2026-09-21T17:59:22Zhttps://escholarship.org/oaioai:escholarship.org:ark:/13030/qt2s0273qm2026-09-18T04:35:31Zqt2s0273qmArchitecture and Selectivity in Aquaporins: 2.5 Å X-Ray Structure of Aquaporin ZSavage, David FEgea, Pascal FRobles-Colmenares, YanethO'Connell, Joseph DStroud, Robert MSanford Simon2003-12-01Aquaporins are a family of water and small molecule channels found in organisms ranging from bacteria to animals. One of these channels, the E. coli protein aquaporin Z (AqpZ), has been shown to selectively conduct only water at high rates. We have expressed, purified, crystallized, and solved the X-ray structure of AqpZ. The 2.5 A resolution structure of AqpZ suggests aquaporin selectivity results both from a steric mechanism due to pore size and from specific amino acid substitutions that regulate the preference for a hydrophobic or hydrophilic substrate. This structure provides direct evidence on the molecular mechanisms of specificity between water and glycerol in this family of channels from a single species. It is to our knowledge the first atomic resolution structure of a recombinant aquaporin and so provides a platform for combined genetic, mutational, functional, and structural determinations of the mechanisms of aquaporins and, more generally, the assembly of multimeric membrane proteins.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Bioengineering (rcdc)Biotechnology (rcdc)Genetics (rcdc)Generic health relevance (hrcs-hc)Amino Acid Sequence (mesh)Aquaporins (mesh)Carbon (mesh)Cell Membrane (mesh)CrystallographyX-Ray (mesh)Detergents (mesh)Escherichia coli (mesh)Escherichia coli Proteins (mesh)Glycerol (mesh)Hydrogen (mesh)Membrane Proteins (mesh)ModelsMolecular (mesh)Molecular Conformation (mesh)Molecular Sequence Data (mesh)Oxygen (mesh)Protein Binding (mesh)Protein Conformation (mesh)Protein StructureSecondary (mesh)Recombinant Proteins (mesh)Sequence HomologyAmino Acid (mesh)Water (mesh)Cell Membrane (mesh)Escherichia coli (mesh)Carbon (mesh)Oxygen (mesh)Hydrogen (mesh)Water (mesh)Glycerol (mesh)Aquaporins (mesh)Escherichia coli Proteins (mesh)Membrane Proteins (mesh)Recombinant Proteins (mesh)Detergents (mesh)CrystallographyX-Ray (mesh)Amino Acid Sequence (mesh)Molecular Conformation (mesh)Protein Conformation (mesh)Protein StructureSecondary (mesh)Protein Binding (mesh)Sequence HomologyAmino Acid (mesh)ModelsMolecular (mesh)Molecular Sequence Data (mesh)Amino Acid Sequence (mesh)Aquaporins (mesh)Carbon (mesh)Cell Membrane (mesh)CrystallographyX-Ray (mesh)Detergents (mesh)Escherichia coli (mesh)Escherichia coli Proteins (mesh)Glycerol (mesh)Hydrogen (mesh)Membrane Proteins (mesh)ModelsMolecular (mesh)Molecular Conformation (mesh)Molecular Sequence Data (mesh)Oxygen (mesh)Protein Binding (mesh)Protein Conformation (mesh)Protein StructureSecondary (mesh)Recombinant Proteins (mesh)Sequence HomologyAmino Acid (mesh)Water (mesh)06 Biological Sciences (for)07 Agricultural and Veterinary Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)30 Agriculturalveterinary and food sciences (for-2020)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2s0273qmhttps://escholarship.org/content/qt2s0273qm/qt2s0273qm.pdfinfo:doi/10.1371/journal.pbio.0000072articlePLOS Biology, vol 1, iss 3e72oai:escholarship.org:ark:/13030/qt2g22r9k62026-09-17T03:21:09Zqt2g22r9k6De novo determination of mosquitocidal Cry11Aa and Cry11Ba structures from naturally-occurring nanocrystalsTetreau, GuillaumeSawaya, Michael RDe Zitter, ElkeAndreeva, Elena ABanneville, Anne-SophieSchibrowsky, NatalieCoquelle, NicolasBrewster, Aaron SGrünbein, Marie LuiseKovacs, Gabriela NassHunter, Mark SKloos, MarcoSierra, Raymond GSchiro, GiorgioQiao, PeiStricker, MyriamBideshi, DennisYoung, Iris DZala, NinonEngilberge, SylvainGorel, AlexanderSignor, LucaTeulon, Jean-MarieHilpert, MarioFoucar, LutzBielecki, JohanBean, Richardde Wijn, RaphaelSato, TokushiKirkwood, HenryLetrun, RomainBatyuk, AlexanderSnigireva, IrinaFenel, DaphnaSchubert, RobinCanfield, Ethan JAlba, Mario MLaporte, FrédéricDesprés, LaurenceBacia, MariaRoux, AmandineChapelle, ChristianRiobé, FrançoisMaury, OlivierLing, Wai LiBoutet, SébastienMancuso, AdrianGutsche, IrinaGirard, EricBarends, Thomas RMPellequer, Jean-LucPark, Hyun-WooLaganowsky, Arthur DRodriguez, JoseBurghammer, ManfredShoeman, Robert LDoak, R BruceWeik, MartinSauter, Nicholas KFederici, BrianCascio, DuilioSchlichting, IlmeColletier, Jacques-Philippe2021-01-01Abstract Cry11Aa and Cry11Ba are the two most potent toxins produced by mosquitocidal Bacillus thuringiensis subsp. israelensis and jegathesan , respectively. The toxins naturally crystallize within the host; however, the crystals are too small for structure determination at synchrotron sources. Therefore, we applied serial femtosecond crystallography at X-ray free electron lasers to in vivo -grown nanocrystals of these toxins. The structure of Cry11Aa was determined de novo using the single-wavelength anomalous dispersion method, which in turn enabled the determination of the Cry11Ba structure by molecular replacement. The two structures reveal a new pattern for in vivo crystallization of Cry toxins, whereby each of their three domains packs with a symmetrically identical domain, and a cleavable crystal packing motif is located within the protoxin rather than at the termini. The diversity of in vivo crystallization patterns suggests explanations for their varied levels of toxicity and rational approaches to improve these toxins for mosquito control.3402 Inorganic Chemistry (for-2020)3101 Biochemistry and Cell Biology (for-2020)34 Chemical Sciences (for-2020)31 Biological Sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2g22r9k6https://escholarship.org/content/qt2g22r9k6/qt2g22r9k6.pdfinfo:doi/10.1101/2021.12.15.472578articleoai:escholarship.org:ark:/13030/qt6ws913x12026-09-15T11:05:37Zqt6ws913x1Divergent roles for KLF4 and TFCP2L1 in naive ground state pluripotency and human primordial germ cell developmentHancock, GVLiu, WPeretz, LChen, DGell, JJCollier, AJZamudioPlath, KClark, AT2021-08-01During embryo development, human primordial germ cells (hPGCs) express a naive gene expression program with similarities to pre-implantation naive epiblast (EPI) cells and naive human embryonic stem cells (hESCs). Previous studies have shown that TFAP2C is required for establishing naive gene expression in these cell types, however the role of additional naive transcription factors in hPGC biology is not known. Here, we show that unlike TFAP2C, the naive transcription factors KLF4 and TFCP2L1 are not required for induction of hPGC-like cells (hPGCLCs) from hESCs, and they have no role in establishing and maintaining a naive-like gene expression program in hPGCLCs with extended time in culture. Taken together, our results suggest a model whereby the molecular mechanisms that drive naive gene expression in hPGCs/hPGCLCs are distinct from those in the naive EPI/hESCs.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Stem Cell Research - Embryonic - Human (rcdc)Stem Cell Research (rcdc)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Cell Differentiation (mesh)Germ Cells (mesh)Human Embryonic Stem Cells (mesh)Humans (mesh)Kruppel-Like Factor 4 (mesh)Repressor Proteins (mesh)Transcription Factors (mesh)Transcriptome (mesh)Primordial Germ CellsPGCshPGCsPluripotencyKLF4Stem cellsGerm Cells (mesh)Humans (mesh)Transcription Factors (mesh)Repressor Proteins (mesh)Cell Differentiation (mesh)Transcriptome (mesh)Human Embryonic Stem Cells (mesh)Kruppel-Like Factor 4 (mesh)KLF4PGCsPluripotencyPrimordial Germ CellsStem cellsTFCP2L1hPGCsCell Differentiation (mesh)Germ Cells (mesh)Human Embryonic Stem Cells (mesh)Humans (mesh)Kruppel-Like Factor 4 (mesh)Repressor Proteins (mesh)Transcription Factors (mesh)Transcriptome (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)3105 Genetics (for-2020)3206 Medical biotechnology (for-2020)3211 Oncology and carcinogenesis (for-2020)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/6ws913x1https://escholarship.org/content/qt6ws913x1/qt6ws913x1.pdfinfo:doi/10.1016/j.scr.2021.102493articleStem Cell Research, vol 55102493oai:escholarship.org:ark:/13030/qt7nv0d5632026-09-14T12:16:41Zqt7nv0d563LXRs link metabolism to inflammation through Abca1-dependent regulation of membrane composition and TLR signalingIto, AyakaHong, CynthiaRong, XinZhu, XueweiTarling, Elizabeth JHedde, Per NiklasGratton, EnricoParks, JohnTontonoz, Peter2015-01-01The liver X receptors (LXRs) are transcriptional regulators of lipid homeostasis that also have potent anti-inflammatory effects. The molecular basis for their anti-inflammatory effects is incompletely understood, but has been proposed to involve the indirect tethering of LXRs to inflammatory gene promoters. Here we demonstrate that the ability of LXRs to repress inflammatory gene expression in cells and mice derives primarily from their ability to regulate lipid metabolism through transcriptional activation and can occur in the absence of SUMOylation. Moreover, we identify the putative lipid transporter Abca1 as a critical mediator of LXR's anti-inflammatory effects. Activation of LXR inhibits signaling from TLRs 2, 4 and 9 to their downstream NF-κB and MAPK effectors through Abca1-dependent changes in membrane lipid organization that disrupt the recruitment of MyD88 and TRAF6. These data suggest that a common mechanism-direct transcriptional activation-underlies the dual biological functions of LXRs in metabolism and inflammation.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Nutrition (rcdc)Genetics (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Inflammatory and immune system (hrcs-hc)ATP Binding Cassette Transporter 1 (mesh)Animals (mesh)Cell Membrane (mesh)CellsCultured (mesh)Chromatin Immunoprecipitation (mesh)Gene Expression Profiling (mesh)Inflammation (mesh)Liver X Receptors (mesh)Mice (mesh)Orphan Nuclear Receptors (mesh)Signal Transduction (mesh)Toll-Like Receptors (mesh)CellsCultured (mesh)Cell Membrane (mesh)Animals (mesh)Mice (mesh)Inflammation (mesh)Chromatin Immunoprecipitation (mesh)Gene Expression Profiling (mesh)Signal Transduction (mesh)Toll-Like Receptors (mesh)Orphan Nuclear Receptors (mesh)ATP Binding Cassette Transporter 1 (mesh)Liver X Receptors (mesh)LXRToll-like receptorcell biologychromosomesgeneslipid metabolismmousenuclear receptorATP Binding Cassette Transporter 1 (mesh)Animals (mesh)Cell Membrane (mesh)CellsCultured (mesh)Chromatin Immunoprecipitation (mesh)Gene Expression Profiling (mesh)Inflammation (mesh)Liver X Receptors (mesh)Mice (mesh)Orphan Nuclear Receptors (mesh)Signal Transduction (mesh)Toll-Like Receptors (mesh)0601 Biochemistry and Cell Biology (for)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/7nv0d563info:doi/10.7554/elife.08009multimediaELIFE, vol 4, iss JULY 2015e08009oai:escholarship.org:ark:/13030/qt5br8j4kn2026-09-14T01:59:34Zqt5br8j4knCRISPR screens in iPSC-derived neurons reveal principles of tau proteostasisSamelson, Avi JAriqat, NabeelaMcKetney, JustinRohanitazangi, GitaBravo, Celeste ParraBose, Rudra STravaglini, Kyle JLam, Victor LGoodness, DarrinTa, ThomasDixon, GaryMarzette, EmilyJin, JulianneTian, RuilinTse, EricAbskharon, RomanyPan, Henry SCarroll, Emma CLawrence, Rosalie EGestwicki, Jason ERexach, Jessica EEisenberg, David SKanaan, Nicholas MSouthworth, Daniel RGross, John DGan, LiSwaney, Danielle LKampmann, Martin2026-03-01Aggregation of the protein tau defines tauopathies, the most common age-related neurodegenerative diseases, which include Alzheimer's disease and frontotemporal dementia. Specific neuronal subtypes are selectively vulnerable to tau aggregation, dysfunction, and death. However, molecular mechanisms underlying cell-type-selective vulnerability are unknown. To systematically uncover the cellular factors controlling the accumulation of tau aggregates in human neurons, we conducted a genome-wide CRISPRi screen in induced pluripotent stem cell (iPSC)-derived neurons. The screen uncovered both known and unexpected pathways, including UFMylation and GPI anchor biosynthesis, which control tau oligomer levels. We discovered that the E3 ubiquitin ligase CRL5SOCS4 controls tau levels in human neurons, ubiquitinates tau, and is correlated with resilience to tauopathies in human disease. Disruption of mitochondrial function promotes proteasomal misprocessing of tau, generating disease-relevant tau proteolytic fragments and changing tau aggregation in vitro. These results systematically reveal principles of tau proteostasis in human neurons and suggest potential therapeutic targets for tauopathies.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Brain Disorders (rcdc)Aging (rcdc)Stem Cell Research (rcdc)Acquired Cognitive Impairment (rcdc)Neurodegenerative (rcdc)Frontotemporal Dementia (FTD) (rcdc)Alzheimer's Disease (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell (rcdc)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)Neurosciences (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell - Human (rcdc)Dementia (rcdc)Alzheimer's Disease Related Dementias (ADRD) (rcdc)2.1 Biological and endogenous factors (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)Neurological (hrcs-hc)Humans (mesh)tau Proteins (mesh)Induced Pluripotent Stem Cells (mesh)Neurons (mesh)Proteostasis (mesh)Tauopathies (mesh)Mitochondria (mesh)Ubiquitination (mesh)CRISPR-Cas Systems (mesh)Neurons (mesh)Mitochondria (mesh)Humans (mesh)Tauopathies (mesh)tau Proteins (mesh)Ubiquitination (mesh)Induced Pluripotent Stem Cells (mesh)CRISPR-Cas Systems (mesh)Proteostasis (mesh)CRISPR screenCUL5SOCS4neurodegenerationprotein aggregationproteostasistauHumans (mesh)tau Proteins (mesh)Induced Pluripotent Stem Cells (mesh)Neurons (mesh)Proteostasis (mesh)Tauopathies (mesh)Mitochondria (mesh)Ubiquitination (mesh)CRISPR-Cas Systems (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)CC-BY-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/5br8j4kninfo:doi/10.1016/j.cell.2025.12.038articleCell, vol 189, iss 51517 - 1534.e19oai:escholarship.org:ark:/13030/qt7tg783zh2026-09-14T00:28:49Zqt7tg783zhViral delivery of an RNA-guided genome editor for transgene-free germline editing in ArabidopsisWeiss, TrevorKamalu, MarisShi, HonglueLi, ZhengAmerasekera, JasmineZhong, ZhenhuiAdler, Benjamin ASong, Michelle MVohra, KamakshiWirnowski, GabrielChitkara, SidharthAmbrose, CharlieSteinmetz, NoahSridharan, AnanyaSahagun, DiegoBanfield, Jillian FDoudna, Jennifer AJacobsen, Steven E2025-05-01Genome editing is transforming plant biology by enabling precise DNA modifications. However, delivery of editing systems into plants remains challenging, often requiring slow, genotype-specific methods such as tissue culture or transformation1. Plant viruses, which naturally infect and spread to most tissues, present a promising delivery system for editing reagents. However, many viruses have limited cargo capacities, restricting their ability to carry large CRISPR-Cas systems. Here we engineered tobacco rattle virus (TRV) to carry the compact RNA-guided TnpB enzyme ISYmu1 and its guide RNA. This innovation allowed transgene-free editing of Arabidopsis thaliana in a single step, with edits inherited in the subsequent generation. By overcoming traditional reagent delivery barriers, this approach offers a novel platform for genome editing, which can greatly accelerate plant biotechnology and basic research.3108 Plant Biology (for-2020)31 Biological Sciences (for-2020)Biotechnology (rcdc)Genetics (rcdc)Bioengineering (rcdc)5.2 Cellular and gene therapies (hrcs-rac)Arabidopsis (mesh)Gene Editing (mesh)Plant Viruses (mesh)CRISPR-Cas Systems (mesh)RNAGuideCRISPR-Cas Systems (mesh)PlantsGenetically Modified (mesh)Transgenes (mesh)GenomePlant (mesh)Plant Viruses (mesh)PlantsGenetically Modified (mesh)Arabidopsis (mesh)GenomePlant (mesh)Transgenes (mesh)CRISPR-Cas Systems (mesh)Gene Editing (mesh)RNAGuideCRISPR-Cas Systems (mesh)Arabidopsis (mesh)Gene Editing (mesh)Plant Viruses (mesh)CRISPR-Cas Systems (mesh)RNAGuideCRISPR-Cas Systems (mesh)PlantsGenetically Modified (mesh)Transgenes (mesh)GenomePlant (mesh)0607 Plant Biology (for)0703 Crop and Pasture Production (for)3103 Ecology (for-2020)3108 Plant biology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/7tg783zhhttps://escholarship.org/content/qt7tg783zh/qt7tg783zh.pdfinfo:doi/10.1038/s41477-025-01989-9articleNature Plants, vol 11, iss 5967 - 976oai:escholarship.org:ark:/13030/qt1cx8v95f2026-09-13T17:24:56Zqt1cx8v95fHepatic nonvesicular cholesterol transport is critical for systemic lipid homeostasisXiao, XuKennelly, John PaulFerrari, AlessandraClifford, Bethan LWhang, EmilyGao, YajingQian, KevinSandhu, JaspreetJarrett, Kelsey EBrearley-Sholto, Madelaine CNguyen, AlexanderNagari, Rohith TLee, Min SubZhang, SichengWeston, Thomas AYoung, Stephen GBensinger, Steven JVillanueva, Claudio Jde Aguiar Vallim, Thomas QTontonoz, Peter2023-01-01In cell models, changes in the ‘accessible’ pool of plasma membrane (PM) cholesterol are linked with the regulation of endoplasmic reticulum sterol synthesis and metabolism by the Aster family of nonvesicular transporters; however, the relevance of such nonvesicular transport mechanisms for lipid homeostasis in vivo has not been defined. Here we reveal two physiological contexts that generate accessible PM cholesterol and engage the Aster pathway in the liver: fasting and reverse cholesterol transport. During fasting, adipose-tissue-derived fatty acids activate hepatocyte sphingomyelinase to liberate sequestered PM cholesterol. Aster-dependent cholesterol transport during fasting facilitates cholesteryl ester formation, cholesterol movement into bile and very low-density lipoprotein production. During reverse cholesterol transport, high-density lipoprotein delivers excess cholesterol to the hepatocyte PM through scavenger receptor class B member 1. Loss of hepatic Asters impairs cholesterol movement into feces, raises plasma cholesterol levels and causes cholesterol accumulation in peripheral tissues. These results reveal fundamental mechanisms by which Aster cholesterol flux contributes to hepatic and systemic lipid homeostasis.3205 Medical Biochemistry and Metabolomics (for-2020)3208 Medical Physiology (for-2020)32 Biomedical and Clinical Sciences (for-2020)3210 Nutrition and Dietetics (for-2020)Digestive Diseases (rcdc)Liver Disease (rcdc)Nutrition (rcdc)Atherosclerosis (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Cholesterol (mesh)Biological Transport (mesh)Liver (mesh)Homeostasis (mesh)Fatty Acids (mesh)Liver (mesh)Cholesterol (mesh)Fatty Acids (mesh)Biological Transport (mesh)Homeostasis (mesh)Cholesterol (mesh)Biological Transport (mesh)Liver (mesh)Homeostasis (mesh)Fatty Acids (mesh)3205 Medical biochemistry and metabolomics (for-2020)3208 Medical physiology (for-2020)3210 Nutrition and dietetics (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1cx8v95fhttps://escholarship.org/content/qt1cx8v95f/qt1cx8v95f.pdfinfo:doi/10.1038/s42255-022-00722-6articleNature Metabolism, vol 5, iss 1165 - 181oai:escholarship.org:ark:/13030/qt28s341mv2026-09-11T16:02:29Zqt28s341mvThe role of ATXR6 expression in modulating genome stability and transposable element repression in ArabidopsisPotok, Magdalena EZhong, ZhenhuiPicard, Colette LLiu, QikunDo, TrumanJacobsen, Cassidy ESakr, OceanNaranbaatar, BilguudeiThilakaratne, RuwanKhnkoyan, ZhannaPurl, MeganCheng, HarrisonVervaet, HelenaFeng, SuhuaRayatpisheh, ShimaWohlschlegel, James AO’Malley, Ronan CEcker, Joseph RJacobsen, Steven E2022-01-18ARABIDOPSIS TRITHORAX-RELATED PROTEIN 5 (ATXR5) AND ATXR6 are required for the deposition of H3K27me1 and for maintaining genomic stability in Arabidopsis Reduction of ATXR5/6 activity results in activation of DNA damage response genes, along with tissue-specific derepression of transposable elements (TEs), chromocenter decompaction, and genomic instability characterized by accumulation of excess DNA from heterochromatin. How loss of ATXR5/6 and H3K27me1 leads to these phenotypes remains unclear. Here we provide extensive characterization of the atxr5/6 hypomorphic mutant by comprehensively examining gene expression and epigenetic changes in the mutant. We found that the tissue-specific phenotypes of TE derepression and excessive DNA in this atxr5/6 mutant correlated with residual ATXR6 expression from the hypomorphic ATXR6 allele. However, up-regulation of DNA damage genes occurred regardless of ATXR6 levels and thus appears to be a separable process. We also isolated an atxr6-null allele which showed that ATXR5 and ATXR6 are required for female germline development. Finally, we characterize three previously reported suppressors of the hypomorphic atxr5/6 mutant and show that these rescue atxr5/6 via distinct mechanisms, two of which involve increasing H3K27me1 levels.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)3105 Genetics (for-2020)Genetics (rcdc)Human Genome (rcdc)Biotechnology (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Generic health relevance (hrcs-hc)Alleles (mesh)Arabidopsis (mesh)Arabidopsis Proteins (mesh)DNA Transposable Elements (mesh)EpigenesisGenetic (mesh)Gene Expression RegulationPlant (mesh)Genomic Instability (mesh)Heterochromatin (mesh)Histones (mesh)Methyltransferases (mesh)Mutation (mesh)Phenotype (mesh)Transcriptome (mesh)H3K27me1ATXR5/6planthistone methyltransferaseHeterochromatin (mesh)Arabidopsis (mesh)Genomic Instability (mesh)Methyltransferases (mesh)Histones (mesh)Arabidopsis Proteins (mesh)DNA Transposable Elements (mesh)EpigenesisGenetic (mesh)Gene Expression RegulationPlant (mesh)Phenotype (mesh)Mutation (mesh)Alleles (mesh)Transcriptome (mesh)ATXR5/6H3K27me1histone methyltransferaseplantAlleles (mesh)Arabidopsis (mesh)Arabidopsis Proteins (mesh)DNA Transposable Elements (mesh)EpigenesisGenetic (mesh)Gene Expression RegulationPlant (mesh)Genomic Instability (mesh)Heterochromatin (mesh)Histones (mesh)Methyltransferases (mesh)Mutation (mesh)Phenotype (mesh)Transcriptome (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/28s341mvhttps://escholarship.org/content/qt28s341mv/qt28s341mv.pdfinfo:doi/10.1073/pnas.2115570119articleProceedings of the National Academy of Sciences of the United States of America, vol 119, iss 3e2115570119oai:escholarship.org:ark:/13030/qt4np471k52026-09-11T00:05:43Zqt4np471k5Temporally distinct 3D multi-omic dynamics in the developing human brainHeffel, Matthew GZhou, JingtianZhang, YiLee, Dong-SungHou, KangchengPastor-Alonso, OierAbuhanna, Kevin DGalasso, JosephKern, ColinTai, Chu-YiGarcia-Padilla, CarlosNafisi, MahsaZhou, YiSchmitt, Anthony DLi, TerenceHaeussler, MaximilianWick, BrittneyZhang, Martin JinyeXie, FangmingZiffra, Ryan SMukamel, Eran AEskin, EleazarNowakowski, Tomasz JDixon, Jesse RPasaniuc, BogdanEcker, Joseph RZhu, QuanBintu, BogdanParedes, Mercedes FLuo, Chongyuan2024-11-14The human hippocampus and prefrontal cortex play critical roles in learning and cognition1,2, yet the dynamic molecular characteristics of their development remain enigmatic. Here we investigated the epigenomic and three-dimensional chromatin conformational reorganization during the development of the hippocampus and prefrontal cortex, using more than 53,000 joint single-nucleus profiles of chromatin conformation and DNA methylation generated by single-nucleus methyl-3C sequencing (snm3C-seq3)3. The remodelling of DNA methylation is temporally separated from chromatin conformation dynamics. Using single-cell profiling and multimodal single-molecule imaging approaches, we have found that short-range chromatin interactions are enriched in neurons, whereas long-range interactions are enriched in glial cells and non-brain tissues. We reconstructed the regulatory programs of cell-type development and differentiation, finding putatively causal common variants for schizophrenia strongly overlapping with chromatin loop-connected, cell-type-specific regulatory regions. Our data provide multimodal resources for studying gene regulatory dynamics in brain development and demonstrate that single-cell three-dimensional multi-omics is a powerful approach for dissecting neuropsychiatric risk loci.31 Biological Sciences (for-2020)3105 Genetics (for-2020)Brain Disorders (rcdc)Human Genome (rcdc)Mental Health (rcdc)Neurosciences (rcdc)Mental Illness (rcdc)Genetics (rcdc)2.1 Biological and endogenous factors (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)Neurological (hrcs-hc)Humans (mesh)Cell Differentiation (mesh)Chromatin (mesh)Disease Susceptibility (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Epigenomics (mesh)Fetus (mesh)Hippocampus (mesh)Multiomics (mesh)Neuroglia (mesh)Neurons (mesh)Prefrontal Cortex (mesh)Schizophrenia (mesh)Single Molecule Imaging (mesh)Single-Cell Analysis (mesh)Time Factors (mesh)InfantNewborn (mesh)Hippocampus (mesh)Prefrontal Cortex (mesh)Neuroglia (mesh)Neurons (mesh)Chromatin (mesh)Fetus (mesh)Humans (mesh)Disease Susceptibility (mesh)Schizophrenia (mesh)Cell Differentiation (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Time Factors (mesh)InfantNewborn (mesh)Epigenomics (mesh)Single-Cell Analysis (mesh)Single Molecule Imaging (mesh)Multiomics (mesh)Humans (mesh)Cell Differentiation (mesh)Chromatin (mesh)Disease Susceptibility (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Epigenomics (mesh)Fetus (mesh)Hippocampus (mesh)Multiomics (mesh)Neuroglia (mesh)Neurons (mesh)Prefrontal Cortex (mesh)Schizophrenia (mesh)Single Molecule Imaging (mesh)Single-Cell Analysis (mesh)Time Factors (mesh)InfantNewborn (mesh)General Science & Technology (science-metrix)CC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/4np471k5info:doi/10.1038/s41586-024-08030-7articleNature, vol 635, iss 8038481 - 489oai:escholarship.org:ark:/13030/qt5b4209gs2026-09-10T13:30:10Zqt5b4209gsA guide to the BRAIN Initiative Cell Census Network data ecosystemHawrylycz, MichaelMartone, Maryann EAscoli, Giorgio ABjaalie, Jan GDong, Hong-WeiGhosh, Satrajit SGillis, JesseHertzano, RonnaHaynor, David RHof, Patrick RKim, YongsooLein, EdLiu, YufengMiller, Jeremy AMitra, Partha PMukamel, EranNg, LydiaOsumi-Sutherland, DavidPeng, HanchuanRay, Patrick LSanchez, RaymondRegev, AvivRopelewski, AlexScheuermann, Richard HTan, Shawn Zheng KaiThompson, Carol LTickle, TimothyTilgner, HagenVarghese, MerinaWester, BrockWhite, OwenZeng, HongkuiAevermann, BrianAllemang, DavidAment, SethAthey, Thomas LBaker, CodyBaker, Katherine SBaker, Pamela MBandrowski, AnitaBanerjee, SamikBishwakarma, PrajalCarr, AmbroseChen, MinChoudhury, RoniCool, JonahCreasy, HeatherD’Orazi, FlorenceDegatano, KyleeDichter, BenjaminDing, Song-LinDolbeare, TimEcker, Joseph RFang, RongxinFillion-Robin, Jean-ChristopheFliss, Timothy PGee, JamesGillespie, TomGouwens, NathanZhang, Guo-QiangHalchenko, Yaroslav OHarris, Nomi LHerb, Brian RHintiryan, HouriHood, GregoryHorvath, SamHuo, BingxingJarecka, DorotaJiang, ShengdianKhajouei, FarzanehKiernan, Elizabeth AKir, HuseyinKruse, LaurenLee, ChangkyuLelieveldt, BoudewijnLi, YangLiu, HanqingLiu, LijuanMarkuhar, AnupMathews, JamesMathews, Kaylee LMezias, ChrisMiller, Michael IMollenkopf, TylerMufti, ShoaibMungall, Christopher JOrvis, JoshuaPuchades, Maja AQu, LeiReceveur, Joseph PRen, BingSjoquist, NathanStaats, BrianTward, Danielvan Velthoven, Cindy TJWang, QuanxinXie, FangmingXu, HuaYao, ZizhenYun, Zhixi2023-06-01Characterizing cellular diversity at different levels of biological organization and across data modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also essential to manipulate cell types in controlled ways and to understand their variation and vulnerability in brain disorders. The BRAIN Initiative Cell Census Network (BICCN) is an integrated network of data-generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate (NHP) brains. Here, we provide a guide to the cellular and spatial approaches employed by the BICCN, and to accessing and using these data and extensive resources, including the BRAIN Cell Data Center (BCDC), which serves to manage and integrate data across the ecosystem. We illustrate the power of the BICCN data ecosystem through vignettes highlighting several BICCN analysis and visualization tools. Finally, we present emerging standards that have been developed or adopted toward Findable, Accessible, Interoperable, and Reusable (FAIR) neuroscience. The combined BICCN ecosystem provides a comprehensive resource for the exploration and analysis of cell types in the brain.31 Biological Sciences (for-2020)3105 Genetics (for-2020)Data Science (rcdc)Neurosciences (rcdc)Mental Health (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Neurological (hrcs-hc)Animals (mesh)Humans (mesh)Mice (mesh)Brain (mesh)Ecosystem (mesh)Neurons (mesh)Neurosciences (mesh)Brain (mesh)Neurons (mesh)Animals (mesh)Humans (mesh)Mice (mesh)Neurosciences (mesh)Ecosystem (mesh)Animals (mesh)Humans (mesh)Mice (mesh)Brain (mesh)Ecosystem (mesh)Neurons (mesh)Neurosciences (mesh)06 Biological Sciences (for)07 Agricultural and Veterinary Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)30 Agriculturalveterinary and food sciences (for-2020)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/5b4209gshttps://escholarship.org/content/qt5b4209gs/qt5b4209gs.pdfinfo:doi/10.1371/journal.pbio.3002133articlePLOS Biology, vol 21, iss 6e3002133oai:escholarship.org:ark:/13030/qt7854q6b52026-09-10T09:03:40Zqt7854q6b5MITF drives endolysosomal biogenesis and potentiates Wnt signaling in melanoma cellsPloper, DiegoTaelman, Vincent FRobert, LidiaPerez, Brian STitz, BjörnChen, Hsiao-WangGraeber, Thomas Gvon Euw, ErikaRibas, AntoniDe Robertis, Edward M2015-02-03Canonical Wnt signaling plays an important role in development and disease, regulating transcription of target genes and stabilizing many proteins phosphorylated by glycogen synthase kinase 3 (GSK3). We observed that the MiT family of transcription factors, which includes the melanoma oncogene MITF (micropthalmia-associated transcription factor) and the lysosomal master regulator TFEB, had the highest phylogenetic conservation of three consecutive putative GSK3 phosphorylation sites in animal proteomes. This finding prompted us to examine the relationship between MITF, endolysosomal biogenesis, and Wnt signaling. Here we report that MITF expression levels correlated with the expression of a large subset of lysosomal genes in melanoma cell lines. MITF expression in the tetracycline-inducible C32 melanoma model caused a marked increase in vesicular structures, and increased expression of late endosomal proteins, such as Rab7, LAMP1, and CD63. These late endosomes were not functional lysosomes as they were less active in proteolysis, yet were able to concentrate Axin1, phospho-LRP6, phospho-β-catenin, and GSK3 in the presence of Wnt ligands. This relocalization significantly enhanced Wnt signaling by increasing the number of multivesicular bodies into which the Wnt signalosome/destruction complex becomes localized upon Wnt signaling. We also show that the MITF protein was stabilized by Wnt signaling, through the novel C-terminal GSK3 phosphorylations identified here. MITF stabilization caused an increase in multivesicular body biosynthesis, which in turn increased Wnt signaling, generating a positive-feedback loop that may function during the proliferative stages of melanoma. The results underscore the importance of misregulated endolysosomal biogenesis in Wnt signaling and cancer.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Cancer (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Cancer (hrcs-hc)Cell LineTumor (mesh)Endosomes (mesh)Glycogen Synthase Kinase 3 (mesh)HEK293 Cells (mesh)Humans (mesh)Lysosomes (mesh)Microphthalmia-Associated Transcription Factor (mesh)Phosphorylation (mesh)Signal Transduction (mesh)Wnt Proteins (mesh)MITFWnt-STOPlysosomemelanomamultivesicular bodyCell LineTumor (mesh)Endosomes (mesh)Lysosomes (mesh)Humans (mesh)Glycogen Synthase Kinase 3 (mesh)Signal Transduction (mesh)Phosphorylation (mesh)Wnt Proteins (mesh)Microphthalmia-Associated Transcription Factor (mesh)HEK293 Cells (mesh)MITFWnt-STOPlysosomemelanomamultivesicular bodyCell LineTumor (mesh)Endosomes (mesh)Glycogen Synthase Kinase 3 (mesh)HEK293 Cells (mesh)Humans (mesh)Lysosomes (mesh)Microphthalmia-Associated Transcription Factor (mesh)Phosphorylation (mesh)Signal Transduction (mesh)Wnt Proteins (mesh)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7854q6b5https://escholarship.org/content/qt7854q6b5/qt7854q6b5.pdfinfo:doi/10.1073/pnas.1424576112articleProceedings of the National Academy of Sciences of the United States of America, vol 112, iss 5e420 - e429oai:escholarship.org:ark:/13030/qt56j017g92026-09-10T08:51:49Zqt56j017g9Single nucleus multi-omics identifies human cortical cell regulatory genome diversityLuo, ChongyuanLiu, HanqingXie, FangmingArmand, Ethan JSiletti, KimberlyBakken, Trygve EFang, RongxinDoyle, Wayne IStuart, TimHodge, Rebecca DHu, LijuanWang, Bang-AnZhang, ZhuzhuPreissl, SebastianLee, Dong-SungZhou, JingtianNiu, Sheng-YongCastanon, RosaBartlett, AnnaRivkin, AngelineWang, XinxinLucero, JacintaNery, Joseph RDavis, David AMash, Deborah CSatija, RahulDixon, Jesse RLinnarsson, StenLein, EdBehrens, M MargaritaRen, BingMukamel, Eran AEcker, Joseph R2022-03-01Single-cell technologies measure unique cellular signatures but are typically limited to a single modality. Computational approaches allow the fusion of diverse single-cell data types, but their efficacy is difficult to validate in the absence of authentic multi-omic measurements. To comprehensively assess the molecular phenotypes of single cells, we devised single-nucleus methylcytosine, chromatin accessibility, and transcriptome sequencing (snmCAT-seq) and applied it to postmortem human frontal cortex tissue. We developed a cross-validation approach using multi-modal information to validate fine-grained cell types and assessed the effectiveness of computational data fusion methods. Correlation analysis in individual cells revealed distinct relations between methylation and gene expression. Our integrative approach enabled joint analyses of the methylome, transcriptome, chromatin accessibility, and conformation for 63 human cortical cell types. We reconstructed regulatory lineages for cortical cell populations and found specific enrichment of genetic risk for neuropsychiatric traits, enabling the prediction of cell types that are associated with diseases.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)3105 Genetics (for-2020)Precision Medicine (rcdc)Cancer (rcdc)Biotechnology (rcdc)Bioengineering (rcdc)Cancer Genomics (rcdc)Human Genome (rcdc)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)3 Good Health and Well Being (sdg)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/56j017g9https://escholarship.org/content/qt56j017g9/qt56j017g9.pdfinfo:doi/10.1016/j.xgen.2022.100107articleCell Genomics, vol 2, iss 3100107oai:escholarship.org:ark:/13030/qt0wz709h32026-09-03T11:24:44Zqt0wz709h3Interaction of chikungunya virus glycoproteins with macrophage factors controls virion productionYao, ZhenlanRamachandran, SangeethaHuang, SerinaKim, ErinJami-Alahmadi, YasamanKaushal, PrashantBouhaddou, MehdiWohlschlegel, James ALi, Melody MH2024-10-15Despite their role as innate sentinels, macrophages can serve as cellular reservoirs of chikungunya virus (CHIKV), a highly-pathogenic arthropod-borne alphavirus that has caused large outbreaks among human populations. Here, with the use of viral chimeras and evolutionary selection analysis, we define CHIKV glycoproteins E1 and E2 as critical for virion production in THP-1 derived human macrophages. Through proteomic analysis and functional validation, we further identify signal peptidase complex subunit 3 (SPCS3) and eukaryotic translation initiation factor 3 subunit K (eIF3k) as E1-binding host proteins with anti-CHIKV activities. We find that E1 residue V220, which has undergone positive selection, is indispensable for CHIKV production in macrophages, as its mutation attenuates E1 interaction with the host restriction factors SPCS3 and eIF3k. Finally, we show that the antiviral activity of eIF3k is translation-independent, and that CHIKV infection promotes eIF3k translocation from the nucleus to the cytoplasm, where it associates with SPCS3. These functions of CHIKV glycoproteins late in the viral life cycle provide a new example of an intracellular evolutionary arms race with host restriction factors, as well as potential targets for therapeutic intervention.3207 Medical Microbiology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Biodefense (rcdc)Infectious Diseases (rcdc)Vector-Borne Diseases (rcdc)Emerging Infectious Diseases (rcdc)Rare Diseases (rcdc)2.2 Factors relating to the physical environment (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Infection (hrcs-hc)3 Good Health and Well Being (sdg)Chikungunya virus (mesh)Humans (mesh)Macrophages (mesh)Viral Envelope Proteins (mesh)Virion (mesh)Chikungunya Fever (mesh)Glycoproteins (mesh)Host-Pathogen Interactions (mesh)Virus Replication (mesh)THP-1 Cells (mesh)Alphavirus E1 GlycoproteinChikungunya ViruseIF3kEvolutionary SelectionMacrophageMacrophages (mesh)Humans (mesh)Chikungunya virus (mesh)Virion (mesh)Glycoproteins (mesh)Viral Envelope Proteins (mesh)Virus Replication (mesh)Host-Pathogen Interactions (mesh)Chikungunya Fever (mesh)THP-1 Cells (mesh)Alphavirus E1 GlycoproteinChikungunya VirusEvolutionary SelectionMacrophageeIF3kChikungunya virus (mesh)Humans (mesh)Macrophages (mesh)Viral Envelope Proteins (mesh)Virion (mesh)Chikungunya Fever (mesh)Glycoproteins (mesh)Host-Pathogen Interactions (mesh)Virus Replication (mesh)THP-1 Cells (mesh)06 Biological Sciences (for)08 Information and Computing Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/0wz709h3https://escholarship.org/content/qt0wz709h3/qt0wz709h3.pdfinfo:doi/10.1038/s44318-024-00193-3articleThe EMBO Journal, vol 43, iss 2010 - 4655oai:escholarship.org:ark:/13030/qt6bb6m6k62026-09-02T10:35:27Zqt6bb6m6k6Structure of Tetrahymena telomerase reveals previously unknown subunits, functions, and interactionsJiang, JiansenChan, HenryCash, Darian DMiracco, Edward JOgorzalek Loo, Rachel RUpton, Heather ECascio, DuilioO'Brien Johnson, ReidCollins, KathleenLoo, Joseph AZhou, Z HongFeigon, Juli2015-10-30Telomerase helps maintain telomeres by processive synthesis of telomere repeat DNA at their 3'-ends, using an integral telomerase RNA (TER) and telomerase reverse transcriptase (TERT). We report the cryo-electron microscopy structure of Tetrahymena telomerase at ~9 angstrom resolution. In addition to seven known holoenzyme proteins, we identify two additional proteins that form a complex (TEB) with single-stranded telomere DNA-binding protein Teb1, paralogous to heterotrimeric replication protein A (RPA). The p75-p45-p19 subcomplex is identified as another RPA-related complex, CST (CTC1-STN1-TEN1). This study reveals the paths of TER in the TERT-TER-p65 catalytic core and single-stranded DNA exit; extensive subunit interactions of the TERT essential N-terminal domain, p50, and TEB; and other subunit identities and structures, including p19 and p45C crystal structures. Our findings provide structural and mechanistic insights into telomerase holoenzyme function.3101 Biochemistry and Cell Biology (for-2020)51 Physical Sciences (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Catalytic Domain (mesh)Cryoelectron Microscopy (mesh)CrystallographyX-Ray (mesh)DNASingle-Stranded (mesh)Holoenzymes (mesh)Protein Binding (mesh)Protein Conformation (mesh)Protein Subunits (mesh)RNA (mesh)Replication Protein A (mesh)Telomerase (mesh)Telomere (mesh)Telomere Homeostasis (mesh)Telomere-Binding Proteins (mesh)Tetrahymena (mesh)Telomere (mesh)Tetrahymena (mesh)Holoenzymes (mesh)Telomerase (mesh)Telomere-Binding Proteins (mesh)Protein Subunits (mesh)DNASingle-Stranded (mesh)RNA (mesh)Cryoelectron Microscopy (mesh)CrystallographyX-Ray (mesh)Catalytic Domain (mesh)Protein Conformation (mesh)Protein Binding (mesh)Replication Protein A (mesh)Telomere Homeostasis (mesh)Catalytic Domain (mesh)Cryoelectron Microscopy (mesh)CrystallographyX-Ray (mesh)DNASingle-Stranded (mesh)Holoenzymes (mesh)Protein Binding (mesh)Protein Conformation (mesh)Protein Subunits (mesh)RNA (mesh)Replication Protein A (mesh)Telomerase (mesh)Telomere (mesh)Telomere Homeostasis (mesh)Telomere-Binding Proteins (mesh)Tetrahymena (mesh)General Science & Technology (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6bb6m6k6https://escholarship.org/content/qt6bb6m6k6/qt6bb6m6k6.pdfinfo:doi/10.1126/science.aab4070articleScience, vol 350, iss 6260aab4070oai:escholarship.org:ark:/13030/qt3jt0c1rr2026-08-31T02:07:09Zqt3jt0c1rrDrp1 regulates mitochondrial health and controls skeletal muscle mass through the Erk1/2-Nur77 pathwayM., AliceTran, Peter HYang, Nicole LNgo, JenniferIwasaki, HirotakaRen, WenjuanLivit, SimoneStiles, LinseyWang, SarahHo, TrinityYim, Emma YMorrow, NoelleJohnson, Morgan MCleary, CarolineZou, KaiCrosbie, Rachelle HJiang, YuweiShirihai, Orian SWanagat, JonathanMahata, SushilWohlschlegel, James AHevener, Andrea LZhou, Zhenqi2026-05-08The maintenance of skeletal muscle mass relies on mitochondrial quality control, including balanced dynamics and mitophagy. Dynamin-related protein 1 (Drp1), a central mediator of mitochondrial fission, is essential for these processes, yet its role in muscle mass regulation remains incompletely defined. Here, we show that acute Drp1 deletion in the skeletal muscle increases Parkin-mediated mitochondrial degradation, reduces mitochondrial DNA (mtDNA) content, and leads to severe muscle atrophy. Although dual deletion of Drp1 and Parkin restores mtDNA content, muscle loss persists. Mechanistically, Drp1 loss impairs mitochondrial respiratory chain activity, suppressing extracellular signal-regulated kinase 1/2 (Erk1/2) signaling and down-regulating the nuclear receptor subfamily 4 group A member 1 (Nur77). Pharmacologic β2-adrenergic receptor activation with clenbuterol reactivated Erk1/2, restored Nur77 expression, and rescued muscle atrophy. These findings define a Drp1-Erk1/2-Nur77 signaling axis linking mitochondrial integrity to skeletal muscle mass and identify a potential therapeutic target for muscle degeneration in mitochondrial and metabolic diseases.3101 Biochemistry and Cell Biology (for-2020)3208 Medical Physiology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)2.1 Biological and endogenous factors (hrcs-rac)Musculoskeletal (hrcs-hc)Animals (mesh)Nuclear Receptor Subfamily 4Group AMember 1 (mesh)Dynamins (mesh)MuscleSkeletal (mesh)Mice (mesh)MAP Kinase Signaling System (mesh)Mitochondria (mesh)Muscular Atrophy (mesh)Signal Transduction (mesh)DNAMitochondrial (mesh)Mitogen-Activated Protein Kinase 3 (mesh)MuscleSkeletal (mesh)Mitochondria (mesh)Animals (mesh)Mice (mesh)Muscular Atrophy (mesh)Dynamins (mesh)Mitogen-Activated Protein Kinase 3 (mesh)DNAMitochondrial (mesh)Signal Transduction (mesh)MAP Kinase Signaling System (mesh)Nuclear Receptor Subfamily 4Group AMember 1 (mesh)Animals (mesh)Nuclear Receptor Subfamily 4Group AMember 1 (mesh)Dynamins (mesh)MuscleSkeletal (mesh)Mice (mesh)MAP Kinase Signaling System (mesh)Mitochondria (mesh)Muscular Atrophy (mesh)Signal Transduction (mesh)DNAMitochondrial (mesh)Mitogen-Activated Protein Kinase 3 (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/3jt0c1rrhttps://escholarship.org/content/qt3jt0c1rr/qt3jt0c1rr.pdfinfo:doi/10.1126/sciadv.aec0795articleScience Advances, vol 12, iss 19eaec0795oai:escholarship.org:ark:/13030/qt6vt828nz2026-08-30T23:53:26Zqt6vt828nzStructure-based discovery of small molecules that disaggregate Alzheimer’s disease tissue derived tau fibrils in vitroSeidler, Paul MMurray, Kevin ABoyer, David RGe, PengSawaya, Michael RHu, Carolyn JCheng, XinyiAbskharon, RomanyPan, HopeDeTure, Michael AWilliams, Christopher KDickson, Dennis WVinters, Harry VEisenberg, David S2022-09-16Alzheimer’s disease (AD) is the consequence of neuronal death and brain atrophy associated with the aggregation of protein tau into fibrils. Thus disaggregation of tau fibrils could be a therapeutic approach to AD. The small molecule EGCG, abundant in green tea, has long been known to disaggregate tau and other amyloid fibrils, but EGCG has poor drug-like properties, failing to fully penetrate the brain. Here we have cryogenically trapped an intermediate of brain-extracted tau fibrils on the kinetic pathway to EGCG-induced disaggregation and have determined its cryoEM structure. The structure reveals that EGCG molecules stack in polar clefts between the paired helical protofilaments that pathologically define AD. Treating the EGCG binding position as a pharmacophore, we computationally screened thousands of drug-like compounds for compatibility for the pharmacophore, discovering several that experimentally disaggregate brain-derived tau fibrils in vitro. This work suggests the potential of structure-based, small-molecule drug discovery for amyloid diseases.3101 Biochemistry and Cell Biology (for-2020)3404 Medicinal and Biomolecular Chemistry (for-2020)34 Chemical Sciences (for-2020)31 Biological Sciences (for-2020)Neurodegenerative (rcdc)Neurosciences (rcdc)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)Dementia (rcdc)Brain Disorders (rcdc)Complementary and Integrative Health (rcdc)Alzheimer's Disease (rcdc)Acquired Cognitive Impairment (rcdc)Aging (rcdc)2.1 Biological and endogenous factors (hrcs-rac)5.1 Pharmaceuticals (hrcs-rac)Neurological (hrcs-hc)Alzheimer Disease (mesh)Amyloid (mesh)Amyloidosis (mesh)Catechin (mesh)Cryoelectron Microscopy (mesh)Drug EvaluationPreclinical (mesh)Humans (mesh)Tea (mesh)tau Proteins (mesh)Humans (mesh)Alzheimer Disease (mesh)Amyloidosis (mesh)Catechin (mesh)Amyloid (mesh)tau Proteins (mesh)Cryoelectron Microscopy (mesh)Drug EvaluationPreclinical (mesh)Tea (mesh)Alzheimer Disease (mesh)Amyloid (mesh)Amyloidosis (mesh)Catechin (mesh)Cryoelectron Microscopy (mesh)Drug EvaluationPreclinical (mesh)Humans (mesh)Tea (mesh)tau Proteins (mesh)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6vt828nzhttps://escholarship.org/content/qt6vt828nz/qt6vt828nz.pdfinfo:doi/10.1038/s41467-022-32951-4articleNature Communications, vol 13, iss 15451oai:escholarship.org:ark:/13030/qt1rb238832026-08-30T14:09:38Zqt1rb23883Efficient and accurate determination of genome-wide DNA methylation patterns in Arabidopsis thaliana with enzymatic methyl sequencingFeng, SuhuaZhong, ZhenhuiWang, MingJacobsen, Steven E2020-12-01Background5′ methylation of cytosines in DNA molecules is an important epigenetic mark in eukaryotes. Bisulfite sequencing is the gold standard of DNA methylation detection, and whole-genome bisulfite sequencing (WGBS) has been widely used to detect methylation at single-nucleotide resolution on a genome-wide scale. However, sodium bisulfite is known to severely degrade DNA, which, in combination with biases introduced during PCR amplification, leads to unbalanced base representation in the final sequencing libraries. Enzymatic conversion of unmethylated cytosines to uracils can achieve the same end product for sequencing as does bisulfite treatment and does not affect the integrity of the DNA; enzymatic methylation sequencing may, thus, provide advantages over bisulfite sequencing.ResultsUsing an enzymatic methyl-seq (EM-seq) technique to selectively deaminate unmethylated cytosines to uracils, we generated and sequenced libraries based on different amounts of Arabidopsis input DNA and different numbers of PCR cycles, and compared these data to results from traditional whole-genome bisulfite sequencing. We found that EM-seq libraries were more consistent between replicates and had higher mapping and lower duplication rates, lower background noise, higher average coverage, and higher coverage of total cytosines. Differential methylation region (DMR) analysis showed that WGBS tended to over-estimate methylation levels especially in CHG and CHH contexts, whereas EM-seq detected higher CG methylation levels in certain highly methylated areas. These phenomena can be mostly explained by a correlation of WGBS methylation estimation with GC content and methylated cytosine density. We used EM-seq to compare methylation between leaves and flowers, and found that CHG methylation level is greatly elevated in flowers, especially in pericentromeric regions.ConclusionWe suggest that EM-seq is a more accurate and reliable approach than WGBS to detect methylation. Compared to WGBS, the results of EM-seq are less affected by differences in library preparation conditions or by the skewed base composition in the converted DNA. It may therefore be more desirable to use EM-seq in methylation studies.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)3105 Genetics (for-2020)Genetics (rcdc)Human Genome (rcdc)Arabidopsis (mesh)DNA Methylation (mesh)Epigenome (mesh)GenomePlant (mesh)Sensitivity and Specificity (mesh)Sequence AnalysisDNA (mesh)DNA methylationBisulfite sequencingWGBSEM-seqTETAPOBECArabidopsis flowersArabidopsis leavesArabidopsis (mesh)Sensitivity and Specificity (mesh)Sequence AnalysisDNA (mesh)DNA Methylation (mesh)GenomePlant (mesh)Epigenome (mesh)APOBECArabidopsis flowersArabidopsis leavesBisulfite sequencingDNA methylationEM-seqTETWGBSArabidopsis (mesh)DNA Methylation (mesh)Epigenome (mesh)GenomePlant (mesh)Sensitivity and Specificity (mesh)Sequence AnalysisDNA (mesh)0604 Genetics (for)3105 Genetics (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/1rb23883https://escholarship.org/content/qt1rb23883/qt1rb23883.pdfinfo:doi/10.1186/s13072-020-00361-9articleEpigenetics & Chromatin, vol 13, iss 142oai:escholarship.org:ark:/13030/qt69h6t8v92026-08-30T04:25:54Zqt69h6t8v9Increased lactate dehydrogenase activity is dispensable in squamous carcinoma cells of originFlores, ASandoval-Gonzalez, STakahashi, RKrall, ASathe, LWei, LRadu, CJoly, JHGraham, NAChristofk, HRLowry, WE2019-01-09Although numerous therapeutic strategies have attempted to target aerobic glycolysis to inhibit tumor progression, these approaches have not resulted in effective clinical outcomes. Murine squamous cell carcinoma (SCC) can be initiated by hair follicle stem cells (HFSCs). HFSCs utilize aerobic glycolysis, and the activity of lactate dehydrogenase (Ldh) is essential for HFSC activation. We sought to determine whether Ldh activity in SCC is critical for tumorigenesis or simply a marker of the cell type of origin. Genetic abrogation or induction of Ldh activity in HFSC-mediated tumorigenesis shows no effect on tumorigenesis as measured by number, time to formation, proliferation, volume, epithelial to mesenchymal transition, gene expression, or immune response. Ldha-null tumors show dramatically reduced levels of glycolytic metabolites by metabolomics, and significantly reduced glucose uptake by FDG-PET live animal imaging. These results suggest that squamous cancer cells of origin do not require increased glycolytic activity to generate cancers.3205 Medical Biochemistry and Metabolomics (for-2020)32 Biomedical and Clinical Sciences (for-2020)3211 Oncology and Carcinogenesis (for-2020)Genetics (rcdc)Stem Cell Research (rcdc)Cancer (rcdc)Biomedical Imaging (rcdc)Stem Cell Research - Nonembryonic - Non-Human (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Cancer (hrcs-hc)Animals (mesh)CarcinomaSquamous Cell (mesh)Enzyme Induction (mesh)Female (mesh)L-Lactate Dehydrogenase (mesh)Male (mesh)Mice (mesh)MiceTransgenic (mesh)NeoplasmsExperimental (mesh)Animals (mesh)MiceTransgenic (mesh)Mice (mesh)CarcinomaSquamous Cell (mesh)NeoplasmsExperimental (mesh)L-Lactate Dehydrogenase (mesh)Enzyme Induction (mesh)Female (mesh)Male (mesh)Animals (mesh)CarcinomaSquamous Cell (mesh)Enzyme Induction (mesh)Female (mesh)L-Lactate Dehydrogenase (mesh)Male (mesh)Mice (mesh)MiceTransgenic (mesh)NeoplasmsExperimental (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/69h6t8v9https://escholarship.org/content/qt69h6t8v9/qt69h6t8v9.pdfinfo:doi/10.1038/s41467-018-07857-9articleNature Communications, vol 10, iss 191oai:escholarship.org:ark:/13030/qt1q76t50g2026-08-29T20:40:44Zqt1q76t50gLactate dehydrogenase activity drives hair follicle stem cell activationFlores, AimeeSchell, JohnKrall, Abigail SJelinek, DavidMiranda, MatildeGrigorian, MelinaBraas, DanielWhite, Andrew CZhou, Jessica LGraham, Nicholas AGraeber, ThomasSeth, PankajEvseenko, DenisColler, Hilary ARutter, JaredChristofk, Heather RLowry, William E2017-09-01Although normally dormant, hair follicle stem cells (HFSCs) quickly become activated to divide during a new hair cycle. The quiescence of HFSCs is known to be regulated by a number of intrinsic and extrinsic mechanisms. Here we provide several lines of evidence to demonstrate that HFSCs utilize glycolytic metabolism and produce significantly more lactate than other cells in the epidermis. Furthermore, lactate generation appears to be critical for the activation of HFSCs as deletion of lactate dehydrogenase (Ldha) prevented their activation. Conversely, genetically promoting lactate production in HFSCs through mitochondrial pyruvate carrier 1 (Mpc1) deletion accelerated their activation and the hair cycle. Finally, we identify small molecules that increase lactate production by stimulating Myc levels or inhibiting Mpc1 carrier activity and can topically induce the hair cycle. These data suggest that HFSCs maintain a metabolic state that allows them to remain dormant and yet quickly respond to appropriate proliferative stimuli.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Regenerative Medicine (rcdc)Genetics (rcdc)Stem Cell Research - Nonembryonic - Non-Human (rcdc)Stem Cell Research (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Acrylates (mesh)Animals (mesh)Anion Transport Proteins (mesh)Cell Proliferation (mesh)Cellular Senescence (mesh)Female (mesh)Genotype (mesh)Glycolysis (mesh)Hair Follicle (mesh)Isoenzymes (mesh)L-Lactate Dehydrogenase (mesh)Lactate Dehydrogenase 5 (mesh)Lactic Acid (mesh)Male (mesh)MiceInbred C57BL (mesh)MiceKnockout (mesh)Mitochondrial Membrane Transport Proteins (mesh)Monocarboxylic Acid Transporters (mesh)Phenotype (mesh)Proto-Oncogene Proteins c-myc (mesh)Signal Transduction (mesh)Stem Cells (mesh)Time Factors (mesh)Hair Follicle (mesh)Stem Cells (mesh)Animals (mesh)MiceInbred C57BL (mesh)MiceKnockout (mesh)Acrylates (mesh)Lactic Acid (mesh)Isoenzymes (mesh)L-Lactate Dehydrogenase (mesh)Anion Transport Proteins (mesh)Monocarboxylic Acid Transporters (mesh)Proto-Oncogene Proteins c-myc (mesh)Mitochondrial Membrane Transport Proteins (mesh)Signal Transduction (mesh)Cell Proliferation (mesh)Glycolysis (mesh)Genotype (mesh)Phenotype (mesh)Time Factors (mesh)Female (mesh)Male (mesh)Cellular Senescence (mesh)Lactate Dehydrogenase 5 (mesh)Acrylates (mesh)Animals (mesh)Anion Transport Proteins (mesh)Cell Proliferation (mesh)Cellular Senescence (mesh)Female (mesh)Genotype (mesh)Glycolysis (mesh)Hair Follicle (mesh)Isoenzymes (mesh)L-Lactate Dehydrogenase (mesh)Lactate Dehydrogenase 5 (mesh)Lactic Acid (mesh)Male (mesh)MiceInbred C57BL (mesh)MiceKnockout (mesh)Mitochondrial Membrane Transport Proteins (mesh)Monocarboxylic Acid Transporters (mesh)Phenotype (mesh)Proto-Oncogene Proteins c-myc (mesh)Signal Transduction (mesh)Stem Cells (mesh)Time Factors (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1q76t50ghttps://escholarship.org/content/qt1q76t50g/qt1q76t50g.pdfinfo:doi/10.1038/ncb3575articleNature Cell Biology, vol 19, iss 91017 - 1026oai:escholarship.org:ark:/13030/qt0zh6x41b2026-08-29T08:13:03Zqt0zh6x41bOrigins of stereoselectivity in evolved ketoreductasesNoey, Elizabeth LTibrewal, NidhiJiménez-Osés, GonzaloOsuna, SílviaPark, JiyongBond, Carly MCascio, DuilioLiang, JackZhang, XiyunHuisman, Gjalt WTang, YiHouk, Kendall N2015-12-22Mutants of Lactobacillus kefir short-chain alcohol dehydrogenase, used here as ketoreductases (KREDs), enantioselectively reduce the pharmaceutically relevant substrates 3-thiacyclopentanone and 3-oxacyclopentanone. These substrates differ by only the heteroatom (S or O) in the ring, but the KRED mutants reduce them with different enantioselectivities. Kinetic studies show that these enzymes are more efficient with 3-thiacyclopentanone than with 3-oxacyclopentanone. X-ray crystal structures of apo- and NADP(+)-bound selected mutants show that the substrate-binding loop conformational preferences are modified by these mutations. Quantum mechanical calculations and molecular dynamics (MD) simulations are used to investigate the mechanism of reduction by the enzyme. We have developed an MD-based method for studying the diastereomeric transition state complexes and rationalize different enantiomeric ratios. This method, which probes the stability of the catalytic arrangement within the theozyme, shows a correlation between the relative fractions of catalytically competent poses for the enantiomeric reductions and the experimental enantiomeric ratio. Some mutations, such as A94F and Y190F, induce conformational changes in the active site that enlarge the small binding pocket, facilitating accommodation of the larger S atom in this region and enhancing S-selectivity with 3-thiacyclopentanone. In contrast, in the E145S mutant and the final variant evolved for large-scale production of the intermediate for the antibiotic sulopenem, R-selectivity is promoted by shrinking the small binding pocket, thereby destabilizing the pro-S orientation.3101 Biochemistry and Cell Biology (for-2020)34 Chemical Sciences (for-2020)31 Biological Sciences (for-2020)Generic health relevance (hrcs-hc)Alcohol Oxidoreductases (mesh)Amino Acid Substitution (mesh)Bacterial Proteins (mesh)Catalytic Domain (mesh)CrystallographyX-Ray (mesh)Directed Molecular Evolution (mesh)Enzyme Stability (mesh)Kinetics (mesh)Lactobacillus (mesh)ModelsMolecular (mesh)Molecular Dynamics Simulation (mesh)MutagenesisSite-Directed (mesh)Protein Conformation (mesh)Quantum Theory (mesh)Stereoisomerism (mesh)Substrate Specificity (mesh)directed evolutioncrystallographic structuresmolecular dynamicstheozymeenantioselectivityLactobacillus (mesh)Alcohol Oxidoreductases (mesh)Bacterial Proteins (mesh)CrystallographyX-Ray (mesh)Directed Molecular Evolution (mesh)Amino Acid Substitution (mesh)MutagenesisSite-Directed (mesh)Enzyme Stability (mesh)Catalytic Domain (mesh)Protein Conformation (mesh)Substrate Specificity (mesh)Kinetics (mesh)Stereoisomerism (mesh)Quantum Theory (mesh)ModelsMolecular (mesh)Molecular Dynamics Simulation (mesh)crystallographic structuresdirected evolutionenantioselectivitymolecular dynamicstheozymeAlcohol Oxidoreductases (mesh)Amino Acid Substitution (mesh)Bacterial Proteins (mesh)Catalytic Domain (mesh)CrystallographyX-Ray (mesh)Directed Molecular Evolution (mesh)Enzyme Stability (mesh)Kinetics (mesh)Lactobacillus (mesh)ModelsMolecular (mesh)Molecular Dynamics Simulation (mesh)MutagenesisSite-Directed (mesh)Protein Conformation (mesh)Quantum Theory (mesh)Stereoisomerism (mesh)Substrate Specificity (mesh)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0zh6x41bhttps://escholarship.org/content/qt0zh6x41b/qt0zh6x41b.pdfinfo:doi/10.1073/pnas.1507910112articleProceedings of the National Academy of Sciences of the United States of America, vol 112, iss 51e7065 - e7072oai:escholarship.org:ark:/13030/qt7b37h0vb2026-08-29T02:10:06Zqt7b37h0vbNovel insights into the composition and function of the Toxoplasma IMC suturesChen, Allan LMoon, Andy SBell, Hannah NHuang, Amy SVashisht, Ajay AToh, Justin YLin, Andrew HNadipuram, Santhosh MKim, Elliot WChoi, Charles PWohlschlegel, James ABradley, Peter J2017-04-01The Toxoplasma inner membrane complex (IMC) is a specialized organelle underlying the parasite's plasma membrane that consists of flattened rectangular membrane sacs that are sutured together and positioned atop a supportive cytoskeleton. We have previously identified a novel class of proteins localizing to the transverse and longitudinal sutures of the IMC, which we named IMC sutures components (ISCs). Here, we have used proximity-dependent biotin identification at the sutures to better define the composition of this IMC subcompartment. Using ISC4 as bait, we demonstrate biotin-dependent labeling of the sutures and have uncovered two new ISCs. We also identified five new proteins that exclusively localize to the transverse sutures that we named transverse sutures components (TSCs), demonstrating that components of the IMC sutures consist of two groups: those that localize to the transverse and longitudinal sutures (ISCs) and those residing only in the transverse sutures (TSCs). In addition, we functionally analyze the ISC protein ISC3 and demonstrate that ISC3-null parasites have morphological defects and reduced fitness in vitro. Most importantly, Δisc3 parasites exhibit a complete loss of virulence in vivo. These studies expand the known composition of the IMC sutures and highlight the contribution of ISCs to the ability of the parasite to proliferate and cause disease.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)2.1 Biological and endogenous factors (hrcs-rac)CellsCultured (mesh)Female (mesh)Gene Knockout Techniques (mesh)Host-Parasite Interactions (mesh)Humans (mesh)Phosphatidate Phosphatase (mesh)Protozoan Proteins (mesh)Toxoplasma (mesh)Virulence (mesh)CellsCultured (mesh)Humans (mesh)Toxoplasma (mesh)Phosphatidate Phosphatase (mesh)Protozoan Proteins (mesh)Virulence (mesh)Female (mesh)Host-Parasite Interactions (mesh)Gene Knockout Techniques (mesh)CellsCultured (mesh)Female (mesh)Gene Knockout Techniques (mesh)Host-Parasite Interactions (mesh)Humans (mesh)Phosphatidate Phosphatase (mesh)Protozoan Proteins (mesh)Toxoplasma (mesh)Virulence (mesh)0605 Microbiology (for)1108 Medical Microbiology (for)Microbiology (science-metrix)3107 Microbiology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7b37h0vbhttps://escholarship.org/content/qt7b37h0vb/qt7b37h0vb.pdfinfo:doi/10.1111/cmi.12678articleCellular Microbiology, vol 19, iss 4e12678oai:escholarship.org:ark:/13030/qt2jj1f6172026-08-29T00:53:33Zqt2jj1f617CryoEM structure of the Methanospirillum hungatei archaellum reveals structural features distinct from the bacterial flagellum and type IV pilusPoweleit, NicoleGe, PengNguyen, Hong HLoo, Rachel R OgorzalekGunsalus, Robert PZhou, Z Hong2017-03-01Archaea use flagella known as archaella—distinct both in protein composition and structure from bacterial flagella—to drive cell motility, but the structural basis of this function is unknown. Here, we report an atomic model of the archaella, based on the cryo electron microscopy (cryoEM) structure of the Methanospirillum hungatei archaellum at 3.4 Å resolution. Each archaellum contains ∼61,500 archaellin subunits organized into a curved helix with a diameter of 10 nm and average length of 10,000 nm. The tadpole-shaped archaellin monomer has two domains, a β-barrel domain and a long, mildly kinked α-helix tail. Our structure reveals multiple post-translational modifications to the archaella, including six O-linked glycans and an unusual N-linked modification. The extensive interactions among neighbouring archaellins explain how the long but thin archaellum maintains the structural integrity required for motility-driving rotation. These extensive inter-subunit interactions and the absence of a central pore in the archaellum distinguish it from both the bacterial flagellum and type IV pili.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Generic health relevance (hrcs-hc)Cryoelectron Microscopy (mesh)Flagella (mesh)Methanospirillum (mesh)Flagella (mesh)Methanospirillum (mesh)Cryoelectron Microscopy (mesh)Cryoelectron Microscopy (mesh)Flagella (mesh)Methanospirillum (mesh)0605 Microbiology (for)1108 Medical Microbiology (for)3107 Microbiology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2jj1f617https://escholarship.org/content/qt2jj1f617/qt2jj1f617.pdfinfo:doi/10.1038/nmicrobiol.2016.222articleNature Microbiology, vol 2, iss 316222oai:escholarship.org:ark:/13030/qt8010v6nq2026-08-29T00:18:49Zqt8010v6nqUniversal chromatin state annotation of the mouse genomeVu, HaErnst, Jason2023-06-27Abstract
A large-scale application of the “stacked modeling” approach for chromatin state discovery previously provides a single “universal” chromatin state annotation of the human genome based jointly on data from many cell and tissue types. Here, we produce an analogous chromatin state annotation for mouse based on 901 datasets assaying 14 chromatin marks in 26 cell or tissue types. To characterize each chromatin state, we relate the states to external annotations and compare them to analogously defined human states. We expect the universal chromatin state annotation for mouse to be a useful resource for studying this key model organism’s genome.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)3105 Genetics (for-2020)Human Genome (rcdc)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Animals (mesh)Mice (mesh)Chromatin (mesh)GenomeHuman (mesh)Molecular Sequence Annotation (mesh)Chromatin (mesh)Animals (mesh)Mice (mesh)GenomeHuman (mesh)Molecular Sequence Annotation (mesh)Animals (mesh)Mice (mesh)Chromatin (mesh)GenomeHuman (mesh)Molecular Sequence Annotation (mesh)05 Environmental Sciences (for)06 Biological Sciences (for)08 Information and Computing Sciences (for)Bioinformatics (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/8010v6nqhttps://escholarship.org/content/qt8010v6nq/qt8010v6nq.pdfinfo:doi/10.1186/s13059-023-02994-xarticleGenome Biology, vol 24, iss 1153oai:escholarship.org:ark:/13030/qt4b8158872026-08-28T16:07:25Zqt4b815887Head organizer: Cerberus and IGF cooperate in brain induction in Xenopus embryosAzbazdar, YagmurPera, Edgar MDe Robertis, Edward M2025-12-01Neural induction by cell-cell signaling was discovered a century ago by the organizer transplantations of Spemann and Mangold in amphibians. Spemann later found that early dorsal blastopore lips induced heads and late organizers trunk-tail structures. Identifying region-specific organizer signals has been a driving force in the progress of animal biology. Head induction in the absence of trunk is designated archencephalic differentiation. Two specific head inducers, Cerberus and Insulin-like growth factors (IGFs), that induce archencephalic brain but not trunk-tail structures have been described previously. However, whether these two signals interact with each other had not been studied to date and was the purpose of the present investigation. It was found that Cerberus, a multivalent growth factor antagonist that inhibits Nodal, BMP and Wnt signals, strongly cooperated with IGF2, a growth factor that provides a positive signal through tyrosine kinase IGF receptors that activate MAPK and other pathways. The ectopic archencephalic structures induced by the combination of Cerberus and IGF2 are of higher frequency and larger than either one alone. They contain brain, a cyclopic eye and multiple olfactory placodes, without trace of trunk structures such as notochord or somites. A dominant-negative secreted IGF receptor 1 blocked Cerberus activity, indicating that endogenous IGF signals are required for ectopic brain formation. In a sensitized embryonic system, in which embryos were depleted of β-catenin, IGF2 did not by itself induce neural tissue while in combination with Cerberus it greatly enhanced formation of circular brain structures expressing the anterior markers Otx2 and Rx2a, but not spinal cord or notochord markers. The main conclusion of this work is that IGF provides a positive signal initially uniformly expressed throughout the embryo that potentiates the effect of an organizer-specific negative signal mediated by Cerberus. The results are discussed in the context of the history of neural induction.3109 Zoology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Neurosciences (rcdc)Pediatric Research Initiative (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Animals (mesh)Brain (mesh)Xenopus Proteins (mesh)Xenopus laevis (mesh)Signal Transduction (mesh)Insulin-Like Growth Factor II (mesh)EmbryoNonmammalian (mesh)Somatomedins (mesh)OrganizersEmbryonic (mesh)Head (mesh)Embryonic Induction (mesh)Gene Expression RegulationDevelopmental (mesh)Spemann organizerEmbryonic inductionIGF signalingArchencephalic developmentTrunk-tail inducersHead (mesh)Brain (mesh)EmbryoNonmammalian (mesh)OrganizersEmbryonic (mesh)Animals (mesh)Xenopus laevis (mesh)Somatomedins (mesh)Insulin-Like Growth Factor II (mesh)Xenopus Proteins (mesh)Embryonic Induction (mesh)Signal Transduction (mesh)Gene Expression RegulationDevelopmental (mesh)Archencephalic developmentEmbryonic inductionIGF signalingSpemann organizerTrunk-tail inducersAnimals (mesh)Brain (mesh)Xenopus Proteins (mesh)Xenopus laevis (mesh)Signal Transduction (mesh)Insulin-Like Growth Factor II (mesh)EmbryoNonmammalian (mesh)Somatomedins (mesh)OrganizersEmbryonic (mesh)Head (mesh)Embryonic Induction (mesh)Gene Expression RegulationDevelopmental (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/4b815887https://escholarship.org/content/qt4b815887/qt4b815887.pdfinfo:doi/10.1016/j.cdev.2023.203897articleCells and Development, vol 184203897oai:escholarship.org:ark:/13030/qt23t0s57q2026-08-27T12:56:24Zqt23t0s57qProximity biotinylation reveals novel secreted dense granule proteins of Toxoplasma gondii bradyzoitesNadipuram, Santhosh MukundThind, Amara CervantesRayatpisheh, ShimaWohlschlegel, James AkiraBradley, Peter JohnMoreno, Silvia N2020-05-06Toxoplasma gondii is an obligate intracellular parasite which is capable of establishing life-long chronic infection in any mammalian host. During the intracellular life cycle, the parasite secretes an array of proteins into the parasitophorous vacuole (PV) where it resides. Specialized organelles called the dense granules secrete GRA proteins that are known to participate in nutrient acquisition, immune evasion, and host cell-cycle manipulation. Although many GRAs have been discovered which are expressed during the acute infection mediated by tachyzoites, little is known about those that participate in the chronic infection mediated by the bradyzoite form of the parasite. In this study, we sought to uncover novel bradyzoite-upregulated GRA proteins using proximity biotinylation, which we previously used to examine the secreted proteome of the tachyzoites. Using a fusion of the bradyzoite upregulated protein MAG1 to BirA* as bait and a strain with improved switch efficiency, we identified a number of novel GRA proteins which are expressed in bradyzoites. After using the CRISPR/Cas9 system to characterize these proteins by gene knockout, we focused on one of these GRAs (GRA55) and found it was important for the establishment or maintenance of cysts in the mouse brain. These findings highlight new components of the GRA proteome of the tissue-cyst life stage of T. gondii and identify potential targets that are important for maintenance of parasite persistence in vivo.3009 Veterinary Sciences (for-2020)30 AgriculturalVeterinary and Food Sciences (for-2020)3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Emerging Infectious Diseases (rcdc)Biotechnology (rcdc)Infectious Diseases (rcdc)Biodefense (rcdc)Genetics (rcdc)2.2 Factors relating to the physical environment (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Infection (hrcs-hc)Generic health relevance (hrcs-hc)Animals (mesh)Biotinylation (mesh)Brain (mesh)CRISPR-Cas Systems (mesh)Female (mesh)Gene Knockout Techniques (mesh)GenesProtozoan (mesh)Humans (mesh)Life Cycle Stages (mesh)Mice (mesh)MiceInbred C57BL (mesh)Proteome (mesh)Protozoan Proteins (mesh)Toxoplasma (mesh)ToxoplasmosisAnimal (mesh)ToxoplasmosisCerebral (mesh)Vacuoles (mesh)Virulence (mesh)Brain (mesh)Vacuoles (mesh)Animals (mesh)MiceInbred C57BL (mesh)Humans (mesh)Mice (mesh)Toxoplasma (mesh)ToxoplasmosisCerebral (mesh)ToxoplasmosisAnimal (mesh)Proteome (mesh)Protozoan Proteins (mesh)Biotinylation (mesh)Virulence (mesh)Life Cycle Stages (mesh)GenesProtozoan (mesh)Female (mesh)Gene Knockout Techniques (mesh)CRISPR-Cas Systems (mesh)Animals (mesh)Biotinylation (mesh)Brain (mesh)CRISPR-Cas Systems (mesh)Female (mesh)Gene Knockout Techniques (mesh)GenesProtozoan (mesh)Humans (mesh)Life Cycle Stages (mesh)Mice (mesh)MiceInbred C57BL (mesh)Proteome (mesh)Protozoan Proteins (mesh)Toxoplasma (mesh)ToxoplasmosisAnimal (mesh)ToxoplasmosisCerebral (mesh)Vacuoles (mesh)Virulence (mesh)General Science & Technology (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/23t0s57qhttps://escholarship.org/content/qt23t0s57q/qt23t0s57q.pdfinfo:doi/10.1371/journal.pone.0232552articlePLOS ONE, vol 15, iss 5e0232552oai:escholarship.org:ark:/13030/qt7zn9049m2026-08-27T09:49:34Zqt7zn9049mStructure of amyloid-β (20-34) with Alzheimer’s-associated isomerization at Asp23 reveals a distinct protofilament interfaceWarmack, Rebeccah ABoyer, David RZee, Chih-TeRichards, Logan SSawaya, Michael RCascio, DuilioGonen, TamirEisenberg, David SClarke, Steven G2019-07-26Amyloid-β (Aβ) harbors numerous posttranslational modifications (PTMs) that may affect Alzheimer’s disease (AD) pathogenesis. Here we present the 1.1 Å resolution MicroED structure of an Aβ 20–34 fibril with and without the disease-associated PTM, L-isoaspartate, at position 23 (L-isoAsp23). Both wild-type and L-isoAsp23 protofilaments adopt β-helix-like folds with tightly packed cores, resembling the cores of full-length fibrillar Aβ structures, and both self-associate through two distinct interfaces. One of these is a unique Aβ interface strengthened by the isoaspartyl modification. Powder diffraction patterns suggest a similar structure may be adopted by protofilaments of an analogous segment containing the heritable Iowa mutation, Asp23Asn. Consistent with its early onset phenotype in patients, Asp23Asn accelerates aggregation of Aβ 20–34, as does the L-isoAsp23 modification. These structures suggest that the enhanced amyloidogenicity of the modified Aβ segments may also reduce the concentration required to achieve nucleation and therefore help spur the pathogenesis of AD.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Neurodegenerative (rcdc)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)Acquired Cognitive Impairment (rcdc)Alzheimer's Disease (rcdc)Brain Disorders (rcdc)Aging (rcdc)Neurosciences (rcdc)Dementia (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Neurological (hrcs-hc)Alzheimer Disease (mesh)Amino Acid Sequence (mesh)Amyloid beta-Peptides (mesh)Aspartic Acid (mesh)Humans (mesh)Isoaspartic Acid (mesh)Isomerism (mesh)Mutation (mesh)Protein Conformation (mesh)Humans (mesh)Alzheimer Disease (mesh)Aspartic Acid (mesh)Isoaspartic Acid (mesh)Amino Acid Sequence (mesh)Protein Conformation (mesh)Mutation (mesh)Isomerism (mesh)Amyloid beta-Peptides (mesh)Alzheimer Disease (mesh)Amino Acid Sequence (mesh)Amyloid beta-Peptides (mesh)Aspartic Acid (mesh)Humans (mesh)Isoaspartic Acid (mesh)Isomerism (mesh)Mutation (mesh)Protein Conformation (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/7zn9049mhttps://escholarship.org/content/qt7zn9049m/qt7zn9049m.pdfinfo:doi/10.1038/s41467-019-11183-zarticleNature Communications, vol 10, iss 13357oai:escholarship.org:ark:/13030/qt4898p2wh2026-08-27T06:33:03Zqt4898p2whINO80C Remodeler Maintains Genomic Stability by Preventing Promiscuous Transcription at Replication OriginsTopal, SalihVan, ChristopherXue, YongCarey, Michael FPeterson, Craig L2020-09-01The proper coordination of transcription with DNA replication and repair is central for genomic stability. We investigate how the INO80C chromatin remodeling enzyme might coordinate these genomic processes. We find that INO80C co-localizes with the origin recognition complex (ORC) at yeast replication origins and is bound to replication initiation sites in mouse embryonic stem cells (mESCs). In yeast, INO80C recruitment requires origin sequences but does not require ORC, suggesting that recruitment is independent of pre-replication complex assembly. In both yeast and ESCs, INO80C co-localizes at origins with Mot1 and NC2 transcription factors, and genetic studies suggest that they function together to promote genome stability. Interestingly, nascent transcript sequencing demonstrates that INO80C and Mot1 prevent pervasive transcription through origin sequences, and absence of these factors leads to formation of new DNA double-strand breaks. We propose that INO80C and Mot1/NC2 function through distinct pathways to limit origin transcription, maintaining genomic stability.31 Biological Sciences (for-2020)3105 Genetics (for-2020)Stem Cell Research - Embryonic - Non-Human (rcdc)Human Genome (rcdc)Genetics (rcdc)Stem Cell Research (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)ATPases Associated with Diverse Cellular Activities (mesh)Chromatin (mesh)DNA-Binding Proteins (mesh)Genomic Instability (mesh)Humans (mesh)Replication Origin (mesh)Transcription Factors (mesh)Chromatin (mesh)Humans (mesh)Genomic Instability (mesh)DNA-Binding Proteins (mesh)Transcription Factors (mesh)Replication Origin (mesh)ATPases Associated with Diverse Cellular Activities (mesh)DSBINO80Mot1NC2NET-seqORCchromatinncRNAreplicationATPases Associated with Diverse Cellular Activities (mesh)Chromatin (mesh)DNA-Binding Proteins (mesh)Genomic Instability (mesh)Humans (mesh)Replication Origin (mesh)Transcription Factors (mesh)0601 Biochemistry and Cell Biology (for)1116 Medical Physiology (for)31 Biological sciences (for-2020)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/4898p2whhttps://escholarship.org/content/qt4898p2wh/qt4898p2wh.pdfinfo:doi/10.1016/j.celrep.2020.108106articleCell Reports, vol 32, iss 10108106oai:escholarship.org:ark:/13030/qt6rf7545c2026-08-27T02:09:56Zqt6rf7545cEstrogen receptor α controls metabolism in white and brown adipocytes by regulating Polg1 and mitochondrial remodelingZhou, ZhenqiMoore, Timothy MDrew, Brian GRibas, VicentWanagat, JonathanCivelek, MeteSegawa, MayukoWolf, Dane MNorheim, FrodeSeldin, Marcus MStrumwasser, Alexander RWhitney, Kate ALester, EllenReddish, Britany RVergnes, LaurentReue, KarenRajbhandari, PrashantTontonoz, PeterLee, JasonMahata, Sushil KHewitt, Sylvia CShirihai, OrianGastonbury, CraigSmall, Kerrin SLaakso, MarkkuJensen, JorgenLee, SindreDrevon, Christian AKorach, Kenneth SLusis, Aldons JHevener, Andrea L2020-08-05Obesity is heightened during aging, and although the estrogen receptor α (ERα) has been implicated in the prevention of obesity, its molecular actions in adipocytes remain inadequately understood. Here, we show that adipose tissue ESR1/Esr1 expression inversely associated with adiposity and positively associated with genes involved in mitochondrial metabolism and markers of metabolic health in 700 Finnish men and 100 strains of inbred mice from the UCLA Hybrid Mouse Diversity Panel. To determine the anti-obesity actions of ERα in fat, we selectively deleted Esr1 from white and brown adipocytes in mice. In white adipose tissue, Esr1 controlled oxidative metabolism by restraining the targeted elimination of mitochondria via the E3 ubiquitin ligase parkin. mtDNA content was elevated, and adipose tissue mass was reduced in adipose-selective parkin knockout mice. In brown fat centrally involved in body temperature maintenance, Esr1 was requisite for both mitochondrial remodeling by dynamin-related protein 1 (Drp1) and uncoupled respiration thermogenesis by uncoupled protein 1 (Ucp1). In both white and brown fat of female mice and adipocytes in culture, mitochondrial dysfunction in the context of Esr1 deletion was paralleled by a reduction in the expression of the mtDNA polymerase γ subunit Polg1 We identified Polg1 as an ERα target gene by showing that ERα binds the Polg1 promoter to control its expression in 3T3L1 adipocytes. These findings support strategies leveraging ERα action on mitochondrial function in adipocytes to combat obesity and metabolic dysfunction.3206 Medical Biotechnology (for-2020)40 Engineering (for-2020)32 Biomedical and Clinical Sciences (for-2020)4003 Biomedical Engineering (for-2020)Genetics (rcdc)Obesity (rcdc)Women's Health (rcdc)Biotechnology (rcdc)Estrogen (rcdc)Nutrition (rcdc)Aging (rcdc)Diabetes (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Metabolic and endocrine (hrcs-hc)AdipocytesBrown (mesh)AdipocytesWhite (mesh)Adipose TissueBrown (mesh)Animals (mesh)Estrogen Receptor alpha (mesh)Female (mesh)Mice (mesh)Mitochondria (mesh)Mitochondrial Proteins (mesh)Thermogenesis (mesh)Uncoupling Protein 1 (mesh)Mitochondria (mesh)Animals (mesh)Mice (mesh)Mitochondrial Proteins (mesh)Estrogen Receptor alpha (mesh)Thermogenesis (mesh)Female (mesh)Adipose TissueBrown (mesh)AdipocytesBrown (mesh)AdipocytesWhite (mesh)Uncoupling Protein 1 (mesh)AdipocytesBrown (mesh)AdipocytesWhite (mesh)Adipose TissueBrown (mesh)Animals (mesh)Estrogen Receptor alpha (mesh)Female (mesh)Mice (mesh)Mitochondria (mesh)Mitochondrial Proteins (mesh)Thermogenesis (mesh)Uncoupling Protein 1 (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)3206 Medical biotechnology (for-2020)4003 Biomedical engineering (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6rf7545chttps://escholarship.org/content/qt6rf7545c/qt6rf7545c.pdfinfo:doi/10.1126/scitranslmed.aax8096articleScience Translational Medicine, vol 12, iss 555eaax8096oai:escholarship.org:ark:/13030/qt4v52f5p52026-08-26T22:13:34Zqt4v52f5p5A genetic signature of the evolution of loss of flight in the Galapagos cormorantBurga, AlejandroWang, WeiguangBen-David, EyalWolf, Paul CRamey, Andrew MVerdugo, ClaudioLyons, KarenParker, Patricia GKruglyak, Leonid2017-06-02We have a limited understanding of the genetic and molecular basis of evolutionary changes in the size and proportion of limbs. We studied wing and pectoral skeleton reduction leading to flightlessness in the Galapagos cormorant (Phalacrocorax harrisi). We sequenced and de novo assembled the genomes of four cormorant species and applied a predictive and comparative genomics approach to find candidate variants that may have contributed to the evolution of flightlessness. These analyses and cross-species experiments in Caenorhabditis elegans and in chondrogenic cell lines implicated variants in genes necessary for transcriptional regulation and function of the primary cilium. Cilia are essential for Hedgehog signaling, and humans affected by skeletal ciliopathies suffer from premature bone growth arrest, mirroring skeletal features associated with loss of flight.31 Biological Sciences (for-2020)3104 Evolutionary Biology (for-2020)3105 Genetics (for-2020)Biotechnology (rcdc)Genetics (rcdc)Human Genome (rcdc)Congenital Structural Anomalies (rcdc)Pediatric Research Initiative (rcdc)Generic health relevance (hrcs-hc)Animals (mesh)Biological Evolution (mesh)Birds (mesh)Bone and Bones (mesh)Caenorhabditis elegans (mesh)Cell Differentiation (mesh)Cell Line (mesh)Chondrogenesis (mesh)Cilia (mesh)Ecuador (mesh)Gene Expression Regulation (mesh)Genetic Variation (mesh)Genome (mesh)Homeodomain Proteins (mesh)Mutation (mesh)Phylogeny (mesh)WingsAnimal (mesh)Bone and Bones (mesh)Cell Line (mesh)Cilia (mesh)Animals (mesh)Birds (mesh)Caenorhabditis elegans (mesh)Homeodomain Proteins (mesh)Phylogeny (mesh)Cell Differentiation (mesh)Gene Expression Regulation (mesh)Chondrogenesis (mesh)Mutation (mesh)Genome (mesh)Ecuador (mesh)Genetic Variation (mesh)Biological Evolution (mesh)WingsAnimal (mesh)Animals (mesh)Biological Evolution (mesh)Birds (mesh)Bone and Bones (mesh)Caenorhabditis elegans (mesh)Cell Differentiation (mesh)Cell Line (mesh)Chondrogenesis (mesh)Cilia (mesh)Ecuador (mesh)Gene Expression Regulation (mesh)Genetic Variation (mesh)Genome (mesh)Homeodomain Proteins (mesh)Mutation (mesh)Phylogeny (mesh)WingsAnimal (mesh)General Science & Technology (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4v52f5p5https://escholarship.org/content/qt4v52f5p5/qt4v52f5p5.pdfinfo:doi/10.1126/science.aal3345articleScience, vol 356, iss 6341eaal3345oai:escholarship.org:ark:/13030/qt6170x28w2026-08-26T19:34:23Zqt6170x28wMolecular sociology of virus-induced cellular condensates supporting reovirus assembly and replicationLiu, XiaoyuXia, XianMartynowycz, Michael WGonen, TamirZhou, Z Hong2024-12-06Virus-induced cellular condensates, or viral factories, are poorly understood high-density phases where replication of many viruses occurs. Here, by cryogenic electron tomography (cryoET) of focused ion beam (FIB) milling-produced lamellae of mammalian reovirus (MRV)-infected cells, we visualized the molecular organization and interplay (i.e., “molecular sociology”) of host and virus in 3D at two time points post-infection, enabling a detailed description of these condensates and a mechanistic understanding of MRV replication within them. Expanding over time, the condensate fashions host ribosomes at its periphery, and host microtubules, lipid membranes, and viral molecules in its interior, forming a 3D architecture that supports the dynamic processes of viral genome replication and capsid assembly. A total of six MRV assembly intermediates are identified inside the condensate: star core, empty and genome-containing cores, empty and full virions, and outer shell particle. Except for star core, these intermediates are visualized at atomic resolution by cryogenic electron microscopy (cryoEM) of cellular extracts. The temporal sequence and spatial rearrangement among these viral intermediates choreograph the viral life cycle within the condensates. Together, the molecular sociology of MRV-induced cellular condensate highlights the functional advantage of transient enrichment of molecules at the right location and time for viral replication.3207 Medical Microbiology (for-2020)32 Biomedical and Clinical Sciences (for-2020)51 Physical Sciences (for-2020)31 Biological Sciences (for-2020)Infectious Diseases (rcdc)2.2 Factors relating to the physical environment (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)Infection (hrcs-hc)Virus Replication (mesh)Virus Assembly (mesh)Cryoelectron Microscopy (mesh)Animals (mesh)Electron Microscope Tomography (mesh)GenomeViral (mesh)Humans (mesh)Capsid (mesh)Virion (mesh)Cell Line (mesh)Reoviridae (mesh)Microtubules (mesh)Ribosomes (mesh)OrthoreovirusMammalian (mesh)Cell Line (mesh)Microtubules (mesh)Ribosomes (mesh)Animals (mesh)Humans (mesh)Reoviridae (mesh)OrthoreovirusMammalian (mesh)Virion (mesh)Capsid (mesh)Cryoelectron Microscopy (mesh)Virus Replication (mesh)Virus Assembly (mesh)GenomeViral (mesh)Electron Microscope Tomography (mesh)Virus Replication (mesh)Virus Assembly (mesh)Cryoelectron Microscopy (mesh)Animals (mesh)Electron Microscope Tomography (mesh)GenomeViral (mesh)Humans (mesh)Capsid (mesh)Virion (mesh)Cell Line (mesh)Reoviridae (mesh)Microtubules (mesh)Ribosomes (mesh)OrthoreovirusMammalian (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/6170x28whttps://escholarship.org/content/qt6170x28w/qt6170x28w.pdfinfo:doi/10.1038/s41467-024-54968-7articleNature Communications, vol 15, iss 110638oai:escholarship.org:ark:/13030/qt2wr7c2jn2026-08-26T13:43:58Zqt2wr7c2jnBioinformatic identification of previously unrecognized amyloidogenic proteinsRosenberg, Gregory MMurray, Kevin ASalwinski, LukaszHughes, Michael PAbskharon, RomanyEisenberg, David S2022-05-01Low-complexity domains (LCDs) of proteins have been shown to self-associate, and pathogenic mutations within these domains often drive the proteins into amyloid aggregation associated with disease. These domains may be especially susceptible to amyloidogenic mutations because they are commonly intrinsically disordered and function in self-association. The question therefore arises whether a search for pathogenic mutations in LCDs of the human proteome can lead to identification of other proteins associated with amyloid disease. Here, we take a computational approach to identify documented pathogenic mutations within LCDs that may favor amyloid formation. Using this approach, we identify numerous known amyloidogenic mutations, including several such mutations within proteins previously unidentified as amyloidogenic. Among the latter group, we focus on two mutations within the TRK-fused gene protein (TFG), known to play roles in protein secretion and innate immunity, which are associated with two different peripheral neuropathies. We show that both mutations increase the propensity of TFG to form amyloid fibrils. We therefore conclude that TFG is a novel amyloid protein and propose that the diseases associated with its mutant forms may be amyloidoses.3101 Biochemistry and Cell Biology (for-2020)3102 Bioinformatics and Computational Biology (for-2020)31 Biological Sciences (for-2020)Alzheimer's Disease (rcdc)Neurodegenerative (rcdc)Brain Disorders (rcdc)Dementia (rcdc)Acquired Cognitive Impairment (rcdc)Aging (rcdc)Rare Diseases (rcdc)Neurosciences (rcdc)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Neurological (hrcs-hc)Amyloid (mesh)Amyloidogenic Proteins (mesh)Amyloidosis (mesh)Computational Biology (mesh)Humans (mesh)Mutation (mesh)Proteome (mesh)Humans (mesh)Amyloidosis (mesh)Amyloid (mesh)Proteome (mesh)Computational Biology (mesh)Mutation (mesh)Amyloidogenic Proteins (mesh)Charcot–Marie–Tooth disease electron microscopyamyloidintrinsically disordered proteinlow-complexity domainprotein structureAmyloid (mesh)Amyloidogenic Proteins (mesh)Amyloidosis (mesh)Computational Biology (mesh)Humans (mesh)Mutation (mesh)Proteome (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biochemistry & Molecular Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/2wr7c2jnhttps://escholarship.org/content/qt2wr7c2jn/qt2wr7c2jn.pdfinfo:doi/10.1016/j.jbc.2022.101920articleJournal of Biological Chemistry, vol 298, iss 5101920oai:escholarship.org:ark:/13030/qt2jz6m0b92026-08-26T13:42:05Zqt2jz6m0b9Low complexity domains of the nucleocapsid protein of SARS-CoV-2 form amyloid fibrilsTayeb-Fligelman, EinavBowler, Jeannette TTai, Christen ESawaya, Michael RJiang, Yi XiaoGarcia, GustavoGriner, Sarah LCheng, XinyiSalwinski, LukaszLutter, LiisaSeidler, Paul MLu, JiahuiRosenberg, Gregory MHou, KeAbskharon, RomanyPan, HopeZee, Chih-TeBoyer, David RLi, YanAnderson, Daniel HMurray, Kevin AFalcon, GenesisCascio, DuilioSaelices, LorenaDamoiseaux, RobertArumugaswami, VaithilingarajaGuo, FengEisenberg, David S2023-04-25The self-assembly of the Nucleocapsid protein (NCAP) of SARS-CoV-2 is crucial for its function. Computational analysis of the amino acid sequence of NCAP reveals low-complexity domains (LCDs) akin to LCDs in other proteins known to self-assemble as phase separation droplets and amyloid fibrils. Previous reports have described NCAP’s propensity to phase-separate. Here we show that the central LCD of NCAP is capable of both, phase separation and amyloid formation. Within this central LCD we identified three adhesive segments and determined the atomic structure of the fibrils formed by each. Those structures guided the design of G12, a peptide that interferes with the self-assembly of NCAP and demonstrates antiviral activity in SARS-CoV-2 infected cells. Our work, therefore, demonstrates the amyloid form of the central LCD of NCAP and suggests that amyloidogenic segments of NCAP could be targeted for drug development.3101 Biochemistry and Cell Biology (for-2020)3102 Bioinformatics and Computational Biology (for-2020)31 Biological Sciences (for-2020)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)Brain Disorders (rcdc)Neurodegenerative (rcdc)Infectious Diseases (rcdc)Alzheimer's Disease (rcdc)Emerging Infectious Diseases (rcdc)Acquired Cognitive Impairment (rcdc)Neurosciences (rcdc)Coronaviruses (rcdc)Dementia (rcdc)Aging (rcdc)Humans (mesh)Amyloid (mesh)Amyloidogenic Proteins (mesh)COVID-19 (mesh)Nucleocapsid Proteins (mesh)Peptides (mesh)Protein Domains (mesh)SARS-CoV-2 (mesh)Coronavirus Nucleocapsid Proteins (mesh)Humans (mesh)Amyloid (mesh)Peptides (mesh)Nucleocapsid Proteins (mesh)Amyloidogenic Proteins (mesh)Protein Domains (mesh)COVID-19 (mesh)SARS-CoV-2 (mesh)Coronavirus Nucleocapsid Proteins (mesh)Humans (mesh)Amyloid (mesh)Amyloidogenic Proteins (mesh)COVID-19 (mesh)Nucleocapsid Proteins (mesh)Peptides (mesh)Protein Domains (mesh)SARS-CoV-2 (mesh)Coronavirus Nucleocapsid Proteins (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/2jz6m0b9https://escholarship.org/content/qt2jz6m0b9/qt2jz6m0b9.pdfinfo:doi/10.1038/s41467-023-37865-3articleNature Communications, vol 14, iss 12379oai:escholarship.org:ark:/13030/qt67d9m09g2026-08-26T13:42:00Zqt67d9m09gFibril structures of TFG protein mutants validate the identification of TFG as a disease-related amyloid protein by the IMPAcT methodRosenberg, Gregory MAbskharon, RomanyBoyer, David RGe, PengSawaya, Michael REisenberg, David SYortsos, Yannis2023-12-01We previously presented a bioinformatic method for identifying diseases that arise from a mutation in a protein's low-complexity domain that drives the protein into pathogenic amyloid fibrils. One protein so identified was the tropomyosin-receptor kinase-fused gene protein (TRK-fused gene protein or TFG). Mutations in TFG are associated with degenerative neurological conditions. Here, we present experimental evidence that confirms our prediction that these conditions are amyloid-related. We find that the low-complexity domain of TFG containing the disease-related mutations G269V or P285L forms amyloid fibrils, and we determine their structures using cryo-electron microscopy (cryo-EM). These structures are unmistakably amyloid in nature and confirm the propensity of the mutant TFG low-complexity domain to form amyloid fibrils. Also, despite resulting from a pathogenic mutation, the fibril structures bear some similarities to other amyloid structures that are thought to be nonpathogenic and even functional, but there are other factors that support these structures' relevance to disease, including an increased propensity to form amyloid compared with the wild-type sequence, structure-stabilizing influence from the mutant residues themselves, and double-protofilament amyloid cores. Our findings elucidate two potentially disease-relevant structures of a previously unknown amyloid and also show how the structural features of pathogenic amyloid fibrils may not conform to the features commonly associated with pathogenicity.3101 Biochemistry and Cell Biology (for-2020)3102 Bioinformatics and Computational Biology (for-2020)31 Biological Sciences (for-2020)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)Acquired Cognitive Impairment (rcdc)Neurodegenerative (rcdc)Neurosciences (rcdc)Alzheimer's Disease (rcdc)Brain Disorders (rcdc)Dementia (rcdc)Aging (rcdc)Rare Diseases (rcdc)Genetics (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Generic health relevance (hrcs-hc)amyloidcryo-electron microscopymutationCharcot-Marie-Tooth diseasehereditary motor and sensory neuropathy with proximal dominant involvementCharcot–Marie–Tooth diseaseamyloidcryo-electron microscopyhereditary motor and sensory neuropathy with proximal dominant involvementmutationapplication/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/67d9m09ghttps://escholarship.org/content/qt67d9m09g/qt67d9m09g.pdfinfo:doi/10.1093/pnasnexus/pgad402articlePNAS Nexus, vol 2, iss 12pgad402oai:escholarship.org:ark:/13030/qt7z03x03w2026-08-26T10:38:25Zqt7z03x03wStructure-based inhibitors of amyloid beta core suggest a common interface with tauGriner, Sarah LSeidler, PaulBowler, JeannetteMurray, Kevin AYang, Tianxiao PeterSahay, ShrutiSawaya, Michael RCascio, DuilioRodriguez, Jose APhilipp, StephanSosna, JustynaGlabe, Charles GGonen, TamirEisenberg, David S2019-10-15Alzheimer's disease (AD) pathology is characterized by plaques of amyloid beta (Aβ) and neurofibrillary tangles of tau. Aβ aggregation is thought to occur at early stages of the disease, and ultimately gives way to the formation of tau tangles which track with cognitive decline in humans. Here, we report the crystal structure of an Aβ core segment determined by MicroED and in it, note characteristics of both fibrillar and oligomeric structure. Using this structure, we designed peptide-based inhibitors that reduce Aβ aggregation and toxicity of already-aggregated species. Unexpectedly, we also found that these inhibitors reduce the efficiency of Aβ-mediated tau aggregation, and moreover reduce aggregation and self-seeding of tau fibrils. The ability of these inhibitors to interfere with both Aβ and tau seeds suggests these fibrils share a common epitope, and supports the hypothesis that cross-seeding is one mechanism by which amyloid is linked to tau aggregation and could promote cognitive decline.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Brain Disorders (rcdc)Aging (rcdc)Neurodegenerative (rcdc)Acquired Cognitive Impairment (rcdc)Dementia (rcdc)Neurosciences (rcdc)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)Alzheimer's Disease (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Neurological (hrcs-hc)Amyloid beta-Peptides (mesh)Animals (mesh)CrystallographyX-Ray (mesh)Humans (mesh)Molecular Structure (mesh)Protein Binding (mesh)Protein Conformation (mesh)tau Proteins (mesh)Animals (mesh)Humans (mesh)tau Proteins (mesh)CrystallographyX-Ray (mesh)Molecular Structure (mesh)Protein Conformation (mesh)Protein Binding (mesh)Amyloid beta-Peptides (mesh)MicroEDamyloidamyloid betabiochemistrychemical biologycross-seedinghumaninhibitormolecular biophysicsstructural biologytauAmyloid beta-Peptides (mesh)Animals (mesh)CrystallographyX-Ray (mesh)Humans (mesh)Molecular Structure (mesh)Protein Binding (mesh)Protein Conformation (mesh)tau Proteins (mesh)0601 Biochemistry and Cell Biology (for)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/7z03x03whttps://escholarship.org/content/qt7z03x03w/qt7z03x03w.pdfinfo:doi/10.7554/elife.46924articleELIFE, vol 8e46924oai:escholarship.org:ark:/13030/qt51q6k2842026-08-26T09:00:59Zqt51q6k284EXP1 is required for organisation of EXP2 in the intraerythrocytic malaria parasite vacuoleNessel, TimothyBeck, John MRayatpisheh, ShimaJami‐Alahmadi, YasamanWohlschlegel, James AGoldberg, Daniel EBeck, Josh R2020-05-01Intraerythrocytic malaria parasites reside within a parasitophorous vacuole membrane (PVM) that closely overlays the parasite plasma membrane. Although the PVM is the site of several transport activities essential to parasite survival, the basis for organisation of this membrane system is unknown. Here, we performed proximity labeling at the PVM with BioID2, which highlighted a group of single-pass integral membrane proteins that constitute a major component of the PVM proteome but whose function remains unclear. We investigated EXP1, the longest known member of this group, by adapting a CRISPR/Cpf1 genome editing system to install the TetR-DOZI-aptamers system for conditional translational control. Importantly, although EXP1 was required for intraerythrocytic development, a previously reported in vitro glutathione S-transferase activity could not account for this essential EXP1 function in vivo. EXP1 knockdown was accompanied by profound changes in vacuole ultrastructure, including apparent increased separation of the PVM from the parasite plasma membrane and formation of abnormal membrane structures. Furthermore, although activity of the Plasmodium translocon of exported proteins was not impacted by depletion of EXP1, the distribution of the translocon pore-forming protein EXP2 but not the HSP101 unfoldase was substantially altered. Collectively, our results reveal a novel PVM defect that indicates a critical role for EXP1 in maintaining proper organisation of EXP2 within the PVM.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Infectious Diseases (rcdc)Rare Diseases (rcdc)Biotechnology (rcdc)Malaria (rcdc)Vector-Borne Diseases (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Infection (hrcs-hc)3 Good Health and Well Being (sdg)Animals (mesh)AntigensProtozoan (mesh)Gene Editing (mesh)Malaria (mesh)Membrane Proteins (mesh)Parasites (mesh)Plasmodium (mesh)Plasmodium falciparum (mesh)Protozoan Proteins (mesh)Vacuoles (mesh)BioID2Cpf1Cas12aEXP1EXP2parasitophorous vacuolePlasmodium falciparumVacuoles (mesh)Animals (mesh)Parasites (mesh)Plasmodium (mesh)Plasmodium falciparum (mesh)Malaria (mesh)Membrane Proteins (mesh)Protozoan Proteins (mesh)AntigensProtozoan (mesh)Gene Editing (mesh)Plasmodium falciparumBioID2Cpf1/Cas12aEXP1EXP2parasitophorous vacuoleAnimals (mesh)AntigensProtozoan (mesh)Gene Editing (mesh)Malaria (mesh)Membrane Proteins (mesh)Parasites (mesh)Plasmodium (mesh)Plasmodium falciparum (mesh)Protozoan Proteins (mesh)Vacuoles (mesh)0605 Microbiology (for)1108 Medical Microbiology (for)Microbiology (science-metrix)3107 Microbiology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/51q6k284https://escholarship.org/content/qt51q6k284/qt51q6k284.pdfinfo:doi/10.1111/cmi.13168articleCellular Microbiology, vol 22, iss 5e13168 - e13168oai:escholarship.org:ark:/13030/qt7268g0j32026-08-26T08:41:30Zqt7268g0j3The Rhoptry Pseudokinase ROP54 Modulates Toxoplasma gondii Virulence and Host GBP2 LoadingKim, Elliot WNadipuram, Santhosh MTetlow, Ashley LBarshop, William DLiu, Philip TWohlschlegel, James ABradley, Peter JBlader, Ira J2016-04-27Toxoplasma gondii uses unique secretory organelles called rhoptries to inject an array of effector proteins into the host cytoplasm that hijack host cell functions. We have discovered a novel rhoptry pseudokinase effector, ROP54, which is injected into the host cell upon invasion and traffics to the cytoplasmic face of the parasitophorous vacuole membrane (PVM). Disruption of ROP54 in a type II strain of T. gondii does not affect growth in vitro but results in a 100-fold decrease in virulence in vivo, suggesting that ROP54 modulates some aspect of the host immune response. We show that parasites lacking ROP54 are more susceptible to macrophage-dependent clearance, further suggesting that ROP54 is involved in evasion of innate immunity. To determine how ROP54 modulates parasite virulence, we examined the loading of two known innate immune effectors, immunity-related GTPase b6 (IRGb6) and guanylate binding protein 2 (GBP2), in wild-type and ∆rop54II mutant parasites. While no difference in IRGb6 loading was seen, we observed a substantial increase in GBP2 loading on the parasitophorous vacuole (PV) of ROP54-disrupted parasites. These results demonstrate that ROP54 is a novel rhoptry effector protein that promotes Toxoplasma infections by modulating GBP2 loading onto parasite-containing vacuoles. IMPORTANCE The interactions between intracellular microbes and their host cells can lead to the discovery of novel drug targets. During Toxoplasma infections, host cells express an array of immunity-related GTPases (IRGs) and guanylate binding proteins (GBPs) that load onto the parasite-containing vacuole to clear the parasite. To counter this mechanism, the parasite secretes effector proteins that traffic to the vacuole to disarm the immunity-related loading proteins and evade the immune response. While the interplay between host IRGs and Toxoplasma effector proteins is well understood, little is known about how Toxoplasma neutralizes the GBP response. We describe here a T. gondii pseudokinase effector, ROP54, that localizes to the vacuole upon invasion and is critical for parasite virulence. Toxoplasma vacuoles lacking ROP54 display an increased loading of the host immune factor GBP2, but not IRGb6, indicating that ROP54 plays a distinct role in immune evasion.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Foodborne Illness (rcdc)Emerging Infectious Diseases (rcdc)Biodefense (rcdc)Infectious Diseases (rcdc)2.1 Biological and endogenous factors (hrcs-rac)2.2 Factors relating to the physical environment (hrcs-rac)Infection (hrcs-hc)Toxoplasma gondiiguanylate binding proteinsimmunity-related GTPasespseudokinaserhoptryvirulenceToxoplasma gondiiguanylate binding proteinsimmunity-related GTPasespseudokinaserhoptryvirulence1107 Immunology (for)Immunology (science-metrix)Microbiology (science-metrix)3204 Immunology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/7268g0j3https://escholarship.org/content/qt7268g0j3/qt7268g0j3.pdfinfo:doi/10.1128/msphere.00045-16articlemSphere, vol 1, iss 210.1128/msphere.00045 - 10.1128/msphere.00016oai:escholarship.org:ark:/13030/qt0781613z2026-08-26T08:39:57Zqt0781613zFumarate Mediates a Chronic Proliferative Signal in Fumarate Hydratase-Inactivated Cancer Cells by Increasing Transcription and Translation of Ferritin GenesKerins, Michael JohnVashisht, Ajay AmarLiang, Benjamin Xi-TongDuckworth, Spencer JordanPraslicka, Brandon JohnWohlschlegel, James AkiraOoi, Aikseng2017-06-01Germ line mutations of the gene encoding the tricarboxylic acid (TCA) cycle enzyme fumarate hydratase (FH) cause a hereditary cancer syndrome known as hereditary leiomyomatosis and renal cell cancer (HLRCC). HLRCC-associated tumors harbor biallelic FH inactivation that results in the accumulation of the TCA cycle metabolite fumarate. Although it is known that fumarate accumulation can alter cellular signaling, if and how fumarate confers a growth advantage remain unclear. Here we show that fumarate accumulation confers a chronic proliferative signal by disrupting cellular iron signaling. Specifically, fumarate covalently modifies cysteine residues on iron regulatory protein 2 (IRP2), rendering it unable to repress ferritin mRNA translation. Simultaneously, fumarate increases ferritin gene transcription by activating the NRF2 (nuclear factor [erythroid-derived 2]-like 2) transcription factor. In turn, increased ferritin protein levels promote the expression of the promitotic transcription factor FOXM1 (Forkhead box protein M1). Consistently, clinical HLRCC tissues showed increased expression levels of both FOXM1 and its proliferation-associated target genes. This finding demonstrates how FH inactivation can endow cells with a growth advantage.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Rare Diseases (rcdc)Cancer (rcdc)Genetics (rcdc)Kidney Disease (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Cancer (hrcs-hc)Amino Acid Sequence (mesh)CarcinomaRenal Cell (mesh)Cell LineTumor (mesh)Cell Proliferation (mesh)Ferritins (mesh)Forkhead Box Protein M1 (mesh)Fumarate Hydratase (mesh)Fumarates (mesh)Humans (mesh)Intracellular Space (mesh)Iron Regulatory Protein 2 (mesh)Kidney Neoplasms (mesh)Leiomyomatosis (mesh)ModelsBiological (mesh)NF-E2-Related Factor 2 (mesh)Protein Biosynthesis (mesh)Signal Transduction (mesh)Succinic Acid (mesh)TranscriptionGenetic (mesh)ferritinFHFOXM1fumarateHLRCCNRF2Cell LineTumor (mesh)Intracellular Space (mesh)Humans (mesh)Leiomyomatosis (mesh)CarcinomaRenal Cell (mesh)Kidney Neoplasms (mesh)Fumarates (mesh)Succinic Acid (mesh)Iron Regulatory Protein 2 (mesh)Fumarate Hydratase (mesh)Signal Transduction (mesh)Cell Proliferation (mesh)Protein Biosynthesis (mesh)TranscriptionGenetic (mesh)Amino Acid Sequence (mesh)ModelsBiological (mesh)NF-E2-Related Factor 2 (mesh)Ferritins (mesh)Forkhead Box Protein M1 (mesh)FHFOXM1HLRCCNRF2ferritinfumarateAmino Acid Sequence (mesh)CarcinomaRenal Cell (mesh)Cell LineTumor (mesh)Cell Proliferation (mesh)Ferritins (mesh)Forkhead Box Protein M1 (mesh)Fumarate Hydratase (mesh)Fumarates (mesh)Humans (mesh)Intracellular Space (mesh)Iron Regulatory Protein 2 (mesh)Kidney Neoplasms (mesh)Leiomyomatosis (mesh)ModelsBiological (mesh)NF-E2-Related Factor 2 (mesh)Protein Biosynthesis (mesh)Signal Transduction (mesh)Succinic Acid (mesh)TranscriptionGenetic (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0781613zhttps://escholarship.org/content/qt0781613z/qt0781613z.pdfinfo:doi/10.1128/mcb.00079-17articleMolecular and Cellular Biology, vol 37, iss 11e00079 - e00017oai:escholarship.org:ark:/13030/qt9kn4v20z2026-08-26T08:35:09Zqt9kn4v20zA photoactivatable crosslinking system reveals protein interactions in the Toxoplasma gondii inner membrane complexChoi, Charles PaulMoon, Andy SeongBack, Peter SungminJami‐Alahmadi, YasamanVashisht, Ajay AmarWohlschlegel, James AkiraBradley, Peter JohnCoppens, Isabelle2019-10-01The Toxoplasma gondii inner membrane complex (IMC) is an important organelle involved in parasite motility and replication. The IMC resides beneath the parasite's plasma membrane and is composed of both membrane and cytoskeletal components. Although the protein composition of the IMC is becoming better understood, the protein-protein associations that enable proper functioning of the organelle remain largely unknown. Determining protein interactions in the IMC cytoskeletal network is particularly challenging, as disrupting the cytoskeleton requires conditions that disrupt protein complexes. To circumvent this problem, we demonstrate the application of a photoreactive unnatural amino acid (UAA) crosslinking system to capture protein interactions in the native intracellular environment. In addition to identifying binding partners, the UAA approach maps the binding interface of the bait protein used for crosslinking, providing structural information of the interacting proteins. We apply this technology to the essential IMC protein ILP1 and demonstrate that distinct regions of its C-terminal coiled-coil domain crosslink to the alveolins IMC3 and IMC6, as well as IMC27. We also show that the IMC3 C-terminal domain and the IMC6 N-terminal domain are necessary for binding to ILP1, further mapping interactions between ILP1 and the cytoskeleton. Together, this study develops a new approach to study protein-protein interactions in Toxoplasma and provides the first insight into the architecture of the cytoskeletal network of the apicomplexan IMC.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Emerging Infectious Diseases (rcdc)Biodefense (rcdc)Infectious Diseases (rcdc)Foodborne Illness (rcdc)2.1 Biological and endogenous factors (hrcs-rac)2.2 Factors relating to the physical environment (hrcs-rac)Azides (mesh)Cell Membrane (mesh)Cross-Linking Reagents (mesh)Cytoskeletal Proteins (mesh)Cytoskeleton (mesh)Gene Expression (mesh)Intracellular Membranes (mesh)Phenylalanine (mesh)Photochemical Processes (mesh)Protein Binding (mesh)Protein Interaction Domains and Motifs (mesh)Protein Interaction Mapping (mesh)Protozoan Proteins (mesh)Toxoplasma (mesh)Ultraviolet Rays (mesh)Cell Membrane (mesh)Intracellular Membranes (mesh)Cytoskeleton (mesh)Toxoplasma (mesh)Azides (mesh)Phenylalanine (mesh)Cytoskeletal Proteins (mesh)Protozoan Proteins (mesh)Cross-Linking Reagents (mesh)Protein Interaction Mapping (mesh)Ultraviolet Rays (mesh)Gene Expression (mesh)Protein Binding (mesh)Protein Interaction Domains and Motifs (mesh)Photochemical Processes (mesh)Azides (mesh)Cell Membrane (mesh)Cross-Linking Reagents (mesh)Cytoskeletal Proteins (mesh)Cytoskeleton (mesh)Gene Expression (mesh)Intracellular Membranes (mesh)Phenylalanine (mesh)Photochemical Processes (mesh)Protein Binding (mesh)Protein Interaction Domains and Motifs (mesh)Protein Interaction Mapping (mesh)Protozoan Proteins (mesh)Toxoplasma (mesh)Ultraviolet Rays (mesh)06 Biological Sciences (for)07 Agricultural and Veterinary Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)30 Agriculturalveterinary and food sciences (for-2020)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/9kn4v20zhttps://escholarship.org/content/qt9kn4v20z/qt9kn4v20z.pdfinfo:doi/10.1371/journal.pbio.3000475articlePLOS Biology, vol 17, iss 10e3000475oai:escholarship.org:ark:/13030/qt39c6323f2026-08-26T01:31:22Zqt39c6323fRationale and design of a multicenter Chronic Kidney Disease (CKD) and at-risk for CKD electronic health records-based registry: CURE-CKDNorris, Keith CDuru, O KenrikAlicic, Radica ZDaratha, Kenn BNicholas, Susanne BMcPherson, Sterling MBell, Douglas SShen, Jenny IJones, Cami RMoin, TannazWaterman, Amy DNeumiller, Joshua JVargas, Roberto BBui, Alex ATMangione, Carol MTuttle, Katherine R2019-12-01BackgroundChronic kidney disease (CKD) is a global public health problem, exhibiting sharp increases in incidence, prevalence, and attributable morbidity and mortality. There is a critical need to better understand the demographics, clinical characteristics, and key risk factors for CKD; and to develop platforms for testing novel interventions to improve modifiable risk factors, particularly for the CKD patients with a rapid decline in kidney function.MethodsWe describe a novel collaboration between two large healthcare systems (Providence St. Joseph Health and University of California, Los Angeles Health) supported by leadership from both institutions, which was created to develop harmonized cohorts of patients with CKD or those at increased risk for CKD (hypertension/HTN, diabetes/DM, pre-diabetes) from electronic health record data.ResultsThe combined repository of candidate records included more than 3.3 million patients with at least a single qualifying measure for CKD and/or at-risk for CKD. The CURE-CKD registry includes over 2.6 million patients with and/or at-risk for CKD identified by stricter guide-line based criteria using a combination of administrative encounter codes, physical examinations, laboratory values and medication use. Notably, data based on race/ethnicity and geography in part, will enable robust analyses to study traditionally disadvantaged or marginalized patients not typically included in clinical trials.DiscussionCURE-CKD project is a unique multidisciplinary collaboration between nephrologists, endocrinologists, primary care physicians with health services research skills, health economists, and those with expertise in statistics, bio-informatics and machine learning. The CURE-CKD registry uses curated observations from real-world settings across two large healthcare systems and has great potential to provide important contributions for healthcare and for improving clinical outcomes in patients with and at-risk for CKD.4203 Health Services and Systems (for-2020)32 Biomedical and Clinical Sciences (for-2020)42 Health Sciences (for-2020)Health Disparities and Racial or Ethnic Minority Health Research (rcdc)Social Determinants of Health (rcdc)Women's Health (rcdc)Kidney Disease (rcdc)Networking and Information Technology R&D (NITRD) (rcdc)Health Services (rcdc)Machine Learning and Artificial Intelligence (rcdc)Prevention (rcdc)Minority Health (rcdc)Patient Safety (rcdc)Primary Health Care (rcdc)Clinical Research (rcdc)Renal and urogenital (hrcs-hc)3 Good Health and Well Being (sdg)Adult (mesh)Comprehensive Health Care (mesh)Diabetes Mellitus (mesh)Disease Progression (mesh)Electronic Health Records (mesh)Female (mesh)Humans (mesh)Hypertension (mesh)Male (mesh)Medical Record Linkage (mesh)Prevalence (mesh)Prognosis (mesh)Quality Improvement (mesh)Registries (mesh)Renal InsufficiencyChronic (mesh)Risk Assessment (mesh)Risk Factors (mesh)United States (mesh)Chronic kidney diseaseElectronic health recordsHealthcare systemsHypertensionDiabetesPre-diabetesRegistryStudy designCURE-CKD investigatorsHumans (mesh)Hypertension (mesh)Diabetes Mellitus (mesh)Disease Progression (mesh)Prognosis (mesh)Medical Record Linkage (mesh)Registries (mesh)Prevalence (mesh)Risk Assessment (mesh)Risk Factors (mesh)Adult (mesh)Comprehensive Health Care (mesh)United States (mesh)Female (mesh)Male (mesh)Renal InsufficiencyChronic (mesh)Electronic Health Records (mesh)Quality Improvement (mesh)Chronic kidney diseaseDiabetesElectronic health recordsHealthcare systemsHypertensionPre-diabetesRegistryStudy designAdult (mesh)Comprehensive Health Care (mesh)Diabetes Mellitus (mesh)Disease Progression (mesh)Electronic Health Records (mesh)Female (mesh)Humans (mesh)Hypertension (mesh)Male (mesh)Medical Record Linkage (mesh)Prevalence (mesh)Prognosis (mesh)Quality Improvement (mesh)Registries (mesh)Renal InsufficiencyChronic (mesh)Risk Assessment (mesh)Risk Factors (mesh)United States (mesh)1103 Clinical Sciences (for)Urology & Nephrology (science-metrix)3202 Clinical sciences (for-2020)4203 Health services and systems (for-2020)4205 Nursing (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/39c6323fhttps://escholarship.org/content/qt39c6323f/qt39c6323f.pdfinfo:doi/10.1186/s12882-019-1558-9articleBMC Nephrology, vol 20, iss 1416oai:escholarship.org:ark:/13030/qt3t8708z12026-08-25T23:44:45Zqt3t8708z1Single cell analysis reveals immune cell–adipocyte crosstalk regulating the transcription of thermogenic adipocytesRajbhandari, PrashantArneson, DouglasHart, Sydney KAhn, In SookDiamante, GracielSantos, Luis CZaghari, NimaFeng, An-ChiehThomas, Brandon JVergnes, LaurentLee, Stephen DRajbhandari, Abha KReue, KarenSmale, Stephen TYang, XiaTontonoz, Peter2019-10-23Immune cells are vital constituents of the adipose microenvironment that influence both local and systemic lipid metabolism. Mice lacking IL10 have enhanced thermogenesis, but the roles of specific cell types in the metabolic response to IL10 remain to be defined. We demonstrate here that selective loss of IL10 receptor α in adipocytes recapitulates the beneficial effects of global IL10 deletion, and that local crosstalk between IL10-producing immune cells and adipocytes is a determinant of thermogenesis and systemic energy balance. Single Nuclei Adipocyte RNA-sequencing (SNAP-seq) of subcutaneous adipose tissue defined a metabolically-active mature adipocyte subtype characterized by robust expression of genes involved in thermogenesis whose transcriptome was selectively responsive to IL10Rα deletion. Furthermore, single-cell transcriptomic analysis of adipose stromal populations identified lymphocytes as a key source of IL10 production in response to thermogenic stimuli. These findings implicate adaptive immune cell-adipocyte communication in the maintenance of adipose subtype identity and function.31 Biological Sciences (for-2020)32 Biomedical and Clinical Sciences (for-2020)3204 Immunology (for-2020)Genetics (rcdc)Human Genome (rcdc)Obesity (rcdc)Nutrition (rcdc)Diabetes (rcdc)2.1 Biological and endogenous factors (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)Metabolic and endocrine (hrcs-hc)7 Affordable and Clean Energy (sdg)Adipocytes (mesh)Animals (mesh)Cell Communication (mesh)Gene Expression Regulation (mesh)Interleukin-10 (mesh)Interleukin-10 Receptor alpha Subunit (mesh)Lymphocytes (mesh)Mice (mesh)Single-Cell Analysis (mesh)Thermogenesis (mesh)TranscriptionGenetic (mesh)Lymphocytes (mesh)Adipocytes (mesh)Animals (mesh)Mice (mesh)Interleukin-10 (mesh)Cell Communication (mesh)TranscriptionGenetic (mesh)Gene Expression Regulation (mesh)Thermogenesis (mesh)Interleukin-10 Receptor alpha Subunit (mesh)Single-Cell Analysis (mesh)adipocytecell biologycytokinehuman biologymedicinemetabolismmouseAdipocytes (mesh)Animals (mesh)Cell Communication (mesh)Gene Expression Regulation (mesh)Interleukin-10 (mesh)Interleukin-10 Receptor alpha Subunit (mesh)Lymphocytes (mesh)Mice (mesh)Single-Cell Analysis (mesh)Thermogenesis (mesh)TranscriptionGenetic (mesh)0601 Biochemistry and Cell Biology (for)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/3t8708z1https://escholarship.org/content/qt3t8708z1/qt3t8708z1.pdfinfo:doi/10.7554/elife.49501articleELIFE, vol 8e49501oai:escholarship.org:ark:/13030/qt3h2657tq2026-08-25T22:42:30Zqt3h2657tqComparison of reprogramming factor targets reveals both species-specific and conserved mechanisms in early iPSC reprogrammingFu, KaiChronis, ConstantinosSoufi, AbdenourBonora, GiancarloEdwards, MiguelSmale, Stephen TZaret, Kenneth SPlath, KathrinPellegrini, Matteo2018-12-01BackgroundBoth human and mouse fibroblasts can be reprogrammed to pluripotency with Oct4, Sox2, Klf4, and c-Myc (OSKM) transcription factors. While both systems generate pluripotency, human reprogramming takes considerably longer than mouse.ResultsTo assess additional similarities and differences, we sought to compare the binding of the reprogramming factors between the two systems. In human fibroblasts, the OSK factors initially target many more closed chromatin sites compared to mouse. Despite this difference, the intra- and intergenic distribution of target sites, target genes, primary binding motifs, and combinatorial binding patterns between the reprogramming factors are largely shared. However, while many OSKM binding events in early mouse cell reprogramming occur in syntenic regions, only a limited number is conserved in human.ConclusionsOur findings suggest similar general effects of OSKM binding across these two species, even though the detailed regulatory networks have diverged significantly.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Stem Cell Research (rcdc)Human Genome (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell - Human (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Generic health relevance (hrcs-hc)Animals (mesh)CellsCultured (mesh)Cellular Reprogramming (mesh)Chromatin (mesh)Fibroblasts (mesh)Humans (mesh)Induced Pluripotent Stem Cells (mesh)Kruppel-Like Factor 4 (mesh)Kruppel-Like Transcription Factors (mesh)Mice (mesh)Octamer Transcription Factor-3 (mesh)Proto-Oncogene Proteins c-myc (mesh)SOXB1 Transcription Factors (mesh)Species Specificity (mesh)Transcription Factors (mesh)ReprogrammingiPS cellsComparative epigenomicsCellsCultured (mesh)Chromatin (mesh)Fibroblasts (mesh)Animals (mesh)Humans (mesh)Mice (mesh)Proto-Oncogene Proteins c-myc (mesh)Transcription Factors (mesh)Species Specificity (mesh)Octamer Transcription Factor-3 (mesh)Kruppel-Like Transcription Factors (mesh)SOXB1 Transcription Factors (mesh)Induced Pluripotent Stem Cells (mesh)Cellular Reprogramming (mesh)Kruppel-Like Factor 4 (mesh)Comparative epigenomicsReprogrammingiPS cellsAnimals (mesh)CellsCultured (mesh)Cellular Reprogramming (mesh)Chromatin (mesh)Fibroblasts (mesh)Humans (mesh)Induced Pluripotent Stem Cells (mesh)Kruppel-Like Factor 4 (mesh)Kruppel-Like Transcription Factors (mesh)Mice (mesh)Octamer Transcription Factor-3 (mesh)Proto-Oncogene Proteins c-myc (mesh)SOXB1 Transcription Factors (mesh)Species Specificity (mesh)Transcription Factors (mesh)06 Biological Sciences (for)08 Information and Computing Sciences (for)11 Medical and Health Sciences (for)Bioinformatics (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/3h2657tqhttps://escholarship.org/content/qt3h2657tq/qt3h2657tq.pdfinfo:doi/10.1186/s12864-018-5326-1articleBMC Genomics, vol 19, iss 1956oai:escholarship.org:ark:/13030/qt2p10p1932026-08-25T22:42:17Zqt2p10p193Phosphorylation and Proteasome Recognition of the mRNA-Binding Protein Cth2 Facilitates Yeast Adaptation to Iron DeficiencyRomero, Antonia MMartínez-Pastor, MarDu, GangSolé, CarmeCarlos, MaríaVergara, Sandra VSanvisens, NereaWohlschlegel, James AToczyski, David PPosas, Francescde Nadal, EulàliaMartínez-Pastor, María TThiele, Dennis JPuig, SergiWickner, Reed B2018-11-07Iron is an indispensable micronutrient for all eukaryotic organisms due to its participation as a redox cofactor in many metabolic pathways. Iron imbalance leads to the most frequent human nutritional deficiency in the world. Adaptation to iron limitation requires a global reorganization of the cellular metabolism directed to prioritize iron utilization for essential processes. In response to iron scarcity, the conserved Saccharomyces cerevisiae mRNA-binding protein Cth2, which belongs to the tristetraprolin family of tandem zinc finger proteins, coordinates a global remodeling of the cellular metabolism by promoting the degradation of multiple mRNAs encoding highly iron-consuming proteins. In this work, we identify a critical mechanism for the degradation of Cth2 protein during the adaptation to iron deficiency. Phosphorylation of a patch of Cth2 serine residues within its amino-terminal region facilitates recognition by the SCFGrr1 ubiquitin ligase complex, accelerating Cth2 turnover by the proteasome. When Cth2 degradation is impaired by either mutagenesis of the Cth2 serine residues or deletion of GRR1, the levels of Cth2 rise and abrogate growth in iron-depleted conditions. Finally, we uncover that the casein kinase Hrr25 phosphorylates and promotes Cth2 destabilization. These results reveal a sophisticated posttranslational regulatory pathway necessary for the adaptation to iron depletion.IMPORTANCE Iron is a vital element for many metabolic pathways, including the synthesis of DNA and proteins, and the generation of energy via oxidative phosphorylation. Therefore, living organisms have developed tightly controlled mechanisms to properly distribute iron, since imbalances lead to nutritional deficiencies, multiple diseases, and vulnerability against pathogens. Saccharomyces cerevisiae Cth2 is a conserved mRNA-binding protein that coordinates a global reprogramming of iron metabolism in response to iron deficiency in order to optimize its utilization. Here we report that the phosphorylation of Cth2 at specific serine residues is essential to regulate the stability of the protein and adaptation to iron depletion. We identify the kinase and ubiquitination machinery implicated in this process to establish a posttranscriptional regulatory model. These results and recent findings for both mammals and plants reinforce the privileged position of E3 ubiquitin ligases and phosphorylation events in the regulation of eukaryotic iron homeostasis.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Nutrition (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)AdaptationPhysiological (mesh)Gene Expression RegulationFungal (mesh)Iron (mesh)Mutagenesis (mesh)Phosphorylation (mesh)Proteasome Endopeptidase Complex (mesh)Protein ProcessingPost-Translational (mesh)Protein Stability (mesh)RNAMessenger (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)Serine (mesh)Tristetraprolin (mesh)iron deficiencyphosphorylationposttranslational regulationprotein stabilityyeastSaccharomyces cerevisiae (mesh)Iron (mesh)Proteasome Endopeptidase Complex (mesh)Serine (mesh)Saccharomyces cerevisiae Proteins (mesh)RNAMessenger (mesh)AdaptationPhysiological (mesh)Gene Expression RegulationFungal (mesh)Protein ProcessingPost-Translational (mesh)Mutagenesis (mesh)Phosphorylation (mesh)Tristetraprolin (mesh)Protein Stability (mesh)iron deficiencyphosphorylationposttranslational regulationprotein stabilityyeastAdaptationPhysiological (mesh)Gene Expression RegulationFungal (mesh)Iron (mesh)Mutagenesis (mesh)Phosphorylation (mesh)Proteasome Endopeptidase Complex (mesh)Protein ProcessingPost-Translational (mesh)Protein Stability (mesh)RNAMessenger (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)Serine (mesh)Tristetraprolin (mesh)0605 Microbiology (for)3101 Biochemistry and cell biology (for-2020)3107 Microbiology (for-2020)3207 Medical microbiology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/2p10p193https://escholarship.org/content/qt2p10p193/qt2p10p193.pdfinfo:doi/10.1128/mbio.01694-18articlemBio, vol 9, iss 510.1128/mbio.01694 - 10.1128/mbio.01618oai:escholarship.org:ark:/13030/qt0sv4s4tq2026-08-25T21:27:53Zqt0sv4s4tqCryo-EM of full-length α-synuclein reveals fibril polymorphs with a common structural kernelLi, BinsenGe, PengMurray, Kevin ASheth, PhorumZhang, MengNair, GayatriSawaya, Michael RShin, Woo ShikBoyer, David RYe, ShulinEisenberg, David SZhou, Z HongJiang, Lin2018-09-06Abstractα-Synuclein (aSyn) fibrillar polymorphs have distinct in vitro and in vivo seeding activities, contributing differently to synucleinopathies. Despite numerous prior attempts, how polymorphic aSyn fibrils differ in atomic structure remains elusive. Here, we present fibril polymorphs from the full-length recombinant human aSyn and their seeding capacity and cytotoxicity in vitro. By cryo-electron microscopy helical reconstruction, we determine the structures of the two predominant species, a rod and a twister, both at 3.7 Å resolution. Our atomic models reveal that both polymorphs share a kernel structure of a bent β-arch, but differ in their inter-protofilament interfaces. Thus, different packing of the same kernel structure gives rise to distinct fibril polymorphs. Analyses of disease-related familial mutations suggest their potential contribution to the pathogenesis of synucleinopathies by altering population distribution of the fibril polymorphs. Drug design targeting amyloid fibrils in neurodegenerative diseases should consider the formation and distribution of concurrent fibril polymorphs.3101 Biochemistry and Cell Biology (for-2020)51 Physical Sciences (for-2020)31 Biological Sciences (for-2020)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)Alzheimer's Disease (rcdc)Acquired Cognitive Impairment (rcdc)Brain Disorders (rcdc)Aging (rcdc)Parkinson's Disease (rcdc)Neurosciences (rcdc)Dementia (rcdc)Neurodegenerative (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Animals (mesh)Biosensing Techniques (mesh)Cryoelectron Microscopy (mesh)Fluorescence Resonance Energy Transfer (mesh)HEK293 Cells (mesh)Humans (mesh)PC12 Cells (mesh)Protein Conformation (mesh)Rats (mesh)Recombinant Proteins (mesh)X-Ray Diffraction (mesh)alpha-Synuclein (mesh)PC12 Cells (mesh)Animals (mesh)Humans (mesh)Rats (mesh)Recombinant Proteins (mesh)Cryoelectron Microscopy (mesh)X-Ray Diffraction (mesh)Fluorescence Resonance Energy Transfer (mesh)Biosensing Techniques (mesh)Protein Conformation (mesh)alpha-Synuclein (mesh)HEK293 Cells (mesh)Animals (mesh)Biosensing Techniques (mesh)Cryoelectron Microscopy (mesh)Fluorescence Resonance Energy Transfer (mesh)HEK293 Cells (mesh)Humans (mesh)PC12 Cells (mesh)Protein Conformation (mesh)Rats (mesh)Recombinant Proteins (mesh)X-Ray Diffraction (mesh)alpha-Synuclein (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/0sv4s4tqhttps://escholarship.org/content/qt0sv4s4tq/qt0sv4s4tq.pdfinfo:doi/10.1038/s41467-018-05971-2articleNature Communications, vol 9, iss 13609oai:escholarship.org:ark:/13030/qt6vs2896r2026-08-25T20:55:14Zqt6vs2896rRecurrent patterns of DNA copy number alterations in tumors reflect metabolic selection pressuresGraham, Nicholas AMinasyan, AspramLomova, AnastasiaCass, AshleyBalanis, Nikolas GFriedman, MichaelChan, ShawnaZhao, SophieDelgado, AdrianGo, JamesBeck, LillieHurtz, ChristianNg, CarinaQiao, Rongten Hoeve, JohannaPalaskas, NicolaosWu, HongMüschen, MarkusMultani, Asha SPort, ElisaLarson, Steven MSchultz, NikolausBraas, DanielChristofk, Heather RMellinghoff, Ingo KGraeber, Thomas G2017-02-01Copy number alteration (CNA) profiling of human tumors has revealed recurrent patterns of DNA amplifications and deletions across diverse cancer types. These patterns are suggestive of conserved selection pressures during tumor evolution but cannot be fully explained by known oncogenes and tumor suppressor genes. Using a pan‐cancer analysis of CNA data from patient tumors and experimental systems, here we show that principal component analysis‐defined CNA signatures are predictive of glycolytic phenotypes, including 18F‐fluorodeoxy‐glucose (FDG) avidity of patient tumors, and increased proliferation. The primary CNA signature is enriched for p53 mutations and is associated with glycolysis through coordinate amplification of glycolytic genes and other cancer‐linked metabolic enzymes. A pan‐cancer and cross‐species comparison of CNAs highlighted 26 consistently altered DNA regions, containing 11 enzymes in the glycolysis pathway in addition to known cancer‐driving genes. Furthermore, exogenous expression of hexokinase and enolase enzymes in an experimental immortalization system altered the subsequent copy number status of the corresponding endogenous loci, supporting the hypothesis that these metabolic genes act as drivers within the conserved CNA amplification regions. Taken together, these results demonstrate that metabolic stress acts as a selective pressure underlying the recurrent CNAs observed in human tumors, and further cast genomic instability as an enabling event in tumorigenesis and metabolic evolution.31 Biological Sciences (for-2020)3105 Genetics (for-2020)Human Genome (rcdc)Cancer (rcdc)Genetics (rcdc)Cancer Genomics (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Cancer (hrcs-hc)Cell LineTumor (mesh)DNA Copy Number Variations (mesh)EvolutionMolecular (mesh)Gene Amplification (mesh)Gene Deletion (mesh)Gene Expression Profiling (mesh)Gene Expression RegulationNeoplastic (mesh)Genomic Instability (mesh)Glycolysis (mesh)Humans (mesh)Metabolic Networks and Pathways (mesh)Neoplasms (mesh)Principal Component Analysis (mesh)SelectionGenetic (mesh)aneuploidyDNA copy number alterationsgenomic instabilityglycolysismetabolismCell LineTumor (mesh)Humans (mesh)Neoplasms (mesh)Genomic Instability (mesh)Gene Expression Profiling (mesh)EvolutionMolecular (mesh)Gene Amplification (mesh)Gene Expression RegulationNeoplastic (mesh)Gene Deletion (mesh)Glycolysis (mesh)Principal Component Analysis (mesh)Metabolic Networks and Pathways (mesh)SelectionGenetic (mesh)DNA Copy Number Variations (mesh)DNA copy number alterationsaneuploidygenomic instabilityglycolysismetabolismCell LineTumor (mesh)DNA Copy Number Variations (mesh)EvolutionMolecular (mesh)Gene Amplification (mesh)Gene Deletion (mesh)Gene Expression Profiling (mesh)Gene Expression RegulationNeoplastic (mesh)Genomic Instability (mesh)Glycolysis (mesh)Humans (mesh)Metabolic Networks and Pathways (mesh)Neoplasms (mesh)Principal Component Analysis (mesh)SelectionGenetic (mesh)0601 Biochemistry and Cell Biology (for)0699 Other Biological Sciences (for)Bioinformatics (science-metrix)3101 Biochemistry and cell biology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/6vs2896rhttps://escholarship.org/content/qt6vs2896r/qt6vs2896r.pdfinfo:doi/10.15252/msb.20167159articleMolecular Systems Biology, vol 13, iss 2msb167159oai:escholarship.org:ark:/13030/qt1wv789fc2026-08-25T11:26:54Zqt1wv789fcMultiple serine transposase dimers assemble the transposon-end synaptic complex during IS607-family transpositionChen, WenyangMandali, SridharHancock, Stephen PKumar, PramodCollazo, MichaelCascio, DuilioJohnson, Reid C2018-10-05IS607-family transposons are unusual because they do not have terminal inverted repeats or generate target site duplications. They encode two protein-coding genes, but only tnpA is required for transposition. Our X-ray structures confirm that TnpA is a member of the serine recombinase (SR) family, but the chemically-inactive quaternary structure of the dimer, along with the N-terminal location of the DNA binding domain, are different from other SRs. TnpA dimers from IS1535 cooperatively associate with multiple subterminal repeats, which together with additional nonspecific binding, form a nucleoprotein filament on one transposon end that efficiently captures a second unbound end to generate the paired-end complex (PEC). Formation of the PEC does not require a change in the dimeric structure of the catalytic domain, but remodeling of the C-terminal α-helical region is involved. We posit that the PEC recruits a chemically-active conformer of TnpA to the transposon end to initiate DNA chemistry.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Cancer (rcdc)AbsorptiometryPhoton (mesh)Bacteria (mesh)DNA (mesh)DNA Transposable Elements (mesh)DNABacterial (mesh)ModelsMolecular (mesh)MutagenesisInsertional (mesh)Nucleic Acid Conformation (mesh)Protein Binding (mesh)Protein Multimerization (mesh)Protein StructureQuaternary (mesh)Recombinases (mesh)Serine (mesh)Transposases (mesh)Bacteria (mesh)Recombinases (mesh)Transposases (mesh)Serine (mesh)DNA (mesh)DNABacterial (mesh)DNA Transposable Elements (mesh)AbsorptiometryPhoton (mesh)MutagenesisInsertional (mesh)Nucleic Acid Conformation (mesh)Protein StructureQuaternary (mesh)Protein Binding (mesh)ModelsMolecular (mesh)Protein Multimerization (mesh)DNA transpositionE. coliHelicobacter pyloriMycobacteria tuberculosisSulfolobus islandicusbiochemistrychemical biologychromosomesgene expressionnucleoprotein complexserine recombinaseAbsorptiometryPhoton (mesh)Bacteria (mesh)DNA (mesh)DNA Transposable Elements (mesh)DNABacterial (mesh)ModelsMolecular (mesh)MutagenesisInsertional (mesh)Nucleic Acid Conformation (mesh)Protein Binding (mesh)Protein Multimerization (mesh)Protein StructureQuaternary (mesh)Recombinases (mesh)Serine (mesh)Transposases (mesh)0601 Biochemistry and Cell Biology (for)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1wv789fchttps://escholarship.org/content/qt1wv789fc/qt1wv789fc.pdfinfo:doi/10.7554/elife.39611articleELIFE, vol 7e39611oai:escholarship.org:ark:/13030/qt8t41v72w2026-08-25T08:34:22Zqt8t41v72wAlternative polyadenylation factors link cell cycle to migrationMitra, MithunJohnson, Elizabeth LSwamy, Vinay SNersesian, Lois ECorney, David CRobinson, David GTaylor, Daniel GAmbrus, Aaron MJelinek, DavidWang, WeiBatista, Sandra LColler, Hilary A2018-12-01BackgroundIn response to a wound, fibroblasts are activated to migrate toward the wound, to proliferate and to contribute to the wound healing process. We hypothesize that changes in pre-mRNA processing occurring as fibroblasts enter the proliferative cell cycle are also important for promoting their migration.ResultsRNA sequencing of fibroblasts induced into quiescence by contact inhibition reveals downregulation of genes involved in mRNA processing, including splicing and cleavage and polyadenylation factors. These genes also show differential exon use, especially increased intron retention in quiescent fibroblasts compared to proliferating fibroblasts. Mapping the 3′ ends of transcripts reveals that longer transcripts from distal polyadenylation sites are more prevalent in quiescent fibroblasts and are associated with increased expression and transcript stabilization based on genome-wide transcript decay analysis. Analysis of dermal excisional wounds in mice reveals that proliferating cells adjacent to wounds express higher levels of cleavage and polyadenylation factors than quiescent fibroblasts in unwounded skin. Quiescent fibroblasts contain reduced levels of the cleavage and polyadenylation factor CstF-64. CstF-64 knockdown recapitulates changes in isoform selection and gene expression associated with quiescence, and results in slower migration.ConclusionsOur findings support cleavage and polyadenylation factors as a link between cellular proliferation state and migration.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)Human Genome (rcdc)Genetics (rcdc)Wound Healing and Care (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Cell Cycle (mesh)Cell Movement (mesh)CellsCultured (mesh)Fibroblasts (mesh)Humans (mesh)Poly A (mesh)Polyadenylation (mesh)RNA Splicing (mesh)Skin (mesh)mRNA Cleavage and Polyadenylation Factors (mesh)mRNA processingProliferationQuiescenceMigrationWound healingCellsCultured (mesh)Fibroblasts (mesh)Skin (mesh)Humans (mesh)mRNA Cleavage and Polyadenylation Factors (mesh)Poly A (mesh)Cell Cycle (mesh)Cell Movement (mesh)Polyadenylation (mesh)RNA Splicing (mesh)MigrationProliferationQuiescenceWound healingmRNA processingCell Cycle (mesh)Cell Movement (mesh)CellsCultured (mesh)Fibroblasts (mesh)Humans (mesh)Poly A (mesh)Polyadenylation (mesh)RNA Splicing (mesh)Skin (mesh)mRNA Cleavage and Polyadenylation Factors (mesh)05 Environmental Sciences (for)06 Biological Sciences (for)08 Information and Computing Sciences (for)Bioinformatics (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/8t41v72whttps://escholarship.org/content/qt8t41v72w/qt8t41v72w.pdfinfo:doi/10.1186/s13059-018-1551-9articleGenome Biology, vol 19, iss 1176oai:escholarship.org:ark:/13030/qt3x99h8gq2026-08-25T07:14:29Zqt3x99h8gqExtracellular Matrix Remodeling Regulates Glucose Metabolism through TXNIP DestabilizationSullivan, William JMullen, Peter JSchmid, Ernst WFlores, AimeeMomcilovic, MilicaSharpley, Mark SJelinek, DavidWhiteley, Andrew EMaxwell, Matthew BWilde, Blake RBanerjee, UtpalColler, Hilary AShackelford, David BBraas, DanielAyer, Donald Ede Aguiar Vallim, Thomas QLowry, William EChristofk, Heather R2018-09-01The metabolic state of a cell is influenced by cell-extrinsic factors, including nutrient availability and growth factor signaling. Here, we present extracellular matrix (ECM) remodeling as another fundamental node of cell-extrinsic metabolic regulation. Unbiased analysis of glycolytic drivers identified the hyaluronan-mediated motility receptor as being among the most highly correlated with glycolysis in cancer. Confirming a mechanistic link between the ECM component hyaluronan and metabolism, treatment of cells and xenografts with hyaluronidase triggers a robust increase in glycolysis. This is largely achieved through rapid receptor tyrosine kinase-mediated induction of the mRNA decay factor ZFP36, which targets TXNIP transcripts for degradation. Because TXNIP promotes internalization of the glucose transporter GLUT1, its acute decline enriches GLUT1 at the plasma membrane. Functionally, induction of glycolysis by hyaluronidase is required for concomitant acceleration of cell migration. This interconnection between ECM remodeling and metabolism is exhibited in dynamic tissue states, including tumorigenesis and embryogenesis.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Cancer (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Carbohydrate Metabolism (mesh)Carrier Proteins (mesh)Cell LineTumor (mesh)Extracellular Matrix (mesh)Glucose (mesh)Glucose Transporter Type 1 (mesh)Glycolysis (mesh)Humans (mesh)Hyaluronic Acid (mesh)Hyaluronoglucosaminidase (mesh)Intercellular Signaling Peptides and Proteins (mesh)Signal Transduction (mesh)Tristetraprolin (mesh)Cell LineTumor (mesh)Extracellular Matrix (mesh)Humans (mesh)Hyaluronoglucosaminidase (mesh)Glucose (mesh)Hyaluronic Acid (mesh)Intercellular Signaling Peptides and Proteins (mesh)Carrier Proteins (mesh)Signal Transduction (mesh)Glycolysis (mesh)Carbohydrate Metabolism (mesh)Glucose Transporter Type 1 (mesh)Tristetraprolin (mesh)GLUT1 traffickingTXNIPZFP36cell biologycell migrationextracellular matrixglucose metabolismhyaluronidasemRNA degradationreceptor tyrosine kinase signalingCarbohydrate Metabolism (mesh)Carrier Proteins (mesh)Cell LineTumor (mesh)Extracellular Matrix (mesh)Glucose (mesh)Glucose Transporter Type 1 (mesh)Glycolysis (mesh)Humans (mesh)Hyaluronic Acid (mesh)Hyaluronoglucosaminidase (mesh)Intercellular Signaling Peptides and Proteins (mesh)Signal Transduction (mesh)Tristetraprolin (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3x99h8gqhttps://escholarship.org/content/qt3x99h8gq/qt3x99h8gq.pdfinfo:doi/10.1016/j.cell.2018.08.017articleCell, vol 175, iss 1117 - 132.e21oai:escholarship.org:ark:/13030/qt04m512v02026-08-25T07:09:15Zqt04m512v04-(Nitrophenylsulfonyl)piperazines mitigate radiation damage to multiple tissuesMicewicz, Ewa DKim, KwangheeIwamoto, Keisuke SRatikan, Josephine ACheng, GenhongBoxx, Gayle MDamoiseaux, Robert DWhitelegge, Julian PRuchala, PiotrNguyen, ChristinePurbey, PrabhatLoo, JosephDeng, GangJung, Michael ESayre, James WNorris, Andrew JSchaue, DörtheMcBride, William HAmendola, Roberto2017-07-21Our ability to use ionizing radiation as an energy source, as a therapeutic agent, and, unfortunately, as a weapon, has evolved tremendously over the past 120 years, yet our tool box to handle the consequences of accidental and unwanted radiation exposure remains very limited. We have identified a novel group of small molecule compounds with a 4-nitrophenylsulfonamide (NPS) backbone in common that dramatically decrease mortality from the hematopoietic acute radiation syndrome (hARS). The group emerged from an in vitro high throughput screen (HTS) for inhibitors of radiation-induced apoptosis. The lead compound also mitigates against death after local abdominal irradiation and after local thoracic irradiation (LTI) in models of subacute radiation pneumonitis and late radiation fibrosis. Mitigation of hARS is through activation of radiation-induced CD11b+Ly6G+Ly6C+ immature myeloid cells. This is consistent with the notion that myeloerythroid-restricted progenitors protect against WBI-induced lethality and extends the possible involvement of the myeloid lineage in radiation effects. The lead compound was active if given to mice before or after WBI and had some anti-tumor action, suggesting that these compounds may find broader applications to cancer radiation therapy.32 Biomedical and Clinical Sciences (for-2020)3211 Oncology and Carcinogenesis (for-2020)Stem Cell Research - Nonembryonic - Non-Human (rcdc)Hematology (rcdc)Biodefense (rcdc)Physical Injury - Accidents and Adverse Effects (rcdc)Stem Cell Research (rcdc)Radiation Oncology (rcdc)Cancer (rcdc)5.1 Pharmaceuticals (hrcs-rac)Cancer (hrcs-hc)Acute Radiation Syndrome (mesh)Animals (mesh)Antineoplastic Agents (mesh)Apoptosis (mesh)CellsCultured (mesh)Female (mesh)Male (mesh)Mice (mesh)MiceInbred C3H (mesh)MiceInbred C57BL (mesh)Myeloid Cells (mesh)Piperazines (mesh)CellsCultured (mesh)Myeloid Cells (mesh)Animals (mesh)MiceInbred C3H (mesh)MiceInbred C57BL (mesh)Mice (mesh)Piperazines (mesh)Antineoplastic Agents (mesh)Apoptosis (mesh)Female (mesh)Male (mesh)Acute Radiation Syndrome (mesh)Acute Radiation Syndrome (mesh)Animals (mesh)Antineoplastic Agents (mesh)Apoptosis (mesh)CellsCultured (mesh)Female (mesh)Male (mesh)Mice (mesh)MiceInbred C3H (mesh)MiceInbred C57BL (mesh)Myeloid Cells (mesh)Piperazines (mesh)General Science & Technology (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/04m512v0https://escholarship.org/content/qt04m512v0/qt04m512v0.pdfinfo:doi/10.1371/journal.pone.0181577articlePLOS ONE, vol 12, iss 7e0181577oai:escholarship.org:ark:/13030/qt9c03z0642026-08-24T22:01:27Zqt9c03z064C-terminal domains of histone demethylase JMJ14 interact with a pair of NAC transcription factors to mediate specific chromatin associationZhang, ShuaibinZhou, BingKang, YanyuanCui, XiaLiu, AoDeleris, AngeliqueGreenberg, Maxim VCCui, XiekuiQiu, QiLu, FalongWohlschlegel, James AJacobsen, Steven ECao, Xiaofeng2015-01-01Jumonji C (JmjC) domain-containing protein 14 (JMJ14) is an H3K4-specific histone demethylase that has important roles in RNA-mediated gene silencing and flowering time regulation in Arabidopsis. However, how JMJ14 is recruited to its target genes remains unclear. Here, we show that the C-terminal FYRN (F/Y-rich N terminus) and FYRC (F/Y-rich C terminus) domains of JMJ14 are required for RNA silencing and flowering time regulation. Chromatin binding of JMJ14 is lost upon deletion of its FYRN and FYRC domains, and H3K4me3 is increased. FYRN and FYRC domains interact with a pair of NAC (NAM, ATAF, CUC) domain-containing transcription factors, NAC050 and NAC052. Genome-wide chromatin immunoprecipitation analysis revealed that JMJ14 and NAC050/052 share a set of common target genes with CTTGNNNNNCAAG consensus sequences. Mutations in either NAC052 or NAC050 impair RNA-mediated gene silencing. Together, our findings demonstrate an important role of FYRN and FYRC domains in targeting JMJ14 through direct interaction with NAC050/052 proteins, which reveals a novel mechanism of histone demethylase recruitment.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Biotechnology (rcdc)Human Genome (rcdc)Cancer (rcdc)JMJ14histone demethylaseNAC050NAC052transgene silencingJMJ14NAC050NAC052histone demethylasetransgene silencing0601 Biochemistry and Cell Biology (for)3101 Biochemistry and cell biology (for-2020)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/9c03z064info:doi/10.1038/celldisc.2015.3articleCell Discovery, vol 1, iss 115003oai:escholarship.org:ark:/13030/qt5p40p6932026-08-24T14:17:57Zqt5p40p693Serial femtosecond crystallography on in vivo-grown crystals drives elucidation of mosquitocidal Cyt1Aa bioactivation cascadeTetreau, GuillaumeBanneville, Anne-SophieAndreeva, Elena ABrewster, Aaron SHunter, Mark SSierra, Raymond GTeulon, Jean-MarieYoung, Iris DBurke, NiamhGrünewald, Tilman ABeaudouin, JoëlSnigireva, IrinaFernandez-Luna, Maria TeresaBurt, AlisterPark, Hyun-WooSignor, LucaBafna, Jayesh ASadir, RabiaFenel, DaphnaBoeri-Erba, ElisabettaBacia, MariaZala, NinonLaporte, FrédéricDesprés, LaurenceWeik, MartinBoutet, SébastienRosenthal, MartinCoquelle, NicolasBurghammer, ManfredCascio, DuilioSawaya, Michael RWinterhalter, MathiasGratton, EnricoGutsche, IrinaFederici, BrianPellequer, Jean-LucSauter, Nicholas KColletier, Jacques-Philippe2020-03-02Cyt1Aa is the one of four crystalline protoxins produced by mosquitocidal bacterium Bacillus thuringiensis israelensis (Bti) that has been shown to delay the evolution of insect resistance in the field. Limiting our understanding of Bti efficacy and the path to improved toxicity and spectrum has been ignorance of how Cyt1Aa crystallizes in vivo and of its mechanism of toxicity. Here, we use serial femtosecond crystallography to determine the Cyt1Aa protoxin structure from sub-micron-sized crystals produced in Bti. Structures determined under various pH/redox conditions illuminate the role played by previously uncharacterized disulfide-bridge and domain-swapped interfaces from crystal formation in Bti to dissolution in the larval mosquito midgut. Biochemical, toxicological and biophysical methods enable the deconvolution of key steps in the Cyt1Aa bioactivation cascade. We additionally show that the size, shape, production yield, pH sensitivity and toxicity of Cyt1Aa crystals grown in Bti can be controlled by single atom substitution.3001 Agricultural Biotechnology (for-2020)30 AgriculturalVeterinary and Food Sciences (for-2020)34 Chemical Sciences (for-2020)Animals (mesh)Bacillus thuringiensis Toxins (mesh)Bacterial Proteins (mesh)Cell Membrane (mesh)CrystallographyX-Ray (mesh)Disulfides (mesh)Endotoxins (mesh)HEK293 Cells (mesh)Hemolysin Proteins (mesh)Humans (mesh)Hydrogen-Ion Concentration (mesh)Insecticides (mesh)Mice (mesh)MicroscopyAtomic Force (mesh)NIH 3T3 Cells (mesh)Protein Conformation (mesh)Sf9 Cells (mesh)NIH 3T3 Cells (mesh)Cell Membrane (mesh)Animals (mesh)Humans (mesh)Mice (mesh)Disulfides (mesh)Bacterial Proteins (mesh)Endotoxins (mesh)Insecticides (mesh)MicroscopyAtomic Force (mesh)CrystallographyX-Ray (mesh)Protein Conformation (mesh)Hydrogen-Ion Concentration (mesh)Hemolysin Proteins (mesh)HEK293 Cells (mesh)Sf9 Cells (mesh)Bacillus thuringiensis Toxins (mesh)Animals (mesh)Bacillus thuringiensis Toxins (mesh)Bacterial Proteins (mesh)Cell Membrane (mesh)CrystallographyX-Ray (mesh)Disulfides (mesh)Endotoxins (mesh)HEK293 Cells (mesh)Hemolysin Proteins (mesh)Humans (mesh)Hydrogen-Ion Concentration (mesh)Insecticides (mesh)Mice (mesh)MicroscopyAtomic Force (mesh)NIH 3T3 Cells (mesh)Protein Conformation (mesh)Sf9 Cells (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/5p40p693https://escholarship.org/content/qt5p40p693/qt5p40p693.pdfinfo:doi/10.1038/s41467-020-14894-warticleNature Communications, vol 11, iss 11153oai:escholarship.org:ark:/13030/qt6zf1324w2026-08-24T13:26:25Zqt6zf1324wMolecular basis for blue light-dependent phosphorylation of Arabidopsis cryptochrome 2Liu, QingWang, QinDeng, WeixianWang, XuPiao, MingxinCai, DaweiLi, YaxingBarshop, William DYu, XiaolanZhou, TingtingLiu, BinOka, YoshitoWohlschlegel, JamesZuo, ZechengLin, Chentao2017-05-11Plant cryptochromes undergo blue light-dependent phosphorylation to regulate their activity and abundance, but the protein kinases that phosphorylate plant cryptochromes have remained unclear. Here we show that photoexcited Arabidopsis cryptochrome 2 (CRY2) is phosphorylated in vivo on as many as 24 different residues, including 7 major phosphoserines. We demonstrate that four closely related Photoregulatory Protein Kinases (previously referred to as MUT9-like kinases) interact with and phosphorylate photoexcited CRY2. Analyses of the ppk123 and ppk124 triple mutants and amiR4k artificial microRNA-expressing lines demonstrate that PPKs catalyse blue light-dependent CRY2 phosphorylation to both activate and destabilize the photoreceptor. Phenotypic analyses of these mutant lines indicate that PPKs may have additional substrates, including those involved in the phytochrome signal transduction pathway. These results reveal a mechanism underlying the co-action of cryptochromes and phytochromes to coordinate plant growth and development in response to different wavelengths of solar radiation in nature.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Amino Acid Sequence (mesh)Arabidopsis (mesh)Arabidopsis Proteins (mesh)Cryptochromes (mesh)Gene Expression RegulationPlant (mesh)Isoenzymes (mesh)Light (mesh)Phosphorylation (mesh)Phosphoserine (mesh)Phosphotransferases (Alcohol Group Acceptor) (mesh)Phytochrome (mesh)Protein ProcessingPost-Translational (mesh)Protein Serine-Threonine Kinases (mesh)Arabidopsis (mesh)Isoenzymes (mesh)Phosphotransferases (Alcohol Group Acceptor) (mesh)Phytochrome (mesh)Phosphoserine (mesh)Arabidopsis Proteins (mesh)Gene Expression RegulationPlant (mesh)Protein ProcessingPost-Translational (mesh)Amino Acid Sequence (mesh)Phosphorylation (mesh)Light (mesh)Cryptochromes (mesh)Protein Serine-Threonine Kinases (mesh)Amino Acid Sequence (mesh)Arabidopsis (mesh)Arabidopsis Proteins (mesh)Cryptochromes (mesh)Gene Expression RegulationPlant (mesh)Isoenzymes (mesh)Light (mesh)Phosphorylation (mesh)Phosphoserine (mesh)Phosphotransferases (Alcohol Group Acceptor) (mesh)Phytochrome (mesh)Protein ProcessingPost-Translational (mesh)Protein Serine-Threonine Kinases (mesh)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6zf1324whttps://escholarship.org/content/qt6zf1324w/qt6zf1324w.pdfinfo:doi/10.1038/ncomms15234articleNature Communications, vol 8, iss 115234oai:escholarship.org:ark:/13030/qt0kt9g5cw2026-08-24T06:31:38Zqt0kt9g5cwTranscriptional, Electrophysiological, and Metabolic Characterizations of hESC-Derived First and Second Heart Fields Demonstrate a Potential Role of TBX5 in Cardiomyocyte MaturationPezhouman, ArashNguyen, Ngoc BSercel, Alexander JNguyen, Thang LDaraei, AliSabri, ShanChapski, Douglas JZheng, MeltonPatananan, Alexander NErnst, JasonPlath, KathrinVondriska, Thomas MTeitell, Michael AArdehali, Reza2021-12-17Background: Human embryonic stem cell-derived cardiomyocytes (hESC-CMs) can be used as a source for cell delivery to remuscularize the heart after myocardial infarction. Despite their therapeutic potential, the emergence of ventricular arrhythmias has limited their application. We previously developed a double reporter hESC line to isolate first heart field (FHF: TBX5 + NKX2-5 +) and second heart field (SHF: TBX5 - NKX2-5 + ) CMs. Herein, we explore the role of TBX5 and its effects on underlying gene regulatory networks driving phenotypical and functional differences between these two populations. Methods: We used a combination of tools and techniques for rapid and unsupervised profiling of FHF and SHF populations at the transcriptional, translational, and functional level including single cell RNA (scRNA) and bulk RNA sequencing, atomic force and quantitative phase microscopy, respirometry, and electrophysiology. Results: Gene ontology analysis revealed three biological processes attributed to TBX5 expression: sarcomeric structure, oxidative phosphorylation, and calcium ion handling. Interestingly, migratory pathways were enriched in SHF population. SHF-like CMs display less sarcomeric organization compared to FHF-like CMs, despite prolonged in vitro culture. Atomic force and quantitative phase microscopy showed increased cellular stiffness and decreased mass distribution over time in FHF compared to SHF populations, respectively. Electrophysiological studies showed longer plateau in action potentials recorded from FHF-like CMs, consistent with their increased expression of calcium handling genes. Interestingly, both populations showed nearly identical respiratory profiles with the only significant functional difference being higher ATP generation-linked oxygen consumption rate in FHF-like CMs. Our findings suggest that FHF-like CMs display more mature features given their enhanced sarcomeric alignment, calcium handling, and decreased migratory characteristics. Finally, pseudotime analyses revealed a closer association of the FHF population to human fetal CMs along the developmental trajectory. Conclusion: Our studies reveal that distinguishing FHF and SHF populations based on TBX5 expression leads to a significant impact on their downstream functional properties. FHF CMs display more mature characteristics such as enhanced sarcomeric organization and improved calcium handling, with closer positioning along the differentiation trajectory to human fetal hearts. These data suggest that the FHF CMs may be a more suitable candidate for cardiac regeneration.3206 Medical Biotechnology (for-2020)31 Biological Sciences (for-2020)32 Biomedical and Clinical Sciences (for-2020)Genetics (rcdc)Cardiovascular (rcdc)Heart Disease (rcdc)Stem Cell Research (rcdc)Human Genome (rcdc)Stem Cell Research - Embryonic - Human (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Cardiovascular (hrcs-hc)first and second heart fieldssingle cell RNA seqaction potentialhESC-derived cardiomyocytematurityregenerative medicinemetabolismaction potentialfirst and second heart fieldshESC-derived cardiomyocytematuritymetabolismregenerative medicinesingle cell RNA seq31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/0kt9g5cwhttps://escholarship.org/content/qt0kt9g5cw/qt0kt9g5cw.pdfinfo:doi/10.3389/fcell.2021.787684articleFrontiers in Cell and Developmental Biology, vol 9787684oai:escholarship.org:ark:/13030/qt0w6619xm2026-08-24T06:30:57Zqt0w6619xmUniversal annotation of the human genome through integration of over a thousand epigenomic datasetsVu, HaErnst, Jason2022-12-01BackgroundGenome-wide maps of chromatin marks such as histone modifications and open chromatin sites provide valuable information for annotating the non-coding genome, including identifying regulatory elements. Computational approaches such as ChromHMM have been applied to discover and annotate chromatin states defined by combinatorial and spatial patterns of chromatin marks within the same cell type. An alternative “stacked modeling” approach was previously suggested, where chromatin states are defined jointly from datasets of multiple cell types to produce a single universal genome annotation based on all datasets. Despite its potential benefits for applications that are not specific to one cell type, such an approach was previously applied only for small-scale specialized purposes. Large-scale applications of stacked modeling have previously posed scalability challenges.ResultsUsing a version of ChromHMM enhanced for large-scale applications, we apply the stacked modeling approach to produce a universal chromatin state annotation of the human genome using over 1000 datasets from more than 100 cell types, with the learned model denoted as the full-stack model. The full-stack model states show distinct enrichments for external genomic annotations, which we use in characterizing each state. Compared to per-cell-type annotations, the full-stack annotations directly differentiate constitutive from cell type-specific activity and is more predictive of locations of external genomic annotations.ConclusionsThe full-stack ChromHMM model provides a universal chromatin state annotation of the genome and a unified global view of over 1000 datasets. We expect this to be a useful resource that complements existing per-cell-type annotations for studying the non-coding human genome.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)Human Genome (rcdc)Genetics (rcdc)Biotechnology (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Chromatin (mesh)Epigenomics (mesh)GenomeHuman (mesh)Genomics (mesh)Humans (mesh)Molecular Sequence Annotation (mesh)Chromatin (mesh)Humans (mesh)Genomics (mesh)GenomeHuman (mesh)Epigenomics (mesh)Molecular Sequence Annotation (mesh)Chromatin (mesh)Epigenomics (mesh)GenomeHuman (mesh)Genomics (mesh)Humans (mesh)Molecular Sequence Annotation (mesh)05 Environmental Sciences (for)06 Biological Sciences (for)08 Information and Computing Sciences (for)Bioinformatics (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/0w6619xmhttps://escholarship.org/content/qt0w6619xm/qt0w6619xm.pdfinfo:doi/10.1186/s13059-021-02572-zarticleGenome Biology, vol 23, iss 19oai:escholarship.org:ark:/13030/qt94g6459n2026-08-24T01:42:34Zqt94g6459nPaths and pathways that generate cell-type heterogeneity and developmental progression in hematopoiesisGirard, Juliet RGoins, Lauren MVuu, Dung MSharpley, Mark SSpratford, Carrie MMantri, Shreya RBanerjee, Utpal2021-10-29Mechanistic studies of Drosophila lymph gland hematopoiesis are limited by the availability of cell-type-specific markers. Using a combination of bulk RNA-Seq of FACS-sorted cells, single-cell RNA-Seq, and genetic dissection, we identify new blood cell subpopulations along a developmental trajectory with multiple paths to mature cell types. This provides functional insights into key developmental processes and signaling pathways. We highlight metabolism as a driver of development, show that graded Pointed expression allows distinct roles in successive developmental steps, and that mature crystal cells specifically express an alternate isoform of Hypoxia-inducible factor (Hif/Sima). Mechanistically, the Musashi-regulated protein Numb facilitates Sima-dependent non-canonical, and inhibits canonical, Notch signaling. Broadly, we find that prior to making a fate choice, a progenitor selects between alternative, biologically relevant, transitory states allowing smooth transitions reflective of combinatorial expressions rather than stepwise binary decisions. Increasingly, this view is gaining support in mammalian hematopoiesis.3101 Biochemistry and Cell Biology (for-2020)3105 Genetics (for-2020)31 Biological Sciences (for-2020)Hematology (rcdc)Genetics (rcdc)2.1 Biological and endogenous factors (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Animals (mesh)DNA-Binding Proteins (mesh)Drosophila Proteins (mesh)Drosophila melanogaster (mesh)Female (mesh)Hematopoiesis (mesh)Hemocytes (mesh)Hemolymph (mesh)Juvenile Hormones (mesh)Larva (mesh)Male (mesh)hematopoiesiscrystal cellslymph glandblood progenitorsstem cellsintermediate progenitorsDmelanogasterHemocytes (mesh)Hemolymph (mesh)Animals (mesh)Drosophila melanogaster (mesh)Juvenile Hormones (mesh)DNA-Binding Proteins (mesh)Drosophila Proteins (mesh)Hematopoiesis (mesh)Larva (mesh)Female (mesh)Male (mesh)D. melanogasterblood progenitorscrystal cellsdevelopmental biologygeneticsgenomicshematopoiesisintermediate progenitorslymph glandstem cellsAnimals (mesh)DNA-Binding Proteins (mesh)Drosophila Proteins (mesh)Drosophila melanogaster (mesh)Female (mesh)Hematopoiesis (mesh)Hemocytes (mesh)Hemolymph (mesh)Juvenile Hormones (mesh)Larva (mesh)Male (mesh)0601 Biochemistry and Cell Biology (for)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/94g6459nhttps://escholarship.org/content/qt94g6459n/qt94g6459n.pdfinfo:doi/10.7554/elife.67516articleELIFE, vol 10e67516oai:escholarship.org:ark:/13030/qt3vt8c06d2026-08-23T17:51:03Zqt3vt8c06dA pathogenic role for histone H3 copper reductase activity in a yeast model of Friedreich’s ataxiaCampos, Oscar AAttar, NarsisCheng, ChenVogelauer, MariaMallipeddi, Nathan VSchmollinger, StefanMatulionis, NedasChristofk, Heather RMerchant, Sabeeha SKurdistani, Siavash K2021-12-17Disruptions to iron-sulfur (Fe-S) clusters, essential cofactors for a broad range of proteins, cause widespread cellular defects resulting in human disease. A source of damage to Fe-S clusters is cuprous (Cu1+) ions. Since histone H3 enzymatically produces Cu1+ for copper-dependent functions, we asked whether this activity could become detrimental to Fe-S clusters. Here, we report that histone H3–mediated Cu1+ toxicity is a major determinant of cellular functional pool of Fe-S clusters. Inadequate Fe-S cluster supply, due to diminished assembly as occurs in Friedreich’s ataxia or defective distribution, causes severe metabolic and growth defects in Saccharomyces cerevisiae. Decreasing Cu1+ abundance, through attenuation of histone cupric reductase activity or depletion of total cellular copper, restored Fe-S cluster–dependent metabolism and growth. Our findings reveal an interplay between chromatin and mitochondria in Fe-S cluster homeostasis and a potential pathogenic role for histone enzyme activity and Cu1+ in diseases with Fe-S cluster dysfunction.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Neurodegenerative (rcdc)Rare Diseases (rcdc)Neurosciences (rcdc)2.1 Biological and endogenous factors (hrcs-rac)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3vt8c06dhttps://escholarship.org/content/qt3vt8c06d/qt3vt8c06d.pdfinfo:doi/10.1126/sciadv.abj9889articleScience Advances, vol 7, iss 51eabj9889oai:escholarship.org:ark:/13030/qt2s42404x2026-08-23T17:43:54Zqt2s42404xComprehensive identification of SWI/SNF complex subunits underpins deep eukaryotic ancestry and reveals new plant componentsHernández-García, JorgeDiego-Martin, BorjaKuo, Peggy HsuanyuJami-Alahmadi, YasamanVashisht, Ajay AWohlschlegel, JamesJacobsen, Steven EBlázquez, Miguel AGallego-Bartolomé, Javier2022-06-06Over millions of years, eukaryotes evolved from unicellular to multicellular organisms with increasingly complex genomes and sophisticated gene expression networks. Consequently, chromatin regulators evolved to support this increased complexity. The ATP-dependent chromatin remodelers of the SWI/SNF family are multiprotein complexes that modulate nucleosome positioning and appear under different configurations, which perform distinct functions. While the composition, architecture, and activity of these subclasses are well understood in a limited number of fungal and animal model organisms, the lack of comprehensive information in other eukaryotic organisms precludes the identification of a reliable evolutionary model of SWI/SNF complexes. Here, we performed a systematic analysis using 36 species from animal, fungal, and plant lineages to assess the conservation of known SWI/SNF subunits across eukaryotes. We identified evolutionary relationships that allowed us to propose the composition of a hypothetical ancestral SWI/SNF complex in the last eukaryotic common ancestor. This last common ancestor appears to have undergone several rounds of lineage-specific subunit gains and losses, shaping the current conformation of the known subclasses in animals and fungi. In addition, our results unravel a plant SWI/SNF complex, reminiscent of the animal BAF subclass, which incorporates a set of plant-specific subunits of still unknown function.31 Biological Sciences (for-2020)3104 Evolutionary Biology (for-2020)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Animals (mesh)Chromatin (mesh)Chromosomal ProteinsNon-Histone (mesh)Eukaryota (mesh)Plant Structures (mesh)Transcription Factors (mesh)Chromatin (mesh)Animals (mesh)Chromosomal ProteinsNon-Histone (mesh)Transcription Factors (mesh)Plant Structures (mesh)Eukaryota (mesh)Animals (mesh)Chromatin (mesh)Chromosomal ProteinsNon-Histone (mesh)Eukaryota (mesh)Plant Structures (mesh)Transcription Factors (mesh)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/2s42404xhttps://escholarship.org/content/qt2s42404x/qt2s42404x.pdfinfo:doi/10.1038/s42003-022-03490-xarticleCommunications Biology, vol 5, iss 1549oai:escholarship.org:ark:/13030/qt96d7f5nz2026-08-23T17:40:28Zqt96d7f5nzLysosomes are required for early dorsal signaling in the Xenopus embryoTejeda-Muñoz, NydiaDe Robertis, Edward M2022-04-26Lysosomes are the digestive center of the cell and play important roles in human diseases, including cancer. Previous work has suggested that late endosomes, also known as multivesicular bodies (MVBs), and lysosomes are essential for canonical Wnt pathway signaling. Sequestration of Glycogen Synthase 3 (GSK3) and of β‐catenin destruction complex components in MVBs is required for sustained canonical Wnt signaling. Little is known about the role of lysosomes during early development. In the Xenopus egg, a Wnt-like cytoplasmic determinant signal initiates formation of the body axis following a cortical rotation triggered by sperm entry. Here we report that cathepsin D was activated in lysosomes specifically on the dorsal marginal zone of the embryo at the 64-cell stage, long before zygotic transcription starts. Expansion of the MVB compartment with low-dose hydroxychloroquine (HCQ) greatly potentiated the dorsalizing effects of the Wnt agonist lithium chloride (LiCl) in embryos, and this effect required macropinocytosis. Formation of the dorsal axis required lysosomes, as indicated by brief treatments with the vacuolar ATPase (V-ATPase) inhibitors Bafilomycin A1 or Concanamycin A at the 32-cell stage. Inhibiting the MVB-forming machinery with a dominant-negative point mutation in Vacuolar Protein Sorting 4 (Vps4-EQ) interfered with the endogenous dorsal axis. The Wnt-like activity of the dorsal cytoplasmic determinant Huluwa (Hwa), and that of microinjected xWnt8 messenger RNA, also required lysosome acidification and the MVB-forming machinery. We conclude that lysosome function is required for early dorsal axis development in Xenopus. The results highlight the intertwining between membrane trafficking, lysosomes, and vertebrate axis formation.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)1.1 Normal biological development and functioning (hrcs-rac)Animals (mesh)Body Patterning (mesh)EmbryoMammalian (mesh)EmbryoNonmammalian (mesh)Lysosomes (mesh)Signal Transduction (mesh)Xenopus Proteins (mesh)Xenopus laevis (mesh)lysosomescytoplasmic determinantXenopus laevisWnt signalingHwaLysosomes (mesh)EmbryoNonmammalian (mesh)Animals (mesh)Xenopus laevis (mesh)Xenopus Proteins (mesh)Signal Transduction (mesh)Body Patterning (mesh)EmbryoMammalian (mesh)HwaWnt signalingXenopus laeviscytoplasmic determinantlysosomesAnimals (mesh)Body Patterning (mesh)EmbryoMammalian (mesh)EmbryoNonmammalian (mesh)Lysosomes (mesh)Signal Transduction (mesh)Xenopus Proteins (mesh)Xenopus laevis (mesh)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/96d7f5nzhttps://escholarship.org/content/qt96d7f5nz/qt96d7f5nz.pdfinfo:doi/10.1073/pnas.2201008119articleProceedings of the National Academy of Sciences of the United States of America, vol 119, iss 17e2201008119oai:escholarship.org:ark:/13030/qt6vm7b7g32026-08-23T17:40:17Zqt6vm7b7g3Canonical Wnt signaling induces focal adhesion and Integrin beta-1 endocytosisTejeda-Muñoz, NydiaMorselli, MarcoMoriyama, YukiSheladiya, PoojaPellegrini, MatteoDe Robertis, Edward M2022-04-01During canonical Wnt signaling, the Wnt receptor complex is sequestered together with glycogen synthase kinase 3 (GSK3) and Axin inside late endosomes, known as multivesicular bodies (MVBs). Here, we present experiments showing that Wnt causes the endocytosis of focal adhesion (FA) proteins and depletion of Integrin β 1 (ITGβ1) from the cell surface. FAs and integrins link the cytoskeleton to the extracellular matrix. Wnt-induced endocytosis caused ITGβ1 depletion from the plasma membrane and was accompanied by striking changes in the actin cytoskeleton. In situ protease protection assays in cultured cells showed that ITGβ1 was sequestered within membrane-bounded organelles that corresponded to Wnt-induced MVBs containing GSK3 and FA-associated proteins. An in vivo model using Xenopus embryos dorsalized by Wnt8 mRNA showed that ITGβ1 depletion decreased Wnt signaling. The finding of a crosstalk between two major signaling pathways, canonical Wnt and focal adhesions, should be relevant to human cancer and cell biology.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Cancer (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Cell biologyDevelopmental biologyOmicsapplication/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/6vm7b7g3https://escholarship.org/content/qt6vm7b7g3/qt6vm7b7g3.pdfinfo:doi/10.1016/j.isci.2022.104123articleiScience, vol 25, iss 4104123oai:escholarship.org:ark:/13030/qt8qn6x00g2026-08-23T17:27:57Zqt8qn6x00gSortase-assembled pili in Corynebacterium diphtheriae are built using a latch mechanismMcConnell, Scott AMcAllister, Rachel AAmer, Brendan RMahoney, Brendan JSue, Christopher KChang, ChungyuTon-That, HungClubb, Robert T2021-03-23Gram-positive bacteria assemble pili (fimbriae) on their surfaces to adhere to host tissues and to promote polymicrobial interactions. These hair-like structures, although very thin (1 to 5 nm), exhibit impressive tensile strengths because their protein components (pilins) are covalently crosslinked together via lysine-isopeptide bonds by pilus-specific sortase enzymes. While atomic structures of isolated pilins have been determined, how they are joined together by sortases and how these interpilin crosslinks stabilize pilus structure are poorly understood. Using a reconstituted pilus assembly system and hybrid structural biology methods, we elucidated the solution structure and dynamics of the crosslinked interface that is repeated to build the prototypical SpaA pilus from Corynebacterium diphtheriae We show that sortase-catalyzed introduction of a K190-T494 isopeptide bond between adjacent SpaA pilins causes them to form a rigid interface in which the LPLTG sorting signal is inserted into a large binding groove. Cellular and quantitative kinetic measurements of the crosslinking reaction shed light onto the mechanism of pilus biogenesis. We propose that the pilus-specific sortase in C. diphtheriae uses a latch mechanism to select K190 on SpaA for crosslinking in which the sorting signal is partially transferred from the enzyme to a binding groove in SpaA in order to facilitate catalysis. This process is facilitated by a conserved loop in SpaA, which after crosslinking forms a stabilizing latch that covers the K190-T494 isopeptide bond. General features of the structure and sortase-catalyzed assembly mechanism of the SpaA pilus are likely conserved in Gram-positive bacteria.3101 Biochemistry and Cell Biology (for-2020)34 Chemical Sciences (for-2020)31 Biological Sciences (for-2020)Infectious Diseases (rcdc)Aminoacyltransferases (mesh)Bacterial Proteins (mesh)Catalysis (mesh)Corynebacterium diphtheriae (mesh)Cysteine Endopeptidases (mesh)Fimbriae Proteins (mesh)FimbriaeBacterial (mesh)Lysine (mesh)Protein Binding (mesh)pilisortaseGram positivelysine isopeptide bondintegrative structural biologyFimbriaeBacterial (mesh)Corynebacterium diphtheriae (mesh)Cysteine Endopeptidases (mesh)Aminoacyltransferases (mesh)Lysine (mesh)Bacterial Proteins (mesh)Fimbriae Proteins (mesh)Protein Binding (mesh)Catalysis (mesh)Gram positiveintegrative structural biologylysine isopeptide bondpilisortaseAminoacyltransferases (mesh)Bacterial Proteins (mesh)Catalysis (mesh)Corynebacterium diphtheriae (mesh)Cysteine Endopeptidases (mesh)Fimbriae Proteins (mesh)FimbriaeBacterial (mesh)Lysine (mesh)Protein Binding (mesh)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8qn6x00ghttps://escholarship.org/content/qt8qn6x00g/qt8qn6x00g.pdfinfo:doi/10.1073/pnas.2019649118articleProceedings of the National Academy of Sciences of the United States of America, vol 118, iss 12e2019649118oai:escholarship.org:ark:/13030/qt0qf6t1ks2026-08-23T15:48:30Zqt0qf6t1ksAtomic structures of fibrillar segments of hIAPP suggest tightly mated β-sheets are important for cytotoxicityKrotee, PascalRodriguez, Jose ASawaya, Michael RCascio, DuilioReyes, Francis EShi, DanHattne, JohanNannenga, Brent LOskarsson, Marie EPhilipp, StephanGriner, SarahJiang, LinGlabe, Charles GWestermark, Gunilla TGonen, TamirEisenberg, David S2017-01-03hIAPP fibrils are associated with Type-II Diabetes, but the link of hIAPP structure to islet cell death remains elusive. Here we observe that hIAPP fibrils are cytotoxic to cultured pancreatic β-cells, leading us to determine the structure and cytotoxicity of protein segments composing the amyloid spine of hIAPP. Using the cryoEM method MicroED, we discover that one segment, 19-29 S20G, forms pairs of β-sheets mated by a dry interface that share structural features with and are similarly cytotoxic to full-length hIAPP fibrils. In contrast, a second segment, 15-25 WT, forms non-toxic labile β-sheets. These segments possess different structures and cytotoxic effects, however, both can seed full-length hIAPP, and cause hIAPP to take on the cytotoxic and structural features of that segment. These results suggest that protein segment structures represent polymorphs of their parent protein and that segment 19-29 S20G may serve as a model for the toxic spine of hIAPP.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Amyloid (mesh)Cell Survival (mesh)CellsCultured (mesh)Cryoelectron Microscopy (mesh)Humans (mesh)Insulin-Secreting Cells (mesh)Islet Amyloid Polypeptide (mesh)Protein Conformationbeta-Strand (mesh)CellsCultured (mesh)Humans (mesh)Amyloid (mesh)Cryoelectron Microscopy (mesh)Cell Survival (mesh)Insulin-Secreting Cells (mesh)Islet Amyloid Polypeptide (mesh)Protein Conformationbeta-Strand (mesh)MicroEDType-II Diabetesamyloid fibrilbiochemistrybiophysicscytotoxicityhumanislet amyloid polypeptidestructural biologyAmyloid (mesh)Cell Survival (mesh)CellsCultured (mesh)Cryoelectron Microscopy (mesh)Humans (mesh)Insulin-Secreting Cells (mesh)Islet Amyloid Polypeptide (mesh)Protein Conformationbeta-Strand (mesh)0601 Biochemistry and Cell Biology (for)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/0qf6t1kshttps://escholarship.org/content/qt0qf6t1ks/qt0qf6t1ks.pdfinfo:doi/10.7554/elife.19273articleELIFE, vol 6e19273oai:escholarship.org:ark:/13030/qt7c35z3bc2026-08-23T13:06:40Zqt7c35z3bcMapping molecular landmarks of human skeletal ontogeny and pluripotent stem cell-derived articular chondrocytesFerguson, Gabriel BVan Handel, BenBay, MaxwellFiziev, PetkoOrg, TonisLee, SiyoungShkhyan, RuzannaBanks, Nicholas WScheinberg, MilaWu, LingSaitta, BiagioElphingstone, JosephLarson, A NoelleRiester, Scott MPyle, April DBernthal, Nicholas MMikkola, Hanna KAErnst, Jasonvan Wijnen, Andre JBonaguidi, MichaelEvseenko, Denis2018-09-07Tissue-specific gene expression defines cellular identity and function, but knowledge of early human development is limited, hampering application of cell-based therapies. Here we profiled 5 distinct cell types at a single fetal stage, as well as chondrocytes at 4 stages in vivo and 2 stages during in vitro differentiation. Network analysis delineated five tissue-specific gene modules; these modules and chromatin state analysis defined broad similarities in gene expression during cartilage specification and maturation in vitro and in vivo, including early expression and progressive silencing of muscle- and bone-specific genes. Finally, ontogenetic analysis of freshly isolated and pluripotent stem cell-derived articular chondrocytes identified that integrin alpha 4 defines 2 subsets of functionally and molecularly distinct chondrocytes characterized by their gene expression, osteochondral potential in vitro and proliferative signature in vivo. These analyses provide new insight into human musculoskeletal development and provide an essential comparative resource for disease modeling and regenerative medicine.3206 Medical Biotechnology (for-2020)32 Biomedical and Clinical Sciences (for-2020)40 Engineering (for-2020)4003 Biomedical Engineering (for-2020)Stem Cell Research - Induced Pluripotent Stem Cell (rcdc)Stem Cell Research (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell - Non-Human (rcdc)Stem Cell Research - Embryonic - Human (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell - Human (rcdc)Regenerative Medicine (rcdc)Biotechnology (rcdc)Genetics (rcdc)5.2 Cellular and gene therapies (hrcs-rac)Musculoskeletal (hrcs-hc)Animals (mesh)Biomarkers (mesh)Chondrocytes (mesh)Chondrogenesis (mesh)EpigenesisGenetic (mesh)Fetal Development (mesh)Gene Expression Profiling (mesh)Histone Code (mesh)Humans (mesh)Mice (mesh)Myoblasts (mesh)Osteoblasts (mesh)Sequence AnalysisRNA (mesh)Swine (mesh)Tenocytes (mesh)TranscriptionGenetic (mesh)Transcriptome (mesh)Chondrocytes (mesh)Osteoblasts (mesh)Myoblasts (mesh)Animals (mesh)Swine (mesh)Humans (mesh)Mice (mesh)Gene Expression Profiling (mesh)Sequence AnalysisRNA (mesh)TranscriptionGenetic (mesh)EpigenesisGenetic (mesh)Histone Code (mesh)Fetal Development (mesh)Chondrogenesis (mesh)Transcriptome (mesh)Biomarkers (mesh)Tenocytes (mesh)Animals (mesh)Biomarkers (mesh)Chondrocytes (mesh)Chondrogenesis (mesh)EpigenesisGenetic (mesh)Fetal Development (mesh)Gene Expression Profiling (mesh)Histone Code (mesh)Humans (mesh)Mice (mesh)Myoblasts (mesh)Osteoblasts (mesh)Sequence AnalysisRNA (mesh)Swine (mesh)Tenocytes (mesh)TranscriptionGenetic (mesh)Transcriptome (mesh)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7c35z3bchttps://escholarship.org/content/qt7c35z3bc/qt7c35z3bc.pdfinfo:doi/10.1038/s41467-018-05573-yarticleNature Communications, vol 9, iss 13634oai:escholarship.org:ark:/13030/qt9xw0p9gs2026-08-23T11:37:43Zqt9xw0p9gsBrap regulates liver morphology and hepatocyte turnover via modulation of the Hippo pathwayPriest, ChristinaNagari, Rohith TBideyan, LaraLee, Stephen DNguyen, AlexanderXiao, XuTontonoz, Peter2022-05-03Regulation of hepatocyte proliferation and liver morphology is of critical importance to tissue and whole-body homeostasis. However, the molecular mechanisms that underlie this complex process are incompletely understood. Here, we describe a role for the ubiquitin ligase BRCA1-associated protein (BRAP) in regulation of hepatocyte morphology and turnover via regulation of MST2, a protein kinase in the Hippo pathway. The Hippo pathway has been implicated in the control of liver morphology, inflammation, and fibrosis. We demonstrate here that liver-specific ablation of Brap in mice results in gross and cellular morphological alterations of the liver. Brap-deficient livers exhibit increased hepatocyte proliferation, cell death, and inflammation. We show that loss of BRAP protein alters Hippo pathway signaling, causing a reduction in phosphorylation of YAP and increased expression of YAP target genes, including those regulating cell growth and interactions with the extracellular environment. Finally, increased Hippo signaling in Brap knockout mice alters the pattern of liver lipid accumulation in dietary models of obesity. These studies identify a role for BRAP as a modulator of the hepatic Hippo pathway with relevance to human liver disease.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Digestive Diseases (rcdc)Chronic Liver Disease and Cirrhosis (rcdc)Liver Disease (rcdc)2.1 Biological and endogenous factors (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)Oral and gastrointestinal (hrcs-hc)Hepatocytes (mesh)Hippo Signaling Pathway (mesh)Liver (mesh)Signal Transduction (mesh)Ubiquitin-Protein Ligases (mesh)liverubiquitin ligaseHippo pathwayLiver (mesh)Hepatocytes (mesh)Ubiquitin-Protein Ligases (mesh)Signal Transduction (mesh)Hippo Signaling Pathway (mesh)Hippo pathwayliverubiquitin ligaseHepatocytes (mesh)Hippo Signaling Pathway (mesh)Liver (mesh)Signal Transduction (mesh)Ubiquitin-Protein Ligases (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/9xw0p9gshttps://escholarship.org/content/qt9xw0p9gs/qt9xw0p9gs.pdfinfo:doi/10.1073/pnas.2201859119articleProceedings of the National Academy of Sciences of the United States of America, vol 119, iss 18e2201859119oai:escholarship.org:ark:/13030/qt5664d8652026-08-23T11:37:23Zqt5664d865Integrative analysis reveals multiple modes of LXR transcriptional regulation in liverBideyan, LaraFan, WenxinKaczor-Urbanowicz, Karolina ElżbietaPriest, ChristinaCasero, DavidTontonoz, Peter2022-02-15The nuclear receptors liver X receptor (LXR) α and β play crucial roles in hepatic metabolism. Many genes induced in response to pharmacologic LXR agonism have been defined; however, the transcriptional consequences of loss of LXR binding to its genomic targets are less well characterized. Here, we addressed how deletion of both LXRα and LXRβ from mouse liver (LXR double knockout [DKO]) affects the transcriptional regulatory landscape by integrating changes in LXR binding, chromatin accessibility, and gene expression. Many genes involved in fatty acid metabolism showed reduced expression and chromatin accessibility at their intergenic and intronic regions in LXRDKO livers. Genes that were up-regulated with LXR deletion had increased chromatin accessibility at their promoter regions and were enriched for functions not linked to lipid metabolism. Loss of LXR binding in liver reduced the activity of a broad set of hepatic transcription factors, inferred through changes in motif accessibility. By contrast, accessibility at promoter nuclear factor Y (NF-Y) motifs was increased in the absence of LXR. Unexpectedly, we also defined a small set of LXR targets for direct ligand-dependent repression. These genes have LXR-binding sites but showed increased expression in LXRDKO liver and reduced expression in response to the LXR agonist. In summary, the binding of LXRs to the hepatic genome has broad effects on the transcriptional landscape that extend beyond its canonical function as an activator of lipid metabolic genes.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Biotechnology (rcdc)Nutrition (rcdc)Human Genome (rcdc)Chronic Liver Disease and Cirrhosis (rcdc)Genetics (rcdc)Liver Disease (rcdc)Digestive Diseases (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Animals (mesh)Benzoates (mesh)Benzylamines (mesh)Gene Expression Regulation (mesh)Liver (mesh)Liver X Receptors (mesh)Mice (mesh)MiceKnockout (mesh)LXRnuclear receptortranscriptionLiver (mesh)Animals (mesh)MiceKnockout (mesh)Mice (mesh)Benzylamines (mesh)Benzoates (mesh)Gene Expression Regulation (mesh)Liver X Receptors (mesh)LXRnuclear receptortranscriptionAnimals (mesh)Benzoates (mesh)Benzylamines (mesh)Gene Expression Regulation (mesh)Liver (mesh)Liver X Receptors (mesh)Mice (mesh)MiceKnockout (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/5664d865https://escholarship.org/content/qt5664d865/qt5664d865.pdfinfo:doi/10.1073/pnas.2122683119articleProceedings of the National Academy of Sciences of the United States of America, vol 119, iss 7e2122683119oai:escholarship.org:ark:/13030/qt4h4495x52026-08-23T09:18:43Zqt4h4495x5Ectopic targeting of CG DNA methylation in Arabidopsis with the bacterial SssI methyltransferaseLiu, WanluGallego-Bartolomé, JavierZhou, YuxingZhong, ZhenhuiWang, MingWongpalee, Somsakul PopGardiner, JasonFeng, SuhuaKuo, Peggy HsuanyuJacobsen, Steven E2021-05-25The ability to target epigenetic marks like DNA methylation to specific loci is important in both basic research and in crop plant engineering. However, heritability of targeted DNA methylation, how it impacts gene expression, and which epigenetic features are required for proper establishment are mostly unknown. Here, we show that targeting the CG-specific methyltransferase M.SssI with an artificial zinc finger protein can establish heritable CG methylation and silencing of a targeted locus in Arabidopsis. In addition, we observe highly heritable widespread ectopic CG methylation mainly over euchromatic regions. This hypermethylation shows little effect on transcription while it triggers a mild but significant reduction in the accumulation of H2A.Z and H3K27me3. Moreover, ectopic methylation occurs preferentially at less open chromatin that lacks positive histone marks. These results outline general principles of the heritability and interaction of CG methylation with other epigenomic features that should help guide future efforts to engineer epigenomes.31 Biological Sciences (for-2020)3105 Genetics (for-2020)Human Genome (rcdc)Genetics (rcdc)Arabidopsis (mesh)Arabidopsis Proteins (mesh)Bacterial Proteins (mesh)Chromatin (mesh)Chromatin Immunoprecipitation Sequencing (mesh)DNA Methylation (mesh)DNA-Cytosine Methylases (mesh)Gene Expression RegulationPlant (mesh)Histones (mesh)PlantsGenetically Modified (mesh)RNA-Seq (mesh)Spiroplasma (mesh)Chromatin (mesh)Spiroplasma (mesh)PlantsGenetically Modified (mesh)Arabidopsis (mesh)Bacterial Proteins (mesh)Histones (mesh)Arabidopsis Proteins (mesh)DNA Methylation (mesh)Gene Expression RegulationPlant (mesh)DNA-Cytosine Methylases (mesh)Chromatin Immunoprecipitation Sequencing (mesh)RNA-Seq (mesh)Arabidopsis (mesh)Arabidopsis Proteins (mesh)Bacterial Proteins (mesh)Chromatin (mesh)Chromatin Immunoprecipitation Sequencing (mesh)DNA Methylation (mesh)DNA-Cytosine Methylases (mesh)Gene Expression RegulationPlant (mesh)Histones (mesh)PlantsGenetically Modified (mesh)RNA-Seq (mesh)Spiroplasma (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/4h4495x5https://escholarship.org/content/qt4h4495x5/qt4h4495x5.pdfinfo:doi/10.1038/s41467-021-23346-yarticleNature Communications, vol 12, iss 13130oai:escholarship.org:ark:/13030/qt7105v6b32026-08-23T09:17:34Zqt7105v6b3A Mouse Model to Investigate the Role of Cancer-associated Fibroblasts in Tumor GrowthJelinek, DavidZhang, Ellen RanAmbrus, AaronHaley, ErinGuinn, EmilyVo, AustinLe, PeterKesaf, Ayse ElifNguyen, JenniferGuo, LilyFrederick, DestinySun, ZhengyangGuo, NatalieSevier, ParkerBilotta, EricAtai, KaiserVoisin, LaurentColler, Hilary A2020-12-01Cancer-associated fibroblasts (CAFs) can play an important role in tumor growth by creating a tumor-promoting microenvironment. Models to study the role of CAFs in the tumor microenvironment can be helpful for understanding the functional importance of fibroblasts, fibroblasts from different tissues, and specific genetic factors in fibroblasts. Mouse models are essential for understanding the contributors to tumor growth and progression in an in vivo context. Here, a protocol in which cancer cells are mixed with fibroblasts and introduced into mice to develop tumors is provided. Tumor sizes over time and final tumor weights are determined and compared among groups. The protocol described can provide more insight into the functional role of CAFs in tumor growth and progression.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Cancer (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Cancer (hrcs-hc)Animals (mesh)Cancer-Associated Fibroblasts (mesh)Cell LineTumor (mesh)Cell Proliferation (mesh)Disease ModelsAnimal (mesh)Humans (mesh)Injections (mesh)Melanoma (mesh)Mice (mesh)Neoplasms (mesh)Tumor Burden (mesh)Tumor Microenvironment (mesh)Cell LineTumor (mesh)Animals (mesh)Humans (mesh)Mice (mesh)Neoplasms (mesh)Melanoma (mesh)Disease ModelsAnimal (mesh)Tumor Burden (mesh)Injections (mesh)Cell Proliferation (mesh)Tumor Microenvironment (mesh)Cancer-Associated Fibroblasts (mesh)Animals (mesh)Cancer-Associated Fibroblasts (mesh)Cell LineTumor (mesh)Cell Proliferation (mesh)Disease ModelsAnimal (mesh)Humans (mesh)Injections (mesh)Melanoma (mesh)Mice (mesh)Neoplasms (mesh)Tumor Burden (mesh)Tumor Microenvironment (mesh)0601 Biochemistry and Cell Biology (for)1701 Psychology (for)1702 Cognitive Sciences (for)3101 Biochemistry and cell biology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7105v6b3https://escholarship.org/content/qt7105v6b3/qt7105v6b3.pdfinfo:doi/10.3791/61883articleJournal of Visualized Experiments, vol 2020, iss 16610.3791/61883oai:escholarship.org:ark:/13030/qt3b00n52h2026-08-23T07:32:37Zqt3b00n52hStructural polymorphism of amyloid fibrils in ATTR amyloidosis revealed by cryo-electron microscopyNguyen, Binh AnSingh, VirenderAfrin, ShumailaYakubovska, AnnaWang, LanieAhmed, YasminPedretti, RoseFernandez-Ramirez, Maria del CarmenSingh, PreetiPękała, MajaCabrera Hernandez, Luis OKumar, SiddharthLemoff, AndrewGonzalez-Prieto, RomanSawaya, Michael REisenberg, David SBenson, Merrill DouglasSaelices, Lorena2024-01-17ATTR amyloidosis is caused by the deposition of transthyretin in the form of amyloid fibrils in virtually every organ of the body, including the heart. This systemic deposition leads to a phenotypic variability that has not been molecularly explained yet. In brain amyloid conditions, previous studies suggest an association between clinical phenotype and the molecular structures of their amyloid fibrils. Here we investigate whether there is such an association in ATTRv amyloidosis patients carrying the mutation I84S. Using cryo-electron microscopy, we determined the structures of cardiac fibrils extracted from three ATTR amyloidosis patients carrying the ATTRv-I84S mutation, associated with a consistent clinical phenotype. We found that in each ATTRv-I84S patient, the cardiac fibrils exhibited different local conformations, and these variations can co-exist within the same fibril. Our finding suggests that one amyloid disease may associate with multiple fibril structures in systemic amyloidoses, calling for further studies.31 Biological Sciences (for-2020)32 Biomedical and Clinical Sciences (for-2020)51 Physical Sciences (for-2020)5104 Condensed Matter Physics (for-2020)Rare Diseases (rcdc)Neurosciences (rcdc)Neurodegenerative (rcdc)Cardiovascular (rcdc)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)Aging (rcdc)Acquired Cognitive Impairment (rcdc)Alzheimer's Disease (rcdc)Dementia (rcdc)Heart Disease (rcdc)Brain Disorders (rcdc)Orphan Drug (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Cardiovascular (hrcs-hc)Humans (mesh)Amyloid (mesh)Amyloid NeuropathiesFamilial (mesh)Cryoelectron Microscopy (mesh)Prealbumin (mesh)Heart (mesh)Brain Diseases (mesh)Heart (mesh)Humans (mesh)Brain Diseases (mesh)Amyloid NeuropathiesFamilial (mesh)Amyloid (mesh)Prealbumin (mesh)Cryoelectron Microscopy (mesh)Humans (mesh)Amyloid (mesh)Amyloid NeuropathiesFamilial (mesh)Cryoelectron Microscopy (mesh)Prealbumin (mesh)Heart (mesh)Brain Diseases (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/3b00n52hhttps://escholarship.org/content/qt3b00n52h/qt3b00n52h.pdfinfo:doi/10.1038/s41467-024-44820-3articleNature Communications, vol 15, iss 1581oai:escholarship.org:ark:/13030/qt8tp9v24s2026-08-23T07:28:47Zqt8tp9v24sSARS-CoV-2 infection rewires host cell metabolism and is potentially susceptible to mTORC1 inhibitionMullen, Peter JGarcia, GustavoPurkayastha, ArunimaMatulionis, NedasSchmid, Ernst WMomcilovic, MilicaSen, ChandaniLangerman, JustinRamaiah, ArunachalamShackelford, David BDamoiseaux, RobertFrench, Samuel WPlath, KathrinGomperts, Brigitte NArumugaswami, VaithilingarajaChristofk, Heather R2021-03-25Viruses hijack host cell metabolism to acquire the building blocks required for replication. Understanding how SARS-CoV-2 alters host cell metabolism may lead to potential treatments for COVID-19. Here we profile metabolic changes conferred by SARS-CoV-2 infection in kidney epithelial cells and lung air-liquid interface (ALI) cultures, and show that SARS-CoV-2 infection increases glucose carbon entry into the TCA cycle via increased pyruvate carboxylase expression. SARS-CoV-2 also reduces oxidative glutamine metabolism while maintaining reductive carboxylation. Consistent with these changes, SARS-CoV-2 infection increases the activity of mTORC1 in cell lines and lung ALI cultures. Lastly, we show evidence of mTORC1 activation in COVID-19 patient lung tissue, and that mTORC1 inhibitors reduce viral replication in kidney epithelial cells and lung ALI cultures. Our results suggest that targeting mTORC1 may be a feasible treatment strategy for COVID-19 patients, although further studies are required to determine the mechanism of inhibition and potential efficacy in patients.3207 Medical Microbiology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Coronaviruses Therapeutics and Interventions (rcdc)Kidney Disease (rcdc)Coronaviruses (rcdc)Infectious Diseases (rcdc)Emerging Infectious Diseases (rcdc)Biodefense (rcdc)Lung (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Infection (hrcs-hc)Animals (mesh)Benzamides (mesh)COVID-19 (mesh)Cell Line (mesh)Chlorocebus aethiops (mesh)Citric Acid Cycle (mesh)Glucose (mesh)Glutamine (mesh)HEK293 Cells (mesh)Humans (mesh)Lung (mesh)Mechanistic Target of Rapamycin Complex 1 (mesh)Morpholines (mesh)Naphthyridines (mesh)Protein Kinase Inhibitors (mesh)Pyrimidines (mesh)Pyruvate Carboxylase (mesh)SARS-CoV-2 (mesh)Vero Cells (mesh)Virus Replication (mesh)Lung (mesh)Cell Line (mesh)Vero Cells (mesh)Animals (mesh)Humans (mesh)Benzamides (mesh)Morpholines (mesh)Pyrimidines (mesh)Naphthyridines (mesh)Pyruvate Carboxylase (mesh)Glucose (mesh)Glutamine (mesh)Protein Kinase Inhibitors (mesh)Virus Replication (mesh)Citric Acid Cycle (mesh)HEK293 Cells (mesh)Mechanistic Target of Rapamycin Complex 1 (mesh)Chlorocebus aethiops (mesh)COVID-19 (mesh)SARS-CoV-2 (mesh)Animals (mesh)Benzamides (mesh)COVID-19 (mesh)Cell Line (mesh)Chlorocebus aethiops (mesh)Citric Acid Cycle (mesh)Glucose (mesh)Glutamine (mesh)HEK293 Cells (mesh)Humans (mesh)Lung (mesh)Mechanistic Target of Rapamycin Complex 1 (mesh)Morpholines (mesh)Naphthyridines (mesh)Protein Kinase Inhibitors (mesh)Pyrimidines (mesh)Pyruvate Carboxylase (mesh)SARS-CoV-2 (mesh)Vero Cells (mesh)Virus Replication (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/8tp9v24shttps://escholarship.org/content/qt8tp9v24s/qt8tp9v24s.pdfinfo:doi/10.1038/s41467-021-22166-4articleNature Communications, vol 12, iss 11876oai:escholarship.org:ark:/13030/qt1799r54v2026-08-23T07:28:43Zqt1799r54vCarboxylate-Modified Magnetic Bead (CMMB)-Based Isopropanol Gradient Peptide Fractionation (CIF) Enables Rapid and Robust Off-Line Peptide Mixture Fractionation in Bottom-Up ProteomicsDeng, WeixianSha, JihuiPlath, KathrinWohlschlegel, James A2021-01-01Deep proteome coverage in bottom-up proteomics requires peptide-level fractionation to simplify the complex peptide mixture before analysis by tandem mass spectrometry. By decreasing the number of coeluting precursor peptide ions, fractionation effectively reduces the complexity of the sample leading to higher sample coverage and reduced bias toward high-abundance precursors that are preferentially identified in data-dependent acquisition strategies. To achieve this goal, we report a bead-based off-line peptide fractionation method termed CIF or carboxylate-modified magnetic bead-based isopropanol gradient peptide fractionation. CIF is an extension of the SP3 (single-pot solid phase-enhanced sample preparation) strategy and provides an effective but complementary approach to other commonly used fractionation methods including strong cation exchange and reversed phase-based chromatography. We demonstrate that CIF is an effective offline separation strategy capable of increasing the depth of peptide analyte coverage both when used alone or as a second dimension of peptide fractionation in conjunction with high pH reversed phase. These features make it ideally suited for a wide range of proteomic applications including the affinity purification of low-abundance bait proteins.3401 Analytical Chemistry (for-2020)34 Chemical Sciences (for-2020)Biotechnology (rcdc)2-Propanol (mesh)Carboxylic Acids (mesh)Chemical Fractionation (mesh)ChromatographyReverse-Phase (mesh)HEK293 Cells (mesh)Humans (mesh)Ion Exchange (mesh)Magnetic Phenomena (mesh)Peptides (mesh)Proteome (mesh)Proteomics (mesh)Humans (mesh)2-Propanol (mesh)Carboxylic Acids (mesh)Peptides (mesh)Proteome (mesh)Chemical Fractionation (mesh)Proteomics (mesh)Ion Exchange (mesh)ChromatographyReverse-Phase (mesh)HEK293 Cells (mesh)Magnetic Phenomena (mesh)Peptide fractionationSP3proteomics2-Propanol (mesh)Carboxylic Acids (mesh)Chemical Fractionation (mesh)ChromatographyReverse-Phase (mesh)HEK293 Cells (mesh)Humans (mesh)Ion Exchange (mesh)Magnetic Phenomena (mesh)Peptides (mesh)Proteome (mesh)Proteomics (mesh)Biochemistry & Molecular Biology (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/1799r54vhttps://escholarship.org/content/qt1799r54v/qt1799r54v.pdfinfo:doi/10.1074/mcp.ra120.002411articleMolecular & Cellular Proteomics, vol 20100039oai:escholarship.org:ark:/13030/qt4rs120hn2026-08-23T07:26:19Zqt4rs120hnIntron retention is a robust marker of intertumoral heterogeneity in pancreatic ductal adenocarcinomaTan, Daniel JMitra, MithunChiu, Alec MColler, Hilary A2020-12-11Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer with a 5-year survival rate of <8%. Unsupervised clustering of 76 PDAC patients based on intron retention (IR) events resulted in two clusters of tumors (IR-1 and IR-2). While gene expression-based clusters are not predictive of patient outcome in this cohort, the clusters we developed based on intron retention were associated with differences in progression-free interval. IR levels are lower and clinical outcome is worse in IR-1 compared with IR-2. Oncogenes were significantly enriched in the set of 262 differentially retained introns between the two IR clusters. Higher IR levels in IR-2 correlate with higher gene expression, consistent with detention of intron-containing transcripts in the nucleus in IR-2. Out of 258 genes encoding RNA-binding proteins (RBP) that were differentially expressed between IR-1 and IR-2, the motifs for seven RBPs were significantly enriched in the 262-intron set, and the expression of 25 RBPs were highly correlated with retention levels of 139 introns. Network analysis suggested that retention of introns in IR-2 could result from disruption of an RBP protein−protein interaction network previously linked to efficient intron removal. Finally, IR-based clusters developed for the majority of the 20 cancer types surveyed had two clusters with asymmetrical distributions of IR events like PDAC, with one cluster containing mostly intron loss events. Taken together, our findings suggest IR may be an important biomarker for subclassifying tumors.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)Digestive Diseases (rcdc)Pancreatic Cancer (rcdc)Genetics (rcdc)Cancer (rcdc)Rare Diseases (rcdc)3105 Genetics (for-2020)3206 Medical biotechnology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/4rs120hnhttps://escholarship.org/content/qt4rs120hn/qt4rs120hn.pdfinfo:doi/10.1038/s41525-020-00159-4articlenpj Genomic Medicine, vol 5, iss 155oai:escholarship.org:ark:/13030/qt4p5520st2026-08-23T07:25:47Zqt4p5520stThe role of MORC3 in silencing transposable elements in mouse embryonic stem cellsDesai, Varsha PChouaref, JihedWu, HaoyuPastor, William AKan, Ryan LOey, Harald MLi, ZhengHo, JamieVonk, Kelly KDSan Leon Granado, DavidChristopher, Michael AClark, Amander TJacobsen, Steven EDaxinger, Lucia2021-10-27BackgroundMicrorchidia proteins (MORCs) are involved in epigenetic gene silencing in a variety of eukaryotic organisms. Deletion of MORCs result in several developmental abnormalities and their dysregulation has been implicated in developmental disease and multiple cancers. Specifically, mammalian MORC3 mutations are associated with immune system defects and human cancers such as bladder, uterine, stomach, lung, and diffuse large B cell lymphomas. While previous studies have shown that MORC3 binds to H3K4me3 in vitro and overlaps with H3K4me3 ChIP-seq peaks in mouse embryonic stem cells, the mechanism by which MORC3 regulates gene expression is unknown.ResultsIn this study, we identified that mutation in Morc3 results in a suppressor of variegation phenotype in a Modifiers of murine metastable epialleles Dominant (MommeD) screen. We also find that MORC3 functions as an epigenetic silencer of transposable elements (TEs) in mouse embryonic stem cells (mESCs). Loss of Morc3 results in upregulation of TEs, specifically those belonging to the LTR class of retrotransposons also referred to as endogenous retroviruses (ERVs). Using ChIP-seq we found that MORC3, in addition to its known localization at H3K4me3 sites, also binds to ERVs, suggesting a direct role in regulating their expression. Previous studies have shown that these ERVs are marked by the repressive histone mark H3K9me3 which plays a key role in their silencing. However, we found that levels of H3K9me3 showed only minor losses in Morc3 mutant mES cells. Instead, we found that loss of Morc3 resulted in increased chromatin accessibility at ERVs as measured by ATAC-seq.ConclusionsOur results reveal MORC3 as a novel regulator of ERV silencing in mouse embryonic stem cells. The relatively minor changes of H3K9me3 in the Morc3 mutant suggests that MORC3 acts mainly downstream of, or in a parallel pathway with, the TRIM28/SETDB1 complex that deposits H3K9me3 at these loci. The increased chromatin accessibility of ERVs in the Morc3 mutant suggests that MORC3 may act at the level of chromatin compaction to effect TE silencing.3101 Biochemistry and Cell Biology (for-2020)3102 Bioinformatics and Computational Biology (for-2020)31 Biological Sciences (for-2020)Stem Cell Research (rcdc)Human Genome (rcdc)Cancer (rcdc)Rare Diseases (rcdc)Genetics (rcdc)Stem Cell Research - Embryonic - Non-Human (rcdc)2.1 Biological and endogenous factors (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Adenosine Triphosphatases (mesh)Animals (mesh)Chromatin (mesh)DNA Transposable Elements (mesh)DNA-Binding Proteins (mesh)Endogenous Retroviruses (mesh)Gene Silencing (mesh)Mice (mesh)Mouse Embryonic Stem Cells (mesh)MORC3Endogenous retrovirusesMommeD screenChromatin regulatorsIAPsChromatin (mesh)Animals (mesh)Mice (mesh)Endogenous Retroviruses (mesh)DNA-Binding Proteins (mesh)DNA Transposable Elements (mesh)Gene Silencing (mesh)Adenosine Triphosphatases (mesh)Mouse Embryonic Stem Cells (mesh)Chromatin regulatorsEndogenous retrovirusesIAPsMORC3MommeD screenAdenosine Triphosphatases (mesh)Animals (mesh)Chromatin (mesh)DNA Transposable Elements (mesh)DNA-Binding Proteins (mesh)Endogenous Retroviruses (mesh)Gene Silencing (mesh)Mice (mesh)Mouse Embryonic Stem Cells (mesh)0604 Genetics (for)3105 Genetics (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/4p5520sthttps://escholarship.org/content/qt4p5520st/qt4p5520st.pdfinfo:doi/10.1186/s13072-021-00420-9articleEpigenetics & Chromatin, vol 14, iss 149oai:escholarship.org:ark:/13030/qt3vh6v6xb2026-08-23T07:25:43Zqt3vh6v6xbDivergent acyl carrier protein decouples mitochondrial Fe-S cluster biogenesis from fatty acid synthesis in malaria parasitesFalekun, SeyiSepulveda, JaimeJami-Alahmadi, YasamanPark, HahnbeomWohlschlegel, James ASigala, Paul A2021-10-06Most eukaryotic cells retain a mitochondrial fatty acid synthesis (FASII) pathway whose acyl carrier protein (mACP) and 4-phosphopantetheine (Ppant) prosthetic group provide a soluble scaffold for acyl chain synthesis and biochemically couple FASII activity to mitochondrial electron transport chain (ETC) assembly and Fe-S cluster biogenesis. In contrast, the mitochondrion of Plasmodium falciparum malaria parasites lacks FASII enzymes yet curiously retains a divergent mACP lacking a Ppant group. We report that ligand-dependent knockdown of mACP is lethal to parasites, indicating an essential FASII-independent function. Decyl-ubiquinone rescues parasites temporarily from death, suggesting a dominant dysfunction of the mitochondrial ETC. Biochemical studies reveal that Plasmodium mACP binds and stabilizes the Isd11-Nfs1 complex required for Fe-S cluster biosynthesis, despite lacking the Ppant group required for this association in other eukaryotes, and knockdown of parasite mACP causes loss of Nfs1 and the Rieske Fe-S protein in ETC complex III. This work reveals that Plasmodium parasites have evolved to decouple mitochondrial Fe-S cluster biogenesis from FASII activity, and this adaptation is a shared metabolic feature of other apicomplexan pathogens, including Toxoplasma and Babesia. This discovery unveils an evolutionary driving force to retain interaction of mitochondrial Fe-S cluster biogenesis with ACP independent of its eponymous function in FASII.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)3202 Clinical Sciences (for-2020)3207 Medical Microbiology (for-2020)Vector-Borne Diseases (rcdc)Rare Diseases (rcdc)Infectious Diseases (rcdc)Malaria (rcdc)2.1 Biological and endogenous factors (hrcs-rac)2.2 Factors relating to the physical environment (hrcs-rac)Infection (hrcs-hc)3 Good Health and Well Being (sdg)Acyl Carrier Protein (mesh)Fatty Acids (mesh)Iron (mesh)Organelle Biogenesis (mesh)Plasmodium falciparum (mesh)Protozoan Proteins (mesh)Sulfur (mesh)malariaorganelle adaptationmitochondriaacyl carrier proteinFe-S cluster synthesisPfalciparumPlasmodium falciparum (mesh)Sulfur (mesh)Iron (mesh)Fatty Acids (mesh)Acyl Carrier Protein (mesh)Protozoan Proteins (mesh)Organelle Biogenesis (mesh)Fe-S cluster synthesisP. falciparumacyl carrier proteinbiochemistrychemical biologyinfectious diseasemalariamicrobiologymitochondriaorganelle adaptationAcyl Carrier Protein (mesh)Fatty Acids (mesh)Iron (mesh)Organelle Biogenesis (mesh)Plasmodium falciparum (mesh)Protozoan Proteins (mesh)Sulfur (mesh)0601 Biochemistry and Cell Biology (for)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/3vh6v6xbhttps://escholarship.org/content/qt3vh6v6xb/qt3vh6v6xb.pdfinfo:doi/10.7554/elife.71636articleELIFE, vol 10e71636oai:escholarship.org:ark:/13030/qt27n3900t2026-08-23T07:14:22Zqt27n3900tWnt-inducible Lrp6-APEX2 interacting proteins identify ESCRT machinery and Trk-fused gene as components of the Wnt signaling pathwayColozza, GabrieleJami-Alahmadi, YasamanDsouza, AlyssaTejeda-Muñoz, NydiaAlbrecht, Lauren VSosa, Eric AWohlschlegel, James ADe Robertis, Edward M2014-09-01The canonical Wnt pathway serves as a hub connecting diverse cellular processes, including β-catenin signaling, differentiation, growth, protein stability, macropinocytosis, and nutrient acquisition in lysosomes. We have proposed that sequestration of β-catenin destruction complex components in multivesicular bodies (MVBs) is required for sustained canonical Wnt signaling. In this study, we investigated the events that follow activation of the canonical Wnt receptor Lrp6 using an APEX2-mediated proximity labeling approach. The Wnt co-receptor Lrp6 was fused to APEX2 and used to biotinylate targets that are recruited near the receptor during Wnt signaling at different time periods. Lrp6 proximity targets were identified by mass spectrometry, and revealed that many endosomal proteins interacted with Lrp6 within 5 min of Wnt3a treatment. Interestingly, we found that Trk-fused gene (TFG), previously known to regulate the cell secretory pathway and to be rearranged in thyroid and lung cancers, was strongly enriched in the proximity of Lrp6. TFG depletion with siRNA, or knock-out with CRISPR/Cas9, significantly reduced Wnt/β-catenin signaling in cell culture. In vivo, studies in the Xenopus system showed that TFG is required for endogenous Wnt-dependent embryonic patterning. The results suggest that the multivesicular endosomal machinery and the novel player TFG have important roles in Wnt signaling.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Biotechnology (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Generic health relevance (hrcs-hc)DNA-(Apurinic or Apyrimidinic Site) Lyase (mesh)Endonucleases (mesh)Endosomal Sorting Complexes Required for Transport (mesh)Gene Fusion (mesh)HEK293 Cells (mesh)Humans (mesh)Low Density Lipoprotein Receptor-Related Protein-6 (mesh)Multifunctional Enzymes (mesh)ReceptortrkA (mesh)Wnt Signaling Pathway (mesh)46 Information and Computing Sciences (for-2020)31 Biological Sciences (for-2020)49 Mathematical Sciences (for-2020)Bioengineering (rcdc)Biotechnology (rcdc)Networking and Information Technology R&D (NITRD) (rcdc)Generic health relevance (hrcs-hc)Data InterpretationStatistical (mesh)Mass Spectrometry (mesh)Peptides (mesh)Proteins (mesh)Proteomics (mesh)Software (mesh)Humans (mesh)DNA-(Apurinic or Apyrimidinic Site) Lyase (mesh)Endonucleases (mesh)ReceptortrkA (mesh)Gene Fusion (mesh)Endosomal Sorting Complexes Required for Transport (mesh)HEK293 Cells (mesh)Low Density Lipoprotein Receptor-Related Protein-6 (mesh)Wnt Signaling Pathway (mesh)Multifunctional Enzymes (mesh)DNA-(Apurinic or Apyrimidinic Site) Lyase (mesh)Endonucleases (mesh)Endosomal Sorting Complexes Required for Transport (mesh)Gene Fusion (mesh)HEK293 Cells (mesh)Humans (mesh)Low Density Lipoprotein Receptor-Related Protein-6 (mesh)Multifunctional Enzymes (mesh)ReceptortrkA (mesh)Wnt Signaling Pathway (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/27n3900thttps://escholarship.org/content/qt27n3900t/qt27n3900t.pdfinfo:doi/10.1038/s41598-020-78019-5articleScientific Reports, vol 10, iss 121555oai:escholarship.org:ark:/13030/qt3fv0k8bt2026-08-23T04:26:35Zqt3fv0k8btGSK3 Inhibits Macropinocytosis and Lysosomal Activity through the Wnt Destruction Complex MachineryAlbrecht, Lauren VTejeda-Muñoz, NydiaBui, Maggie HCicchetto, Andrew CDi Biagio, DanieleColozza, GabrieleSchmid, ErnstPiccolo, StefanoChristofk, Heather RDe Robertis, Edward M2020-07-01Canonical Wnt signaling is emerging as a major regulator of endocytosis. Here, we report that Wnt-induced macropinocytosis is regulated through glycogen synthase kinase 3 (GSK3) and the β-catenin destruction complex. We find that mutation of Axin1, a tumor suppressor and component of the destruction complex, results in the activation of macropinocytosis. Surprisingly, inhibition of GSK3 by lithium chloride (LiCl), CHIR99021, or dominant-negative GSK3 triggers macropinocytosis. GSK3 inhibition causes a rapid increase in acidic endolysosomes that is independent of new protein synthesis. GSK3 inhibition or Axin1 mutation increases lysosomal activity, which can be followed with tracers of active cathepsin D, β-glucosidase, and ovalbumin degradation. Microinjection of LiCl into the blastula cavity of Xenopus embryos causes a striking increase in dextran macropinocytosis. The effects of GSK3 inhibition on protein degradation in endolysosomes are blocked by the macropinocytosis inhibitors EIPA or IPA-3, suggesting that increases in membrane trafficking drive lysosomal activity.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Animals (mesh)Axin Protein (mesh)Cell LineTumor (mesh)Endocytosis (mesh)Endosomes (mesh)Glycogen Synthase Kinase 3 (mesh)Lysosomes (mesh)Phosphorylation (mesh)Pinocytosis (mesh)Wnt Proteins (mesh)Wnt Signaling Pathway (mesh)Xenopus Proteins (mesh)Xenopus laevis (mesh)beta Catenin (mesh)Cell LineTumor (mesh)Endosomes (mesh)Lysosomes (mesh)Animals (mesh)Xenopus laevis (mesh)Glycogen Synthase Kinase 3 (mesh)Xenopus Proteins (mesh)Endocytosis (mesh)Pinocytosis (mesh)Phosphorylation (mesh)Wnt Proteins (mesh)beta Catenin (mesh)Axin Protein (mesh)Wnt Signaling Pathway (mesh)Axin1Pak1cathepsin Dcolorectal carcinomahepatocellular carcinomalysosomemembrane traffickingmultivesicular bodiesnutrient acquisitionβ-glucosidaseAnimals (mesh)Axin Protein (mesh)Cell LineTumor (mesh)Endocytosis (mesh)Endosomes (mesh)Glycogen Synthase Kinase 3 (mesh)Lysosomes (mesh)Phosphorylation (mesh)Pinocytosis (mesh)Wnt Proteins (mesh)Wnt Signaling Pathway (mesh)Xenopus Proteins (mesh)Xenopus laevis (mesh)beta Catenin (mesh)0601 Biochemistry and Cell Biology (for)1116 Medical Physiology (for)31 Biological sciences (for-2020)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/3fv0k8bthttps://escholarship.org/content/qt3fv0k8bt/qt3fv0k8bt.pdfinfo:doi/10.1016/j.celrep.2020.107973articleCell Reports, vol 32, iss 4107973oai:escholarship.org:ark:/13030/qt8076v3g02026-08-23T04:19:18Zqt8076v3g0The characterization of Mediator 12 and 13 as conditional positive gene regulators in ArabidopsisLiu, QikunBischof, SylvainHarris, C JakeZhong, ZhenhuiZhan, LingyuNguyen, CalvinRashoff, AndrewBarshop, William DSun, FeiFeng, SuhuaPotok, MagdalenaGallego-Bartolome, JavierZhai, JixianWohlschlegel, James ACarey, Michael FLong, Jeffrey AJacobsen, Steven E2020-06-03Mediator 12 (MED12) and MED13 are components of the Mediator multi-protein complex, that facilitates the initial steps of gene transcription. Here, in an Arabidopsis mutant screen, we identify MED12 and MED13 as positive gene regulators, both of which contribute broadly to morc1 de-repressed gene expression. Both MED12 and MED13 are preferentially required for the expression of genes depleted in active chromatin marks, a chromatin signature shared with morc1 re-activated loci. We further discover that MED12 tends to interact with genes that are responsive to environmental stimuli, including light and radiation. We demonstrate that light-induced transient gene expression depends on MED12, and is accompanied by a concomitant increase in MED12 enrichment during induction. In contrast, the steady-state expression level of these genes show little dependence on MED12, suggesting that MED12 is primarily required to aid the expression of genes in transition from less-active to more active states.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)3105 Genetics (for-2020)Genetics (rcdc)Arabidopsis (mesh)Arabidopsis Proteins (mesh)Chromatin (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Gene Expression RegulationPlant (mesh)GenesPlant (mesh)GenesSuppressor (mesh)Genetic Loci (mesh)Green Fluorescent Proteins (mesh)Light (mesh)PlantsGenetically Modified (mesh)Repressor Proteins (mesh)Up-Regulation (mesh)Chromatin (mesh)PlantsGenetically Modified (mesh)Arabidopsis (mesh)Green Fluorescent Proteins (mesh)Arabidopsis Proteins (mesh)Repressor Proteins (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Gene Expression RegulationPlant (mesh)Up-Regulation (mesh)GenesPlant (mesh)GenesSuppressor (mesh)Light (mesh)Genetic Loci (mesh)Arabidopsis (mesh)Arabidopsis Proteins (mesh)Chromatin (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Gene Expression RegulationPlant (mesh)GenesPlant (mesh)GenesSuppressor (mesh)Genetic Loci (mesh)Green Fluorescent Proteins (mesh)Light (mesh)PlantsGenetically Modified (mesh)Repressor Proteins (mesh)Up-Regulation (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/8076v3g0https://escholarship.org/content/qt8076v3g0/qt8076v3g0.pdfinfo:doi/10.1038/s41467-020-16651-5articleNature Communications, vol 11, iss 12798oai:escholarship.org:ark:/13030/qt15t2099n2026-08-23T04:17:50Zqt15t2099nNAP1-RELATED PROTEIN1 and 2 negatively regulate H2A.Z abundance in chromatin in ArabidopsisWang, YafeiZhong, ZhenhuiZhang, YaxinXu, LinhaoFeng, SuhuaRayatpisheh, ShimaWohlschlegel, James AWang, ZonghuaJacobsen, Steven EAusin, Israel2020-06-08In eukaryotes, DNA wraps around histones to form nucleosomes, which are compacted into chromatin. DNA-templated processes, including transcription, require chromatin disassembly and reassembly mediated by histone chaperones. Additionally, distinct histone variants can replace core histones to regulate chromatin structure and function. Although replacement of H2A with the evolutionarily conserved H2A.Z via the SWR1 histone chaperone complex has been extensively studied, in plants little is known about how a reduction of H2A.Z levels can be achieved. Here, we show that NRP proteins cause a decrease of H2A.Z-containing nucleosomes in Arabidopsis under standard growing conditions. nrp1-1 nrp2-2 double mutants show an over-accumulation of H2A.Z genome-wide, especially at heterochromatic regions normally H2A.Z-depleted in wild-type plants. Our work suggests that NRP proteins regulate gene expression by counteracting SWR1, thereby preventing excessive accumulation of H2A.Z.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Adenosine Triphosphatases (mesh)Arabidopsis (mesh)Arabidopsis Proteins (mesh)Chromatin (mesh)Chromatin Assembly and Disassembly (mesh)Gene Expression RegulationPlant (mesh)GenomePlant (mesh)Histones (mesh)Molecular Chaperones (mesh)Mutation (mesh)Nucleosomes (mesh)Whole Genome Sequencing (mesh)Chromatin (mesh)Nucleosomes (mesh)Arabidopsis (mesh)Molecular Chaperones (mesh)Histones (mesh)Arabidopsis Proteins (mesh)Chromatin Assembly and Disassembly (mesh)Gene Expression RegulationPlant (mesh)Mutation (mesh)GenomePlant (mesh)Adenosine Triphosphatases (mesh)Whole Genome Sequencing (mesh)Adenosine Triphosphatases (mesh)Arabidopsis (mesh)Arabidopsis Proteins (mesh)Chromatin (mesh)Chromatin Assembly and Disassembly (mesh)Gene Expression RegulationPlant (mesh)GenomePlant (mesh)Histones (mesh)Molecular Chaperones (mesh)Mutation (mesh)Nucleosomes (mesh)Whole Genome Sequencing (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/15t2099nhttps://escholarship.org/content/qt15t2099n/qt15t2099n.pdfinfo:doi/10.1038/s41467-020-16691-xarticleNature Communications, vol 11, iss 12887oai:escholarship.org:ark:/13030/qt8ds763672026-08-23T04:04:15Zqt8ds76367Therapeutic IDOL Reduction Ameliorates Amyloidosis and Improves Cognitive Function in APP/PS1 MiceGao, JieLittman, RussellDiamante, GracielXiao, XuAhn, In SookYang, XiaCole, Tracy ATontonoz, Peter2020-03-30Brain lipoprotein receptors have been shown to regulate the metabolism of ApoE and β-amyloid (Aβ) and are potential therapeutic targets for Alzheimer's disease (AD). Previously, we identified E3 ubiquitin ligase IDOL as a negative regulator of brain lipoprotein receptors. Genetic ablation of Idol increases low-density lipoprotein receptor protein levels, which facilitates Aβ uptake and clearance by microglia. In this study, we utilized an antisense oligonucleotide (ASO) to reduce IDOL expression therapeutically in the brains of APP/PS1 male mice. ASO treatment led to decreased Aβ pathology and improved spatial learning and memory. Single-cell transcriptomic analysis of hippocampus revealed that IDOL inhibition upregulated lysosomal/phagocytic genes in microglia. Furthermore, clustering of microglia revealed that IDOL-ASO treatment shifted the composition of the microglia population by increasing the prevalence of disease-associated microglia. Our results suggest that reducing IDOL expression in the adult brain promotes the phagocytic clearance of Aβ and ameliorates Aβ-dependent pathology. Pharmacological inhibition of IDOL activity in the brain may represent a therapeutic strategy for the treatment of AD.3214 Pharmacology and Pharmaceutical Sciences (for-2020)3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Dementia (rcdc)Acquired Cognitive Impairment (rcdc)Aging (rcdc)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)Neurodegenerative (rcdc)Neurosciences (rcdc)Alzheimer's Disease (rcdc)Brain Disorders (rcdc)2.1 Biological and endogenous factors (hrcs-rac)5.1 Pharmaceuticals (hrcs-rac)Mental health (hrcs-hc)Neurological (hrcs-hc)Alzheimer Disease (mesh)Amyloid beta-Peptides (mesh)Amyloid beta-Protein Precursor (mesh)Amyloidosis (mesh)Animals (mesh)Apolipoproteins E (mesh)Brain (mesh)Cognition (mesh)Disease ModelsAnimal (mesh)Hippocampus (mesh)Male (mesh)Mice (mesh)MiceInbred C57BL (mesh)MiceTransgenic (mesh)Microglia (mesh)OligodeoxyribonucleotidesAntisense (mesh)ReceptorsLDL (mesh)Ubiquitin-Protein Ligases (mesh)AlzheimersIDOLLXRmacrophagemicrogliaBrain (mesh)Hippocampus (mesh)Microglia (mesh)Animals (mesh)MiceInbred C57BL (mesh)MiceTransgenic (mesh)Mice (mesh)Alzheimer Disease (mesh)Amyloidosis (mesh)Disease ModelsAnimal (mesh)Ubiquitin-Protein Ligases (mesh)Amyloid beta-Protein Precursor (mesh)Apolipoproteins E (mesh)ReceptorsLDL (mesh)OligodeoxyribonucleotidesAntisense (mesh)Cognition (mesh)Male (mesh)Amyloid beta-Peptides (mesh)AlzheimersIDOLLXRmacrophagemicrogliaAlzheimer Disease (mesh)Amyloid beta-Peptides (mesh)Amyloid beta-Protein Precursor (mesh)Amyloidosis (mesh)Animals (mesh)Apolipoproteins E (mesh)Brain (mesh)Cognition (mesh)Disease ModelsAnimal (mesh)Hippocampus (mesh)Male (mesh)Mice (mesh)MiceInbred C57BL (mesh)MiceTransgenic (mesh)Microglia (mesh)OligodeoxyribonucleotidesAntisense (mesh)ReceptorsLDL (mesh)Ubiquitin-Protein Ligases (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8ds76367https://escholarship.org/content/qt8ds76367/qt8ds76367.pdfinfo:doi/10.1128/mcb.00518-19articleMolecular and Cellular Biology, vol 40, iss 8e00518 - e00519oai:escholarship.org:ark:/13030/qt9w12f76w2026-08-23T02:25:49Zqt9w12f76wLong term surgical outcomes for infective endocarditis in people who inject drugs: a systematic review and meta-analysisGoodman-Meza, DavidWeiss, Robert EGamboa, SebastiánGallegos, AbelBui, Alex ATGoetz, Matthew BShoptaw, StevenLandovitz, Raphael J2019-12-01BackgroundIn recent years, the number of infective endocarditis (IE) cases associated with injection drug use has increased. Clinical guidelines suggest deferring surgery for IE in people who inject drugs (PWID) due to a concern for worse outcomes in comparison to non-injectors (non-PWID). We performed a systematic review and meta-analysis of long-term outcomes in PWID who underwent cardiac surgery and compared these outcomes to non-PWID.MethodsWe systematically searched for studies reported between 1965 and 2018. We used an algorithm to estimate individual patient data (eIPD) from Kaplan-Meier (KM) curves and combined it with published individual patient data (IPD) to analyze long-term outcomes after cardiac surgery for IE in PWID. Our primary outcome was survival. Secondary outcomes were reoperation and mortality at 30-days, one-, five-, and 10-years. Random effects Cox regression was used for estimating survival.ResultsWe included 27 studies in the systematic review and 19 provided data (KM or IPD) for the meta-analysis. PWID were younger and more likely to have S. aureus than non-PWID. Survival at 30-days, one-, five-, and 10-years was 94.3, 81.0, 62.1, and 56.6% in PWID, respectively; and 96.4, 85.0, 70.3, and 63.4% in non-PWID. PWID had 47% greater hazard of death (HR 1.47, 95% CI, 1.05–2.05) and more than twice the hazard of reoperation (HR 2.37, 95% CI, 1.25–4.50) than non-PWID.ConclusionPWID had shorter survival that non-PWID. Implementing evidence-based interventions and testing new modalities are urgently needed to improve outcomes in PWID after cardiac surgery.32 Biomedical and Clinical Sciences (for-2020)3202 Clinical Sciences (for-2020)Patient Safety (rcdc)Cardiovascular (rcdc)Substance Misuse (rcdc)Rare Diseases (rcdc)Drug Abuse (NIDA only) (rcdc)Heart Disease (rcdc)Infectious Diseases (rcdc)3 Good Health and Well Being (sdg)Cardiac Surgical Procedures (mesh)Endocarditis (mesh)Humans (mesh)Kaplan-Meier Estimate (mesh)Proportional Hazards Models (mesh)Staphylococcal Infections (mesh)Substance AbuseIntravenous (mesh)Treatment Outcome (mesh)People who inject drugsEndocarditisSurgeryMeta-analysisHumans (mesh)Staphylococcal Infections (mesh)Endocarditis (mesh)Substance AbuseIntravenous (mesh)Treatment Outcome (mesh)Cardiac Surgical Procedures (mesh)Proportional Hazards Models (mesh)Kaplan-Meier Estimate (mesh)EndocarditisMeta-analysisPeople who inject drugsSurgeryCardiac Surgical Procedures (mesh)Endocarditis (mesh)Humans (mesh)Kaplan-Meier Estimate (mesh)Proportional Hazards Models (mesh)Staphylococcal Infections (mesh)Substance AbuseIntravenous (mesh)Treatment Outcome (mesh)0605 Microbiology (for)1103 Clinical Sciences (for)1108 Medical Microbiology (for)Microbiology (science-metrix)3202 Clinical sciences (for-2020)3207 Medical microbiology (for-2020)4206 Public health (for-2020)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/9w12f76winfo:doi/10.1186/s12879-019-4558-2articleBMC Infectious Diseases, vol 19, iss 1918oai:escholarship.org:ark:/13030/qt5241d41s2026-08-23T02:12:24Zqt5241d41sAnalysis of cardiomyocyte clonal expansion during mouse heart development and injurySereti, Konstantina-IoannaNguyen, Ngoc BKamran, PanizZhao, PengRanjbarvaziri, SaraPark, ShuinSabri, ShanEngel, James LSung, KevinKulkarni, Rajan PDing, YichenHsiai, Tzung KPlath, KathrinErnst, JasonSahoo, DebashisMikkola, Hanna KAIruela-Arispe, M LuisaArdehali, Reza2018-02-21The cellular mechanisms driving cardiac tissue formation remain poorly understood, largely due to the structural and functional complexity of the heart. It is unclear whether newly generated myocytes originate from cardiac stem/progenitor cells or from pre-existing cardiomyocytes that re-enter the cell cycle. Here, we identify the source of new cardiomyocytes during mouse development and after injury. Our findings suggest that cardiac progenitors maintain proliferative potential and are the main source of cardiomyocytes during development; however, the onset of αMHC expression leads to reduced cycling capacity. Single-cell RNA sequencing reveals a proliferative, “progenitor-like” population abundant in early embryonic stages that decreases to minimal levels postnatally. Furthermore, cardiac injury by ligation of the left anterior descending artery was found to activate cardiomyocyte proliferation in neonatal but not adult mice. Our data suggest that clonal dominance of differentiating progenitors mediates cardiac development, while a distinct subpopulation of cardiomyocytes may have the potential for limited proliferation during late embryonic development and shortly after birth.32 Biomedical and Clinical Sciences (for-2020)3201 Cardiovascular Medicine and Haematology (for-2020)Pediatric Research Initiative (rcdc)Rare Diseases (rcdc)Heart Disease - Coronary Heart Disease (rcdc)Stem Cell Research (rcdc)Congenital Structural Anomalies (rcdc)Congenital Heart Disease (rcdc)Cardiovascular (rcdc)Genetics (rcdc)Stem Cell Research - Nonembryonic - Non-Human (rcdc)Heart Disease (rcdc)Regenerative Medicine (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Cardiovascular (hrcs-hc)Animals (mesh)AnimalsNewborn (mesh)Cell Differentiation (mesh)Cell Lineage (mesh)Cell Proliferation (mesh)Embryonic Stem Cells (mesh)Female (mesh)Fetal Heart (mesh)Heart (mesh)Heart Injuries (mesh)Male (mesh)Mice (mesh)MiceTransgenic (mesh)MyoblastsCardiac (mesh)Myocardial Infarction (mesh)MyocytesCardiac (mesh)Pericardium (mesh)Pregnancy (mesh)Sequence AnalysisRNA (mesh)Heart (mesh)Fetal Heart (mesh)Pericardium (mesh)MyocytesCardiac (mesh)MyoblastsCardiac (mesh)Animals (mesh)AnimalsNewborn (mesh)MiceTransgenic (mesh)Mice (mesh)Myocardial Infarction (mesh)Heart Injuries (mesh)Sequence AnalysisRNA (mesh)Cell Differentiation (mesh)Cell Proliferation (mesh)Cell Lineage (mesh)Pregnancy (mesh)Female (mesh)Male (mesh)Embryonic Stem Cells (mesh)Animals (mesh)AnimalsNewborn (mesh)Cell Differentiation (mesh)Cell Lineage (mesh)Cell Proliferation (mesh)Embryonic Stem Cells (mesh)Female (mesh)Fetal Heart (mesh)Heart (mesh)Heart Injuries (mesh)Male (mesh)Mice (mesh)MiceTransgenic (mesh)MyoblastsCardiac (mesh)Myocardial Infarction (mesh)MyocytesCardiac (mesh)Pericardium (mesh)Pregnancy (mesh)Sequence AnalysisRNA (mesh)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/5241d41sinfo:doi/10.1038/s41467-018-02891-zarticleNature Communications, vol 9, iss 1754oai:escholarship.org:ark:/13030/qt5j63d3702026-08-23T02:03:03Zqt5j63d370Viral hijacking of cellular metabolismThaker, Shivani KCh’ng, JamesChristofk, Heather R2019-12-01This review discusses the current state of the viral metabolism field and gaps in knowledge that will be important for future studies to investigate. We discuss metabolic rewiring caused by viruses, the influence of oncogenic viruses on host cell metabolism, and the use of viruses as guides to identify critical metabolic nodes for cancer anabolism. We also discuss the need for more mechanistic studies identifying viral proteins responsible for metabolic hijacking and for in vivo studies of viral-induced metabolic rewiring. Improved technologies for detailed metabolic measurements and genetic manipulation will lead to important discoveries over the next decade.3107 Microbiology (for-2020)31 Biological Sciences (for-2020)Infectious Diseases (rcdc)Cancer (rcdc)Biotechnology (rcdc)2.1 Biological and endogenous factors (hrcs-rac)2.2 Factors relating to the physical environment (hrcs-rac)Infection (hrcs-hc)Host-Pathogen Interactions (mesh)Metabolic Networks and Pathways (mesh)Neoplasms (mesh)Viruses (mesh)Viruses (mesh)Neoplasms (mesh)Metabolic Networks and Pathways (mesh)Host-Pathogen Interactions (mesh)Host-Pathogen Interactions (mesh)Metabolic Networks and Pathways (mesh)Neoplasms (mesh)Viruses (mesh)Developmental Biology (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/5j63d370https://escholarship.org/content/qt5j63d370/qt5j63d370.pdfinfo:doi/10.1186/s12915-019-0678-9articleBMC Biology, vol 17, iss 159oai:escholarship.org:ark:/13030/qt3r48d0h32026-08-23T01:56:31Zqt3r48d0h3CryoEM structures of Arabidopsis DDR complexes involved in RNA-directed DNA methylationWongpalee, Somsakul PopLiu, ShihengGallego-Bartolomé, JavierLeitner, AlexanderAebersold, RuediLiu, WanluYen, LindaNohales, Maria AKuo, Peggy HsuanyuVashisht, Ajay AWohlschlegel, James AFeng, SuhuaKay, Steve AZhou, Z HongJacobsen, Steven E2019-09-02Transcription by RNA polymerase V (Pol V) in plants is required for RNA-directed DNA methylation, leading to transcriptional gene silencing. Global chromatin association of Pol V requires components of the DDR complex DRD1, DMS3 and RDM1, but the assembly process of this complex and the underlying mechanism for Pol V recruitment remain unknown. Here we show that all DDR complex components co-localize with Pol V, and we report the cryoEM structures of two complexes associated with Pol V recruitment—DR (DMS3-RDM1) and DDR′ (DMS3-RDM1-DRD1 peptide), at 3.6 Å and 3.5 Å resolution, respectively. RDM1 dimerization at the center frames the assembly of the entire complex and mediates interactions between DMS3 and DRD1 with a stoichiometry of 1 DRD1:4 DMS3:2 RDM1. DRD1 binding to the DR complex induces a drastic movement of a DMS3 coiled-coil helix bundle. We hypothesize that both complexes are functional intermediates that mediate Pol V recruitment.31 Biological Sciences (for-2020)3105 Genetics (for-2020)Genetics (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Generic health relevance (hrcs-hc)Arabidopsis (mesh)Arabidopsis Proteins (mesh)Chromosomal ProteinsNon-Histone (mesh)Cryoelectron Microscopy (mesh)DNA Methylation (mesh)DNAPlant (mesh)DNA-Binding Proteins (mesh)DNA-Directed RNA Polymerases (mesh)Gene Expression RegulationPlant (mesh)ModelsMolecular (mesh)Multiprotein Complexes (mesh)Protein Binding (mesh)Protein Conformation (mesh)RNAPlant (mesh)Arabidopsis (mesh)Multiprotein Complexes (mesh)DNA-Directed RNA Polymerases (mesh)DNA-Binding Proteins (mesh)Chromosomal ProteinsNon-Histone (mesh)Arabidopsis Proteins (mesh)DNAPlant (mesh)RNAPlant (mesh)Cryoelectron Microscopy (mesh)DNA Methylation (mesh)Gene Expression RegulationPlant (mesh)Protein Conformation (mesh)Protein Binding (mesh)ModelsMolecular (mesh)Arabidopsis (mesh)Arabidopsis Proteins (mesh)Chromosomal ProteinsNon-Histone (mesh)Cryoelectron Microscopy (mesh)DNA Methylation (mesh)DNAPlant (mesh)DNA-Binding Proteins (mesh)DNA-Directed RNA Polymerases (mesh)Gene Expression RegulationPlant (mesh)ModelsMolecular (mesh)Multiprotein Complexes (mesh)Protein Binding (mesh)Protein Conformation (mesh)RNAPlant (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/3r48d0h3https://escholarship.org/content/qt3r48d0h3/qt3r48d0h3.pdfinfo:doi/10.1038/s41467-019-11759-9articleNature Communications, vol 10, iss 13916oai:escholarship.org:ark:/13030/qt8072h8r82026-08-23T01:51:38Zqt8072h8r8Structure of the human ClC-1 chloride channelWang, KaituoPreisler, Sarah SpruceZhang, LiyingCui, YanxiangMissel, Julie WinkelGrønberg, ChristinaGotfryd, KamilLindahl, ErikAndersson, MagnusCalloe, KirstineEgea, Pascal FKlaerke, Dan ArnePusch, MichaelPedersen, Per AmstrupZhou, Z HongGourdon, PontusLieberman, Raquel L2019-04-01ClC-1 protein channels facilitate rapid passage of chloride ions across cellular membranes, thereby orchestrating skeletal muscle excitability. Malfunction of ClC-1 is associated with myotonia congenita, a disease impairing muscle relaxation. Here, we present the cryo-electron microscopy (cryo-EM) structure of human ClC-1, uncovering an architecture reminiscent of that of bovine ClC-K and CLC transporters. The chloride conducting pathway exhibits distinct features, including a central glutamate residue ("fast gate") known to confer voltage-dependence (a mechanistic feature not present in ClC-K), linked to a somewhat rearranged central tyrosine and a narrower aperture of the pore toward the extracellular vestibule. These characteristics agree with the lower chloride flux of ClC-1 compared with ClC-K and enable us to propose a model for chloride passage in voltage-dependent CLC channels. Comparison of structures derived from protein studied in different experimental conditions supports the notion that pH and adenine nucleotides regulate ClC-1 through interactions between the so-called cystathionine-β-synthase (CBS) domains and the intracellular vestibule ("slow gating"). The structure also provides a framework for analysis of mutations causing myotonia congenita and reveals a striking correlation between mutated residues and the phenotypic effect on voltage gating, opening avenues for rational design of therapies against ClC-1-related diseases.3101 Biochemistry and Cell Biology (for-2020)3208 Medical Physiology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Rare Diseases (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Amino Acid Sequence (mesh)Cell Membrane (mesh)Chloride Channels (mesh)Cryoelectron Microscopy (mesh)Humans (mesh)Ion Channel Gating (mesh)Kinetics (mesh)Membrane Potentials (mesh)ModelsMolecular (mesh)Cell Membrane (mesh)Humans (mesh)Chloride Channels (mesh)Cryoelectron Microscopy (mesh)Ion Channel Gating (mesh)Amino Acid Sequence (mesh)Membrane Potentials (mesh)Kinetics (mesh)ModelsMolecular (mesh)Amino Acid Sequence (mesh)Cell Membrane (mesh)Chloride Channels (mesh)Cryoelectron Microscopy (mesh)Humans (mesh)Ion Channel Gating (mesh)Kinetics (mesh)Membrane Potentials (mesh)ModelsMolecular (mesh)06 Biological Sciences (for)07 Agricultural and Veterinary Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)30 Agriculturalveterinary and food sciences (for-2020)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/8072h8r8https://escholarship.org/content/qt8072h8r8/qt8072h8r8.pdfinfo:doi/10.1371/journal.pbio.3000218articlePLOS Biology, vol 17, iss 4e3000218oai:escholarship.org:ark:/13030/qt70b2315v2026-08-23T01:49:29Zqt70b2315vDNA methylation estimation using methylation-sensitive restriction enzyme bisulfite sequencing (MREBS)Bonora, GiancarloRubbi, LiudmillaMorselli, MarcoMa, FeiyangChronis, ConstantinosPlath, KathrinPellegrini, MatteoAlbertini, Emidio2019-04-04Whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) are widely used for measuring DNA methylation levels on a genome-wide scale. Both methods have limitations: WGBS is expensive and prohibitive for most large-scale projects; RRBS only interrogates 6-12% of the CpGs in the human genome. Here, we introduce methylation-sensitive restriction enzyme bisulfite sequencing (MREBS) which has the reduced sequencing requirements of RRBS, but significantly expands the coverage of CpG sites in the genome. We built a multiple regression model that combines the two features of MREBS: the bisulfite conversion ratios of single cytosines (as in WGBS and RRBS) as well as the number of reads that cover each locus (as in MRE-seq). This combined approach allowed us to estimate differential methylation across 60% of the genome using read count data alone, and where counts were sufficiently high in both samples (about 1.5% of the genome), our estimates were significantly improved by the single CpG conversion information. We show that differential DNA methylation values based on MREBS data correlate well with those based on WGBS and RRBS. This newly developed technique combines the sequencing cost of RRBS and DNA methylation estimates on a portion of the genome similar to WGBS, making it ideal for large-scale projects of mammalian genomes.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)3105 Genetics (for-2020)Genetics (rcdc)Human Genome (rcdc)Generic health relevance (hrcs-hc)Animals (mesh)Cell Line (mesh)Cellular Reprogramming (mesh)Chromatin (mesh)CpG Islands (mesh)DNA Methylation (mesh)DNA Restriction Enzymes (mesh)Genome (mesh)Mice (mesh)Sequence AnalysisDNA (mesh)Sulfites (mesh)Cell Line (mesh)Chromatin (mesh)Animals (mesh)Mice (mesh)Sulfites (mesh)DNA Restriction Enzymes (mesh)Sequence AnalysisDNA (mesh)DNA Methylation (mesh)CpG Islands (mesh)Genome (mesh)Cellular Reprogramming (mesh)Animals (mesh)Cell Line (mesh)Cellular Reprogramming (mesh)Chromatin (mesh)CpG Islands (mesh)DNA Methylation (mesh)DNA Restriction Enzymes (mesh)Genome (mesh)Mice (mesh)Sequence AnalysisDNA (mesh)Sulfites (mesh)General Science & Technology (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/70b2315vhttps://escholarship.org/content/qt70b2315v/qt70b2315v.pdfinfo:doi/10.1371/journal.pone.0214368articlePLOS ONE, vol 14, iss 4e0214368oai:escholarship.org:ark:/13030/qt0dn1v4hx2026-08-23T00:18:10Zqt0dn1v4hxThe MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation statusLi, DongmingPalanca, Ana Marie SWon, So YounGao, LeiFeng, YingVashisht, Ajay ALiu, LiZhao, YuanyuanLiu, XigangWu, XiuyunLi, ShaofangLe, BrandonKim, Yun JuYang, GuodongLi, ShengbenLiu, JinyuanWohlschlegel, James AGuo, HongweiMo, BeixinChen, XuemeiLaw, Julie A2017-04-28DNA methylation is associated with gene silencing in eukaryotic organisms. Although pathways controlling the establishment, maintenance and removal of DNA methylation are known, relatively little is understood about how DNA methylation influences gene expression. Here we identified a METHYL-CpG-BINDING DOMAIN 7 (MBD7) complex in Arabidopsis thaliana that suppresses the transcriptional silencing of two LUCIFERASE (LUC) reporters via a mechanism that is largely downstream of DNA methylation. Although mutations in components of the MBD7 complex resulted in modest increases in DNA methylation concomitant with decreased LUC expression, we found that these hyper-methylation and gene expression phenotypes can be genetically uncoupled. This finding, along with genome-wide profiling experiments showing minimal changes in DNA methylation upon disruption of the MBD7 complex, places the MBD7 complex amongst a small number of factors acting downstream of DNA methylation. This complex, however, is unique as it functions to suppress, rather than enforce, DNA methylation-mediated gene silencing.3108 Plant Biology (for-2020)31 Biological Sciences (for-2020)3105 Genetics (for-2020)Genetics (rcdc)Human Genome (rcdc)Cancer (hrcs-hc)Generic health relevance (hrcs-hc)Arabidopsis (mesh)DNA Methylation (mesh)DNA-Binding Proteins (mesh)Gene Expression RegulationPlant (mesh)GenesReporter (mesh)Luciferases (mesh)Plant Proteins (mesh)Transgenes (mesh)Arabidopsis (mesh)Luciferases (mesh)DNA-Binding Proteins (mesh)Plant Proteins (mesh)DNA Methylation (mesh)Gene Expression RegulationPlant (mesh)GenesReporter (mesh)Transgenes (mesh)A. thalianaDNA methylationHSP20Methyl-CpG-Binding Domain (MBD)RNA-directed DNA methylation (RdDM)chromosomesgenesplant biologytranscriptional gene silencingα-crystallin domain (ACD)Arabidopsis (mesh)DNA Methylation (mesh)DNA-Binding Proteins (mesh)Gene Expression RegulationPlant (mesh)GenesReporter (mesh)Luciferases (mesh)Plant Proteins (mesh)Transgenes (mesh)0601 Biochemistry and Cell Biology (for)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/0dn1v4hxhttps://escholarship.org/content/qt0dn1v4hx/qt0dn1v4hx.pdfinfo:doi/10.7554/elife.19893articleELIFE, vol 6e19893oai:escholarship.org:ark:/13030/qt8qv8s1c52026-08-22T23:58:16Zqt8qv8s1c5Protocol for culturing and imaging of ectodermal cells from XenopusTejeda-Muñoz, NydiaMonka, JuliaDe Robertis, Edward M2022-09-01The Xenopus embryo provides an advantageous model system where genes can be readily transplanted as DNA or mRNA or depleted with antisense techniques. Here, we present a protocol to culture and image the cell biological properties of explanted Xenopus cap cells in tissue culture. We illustrate how this protocol can be applied to visualize lysosomes, macropinocytosis, focal adhesions, Wnt signaling, and cell migration. For complete details on the use and execution of this protocol, please refer to Tejeda-Muñoz et al. (2022).3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Animals (mesh)BlottingWestern (mesh)RNAMessenger (mesh)Wnt Signaling Pathway (mesh)Xenopus Proteins (mesh)Xenopus laevis (mesh)Animals (mesh)Xenopus laevis (mesh)Xenopus Proteins (mesh)RNAMessenger (mesh)BlottingWestern (mesh)Wnt Signaling Pathway (mesh)Cell BiologyCell cultureDevelopmental biologyMicroscopyModel OrganismsSignal TransductionAnimals (mesh)BlottingWestern (mesh)RNAMessenger (mesh)Wnt Signaling Pathway (mesh)Xenopus Proteins (mesh)Xenopus laevis (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/8qv8s1c5https://escholarship.org/content/qt8qv8s1c5/qt8qv8s1c5.pdfinfo:doi/10.1016/j.xpro.2022.101455articleSTAR Protocols, vol 3, iss 3101455oai:escholarship.org:ark:/13030/qt9rx2m4gq2026-08-22T21:54:14Zqt9rx2m4gqCrystal Structure of the Streptomyces coelicolor Sortase E1 Transpeptidase Provides Insight into the Binding Mode of the Novel Class E Sorting SignalKattke, Michele DChan, Albert HDuong, AndrewSexton, Danielle LSawaya, Michael RCascio, DuilioElliot, Marie AClubb, Robert TTon-That, Hung2016-12-09Many species of Gram-positive bacteria use sortase transpeptidases to covalently affix proteins to their cell wall or to assemble pili. Sortase-displayed proteins perform critical and diverse functions for cell survival, including cell adhesion, nutrient acquisition, and morphological development, among others. Based on their amino acid sequences, there are at least six types of sortases (class A to F enzymes); however, class E enzymes have not been extensively studied. Class E sortases are used by soil and freshwater-dwelling Actinobacteria to display proteins that contain a non-canonical LAXTG sorting signal, which differs from 90% of known sorting signals by substitution of alanine for proline. Here we report the first crystal structure of a class E sortase, the 1.93 Å resolution structure of the SrtE1 enzyme from Streptomyces coelicolor. The active site is bound to a tripeptide, providing insight into the mechanism of substrate binding. SrtE1 possesses β3/β4 and β6/β7 active site loops that contact the LAXTG substrate and are structurally distinct from other classes. We propose that SrtE1 and other class E sortases employ a conserved tyrosine residue within their β3/β4 loop to recognize the amide nitrogen of alanine at position P3 of the sorting signal through a hydrogen bond, as seen here. Incapability of hydrogen-bonding with canonical proline-containing sorting signals likely contributes to class E substrate specificity. Furthermore, we demonstrate that surface anchoring of proteins involved in aerial hyphae formation requires an N-terminal segment in SrtE1 that is presumably positioned within the cytoplasm. Combined, our results reveal unique features within class E enzymes that enable them to recognize distinct sorting signals, and could facilitate the development of substrate-based inhibitors of this important enzyme family.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Infectious Diseases (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Amino Acid Sequence (mesh)Aminoacyltransferases (mesh)Bacterial Proteins (mesh)Catalytic Domain (mesh)CrystallographyX-Ray (mesh)Cysteine Endopeptidases (mesh)ModelsMolecular (mesh)Oligopeptides (mesh)Protein Conformation (mesh)Protein Sorting Signals (mesh)Streptomyces coelicolor (mesh)Substrate Specificity (mesh)Streptomyces coelicolor (mesh)Cysteine Endopeptidases (mesh)Aminoacyltransferases (mesh)Oligopeptides (mesh)Protein Sorting Signals (mesh)Bacterial Proteins (mesh)CrystallographyX-Ray (mesh)Amino Acid Sequence (mesh)Catalytic Domain (mesh)Protein Conformation (mesh)Substrate Specificity (mesh)ModelsMolecular (mesh)Amino Acid Sequence (mesh)Aminoacyltransferases (mesh)Bacterial Proteins (mesh)Catalytic Domain (mesh)CrystallographyX-Ray (mesh)Cysteine Endopeptidases (mesh)ModelsMolecular (mesh)Oligopeptides (mesh)Protein Conformation (mesh)Protein Sorting Signals (mesh)Streptomyces coelicolor (mesh)Substrate Specificity (mesh)General Science & Technology (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/9rx2m4gqhttps://escholarship.org/content/qt9rx2m4gq/qt9rx2m4gq.pdfinfo:doi/10.1371/journal.pone.0167763articlePLOS ONE, vol 11, iss 12e0167763oai:escholarship.org:ark:/13030/qt86z9032w2026-08-22T19:08:09Zqt86z9032wHigh Confidence Fission Yeast SUMO Conjugates Identified by Tandem Denaturing Affinity PurificationNie, MinghuaVashisht, Ajay AWohlschlegel, James ABoddy, Michael N2015-09-25Covalent attachment of the small ubiquitin-like modifier (SUMO) to key targets in the proteome critically regulates the evolutionarily conserved processes of cell cycle control, transcription, DNA replication and maintenance of genome stability. The proteome-wide identification of SUMO conjugates in budding yeast has been invaluable in helping to define roles of SUMO in these processes. Like budding yeast, fission yeast is an important and popular model organism; however, the fission yeast Schizosaccharomyces pombe community currently lacks proteome-wide knowledge of SUMO pathway targets. To begin to address this deficiency, we adapted and used a highly stringent Tandem Denaturing Affinity Purification (TDAP) method, coupled with mass spectrometry, to identify fission yeast SUMO conjugates. Comparison of our data with that compiled in budding yeast reveals conservation of SUMO target enrichment in nuclear and chromatin-associated processes. Moreover, the SUMO “cloud” phenomenon, whereby multiple components of a single protein complex are SUMOylated, is also conserved. Overall, SUMO TDAP provides both a key resource of high confidence SUMO-modified target proteins in fission yeast and a robust method for future analyses of SUMO function.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)ChromatographyAffinity (mesh)Computational Biology (mesh)Mass Spectrometry (mesh)Multiprotein Complexes (mesh)Protein Binding (mesh)Reproducibility of Results (mesh)Schizosaccharomyces (mesh)Small Ubiquitin-Related Modifier Proteins (mesh)Sumoylation (mesh)Schizosaccharomyces (mesh)Multiprotein Complexes (mesh)Small Ubiquitin-Related Modifier Proteins (mesh)ChromatographyAffinity (mesh)Reproducibility of Results (mesh)Computational Biology (mesh)Protein Binding (mesh)Mass Spectrometry (mesh)Sumoylation (mesh)ChromatographyAffinity (mesh)Computational Biology (mesh)Mass Spectrometry (mesh)Multiprotein Complexes (mesh)Protein Binding (mesh)Reproducibility of Results (mesh)Schizosaccharomyces (mesh)Small Ubiquitin-Related Modifier Proteins (mesh)Sumoylation (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/86z9032whttps://escholarship.org/content/qt86z9032w/qt86z9032w.pdfinfo:doi/10.1038/srep14389articleScientific Reports, vol 5, iss 114389oai:escholarship.org:ark:/13030/qt3dd7115g2026-08-22T19:08:05Zqt3dd7115gThree Different Pathways Prevent Chromosome Segregation in the Presence of DNA Damage or Replication Stress in Budding YeastPalou, GloriaPalou, RogerZeng, FanliVashisht, Ajay AWohlschlegel, James AQuintana, David GMcKinnon, Peter2015-09-01A surveillance mechanism, the S phase checkpoint, blocks progression into mitosis in response to DNA damage and replication stress. Segregation of damaged or incompletely replicated chromosomes results in genomic instability. In humans, the S phase checkpoint has been shown to constitute an anti-cancer barrier. Inhibition of mitotic cyclin dependent kinase (M-CDK) activity by Wee1 kinases is critical to block mitosis in some organisms. However, such mechanism is dispensable in the response to genotoxic stress in the model eukaryotic organism Saccharomyces cerevisiae. We show here that the Wee1 ortholog Swe1 does indeed inhibit M-CDK activity and chromosome segregation in response to genotoxic insults. Swe1 dispensability in budding yeast is the result of a redundant control of M-CDK activity by the checkpoint kinase Rad53. In addition, our results indicate that Swe1 is an effector of the checkpoint central kinase Mec1. When checkpoint control on M-CDK and on Pds1/securin stabilization are abrogated, cells undergo aberrant chromosome segregation.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Cancer (hrcs-hc)Chromosome Segregation (mesh)ChromosomesFungal (mesh)Cyclin-Dependent Kinases (mesh)DNA Damage (mesh)DNA Replication (mesh)Mutagens (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)ChromosomesFungal (mesh)Saccharomyces cerevisiae (mesh)DNA Damage (mesh)Cyclin-Dependent Kinases (mesh)Saccharomyces cerevisiae Proteins (mesh)Mutagens (mesh)Chromosome Segregation (mesh)DNA Replication (mesh)Chromosome Segregation (mesh)ChromosomesFungal (mesh)Cyclin-Dependent Kinases (mesh)DNA Damage (mesh)DNA Replication (mesh)Mutagens (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)0604 Genetics (for)Developmental Biology (science-metrix)3105 Genetics (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/3dd7115ghttps://escholarship.org/content/qt3dd7115g/qt3dd7115g.pdfinfo:doi/10.1371/journal.pgen.1005468articlePLOS Genetics, vol 11, iss 9e1005468oai:escholarship.org:ark:/13030/qt1h15q0602026-08-22T18:05:19Zqt1h15q060Large-scale remodeling of a repressed exon ribonucleoprotein to an exon definition complex active for splicingWongpalee, Somsakul PopVashisht, AjaySharma, ShaliniChui, DarrylWohlschlegel, James ABlack, Douglas L2016-11-24Polypyrimidine-tract binding protein PTBP1 can repress splicing during the exon definition phase of spliceosome assembly, but the assembly steps leading to an exon definition complex (EDC) and how PTBP1 might modulate them are not clear. We found that PTBP1 binding in the flanking introns allowed normal U2AF and U1 snRNP binding to the target exon splice sites but blocked U2 snRNP assembly in HeLa nuclear extract. Characterizing a purified PTBP1-repressed complex, as well as an active early complex and the final EDC by SILAC-MS, we identified extensive PTBP1-modulated changes in exon RNP composition. The active early complex formed in the absence of PTBP1 proceeded to assemble an EDC with the eviction of hnRNP proteins, the late recruitment of SR proteins, and binding of the U2 snRNP. These results demonstrate that during early stages of splicing, exon RNP complexes are highly dynamic with many proteins failing to bind during PTBP1 arrest.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Generic health relevance (hrcs-hc)Exons (mesh)HeLa Cells (mesh)Heterogeneous-Nuclear Ribonucleoproteins (mesh)Humans (mesh)Mass Spectrometry (mesh)Polypyrimidine Tract-Binding Protein (mesh)RNA Splicing (mesh)RNASmall Nuclear (mesh)Spliceosomes (mesh)Splicing Factor U2AF (mesh)Hela Cells (mesh)Spliceosomes (mesh)Humans (mesh)Polypyrimidine Tract-Binding Protein (mesh)Heterogeneous-Nuclear Ribonucleoproteins (mesh)RNASmall Nuclear (mesh)RNA Splicing (mesh)Exons (mesh)Mass Spectrometry (mesh)Splicing Factor U2AF (mesh)RNA binding proteinbiochemistryevolutionary biologygene regulationgenomicshumanribonucleoproteinsplicingExons (mesh)HeLa Cells (mesh)Heterogeneous-Nuclear Ribonucleoproteins (mesh)Humans (mesh)Mass Spectrometry (mesh)Polypyrimidine Tract-Binding Protein (mesh)RNA Splicing (mesh)RNASmall Nuclear (mesh)Spliceosomes (mesh)Splicing Factor U2AF (mesh)0601 Biochemistry and Cell Biology (for)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/1h15q060https://escholarship.org/content/qt1h15q060/qt1h15q060.pdfinfo:doi/10.7554/elife.19743articleeLife, vol 5e19743oai:escholarship.org:ark:/13030/qt2q13x78d2026-08-22T15:53:06Zqt2q13x78dKinetics of mRNA nuclear export regulate innate immune response gene expressionLefaudeux, DianeSen, SupriyaJiang, KevinHoffmann, Alexander2022-11-23The abundance and stimulus-responsiveness of mature mRNA is thought to be determined by nuclear synthesis, processing, and cytoplasmic decay. However, the rate and efficiency of moving mRNA to the cytoplasm almost certainly contributes, but has rarely been measured. Here, we investigated mRNA export rates for innate immune genes. We generated high spatio-temporal resolution RNA-seq data from endotoxin-stimulated macrophages and parameterized a mathematical model to infer kinetic parameters with confidence intervals. We find that the effective chromatin-to-cytoplasm export rate is gene-specific, varying 100-fold: for some genes, less than 5% of synthesized transcripts arrive in the cytoplasm as mature mRNAs, while others show high export efficiency. Interestingly, effective export rates do not determine temporal gene responsiveness, but complement the wide range of mRNA decay rates; this ensures similar abundances of short- and long-lived mRNAs, which form successive innate immune response expression waves.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)Genetics (rcdc)Human Genome (rcdc)2.1 Biological and endogenous factors (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)Active TransportCell Nucleus (mesh)RNA Transport (mesh)ImmunityInnate (mesh)RNAMessenger (mesh)Gene Expression (mesh)UCLA Ribonomics GroupRNAMessenger (mesh)Gene Expression (mesh)Active TransportCell Nucleus (mesh)RNA Transport (mesh)ImmunityInnate (mesh)Active TransportCell Nucleus (mesh)RNA Transport (mesh)ImmunityInnate (mesh)RNAMessenger (mesh)Gene Expression (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/2q13x78dhttps://escholarship.org/content/qt2q13x78d/qt2q13x78d.pdfinfo:doi/10.1038/s41467-022-34635-5articleNature Communications, vol 13, iss 17197oai:escholarship.org:ark:/13030/qt2kg2g8bz2026-08-22T14:38:04Zqt2kg2g8bzNatural Language Processing and Machine Learning to Identify People Who Inject Drugs in Electronic Health RecordsGoodman-Meza, DavidTang, AmberAryanfar, BabakVazquez, SergioGordon, Adam JGoto, MichihikoGoetz, Matthew BidwellShoptaw, StevenBui, Alex AT2022-09-02Background: Improving the identification of people who inject drugs (PWID) in electronic medical records can improve clinical decision making, risk assessment and mitigation, and health service research. Identification of PWID currently consists of heterogeneous, nonspecific International Classification of Diseases (ICD) codes as proxies. Natural language processing (NLP) and machine learning (ML) methods may have better diagnostic metrics than nonspecific ICD codes for identifying PWID.
Methods: We manually reviewed 1000 records of patients diagnosed with Staphylococcus aureus bacteremia admitted to Veterans Health Administration hospitals from 2003 through 2014. The manual review was the reference standard. We developed and trained NLP/ML algorithms with and without regular expression filters for negation (NegEx) and compared these with 11 proxy combinations of ICD codes to identify PWID. Data were split 70% for training and 30% for testing. We calculated diagnostic metrics and estimated 95% confidence intervals (CIs) by bootstrapping the hold-out test set. Best models were determined by best F-score, a summary of sensitivity and positive predictive value.
Results: Random forest with and without NegEx were the best-performing NLP/ML algorithms in the training set. Random forest with NegEx outperformed all ICD-based algorithms. F-score for the best NLP/ML algorithm was 0.905 (95% CI, .786-.967) and 0.592 (95% CI, .550-.632) for the best ICD-based algorithm. The NLP/ML algorithm had a sensitivity of 92.6% and specificity of 95.4%.
Conclusions: NLP/ML outperformed ICD-based coding algorithms at identifying PWID in electronic health records. NLP/ML models should be considered in identifying cohorts of PWID to improve clinical decision making, health services research, and administrative surveillance.32 Biomedical and Clinical Sciences (for-2020)3202 Clinical Sciences (for-2020)Patient Safety (rcdc)Data Science (rcdc)Networking and Information Technology R&D (NITRD) (rcdc)Machine Learning and Artificial Intelligence (rcdc)3 Good Health and Well Being (sdg)EHRmachine learningNLPPWIDEHRNLPPWIDmachine learning3202 Clinical sciences (for-2020)3207 Medical microbiology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2kg2g8bzhttps://escholarship.org/content/qt2kg2g8bz/qt2kg2g8bz.pdfinfo:doi/10.1093/ofid/ofac471articleOpen Forum Infectious Diseases, vol 9, iss 9ofac471oai:escholarship.org:ark:/13030/qt7vp9b5w92026-08-21T20:49:57Zqt7vp9b5w9Neural Induction in Xenopus: Requirement for Ectodermal and Endomesodermal Signals via Chordin, Noggin, β-Catenin, and CerberusKuroda, HirokiWessely, OliverRobertis, EM DeChristof Niehrs2004-05-01The origin of the signals that induce the differentiation of the central nervous system (CNS) is a long-standing question in vertebrate embryology. Here we show that Xenopus neural induction starts earlier than previously thought, at the blastula stage, and requires the combined activity of two distinct signaling centers. One is the well-known Nieuwkoop center, located in dorsal-vegetal cells, which expresses Nodal-related endomesodermal inducers. The other is a blastula Chordin- and Noggin-expressing (BCNE) center located in dorsal animal cells that contains both prospective neuroectoderm and Spemann organizer precursor cells. Both centers are downstream of the early beta-Catenin signal. Molecular analyses demonstrated that the BCNE center was distinct from the Nieuwkoop center, and that the Nieuwkoop center expressed the secreted protein Cerberus (Cer). We found that explanted blastula dorsal animal cap cells that have not yet contacted a mesodermal substratum can, when cultured in saline solution, express definitive neural markers and differentiate histologically into CNS tissue. Transplantation experiments showed that the BCNE region was required for brain formation, even though it lacked CNS-inducing activity when transplanted ventrally. Cell-lineage studies demonstrated that BCNE cells give rise to a large part of the brain and retina and, in more posterior regions of the embryo, to floor plate and notochord. Loss-of-function experiments with antisense morpholino oligos (MO) showed that the CNS that forms in mesoderm-less Xenopus embryos (generated by injection with Cerberus-Short [CerS] mRNA) required Chordin (Chd), Noggin (Nog), and their upstream regulator beta-Catenin. When mesoderm involution was prevented in dorsal marginal-zone explants, the anterior neural tissue formed in ectoderm was derived from BCNE cells and had a complete requirement for Chd. By injecting Chd morpholino oligos (Chd-MO) into prospective neuroectoderm and Cerberus morpholino oligos (Cer-MO) into prospective endomesoderm at the 8-cell stage, we showed that both layers cooperate in CNS formation. The results suggest a model for neural induction in Xenopus in which an early blastula beta-Catenin signal predisposes the prospective neuroectoderm to neural induction by endomesodermal signals emanating from Spemann's organizer.32 Biomedical and Clinical Sciences (for-2020)Neurosciences (rcdc)Stem Cell Research (rcdc)Stem Cell Research - Nonembryonic - Non-Human (rcdc)Pediatric Research Initiative (rcdc)Animals (mesh)Brain (mesh)Carrier Proteins (mesh)Cell Differentiation (mesh)Cell Line (mesh)Cell Lineage (mesh)Cell Transplantation (mesh)Central Nervous System (mesh)Cytoskeletal Proteins (mesh)Ectoderm (mesh)Female (mesh)Gene Expression RegulationDevelopmental (mesh)Glycoproteins (mesh)Intercellular Signaling Peptides and Proteins (mesh)Male (mesh)Mesoderm (mesh)Neurons (mesh)Oligonucleotides (mesh)OligonucleotidesAntisense (mesh)OrganizersEmbryonic (mesh)Proteins (mesh)RNA (mesh)RNAMessenger (mesh)Signal Transduction (mesh)Time Factors (mesh)Trans-Activators (mesh)Xenopus (mesh)Xenopus Proteins (mesh)beta Catenin (mesh)Noggin Protein (mesh)Central Nervous System (mesh)Brain (mesh)Neurons (mesh)Cell Line (mesh)Ectoderm (mesh)Mesoderm (mesh)OrganizersEmbryonic (mesh)Animals (mesh)Xenopus (mesh)Glycoproteins (mesh)Intercellular Signaling Peptides and Proteins (mesh)Proteins (mesh)Xenopus Proteins (mesh)Carrier Proteins (mesh)Cytoskeletal Proteins (mesh)Trans-Activators (mesh)OligonucleotidesAntisense (mesh)RNA (mesh)RNAMessenger (mesh)Oligonucleotides (mesh)Cell Transplantation (mesh)Signal Transduction (mesh)Cell Differentiation (mesh)Gene Expression RegulationDevelopmental (mesh)Cell Lineage (mesh)Time Factors (mesh)Female (mesh)Male (mesh)beta Catenin (mesh)Noggin Protein (mesh)Animals (mesh)Brain (mesh)Carrier Proteins (mesh)Cell Differentiation (mesh)Cell Line (mesh)Cell Lineage (mesh)Cell Transplantation (mesh)Central Nervous System (mesh)Cytoskeletal Proteins (mesh)Ectoderm (mesh)Female (mesh)Gene Expression RegulationDevelopmental (mesh)Glycoproteins (mesh)Intercellular Signaling Peptides and Proteins (mesh)Male (mesh)Mesoderm (mesh)Neurons (mesh)Oligonucleotides (mesh)OligonucleotidesAntisense (mesh)OrganizersEmbryonic (mesh)Proteins (mesh)RNA (mesh)RNAMessenger (mesh)Signal Transduction (mesh)Time Factors (mesh)Trans-Activators (mesh)Xenopus (mesh)Xenopus Proteins (mesh)beta Catenin (mesh)Noggin Protein (mesh)06 Biological Sciences (for)07 Agricultural and Veterinary Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)30 Agriculturalveterinary and food sciences (for-2020)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7vp9b5w9https://escholarship.org/content/qt7vp9b5w9/qt7vp9b5w9.pdfinfo:doi/10.1371/journal.pbio.0020092articlePLOS Biology, vol 2, iss 5e92oai:escholarship.org:ark:/13030/qt4jc931m42026-08-21T20:49:53Zqt4jc931m4Drosophila Smad2 Opposes Mad Signaling during Wing Vein DevelopmentSander, VeronikaEivers, EdwardChoi, Renee HDe Robertis, Edward MMcCabe, Brian D2010-04-28In the vertebrates, the BMP/Smad1 and TGF-beta/Smad2 signaling pathways execute antagonistic functions in different contexts of development. The differentiation of specific structures results from the balance between these two pathways. For example, the gastrula organizer/node of the vertebrates requires a region of low Smad1 and high Smad2 signaling. In Drosophila, Mad regulates tissue determination and growth in the wing, but the function of dSmad2 in wing patterning is largely unknown. In this study, we used an RNAi loss-of-function approach to investigate dSmad2 signaling during wing development. RNAi-mediated knockdown of dSmad2 caused formation of extra vein tissue, with phenotypes similar to those seen in Dpp/Mad gain-of-function. Clonal analyses revealed that the normal function of dSmad2 is to inhibit the response of wing intervein cells to the extracellular Dpp morphogen gradient that specifies vein formation, as measured by expression of the activated phospho-Mad protein. The effect of dSmad2 depletion in promoting vein differentiation was dependent on Medea, the co-factor shared by Mad and dSmad2. Furthermore, double RNAi experiments showed that Mad is epistatic to dSmad2. In other words, depletion of Smad2 had no effect in Mad-deficient wings. Our results demonstrate a novel role for dSmad2 in opposing Mad-mediated vein formation in the wing. We propose that the main function of dActivin/dSmad2 in Drosophila wing development is to antagonize Dpp/Mad signaling. Possible molecular mechanisms for the opposition between dSmad2 and Mad signaling are discussed.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Biotechnology (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Activins (mesh)Animals (mesh)DNA-Binding Proteins (mesh)Drosophila (mesh)Drosophila Proteins (mesh)Female (mesh)Signal Transduction (mesh)Smad ProteinsReceptor-Regulated (mesh)Smad2 Protein (mesh)Transcription Factors (mesh)Veins (mesh)WingsAnimal (mesh)Veins (mesh)Animals (mesh)Drosophila (mesh)Activins (mesh)DNA-Binding Proteins (mesh)Drosophila Proteins (mesh)Transcription Factors (mesh)Signal Transduction (mesh)Female (mesh)Smad ProteinsReceptor-Regulated (mesh)Smad2 Protein (mesh)WingsAnimal (mesh)Activins (mesh)Animals (mesh)DNA-Binding Proteins (mesh)Drosophila (mesh)Drosophila Proteins (mesh)Female (mesh)Signal Transduction (mesh)Smad ProteinsReceptor-Regulated (mesh)Smad2 Protein (mesh)Transcription Factors (mesh)Veins (mesh)WingsAnimal (mesh)General Science & Technology (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4jc931m4https://escholarship.org/content/qt4jc931m4/qt4jc931m4.pdfinfo:doi/10.1371/journal.pone.0010383articlePLOS ONE, vol 5, iss 4e10383oai:escholarship.org:ark:/13030/qt1sn7r2vj2026-08-21T20:49:49Zqt1sn7r2vjMad Is Required for Wingless Signaling in Wing Development and Segment Patterning in DrosophilaEivers, EdwardFuentealba, Luis CSander, VeronikaClemens, James CHartnett, LoriDe Robertis, EMSham, Mai Har2009-08-06A key question in developmental biology is how growth factor signals are integrated to generate pattern. In this study we investigated the integration of the Drosophila BMP and Wingless/GSK3 signaling pathways via phosphorylations of the transcription factor Mad. Wingless was found to regulate the phosphorylation of Mad by GSK3 in vivo. In epistatic experiments, the effects of Wingless on wing disc molecular markers (senseless, distalless and vestigial) were suppressed by depletion of Mad with RNAi. Wingless overexpression phenotypes, such as formation of ectopic wing margins, were induced by Mad GSK3 phosphorylation-resistant mutant protein. Unexpectedly, we found that Mad phosphorylation by GSK3 and MAPK occurred in segmental patterns. Mad depletion or overexpression produced Wingless-like embryonic segmentation phenotypes. In Xenopus embryos, segmental border formation was disrupted by Smad8 depletion. The results show that Mad is required for Wingless signaling and for the integration of gradients of positional information.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Animals (mesh)Body Patterning (mesh)DNA-Binding Proteins (mesh)Drosophila (mesh)Drosophila Proteins (mesh)Mutation (mesh)Phenotype (mesh)RNA Interference (mesh)Signal Transduction (mesh)Transcription Factors (mesh)WingsAnimal (mesh)Wnt1 Protein (mesh)Animals (mesh)Drosophila (mesh)DNA-Binding Proteins (mesh)Drosophila Proteins (mesh)Transcription Factors (mesh)Signal Transduction (mesh)RNA Interference (mesh)Body Patterning (mesh)Phenotype (mesh)Mutation (mesh)Wnt1 Protein (mesh)WingsAnimal (mesh)Animals (mesh)Body Patterning (mesh)DNA-Binding Proteins (mesh)Drosophila (mesh)Drosophila Proteins (mesh)Mutation (mesh)Phenotype (mesh)RNA Interference (mesh)Signal Transduction (mesh)Transcription Factors (mesh)WingsAnimal (mesh)Wnt1 Protein (mesh)General Science & Technology (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1sn7r2vjhttps://escholarship.org/content/qt1sn7r2vj/qt1sn7r2vj.pdfinfo:doi/10.1371/journal.pone.0006543articlePLOS ONE, vol 4, iss 8e6543oai:escholarship.org:ark:/13030/qt47j7d02f2026-08-21T13:41:49Zqt47j7d02fHighlighting membrane protein structure and function: A celebration of the Protein Data BankLi, FeiEgea, Pascal FVecchio, Alex JAsial, IgnacioGupta, MeghnaPaulino, JoanaBajaj, RuchikaDickinson, Miles SashaFerguson-Miller, ShelaghMonk, Brian CStroud, Robert M2021-01-01Biological membranes define the boundaries of cells and compartmentalize the chemical and physical processes required for life. Many biological processes are carried out by proteins embedded in or associated with such membranes. Determination of membrane protein (MP) structures at atomic or near-atomic resolution plays a vital role in elucidating their structural and functional impact in biology. This endeavor has determined 1198 unique MP structures as of early 2021. The value of these structures is expanded greatly by deposition of their three-dimensional (3D) coordinates into the Protein Data Bank (PDB) after the first atomic MP structure was elucidated in 1985. Since then, free access to MP structures facilitates broader and deeper understanding of MPs, which provides crucial new insights into their biological functions. Here we highlight the structural and functional biology of representative MPs and landmarks in the evolution of new technologies, with insights into key developments influenced by the PDB in magnifying their impact.3101 Biochemistry and Cell Biology (for-2020)3102 Bioinformatics and Computational Biology (for-2020)31 Biological Sciences (for-2020)1.1 Normal biological development and functioning (hrcs-rac)1.5 Resources and infrastructure (underpinning) (hrcs-rac)Generic health relevance (hrcs-hc)DatabasesProtein (mesh)History20th Century (mesh)History21st Century (mesh)Membrane Proteins (mesh)Protein Conformation (mesh)Structure-Activity Relationship (mesh)Membrane Proteins (mesh)Protein Conformation (mesh)Structure-Activity Relationship (mesh)History20th Century (mesh)History21st Century (mesh)DatabasesProtein (mesh)bioenergeticschanneldrug discoverylipid mimeticsmembrane proteinmembrane protein biogenesisprotein designreceptorstructure-functiontransmembrane transportDatabasesProtein (mesh)History20th Century (mesh)History21st Century (mesh)Membrane Proteins (mesh)Protein Conformation (mesh)Structure-Activity Relationship (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biochemistry & Molecular Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/47j7d02fhttps://escholarship.org/content/qt47j7d02f/qt47j7d02f.pdfinfo:doi/10.1016/j.jbc.2021.100557articleJournal of Biological Chemistry, vol 296100557oai:escholarship.org:ark:/13030/qt6pj2t9632026-08-21T11:52:23Zqt6pj2t963Molecular basis for lipid recognition by the prostaglandin D2 receptor CRTH2Liu, HengDeepak, RNV KrishnaShiriaeva, AnnaGati, CorneliusBatyuk, AlexanderHu, HaoWeierstall, UweLiu, WeiWang, LeiCherezov, VadimFan, HaoZhang, Cheng2021-08-10Prostaglandin D2 (PGD2) signals through the G protein-coupled receptor (GPCR) CRTH2 to mediate various inflammatory responses. CRTH2 is the only member of the prostanoid receptor family that is phylogenetically distant from others, implying a nonconserved mechanism of lipid action on CRTH2. Here, we report a crystal structure of human CRTH2 bound to a PGD2 derivative, 15R-methyl-PGD2 (15mPGD2), by serial femtosecond crystallography. The structure revealed a "polar group in"-binding mode of 15mPGD2 contrasting the "polar group out"-binding mode of PGE2 in its receptor EP3. Structural comparison analysis suggested that these two lipid-binding modes, associated with distinct charge distributions of ligand-binding pockets, may apply to other lipid GPCRs. Molecular dynamics simulations together with mutagenesis studies also identified charged residues at the ligand entry port that function to capture lipid ligands of CRTH2 from the lipid bilayer. Together, our studies suggest critical roles of charge environment in lipid recognition by GPCRs.3101 Biochemistry and Cell Biology (for-2020)34 Chemical Sciences (for-2020)31 Biological Sciences (for-2020)1.1 Normal biological development and functioning (hrcs-rac)CrystallographyX-Ray (mesh)Humans (mesh)Lipid Metabolism (mesh)Molecular Dynamics Simulation (mesh)Mutation (mesh)Prostaglandin D2 (mesh)Protein Conformation (mesh)ReceptorsImmunologic (mesh)ReceptorsProstaglandin (mesh)CRTH2 (DP2)prostaglandin D-2lipid bindingcrystal structureMD simulationsHumans (mesh)Prostaglandin D2 (mesh)ReceptorsProstaglandin (mesh)ReceptorsImmunologic (mesh)CrystallographyX-Ray (mesh)Protein Conformation (mesh)Mutation (mesh)Lipid Metabolism (mesh)Molecular Dynamics Simulation (mesh)CRTH2 (DP2)MD simulationscrystal structurelipid bindingprostaglandin D2CrystallographyX-Ray (mesh)Humans (mesh)Lipid Metabolism (mesh)Molecular Dynamics Simulation (mesh)Mutation (mesh)Prostaglandin D2 (mesh)Protein Conformation (mesh)ReceptorsImmunologic (mesh)ReceptorsProstaglandin (mesh)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6pj2t963https://escholarship.org/content/qt6pj2t963/qt6pj2t963.pdfinfo:doi/10.1073/pnas.2102813118articleProceedings of the National Academy of Sciences of the United States of America, vol 118, iss 32e2102813118oai:escholarship.org:ark:/13030/qt5pk8q2b02026-08-21T09:18:03Zqt5pk8q2b0FAP106 is an interaction hub for assembling microtubule inner proteins at the cilium inner junctionShimogawa, Michelle MWijono, Angeline SWang, HuiZhang, JiayanSha, JihuiSzombathy, NatashaVadakkan, SabeecaPelayo, PaulaJonnalagadda, KeyaWohlschlegel, JamesZhou, Z HongHill, Kent L2023-08-26Motility of pathogenic protozoa depends on flagella (synonymous with cilia) with axonemes containing nine doublet microtubules (DMTs) and two singlet microtubules. Microtubule inner proteins (MIPs) within DMTs influence axoneme stability and motility and provide lineage-specific adaptations, but individual MIP functions and assembly mechanisms are mostly unknown. Here, we show in the sleeping sickness parasite Trypanosoma brucei, that FAP106, a conserved MIP at the DMT inner junction, is required for trypanosome motility and functions as a critical interaction hub, directing assembly of several conserved and lineage-specific MIPs. We use comparative cryogenic electron tomography (cryoET) and quantitative proteomics to identify MIP candidates. Using RNAi knockdown together with fitting of AlphaFold models into cryoET maps, we demonstrate that one of these candidates, MC8, is a trypanosome-specific MIP required for parasite motility. Our work advances understanding of MIP assembly mechanisms and identifies lineage-specific motility proteins that are attractive targets to consider for therapeutic intervention.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Biotechnology (rcdc)Infectious Diseases (rcdc)Rare Diseases (rcdc)Vector-Borne Diseases (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.2 Factors relating to the physical environment (hrcs-rac)Infection (hrcs-hc)3 Good Health and Well Being (sdg)Cilia (mesh)Flagella (mesh)Microtubules (mesh)Acclimatization (mesh)Axoneme (mesh)Microtubule Proteins (mesh)Cilia (mesh)Flagella (mesh)Microtubules (mesh)Microtubule Proteins (mesh)Acclimatization (mesh)Axoneme (mesh)Cilia (mesh)Flagella (mesh)Microtubules (mesh)Acclimatization (mesh)Axoneme (mesh)Microtubule Proteins (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/5pk8q2b0https://escholarship.org/content/qt5pk8q2b0/qt5pk8q2b0.pdfinfo:doi/10.1038/s41467-023-40230-zarticleNature Communications, vol 14, iss 15225oai:escholarship.org:ark:/13030/qt9f32f8vq2026-08-20T21:03:50Zqt9f32f8vqZFP36-mediated mRNA decay regulates metabolismCicchetto, Andrew CJacobson, Elsie CSunshine, HannahWilde, Blake RKrall, Abigail SJarrett, Kelsey ESedgeman, LeslieTurner, MartinPlath, KathrinIruela-Arispe, M Luisade Aguiar Vallim, Thomas QChristofk, Heather R2023-05-01Cellular metabolism is tightly regulated by growth factor signaling, which promotes metabolic rewiring to support growth and proliferation. While growth factor-induced transcriptional and post-translational modes of metabolic regulation have been well defined, whether post-transcriptional mechanisms impacting mRNA stability regulate this process is less clear. Here, we present the ZFP36/L1/L2 family of RNA-binding proteins and mRNA decay factors as key drivers of metabolic regulation downstream of acute growth factor signaling. We quantitatively catalog metabolic enzyme and nutrient transporter mRNAs directly bound by ZFP36 following growth factor stimulation-many of which encode rate-limiting steps in metabolic pathways. Further, we show that ZFP36 directly promotes the mRNA decay of Enolase 2 (Eno2), altering Eno2 protein expression and enzymatic activity, and provide evidence of a ZFP36/Eno2 axis during VEGF-stimulated developmental retinal angiogenesis. Thus, ZFP36-mediated mRNA decay serves as an important mode of metabolic regulation downstream of growth factor signaling within dynamic cell and tissue states.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Generic health relevance (hrcs-hc)RNA-Binding Proteins (mesh)Signal Transduction (mesh)Intercellular Signaling Peptides and Proteins (mesh)RNA Stability (mesh)Tristetraprolin (mesh)Intercellular Signaling Peptides and Proteins (mesh)RNA-Binding Proteins (mesh)Signal Transduction (mesh)RNA Stability (mesh)Tristetraprolin (mesh)CP: MetabolismCP: Molecular biologyRNA-binding proteinsgrowth factor signalingmRNA stabilitymetabolismRNA-Binding Proteins (mesh)Signal Transduction (mesh)Intercellular Signaling Peptides and Proteins (mesh)RNA Stability (mesh)Tristetraprolin (mesh)0601 Biochemistry and Cell Biology (for)1116 Medical Physiology (for)31 Biological sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/9f32f8vqhttps://escholarship.org/content/qt9f32f8vq/qt9f32f8vq.pdfinfo:doi/10.1016/j.celrep.2023.112411articleCell Reports, vol 42, iss 5112411oai:escholarship.org:ark:/13030/qt7tr534mp2026-08-20T20:24:57Zqt7tr534mpStructural basis for HIV-1 antagonism of host APOBEC3G via Cullin E3 ligaseIto, FumiakiAlvarez-Cabrera, Ana LLiu, ShihengYang, HanjingShiriaeva, AnnaZhou, Z HongChen, Xiaojiang S2023-01-06Human APOBEC3G (A3G) is a virus restriction factor that inhibits HIV-1 replication and triggers lethal hypermutation on viral reverse transcripts. HIV-1 viral infectivity factor (Vif) breaches this host A3G immunity by hijacking a cellular E3 ubiquitin ligase complex to target A3G for ubiquitination and degradation. The molecular mechanism of A3G targeting by Vif-E3 ligase is unknown, limiting the antiviral efforts targeting this host-pathogen interaction crucial for HIV-1 infection. Here, we report the cryo-electron microscopy structures of A3G bound to HIV-1 Vif in complex with T cell transcription cofactor CBF-β and multiple components of the Cullin-5 RING E3 ubiquitin ligase. The structures reveal unexpected RNA-mediated interactions of Vif with A3G primarily through A3G's noncatalytic domain, while A3G's catalytic domain is poised for ubiquitin transfer. These structures elucidate the molecular mechanism by which HIV-1 Vif hijacks the host ubiquitin ligase to specifically target A3G to establish infection and offer structural information for the rational development of antiretroviral therapeutics.3207 Medical Microbiology (for-2020)32 Biomedical and Clinical Sciences (for-2020)3204 Immunology (for-2020)Infectious Diseases (rcdc)Genetics (rcdc)HIV/AIDS (rcdc)2.1 Biological and endogenous factors (hrcs-rac)2.2 Factors relating to the physical environment (hrcs-rac)Infection (hrcs-hc)Humans (mesh)Ubiquitin-Protein Ligases (mesh)vif Gene ProductsHuman Immunodeficiency Virus (mesh)HIV-1 (mesh)Cullin Proteins (mesh)Cryoelectron Microscopy (mesh)HIV Infections (mesh)Ubiquitin (mesh)Protein Binding (mesh)APOBEC-3G Deaminase (mesh)Humans (mesh)HIV-1 (mesh)HIV Infections (mesh)Ubiquitin-Protein Ligases (mesh)Cullin Proteins (mesh)Ubiquitin (mesh)Cryoelectron Microscopy (mesh)Protein Binding (mesh)vif Gene ProductsHuman Immunodeficiency Virus (mesh)APOBEC-3G Deaminase (mesh)Humans (mesh)Ubiquitin-Protein Ligases (mesh)vif Gene ProductsHuman Immunodeficiency Virus (mesh)HIV-1 (mesh)Cullin Proteins (mesh)Cryoelectron Microscopy (mesh)HIV Infections (mesh)Ubiquitin (mesh)Protein Binding (mesh)APOBEC-3G Deaminase (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/7tr534mphttps://escholarship.org/content/qt7tr534mp/qt7tr534mp.pdfinfo:doi/10.1126/sciadv.ade3168articleScience Advances, vol 9, iss 1eade3168oai:escholarship.org:ark:/13030/qt79f657sn2026-08-20T11:22:18Zqt79f657snThe Shr receptor from Streptococcus pyogenes uses a cap and release mechanism to acquire heme–iron from human hemoglobinMacdonald, RamsayMahoney, Brendan JSoule, JessGoring, Andrew KFord, JordanLoo, Joseph ACascio, DuilioClubb, Robert T2023-01-31Streptococcus pyogenes (group A Streptococcus) is a clinically important microbial pathogen that requires iron in order to proliferate. During infections, S. pyogenes uses the surface displayed Shr receptor to capture human hemoglobin (Hb) and acquires its iron-laden heme molecules. Through a poorly understood mechanism, Shr engages Hb via two structurally unique N-terminal Hb-interacting domains (HID1 and HID2) which facilitate heme transfer to proximal NEAr Transporter (NEAT) domains. Based on the results of X-ray crystallography, small angle X-ray scattering, NMR spectroscopy, native mass spectrometry, and heme transfer experiments, we propose that Shr utilizes a "cap and release" mechanism to gather heme from Hb. In the mechanism, Shr uses the HID1 and HID2 modules to preferentially recognize only heme-loaded forms of Hb by contacting the edges of its protoporphyrin rings. Heme transfer is enabled by significant receptor dynamics within the Shr-Hb complex which function to transiently uncap HID1 from the heme bound to Hb's β subunit, enabling the gated release of its relatively weakly bound heme molecule and subsequent capture by Shr's NEAT domains. These dynamics may maximize the efficiency of heme scavenging by S. pyogenes, enabling it to preferentially recognize and remove heme from only heme-loaded forms of Hb that contain iron.3101 Biochemistry and Cell Biology (for-2020)34 Chemical Sciences (for-2020)31 Biological Sciences (for-2020)Hematology (rcdc)Infectious Diseases (rcdc)Emerging Infectious Diseases (rcdc)Humans (mesh)Hemoglobins (mesh)Streptococcus pyogenes (mesh)Carrier Proteins (mesh)Heme (mesh)Iron (mesh)group A Streptococcusheme capturehemoglobinX-ray crystallographyNMRHumans (mesh)Streptococcus pyogenes (mesh)Iron (mesh)Heme (mesh)Hemoglobins (mesh)Carrier Proteins (mesh)NMRX-ray crystallographygroup A Streptococcusheme capturehemoglobinHumans (mesh)Hemoglobins (mesh)Streptococcus pyogenes (mesh)Carrier Proteins (mesh)Heme (mesh)Iron (mesh)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/79f657snhttps://escholarship.org/content/qt79f657sn/qt79f657sn.pdfinfo:doi/10.1073/pnas.2211939120articleProceedings of the National Academy of Sciences of the United States of America, vol 120, iss 5e2211939120oai:escholarship.org:ark:/13030/qt6n64w5wb2026-08-20T08:01:40Zqt6n64w5wbRegulation of Arabidopsis photoreceptor CRY2 by two distinct E3 ubiquitin ligasesChen, YadiHu, XiaohuaLiu, SiyuanSu, TiantianHuang, HsiaochiRen, HuiboGao, ZhenshengWang, XuLin, DeshuWohlschlegel, James AWang, QinLin, Chentao2021-04-12Cryptochromes (CRYs) are photoreceptors or components of the molecular clock in various evolutionary lineages, and they are commonly regulated by polyubiquitination and proteolysis. Multiple E3 ubiquitin ligases regulate CRYs in animal models, and previous genetics study also suggest existence of multiple E3 ubiquitin ligases for plant CRYs. However, only one E3 ligase, Cul4COP1/SPAs, has been reported for plant CRYs so far. Here we show that Cul3LRBs is the second E3 ligase of CRY2 in Arabidopsis. We demonstrate the blue light-specific and CRY-dependent activity of LRBs (Light-Response Bric-a-Brack/Tramtrack/Broad 1, 2 & 3) in blue-light regulation of hypocotyl elongation. LRBs physically interact with photoexcited and phosphorylated CRY2, at the CCE domain of CRY2, to facilitate polyubiquitination and degradation of CRY2 in response to blue light. We propose that Cul4COP1/SPAs and Cul3LRBs E3 ligases interact with CRY2 via different structure elements to regulate the abundance of CRY2 photoreceptor under different light conditions, facilitating optimal photoresponses of plants grown in nature.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Arabidopsis (mesh)Arabidopsis Proteins (mesh)Cryptochromes (mesh)HEK293 Cells (mesh)Humans (mesh)Light (mesh)ModelsBiological (mesh)Mutation (mesh)Phosphorylation (mesh)PhotoreceptorsPlant (mesh)Polyubiquitin (mesh)Protein Binding (mesh)Proteolysis (mesh)Seedlings (mesh)Ubiquitin-Protein Ligases (mesh)Ubiquitination (mesh)Humans (mesh)Arabidopsis (mesh)Ubiquitin-Protein Ligases (mesh)Arabidopsis Proteins (mesh)Polyubiquitin (mesh)Protein Binding (mesh)Phosphorylation (mesh)Mutation (mesh)Light (mesh)ModelsBiological (mesh)Ubiquitination (mesh)PhotoreceptorsPlant (mesh)Cryptochromes (mesh)HEK293 Cells (mesh)Proteolysis (mesh)Seedlings (mesh)Arabidopsis (mesh)Arabidopsis Proteins (mesh)Cryptochromes (mesh)HEK293 Cells (mesh)Humans (mesh)Light (mesh)ModelsBiological (mesh)Mutation (mesh)Phosphorylation (mesh)PhotoreceptorsPlant (mesh)Polyubiquitin (mesh)Protein Binding (mesh)Proteolysis (mesh)Seedlings (mesh)Ubiquitin-Protein Ligases (mesh)Ubiquitination (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/6n64w5wbhttps://escholarship.org/content/qt6n64w5wb/qt6n64w5wb.pdfinfo:doi/10.1038/s41467-021-22410-xarticleNature Communications, vol 12, iss 12155oai:escholarship.org:ark:/13030/qt2db7f0tv2026-08-20T07:04:22Zqt2db7f0tvImpact of isolation methods on the biophysical heterogeneity of single extracellular vesiclesSharma, ShivaniLeClaire, MichaelWohlschlegel, JamesGimzewski, James2020-08-07Extracellular vesicles (EVs) have raised high expectations as a novel class of diagnostics and therapeutics. However, variabilities in EV isolation methods and the unresolved structural complexity of these biological-nanoparticles (sub-100 nm) necessitate rigorous biophysical characterization of single EVs. Here, using atomic force microscopy (AFM) in conjunction with direct stochastic optical reconstruction microscopy (dSTORM), micro-fluidic resistive pore sizing (MRPS), and multi-angle light scattering (MALS) techniques, we compared the size, structure and unique surface properties of breast cancer cell-derived small EVs (sEV) obtained using four different isolation methods. AFM and dSTORM particle size distributions showed coherent unimodal and bimodal particle size populations isolated via centrifugation and immune-affinity methods respectively. More importantly, AFM imaging revealed striking differences in sEV nanoscale morphology, surface nano-roughness, and relative abundance of non-vesicles among different isolation methods. Precipitation-based isolation method exhibited the highest particle counts, yet nanoscale imaging revealed the additional presence of aggregates and polymeric residues. Together, our findings demonstrate the significance of orthogonal label-free surface characteristics of single sEVs, not discernable via conventional particle sizing and counts alone. Quantifying key nanoscale structural characteristics of sEVs, collectively termed ‘EV-nano-metrics’ enhances the understanding of the complexity and heterogeneity of sEV isolates, with broad implications for EV-analyte based research and clinical use.40 Engineering (for-2020)4018 Nanotechnology (for-2020)Bioengineering (rcdc)Women's Health (rcdc)Nanotechnology (rcdc)Breast Cancer (rcdc)Biotechnology (rcdc)Cancer (rcdc)Generic health relevance (hrcs-hc)Biophysics (mesh)Breast Neoplasms (mesh)Cell LineTumor (mesh)Extracellular Vesicles (mesh)Female (mesh)Humans (mesh)MCF-7 Cells (mesh)MicroscopyAtomic Force (mesh)Particle Size (mesh)Cell LineTumor (mesh)Humans (mesh)Breast Neoplasms (mesh)MicroscopyAtomic Force (mesh)Biophysics (mesh)Particle Size (mesh)Female (mesh)MCF-7 Cells (mesh)Extracellular Vesicles (mesh)Biophysics (mesh)Breast Neoplasms (mesh)Cell LineTumor (mesh)Extracellular Vesicles (mesh)Female (mesh)Humans (mesh)MCF-7 Cells (mesh)MicroscopyAtomic Force (mesh)Particle Size (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/2db7f0tvhttps://escholarship.org/content/qt2db7f0tv/qt2db7f0tv.pdfinfo:doi/10.1038/s41598-020-70245-1articleScientific Reports, vol 10, iss 113327oai:escholarship.org:ark:/13030/qt5272f4bc2026-08-19T08:25:04Zqt5272f4bcA functional genomics screen identifying blood cell development genes in Drosophila by undergraduates participating in a course-based research experienceEvans, Cory JOlson, John MMondal, Bama CharanKandimalla, PratyushAbbasi, ArianoAbdusamad, Mai MAcosta, OsvaldoAinsworth, Julia AAkram, Haris MAlbert, Ralph BAlegria-Leal, ElitzanderAlexander, Kai YAyala, Angelica CBalashova, Nataliya SBarber, Rebecca MBassi, HarmanjitBennion, Sean PBeyder, MiriamBhatt, Kush VBhoot, ChinmayBradshaw, Aaron WBrannigan, Tierney GCao, BoyuCashell, Yancey YChai, TimothyChan, Alex WChan, CarissaChang, InhoChang, JonathanChang, Michael TChang, Patrick WChang, StephenChari, NeelChassiakos, Alexander JChen, Iris EChen, Vivian KChen, ZheyingCheng, Marsha RChiang, MimiChiu, VivianChoi, SharonChung, Jun HoContreras, LisetCorona, EdgarCruz, Courtney JCruz, Renae LDang, Jefferson MDasari, Suhas PDe La Fuente, Justin RODel Rio, Oscar MADennis, Emily RDertsakyan, Petros SDey, IpsitaDistler, Rachel SDong, ZhiqiaoDorman, Leah CDouglass, Mark AEhresman, Allysen BFu, Ivy HFua, AndreaFull, Sean MGhaffari-Rafi, ArashGhani, Asmar AbdulGiap, BoscoGill, SoniaGill, Zafar SGills, Nicholas JGodavarthi, SindhujaGolnazarian, TalinGoyal, RaghavGray, RicardoGrunfeld, Alexander MGu, Kelly MGutierrez, Natalia CHa, An NHamid, ImanHanson, AshleyHao, CelestiHe, ChongbinHe, MengshiHedtke, Joshua PHernandez, Ysrael KHlaing, HninHobby, Faith AHoi, KarenHope, Ashley CHosseinian, Sahra MHsu, AliceHsueh, JenniferHu, EileenHu, Spencer SHuang, StephanieHuang, WilsonHuynh, MelanieJavier, CarmenJeon, Na EunJi, SunjongJohal, JasminJohn, AmalaJohnson, LaurenTennessen, J2021-03-10Undergraduate students participating in the UCLA Undergraduate Research Consortium for Functional Genomics (URCFG) have conducted a two-phased screen using RNA interference (RNAi) in combination with fluorescent reporter proteins to identify genes important for hematopoiesis in Drosophila. This screen disrupted the function of approximately 3500 genes and identified 137 candidate genes for which loss of function leads to observable changes in the hematopoietic development. Targeting RNAi to maturing, progenitor, and regulatory cell types identified key subsets that either limit or promote blood cell maturation. Bioinformatic analysis reveals gene enrichment in several previously uncharacterized areas, including RNA processing and export and vesicular trafficking. Lastly, the participation of students in this course-based undergraduate research experience (CURE) correlated with increased learning gains across several areas, as well as increased STEM retention, indicating that authentic, student-driven research in the form of a CURE represents an impactful and enriching pedagogical approach.31 Biological Sciences (for-2020)3105 Genetics (for-2020)Stem Cell Research - Nonembryonic - Non-Human (rcdc)Biotechnology (rcdc)Human Genome (rcdc)Hematology (rcdc)Genetics (rcdc)Stem Cell Research (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Animals (mesh)Blood Cells (mesh)Drosophila (mesh)Genomics (mesh)Humans (mesh)Students (mesh)Universities (mesh)hematopoiesisbloodRNAieducationCUREBlood Cells (mesh)Animals (mesh)Humans (mesh)Drosophila (mesh)Genomics (mesh)Students (mesh)Universities (mesh)CURERNAibloodeducationhematopoiesisAnimals (mesh)Blood Cells (mesh)Drosophila (mesh)Genomics (mesh)Humans (mesh)Students (mesh)Universities (mesh)0604 Genetics (for)3101 Biochemistry and cell biology (for-2020)3105 Genetics (for-2020)4905 Statistics (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/5272f4bchttps://escholarship.org/content/qt5272f4bc/qt5272f4bc.pdfinfo:doi/10.1093/g3journal/jkaa028articleG3: Genes, Genomes, Genetics, vol 11, iss 1jkaa028oai:escholarship.org:ark:/13030/qt824438bw2026-08-19T06:44:55Zqt824438bwIntegration of evidence across human and model organism studies: A meeting reportPalmer, Rohan HCJohnson, Emma CWon, HyejungPolimanti, RenatoKapoor, ManavChitre, ApurvaBogue, Molly ABenca‐Bachman, Chelsie EParker, Clarissa CVerma, AnuragReynolds, TimothyErnst, JasonBray, MichaelBin Kwon, SooLai, DongbingQuach, Bryan CGaddis, Nathan CSaba, LauraChen, HaoHawrylycz, MichaelZhang, ShanZhou, YuanMahaffey, SpencerFischer, ChristianSanchez‐Roige, SandraBandrowski, AnitaLu, QingShen, LiPhilip, VivekGelernter, JoelBierut, Laura JHancock, Dana BEdenberg, Howard JJohnson, Eric ONestler, Eric JBarr, Peter BPrins, PjotrSmith, Desmond JAkbarian, SchahramThorgeirsson, ThorgeirWalton, DaveBaker, ErichJacobson, DanielPalmer, Abraham AMiles, MichaelChesler, Elissa JEmerson, JakeAgrawal, ArpanaMartone, MaryannWilliams, Robert W2021-07-01The National Institute on Drug Abuse and Joint Institute for Biological Sciences at the Oak Ridge National Laboratory hosted a meeting attended by a diverse group of scientists with expertise in substance use disorders (SUDs), computational biology, and FAIR (Findability, Accessibility, Interoperability, and Reusability) data sharing. The meeting's objective was to discuss and evaluate better strategies to integrate genetic, epigenetic, and 'omics data across human and model organisms to achieve deeper mechanistic insight into SUDs. Specific topics were to (a) evaluate the current state of substance use genetics and genomics research and fundamental gaps, (b) identify opportunities and challenges of integration and sharing across species and data types, (c) identify current tools and resources for integration of genetic, epigenetic, and phenotypic data, (d) discuss steps and impediment related to data integration, and (e) outline future steps to support more effective collaboration-particularly between animal model research communities and human genetics and clinical research teams. This review summarizes key facets of this catalytic discussion with a focus on new opportunities and gaps in resources and knowledge on SUDs.31 Biological Sciences (for-2020)32 Biomedical and Clinical Sciences (for-2020)3105 Genetics (for-2020)Genetics (rcdc)Data Science (rcdc)Substance Misuse (rcdc)Brain Disorders (rcdc)Human Genome (rcdc)Networking and Information Technology R&D (NITRD) (rcdc)Drug Abuse (NIDA only) (rcdc)1.5 Resources and infrastructure (underpinning) (hrcs-rac)2.6 Resources and infrastructure (aetiology) (hrcs-rac)3 Good Health and Well Being (sdg)cross-speciesdata integrationdrug abusegenomicsGWASmodel organismsmulti-omicsubstance use disordersworking groupcross-speciesdata integrationdrug abusegenomicsGWASmodel organismsmulti-omicsubstance use disordersworking groupGWAScross-speciesdata integrationdrug abusegenomicsmodel organismsmulti-omicsubstance use disordersworking group06 Biological Sciences (for)11 Medical and Health Sciences (for)17 Psychology and Cognitive Sciences (for)Neurology & Neurosurgery (science-metrix)3105 Genetics (for-2020)3209 Neurosciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/824438bwhttps://escholarship.org/content/qt824438bw/qt824438bw.pdfinfo:doi/10.1111/gbb.12738articleGenes Brain & Behavior, vol 20, iss 6e12738oai:escholarship.org:ark:/13030/qt4kx9787c2026-08-18T20:37:38Zqt4kx9787cMapping Metabolism: Monitoring Lactate Dehydrogenase Activity Directly in Tissue.Jelinek, DavidFlores, AimeeUebelhoer, MelaniePasque, VincentPlath, KathrinIruela-Arispe, M LuisaChristofk, Heather RLowry, William EColler, Hilary A2018-06-01Mapping enzymatic activity in space and time is critical for understanding the molecular basis of cell behavior in normal tissue and disease. In situ metabolic activity assays can provide information about the spatial distribution of metabolic activity within a tissue. We provide here a detailed protocol for monitoring the activity of the enzyme lactate dehydrogenase directly in tissue samples. Lactate dehydrogenase is an important determinant of whether consumed glucose will be converted to energy via aerobic or anaerobic glycolysis. A solution containing lactate and NAD is provided to a frozen tissue section. Cells with high lactate dehydrogenase activity will convert the provided lactate to pyruvate, while simultaneously converting provided nicotinamide adenine dinucleotide (NAD) to NADH and a proton, which can be detected based on the reduction of nitrotetrazolium blue to formazan, which is visualized as a blue precipitate. We describe a detailed protocol for monitoring lactate dehydrogenase activity in mouse skin. Applying this protocol, we found that lactate dehydrogenase activity is high in the quiescent hair follicle stem cells within the skin. Applying the protocol to cultured mouse embryonic stem cells revealed higher staining in cultured embryonic stem cells than mouse embryonic fibroblasts. Analysis of freshly isolated mouse aorta revealed staining in smooth muscle cells perpendicular to the aorta. The methodology provided can be used to spatially map the activity of enzymes that generate a proton in frozen or fresh tissue.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Regenerative Medicine (rcdc)Stem Cell Research (rcdc)Stem Cell Research - Embryonic - Non-Human (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Animals (mesh)L-Lactate Dehydrogenase (mesh)Mice (mesh)BiochemistryIssue 136Lactate dehydrogenasein situenzymatic activitymouse skinmetabolismmetabolic mapAnimals (mesh)Mice (mesh)L-Lactate Dehydrogenase (mesh)Animals (mesh)L-Lactate Dehydrogenase (mesh)Mice (mesh)0601 Biochemistry and Cell Biology (for)1701 Psychology (for)1702 Cognitive Sciences (for)3101 Biochemistry and cell biology (for-2020)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/4kx9787cinfo:doi/10.3791/57760articleJournal of Visualized Experiments, vol 2018, iss 136oai:escholarship.org:ark:/13030/qt62z7188k2026-08-18T20:27:34Zqt62z7188kThe SET-Domain Protein SUVR5 Mediates H3K9me2 Deposition and Silencing at Stimulus Response Genes in a DNA Methylation–Independent MannerCaro, ElenaStroud, HumeGreenberg, Maxim VCBernatavichute, Yana VFeng, SuhuaGroth, MartinVashisht, Ajay AWohlschlegel, JamesJacobsen, Steve EGrewal, Shiv2012-01-01In eukaryotic cells, environmental and developmental signals alter chromatin structure and modulate gene expression. Heterochromatin constitutes the transcriptionally inactive state of the genome and in plants and mammals is generally characterized by DNA methylation and histone modifications such as histone H3 lysine 9 (H3K9) methylation. In Arabidopsis thaliana, DNA methylation and H3K9 methylation are usually colocated and set up a mutually self-reinforcing and stable state. Here, in contrast, we found that SUVR5, a plant Su(var)3-9 homolog with a SET histone methyltransferase domain, mediates H3K9me2 deposition and regulates gene expression in a DNA methylation-independent manner. SUVR5 binds DNA through its zinc fingers and represses the expression of a subset of stimulus response genes. This represents a novel mechanism for plants to regulate their chromatin and transcriptional state, which may allow for the adaptability and modulation necessary to rapidly respond to extracellular cues.3108 Plant Biology (for-2020)3101 Biochemistry and Cell Biology (for-2020)3105 Genetics (for-2020)31 Biological Sciences (for-2020)Human Genome (rcdc)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Arabidopsis (mesh)Arabidopsis Proteins (mesh)Base Sequence (mesh)Binding Sites (mesh)DNA Methylation (mesh)DNA-Binding Proteins (mesh)Gene Expression RegulationPlant (mesh)Gene Silencing (mesh)Histone Demethylases (mesh)Histone-Lysine N-Methyltransferase (mesh)Histones (mesh)Nucleotide Motifs (mesh)Promoter RegionsGenetic (mesh)Protein Binding (mesh)Protein Interaction Domains and Motifs (mesh)Zinc Fingers (mesh)Arabidopsis (mesh)Histone-Lysine N-Methyltransferase (mesh)DNA-Binding Proteins (mesh)Histones (mesh)Arabidopsis Proteins (mesh)DNA Methylation (mesh)Gene Expression RegulationPlant (mesh)Gene Silencing (mesh)Binding Sites (mesh)Base Sequence (mesh)Zinc Fingers (mesh)Protein Binding (mesh)Protein Interaction Domains and Motifs (mesh)Promoter RegionsGenetic (mesh)Histone Demethylases (mesh)Nucleotide Motifs (mesh)Arabidopsis (mesh)Arabidopsis Proteins (mesh)Base Sequence (mesh)Binding Sites (mesh)DNA Methylation (mesh)DNA-Binding Proteins (mesh)Gene Expression RegulationPlant (mesh)Gene Silencing (mesh)Histone Demethylases (mesh)Histone-Lysine N-Methyltransferase (mesh)Histones (mesh)Nucleotide Motifs (mesh)Promoter RegionsGenetic (mesh)Protein Binding (mesh)Protein Interaction Domains and Motifs (mesh)Zinc Fingers (mesh)0604 Genetics (for)Developmental Biology (science-metrix)3105 Genetics (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/62z7188khttps://escholarship.org/content/qt62z7188k/qt62z7188k.pdfinfo:doi/10.1371/journal.pgen.1002995articlePLOS Genetics, vol 8, iss 10e1002995oai:escholarship.org:ark:/13030/qt0r44v85k2026-08-18T20:26:40Zqt0r44v85kTime‐Dependent Measurement of Nrf2‐Regulated Antioxidant Response to Ionizing Radiation Toward Identifying Potential Protein Biomarkers for Acute Radiation InjuryLiu, KateSinger, ElizabethCohn, WhitakerMicewicz, Ewa DMcBride, William HWhitelegge, Julian PLoo, Joseph A2019-11-01PURPOSE: Potential acute exposure to ionizing radiation in nuclear or radiological accidents presents complex mass casualty scenarios that demand prompt triage and treatment decisions. Due to delayed symptoms and varied response of radiation victims, there is an urgent need to develop robust biomarkers to assess the extent of injuries in individuals.
EXPERIMENTAL DESIGN: The transcription factor Nrf2 is the master of redox homeostasis and there is transcriptional evidence of Nrf2-dependent antioxidant response activation upon radiation. The biomarker potential of Nrf2-dependent downstream target enzymes is investigated by measuring their response in bone marrow extracted from C57Bl/6 and C3H mice of both genders for up to 4 days following 6 Gy total body irradiation using targeted MS.
RESULTS: Overall, C57Bl/6 mice have a stronger proteomic response than C3H mice. In both strains, male mice have more occurrences of upregulation in antioxidant enzymes than female mice. For C57Bl/6 male mice, three proteins show elevated abundances after radiation exposure: catalase, superoxide dismutase 1, and heme oxygenase 1. Across both strains and genders, glutathione S-transferase Mu 1 is consistently decreased.
CONCLUSIONS AND CLINICAL RELEVANCE: This study provides the basis for future development of organ-specific protein biomarkers used in diagnostic blood test for radiation injury.32 Biomedical and Clinical Sciences (for-2020)3202 Clinical Sciences (for-2020)Prevention (rcdc)Biotechnology (rcdc)Cancer (rcdc)Radiation Oncology (rcdc)Biodefense (rcdc)Physical Injury - Accidents and Adverse Effects (rcdc)4.2 Evaluation of markers and technologies (hrcs-rac)3 Good Health and Well Being (sdg)Animals (mesh)Antioxidants (mesh)Biomarkers (mesh)Bone Marrow (mesh)Catalase (mesh)ChromatographyHigh Pressure Liquid (mesh)Female (mesh)Glutathione Transferase (mesh)Isotope Labeling (mesh)Male (mesh)Mass Spectrometry (mesh)Mice (mesh)MiceInbred C3H (mesh)MiceInbred C57BL (mesh)NF-E2-Related Factor 2 (mesh)Peptides (mesh)Proteomics (mesh)Radiation Injuries (mesh)RadiationIonizing (mesh)Superoxide Dismutase (mesh)antioxidant responsebone marrowgender differenceionizing radiationtargeted proteomicsBone Marrow (mesh)Animals (mesh)MiceInbred C3H (mesh)MiceInbred C57BL (mesh)Mice (mesh)Radiation Injuries (mesh)Catalase (mesh)Superoxide Dismutase (mesh)Glutathione Transferase (mesh)Peptides (mesh)Antioxidants (mesh)ChromatographyHigh Pressure Liquid (mesh)Isotope Labeling (mesh)Proteomics (mesh)RadiationIonizing (mesh)Female (mesh)Male (mesh)NF-E2-Related Factor 2 (mesh)Mass Spectrometry (mesh)Biomarkers (mesh)antioxidant responsebone marrowgender differenceionizing radiationtargeted proteomicsAnimals (mesh)Antioxidants (mesh)Biomarkers (mesh)Bone Marrow (mesh)Catalase (mesh)ChromatographyHigh Pressure Liquid (mesh)Female (mesh)Glutathione Transferase (mesh)Isotope Labeling (mesh)Male (mesh)Mass Spectrometry (mesh)Mice (mesh)MiceInbred C3H (mesh)MiceInbred C57BL (mesh)NF-E2-Related Factor 2 (mesh)Peptides (mesh)Proteomics (mesh)Radiation Injuries (mesh)RadiationIonizing (mesh)Superoxide Dismutase (mesh)1101 Medical Biochemistry and Metabolomics (for)Biochemistry & Molecular Biology (science-metrix)3205 Medical biochemistry and metabolomics (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0r44v85khttps://escholarship.org/content/qt0r44v85k/qt0r44v85k.pdfinfo:doi/10.1002/prca.201900035articleProteomics Clinical Applications, vol 13, iss 6e1900035 - e1900035oai:escholarship.org:ark:/13030/qt0762597g2026-08-18T18:12:13Zqt0762597gDetermining Genome-wide Transcript Decay Rates in Proliferating and Quiescent Human Fibroblasts.Mitra, MithunLee, Ha NeulColler, Hilary A2018-01-01Quiescence is a temporary, reversible state in which cells have ceased cell division, but retain the capacity to proliferate. Multiple studies, including ours, have demonstrated that quiescence is associated with widespread changes in gene expression. Some of these changes occur through changes in the level or activity of proliferation-associated transcription factors, such as E2F and MYC. We have demonstrated that mRNA decay can also contribute to changes in gene expression between proliferating and quiescent cells. In this protocol, we describe the procedure for establishing proliferating and quiescent cultures of human dermal foreskin fibroblasts. We then describe the procedures for inhibiting new transcription in proliferating and quiescent cells with Actinomycin D (ActD). ActD treatment represents a straightforward and reproducible approach to dissociating new transcription from transcript decay. A disadvantage of ActD treatment is that the time course must be limited to a short time frame because ActD affects cell viability. Transcript levels are monitored over time to determine transcript decay rates. This procedure allows for the identification of genes and isoforms that exhibit differential decay in proliferating versus quiescent fibroblasts.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)Genetics (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Cell Proliferation (mesh)Fibroblasts (mesh)Genomics (mesh)Humans (mesh)RNA Stability (mesh)Transcript decayquiescencefibroblastscontact inhibitionhalf-lifeactinomycin DmiR-29Fibroblasts (mesh)Humans (mesh)Genomics (mesh)Cell Proliferation (mesh)RNA Stability (mesh)Cell Proliferation (mesh)Fibroblasts (mesh)Genomics (mesh)Humans (mesh)RNA Stability (mesh)0601 Biochemistry and Cell Biology (for)1701 Psychology (for)1702 Cognitive Sciences (for)3101 Biochemistry and cell biology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0762597ghttps://escholarship.org/content/qt0762597g/qt0762597g.pdfinfo:doi/10.3791/56423articleJournal of Visualized Experiments, vol 2018, iss 131oai:escholarship.org:ark:/13030/qt0g70d8mz2026-08-18T17:16:01Zqt0g70d8mzCatastrophic disassembly of actin filaments via Mical-mediated oxidationGrintsevich, Elena EGe, PengSawaya, Michael RYesilyurt, Hunkar GizemTerman, Jonathan RZhou, Z HongReisler, Emil2017-12-19Actin filament assembly and disassembly are vital for cell functions. MICAL Redox enzymes are important post-translational effectors of actin that stereo-specifically oxidize actin’s M44 and M47 residues to induce cellular F-actin disassembly. Here we show that Mical-oxidized (Mox) actin can undergo extremely fast (84 subunits/s) disassembly, which depends on F-actin’s nucleotide-bound state. Using near-atomic resolution cryoEM reconstruction and single filament TIRF microscopy we identify two dynamic and structural states of Mox-actin. Modeling actin’s D-loop region based on our 3.9 Å cryoEM reconstruction suggests that oxidation by Mical reorients the side chain of M44 and induces a new intermolecular interaction of actin residue M47 (M47-O-T351). Site-directed mutagenesis reveals that this interaction promotes Mox-actin instability. Moreover, we find that Mical oxidation of actin allows for cofilin-mediated severing even in the presence of inorganic phosphate. Thus, in conjunction with cofilin, Mical oxidation of actin promotes F-actin disassembly independent of the nucleotide-bound state.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Actin Cytoskeleton (mesh)Actin Depolymerizing Factors (mesh)Actins (mesh)Cryoelectron Microscopy (mesh)CrystallographyX-Ray (mesh)DNA-Binding Proteins (mesh)Methionine (mesh)Molecular Docking Simulation (mesh)MutagenesisSite-Directed (mesh)Oxidation-Reduction (mesh)Protein Binding (mesh)Protein Domains (mesh)Protein Multimerization (mesh)Recombinant Proteins (mesh)Actins (mesh)Methionine (mesh)DNA-Binding Proteins (mesh)Recombinant Proteins (mesh)Cryoelectron Microscopy (mesh)CrystallographyX-Ray (mesh)MutagenesisSite-Directed (mesh)Protein Binding (mesh)Oxidation-Reduction (mesh)Actin Depolymerizing Factors (mesh)Protein Multimerization (mesh)Actin Cytoskeleton (mesh)Molecular Docking Simulation (mesh)Protein Domains (mesh)Actin Cytoskeleton (mesh)Actin Depolymerizing Factors (mesh)Actins (mesh)Cryoelectron Microscopy (mesh)CrystallographyX-Ray (mesh)DNA-Binding Proteins (mesh)Methionine (mesh)Molecular Docking Simulation (mesh)MutagenesisSite-Directed (mesh)Oxidation-Reduction (mesh)Protein Binding (mesh)Protein Domains (mesh)Protein Multimerization (mesh)Recombinant Proteins (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/0g70d8mzhttps://escholarship.org/content/qt0g70d8mz/qt0g70d8mz.pdfinfo:doi/10.1038/s41467-017-02357-8articleNature Communications, vol 8, iss 12183oai:escholarship.org:ark:/13030/qt97w8q3tz2026-08-18T15:26:37Zqt97w8q3tzRegulation of X-chromosome dosage compensation in human: mechanisms and model systemsSahakyan, AnnaPlath, KathrinRougeulle, Claire2017-11-05The human blastocyst forms 5 days after one of the smallest human cells (the sperm) fertilizes one of the largest human cells (the egg). Depending on the sex-chromosome contribution from the sperm, the resulting embryo will either be female, with two X chromosomes (XX), or male, with an X and a Y chromosome (XY). In early development, one of the major differences between XX female and XY male embryos is the conserved process of X-chromosome inactivation (XCI), which compensates gene expression of the two female X chromosomes to match the dosage of the single X chromosome of males. Most of our understanding of the pre-XCI state and XCI establishment is based on mouse studies, but recent evidence from human pre-implantation embryo research suggests that many of the molecular steps defined in the mouse are not conserved in human. Here, we will discuss recent advances in understanding the control of X-chromosome dosage compensation in early human embryonic development and compare it to that of the mouse.This article is part of the themed issue 'X-chromosome inactivation: a tribute to Mary Lyon'.3101 Biochemistry and Cell Biology (for-2020)3215 Reproductive Medicine (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Contraception/Reproduction (rcdc)Infertility (rcdc)Genetics (rcdc)Human Genome (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Reproductive health and childbirth (hrcs-hc)Generic health relevance (hrcs-hc)Animals (mesh)ChromosomesHumanX (mesh)Dosage CompensationGenetic (mesh)Embryonic Development (mesh)Female (mesh)Humans (mesh)Male (mesh)Mice (mesh)X Chromosome (mesh)X Chromosome Inactivation (mesh)X-chromosome inactivationpluripotent stem cellsX-chromosome dampeningXistXactChromosomesHumanX (mesh)X Chromosome (mesh)Animals (mesh)Humans (mesh)Mice (mesh)Embryonic Development (mesh)Dosage CompensationGenetic (mesh)Female (mesh)Male (mesh)X Chromosome Inactivation (mesh)X-chromosome dampeningX-chromosome inactivationXactXistpluripotent stem cellsAnimals (mesh)ChromosomesHumanX (mesh)Dosage CompensationGenetic (mesh)Embryonic Development (mesh)Female (mesh)Humans (mesh)Male (mesh)Mice (mesh)X Chromosome (mesh)X Chromosome Inactivation (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Evolutionary Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/97w8q3tzhttps://escholarship.org/content/qt97w8q3tz/qt97w8q3tz.pdfinfo:doi/10.1098/rstb.2016.0363articlePhilosophical Transactions of the Royal Society B Biological Sciences, vol 372, iss 173320160363oai:escholarship.org:ark:/13030/qt6dj2s3qr2026-08-18T06:41:54Zqt6dj2s3qrA lifelong duty: how Xist maintains the inactive X chromosomeJacobson, Elsie CPandya-Jones, AmyPlath, Kathrin2022-08-01Female eutherians transcriptionally silence one X chromosome to balance gene dosage between the sexes. X-chromosome inactivation (XCI) is initiated by the lncRNA Xist, which assembles many proteins within the inactive X chromosome (Xi) to trigger gene silencing and heterochromatin formation. It is well established that gene silencing on the Xi is maintained through repressive epigenetic processes, including histone deacetylation and DNA methylation. Recent studies revealed a new mechanism where RNA-binding proteins that interact directly with the RNA contribute to the maintenance of Xist localization and gene silencing. In addition, a surprising plasticity of the Xi was uncovered with many genes becoming upregulated upon experimental deletion of Xist. Intriguingly, immune cells normally lose Xist from the Xi, suggesting that thisXist dependence is utilized in vivo to dynamically regulate gene expression from the Xi. These new studies expose fundamental regulatory mechanisms for the chromatin association of RNAs, highlight the need for studying the maintenance of XCI and Xist localization in a gene- and cell-type-specific manner, and are likely to have clinical impact.3101 Biochemistry and Cell Biology (for-2020)3105 Genetics (for-2020)31 Biological Sciences (for-2020)Human Genome (rcdc)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Chromatin (mesh)Female (mesh)Gene Silencing (mesh)Humans (mesh)RNALong Noncoding (mesh)X Chromosome (mesh)X Chromosome Inactivation (mesh)X Chromosome (mesh)Chromatin (mesh)Humans (mesh)Gene Silencing (mesh)Female (mesh)X Chromosome Inactivation (mesh)RNALong Noncoding (mesh)Chromatin (mesh)Female (mesh)Gene Silencing (mesh)Humans (mesh)RNALong Noncoding (mesh)X Chromosome (mesh)X Chromosome Inactivation (mesh)0604 Genetics (for)Developmental Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)3105 Genetics (for-2020)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/6dj2s3qrhttps://escholarship.org/content/qt6dj2s3qr/qt6dj2s3qr.pdfinfo:doi/10.1016/j.gde.2022.101927articleCurrent Opinion in Genetics & Development, vol 75101927oai:escholarship.org:ark:/13030/qt9gw3v5h82026-08-17T02:26:08Zqt9gw3v5h8Missing Data Imputation for Remote CHF Patient Monitoring SystemsSuh, Myung-kyungWoodbridge, JonathanLan, MarsBui, AlexEvangelista, Lorraine SSarrafzadeh, Majid2011-01-01Congestive heart failure (CHF) is a leading cause of death in the United States. WANDA is a wireless health project that leverages sensor technology and wireless communication to monitor the health status of patients with CHF. The first pilot study of WANDA showed the system's effectiveness for patients with CHF. However, WANDA experienced a considerable amount of missing data due to system misuse, nonuse, and failure. Missing data is highly undesirable as automated alarms may fail to notify healthcare professionals of potentially dangerous patient conditions. In this study, we exploit machine learning techniques including projection adjustment by contribution estimation regression (PACE), Bayesian methods, and voting feature interval (VFI) algorithms to predict both non-binomial and binomial data. The experimental results show that the aforementioned algorithms are superior to other methods with high accuracy and recall. This approach also shows an improved ability to predict missing data when training on entire populations, as opposed to training unique classifiers for each individual.4605 Data Management and Data Science (for-2020)46 Information and Computing Sciences (for-2020)Networking and Information Technology R&D (NITRD) (rcdc)Heart Disease (rcdc)Health Services (rcdc)Machine Learning and Artificial Intelligence (rcdc)Cardiovascular (rcdc)Patient Safety (rcdc)Clinical Research (rcdc)Bioengineering (rcdc)Bayes Theorem (mesh)Heart Failure (mesh)Humans (mesh)MonitoringPhysiologic (mesh)Telemedicine (mesh)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9gw3v5h8https://escholarship.org/content/qt9gw3v5h8/qt9gw3v5h8.pdfinfo:doi/10.1109/iembs.2011.6090867articleAnnual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), vol 20113184 - 3187oai:escholarship.org:ark:/13030/qt1xk6z95n2026-08-15T04:47:43Zqt1xk6z95nMEF2C protects bone marrow B-lymphoid progenitors during stress haematopoiesisWang, WenyuanOrg, TonisMontel-Hagen, AméliePioli, Peter DDuan, DanIsraely, EdoMalkin, DanielSu, TrentFlach, JohannaKurdistani, Siavash KSchiestl, Robert HMikkola, Hanna KA2016-08-01DNA double strand break (DSB) repair is critical for generation of B-cell receptors, which are pre-requisite for B-cell progenitor survival. However, the transcription factors that promote DSB repair in B cells are not known. Here we show that MEF2C enhances the expression of DNA repair and recombination factors in B-cell progenitors, promoting DSB repair, V(D)J recombination and cell survival. Although Mef2c-deficient mice maintain relatively intact peripheral B-lymphoid cellularity during homeostasis, they exhibit poor B-lymphoid recovery after sub-lethal irradiation and 5-fluorouracil injection. MEF2C binds active regulatory regions with high-chromatin accessibility in DNA repair and V(D)J genes in both mouse B-cell progenitors and human B lymphoblasts. Loss of Mef2c in pre-B cells reduces chromatin accessibility in multiple regulatory regions of the MEF2C-activated genes. MEF2C therefore protects B lymphopoiesis during stress by ensuring proper expression of genes that encode DNA repair and B-cell factors.32 Biomedical and Clinical Sciences (for-2020)3202 Clinical Sciences (for-2020)Genetics (rcdc)Stem Cell Research - Nonembryonic - Non-Human (rcdc)Stem Cell Research (rcdc)Biotechnology (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Cancer (hrcs-hc)Animals (mesh)Cell Survival (mesh)Chromatin (mesh)DNA BreaksDouble-Stranded (mesh)Female (mesh)Fluorouracil (mesh)Hematopoiesis (mesh)MEF2 Transcription Factors (mesh)Male (mesh)Mice (mesh)Precursor CellsB-Lymphoid (mesh)V(D)J Recombination (mesh)Whole-Body Irradiation (mesh)Chromatin (mesh)Animals (mesh)Mice (mesh)Fluorouracil (mesh)Whole-Body Irradiation (mesh)Hematopoiesis (mesh)Cell Survival (mesh)Female (mesh)Male (mesh)DNA BreaksDouble-Stranded (mesh)Precursor CellsB-Lymphoid (mesh)V(D)J Recombination (mesh)MEF2 Transcription Factors (mesh)Animals (mesh)Cell Survival (mesh)Chromatin (mesh)DNA BreaksDouble-Stranded (mesh)Female (mesh)Fluorouracil (mesh)Hematopoiesis (mesh)MEF2 Transcription Factors (mesh)Male (mesh)Mice (mesh)Precursor CellsB-Lymphoid (mesh)V(D)J Recombination (mesh)Whole-Body Irradiation (mesh)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1xk6z95nhttps://escholarship.org/content/qt1xk6z95n/qt1xk6z95n.pdfinfo:doi/10.1038/ncomms12376articleNature Communications, vol 7, iss 112376oai:escholarship.org:ark:/13030/qt3w34v6mm2026-08-14T21:49:46Zqt3w34v6mmA high-throughput screen of inactive X chromosome reactivation identifies the enhancement of DNA demethylation by 5-aza-2′-dC upon inhibition of ribonucleotide reductaseMinkovsky, AlissaSahakyan, AnnaBonora, GiancarloDamoiseaux, RobertDimitrova, ElizabethRubbi, LiudmillaPellegrini, MatteoRadu, Caius GPlath, Kathrin2015-12-01BackgroundDNA methylation is important for the maintenance of the silent state of genes on the inactive X chromosome (Xi). Here, we screened for siRNAs and chemicals that reactivate an Xi-linked reporter in the presence of 5-aza-2′-deoxycytidine (5-aza-2′-dC), an inhibitor of DNA methyltransferase 1, at a concentration that, on its own, is not sufficient for Xi-reactivation.ResultsWe found that inhibition of ribonucleotide reductase (RNR) induced expression of the reporter. RNR inhibition potentiated the effect of 5-aza-2′-dC by enhancing its DNA incorporation, thereby decreasing DNA methylation levels genome-wide. Since both 5-aza-2′-dC and RNR-inhibitors are used in the treatment of hematological malignancies, we treated myeloid leukemia cell lines with 5-aza-2′-dC and the RNR-inhibitor hydroxyurea, and observed synergistic inhibition of cell growth and a decrease in genome-wide DNA methylation.ConclusionsTaken together, our study identifies a drug combination that enhances DNA demethylation by altering nucleotide metabolism. This demonstrates that Xi-reactivation assays can be used to optimize the epigenetic activity of drug combinations.31 Biological Sciences (for-2020)3105 Genetics (for-2020)Genetics (rcdc)Rare Diseases (rcdc)Cancer (rcdc)Hematology (rcdc)Orphan Drug (rcdc)Human Genome (rcdc)Cancer (hrcs-hc)X chromosome inactivationDNA methylation5-aza-2 '-dCRibonucleotide reductaseHydroxyurea5-aza-2′-dCDNA methylationHydroxyureaRibonucleotide reductaseX chromosome inactivation0604 Genetics (for)3105 Genetics (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3w34v6mmhttps://escholarship.org/content/qt3w34v6mm/qt3w34v6mm.pdfinfo:doi/10.1186/s13072-015-0034-4articleEpigenetics & Chromatin, vol 8, iss 142oai:escholarship.org:ark:/13030/qt3wp8t7sx2026-08-14T20:18:53Zqt3wp8t7sxArabidopsis AtMORC4 and AtMORC7 Form Nuclear Bodies and Repress a Large Number of Protein-Coding GenesHarris, C JakeHusmann, DylanLiu, WanluKasmi, Farid ElWang, HaifengPapikian, AshotPastor, William AMoissiard, GuillaumeVashisht, Ajay ADangl, Jeffery LWohlschlegel, James AJacobsen, Steven EGilbert, Nick2016-05-01The MORC family of GHKL ATPases are an enigmatic class of proteins with diverse chromatin related functions. In Arabidopsis, AtMORC1, AtMORC2, and AtMORC6 act together in heterodimeric complexes to mediate transcriptional silencing of methylated DNA elements. Here, we studied Arabidopsis AtMORC4 and AtMORC7. We found that, in contrast to AtMORC1,2,6, they act to suppress a wide set of non-methylated protein-coding genes that are enriched for those involved in pathogen response. Furthermore, atmorc4 atmorc7 double mutants show a pathogen response phenotype. We found that AtMORC4 and AtMORC7 form homomeric complexes in vivo and are concentrated in discrete nuclear bodies adjacent to chromocenters. Analysis of an atmorc1,2,4,5,6,7 hextuple mutant demonstrates that transcriptional de-repression is largely uncoupled from changes in DNA methylation in plants devoid of MORC function. However, we also uncover a requirement for MORC in both DNA methylation and silencing at a small but distinct subset of RNA-directed DNA methylation target loci. These regions are characterized by poised transcriptional potential and a low density of sites for symmetric cytosine methylation. These results provide insight into the biological function of MORC proteins in higher eukaryotes.3108 Plant Biology (for-2020)31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)3105 Genetics (for-2020)Genetics (rcdc)Human Genome (rcdc)Adenosine Triphosphatases (mesh)Arabidopsis (mesh)Arabidopsis Proteins (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Gene Expression RegulationPlant (mesh)Multigene Family (mesh)Phenotype (mesh)TranscriptionGenetic (mesh)Arabidopsis (mesh)Arabidopsis Proteins (mesh)DNA Methylation (mesh)TranscriptionGenetic (mesh)EpigenesisGenetic (mesh)Gene Expression RegulationPlant (mesh)Phenotype (mesh)Multigene Family (mesh)Adenosine Triphosphatases (mesh)Adenosine Triphosphatases (mesh)Arabidopsis (mesh)Arabidopsis Proteins (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Gene Expression RegulationPlant (mesh)Multigene Family (mesh)Phenotype (mesh)TranscriptionGenetic (mesh)0604 Genetics (for)Developmental Biology (science-metrix)3105 Genetics (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/3wp8t7sxhttps://escholarship.org/content/qt3wp8t7sx/qt3wp8t7sx.pdfinfo:doi/10.1371/journal.pgen.1005998articlePLOS Genetics, vol 12, iss 5e1005998oai:escholarship.org:ark:/13030/qt4xh0s9d92026-08-14T08:59:18Zqt4xh0s9d9Evidence for Ubiquitin-Regulated Nuclear and Subnuclear Trafficking among Paramyxovirinae Matrix ProteinsPentecost, MickeyVashisht, Ajay ALester, TaliaVoros, TimBeaty, Shannon MPark, ArnoldWang, Yao EYun, Tatyana EFreiberg, Alexander NWohlschlegel, James ALee, BenhurCoyne, Carolyn B2015-03-01The paramyxovirus matrix (M) protein is a molecular scaffold required for viral morphogenesis and budding at the plasma membrane. Transient nuclear residence of some M proteins hints at non-structural roles. However, little is known regarding the mechanisms that regulate the nuclear sojourn. Previously, we found that the nuclear-cytoplasmic trafficking of Nipah virus M (NiV-M) is a prerequisite for budding, and is regulated by a bipartite nuclear localization signal (NLSbp), a leucine-rich nuclear export signal (NES), and monoubiquitination of the K258 residue within the NLSbp itself (NLSbp-lysine). To define whether the sequence determinants of nuclear trafficking identified in NiV-M are common among other Paramyxovirinae M proteins, we generated the homologous NES and NLSbp-lysine mutations in M proteins from the five major Paramyxovirinae genera. Using quantitative 3D confocal microscopy, we determined that the NES and NLSbp-lysine are required for the efficient nuclear export of the M proteins of Nipah virus, Hendra virus, Sendai virus, and Mumps virus. Pharmacological depletion of free ubiquitin or mutation of the conserved NLSbp-lysine to an arginine, which inhibits M ubiquitination, also results in nuclear and nucleolar retention of these M proteins. Recombinant Sendai virus (rSeV-eGFP) bearing the NES or NLSbp-lysine M mutants rescued at similar efficiencies to wild type. However, foci of cells expressing the M mutants displayed marked fusogenicity in contrast to wild type, and infection did not spread. Recombinant Mumps virus (rMuV-eGFP) bearing the homologous mutations showed similar defects in viral morphogenesis. Finally, shotgun proteomics experiments indicated that the interactomes of Paramyxovirinae M proteins are significantly enriched for components of the nuclear pore complex, nuclear transport receptors, and nucleolar proteins. We then synthesize our functional and proteomics data to propose a working model for the ubiquitin-regulated nuclear-cytoplasmic trafficking of cognate paramyxovirus M proteins that show a consistent nuclear trafficking phenotype.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Emerging Infectious Diseases (rcdc)Infectious Diseases (rcdc)Rare Diseases (rcdc)Biodefense (rcdc)Amino Acid Sequence (mesh)Animals (mesh)Cell Nucleus (mesh)Chlorocebus aethiops (mesh)HeLa Cells (mesh)Humans (mesh)ImagingThree-Dimensional (mesh)Immunoblotting (mesh)Immunoprecipitation (mesh)MicroscopyConfocal (mesh)Nuclear Localization Signals (mesh)Paramyxovirinae (mesh)Protein Transport (mesh)Transfection (mesh)Ubiquitin (mesh)Vero Cells (mesh)Viral Matrix Proteins (mesh)Hela Cells (mesh)Vero Cells (mesh)Cell Nucleus (mesh)Animals (mesh)Humans (mesh)Paramyxovirinae (mesh)Ubiquitin (mesh)Viral Matrix Proteins (mesh)ImagingThree-Dimensional (mesh)MicroscopyConfocal (mesh)Immunoblotting (mesh)Transfection (mesh)Immunoprecipitation (mesh)Amino Acid Sequence (mesh)Protein Transport (mesh)Nuclear Localization Signals (mesh)Chlorocebus aethiops (mesh)Amino Acid Sequence (mesh)Animals (mesh)Cell Nucleus (mesh)Chlorocebus aethiops (mesh)HeLa Cells (mesh)Humans (mesh)ImagingThree-Dimensional (mesh)Immunoblotting (mesh)Immunoprecipitation (mesh)MicroscopyConfocal (mesh)Nuclear Localization Signals (mesh)Paramyxovirinae (mesh)Protein Transport (mesh)Transfection (mesh)Ubiquitin (mesh)Vero Cells (mesh)Viral Matrix Proteins (mesh)0605 Microbiology (for)1107 Immunology (for)1108 Medical Microbiology (for)Virology (science-metrix)3107 Microbiology (for-2020)3204 Immunology (for-2020)3207 Medical microbiology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/4xh0s9d9https://escholarship.org/content/qt4xh0s9d9/qt4xh0s9d9.pdfinfo:doi/10.1371/journal.ppat.1004739articlePLOS Pathogens, vol 11, iss 3e1004739oai:escholarship.org:ark:/13030/qt6m57d1kd2026-08-14T07:23:05Zqt6m57d1kdLpcat3-dependent production of arachidonoyl phospholipids is a key determinant of triglyceride secretionRong, XinWang, BoDunham, Merlow MHedde, Per NiklasWong, Jinny SGratton, EnricoYoung, Stephen GFord, David ATontonoz, Peter2015-01-01The role of specific phospholipids (PLs) in lipid transport has been difficult to assess due to an inability to selectively manipulate membrane composition in vivo. Here we show that the phospholipid remodeling enzyme lysophosphatidylcholine acyltransferase 3 (Lpcat3) is a critical determinant of triglyceride (TG) secretion due to its unique ability to catalyze the incorporation of arachidonate into membranes. Mice lacking Lpcat3 in the intestine fail to thrive during weaning and exhibit enterocyte lipid accumulation and reduced plasma TGs. Mice lacking Lpcat3 in the liver show reduced plasma TGs, hepatosteatosis, and secrete lipid-poor very low-density lipoprotein (VLDL) lacking arachidonoyl PLs. Mechanistic studies indicate that Lpcat3 activity impacts membrane lipid mobility in living cells, suggesting a biophysical basis for the requirement of arachidonoyl PLs in lipidating lipoprotein particles. These data identify Lpcat3 as a key factor in lipoprotein production and illustrate how manipulation of membrane composition can be used as a regulatory mechanism to control metabolic pathways.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Digestive Diseases (rcdc)1-Acylglycerophosphocholine O-Acyltransferase (mesh)Animals (mesh)Apolipoproteins B (mesh)Arachidonic Acid (mesh)Breeding (mesh)Diet (mesh)Golgi Apparatus (mesh)Hepatocytes (mesh)Inflammation (mesh)Lipid Metabolism (mesh)LipoproteinsVLDL (mesh)Liver (mesh)Liver X Receptors (mesh)Lysophosphatidylcholines (mesh)Membrane Lipids (mesh)MiceInbred C57BL (mesh)MiceKnockout (mesh)Organ Specificity (mesh)Orphan Nuclear Receptors (mesh)Phenotype (mesh)Phospholipids (mesh)Triglycerides (mesh)Liver (mesh)Golgi Apparatus (mesh)Hepatocytes (mesh)Animals (mesh)MiceInbred C57BL (mesh)MiceKnockout (mesh)Inflammation (mesh)1-Acylglycerophosphocholine O-Acyltransferase (mesh)Arachidonic Acid (mesh)Triglycerides (mesh)LipoproteinsVLDL (mesh)Membrane Lipids (mesh)Phospholipids (mesh)Lysophosphatidylcholines (mesh)Apolipoproteins B (mesh)Diet (mesh)Breeding (mesh)Organ Specificity (mesh)Phenotype (mesh)Lipid Metabolism (mesh)Orphan Nuclear Receptors (mesh)Liver X Receptors (mesh)cell biologyhuman biologylipoproteinmedicinemousenuclear receptorphospholipid1-Acylglycerophosphocholine O-Acyltransferase (mesh)Animals (mesh)Apolipoproteins B (mesh)Arachidonic Acid (mesh)Breeding (mesh)Diet (mesh)Golgi Apparatus (mesh)Hepatocytes (mesh)Inflammation (mesh)Lipid Metabolism (mesh)LipoproteinsVLDL (mesh)Liver (mesh)Liver X Receptors (mesh)Lysophosphatidylcholines (mesh)Membrane Lipids (mesh)MiceInbred C57BL (mesh)MiceKnockout (mesh)Organ Specificity (mesh)Orphan Nuclear Receptors (mesh)Phenotype (mesh)Phospholipids (mesh)Triglycerides (mesh)0601 Biochemistry and Cell Biology (for)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/6m57d1kdhttps://escholarship.org/content/qt6m57d1kd/qt6m57d1kd.pdfinfo:doi/10.7554/elife.06557articleELIFE, vol 4, iss 4e06557oai:escholarship.org:ark:/13030/qt9c5905232026-08-14T07:22:18Zqt9c590523Novel Components of the Toxoplasma Inner Membrane Complex Revealed by BioIDChen, Allan LKim, Elliot WToh, Justin YVashisht, Ajay ARashoff, Andrew QVan, ChristinaHuang, Amy SMoon, Andy SBell, Hannah NBentolila, Laurent AWohlschlegel, James ABradley, Peter JWeiss, Louis M2015-02-27The inner membrane complex (IMC) of Toxoplasma gondii is a peripheral membrane system that is composed of flattened alveolar sacs that underlie the plasma membrane, coupled to a supporting cytoskeletal network. The IMC plays important roles in parasite replication, motility, and host cell invasion. Despite these central roles in the biology of the parasite, the proteins that constitute the IMC are largely unknown. In this study, we have adapted a technique named proximity-dependent biotin identification (BioID) for use in T. gondii to identify novel components of the IMC. Using IMC proteins in both the alveoli and the cytoskeletal network as bait, we have uncovered a total of 19 new IMC proteins in both of these suborganellar compartments, two of which we functionally evaluate by gene knockout. Importantly, labeling of IMC proteins using this approach has revealed a group of proteins that localize to the sutures of the alveolar sacs that have been seen in their entirety in Toxoplasma species only by freeze fracture electron microscopy. Collectively, our study greatly expands the repertoire of known proteins in the IMC and experimentally validates BioID as a strategy for discovering novel constituents of specific cellular compartments of T. gondii.
IMPORTANCE: The identification of binding partners is critical for determining protein function within cellular compartments. However, discovery of protein-protein interactions within membrane or cytoskeletal compartments is challenging, particularly for transient or unstable interactions that are often disrupted by experimental manipulation of these compartments. To circumvent these problems, we adapted an in vivo biotinylation technique called BioID for Toxoplasma species to identify binding partners and proximal proteins within native cellular environments. We used BioID to identify 19 novel proteins in the parasite IMC, an organelle consisting of fused membrane sacs and an underlying cytoskeleton, whose protein composition is largely unknown. We also demonstrate the power of BioID for targeted discovery of proteins within specific compartments, such as the IMC cytoskeleton. In addition, we uncovered a new group of proteins localizing to the alveolar sutures of the IMC. BioID promises to reveal new insights on protein constituents and interactions within cellular compartments of Toxoplasma.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Infectious Diseases (rcdc)Biodefense (rcdc)Emerging Infectious Diseases (rcdc)2.2 Factors relating to the physical environment (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Infection (hrcs-hc)Cell Membrane (mesh)Chemistry TechniquesAnalytical (mesh)Cytological Techniques (mesh)Gene Knockout Techniques (mesh)Parasitology (mesh)Proteome (mesh)Protozoan Proteins (mesh)Staining and Labeling (mesh)Toxoplasma (mesh)Cell Membrane (mesh)Toxoplasma (mesh)Proteome (mesh)Protozoan Proteins (mesh)Cytological Techniques (mesh)Staining and Labeling (mesh)Parasitology (mesh)Gene Knockout Techniques (mesh)Chemistry TechniquesAnalytical (mesh)Cell Membrane (mesh)Chemistry TechniquesAnalytical (mesh)Cytological Techniques (mesh)Gene Knockout Techniques (mesh)Parasitology (mesh)Proteome (mesh)Protozoan Proteins (mesh)Staining and Labeling (mesh)Toxoplasma (mesh)0605 Microbiology (for)3101 Biochemistry and cell biology (for-2020)3107 Microbiology (for-2020)3207 Medical microbiology (for-2020)application/pdfCC-BY-NC-SAeScholarship, University of Californiahttps://escholarship.org/uc/item/9c590523https://escholarship.org/content/qt9c590523/qt9c590523.pdfinfo:doi/10.1128/mbio.02357-14articlemBio, vol 6, iss 110.1128/mbio.02357 - 10.1128/mbio.02314oai:escholarship.org:ark:/13030/qt1fd0d0kw2026-08-14T07:03:47Zqt1fd0d0kwCharacterization of the SAM domain of the PKD-related protein ANKS6 and its interaction with ANKS3Leettola, Catherine NKnight, Mary JaneCascio, DuilioHoffman, SigridBowie, James U2014-12-01BackgroundAutosomal dominant polycystic kidney disease (ADPKD) is the most common genetic disorder leading to end-stage renal failure in humans. In the PKD/Mhm(cy/+) rat model of ADPKD, the point mutation R823W in the sterile alpha motif (SAM) domain of the protein ANKS6 is responsible for disease. SAM domains are known protein-protein interaction domains, capable of binding each other to form polymers and heterodimers. Despite its physiological importance, little is known about the function of ANKS6 and how the R823W point mutation leads to PKD. Recent work has revealed that ANKS6 interacts with a related protein called ANKS3. Both ANKS6 and ANKS3 have a similar domain structure, with ankyrin repeats at the N-terminus and a SAM domain at the C-terminus.ResultsThe SAM domain of ANKS3 is identified as a direct binding partner of the ANKS6 SAM domain. We find that ANKS3-SAM polymerizes and ANKS6-SAM can bind to one end of the polymer. We present crystal structures of both the ANKS3-SAM polymer and the ANKS3-SAM/ANKS6-SAM complex, revealing the molecular details of their association. We also learn how the R823W mutation disrupts ANKS6 function by dramatically destabilizing the SAM domain such that the interaction with ANKS3-SAM is lost.ConclusionsANKS3 is a direct interacting partner of ANKS6. By structurally and biochemically characterizing the interaction between the ANKS3 and ANKS6 SAM domains, our work provides a basis for future investigation of how the interaction between these proteins mediates kidney function.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Polycystic Kidney Disease (rcdc)Genetics (rcdc)Congenital Structural Anomalies (rcdc)Kidney Disease (rcdc)Pediatric Research Initiative (rcdc)2.1 Biological and endogenous factors (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)Renal and urogenital (hrcs-hc)Amino Acid Sequence (mesh)Animals (mesh)Ankyrin Repeat (mesh)Binding Sites (mesh)Carrier Proteins (mesh)Circular Dichroism (mesh)Humans (mesh)ModelsMolecular (mesh)Mutation (mesh)Nuclear Proteins (mesh)Protein Conformation (mesh)Protein StructureSecondary (mesh)Protein StructureTertiary (mesh)Rats (mesh)Surface Plasmon Resonance (mesh)Polycystic kidney diseaseProtein-protein interactionPolymerizationCrystal structureAnimals (mesh)Humans (mesh)Rats (mesh)Carrier Proteins (mesh)Nuclear Proteins (mesh)Circular Dichroism (mesh)Surface Plasmon Resonance (mesh)Binding Sites (mesh)Amino Acid Sequence (mesh)Ankyrin Repeat (mesh)Protein Conformation (mesh)Protein StructureSecondary (mesh)Protein StructureTertiary (mesh)Mutation (mesh)ModelsMolecular (mesh)Amino Acid Sequence (mesh)Animals (mesh)Ankyrin Repeat (mesh)Binding Sites (mesh)Carrier Proteins (mesh)Circular Dichroism (mesh)Humans (mesh)ModelsMolecular (mesh)Mutation (mesh)Nuclear Proteins (mesh)Protein Conformation (mesh)Protein StructureSecondary (mesh)Protein StructureTertiary (mesh)Rats (mesh)Surface Plasmon Resonance (mesh)0601 Biochemistry and Cell Biology (for)0605 Microbiology (for)Biochemistry & Molecular Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/1fd0d0kwhttps://escholarship.org/content/qt1fd0d0kw/qt1fd0d0kw.pdfinfo:doi/10.1186/1472-6807-14-17articleBMC Molecular and Cell Biology, vol 14, iss 117oai:escholarship.org:ark:/13030/qt9pf4p8tt2026-08-14T06:58:21Zqt9pf4p8ttThe Mbd1-Atf7ip-Setdb1 pathway contributes to the maintenance of X chromosome inactivationMinkovsky, AlissaSahakyan, AnnaRankin-Gee, ElyseBonora, GiancarloPatel, SanjeetPlath, Kathrin2014-12-01BackgroundX chromosome inactivation (XCI) is a developmental program of heterochromatin formation that initiates during early female mammalian embryonic development and is maintained through a lifetime of cell divisions in somatic cells. Despite identification of the crucial long non-coding RNA Xist and involvement of specific chromatin modifiers in the establishment and maintenance of the heterochromatin of the inactive X chromosome (Xi), interference with known pathways only partially reactivates the Xi once silencing has been established. Here, we studied ATF7IP (MCAF1), a protein previously characterized to coordinate DNA methylation and histone H3K9 methylation through interactions with the methyl-DNA binding protein MBD1 and the histone H3K9 methyltransferase SETDB1, as a candidate maintenance factor of the Xi.ResultsWe found that siRNA-mediated knockdown of Atf7ip in mouse embryonic fibroblasts (MEFs) induces the activation of silenced reporter genes on the Xi in a low number of cells. Additional inhibition of two pathways known to contribute to Xi maintenance, DNA methylation and Xist RNA coating of the X chromosome, strongly increased the number of cells expressing Xi-linked genes upon Atf7ip knockdown. Despite its functional importance in Xi maintenance, ATF7IP does not accumulate on the Xi in MEFs or differentiating mouse embryonic stem cells. However, we found that depletion of two known repressive biochemical interactors of ATF7IP, MBD1 and SETDB1, but not of other unrelated H3K9 methyltransferases, also induces the activation of an Xi-linked reporter in MEFs.ConclusionsTogether, these data indicate that Atf7ip acts in a synergistic fashion with DNA methylation and Xist RNA to maintain the silent state of the Xi in somatic cells, and that Mbd1 and Setdb1, similar to Atf7ip, play a functional role in Xi silencing. We therefore propose that ATF7IP links DNA methylation on the Xi to SETDB1-mediated H3K9 trimethylation via its interaction with MBD1, and that this function is a crucial feature of the stable silencing of the Xi in female mammalian cells.3101 Biochemistry and Cell Biology (for-2020)3105 Genetics (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Stem Cell Research (rcdc)Human Genome (rcdc)Stem Cell Research - Embryonic - Non-Human (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)X chromosome inactivationXistH3K9 methylationAtf7ipMcaf1Mbd1Setdb1Atf7ipH3K9 methylationMbd1Mcaf1Setdb1X chromosome inactivationXist0604 Genetics (for)3105 Genetics (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/9pf4p8tthttps://escholarship.org/content/qt9pf4p8tt/qt9pf4p8tt.pdfinfo:doi/10.1186/1756-8935-7-12articleEpigenetics & Chromatin, vol 7, iss 112oai:escholarship.org:ark:/13030/qt0cb4h8bs2026-08-14T06:14:38Zqt0cb4h8bsEvolution of histone 2A for chromatin compaction in eukaryotesMacadangdang, Benjamin ROberai, AmitSpektor, TanyaCampos, Oscar ASheng, FangCarey, Michael FVogelauer, MariaKurdistani, Siavash K2014-01-01During eukaryotic evolution, genome size has increased disproportionately to nuclear volume, necessitating greater degrees of chromatin compaction in higher eukaryotes, which have evolved several mechanisms for genome compaction. However, it is unknown whether histones themselves have evolved to regulate chromatin compaction. Analysis of histone sequences from 160 eukaryotes revealed that the H2A N-terminus has systematically acquired arginines as genomes expanded. Insertion of arginines into their evolutionarily conserved position in H2A of a small-genome organism increased linear compaction by as much as 40%, while their absence markedly diminished compaction in cells with large genomes. This effect was recapitulated in vitro with nucleosomal arrays using unmodified histones, indicating that the H2A N-terminus directly modulates the chromatin fiber likely through intra- and inter-nucleosomal arginine-DNA contacts to enable tighter nucleosomal packing. Our findings reveal a novel evolutionary mechanism for regulation of chromatin compaction and may explain the frequent mutations of the H2A N-terminus in cancer.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)Genetics (rcdc)Cancer (rcdc)Human Genome (rcdc)Cancer Genomics (rcdc)Generic health relevance (hrcs-hc)Animals (mesh)Arginine (mesh)Cell LineTumor (mesh)Chromatin (mesh)Chromatin Assembly and Disassembly (mesh)EvolutionMolecular (mesh)GenomeFungal (mesh)HEK293 Cells (mesh)Histones (mesh)Humans (mesh)Neoplasms (mesh)Nucleosomes (mesh)Protein StructureTertiary (mesh)Saccharomyces cerevisiae (mesh)Xenopus laevis (mesh)Cell LineTumor (mesh)Chromatin (mesh)Nucleosomes (mesh)Animals (mesh)Xenopus laevis (mesh)Humans (mesh)Saccharomyces cerevisiae (mesh)Neoplasms (mesh)Arginine (mesh)Histones (mesh)EvolutionMolecular (mesh)Chromatin Assembly and Disassembly (mesh)Protein StructureTertiary (mesh)GenomeFungal (mesh)HEK293 Cells (mesh)S. cerevisiaeargininecell biologychromatinevolutionevolutionary biologygenomicshumanxenopusAnimals (mesh)Arginine (mesh)Cell LineTumor (mesh)Chromatin (mesh)Chromatin Assembly and Disassembly (mesh)EvolutionMolecular (mesh)GenomeFungal (mesh)HEK293 Cells (mesh)Histones (mesh)Humans (mesh)Neoplasms (mesh)Nucleosomes (mesh)Protein StructureTertiary (mesh)Saccharomyces cerevisiae (mesh)Xenopus laevis (mesh)0601 Biochemistry and Cell Biology (for)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/0cb4h8bshttps://escholarship.org/content/qt0cb4h8bs/qt0cb4h8bs.pdfinfo:doi/10.7554/elife.02792articleELIFE, vol 3, iss 3e02792oai:escholarship.org:ark:/13030/qt9jx4r4s52026-08-14T00:32:54Zqt9jx4r4s5Data publication with the structural biology data grid supports live analysisMeyer, Peter ASocias, StephanieKey, JasonRansey, ElizabethTjon, Emily CBuschiazzo, AlejandroLei, MingBotka, ChrisWithrow, JamesNeau, DavidRajashankar, KanagalaghattaAnderson, Karen SBaxter, Richard HBlacklow, Stephen CBoggon, Titus JBonvin, Alexandre MJJBorek, DominikaBrett, Tom JCaflisch, AmedeoChang, Chung-IChazin, Walter JCorbett, Kevin DCosgrove, Michael SCrosson, SeanDhe-Paganon, SiranoDi Cera, EnricoDrennan, Catherine LEck, Michael JEichman, Brandt FFan, Qing RFerré-D'Amaré, Adrian RChristopher Fromme, JGarcia, K ChristopherGaudet, RachelleGong, PengHarrison, Stephen CHeldwein, Ekaterina EJia, ZongchaoKeenan, Robert JKruse, Andrew CKvansakul, MarcMcLellan, Jason SModis, YorgoNam, YunsunOtwinowski, ZbyszekPai, Emil FPereira, Pedro José BarbosaPetosa, CarloRaman, CSRapoport, Tom ARoll-Mecak, AntoninaRosen, Michael KRudenko, GabbySchlessinger, JosephSchwartz, Thomas UShamoo, YousifSondermann, HolgerTao, Yizhi JTolia, Niraj HTsodikov, Oleg VWestover, Kenneth DWu, HaoFoster, IanFraser, James SMaia, Filipe RNCGonen, TamirKirchhausen, TomDiederichs, KayCrosas, MercèSliz, Piotr2016-03-01Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. It is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)1.5 Resources and infrastructure (underpinning) (hrcs-rac)CrystallographyX-Ray (mesh)DatabasesGenetic (mesh)Internet (mesh)Macromolecular Substances (mesh)Publications (mesh)Software (mesh)Macromolecular Substances (mesh)CrystallographyX-Ray (mesh)Publications (mesh)Internet (mesh)Software (mesh)DatabasesGenetic (mesh)CrystallographyX-Ray (mesh)DatabasesGenetic (mesh)Internet (mesh)Macromolecular Substances (mesh)Publications (mesh)Software (mesh)Macromolecular SubstancesCrystallographyX-RayPublicationsInternetSoftwareDatabasesGeneticapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9jx4r4s5https://escholarship.org/content/qt9jx4r4s5/qt9jx4r4s5.pdfinfo:doi/10.1038/ncomms10882articleNature Communications, vol 7, iss 110882oai:escholarship.org:ark:/13030/qt91b1q0rr2026-08-13T21:42:12Zqt91b1q0rrCell biological mechanisms of activity-dependent synapse to nucleus translocation of CRTC1 in neuronsCh'ng, Toh HeanDeSalvo, MartinaLin, PeterVashisht, AjayWohlschlegel, James AMartin, Kelsey C2015-09-04Previous studies have revealed a critical role for CREB-regulated transcriptional coactivator (CRTC1) in regulating neuronal gene expression during learning and memory. CRTC1 localizes to synapses but undergoes activity-dependent nuclear translocation to regulate the transcription of CREB target genes. Here we investigate the long-distance retrograde transport of CRTC1 in hippocampal neurons. We show that local elevations in calcium, triggered by activation of glutamate receptors and L-type voltage-gated calcium channels, initiate active, dynein-mediated retrograde transport of CRTC1 along microtubules. We identify a nuclear localization signal within CRTC1, and characterize three conserved serine residues whose dephosphorylation is required for nuclear import. Domain analysis reveals that the amino-terminal third of CRTC1 contains all of the signals required for regulated nucleocytoplasmic trafficking. We fuse this region to Dendra2 to generate a reporter construct and perform live-cell imaging coupled with local uncaging of glutamate and photoconversion to characterize the dynamics of stimulus-induced retrograde transport and nuclear accumulation.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)3209 Neurosciences (for-2020)31 Biological Sciences (for-2020)Neurosciences (rcdc)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Neurological (hrcs-hc)CREBCRTC1learning and memorysynapse to nucleus signalingsynaptic plasticitytranscription-dependent plasticityactive transportCREBCRTC1active transportlearning and memorysynapse to nucleus signalingsynaptic plasticitytranscription-dependent plasticity1103 Clinical Sciences (for)1109 Neurosciences (for)3101 Biochemistry and cell biology (for-2020)3209 Neurosciences (for-2020)5202 Biological psychology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/91b1q0rrhttps://escholarship.org/content/qt91b1q0rr/qt91b1q0rr.pdfinfo:doi/10.3389/fnmol.2015.00048articleFrontiers in Molecular Neuroscience, vol 8, iss september48oai:escholarship.org:ark:/13030/qt5kz4z04z2026-08-13T21:36:24Zqt5kz4z04zMYC-induced reprogramming of glutamine catabolism supports optimal virus replicationThai, MinhThaker, Shivani KFeng, JunDu, YushenHu, HailiangTing Wu, TingGraeber, Thomas GBraas, DanielChristofk, Heather R2015-11-01Viruses rewire host cell glucose and glutamine metabolism to meet the bioenergetic and biosynthetic demands of viral propagation. However, the mechanism by which viruses reprogram glutamine metabolism and the metabolic fate of glutamine during adenovirus infection have remained elusive. Here, we show MYC activation is necessary for adenovirus-induced upregulation of host cell glutamine utilization and increased expression of glutamine transporters and glutamine catabolism enzymes. Adenovirus-induced MYC activation promotes increased glutamine uptake, increased use of glutamine in reductive carboxylation and increased use of glutamine in generating hexosamine pathway intermediates and specific amino acids. We identify glutaminase (GLS) as a critical enzyme for optimal adenovirus replication and demonstrate that GLS inhibition decreases replication of adenovirus, herpes simplex virus 1 and influenza A in cultured primary cells. Our findings show that adenovirus-induced reprogramming of glutamine metabolism through MYC activation promotes optimal progeny virion generation, and suggest that GLS inhibitors may be useful therapeutically to reduce replication of diverse viruses.3101 Biochemistry and Cell Biology (for-2020)3207 Medical Microbiology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Infectious Diseases (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Infection (hrcs-hc)Adenoviridae (mesh)Cell Line (mesh)Glutamine (mesh)Humans (mesh)Mutation (mesh)Proto-Oncogene Proteins c-myc (mesh)Virus Replication (mesh)Cell Line (mesh)Humans (mesh)Adenoviridae (mesh)Glutamine (mesh)Proto-Oncogene Proteins c-myc (mesh)Virus Replication (mesh)Mutation (mesh)Adenoviridae (mesh)Cell Line (mesh)Glutamine (mesh)Humans (mesh)Mutation (mesh)Proto-Oncogene Proteins c-myc (mesh)Virus Replication (mesh)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/5kz4z04zinfo:doi/10.1038/ncomms9873articleNature Communications, vol 6, iss 18873oai:escholarship.org:ark:/13030/qt1586z5182026-08-13T21:25:59Zqt1586z518DNA Sequence Determinants Controlling Affinity, Stability and Shape of DNA Complexes Bound by the Nucleoid Protein FisHancock, Stephen PStella, StefanoCascio, DuilioJohnson, Reid CLeng, Fenfei2016-03-09The abundant Fis nucleoid protein selectively binds poorly related DNA sequences with high affinities to regulate diverse DNA reactions. Fis binds DNA primarily through DNA backbone contacts and selects target sites by reading conformational properties of DNA sequences, most prominently intrinsic minor groove widths. High-affinity binding requires Fis-stabilized DNA conformational changes that vary depending on DNA sequence. In order to better understand the molecular basis for high affinity site recognition, we analyzed the effects of DNA sequence within and flanking the core Fis binding site on binding affinity and DNA structure. X-ray crystal structures of Fis-DNA complexes containing variable sequences in the noncontacted center of the binding site or variations within the major groove interfaces show that the DNA can adapt to the Fis dimer surface asymmetrically. We show that the presence and position of pyrimidine-purine base steps within the major groove interfaces affect both local DNA bending and minor groove compression to modulate affinities and lifetimes of Fis-DNA complexes. Sequences flanking the core binding site also modulate complex affinities, lifetimes, and the degree of local and global Fis-induced DNA bending. In particular, a G immediately upstream of the 15 bp core sequence inhibits binding and bending, and A-tracts within the flanking base pairs increase both complex lifetimes and global DNA curvatures. Taken together, our observations support a revised DNA motif specifying high-affinity Fis binding and highlight the range of conformations that Fis-bound DNA can adopt. The affinities and DNA conformations of individual Fis-DNA complexes are likely to be tailored to their context-specific biological functions.3101 Biochemistry and Cell Biology (for-2020)34 Chemical Sciences (for-2020)31 Biological Sciences (for-2020)Generic health relevance (hrcs-hc)Base Pairing (mesh)Base Sequence (mesh)Binding Sites (mesh)CrystallographyX-Ray (mesh)DNA (mesh)Factor For Inversion Stimulation Protein (mesh)Molecular Sequence Data (mesh)Nucleic Acid Conformation (mesh)Protein Binding (mesh)Protein Stability (mesh)Factor For Inversion Stimulation Protein (mesh)DNA (mesh)CrystallographyX-Ray (mesh)Binding Sites (mesh)Base Sequence (mesh)Nucleic Acid Conformation (mesh)Base Pairing (mesh)Protein Binding (mesh)Molecular Sequence Data (mesh)Protein Stability (mesh)Base Pairing (mesh)Base Sequence (mesh)Binding Sites (mesh)CrystallographyX-Ray (mesh)DNA (mesh)Factor For Inversion Stimulation Protein (mesh)Molecular Sequence Data (mesh)Nucleic Acid Conformation (mesh)Protein Binding (mesh)Protein Stability (mesh)General Science & Technology (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/1586z518https://escholarship.org/content/qt1586z518/qt1586z518.pdfinfo:doi/10.1371/journal.pone.0150189articlePLOS ONE, vol 11, iss 3e0150189oai:escholarship.org:ark:/13030/qt8ws7114h2026-08-13T19:44:57Zqt8ws7114hIdentification of the Mitochondrial Heme Metabolism ComplexMedlock, Amy EShiferaw, Mesafint TMarcero, Jason RVashisht, Ajay AWohlschlegel, James APhillips, John DDailey, Harry ALiesa, Marc2015-08-19Heme is an essential cofactor for most organisms and all metazoans. While the individual enzymes involved in synthesis and utilization of heme are fairly well known, less is known about the intracellular trafficking of porphyrins and heme, or regulation of heme biosynthesis via protein complexes. To better understand this process we have undertaken a study of macromolecular assemblies associated with heme synthesis. Herein we have utilized mass spectrometry with coimmunoprecipitation of tagged enzymes of the heme biosynthetic pathway in a developing erythroid cell culture model to identify putative protein partners. The validity of these data obtained in the tagged protein system is confirmed by normal porphyrin/heme production by the engineered cells. Data obtained are consistent with the presence of a mitochondrial heme metabolism complex which minimally consists of ferrochelatase, protoporphyrinogen oxidase and aminolevulinic acid synthase-2. Additional proteins involved in iron and intermediary metabolism as well as mitochondrial transporters were identified as potential partners in this complex. The data are consistent with the known location of protein components and support a model of transient protein-protein interactions within a dynamic protein complex.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Hematology (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)5-Aminolevulinate Synthetase (mesh)ATP-Binding Cassette Transporters (mesh)Animals (mesh)Cell LineTumor (mesh)Ferrochelatase (mesh)Heme (mesh)Humans (mesh)Mice (mesh)Mitochondria (mesh)Multiprotein Complexes (mesh)Porphyrins (mesh)Protoporphyrinogen Oxidase (mesh)Cell LineTumor (mesh)Mitochondria (mesh)Animals (mesh)Humans (mesh)Mice (mesh)Porphyrins (mesh)Heme (mesh)Multiprotein Complexes (mesh)Ferrochelatase (mesh)5-Aminolevulinate Synthetase (mesh)ATP-Binding Cassette Transporters (mesh)Protoporphyrinogen Oxidase (mesh)5-Aminolevulinate Synthetase (mesh)ATP-Binding Cassette Transporters (mesh)Animals (mesh)Cell LineTumor (mesh)Ferrochelatase (mesh)Heme (mesh)Humans (mesh)Mice (mesh)Mitochondria (mesh)Multiprotein Complexes (mesh)Porphyrins (mesh)Protoporphyrinogen Oxidase (mesh)General Science & Technology (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/8ws7114hhttps://escholarship.org/content/qt8ws7114h/qt8ws7114h.pdfinfo:doi/10.1371/journal.pone.0135896articlePLOS ONE, vol 10, iss 8e0135896oai:escholarship.org:ark:/13030/qt6bw2n16j2026-08-13T19:42:55Zqt6bw2n16jDefining metabolic flexibility in hair follicle stem cell induced squamous cell carcinomaGalvan, CarlosFlores, Aimee ACerrilos, VictoriaAvila, ItzetlMurphy, ConorZheng, WilsonChristofk, Heather RLowry, William E2024-09-20We previously showed that inhibition of glycolysis in cutaneous squamous cell carcinoma (SCC)-initiating cells had no effect on tumorigenesis, despite the perceived requirement of the Warburg effect, which was thought to drive carcinogenesis. Instead, these SCCs were metabolically flexible and sustained growth through glutaminolysis, another metabolic process frequently implicated to fuel tumorigenesis in various cancers. Here, we focused on glutaminolysis and genetically blocked this process through glutaminase (GLS) deletion in SCC cells of origin. Genetic deletion of GLS had little effect on tumorigenesis due to the up-regulated lactate consumption and utilization for the TCA cycle, providing further evidence of metabolic flexibility. We went on to show that posttranscriptional regulation of nutrient transporters appears to mediate metabolic flexibility in this SCC model. To define the limits of this flexibility, we genetically blocked both glycolysis and glutaminolysis simultaneously and found the abrogation of both of these carbon utilization pathways was enough to prevent both papilloma and frank carcinoma.31 Biological Sciences (for-2020)32 Biomedical and Clinical Sciences (for-2020)3211 Oncology and Carcinogenesis (for-2020)Stem Cell Research (rcdc)Cancer (rcdc)Stem Cell Research - Nonembryonic - Non-Human (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Cancer (hrcs-hc)CarcinomaSquamous Cell (mesh)Animals (mesh)Hair Follicle (mesh)Glutaminase (mesh)Mice (mesh)Glycolysis (mesh)Skin Neoplasms (mesh)Stem Cells (mesh)Glutamine (mesh)Humans (mesh)Cell TransformationNeoplastic (mesh)Carcinogenesis (mesh)Hair Follicle (mesh)Stem Cells (mesh)Animals (mesh)Humans (mesh)Mice (mesh)CarcinomaSquamous Cell (mesh)Skin Neoplasms (mesh)Cell TransformationNeoplastic (mesh)Glutaminase (mesh)Glutamine (mesh)Glycolysis (mesh)Carcinogenesis (mesh)CarcinomaSquamous Cell (mesh)Animals (mesh)Hair Follicle (mesh)Glutaminase (mesh)Mice (mesh)Glycolysis (mesh)Skin Neoplasms (mesh)Stem Cells (mesh)Glutamine (mesh)Humans (mesh)Cell TransformationNeoplastic (mesh)Carcinogenesis (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/6bw2n16jhttps://escholarship.org/content/qt6bw2n16j/qt6bw2n16j.pdfinfo:doi/10.1126/sciadv.adn2806articleScience Advances, vol 10, iss 38eadn2806oai:escholarship.org:ark:/13030/qt1535z6612026-08-13T19:38:29Zqt1535z661Anthrax Lethal Toxin Induced Lysosomal Membrane Permeabilization and Cytosolic Cathepsin Release Is Nlrp1b/Nalp1b-DependentAverette, Kathleen MPratt, Matthew RYang, YananBassilian, SaraWhitelegge, Julian PLoo, Joseph AMuir, Tom WBradley, Kenneth ARatner, Adam J2009-11-18NOD-like receptors (NLRs) are a group of cytoplasmic molecules that recognize microbial invasion or 'danger signals'. Activation of NLRs can induce rapid caspase-1 dependent cell death termed pyroptosis, or a caspase-1 independent cell death termed pyronecrosis. Bacillus anthracis lethal toxin (LT), is recognized by a subset of alleles of the NLR protein Nlrp1b, resulting in pyroptotic cell death of macrophages and dendritic cells. Here we show that LT induces lysosomal membrane permeabilization (LMP). The presentation of LMP requires expression of an LT-responsive allele of Nlrp1b, and is blocked by proteasome inhibitors and heat shock, both of which prevent LT-mediated pyroptosis. Further the lysosomal protease cathepsin B is released into the cell cytosol and cathepsin inhibitors block LT-mediated cell death. These data reveal a role for lysosomal membrane permeabilization in the cellular response to bacterial pathogens and demonstrate a shared requirement for cytosolic relocalization of cathepsins in pyroptosis and pyronecrosis.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Infectious Diseases (rcdc)Anthrax (rcdc)Emerging Infectious Diseases (rcdc)Orphan Drug (rcdc)Rare Diseases (rcdc)Biodefense (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Infection (hrcs-hc)Adaptor ProteinsSignal Transducing (mesh)Alleles (mesh)Animals (mesh)AntigensBacterial (mesh)Apoptosis Regulatory Proteins (mesh)Bacillus anthracis (mesh)Bacterial Toxins (mesh)Cathepsin B (mesh)Cell Line (mesh)Cytosol (mesh)Lysosomes (mesh)Macrophages (mesh)Mice (mesh)MiceInbred C57BL (mesh)ModelsBiological (mesh)NLR Proteins (mesh)Necrosis (mesh)Proteasome Endopeptidase Complex (mesh)Cell Line (mesh)Lysosomes (mesh)Cytosol (mesh)Macrophages (mesh)Animals (mesh)MiceInbred C57BL (mesh)Mice (mesh)Bacillus anthracis (mesh)Necrosis (mesh)Proteasome Endopeptidase Complex (mesh)Cathepsin B (mesh)Adaptor ProteinsSignal Transducing (mesh)Bacterial Toxins (mesh)AntigensBacterial (mesh)Alleles (mesh)ModelsBiological (mesh)Apoptosis Regulatory Proteins (mesh)NLR Proteins (mesh)Adaptor ProteinsSignal Transducing (mesh)Alleles (mesh)Animals (mesh)AntigensBacterial (mesh)Apoptosis Regulatory Proteins (mesh)Bacillus anthracis (mesh)Bacterial Toxins (mesh)Cathepsin B (mesh)Cell Line (mesh)Cytosol (mesh)Lysosomes (mesh)Macrophages (mesh)Mice (mesh)MiceInbred C57BL (mesh)ModelsBiological (mesh)NLR Proteins (mesh)Necrosis (mesh)Proteasome Endopeptidase Complex (mesh)General Science & Technology (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/1535z661https://escholarship.org/content/qt1535z661/qt1535z661.pdfinfo:doi/10.1371/journal.pone.0007913articlePLOS ONE, vol 4, iss 11e7913oai:escholarship.org:ark:/13030/qt9t79q6012026-08-13T18:24:13Zqt9t79q601ACD15, ACD21, and SLN regulate the accumulation and mobility of MBD6 to silence genes and transposable elementsBoone, Brandon AIchino, LuciaWang, ShuyaGardiner, JasonYun, JaewonJami-Alahmadi, YasamanSha, JihuiMendoza, Cristy PSteelman, Bailey Jvan Aardenne, AliyaKira-Lucas, SophiaTrentchev, IsabelleWohlschlegel, James AJacobsen, Steven E2023-11-17DNA methylation mediates silencing of transposable elements and genes in part via recruitment of the Arabidopsis MBD5/6 complex, which contains the methyl-CpG binding domain (MBD) proteins MBD5 and MBD6, and the J-domain containing protein SILENZIO (SLN). Here, we characterize two additional complex members: α-crystalline domain (ACD) containing proteins ACD15 and ACD21. We show that they are necessary for gene silencing, bridge SLN to the complex, and promote higher-order multimerization of MBD5/6 complexes within heterochromatin. These complexes are also highly dynamic, with the mobility of MBD5/6 complexes regulated by the activity of SLN. Using a dCas9 system, we demonstrate that tethering the ACDs to an ectopic site outside of heterochromatin can drive a massive accumulation of MBD5/6 complexes into large nuclear bodies. These results demonstrate that ACD15 and ACD21 are critical components of the gene-silencing MBD5/6 complex and act to drive the formation of higher-order, dynamic assemblies at CG methylation (meCG) sites.31 Biological Sciences (for-2020)3105 Genetics (for-2020)Genetics (rcdc)Human Genome (rcdc)Biotechnology (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)DNA-Binding Proteins (mesh)Heterochromatin (mesh)DNA Transposable Elements (mesh)Arabidopsis (mesh)DNA Methylation (mesh)Arabidopsis Proteins (mesh)Heterochromatin (mesh)Arabidopsis (mesh)DNA-Binding Proteins (mesh)Arabidopsis Proteins (mesh)DNA Transposable Elements (mesh)DNA Methylation (mesh)DNA-Binding Proteins (mesh)Heterochromatin (mesh)DNA Transposable Elements (mesh)Arabidopsis (mesh)DNA Methylation (mesh)Arabidopsis Proteins (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/9t79q601https://escholarship.org/content/qt9t79q601/qt9t79q601.pdfinfo:doi/10.1126/sciadv.adi9036articleScience Advances, vol 9, iss 46eadi9036oai:escholarship.org:ark:/13030/qt92h2c60t2026-08-13T13:25:03Zqt92h2c60tVariability of rRNA Operon Copy Number and Growth Rate Dynamics of Bacillus Isolated from an Extremely Oligotrophic Aquatic EcosystemValdivia-Anistro, Jorge AEguiarte-Fruns, Luis EDelgado-Sapién, GabrielaMárquez-Zacarías, PedroGasca-Pineda, JaimeLearned, JenniferElser, James JOlmedo-Alvarez, GabrielaSouza, Valeria2016-09-13The ribosomal RNA (rrn) operon is a key suite of genes related to the production of protein synthesis machinery and thus to bacterial growth physiology. Experimental evidence has suggested an intrinsic relationship between the number of copies of this operon and environmental resource availability, especially the availability of phosphorus (P), because bacteria that live in oligotrophic ecosystems usually have few rrn operons and a slow growth rate. The Cuatro Ciénegas Basin (CCB) is a complex aquatic ecosystem that contains an unusually high microbial diversity that is able to persist under highly oligotrophic conditions. These environmental conditions impose a variety of strong selective pressures that shape the genome dynamics of their inhabitants. The genus Bacillus is one of the most abundant cultivable bacterial groups in the CCB and usually possesses a relatively large number of rrn operon copies (6-15 copies). The main goal of this study was to analyze the variation in the number of rrn operon copies of Bacillus in the CCB and to assess their growth-related properties as well as their stoichiometric balance (N and P content). We defined 18 phylogenetic groups within the Bacilli clade and documented a range of from six to 14 copies of the rrn operon. The growth dynamic of these Bacilli was heterogeneous and did not show a direct relation to the number of operon copies. Physiologically, our results were not consistent with the Growth Rate Hypothesis, since the copies of the rrn operon were decoupled from growth rate. However, we speculate that the diversity of the growth properties of these Bacilli as well as the low P content of their cells in an ample range of rrn copy number is an adaptive response to oligotrophy of the CCB and could represent an ecological mechanism that allows these taxa to coexist. These findings increase the knowledge of the variability in the number of copies of the rrn operon in the genus Bacillus and give insights about the physiology of this bacterial group under extreme oligotrophic conditions.3107 Microbiology (for-2020)31 Biological Sciences (for-2020)3103 Ecology (for-2020)Genetics (rcdc)3107 Microbiology (for-2020)3207 Medical Microbiology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Biodefense (rcdc)Infectious Diseases (rcdc)Emerging Infectious Diseases (rcdc)2.1 Biological and endogenous factors (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)Infection (hrcs-hc)Inflammatory and immune system (hrcs-hc)N.caninumimmuneresponsep38/MAPkevasionIL-12IL-12N. caninumevasionimmune responsep38/MAPk0502 Environmental Science and Management (for)0503 Soil Sciences (for)0605 Microbiology (for)3107 Microbiology (for-2020)3207 Medical microbiology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/92h2c60thttps://escholarship.org/content/qt92h2c60t/qt92h2c60t.pdfinfo:doi/10.3389/fmicb.2015.01486articleFrontiers in Microbiology, vol 61486oai:escholarship.org:ark:/13030/qt74r8m9522026-08-13T13:24:29Zqt74r8m952In Vivo Biotinylation of the Toxoplasma Parasitophorous Vacuole Reveals Novel Dense Granule Proteins Important for Parasite Growth and PathogenesisNadipuram, Santhosh MKim, Elliot WVashisht, Ajay ALin, Andrew HBell, Hannah NCoppens, IsabelleWohlschlegel, James ABradley, Peter JBoothroyd, John C2016-09-07Toxoplasma gondii is an obligate intracellular parasite that invades host cells and replicates within a unique parasitophorous vacuole. To maintain this intracellular niche, the parasite secretes an array of dense granule proteins (GRAs) into the nascent parasitophorous vacuole. These GRAs are believed to play key roles in vacuolar remodeling, nutrient uptake, and immune evasion while the parasite is replicating within the host cell. Despite the central role of GRAs in the Toxoplasma life cycle, only a subset of these proteins have been identified, and many of their roles have not been fully elucidated. In this report, we utilize the promiscuous biotin ligase BirA* to biotinylate GRA proteins secreted into the vacuole and then identify those proteins by affinity purification and mass spectrometry. Using GRA-BirA* fusion proteins as bait, we have identified a large number of known and candidate GRAs and verified localization of 13 novel GRA proteins by endogenous gene tagging. We proceeded to functionally characterize three related GRAs from this group (GRA38, GRA39, and GRA40) by gene knockout. While Δgra38 and Δgra40 parasites showed no altered phenotype, disruption of GRA39 results in slow-growing parasites that contain striking lipid deposits in the parasitophorous vacuole, suggesting a role in lipid regulation that is important for parasite growth. In addition, parasites lacking GRA39 showed dramatically reduced virulence and a lower tissue cyst burden in vivo Together, the findings from this work reveal a partial vacuolar proteome of T. gondii and identify a novel GRA that plays a key role in parasite replication and pathogenesis.
IMPORTANCE: Most intracellular pathogens reside inside a membrane-bound vacuole within their host cell that is extensively modified by the pathogen to optimize intracellular growth and avoid host defenses. In Toxoplasma, this vacuole is modified by a host of secretory GRA proteins, many of which remain unidentified. Here we demonstrate that in vivo biotinylation of proximal and interacting proteins using the promiscuous biotin ligase BirA* is a powerful approach to rapidly identify vacuolar GRA proteins. We further demonstrate that one factor identified by this approach, GRA39, plays an important role in the ability of the parasite to replicate within its host cell and cause disease.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Biodefense (rcdc)Infectious Diseases (rcdc)Emerging Infectious Diseases (rcdc)2.1 Biological and endogenous factors (hrcs-rac)2.2 Factors relating to the physical environment (hrcs-rac)Infection (hrcs-hc)Biotinylation (mesh)CellsCultured (mesh)ChromatographyAffinity (mesh)Fibroblasts (mesh)Humans (mesh)Mass Spectrometry (mesh)Protozoan Proteins (mesh)Staining and Labeling (mesh)Toxoplasma (mesh)Vacuoles (mesh)Virulence Factors (mesh)CellsCultured (mesh)Vacuoles (mesh)Fibroblasts (mesh)Humans (mesh)Toxoplasma (mesh)Protozoan Proteins (mesh)Virulence Factors (mesh)ChromatographyAffinity (mesh)Staining and Labeling (mesh)Biotinylation (mesh)Mass Spectrometry (mesh)Biotinylation (mesh)CellsCultured (mesh)ChromatographyAffinity (mesh)Fibroblasts (mesh)Humans (mesh)Mass Spectrometry (mesh)Protozoan Proteins (mesh)Staining and Labeling (mesh)Toxoplasma (mesh)Vacuoles (mesh)Virulence Factors (mesh)0605 Microbiology (for)3101 Biochemistry and cell biology (for-2020)3107 Microbiology (for-2020)3207 Medical microbiology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/74r8m952https://escholarship.org/content/qt74r8m952/qt74r8m952.pdfinfo:doi/10.1128/mbio.00808-16articlemBio, vol 7, iss 410.1128/mbio.00808 - 10.1128/mbio.00816oai:escholarship.org:ark:/13030/qt04b2j2qc2026-08-13T13:09:14Zqt04b2j2qcSHH1, a Homeodomain Protein Required for DNA Methylation, As Well As RDR2, RDM4, and Chromatin Remodeling Factors, Associate with RNA Polymerase IVLaw, Julie AVashisht, Ajay AWohlschlegel, James AJacobsen, Steven ECopenhaver, Gregory P2011-07-01DNA methylation is an evolutionarily conserved epigenetic modification that is critical for gene silencing and the maintenance of genome integrity. In Arabidopsis thaliana, the de novo DNA methyltransferase, domains rearranged methyltransferase 2 (DRM2), is targeted to specific genomic loci by 24 nt small interfering RNAs (siRNAs) through a pathway termed RNA-directed DNA methylation (RdDM). Biogenesis of the targeting siRNAs is thought to be initiated by the activity of the plant-specific RNA polymerase IV (Pol-IV). However, the mechanism through which Pol-IV is targeted to specific genomic loci and whether factors other than the core Pol-IV machinery are required for Pol-IV activity remain unknown. Through the affinity purification of nuclear RNA polymerase D1 (NRPD1), the largest subunit of the Pol-IV polymerase, we found that several previously identified RdDM components co-purify with Pol-IV, namely RNA-dependent RNA polymerase 2 (RDR2), CLASSY1 (CLSY1), and RNA-directed DNA methylation 4 (RDM4), suggesting that the upstream siRNA generating portion of the RdDM pathway may be more physically coupled than previously envisioned. A homeodomain protein, SAWADEE homeodomain homolog 1 (SHH1), was also found to co-purify with NRPD1; and we demonstrate that SHH1 is required for de novo and maintenance DNA methylation, as well as for the accumulation of siRNAs at specific loci, confirming it is a bonafide component of the RdDM pathway.3108 Plant Biology (for-2020)31 Biological Sciences (for-2020)3105 Genetics (for-2020)Biotechnology (rcdc)Genetics (rcdc)Human Genome (rcdc)Generic health relevance (hrcs-hc)Arabidopsis (mesh)Arabidopsis Proteins (mesh)Chromatin Assembly and Disassembly (mesh)DNA Methylation (mesh)DNA Polymerase beta (mesh)DNA-Directed RNA Polymerases (mesh)Gene Expression RegulationPlant (mesh)Homeodomain Proteins (mesh)Immunoprecipitation (mesh)Intracellular Signaling Peptides and Proteins (mesh)Mutation (mesh)PlantsGenetically Modified (mesh)Protein Binding (mesh)Protein Subunits (mesh)RNASmall Interfering (mesh)RNA-Dependent RNA Polymerase (mesh)Reverse Transcriptase Polymerase Chain Reaction (mesh)PlantsGenetically Modified (mesh)Arabidopsis (mesh)DNA Polymerase beta (mesh)DNA-Directed RNA Polymerases (mesh)Intracellular Signaling Peptides and Proteins (mesh)Homeodomain Proteins (mesh)Arabidopsis Proteins (mesh)Protein Subunits (mesh)RNASmall Interfering (mesh)Reverse Transcriptase Polymerase Chain Reaction (mesh)Immunoprecipitation (mesh)Chromatin Assembly and Disassembly (mesh)DNA Methylation (mesh)Gene Expression RegulationPlant (mesh)Protein Binding (mesh)Mutation (mesh)RNA-Dependent RNA Polymerase (mesh)Arabidopsis (mesh)Arabidopsis Proteins (mesh)Chromatin Assembly and Disassembly (mesh)DNA Methylation (mesh)DNA Polymerase beta (mesh)DNA-Directed RNA Polymerases (mesh)Gene Expression RegulationPlant (mesh)Homeodomain Proteins (mesh)Immunoprecipitation (mesh)Intracellular Signaling Peptides and Proteins (mesh)Mutation (mesh)PlantsGenetically Modified (mesh)Protein Binding (mesh)Protein Subunits (mesh)RNASmall Interfering (mesh)RNA-Dependent RNA Polymerase (mesh)Reverse Transcriptase Polymerase Chain Reaction (mesh)0604 Genetics (for)Developmental Biology (science-metrix)3105 Genetics (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/04b2j2qchttps://escholarship.org/content/qt04b2j2qc/qt04b2j2qc.pdfinfo:doi/10.1371/journal.pgen.1002195articlePLOS Genetics, vol 7, iss 7e1002195oai:escholarship.org:ark:/13030/qt9q72d0dk2026-08-13T12:54:30Zqt9q72d0dkCRISPR-based targeting of DNA methylation in Arabidopsis thaliana by a bacterial CG-specific DNA methyltransferaseGhoshal, BasudevPicard, Colette LVong, BrandonFeng, SuhuaJacobsen, Steven E2021-06-08CRISPR-based targeted modification of epigenetic marks such as DNA cytosine methylation is an important strategy to regulate the expression of genes and their associated phenotypes. Although plants have DNA methylation in all sequence contexts (CG, CHG, CHH, where H = A, T, C), methylation in the symmetric CG context is particularly important for gene silencing and is very efficiently maintained through mitotic and meiotic cell divisions. Tools that can directly add CG methylation to specific loci are therefore highly desirable but are currently lacking in plants. Here we have developed two CRISPR-based CG-specific targeted DNA methylation systems for plants using a variant of the bacterial CG-specific DNA methyltransferase MQ1 with reduced activity but high specificity. We demonstrate that the methylation added by MQ1 is highly target specific and can be heritably maintained in the absence of the effector. These tools should be valuable both in crop engineering and in plant genetic research.3108 Plant Biology (for-2020)31 Biological Sciences (for-2020)3105 Genetics (for-2020)Biotechnology (rcdc)Genetics (rcdc)Arabidopsis (mesh)Bacterial Proteins (mesh)CRISPR-Cas Systems (mesh)DNA Methylation (mesh)DNAPlant (mesh)DNA-Cytosine Methylases (mesh)PlantsGenetically Modified (mesh)Tenericutes (mesh)DNA methylationArabidopsisCRISPR-Cas9 SunTagPlantsGenetically Modified (mesh)Arabidopsis (mesh)Bacterial Proteins (mesh)DNAPlant (mesh)DNA Methylation (mesh)DNA-Cytosine Methylases (mesh)Tenericutes (mesh)CRISPR-Cas Systems (mesh)ArabidopsisCRISPR-Cas9DNA methylationSunTagArabidopsis (mesh)Bacterial Proteins (mesh)CRISPR-Cas Systems (mesh)DNA Methylation (mesh)DNAPlant (mesh)DNA-Cytosine Methylases (mesh)PlantsGenetically Modified (mesh)Tenericutes (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/9q72d0dkhttps://escholarship.org/content/qt9q72d0dk/qt9q72d0dk.pdfinfo:doi/10.1073/pnas.2125016118articleProceedings of the National Academy of Sciences of the United States of America, vol 118, iss 23e2125016118oai:escholarship.org:ark:/13030/qt09v8x8nq2026-08-13T12:51:13Zqt09v8x8nqArabidopsis MORC proteins function in the efficient establishment of RNA directed DNA methylationXue, YanZhong, ZhenhuiHarris, C JakeGallego-Bartolomé, JavierWang, MingPicard, ColetteCao, XueshiHua, ShanKwok, IvyFeng, SuhuaJami-Alahmadi, YasamanSha, JihuiGardiner, JasonWohlschlegel, JamesJacobsen, Steven E2021-07-13The Microrchidia (MORC) family of ATPases are required for transposable element (TE) silencing and heterochromatin condensation in plants and animals, and C. elegans MORC-1 has been shown to topologically entrap and condense DNA. In Arabidopsis thaliana, mutation of MORCs has been shown to reactivate silent methylated genes and transposons and to decondense heterochromatic chromocenters, despite only minor changes in the maintenance of DNA methylation. Here we provide the first evidence localizing Arabidopsis MORC proteins to specific regions of chromatin and find that MORC4 and MORC7 are closely co-localized with sites of RNA-directed DNA methylation (RdDM). We further show that MORC7, when tethered to DNA by an artificial zinc finger, can facilitate the establishment of RdDM. Finally, we show that MORCs are required for the efficient RdDM mediated establishment of DNA methylation and silencing of a newly integrated FWA transgene, even though morc mutations have no effect on the maintenance of preexisting methylation at the endogenous FWA gene. We propose that MORCs function as a molecular tether in RdDM complexes to reinforce RdDM activity for methylation establishment. These findings have implications for MORC protein function in a variety of other eukaryotic organisms.3108 Plant Biology (for-2020)31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)3105 Genetics (for-2020)Human Genome (rcdc)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Adenosine Triphosphatases (mesh)Arabidopsis (mesh)Arabidopsis Proteins (mesh)DNA Methylation (mesh)Gene Expression RegulationPlant (mesh)Gene Silencing (mesh)Arabidopsis (mesh)Arabidopsis Proteins (mesh)DNA Methylation (mesh)Gene Expression RegulationPlant (mesh)Gene Silencing (mesh)Adenosine Triphosphatases (mesh)Adenosine Triphosphatases (mesh)Arabidopsis (mesh)Arabidopsis Proteins (mesh)DNA Methylation (mesh)Gene Expression RegulationPlant (mesh)Gene Silencing (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/09v8x8nqhttps://escholarship.org/content/qt09v8x8nq/qt09v8x8nq.pdfinfo:doi/10.1038/s41467-021-24553-3articleNature Communications, vol 12, iss 14292oai:escholarship.org:ark:/13030/qt3fq2250n2026-08-13T11:29:37Zqt3fq2250nLoss of Pten Causes Tumor Initiation Following Differentiation of Murine Pluripotent Stem Cells Due to Failed Repression of NanogLindgren, Anne GNatsuhara, KyleTian, EVincent, John JLi, XinminJiao, JingWu, HongBanerjee, UtpalClark, Amander TNguyen, Hang2011-01-27Pluripotent stem cells (PSCs) hold significant promise in regenerative medicine due to their unlimited capacity for self-renewal and potential to differentiate into every cell type in the body. One major barrier to the use of PSCs is their potential risk for tumor initiation following differentiation and transplantation in vivo. In the current study we sought to evaluate the role of the tumor suppressor Pten in murine PSC neoplastic progression. Using eight functional assays that have previously been used to indicate PSC adaptation or transformation, Pten null embryonic stem cells (ESCs) failed to rate as significant in five of them. Instead, our data demonstrate that the loss of Pten causes the emergence of a small number of aggressive, teratoma-initiating embryonic carcinoma cells (ECCs) during differentiation in vitro, while the remaining 90-95% of differentiated cells are non-tumorigenic. Furthermore, our data show that the mechanism by which Pten null ECCs emerge in vitro and cause tumors in vivo is through increased survival and self-renewal, due to failed repression of the transcription factor Nanog.3206 Medical Biotechnology (for-2020)32 Biomedical and Clinical Sciences (for-2020)Stem Cell Research - Nonembryonic - Non-Human (rcdc)Transplantation (rcdc)Stem Cell Research (rcdc)Cancer (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell - Human (rcdc)Stem Cell Research - Nonembryonic - Human (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell - Non-Human (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell (rcdc)Stem Cell Research - Embryonic - Non-Human (rcdc)Regenerative Medicine (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Animals (mesh)Cell Differentiation (mesh)Cell Survival (mesh)Cell TransformationNeoplastic (mesh)Embryonic Stem Cells (mesh)Homeodomain Proteins (mesh)Mice (mesh)Nanog Homeobox Protein (mesh)Neoplastic Stem Cells (mesh)PTEN Phosphohydrolase (mesh)Pluripotent Stem Cells (mesh)Pluripotent Stem Cells (mesh)Animals (mesh)Mice (mesh)Cell TransformationNeoplastic (mesh)Homeodomain Proteins (mesh)Cell Differentiation (mesh)Cell Survival (mesh)PTEN Phosphohydrolase (mesh)Embryonic Stem Cells (mesh)Neoplastic Stem Cells (mesh)Nanog Homeobox Protein (mesh)Animals (mesh)Cell Differentiation (mesh)Cell Survival (mesh)Cell TransformationNeoplastic (mesh)Embryonic Stem Cells (mesh)Homeodomain Proteins (mesh)Mice (mesh)Nanog Homeobox Protein (mesh)Neoplastic Stem Cells (mesh)PTEN Phosphohydrolase (mesh)Pluripotent Stem Cells (mesh)General Science & Technology (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/3fq2250nhttps://escholarship.org/content/qt3fq2250n/qt3fq2250n.pdfinfo:doi/10.1371/journal.pone.0016478articlePLOS ONE, vol 6, iss 1e16478oai:escholarship.org:ark:/13030/qt6r3949n02026-08-13T11:00:08Zqt6r3949n0Single Particle Electron Microscopy Analysis of the Bovine Anion Exchanger 1 Reveals a Flexible Linker Connecting the Cytoplasmic and Membrane DomainsJiang, JiansenMagilnick, NathanielTsirulnikov, KirillAbuladze, NataliaAtanasov, IvoGe, PengNarla, MohandasPushkin, AlexanderZhou, Z HongKurtz, IraKoval, Michael2013-01-01Anion exchanger 1 (AE1) is the major erythrocyte membrane protein that mediates chloride/bicarbonate exchange across the erythrocyte membrane facilitating CO₂ transport by the blood, and anchors the plasma membrane to the spectrin-based cytoskeleton. This multi-protein cytoskeletal complex plays an important role in erythrocyte elasticity and membrane stability. An in-frame AE1 deletion of nine amino acids in the cytoplasmic domain in a proximity to the membrane domain results in a marked increase in membrane rigidity and ovalocytic red cells in the disease Southeast Asian Ovalocytosis (SAO). We hypothesized that AE1 has a flexible region connecting the cytoplasmic and membrane domains, which is partially deleted in SAO, thus causing the loss of erythrocyte elasticity. To explore this hypothesis, we developed a new non-denaturing method of AE1 purification from bovine erythrocyte membranes. A three-dimensional (3D) structure of bovine AE1 at 2.4 nm resolution was obtained by negative staining electron microscopy, orthogonal tilt reconstruction and single particle analysis. The cytoplasmic and membrane domains are connected by two parallel linkers. Image classification demonstrated substantial flexibility in the linker region. We propose a mechanism whereby flexibility of the linker region plays a critical role in regulating red cell elasticity.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Animals (mesh)Anion Exchange Protein 1Erythrocyte (mesh)Cattle (mesh)Cytoplasm (mesh)ElectrophoresisPolyacrylamide Gel (mesh)Immunoblotting (mesh)MicroscopyElectron (mesh)Protein StructureTertiary (mesh)Cytoplasm (mesh)Animals (mesh)Cattle (mesh)Anion Exchange Protein 1Erythrocyte (mesh)MicroscopyElectron (mesh)Immunoblotting (mesh)ElectrophoresisPolyacrylamide Gel (mesh)Protein StructureTertiary (mesh)Animals (mesh)Anion Exchange Protein 1Erythrocyte (mesh)Cattle (mesh)Cytoplasm (mesh)ElectrophoresisPolyacrylamide Gel (mesh)Immunoblotting (mesh)MicroscopyElectron (mesh)Protein StructureTertiary (mesh)General Science & Technology (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/6r3949n0https://escholarship.org/content/qt6r3949n0/qt6r3949n0.pdfinfo:doi/10.1371/journal.pone.0055408articlePLOS ONE, vol 8, iss 2e55408oai:escholarship.org:ark:/13030/qt3hm191d02026-08-13T10:56:45Zqt3hm191d0The Metabolic Landscape of Thymic T Cell Development In Vivo and In VitroSun, VictoriaSharpley, MarkKaczor-Urbanowicz, Karolina EChang, PatrickMontel-Hagen, AmélieLopez, ShawnZampieri, AlexandreZhu, Yuhuade Barros, Stéphanie CParekh, ChintanCasero, DavidBanerjee, UtpalCrooks, Gay M2021-07-28Although metabolic pathways have been shown to control differentiation and activation in peripheral T cells, metabolic studies on thymic T cell development are still lacking, especially in human tissue. In this study, we use transcriptomics and extracellular flux analyses to investigate the metabolic profiles of primary thymic and in vitro-derived mouse and human thymocytes. Core metabolic pathways, specifically glycolysis and oxidative phosphorylation, undergo dramatic changes between the double-negative (DN), double-positive (DP), and mature single-positive (SP) stages in murine and human thymus. Remarkably, despite the absence of the complex multicellular thymic microenvironment, in vitro murine and human T cell development recapitulated the coordinated decrease in glycolytic and oxidative phosphorylation activity between the DN and DP stages seen in primary thymus. Moreover, by inducing in vitro T cell differentiation from Rag1-/- mouse bone marrow, we show that reduced metabolic activity at the DP stage is independent of TCR rearrangement. Thus, our findings suggest that highly conserved metabolic transitions are critical for thymic T cell development.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Inflammatory and immune system (hrcs-hc)Animals (mesh)Biological Evolution (mesh)Biomarkers (mesh)Cell Differentiation (mesh)Cell Line (mesh)Computational Biology (mesh)Energy Metabolism (mesh)Gene Expression Profiling (mesh)Hematopoietic Stem Cells (mesh)Humans (mesh)Lymphopoiesis (mesh)Metabolome (mesh)Metabolomics (mesh)Mice (mesh)Organoids (mesh)T-Lymphocytes (mesh)Thymocytes (mesh)Tissue Culture Techniques (mesh)thymusmetabolismT cellorganoidthymopoiesishumanmousein vitroOrganoids (mesh)T-Lymphocytes (mesh)Hematopoietic Stem Cells (mesh)Cell Line (mesh)Animals (mesh)Humans (mesh)Mice (mesh)Tissue Culture Techniques (mesh)Gene Expression Profiling (mesh)Computational Biology (mesh)Cell Differentiation (mesh)Lymphopoiesis (mesh)Energy Metabolism (mesh)Metabolomics (mesh)Metabolome (mesh)Biological Evolution (mesh)Thymocytes (mesh)Biomarkers (mesh)T cellhumanin vitrometabolismmouseorganoidthymopoiesisthymusAnimals (mesh)Biological Evolution (mesh)Biomarkers (mesh)Cell Differentiation (mesh)Cell Line (mesh)Computational Biology (mesh)Energy Metabolism (mesh)Gene Expression Profiling (mesh)Hematopoietic Stem Cells (mesh)Humans (mesh)Lymphopoiesis (mesh)Metabolome (mesh)Metabolomics (mesh)Mice (mesh)Organoids (mesh)T-Lymphocytes (mesh)Thymocytes (mesh)Tissue Culture Techniques (mesh)1107 Immunology (for)1108 Medical Microbiology (for)3101 Biochemistry and cell biology (for-2020)3105 Genetics (for-2020)3204 Immunology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/3hm191d0https://escholarship.org/content/qt3hm191d0/qt3hm191d0.pdfinfo:doi/10.3389/fimmu.2021.716661articleFrontiers in Immunology, vol 12716661oai:escholarship.org:ark:/13030/qt40g5h7502026-08-13T09:31:37Zqt40g5h750Structures of the Signal Recognition Particle Receptor from the Archaeon Pyrococcus furiosus: Implications for the Targeting Step at the MembraneEgea, Pascal FTsuruta, Hirode Leon, Gladys PNapetschnig, JohannaWalter, PeterStroud, Robert MZhang, Shuguang2008-01-01In all organisms, a ribonucleoprotein called the signal recognition particle (SRP) and its receptor (SR) target nascent proteins from the ribosome to the translocon for secretion or membrane insertion. We present the first X-ray structures of an archeal FtsY, the receptor from the hyper-thermophile Pyrococcus furiosus (Pfu), in its free and GDP*magnesium-bound forms. The highly charged N-terminal domain of Pfu-FtsY is distinguished by a long N-terminal helix. The basic charges on the surface of this helix are likely to regulate interactions at the membrane. A peripheral GDP bound near a regulatory motif could indicate a site of interaction between the receptor and ribosomal or SRP RNAs. Small angle X-ray scattering and analytical ultracentrifugation indicate that the crystal structure of Pfu-FtsY correlates well with the average conformation in solution. Based on previous structures of two sub-complexes, we propose a model of the core of archeal and eukaryotic SRP*SR targeting complexes.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Amino Acid Sequence (mesh)Arabidopsis Proteins (mesh)Cell Membrane (mesh)Chloroplast Proteins (mesh)CrystallographyX-Ray (mesh)DNA-Directed DNA Polymerase (mesh)Guanosine Diphosphate (mesh)Membrane Proteins (mesh)ModelsMolecular (mesh)Protein Binding (mesh)Protein Stability (mesh)Protein StructureSecondary (mesh)Protein StructureTertiary (mesh)Protein Transport (mesh)Pyrococcus furiosus (mesh)ReceptorsCytoplasmic and Nuclear (mesh)ReceptorsPeptide (mesh)Sequence HomologyAmino Acid (mesh)Cell Membrane (mesh)Pyrococcus furiosus (mesh)DNA-Directed DNA Polymerase (mesh)Membrane Proteins (mesh)ReceptorsPeptide (mesh)Arabidopsis Proteins (mesh)ReceptorsCytoplasmic and Nuclear (mesh)Guanosine Diphosphate (mesh)CrystallographyX-Ray (mesh)Amino Acid Sequence (mesh)Protein StructureSecondary (mesh)Protein StructureTertiary (mesh)Protein Binding (mesh)Sequence HomologyAmino Acid (mesh)Protein Transport (mesh)ModelsMolecular (mesh)Protein Stability (mesh)Chloroplast Proteins (mesh)Amino Acid Sequence (mesh)Arabidopsis Proteins (mesh)Cell Membrane (mesh)Chloroplast Proteins (mesh)CrystallographyX-Ray (mesh)DNA-Directed DNA Polymerase (mesh)Guanosine Diphosphate (mesh)Membrane Proteins (mesh)ModelsMolecular (mesh)Protein Binding (mesh)Protein Stability (mesh)Protein StructureSecondary (mesh)Protein StructureTertiary (mesh)Protein Transport (mesh)Pyrococcus furiosus (mesh)ReceptorsCytoplasmic and Nuclear (mesh)ReceptorsPeptide (mesh)Sequence HomologyAmino Acid (mesh)General Science & Technology (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/40g5h750https://escholarship.org/content/qt40g5h750/qt40g5h750.pdfinfo:doi/10.1371/journal.pone.0003619articlePLOS ONE, vol 3, iss 11e3619oai:escholarship.org:ark:/13030/qt661926qh2026-08-13T09:31:24Zqt661926qhInsights into the Mechanism of Bovine CD38/NAD+Glycohydrolase from the X-Ray Structures of Its Michaelis Complex and Covalently-Trapped IntermediatesEgea, Pascal FMuller-Steffner, HélèneKuhn, IsabelleCakir-Kiefer, CélineOppenheimer, Norman JStroud, Robert MKellenberger, EstherSchuber, FrancisVertessy, Beata G2012-01-01Bovine CD38/NAD(+)glycohydrolase (bCD38) catalyses the hydrolysis of NAD(+) into nicotinamide and ADP-ribose and the formation of cyclic ADP-ribose (cADPR). We solved the crystal structures of the mono N-glycosylated forms of the ecto-domain of bCD38 or the catalytic residue mutant Glu218Gln in their apo state or bound to aFNAD or rFNAD, two 2'-fluorinated analogs of NAD(+). Both compounds behave as mechanism-based inhibitors, allowing the trapping of a reaction intermediate covalently linked to Glu218. Compared to the non-covalent (Michaelis) complex, the ligands adopt a more folded conformation in the covalent complexes. Altogether these crystallographic snapshots along the reaction pathway reveal the drastic conformational rearrangements undergone by the ligand during catalysis with the repositioning of its adenine ring from a solvent-exposed position stacked against Trp168 to a more buried position stacked against Trp181. This adenine flipping between conserved tryptophans is a prerequisite for the proper positioning of the N1 of the adenine ring to perform the nucleophilic attack on the C1' of the ribofuranoside ring ultimately yielding cADPR. In all structures, however, the adenine ring adopts the most thermodynamically favorable anti conformation, explaining why cyclization, which requires a syn conformation, remains a rare alternate event in the reactions catalyzed by bCD38 (cADPR represents only 1% of the reaction products). In the Michaelis complex, the substrate is bound in a constrained conformation; the enzyme uses this ground-state destabilization, in addition to a hydrophobic environment and desolvation of the nicotinamide-ribosyl bond, to destabilize the scissile bond leading to the formation of a ribooxocarbenium ion intermediate. The Glu218 side chain stabilizes this reaction intermediate and plays another important role during catalysis by polarizing the 2'-OH of the substrate NAD(+). Based on our structural analysis and data on active site mutants, we propose a detailed analysis of the catalytic mechanism.3101 Biochemistry and Cell Biology (for-2020)3402 Inorganic Chemistry (for-2020)31 Biological Sciences (for-2020)3405 Organic Chemistry (for-2020)34 Chemical Sciences (for-2020)Generic health relevance (hrcs-hc)ADP-ribosyl Cyclase (mesh)ADP-ribosyl Cyclase 1 (mesh)Adenosine Monophosphate (mesh)Amino Acid Substitution (mesh)Animals (mesh)Catalysis (mesh)Catalytic Domain (mesh)Cattle (mesh)CrystallographyX-Ray (mesh)Glycosylation (mesh)Ligands (mesh)ModelsMolecular (mesh)MutagenesisSite-Directed (mesh)Mutant Proteins (mesh)NAD (mesh)Protein Binding (mesh)Protein Multimerization (mesh)Protein StructureTertiary (mesh)Substrate Specificity (mesh)Animals (mesh)Cattle (mesh)NAD (mesh)ADP-ribosyl Cyclase (mesh)Adenosine Monophosphate (mesh)Ligands (mesh)CrystallographyX-Ray (mesh)Amino Acid Substitution (mesh)MutagenesisSite-Directed (mesh)Catalytic Domain (mesh)Protein StructureTertiary (mesh)Protein Binding (mesh)Substrate Specificity (mesh)Glycosylation (mesh)Catalysis (mesh)ModelsMolecular (mesh)Mutant Proteins (mesh)Protein Multimerization (mesh)ADP-ribosyl Cyclase 1 (mesh)ADP-ribosyl Cyclase (mesh)ADP-ribosyl Cyclase 1 (mesh)Adenosine Monophosphate (mesh)Amino Acid Substitution (mesh)Animals (mesh)Catalysis (mesh)Catalytic Domain (mesh)Cattle (mesh)CrystallographyX-Ray (mesh)Glycosylation (mesh)Ligands (mesh)ModelsMolecular (mesh)MutagenesisSite-Directed (mesh)Mutant Proteins (mesh)NAD (mesh)Protein Binding (mesh)Protein Multimerization (mesh)Protein StructureTertiary (mesh)Substrate Specificity (mesh)General Science & Technology (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/661926qhhttps://escholarship.org/content/qt661926qh/qt661926qh.pdfinfo:doi/10.1371/journal.pone.0034918articlePLOS ONE, vol 7, iss 4e34918oai:escholarship.org:ark:/13030/qt8w3084tc2026-08-13T09:31:18Zqt8w3084tcStructures of SRP54 and SRP19, the Two Proteins that Organize the Ribonucleic Core of the Signal Recognition Particle from Pyrococcus furiosusEgea, Pascal FNapetschnig, JohannaWalter, PeterStroud, Robert MZhang, Shuguang2008-01-01In all organisms the Signal Recognition Particle (SRP), binds to signal sequences of proteins destined for secretion or membrane insertion as they emerge from translating ribosomes. In Archaea and Eucarya, the conserved ribonucleoproteic core is composed of two proteins, the accessory protein SRP19, the essential GTPase SRP54, and an evolutionarily conserved and essential SRP RNA. Through the GTP-dependent interaction between the SRP and its cognate receptor SR, ribosomes harboring nascent polypeptidic chains destined for secretion are dynamically transferred to the protein translocation apparatus at the membrane. We present here high-resolution X-ray structures of SRP54 and SRP19, the two RNA binding components forming the core of the signal recognition particle from the hyper-thermophilic archaeon Pyrococcus furiosus (Pfu). The 2.5 A resolution structure of free Pfu-SRP54 is the first showing the complete domain organization of a GDP bound full-length SRP54 subunit. In its ras-like GTPase domain, GDP is found tightly associated with the protein. The flexible linker that separates the GTPase core from the hydrophobic signal sequence binding M domain, adopts a purely alpha-helical structure and acts as an articulated arm allowing the M domain to explore multiple regions as it scans for signal peptides as they emerge from the ribosomal tunnel. This linker is structurally coupled to the GTPase catalytic site and likely to propagate conformational changes occurring in the M domain through the SRP RNA upon signal sequence binding. Two different 1.8 A resolution crystal structures of free Pfu-SRP19 reveal a compact, rigid and well-folded protein even in absence of its obligate SRP RNA partner. Comparison with other SRP19*SRP RNA structures suggests the rearrangement of a disordered loop upon binding with the RNA through a reciprocal induced-fit mechanism and supports the idea that SRP19 acts as a molecular scaffold and a chaperone, assisting the SRP RNA in adopting the conformation required for its optimal interaction with the essential subunit SRP54, and proper assembly of a functional SRP.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Amino Acid Sequence (mesh)Base Sequence (mesh)Binding Sites (mesh)CrystallographyX-Ray (mesh)GTP Phosphohydrolases (mesh)ModelsBiological (mesh)ModelsMolecular (mesh)Molecular Sequence Data (mesh)Nucleic Acid Conformation (mesh)Protein Binding (mesh)Protein Conformation (mesh)Pyrococcus furiosus (mesh)Ribonucleoproteins (mesh)Sequence HomologyAmino Acid (mesh)Signal Recognition Particle (mesh)Pyrococcus furiosus (mesh)GTP Phosphohydrolases (mesh)Ribonucleoproteins (mesh)Signal Recognition Particle (mesh)CrystallographyX-Ray (mesh)Binding Sites (mesh)Amino Acid Sequence (mesh)Base Sequence (mesh)Nucleic Acid Conformation (mesh)Protein Conformation (mesh)Protein Binding (mesh)Sequence HomologyAmino Acid (mesh)ModelsBiological (mesh)ModelsMolecular (mesh)Molecular Sequence Data (mesh)Amino Acid Sequence (mesh)Base Sequence (mesh)Binding Sites (mesh)CrystallographyX-Ray (mesh)GTP Phosphohydrolases (mesh)ModelsBiological (mesh)ModelsMolecular (mesh)Molecular Sequence Data (mesh)Nucleic Acid Conformation (mesh)Protein Binding (mesh)Protein Conformation (mesh)Pyrococcus furiosus (mesh)Ribonucleoproteins (mesh)Sequence HomologyAmino Acid (mesh)Signal Recognition Particle (mesh)General Science & Technology (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8w3084tchttps://escholarship.org/content/qt8w3084tc/qt8w3084tc.pdfinfo:doi/10.1371/journal.pone.0003528articlePLOS ONE, vol 3, iss 10e3528oai:escholarship.org:ark:/13030/qt3ww660hs2026-08-11T23:59:47Zqt3ww660hsSkeletal muscle action of estrogen receptor α is critical for the maintenance of mitochondrial function and metabolic homeostasis in femalesRibas, VicentDrew, Brian GZhou, ZhenqiPhun, JenniferKalajian, Nareg YSoleymani, TeoDaraei, PedramWidjaja, KevinWanagat, Jonathande Aguiar Vallim, Thomas QFluitt, Amy HBensinger, StevenLe, ThucRadu, CaiusWhitelegge, Julian PBeaven, Simon WTontonoz, PeterLusis, Aldons JParks, Brian WVergnes, LaurentReue, KarenSingh, HarpreetBopassa, Jean CToro, LigiaStefani, EnricoWatt, Matthew JSchenk, SimonAkerstrom, ThorbjornKelly, MeghanPedersen, Bente KHewitt, Sylvia CKorach, Kenneth SHevener, Andrea L2016-04-13Impaired estrogen receptor α (ERα) action promotes obesity and metabolic dysfunction in humans and mice; however, the mechanisms underlying these phenotypes remain unknown. Considering that skeletal muscle is a primary tissue responsible for glucose disposal and oxidative metabolism, we established that reduced ERα expression in muscle is associated with glucose intolerance and adiposity in women and female mice. To test this relationship, we generated muscle-specific ERα knockout (MERKO) mice. Impaired glucose homeostasis and increased adiposity were paralleled by diminished muscle oxidative metabolism and bioactive lipid accumulation in MERKO mice. Aberrant mitochondrial morphology, overproduction of reactive oxygen species, and impairment in basal and stress-induced mitochondrial fission dynamics, driven by imbalanced protein kinase A-regulator of calcineurin 1-calcineurin signaling through dynamin-related protein 1, tracked with reduced oxidative metabolism in MERKO muscle. Although muscle mitochondrial DNA (mtDNA) abundance was similar between the genotypes, ERα deficiency diminished mtDNA turnover by a balanced reduction in mtDNA replication and degradation. Our findings indicate the retention of dysfunctional mitochondria in MERKO muscle and implicate ERα in the preservation of mitochondrial health and insulin sensitivity as a defense against metabolic disease in women.3206 Medical Biotechnology (for-2020)40 Engineering (for-2020)32 Biomedical and Clinical Sciences (for-2020)4003 Biomedical Engineering (for-2020)Diabetes (rcdc)Women's Health (rcdc)Aging (rcdc)Estrogen (rcdc)Genetics (rcdc)Obesity (rcdc)Nutrition (rcdc)2.1 Biological and endogenous factors (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)5.1 Pharmaceuticals (hrcs-rac)Animals (mesh)Autophagy (mesh)Calcium-Binding Proteins (mesh)DNA Replication (mesh)DNAMitochondrial (mesh)Dynamins (mesh)Estrogen Receptor alpha (mesh)Female (mesh)Gene Deletion (mesh)Glucose (mesh)Homeostasis (mesh)Humans (mesh)Insulin (mesh)Intracellular Signaling Peptides and Proteins (mesh)Lipid Metabolism (mesh)Mice (mesh)MiceKnockout (mesh)MitochondriaMuscle (mesh)Mitochondrial Dynamics (mesh)Muscle Proteins (mesh)MuscleSkeletal (mesh)Organ Specificity (mesh)Oxidation-Reduction (mesh)Oxidative Stress (mesh)Reactive Oxygen Species (mesh)Signal Transduction (mesh)MuscleSkeletal (mesh)MitochondriaMuscle (mesh)Animals (mesh)MiceKnockout (mesh)Humans (mesh)Mice (mesh)Reactive Oxygen Species (mesh)Insulin (mesh)Dynamins (mesh)Glucose (mesh)Intracellular Signaling Peptides and Proteins (mesh)Calcium-Binding Proteins (mesh)Muscle Proteins (mesh)Estrogen Receptor alpha (mesh)DNAMitochondrial (mesh)Signal Transduction (mesh)Organ Specificity (mesh)DNA Replication (mesh)Gene Deletion (mesh)Oxidation-Reduction (mesh)Oxidative Stress (mesh)Homeostasis (mesh)Autophagy (mesh)Female (mesh)Lipid Metabolism (mesh)Mitochondrial Dynamics (mesh)Animals (mesh)Autophagy (mesh)Calcium-Binding Proteins (mesh)DNA Replication (mesh)DNAMitochondrial (mesh)Dynamins (mesh)Estrogen Receptor alpha (mesh)Female (mesh)Gene Deletion (mesh)Glucose (mesh)Homeostasis (mesh)Humans (mesh)Insulin (mesh)Intracellular Signaling Peptides and Proteins (mesh)Lipid Metabolism (mesh)Mice (mesh)MiceKnockout (mesh)MitochondriaMuscle (mesh)Mitochondrial Dynamics (mesh)Muscle Proteins (mesh)MuscleSkeletal (mesh)Organ Specificity (mesh)Oxidation-Reduction (mesh)Oxidative Stress (mesh)Reactive Oxygen Species (mesh)Signal Transduction (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)3206 Medical biotechnology (for-2020)4003 Biomedical engineering (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3ww660hshttps://escholarship.org/content/qt3ww660hs/qt3ww660hs.pdfinfo:doi/10.1126/scitranslmed.aad3815articleScience Translational Medicine, vol 8, iss 334334ra54oai:escholarship.org:ark:/13030/qt40f6t9vn2026-08-11T21:18:03Zqt40f6t9vnElucidation of TRIM25 ubiquitination targets involved in diverse cellular and antiviral processesYang, EmilyHuang, SerinaJami-Alahmadi, YasamanMcInerney, Gerald MWohlschlegel, James ALi, Melody MHHeise, Mark T2022-09-01The tripartite motif (TRIM) family of E3 ubiquitin ligases is well known for its roles in antiviral restriction and innate immunity regulation, in addition to many other cellular pathways. In particular, TRIM25-mediated ubiquitination affects both carcinogenesis and antiviral response. While individual substrates have been identified for TRIM25, it remains unclear how it regulates diverse processes. Here we characterized a mutation, R54P, critical for TRIM25 catalytic activity, which we successfully utilized to "trap" substrates. We demonstrated that TRIM25 targets proteins implicated in stress granule formation (G3BP1/2), nonsense-mediated mRNA decay (UPF1), nucleoside synthesis (NME1), and mRNA translation and stability (PABPC4). The R54P mutation abolishes TRIM25 inhibition of alphaviruses independently of the host interferon response, suggesting that this antiviral effect is a direct consequence of ubiquitination. Consistent with that, we observed diminished antiviral activity upon knockdown of several TRIM25-R54P specific interactors including NME1 and PABPC4. Our findings highlight that multiple substrates mediate the cellular and antiviral activities of TRIM25, illustrating the multi-faceted role of this ubiquitination network in modulating diverse biological processes.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Antiviral Agents (mesh)DNA Helicases (mesh)Interferons (mesh)Nucleosides (mesh)Poly-ADP-Ribose Binding Proteins (mesh)RNA Helicases (mesh)RNA Recognition Motif Proteins (mesh)Tripartite Motif Proteins (mesh)Ubiquitin-Protein Ligases (mesh)Ubiquitination (mesh)Ubiquitins (mesh)DNA Helicases (mesh)Ubiquitin-Protein Ligases (mesh)RNA Helicases (mesh)Nucleosides (mesh)Interferons (mesh)Ubiquitins (mesh)Antiviral Agents (mesh)Ubiquitination (mesh)Tripartite Motif Proteins (mesh)RNA Recognition Motif Proteins (mesh)Poly-ADP-Ribose Binding Proteins (mesh)Antiviral Agents (mesh)DNA Helicases (mesh)Interferons (mesh)Nucleosides (mesh)Poly-ADP-Ribose Binding Proteins (mesh)RNA Helicases (mesh)RNA Recognition Motif Proteins (mesh)Tripartite Motif Proteins (mesh)Ubiquitin-Protein Ligases (mesh)Ubiquitination (mesh)Ubiquitins (mesh)0605 Microbiology (for)1107 Immunology (for)1108 Medical Microbiology (for)Virology (science-metrix)3107 Microbiology (for-2020)3204 Immunology (for-2020)3207 Medical microbiology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/40f6t9vnhttps://escholarship.org/content/qt40f6t9vn/qt40f6t9vn.pdfinfo:doi/10.1371/journal.ppat.1010743articlePLOS Pathogens, vol 18, iss 9e1010743oai:escholarship.org:ark:/13030/qt710778pf2026-08-11T20:43:11Zqt710778pfDoxycycline Alters Metabolism and Proliferation of Human Cell LinesAhler, EthanSullivan, William JCass, AshleyBraas, DanielYork, Autumn GBensinger, Steven JGraeber, Thomas GChristofk, Heather RSamant, Rajeev2013-01-01The tetracycline antibiotics are widely used in biomedical research as mediators of inducible gene expression systems. Despite many known effects of tetracyclines on mammalian cells-including inhibition of the mitochondrial ribosome-there have been few reports on potential off-target effects at concentrations commonly used in inducible systems. Here, we report that in human cell lines, commonly used concentrations of doxycycline change gene expression patterns and concomitantly shift metabolism towards a more glycolytic phenotype, evidenced by increased lactate secretion and reduced oxygen consumption. We also show that these concentrations are sufficient to slow proliferation. These findings suggest that researchers using doxycycline in inducible expression systems should design appropriate controls to account for potential confounding effects of the drug on cellular metabolism.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Biotechnology (rcdc)2.1 Biological and endogenous factors (hrcs-rac)5.1 Pharmaceuticals (hrcs-rac)Generic health relevance (hrcs-hc)Anti-Bacterial Agents (mesh)Cell Cycle (mesh)Cell LineTumor (mesh)Cell Proliferation (mesh)Doxycycline (mesh)Female (mesh)Gene Expression (mesh)Gene Expression Profiling (mesh)Humans (mesh)Male (mesh)Metabolic Networks and Pathways (mesh)Metabolome (mesh)Oxygen Consumption (mesh)Cell LineTumor (mesh)Humans (mesh)Doxycycline (mesh)Anti-Bacterial Agents (mesh)Gene Expression Profiling (mesh)Cell Cycle (mesh)Cell Proliferation (mesh)Gene Expression (mesh)Oxygen Consumption (mesh)Female (mesh)Male (mesh)Metabolic Networks and Pathways (mesh)Metabolome (mesh)Anti-Bacterial Agents (mesh)Cell Cycle (mesh)Cell LineTumor (mesh)Cell Proliferation (mesh)Doxycycline (mesh)Female (mesh)Gene Expression (mesh)Gene Expression Profiling (mesh)Humans (mesh)Male (mesh)Metabolic Networks and Pathways (mesh)Metabolome (mesh)Oxygen Consumption (mesh)General Science & Technology (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/710778pfhttps://escholarship.org/content/qt710778pf/qt710778pf.pdfinfo:doi/10.1371/journal.pone.0064561articlePLOS ONE, vol 8, iss 5e64561oai:escholarship.org:ark:/13030/qt0cd9r1232026-08-11T20:14:09Zqt0cd9r123Identification of IMC43, a novel IMC protein that collaborates with IMC32 to form an essential daughter bud assembly complex in Toxoplasma gondiiPasquarelli, Rebecca RBack, Peter SSha, JihuiWohlschlegel, James ABradley, Peter JTonkin, Christopher J2023-10-01The inner membrane complex (IMC) of Toxoplasma gondii is essential for all phases of the parasite's life cycle. One of its most critical roles is to act as a scaffold for the assembly of daughter buds during replication by endodyogeny. While many daughter IMC proteins have been identified, most are recruited after bud initiation and are not essential for parasite fitness. Here, we report the identification of IMC43, a novel daughter IMC protein that is recruited at the earliest stages of daughter bud initiation. Using an auxin-inducible degron system we show that depletion of IMC43 results in aberrant morphology, dysregulation of endodyogeny, and an extreme defect in replication. Deletion analyses reveal a region of IMC43 that plays a role in localization and a C-terminal domain that is essential for the protein's function. TurboID proximity labelling and a yeast two-hybrid screen using IMC43 as bait identify 30 candidate IMC43 binding partners. We investigate two of these: the essential daughter protein IMC32 and a novel daughter IMC protein we named IMC44. We show that IMC43 is responsible for regulating the localization of both IMC32 and IMC44 at specific stages of endodyogeny and that this regulation is dependent on the essential C-terminal domain of IMC43. Using pairwise yeast two-hybrid assays, we determine that this region is also sufficient for binding to both IMC32 and IMC44. As IMC43 and IMC32 are both essential proteins, this work reveals the existence of a bud assembly complex that forms the foundation of the daughter IMC during endodyogeny.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Biodefense (rcdc)Genetics (rcdc)Emerging Infectious Diseases (rcdc)Infectious Diseases (rcdc)Toxoplasma (mesh)Nuclear Family (mesh)Protozoan Proteins (mesh)Membrane Proteins (mesh)Two-Hybrid System Techniques (mesh)Toxoplasma (mesh)Membrane Proteins (mesh)Protozoan Proteins (mesh)Two-Hybrid System Techniques (mesh)Nuclear Family (mesh)Toxoplasma (mesh)Nuclear Family (mesh)Protozoan Proteins (mesh)Membrane Proteins (mesh)Two-Hybrid System Techniques (mesh)0605 Microbiology (for)1107 Immunology (for)1108 Medical Microbiology (for)Virology (science-metrix)3107 Microbiology (for-2020)3204 Immunology (for-2020)3207 Medical microbiology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/0cd9r123https://escholarship.org/content/qt0cd9r123/qt0cd9r123.pdfinfo:doi/10.1371/journal.ppat.1011707articlePLOS Pathogens, vol 19, iss 10e1011707oai:escholarship.org:ark:/13030/qt13n748492026-08-11T20:00:07Zqt13n74849Direct tests of cytochrome c and c1 functions in the electron transport chain of malaria parasitesEspino-Sanchez, Tanya JWienkers, HenryMarvin, Rebecca GNalder, Shai-anneGarcía-Guerrero, Aldo EVanNatta, Peter EJami-Alahmadi, YasamanBlackwell, Amanda MixonWhitby, Frank GWohlschlegel, James AKieber-Emmons, Matthew THill, Christopher PSigala, Paul A2023-05-09The mitochondrial electron transport chain (ETC) of Plasmodium malaria parasites is a major antimalarial drug target, but critical cytochrome (cyt) functions remain unstudied and enigmatic. Parasites express two distinct cyt c homologs (c and c-2) with unusually sparse sequence identity and uncertain fitness contributions. P. falciparum cyt c-2 is the most divergent eukaryotic cyt c homolog currently known and has sequence features predicted to be incompatible with canonical ETC function. We tagged both cyt c homologs and the related cyt c1 for inducible knockdown. Translational repression of cyt c and cyt c1 was lethal to parasites, which died from ETC dysfunction and impaired ubiquinone recycling. In contrast, cyt c-2 knockdown or knockout had little impact on blood-stage growth, indicating that parasites rely fully on the more conserved cyt c for ETC function. Biochemical and structural studies revealed that both cyt c and c-2 are hemylated by holocytochrome c synthase, but UV-vis absorbance and EPR spectra strongly suggest that cyt c-2 has an unusually open active site in which heme is stably coordinated by only a single axial amino acid ligand and can bind exogenous small molecules. These studies provide a direct dissection of cytochrome functions in the ETC of malaria parasites and identify a highly divergent Plasmodium cytochrome c with molecular adaptations that defy a conserved role in eukaryotic evolution.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)3202 Clinical Sciences (for-2020)3207 Medical Microbiology (for-2020)Genetics (rcdc)Malaria (rcdc)Rare Diseases (rcdc)Antimicrobial Resistance (rcdc)Infectious Diseases (rcdc)Vector-Borne Diseases (rcdc)Infection (hrcs-hc)3 Good Health and Well Being (sdg)Animals (mesh)Cytochromes c (mesh)Electron Transport (mesh)Parasites (mesh)Antimalarials (mesh)MalariaFalciparum (mesh)Eukaryota (mesh)Cytochromes c1 (mesh)mitochondriamalariaPlasmodiumelectron transport chaincytochromeAnimals (mesh)Parasites (mesh)MalariaFalciparum (mesh)Cytochromes c (mesh)Cytochromes c1 (mesh)Antimalarials (mesh)Electron Transport (mesh)Eukaryota (mesh)Plasmodiumcytochromeelectron transport chainmalariamitochondriaAnimals (mesh)Cytochromes c (mesh)Electron Transport (mesh)Parasites (mesh)Antimalarials (mesh)MalariaFalciparum (mesh)Eukaryota (mesh)Cytochromes c1 (mesh)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/13n74849https://escholarship.org/content/qt13n74849/qt13n74849.pdfinfo:doi/10.1073/pnas.2301047120articleProceedings of the National Academy of Sciences of the United States of America, vol 120, iss 19e2301047120oai:escholarship.org:ark:/13030/qt5bs2s9wz2026-08-11T16:55:04Zqt5bs2s9wzGenome-wide screening identifies Polycomb repressive complex 1.3 as an essential regulator of human naïve pluripotent cell reprogrammingCollier, Amanda JBendall, AdamFabian, CharleneMalcolm, Andrew ATilgner, KatarzynaSemprich, Claudia IWojdyla, KatarzynaNisi, Paola SerenaKishore, KamalFranklin, Valar Nila RoamioMirshekar-Syahkal, BaharD’Santos, ClivePlath, KathrinYusa, KosukeRugg-Gunn, Peter J2022-03-25Uncovering the mechanisms that establish naïve pluripotency in humans is crucial for the future applications of pluripotent stem cells including the production of human blastoids. However, the regulatory pathways that control the establishment of naïve pluripotency by reprogramming are largely unknown. Here, we use genome-wide screening to identify essential regulators as well as major impediments of human primed to naïve pluripotent stem cell reprogramming. We discover that factors essential for cell state change do not typically undergo changes at the level of gene expression but rather are repurposed with new functions. Mechanistically, we establish that the variant Polycomb complex PRC1.3 and PRDM14 jointly repress developmental and gene regulatory factors to ensure naïve cell reprogramming. In addition, small-molecule inhibitors of reprogramming impediments improve naïve cell reprogramming beyond current methods. Collectively, this work defines the principles controlling the establishment of human naïve pluripotency and also provides new insights into mechanisms that destabilize and reconfigure cell identity during cell state transitions.3206 Medical Biotechnology (for-2020)31 Biological Sciences (for-2020)32 Biomedical and Clinical Sciences (for-2020)Stem Cell Research - Induced Pluripotent Stem Cell - Human (rcdc)Stem Cell Research - Embryonic - Human (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell (rcdc)Genetics (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell - Non-Human (rcdc)Human Genome (rcdc)Stem Cell Research - Embryonic - Non-Human (rcdc)Regenerative Medicine (rcdc)Stem Cell Research (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Cell Differentiation (mesh)Cellular Reprogramming (mesh)Gene Expression Regulation (mesh)Humans (mesh)Pluripotent Stem Cells (mesh)Polycomb Repressive Complex 1 (mesh)Pluripotent Stem Cells (mesh)Humans (mesh)Cell Differentiation (mesh)Gene Expression Regulation (mesh)Polycomb Repressive Complex 1 (mesh)Cellular Reprogramming (mesh)Cell Differentiation (mesh)Cellular Reprogramming (mesh)Gene Expression Regulation (mesh)Humans (mesh)Pluripotent Stem Cells (mesh)Polycomb Repressive Complex 1 (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/5bs2s9wzhttps://escholarship.org/content/qt5bs2s9wz/qt5bs2s9wz.pdfinfo:doi/10.1126/sciadv.abk0013articleScience Advances, vol 8, iss 12eabk0013oai:escholarship.org:ark:/13030/qt9bd0m7ws2026-08-11T16:54:56Zqt9bd0m7wsSP3-Enabled Rapid and High Coverage Chemoproteomic Identification of Cell-State–Dependent Redox-Sensitive CysteinesDesai, Heta SYan, TianyangYu, FengchaoSun, Alexander WVillanueva, MirandaNesvizhskii, Alexey IBackus, Keriann M2022-04-01Proteinaceous cysteine residues act as privileged sensors of oxidative stress. As reactive oxygen and nitrogen species have been implicated in numerous pathophysiological processes, deciphering which cysteines are sensitive to oxidative modification and the specific nature of these modifications is essential to understanding protein and cellular function in health and disease. While established mass spectrometry-based proteomic platforms have improved our understanding of the redox proteome, the widespread adoption of these methods is often hindered by complex sample preparation workflows, prohibitive cost of isotopic labeling reagents, and requirements for custom data analysis workflows. Here, we present the SP3-Rox redox proteomics method that combines tailored low cost isotopically labeled capture reagents with SP3 sample cleanup to achieve high throughput and high coverage proteome-wide identification of redox-sensitive cysteines. By implementing a customized workflow in the free FragPipe computational pipeline, we achieve accurate MS1-based quantitation, including for peptides containing multiple cysteine residues. Application of the SP3-Rox method to cellular proteomes identified cysteines sensitive to the oxidative stressor GSNO and cysteine oxidation state changes that occur during T cell activation.3401 Analytical Chemistry (for-2020)3101 Biochemistry and Cell Biology (for-2020)34 Chemical Sciences (for-2020)31 Biological Sciences (for-2020)Biotechnology (rcdc)Generic health relevance (hrcs-hc)Cysteine (mesh)Mass Spectrometry (mesh)Oxidation-Reduction (mesh)Proteome (mesh)Proteomics (mesh)Cysteine (mesh)Proteome (mesh)Proteomics (mesh)Oxidation-Reduction (mesh)Mass Spectrometry (mesh)Cysteine (mesh)Mass Spectrometry (mesh)Oxidation-Reduction (mesh)Proteome (mesh)Proteomics (mesh)Biochemistry & Molecular Biology (science-metrix)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/9bd0m7wshttps://escholarship.org/content/qt9bd0m7ws/qt9bd0m7ws.pdfinfo:doi/10.1016/j.mcpro.2022.100218articleMolecular & Cellular Proteomics, vol 21, iss 4100218oai:escholarship.org:ark:/13030/qt2x46d2gj2026-08-11T03:24:44Zqt2x46d2gjCLSY docking to Pol IV requires a conserved domain critical for small RNA biogenesis and transposon silencingFelgines, LuisaRymen, BartMartins, Laura MXu, GuanghuiMatteoli, CalvinHimber, ChristopheZhou, MingEis, JoshCoruh, CeydaBöhrer, MarcelKuhn, LaurianeChicher, JohanaPandey, VijayaHammann, PhilippeWohlschlegel, JamesWaltz, FlorentLaw, Julie ABlevins, Todd2024-11-27Eukaryotes must balance the need for gene transcription by RNA polymerase II (Pol II) against the danger of mutations caused by transposable element (TE) proliferation. In plants, these gene expression and TE silencing activities are divided between different RNA polymerases. Specifically, RNA polymerase IV (Pol IV), which evolved from Pol II, transcribes TEs to generate small interfering RNAs (siRNAs) that guide DNA methylation and block TE transcription by Pol II. While the Pol IV complex is recruited to TEs via SNF2-like CLASSY (CLSY) proteins, how Pol IV partners with the CLSYs remains unknown. Here, we identified a conserved CYC-YPMF motif that is specific to Pol IV and is positioned on the complex exterior. Furthermore, we found that this motif is essential for the co-purification of all four CLSYs with Pol IV, but that only one CLSY is present in any given Pol IV complex. These findings support a “one CLSY per Pol IV” model where the CYC-YPMF motif acts as a CLSY-docking site. Indeed, mutations in and around this motif phenocopy pol iv null and clsy quadruple mutants. Together, these findings provide structural and functional insights into a critical protein feature that distinguishes Pol IV from other RNA polymerases, allowing it to promote genome stability by targeting TEs for silencing.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)Human Genome (rcdc)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Generic health relevance (hrcs-hc)DNA Transposable Elements (mesh)Arabidopsis Proteins (mesh)DNA-Directed RNA Polymerases (mesh)Gene Silencing (mesh)Arabidopsis (mesh)RNASmall Interfering (mesh)Gene Expression RegulationPlant (mesh)RNA Polymerase II (mesh)Protein Binding (mesh)Protein Domains (mesh)Conserved Sequence (mesh)Arabidopsis (mesh)DNA-Directed RNA Polymerases (mesh)RNA Polymerase II (mesh)Arabidopsis Proteins (mesh)RNASmall Interfering (mesh)DNA Transposable Elements (mesh)Gene Expression RegulationPlant (mesh)Gene Silencing (mesh)Conserved Sequence (mesh)Protein Binding (mesh)Protein Domains (mesh)DNA Transposable Elements (mesh)Arabidopsis Proteins (mesh)DNA-Directed RNA Polymerases (mesh)Gene Silencing (mesh)Arabidopsis (mesh)RNASmall Interfering (mesh)Gene Expression RegulationPlant (mesh)RNA Polymerase II (mesh)Protein Binding (mesh)Protein Domains (mesh)Conserved Sequence (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/2x46d2gjhttps://escholarship.org/content/qt2x46d2gj/qt2x46d2gj.pdfinfo:doi/10.1038/s41467-024-54268-0articleNature Communications, vol 15, iss 110298oai:escholarship.org:ark:/13030/qt151304t12026-08-11T03:18:33Zqt151304t1Aster-dependent nonvesicular transport facilitates dietary cholesterol uptakeFerrari, AlessandraWhang, EmilyXiao, XuKennelly, John PRomartinez-Alonso, BeatrizMack, Julia JWeston, ThomasChen, KaiKim, YoungjaeTol, Marcus JBideyan, LaraNguyen, AlexanderGao, YajingCui, LiujuanBedard, Alexander HSandhu, JaspreetLee, Stephen DFairall, LouiseWilliams, Kevin JSong, WenxinMunguia, PriscillaRussell, Robert AMartin, Martin GJung, Michael EJiang, HaiboSchwabe, John WRYoung, Stephen GTontonoz, Peter2023-11-10Intestinal absorption is an important contributor to systemic cholesterol homeostasis. Niemann-Pick C1 Like 1 (NPC1L1) assists in the initial step of dietary cholesterol uptake, but how cholesterol moves downstream of NPC1L1 is unknown. We show that Aster-B and Aster-C are critical for nonvesicular cholesterol movement in enterocytes. Loss of NPC1L1 diminishes accessible plasma membrane (PM) cholesterol and abolishes Aster recruitment to the intestinal brush border. Enterocytes lacking Asters accumulate PM cholesterol and show endoplasmic reticulum cholesterol depletion. Aster-deficient mice have impaired cholesterol absorption and are protected against diet-induced hypercholesterolemia. Finally, the Aster pathway can be targeted with a small-molecule inhibitor to manipulate cholesterol uptake. These findings identify the Aster pathway as a physiologically important and pharmacologically tractable node in dietary lipid absorption.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Nutrition (rcdc)Digestive Diseases (rcdc)Animals (mesh)Mice (mesh)Biological Transport (mesh)CholesterolDietary (mesh)Intestinal Absorption (mesh)Membrane Transport Proteins (mesh)MiceInbred C57BL (mesh)Enterocytes (mesh)Liver X Receptors (mesh)Humans (mesh)Jejunum (mesh)MiceKnockout (mesh)Membrane Proteins (mesh)Enterocytes (mesh)Jejunum (mesh)Animals (mesh)MiceInbred C57BL (mesh)MiceKnockout (mesh)Humans (mesh)Mice (mesh)CholesterolDietary (mesh)Membrane Transport Proteins (mesh)Membrane Proteins (mesh)Biological Transport (mesh)Intestinal Absorption (mesh)Liver X Receptors (mesh)Animals (mesh)Mice (mesh)Biological Transport (mesh)CholesterolDietary (mesh)Intestinal Absorption (mesh)Membrane Transport Proteins (mesh)MiceInbred C57BL (mesh)Enterocytes (mesh)Liver X Receptors (mesh)Humans (mesh)Jejunum (mesh)MiceKnockout (mesh)Membrane Proteins (mesh)General Science & Technology (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/151304t1https://escholarship.org/content/qt151304t1/qt151304t1.pdfinfo:doi/10.1126/science.adf0966articleScience, vol 382, iss 6671eadf0966 - eadf0966oai:escholarship.org:ark:/13030/qt90q2h92g2026-08-11T03:04:16Zqt90q2h92gTargeting Asparagine Metabolism in Well-Differentiated/Dedifferentiated LiposarcomaKlingbeil, Kyle DWilde, Blake RGraham, Danielle SLofftus, SerenaMcCaw, TylerMatulionis, NedasDry, Sarah MCrompton, Joseph GEilber, Fritz CGraeber, Thomas GShackelford, David BChristofk, Heather RKadera, Brian E2024-09-01BACKGROUND: mTORC1 activity is dependent on the presence of micronutrients, including Asparagine (Asn), to promote anabolic cell signaling in many cancers. We hypothesized that targeting Asn metabolism would inhibit tumor growth by reducing mTORC1 activity in well-differentiated (WD)/dedifferentiated (DD) liposarcoma (LPS).
METHODS: Human tumor metabolomic analysis was utilized to compare abundance of Asn in WD vs. DD LPS. Gene set enrichment analysis (GSEA) compared relative expression among metabolic pathways upregulated in DD vs. WD LPS. Proliferation assays were performed for LPS cell lines and organoid models by using the combination treatment of electron transport chain (ETC) inhibitors with Asn-free media. 13C-Glucose-labeling metabolomics evaluated the effects of combination treatment on nucleotide synthesis. Murine xenograft models were used to assess the effects of ETC inhibition combined with PEGylated L-Asparaginase (PEG-Asnase) on tumor growth and mTORC1 signaling.
RESULTS: Asn was enriched in DD LPS compared to WD LPS. GSEA indicated that mTORC1 signaling was upregulated in DD LPS. Within available LPS cell lines and organoid models, the combination of ETC inhibition with Asn-free media resulted in reduced cell proliferation. Combination treatment inhibited nucleotide synthesis and promoted cell cycle arrest. In vivo, the combination of ETC inhibition with PEG-Asnase restricted tumor growth.
CONCLUSIONS: Asn enrichment and mTORC1 upregulation are important factors contributing to WD/DD LPS tumor progression. Effective targeting strategies require limiting access to extracellular Asn and inhibition of de novo synthesis mechanisms. The combination of PEG-Asnase with ETC inhibition is an effective therapy to restrict tumor growth in WD/DD LPS.3205 Medical Biochemistry and Metabolomics (for-2020)32 Biomedical and Clinical Sciences (for-2020)Rare Diseases (rcdc)Cancer (rcdc)5.1 Pharmaceuticals (hrcs-rac)Cancer (hrcs-hc)3 Good Health and Well Being (sdg)well-differentiated/dedifferentiated liposarcomaasparagine metabolismmTORC1 signalingATF4asparaginasecomplex I inhibitorelectron transport chainpatient-derived organoidspatient-derived xenograftATF4asparaginaseasparagine metabolismcomplex I inhibitorelectron transport chainmTORC1 signalingpatient-derived organoidspatient-derived xenograftwell-differentiated/dedifferentiated liposarcoma1112 Oncology and Carcinogenesis (for)3211 Oncology and carcinogenesis (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/90q2h92ghttps://escholarship.org/content/qt90q2h92g/qt90q2h92g.pdfinfo:doi/10.3390/cancers16173031articleCancers, vol 16, iss 173031oai:escholarship.org:ark:/13030/qt18t6t5582026-08-11T00:58:08Zqt18t6t558BCC0 collaborates with IMC32 and IMC43 to form the Toxoplasma gondii essential daughter bud assembly complexPasquarelli, Rebecca RSha, JihuiWohlschlegel, James ABradley, Peter JBesteiro, Sébastien2024-07-01Toxoplasma gondii divides by endodyogeny, in which two daughter buds are formed within the cytoplasm of the maternal cell using the inner membrane complex (IMC) as a scaffold. During endodyogeny, components of the IMC are synthesized and added sequentially to the nascent daughter buds in a tightly regulated manner. We previously showed that the early recruiting proteins IMC32 and IMC43 form an essential daughter bud assembly complex which lays the foundation of the daughter cell scaffold in T. gondii. In this study, we identify the essential, early recruiting IMC protein BCC0 as a third member of this complex by using IMC32 as bait in both proximity labeling and yeast two-hybrid screens. We demonstrate that BCC0's localization to daughter buds depends on the presence of both IMC32 and IMC43. Deletion analyses and functional complementation studies reveal that residues 701-877 of BCC0 are essential for both its localization and function and that residues 1-899 are sufficient for function despite minor mislocalization. Pairwise yeast two-hybrid assays additionally demonstrate that BCC0's essential domain binds to the coiled-coil region of IMC32 and that BCC0 and IMC43 do not directly interact. This data supports a model for complex assembly in which an IMC32-BCC0 subcomplex initially recruits to nascent buds via palmitoylation of IMC32 and is locked into the scaffold once bud elongation begins by IMC32 binding to IMC43. Together, this study dissects the organization and function of a complex of three early recruiting daughter proteins which are essential for the proper assembly of the IMC during endodyogeny.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Emerging Infectious Diseases (rcdc)Infectious Diseases (rcdc)Biodefense (rcdc)Toxoplasma (mesh)Protozoan Proteins (mesh)Cell Division (mesh)Two-Hybrid System Techniques (mesh)Membrane Proteins (mesh)Toxoplasma (mesh)Membrane Proteins (mesh)Protozoan Proteins (mesh)Two-Hybrid System Techniques (mesh)Cell Division (mesh)Toxoplasma (mesh)Protozoan Proteins (mesh)Cell Division (mesh)Two-Hybrid System Techniques (mesh)Membrane Proteins (mesh)0605 Microbiology (for)1107 Immunology (for)1108 Medical Microbiology (for)Virology (science-metrix)3107 Microbiology (for-2020)3204 Immunology (for-2020)3207 Medical microbiology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/18t6t558https://escholarship.org/content/qt18t6t558/qt18t6t558.pdfinfo:doi/10.1371/journal.ppat.1012411articlePLOS Pathogens, vol 20, iss 7e1012411oai:escholarship.org:ark:/13030/qt3jr1x3km2026-08-11T00:57:46Zqt3jr1x3kmAster-B-dependent estradiol synthesis protects female mice from diet-induced obesityXiao, XuKennelly, John PaulFeng, An-ChiehCheng, LijingRomartinez-Alonso, BeatrizBedard, Alexander HGao, YajingCui, LiujuanYoung, Stephen GSchwabe, John WRTontonoz, Peter2024-02-15Aster proteins mediate the nonvesicular transport of cholesterol from the plasma membrane (PM) to the endoplasmic reticulum (ER). However, the importance of nonvesicular sterol movement for physiology and pathophysiology in various tissues is incompletely understood. Here we show that loss of Aster-B leads to diet-induced obesity in female but not in male mice, and that this sex difference is abolished by ovariectomy. We further demonstrate that Aster-B deficiency impairs nonvesicular cholesterol transport from the PM to the ER in ovaries in vivo, leading to hypogonadism and reduced estradiol synthesis. Female Aster-B-deficient mice exhibit reduced locomotor activity and energy expenditure, consistent with established effects of estrogens on systemic metabolism. Administration of exogenous estradiol ameliorates the diet-induced obesity phenotype of Aster-B-deficient female mice. These findings highlight the key role of Aster-B-dependent nonvesicular cholesterol transport in regulating estradiol production and protecting females from obesity.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Obesity (rcdc)Nutrition (rcdc)Estrogen (rcdc)Women's Health (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Female (mesh)Mice (mesh)Male (mesh)Animals (mesh)Estradiol (mesh)Cell Membrane (mesh)Cholesterol (mesh)Obesity (mesh)Diet (mesh)Cell Membrane (mesh)Animals (mesh)Mice (mesh)Obesity (mesh)Cholesterol (mesh)Estradiol (mesh)Diet (mesh)Female (mesh)Male (mesh)Adipose tissueCholesterolMetabolismFemale (mesh)Mice (mesh)Male (mesh)Animals (mesh)Estradiol (mesh)Cell Membrane (mesh)Cholesterol (mesh)Obesity (mesh)Diet (mesh)11 Medical and Health Sciences (for)Immunology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/3jr1x3kmhttps://escholarship.org/content/qt3jr1x3km/qt3jr1x3km.pdfinfo:doi/10.1172/jci173002articleJournal of Clinical Investigation, vol 134, iss 4e173002oai:escholarship.org:ark:/13030/qt44c6j6x92026-08-11T00:41:04Zqt44c6j6x9Molecular analysis of a self-organizing signaling pathway for Xenopus axial patterning from egg to tailbudAzbazdar, YagmurDe Robertis, Edward M2024-07-09Xenopus embryos provide a favorable material to dissect the sequential steps that lead to dorsal-ventral (D-V) and anterior-posterior (A-P) cell differentiation. Here, we analyze the signaling pathways involved in this process using loss-of-function and gain-of-function approaches. The initial step was provided by Hwa, a transmembrane protein that robustly activates early β-catenin signaling when microinjected into the ventral side of the embryo leading to complete twinned axes. The following step was the activation of Xenopus Nodal-related growth factors, which could rescue the depletion of β-catenin and were themselves blocked by the extracellular Nodal antagonists Cerberus-Short and Lefty. During gastrulation, the Spemann-Mangold organizer secretes a cocktail of growth factor antagonists, of which the BMP antagonists Chordin and Noggin could rescue simultaneously D-V and A-P tissues in β-catenin-depleted embryos. Surprisingly, this rescue occurred in the absence of any β-catenin transcriptional activity as measured by β-catenin activated Luciferase reporters. The Wnt antagonist Dickkopf (Dkk1) strongly synergized with the early Hwa signal by inhibiting late Wnt signals. Depletion of Sizzled (Szl), an antagonist of the Tolloid chordinase, was epistatic over the Hwa and Dkk1 synergy. BMP4 mRNA injection blocked Hwa-induced ectopic axes, and Dkk1 inhibited BMP signaling late, but not early, during gastrulation. Several unexpected findings were made, e.g., well-patterned complete embryonic axes are induced by Chordin or Nodal in β-catenin knockdown embryos, dorsalization by Lithium chloride (LiCl) is mediated by Nodals, Dkk1 exerts its anteriorizing and dorsalizing effects by regulating late BMP signaling, and the Dkk1 phenotype requires Szl.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Pediatric Research Initiative (rcdc)Animals (mesh)Body Patterning (mesh)Signal Transduction (mesh)Xenopus Proteins (mesh)beta Catenin (mesh)Intercellular Signaling Peptides and Proteins (mesh)Xenopus laevis (mesh)Gene Expression RegulationDevelopmental (mesh)Gastrulation (mesh)Nodal Protein (mesh)EmbryoNonmammalian (mesh)OrganizersEmbryonic (mesh)Glycoproteins (mesh)Huluwabeta- cateninCerberusChordinDickkopf 1EmbryoNonmammalian (mesh)OrganizersEmbryonic (mesh)Animals (mesh)Xenopus laevis (mesh)Glycoproteins (mesh)Intercellular Signaling Peptides and Proteins (mesh)Xenopus Proteins (mesh)Signal Transduction (mesh)Gene Expression RegulationDevelopmental (mesh)Body Patterning (mesh)beta Catenin (mesh)Gastrulation (mesh)Nodal Protein (mesh)CerberusChordinDickkopf 1Huluwaβ-cateninAnimals (mesh)Body Patterning (mesh)Signal Transduction (mesh)Xenopus Proteins (mesh)beta Catenin (mesh)Intercellular Signaling Peptides and Proteins (mesh)Xenopus laevis (mesh)Gene Expression RegulationDevelopmental (mesh)Gastrulation (mesh)Nodal Protein (mesh)EmbryoNonmammalian (mesh)OrganizersEmbryonic (mesh)Glycoproteins (mesh)application/pdfCC-BY-NCeScholarship, University of Californiahttps://escholarship.org/uc/item/44c6j6x9https://escholarship.org/content/qt44c6j6x9/qt44c6j6x9.pdfinfo:doi/10.1073/pnas.2408346121articleProceedings of the National Academy of Sciences of the United States of America, vol 121, iss 28e2408346121oai:escholarship.org:ark:/13030/qt25q3p1rc2026-08-10T23:03:54Zqt25q3p1rcSystematic characterization of all Toxoplasma gondii TBC domain-containing proteins identifies an essential regulator of Rab2 in the secretory pathwayQuan, Justin JNikolov, Lachezar ASha, JihuiWohlschlegel, James ACoppens, IsabelleBradley, Peter Jde Koning-Ward, Tania F2024-05-01Toxoplasma gondii resides in its intracellular niche by employing a series of specialized secretory organelles that play roles in invasion, host cell manipulation, and parasite replication. Rab GTPases are major regulators of the parasite's secretory traffic that function as nucleotide-dependent molecular switches to control vesicle trafficking. While many of the Rab proteins have been characterized in T. gondii, precisely how these Rabs are regulated remains poorly understood. To better understand the parasite's secretory traffic, we investigated the entire family of Tre2-Bub2-Cdc16 (TBC) domain-containing proteins, which are known to be involved in vesicle fusion and secretory protein trafficking. We first determined the localization of all 18 TBC domain-containing proteins to discrete regions of the secretory pathway or other vesicles in the parasite. Second, we use an auxin-inducible degron approach to demonstrate that the protozoan-specific TgTBC9 protein, which localizes to the endoplasmic reticulum (ER), is essential for parasite survival. Knockdown of TgTBC9 results in parasite growth arrest and affects the organization of the ER and mitochondrial morphology. TgTBC9 knockdown also results in the formation of large lipid droplets (LDs) and multi-membranous structures surrounded by ER membranes, further indicating a disruption of ER functions. We show that the conserved dual-finger active site in the TBC domain of the protein is critical for its GTPase-activating protein (GAP) function and that the Plasmodium falciparum orthologue of TgTBC9 can rescue the lethal knockdown. We additionally show by immunoprecipitation and yeast 2 hybrid analyses that TgTBC9 preferentially binds Rab2, indicating that the TBC9-Rab2 pair controls ER morphology and vesicular trafficking in the parasite. Together, these studies identify the first essential TBC protein described in any protozoan and provide new insight into intracellular vesicle trafficking in T. gondii.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Infectious Diseases (rcdc)Biodefense (rcdc)Emerging Infectious Diseases (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Toxoplasma (mesh)Protozoan Proteins (mesh)Endoplasmic Reticulum (mesh)rab2 GTP-Binding Protein (mesh)Secretory Pathway (mesh)Protein Domains (mesh)Protein Transport (mesh)Lipid Droplets (mesh)Animals (mesh)Humans (mesh)Endoplasmic Reticulum (mesh)Animals (mesh)Humans (mesh)Toxoplasma (mesh)rab2 GTP-Binding Protein (mesh)Protozoan Proteins (mesh)Protein Transport (mesh)Secretory Pathway (mesh)Lipid Droplets (mesh)Protein Domains (mesh)Toxoplasma (mesh)Protozoan Proteins (mesh)Endoplasmic Reticulum (mesh)rab2 GTP-Binding Protein (mesh)Secretory Pathway (mesh)Protein Domains (mesh)Protein Transport (mesh)Lipid Droplets (mesh)Animals (mesh)Humans (mesh)06 Biological Sciences (for)07 Agricultural and Veterinary Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)30 Agriculturalveterinary and food sciences (for-2020)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/25q3p1rchttps://escholarship.org/content/qt25q3p1rc/qt25q3p1rc.pdfinfo:doi/10.1371/journal.pbio.3002634articlePLOS Biology, vol 22, iss 5e3002634oai:escholarship.org:ark:/13030/qt8v1624v92026-08-10T23:03:26Zqt8v1624v9The Toxoplasma gondii effector GRA83 modulates the host’s innate immune response to regulate parasite infectionThind, Amara CMota, Caroline MGonçalves, Ana Paula NSha, JihuiWohlschlegel, James AMineo, Tiago WPBradley, Peter JMoreno, Silvia NJ2023-10-24Toxoplasma gondii's propensity to infect its host and cause disease is highly dependent on its ability to modulate host cell functions. One of the strategies the parasite uses to accomplish this is via the export of effector proteins from the secretory dense granules. Dense granule (GRA) proteins are known to play roles in nutrient acquisition, host cell cycle manipulation, and immune regulation. Here, we characterize a novel dense granule protein named GRA83, which localizes to the parasitophorous vacuole (PV) in tachyzoites and bradyzoites. Disruption of GRA83 results in increased virulence, weight loss, and parasitemia during the acute infection, as well as a marked increase in the cyst burden during the chronic infection. This increased parasitemia was associated with an accumulation of inflammatory infiltrates in tissues in both acute and chronic infections. Murine macrophages infected with ∆gra83 tachyzoites produced less interleukin-12 (IL-12) in vitro, which was confirmed with reduced IL-12 and interferon-gamma in vivo. This dysregulation of cytokines correlates with reduced nuclear translocation of the p65 subunit of the nuclear factor-κB (NF-κB) complex. While GRA15 similarly regulates NF-κB, infection with ∆gra83/∆gra15 parasites did not further reduce p65 translocation to the host cell nucleus, suggesting these GRAs function in converging pathways. We also used proximity labeling experiments to reveal candidate GRA83 interacting T. gondii-derived partners. Taken together, this work reveals a novel effector that stimulates the innate immune response, enabling the host to limit the parasite burden. Importance Toxoplasma gondii poses a significant public health concern as it is recognized as one of the leading foodborne pathogens in the United States. Infection with the parasite can cause congenital defects in neonates, life-threatening complications in immunosuppressed patients, and ocular disease. Specialized secretory organelles, including the dense granules, play an important role in the parasite's ability to efficiently invade and regulate components of the host's infection response machinery to limit parasite clearance and establish an acute infection. Toxoplasma's ability to avoid early clearance, while also successfully infecting the host long enough to establish a persistent chronic infection, is crucial in allowing for its transmission to a new host. While multiple GRAs directly modulate host signaling pathways, they do so in various ways highlighting the parasite's diverse arsenal of effectors that govern infection. Understanding how parasite-derived effectors harness host functions to evade defenses yet ensure a robust infection is important for understanding the complexity of the pathogen's tightly regulated infection. In this study, we characterize a novel secreted protein named GRA83 that stimulates the host cell's response to limit infection.3107 Microbiology (for-2020)31 Biological Sciences (for-2020)Emerging Infectious Diseases (rcdc)Foodborne Illness (rcdc)Infectious Diseases (rcdc)Biodefense (rcdc)2.1 Biological and endogenous factors (hrcs-rac)2.2 Factors relating to the physical environment (hrcs-rac)Infection (hrcs-hc)InfantNewborn (mesh)Humans (mesh)Animals (mesh)Mice (mesh)Toxoplasma (mesh)NF-kappa B (mesh)Protozoan Proteins (mesh)Parasitemia (mesh)Persistent Infection (mesh)CellsCultured (mesh)Parasitic Diseases (mesh)ImmunityInnate (mesh)Interleukin-12 (mesh)Toxoplasma gondiidense granulesGRA83GRA15NF-kappa Binnate immunityCellsCultured (mesh)Animals (mesh)Humans (mesh)Mice (mesh)Toxoplasma (mesh)Parasitemia (mesh)Parasitic Diseases (mesh)NF-kappa B (mesh)Protozoan Proteins (mesh)Interleukin-12 (mesh)InfantNewborn (mesh)ImmunityInnate (mesh)Persistent Infection (mesh)GRA15GRA83NF-κBToxoplasma gondiidense granulesinnate immunityInfantNewborn (mesh)Humans (mesh)Animals (mesh)Mice (mesh)Toxoplasma (mesh)NF-kappa B (mesh)Protozoan Proteins (mesh)Parasitemia (mesh)Persistent Infection (mesh)CellsCultured (mesh)Parasitic Diseases (mesh)ImmunityInnate (mesh)Interleukin-12 (mesh)1107 Immunology (for)Immunology (science-metrix)Microbiology (science-metrix)3204 Immunology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/8v1624v9https://escholarship.org/content/qt8v1624v9/qt8v1624v9.pdfinfo:doi/10.1128/msphere.00263-23articlemSphere, vol 8, iss 5e00263 - e00223oai:escholarship.org:ark:/13030/qt0gz1n6nw2026-08-10T22:45:37Zqt0gz1n6nwNa,K-ATPase activity promotes macropinocytosis in colon cancer via Wnt signalingTejeda-Muñoz, NydiaAzbazdar, YagmurSosa, Eric AMonka, JuliaWei, Pu-ShengBinder, GraceMei, Kuo-ChingKurmangaliyev, Yerbol ZDe Robertis, Edward M2024-05-15Recent research has shown that membrane trafficking plays an important role in canonical Wnt signaling through sequestration of the β-catenin destruction complex inside multivesicular bodies (MVBs) and lysosomes. In this study, we introduce Ouabain, an inhibitor of the Na,K-ATPase pump that establishes electric potentials across membranes, as a potent inhibitor of Wnt signaling. We find that Na,K-ATPase levels are elevated in advanced colon carcinoma, that this enzyme is elevated in cancer cells with constitutively activated Wnt pathway and is activated by GSK3 inhibitors that increase macropinocytosis. Ouabain blocks macropinocytosis, which is an essential step in Wnt signaling, probably explaining the strong effects of Ouabain on this pathway. In Xenopus embryos, brief Ouabain treatment at the 32-cell stage, critical for the earliest Wnt signal in development-inhibited brains, could be reversed by treatment with Lithium chloride, a Wnt mimic. Inhibiting membrane trafficking may provide a way of targeting Wnt-driven cancers.3101 Biochemistry and Cell Biology (for-2020)3208 Medical Physiology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Cancer (rcdc)Digestive Diseases (rcdc)Colo-Rectal Cancer (rcdc)Cancer (hrcs-hc)Animals (mesh)Humans (mesh)Cell LineTumor (mesh)Colonic Neoplasms (mesh)Ouabain (mesh)Pinocytosis (mesh)Sodium-Potassium-Exchanging ATPase (mesh)Wnt Signaling Pathway (mesh)Xenopus (mesh)Wnt signalingNaK-ATPaseOuabainMacropinocytosisColorectal carcinomaMultivesicular bodiesXenopus laevisCell LineTumor (mesh)Animals (mesh)Xenopus (mesh)Humans (mesh)Colonic Neoplasms (mesh)Ouabain (mesh)Pinocytosis (mesh)Sodium-Potassium-Exchanging ATPase (mesh)Wnt Signaling Pathway (mesh)Xenopus laevisColorectal carcinomaK-ATPaseMacropinocytosisMultivesicular bodiesNaOuabainWnt signalingAnimals (mesh)Humans (mesh)Cell LineTumor (mesh)Colonic Neoplasms (mesh)Ouabain (mesh)Pinocytosis (mesh)Sodium-Potassium-Exchanging ATPase (mesh)Wnt Signaling Pathway (mesh)Xenopus (mesh)0699 Other Biological Sciences (for)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)41 Environmental sciences (for-2020)application/pdfCC-BY-NCeScholarship, University of Californiahttps://escholarship.org/uc/item/0gz1n6nwhttps://escholarship.org/content/qt0gz1n6nw/qt0gz1n6nw.pdfinfo:doi/10.1242/bio.060269articleBiology Open, vol 13, iss 5bio060269oai:escholarship.org:ark:/13030/qt1jt0k2r02026-08-10T22:09:50Zqt1jt0k2r0The PMA phorbol ester tumor promoter increases canonical Wnt signaling via macropinocytosisTejeda-Munoz, NydiaAzbazdar, YagmurMonka, JuliaBinder, GraceDayrit, AlexAyala, RaulO'Brien, NeilDe Robertis, Edward M2023-10-30Activation of the Wnt pathway lies at the core of many human cancers. Wnt and macropinocytosis are often active in the same processes, and understanding how Wnt signaling and membrane trafficking cooperate should improve our understanding of embryonic development and cancer. Here, we show that a macropinocytosis activator, the tumor promoter phorbol 12-myristate 13-acetate (PMA), enhances Wnt signaling. Experiments using the Xenopus embryo as an in vivo model showed marked cooperation between the PMA phorbol ester and Wnt signaling, which was blocked by inhibitors of macropinocytosis, Rac1 activity, and lysosome acidification. Human colorectal cancer tissue arrays and xenografts in mice showed a correlation of cancer progression with increased macropinocytosis/multivesicular body/lysosome markers and decreased GSK3 levels. The crosstalk between canonical Wnt, focal adhesions, lysosomes, and macropinocytosis suggests possible therapeutic targets for cancer progression in Wnt-driven cancers.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)3211 Oncology and Carcinogenesis (for-2020)31 Biological Sciences (for-2020)Cancer (rcdc)Digestive Diseases (rcdc)Biotechnology (rcdc)Colo-Rectal Cancer (rcdc)Cancer (hrcs-hc)Female (mesh)Pregnancy (mesh)Humans (mesh)Animals (mesh)Mice (mesh)Carcinogens (mesh)Wnt Signaling Pathway (mesh)Glycogen Synthase Kinase 3 (mesh)Phorbol Esters (mesh)Esters (mesh)Neoplasms (mesh)Wnt signalingmacropinocytosislysosomescolorectal cancerbeta-cateninXenopusAnimals (mesh)Humans (mesh)Mice (mesh)Neoplasms (mesh)Esters (mesh)Phorbol Esters (mesh)Glycogen Synthase Kinase 3 (mesh)Carcinogens (mesh)Pregnancy (mesh)Female (mesh)Wnt Signaling Pathway (mesh)Wnt signalingcancer biologycolorectal cancerdevelopmental biologylysosomesmacropinocytosisxenopusβ-cateninFemale (mesh)Pregnancy (mesh)Humans (mesh)Animals (mesh)Mice (mesh)Carcinogens (mesh)Wnt Signaling Pathway (mesh)Glycogen Synthase Kinase 3 (mesh)Phorbol Esters (mesh)Esters (mesh)Neoplasms (mesh)0601 Biochemistry and Cell Biology (for)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/1jt0k2r0https://escholarship.org/content/qt1jt0k2r0/qt1jt0k2r0.pdfinfo:doi/10.7554/elife.89141articleELIFE, vol 12rp89141oai:escholarship.org:ark:/13030/qt54z5261r2026-08-10T20:54:05Zqt54z5261rMitochondrial contact site and cristae organizing system (MICOS) machinery supports heme biosynthesis by enabling optimal performance of ferrochelataseDietz, Jonathan VWilloughby, Mathilda MPiel, Robert BRoss, Teresa ABohovych, IrynaAddis, Hannah GFox, Jennifer LLanzilotta, William NDailey, Harry AWohlschlegel, James AReddi, Amit RMedlock, Amy EKhalimonchuk, Oleh2021-10-01Heme is an essential cofactor required for a plethora of cellular processes in eukaryotes. In metazoans the heme biosynthetic pathway is typically partitioned between the cytosol and mitochondria, with the first and final steps taking place in the mitochondrion. The pathway has been extensively studied and its biosynthetic enzymes structurally characterized to varying extents. Nevertheless, understanding of the regulation of heme synthesis and factors that influence this process in metazoans remains incomplete. Therefore, we investigated the molecular organization as well as the physical and genetic interactions of the terminal pathway enzyme, ferrochelatase (Hem15), in the yeast Saccharomyces cerevisiae. Biochemical and genetic analyses revealed dynamic association of Hem15 with Mic60, a core component of the mitochondrial contact site and cristae organizing system (MICOS). Loss of MICOS negatively impacts Hem15 activity, affects the size of the Hem15 high-mass complex, and results in accumulation of reactive and potentially toxic tetrapyrrole precursors that may cause oxidative damage. Restoring intermembrane connectivity in MICOS-deficient cells mitigates these cytotoxic effects. These data provide new insights into how heme biosynthetic machinery is organized and regulated, linking mitochondrial architecture-organizing factors to heme homeostasis.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Ferrochelatase (mesh)Heme (mesh)Mitochondria (mesh)Mitochondrial Membranes (mesh)Mitochondrial Proteins (mesh)MitochondriaHemeMICOSFerrochelataseYeastMitochondria (mesh)Heme (mesh)Ferrochelatase (mesh)Mitochondrial Proteins (mesh)Mitochondrial Membranes (mesh)FerrochelataseHemeMICOSMitochondriaYeastFerrochelatase (mesh)Heme (mesh)Mitochondria (mesh)Mitochondrial Membranes (mesh)Mitochondrial Proteins (mesh)0601 Biochemistry and Cell Biology (for)1101 Medical Biochemistry and Metabolomics (for)1115 Pharmacology and Pharmaceutical Sciences (for)3101 Biochemistry and cell biology (for-2020)3404 Medicinal and biomolecular chemistry (for-2020)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/54z5261rhttps://escholarship.org/content/qt54z5261r/qt54z5261r.pdfinfo:doi/10.1016/j.redox.2021.102125articleRedox Biology, vol 46102125oai:escholarship.org:ark:/13030/qt7k4312v22026-08-10T16:26:43Zqt7k4312v2Physical and in silico immunopeptidomic profiling of a cancer antigen prostatic acid phosphatase reveals targets enabling TCR isolationMao, ZhiyuanNesterenko, Pavlo AMcLaughlin, JamiDeng, WeixianSojo, Giselle BurtonCheng, DonghuiNoguchi, MiyakoChour, WilliamDeLucia, Diana CFinton, Kathryn AQin, YuObusan, Matthew BTran, WendyWang, LiangBangayan, Nathanael JTa, LisaChen, Chia-ChunSeet, Christopher SCrooks, Gay MPhillips, John WHeath, James RStrong, Roland KLee, John KWohlschlegel, James AWitte, Owen N2022-08-02Tissue-specific antigens can serve as targets for adoptive T cell transfer-based cancer immunotherapy. Recognition of tumor by T cells is mediated by interaction between peptide-major histocompatibility complexes (pMHCs) and T cell receptors (TCRs). Revealing the identity of peptides bound to MHC is critical in discovering cognate TCRs and predicting potential toxicity. We performed multimodal immunopeptidomic analyses for human prostatic acid phosphatase (PAP), a well-recognized tissue antigen. Three physical methods, including mild acid elution, coimmunoprecipitation, and secreted MHC precipitation, were used to capture a thorough signature of PAP on HLA-A*02:01. Eleven PAP peptides that are potentially A*02:01-restricted were identified, including five predicted strong binders by NetMHCpan 4.0. Peripheral blood mononuclear cells (PBMCs) from more than 20 healthy donors were screened with the PAP peptides. Seven cognate TCRs were isolated which can recognize three distinct epitopes when expressed in PBMCs. One TCR shows reactivity toward cell lines expressing both full-length PAP and HLA-A*02:01. Our results show that a combined multimodal immunopeptidomic approach is productive in revealing target peptides and defining the cloned TCR sequences reactive with prostatic acid phosphatase epitopes.32 Biomedical and Clinical Sciences (for-2020)3211 Oncology and Carcinogenesis (for-2020)3204 Immunology (for-2020)Cancer (rcdc)Immunization (rcdc)Vaccine Related (rcdc)Biotechnology (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Cancer (hrcs-hc)Acid Phosphatase (mesh)AntigensNeoplasm (mesh)Epitopes (mesh)HLA-A Antigens (mesh)HLA-A2 Antigen (mesh)Humans (mesh)LeukocytesMononuclear (mesh)Neoplasms (mesh)Peptides (mesh)ReceptorsAntigenT-Cell (mesh)T cell receptor (TCR)prostate cancerimmunopeptidomeprostatic acid phosphatasemajor histocompatibility complexes (MHC)LeukocytesMononuclear (mesh)Humans (mesh)Neoplasms (mesh)Acid Phosphatase (mesh)Peptides (mesh)ReceptorsAntigenT-Cell (mesh)AntigensNeoplasm (mesh)HLA-A Antigens (mesh)HLA-A2 Antigen (mesh)Epitopes (mesh)T cell receptor (TCR)immunopeptidomemajor histocompatibility complexes (MHC)prostate cancerprostatic acid phosphataseAcid Phosphatase (mesh)AntigensNeoplasm (mesh)Epitopes (mesh)HLA-A Antigens (mesh)HLA-A2 Antigen (mesh)Humans (mesh)LeukocytesMononuclear (mesh)Neoplasms (mesh)Peptides (mesh)ReceptorsAntigenT-Cell (mesh)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/7k4312v2https://escholarship.org/content/qt7k4312v2/qt7k4312v2.pdfinfo:doi/10.1073/pnas.2203410119articleProceedings of the National Academy of Sciences of the United States of America, vol 119, iss 31e2203410119oai:escholarship.org:ark:/13030/qt7f49k05g2026-08-10T13:22:14Zqt7f49k05gPRB1 Is Required for Clipping of the Histone H3 N Terminal Tail in Saccharomyces cerevisiaeXue, YongVashisht, Ajay ATan, YuliangSu, TrentWohlschlegel, James ABeh, Christopher2014-02-28Cathepsin L, a lysosomal protein in mouse embryonic stem cells has been shown to clip the histone H3 N- terminus, an activity associated with gene activity during mouse cell development. Glutamate dehydrogenase (GDH) was also identified as histone H3 specific protease in chicken liver, which has been connected to gene expression during aging. In baker's yeast, Saccharomyces cerevisiae, clipping the histone H3 N-terminus has been associated with gene activation in stationary phase but the protease responsible for the yeast histone H3 endopeptidase activity had not been identified. In searching for a yeast histone H3 endopeptidase, we found that yeast vacuolar protein Prb1 is present in the cellular fraction enriched for the H3 N-terminus endopeptidase activity and this endopeptidase activity is lost in the PRB1 deletion mutant (prb1Δ). In addition, like Cathepsin L and GDH, purified Prb1 from yeast cleaves H3 between Lys23 and Ala24 in the N-terminus in vitro as shown by Edman degradation. In conclusion, our data argue that PRB1 is required for clipping of the histone H3 N-terminal tail in Saccharomyces cerevisiae.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Alanine (mesh)BlottingWestern (mesh)Endopeptidases (mesh)Histones (mesh)Lysine (mesh)Mass Spectrometry (mesh)Mutation (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)Saccharomyces cerevisiae (mesh)Endopeptidases (mesh)Alanine (mesh)Lysine (mesh)Saccharomyces cerevisiae Proteins (mesh)Histones (mesh)BlottingWestern (mesh)Mutation (mesh)Mass Spectrometry (mesh)Alanine (mesh)BlottingWestern (mesh)Endopeptidases (mesh)Histones (mesh)Lysine (mesh)Mass Spectrometry (mesh)Mutation (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)General Science & Technology (science-metrix)application/pdfhttps://creativecommons.org/publicdomain/zero/1.0/eScholarship, University of Californiahttps://escholarship.org/uc/item/7f49k05ghttps://escholarship.org/content/qt7f49k05g/qt7f49k05g.pdfinfo:doi/10.1371/journal.pone.0090496articlePLOS ONE, vol 9, iss 2e90496oai:escholarship.org:ark:/13030/qt5g14b1872026-08-09T13:52:27Zqt5g14b187Glucose inhibits cardiac muscle maturation through nucleotide biosynthesisNakano, HarukoMinami, ItsunariBraas, DanielPappoe, HermanWu, XiujuSagadevan, AddelynnVergnes, LaurentFu, KaiMorselli, MarcoDunham, ChristopherDing, XueqinStieg, Adam ZGimzewski, James KPellegrini, MatteoClark, Peter MReue, KarenLusis, Aldons JRibalet, BernardKurdistani, Siavash KChristofk, HeatherNakatsuji, NorioNakano, Atsushi2016-01-01The heart switches its energy substrate from glucose to fatty acids at birth, and maternal hyperglycemia is associated with congenital heart disease. However, little is known about how blood glucose impacts heart formation. Using a chemically defined human pluripotent stem-cell-derived cardiomyocyte differentiation system, we found that high glucose inhibits the maturation of cardiomyocytes at genetic, structural, metabolic, electrophysiological, and biomechanical levels by promoting nucleotide biosynthesis through the pentose phosphate pathway. Blood glucose level in embryos is stable in utero during normal pregnancy, but glucose uptake by fetal cardiac tissue is drastically reduced in late gestational stages. In a murine model of diabetic pregnancy, fetal hearts showed cardiomyopathy with increased mitotic activity and decreased maturity. These data suggest that high glucose suppresses cardiac maturation, providing a possible mechanistic basis for congenital heart disease in diabetic pregnancy.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)3201 Cardiovascular Medicine and Haematology (for-2020)3215 Reproductive Medicine (for-2020)Heart Disease (rcdc)Congenital Heart Disease (rcdc)Pregnancy (rcdc)Cardiovascular (rcdc)Stem Cell Research - Embryonic - Human (rcdc)Diabetes (rcdc)Stem Cell Research (rcdc)Perinatal Period - Conditions Originating in Perinatal Period (rcdc)Congenital Structural Anomalies (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell (rcdc)Regenerative Medicine (rcdc)Women's Health (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell - Human (rcdc)Pediatric Research Initiative (rcdc)Rare Diseases (rcdc)Nutrition (rcdc)5.1 Pharmaceuticals (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Cardiovascular (hrcs-hc)Reproductive health and childbirth (hrcs-hc)Animals (mesh)Cell Differentiation (mesh)Embryonic Stem Cells (mesh)Female (mesh)Gene Expression Profiling (mesh)Glucose (mesh)Humans (mesh)Mice (mesh)MiceInbred C57BL (mesh)Muscle Development (mesh)Myocardium (mesh)MyocytesCardiac (mesh)Nucleotides (mesh)Pentose Phosphate Pathway (mesh)Pregnancy (mesh)Sweetening Agents (mesh)Myocardium (mesh)MyocytesCardiac (mesh)Animals (mesh)MiceInbred C57BL (mesh)Humans (mesh)Mice (mesh)Nucleotides (mesh)Glucose (mesh)Sweetening Agents (mesh)Gene Expression Profiling (mesh)Cell Differentiation (mesh)Muscle Development (mesh)Pregnancy (mesh)Female (mesh)Pentose Phosphate Pathway (mesh)Embryonic Stem Cells (mesh)cardiacdevelopmental biologydiabeteshumanhuman pluripotent stem cellmousestem cellsAnimals (mesh)Cell Differentiation (mesh)Embryonic Stem Cells (mesh)Female (mesh)Gene Expression Profiling (mesh)Glucose (mesh)Humans (mesh)Mice (mesh)MiceInbred C57BL (mesh)Muscle Development (mesh)Myocardium (mesh)MyocytesCardiac (mesh)Nucleotides (mesh)Pentose Phosphate Pathway (mesh)Pregnancy (mesh)Sweetening Agents (mesh)0601 Biochemistry and Cell Biology (for)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/5g14b187https://escholarship.org/content/qt5g14b187/qt5g14b187.pdfinfo:doi/10.7554/elife.29330articleMOLECULAR BIOLOGY OF THE CELL, vol 6e29330oai:escholarship.org:ark:/13030/qt7gd458dv2026-08-09T07:04:19Zqt7gd458dvMammalian miRNA RISC Recruits CAF1 and PABP to Affect PABP-Dependent DeadenylationFabian, Marc RMathonnet, GéraldineSundermeier, ThomasMathys, HansruediZipprich, Jakob TSvitkin, Yuri VRivas, FabiolaJinek, MartinWohlschlegel, JamesDoudna, Jennifer AChen, Chyi-Ying AShyu, Ann-BinYates, John RHannon, Gregory JFilipowicz, WitoldDuchaine, Thomas FSonenberg, Nahum2009-09-01MicroRNAs (miRNAs) inhibit mRNA expression in general by base pairing to the 3'UTR of target mRNAs and consequently inhibiting translation and/or initiating poly(A) tail deadenylation and mRNA destabilization. Here we examine the mechanism and kinetics of miRNA-mediated deadenylation in mouse Krebs-2 ascites extract. We demonstrate that miRNA-mediated mRNA deadenylation occurs subsequent to initial translational inhibition, indicating a two-step mechanism of miRNA action, which serves to consolidate repression. We show that a let-7 miRNA-loaded RNA-induced silencing complex (miRISC) interacts with the poly(A)-binding protein (PABP) and the CAF1 and CCR4 deadenylases. In addition, we demonstrate that miRNA-mediated deadenylation is dependent upon CAF1 activity and PABP, which serves as a bona fide miRNA coactivator. Importantly, we present evidence that GW182, a core component of the miRISC, directly interacts with PABP via its C-terminal region and that this interaction is required for miRNA-mediated deadenylation.31 Biological Sciences (for-2020)Biotechnology (rcdc)Genetics (rcdc)5.1 Pharmaceuticals (hrcs-rac)Animals (mesh)Argonaute Proteins (mesh)Ascites (mesh)Autoantigens (mesh)Binding Sites (mesh)CarcinomaKrebs 2 (mesh)Cell-Free System (mesh)Eukaryotic Initiation Factor-2 (mesh)Eukaryotic Initiation Factor-4G (mesh)Exoribonucleases (mesh)Gene Silencing (mesh)HeLa Cells (mesh)Humans (mesh)Kinetics (mesh)Mice (mesh)MicroRNAs (mesh)Poly(A)-Binding Proteins (mesh)Protein Biosynthesis (mesh)Protein StructureTertiary (mesh)Proteins (mesh)RNA ProcessingPost-Transcriptional (mesh)RNA Stability (mesh)RNAMessenger (mesh)RNA-Induced Silencing Complex (mesh)ReceptorsCCR4 (mesh)Repressor Proteins (mesh)Ribonucleases (mesh)Transfection (mesh)Hela Cells (mesh)Cell-Free System (mesh)Animals (mesh)Humans (mesh)Mice (mesh)CarcinomaKrebs 2 (mesh)Ascites (mesh)RNA-Induced Silencing Complex (mesh)Exoribonucleases (mesh)Ribonucleases (mesh)Proteins (mesh)Poly(A)-Binding Proteins (mesh)Eukaryotic Initiation Factor-2 (mesh)Eukaryotic Initiation Factor-4G (mesh)Repressor Proteins (mesh)MicroRNAs (mesh)RNAMessenger (mesh)Autoantigens (mesh)Transfection (mesh)Protein Biosynthesis (mesh)Gene Silencing (mesh)RNA ProcessingPost-Transcriptional (mesh)Binding Sites (mesh)Protein StructureTertiary (mesh)RNA Stability (mesh)Kinetics (mesh)ReceptorsCCR4 (mesh)Argonaute Proteins (mesh)Animals (mesh)Argonaute Proteins (mesh)Ascites (mesh)Autoantigens (mesh)Binding Sites (mesh)CarcinomaKrebs 2 (mesh)Cell-Free System (mesh)Eukaryotic Initiation Factor-2 (mesh)Eukaryotic Initiation Factor-4G (mesh)Exoribonucleases (mesh)Gene Silencing (mesh)HeLa Cells (mesh)Humans (mesh)Kinetics (mesh)Mice (mesh)MicroRNAs (mesh)Poly(A)-Binding Proteins (mesh)Protein Biosynthesis (mesh)Protein StructureTertiary (mesh)Proteins (mesh)RNA ProcessingPost-Transcriptional (mesh)RNA Stability (mesh)RNAMessenger (mesh)RNA-Induced Silencing Complex (mesh)ReceptorsCCR4 (mesh)Repressor Proteins (mesh)Ribonucleases (mesh)Transfection (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/7gd458dvhttps://escholarship.org/content/qt7gd458dv/qt7gd458dv.pdfinfo:doi/10.1016/j.molcel.2009.08.004articleMolecular Cell, vol 35, iss 6868 - 880oai:escholarship.org:ark:/13030/qt2690z67z2026-08-09T03:32:24Zqt2690z67zProteomic Analysis of Ferrochelatase Interactome in Erythroid and Non-Erythroid CellsDavid, ChibuikeDailey, Harry AJami-Alahmadi, YasamanWohlschlegel, James AMedlock, Amy E2023-02-01Heme is an essential cofactor for multiple cellular processes in most organisms. In developing erythroid cells, the demand for heme synthesis is high, but is significantly lower in non-erythroid cells. While the biosynthesis of heme in metazoans is well understood, the tissue-specific regulation of the pathway is less explored. To better understand this, we analyzed the mitochondrial heme metabolon in erythroid and non-erythroid cell lines from the perspective of ferrochelatase (FECH), the terminal enzyme in the heme biosynthetic pathway. Affinity purification of FLAG-tagged-FECH, together with mass spectrometric analysis, was carried out to identify putative protein partners in human and murine cell lines. Proteins involved in the heme biosynthetic process and mitochondrial organization were identified as the core components of the FECH interactome. Interestingly, in non-erythroid cell lines, the FECH interactome is highly enriched with proteins associated with the tricarboxylic acid (TCA) cycle. Overall, our study shows that the mitochondrial heme metabolon in erythroid and non-erythroid cells has similarities and differences, and suggests new roles for the mitochondrial heme metabolon and heme in regulating metabolic flux and key cellular processes.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Biotechnology (rcdc)Hematology (rcdc)1.1 Normal biological development and functioning (hrcs-rac)erythroidferrochelatasehemeheme biosynthesisinteractomemetabolonmitochondrianon-erythroidtricarboxylic acid cycleerythroidferrochelatasehemeheme biosynthesisinteractomemetabolonmitochondrianon-erythroidtricarboxylic acid cycle3101 Biochemistry and cell biology (for-2020)3104 Evolutionary biology (for-2020)4601 Applied computing (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/2690z67zhttps://escholarship.org/content/qt2690z67z/qt2690z67z.pdfinfo:doi/10.3390/life13020577articleLife, vol 13, iss 2577oai:escholarship.org:ark:/13030/qt0t7504jq2026-08-09T01:26:37Zqt0t7504jqThe role of histone H3 leucine 126 in fine-tuning the copper reductase activity of nucleosomesTod, Nataliya PVogelauer, MariaCheng, ChenKarimian, AnsarSchmollinger, StefanCamacho, DimitriosKurdistani, Siavash K2024-06-01The copper reductase activity of histone H3 suggests undiscovered characteristics within the protein. Here, we investigated the function of leucine 126 (H3L126), which occupies an axial position relative to the copper binding. Typically found as methionine or leucine in copper-binding proteins, the axial ligand influences the reduction potential of the bound ion, modulating its tendency to accept or yield electrons. We found that mutation of H3L126 to methionine (H3L126M) enhanced the enzymatic activity of native yeast nucleosomes in vitro and increased intracellular levels of Cu1+, leading to improved copper-dependent activities including mitochondrial respiration and growth in oxidative media with low copper. Conversely, H3L126 to histidine (H3L126H) mutation decreased nucleosome's enzymatic activity and adversely affected copper-dependent activities in vivo. Our findings demonstrate that H3L126 fine-tunes the copper reductase activity of nucleosomes and highlights the utility of nucleosome enzymatic activity as a novel paradigm to uncover previously unnoticed features of histones.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)2.1 Biological and endogenous factors (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)Nucleosomes (mesh)Histones (mesh)Copper (mesh)Saccharomyces cerevisiae (mesh)Leucine (mesh)Saccharomyces cerevisiae Proteins (mesh)Oxidoreductases (mesh)Amino Acid Substitution (mesh)MutationMissense (mesh)Nucleosomes (mesh)Saccharomyces cerevisiae (mesh)Copper (mesh)Oxidoreductases (mesh)Leucine (mesh)Saccharomyces cerevisiae Proteins (mesh)Histones (mesh)Amino Acid Substitution (mesh)MutationMissense (mesh)chromatincopperhistonereductaseyeastNucleosomes (mesh)Histones (mesh)Copper (mesh)Saccharomyces cerevisiae (mesh)Leucine (mesh)Saccharomyces cerevisiae Proteins (mesh)Oxidoreductases (mesh)Amino Acid Substitution (mesh)MutationMissense (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biochemistry & Molecular Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/0t7504jqhttps://escholarship.org/content/qt0t7504jq/qt0t7504jq.pdfinfo:doi/10.1016/j.jbc.2024.107314articleJournal of Biological Chemistry, vol 300, iss 6107314oai:escholarship.org:ark:/13030/qt9tx7920r2026-08-09T01:08:03Zqt9tx7920rTranscription factor PATZ1 promotes adipogenesis by controlling promoter regulatory loci of adipogenic factorsPatel, SanilGanbold, KhatanzulCho, Chung HwanSiddiqui, JuwairriyyahYildiz, RamazanSparman, NjeriSadeh, ShaniNguyen, Christy MWang, JiexinWhitelegge, Julian PFried, Susan KWaki, HironoriVillanueva, Claudio JSeldin, Marcus MSakaguchi, ShinyaEllmeier, WilfriedTontonoz, PeterRajbhandari, Prashant2024-10-02White adipose tissue (WAT) is essential for lipid storage and systemic energy homeostasis. Understanding adipocyte formation and stability is key to developing therapies for obesity and metabolic disorders. Through a high-throughput cDNA screen, we identified PATZ1, a POZ/BTB and AT-Hook Containing Zinc Finger 1 protein, as an important adipogenic transcription factor. PATZ1 is expressed in human and mouse adipocyte precursor cells (APCs) and adipocytes. In cellular models, PATZ1 promotes adipogenesis via protein-protein interactions and DNA binding. PATZ1 ablation in mouse adipocytes and APCs leads to a reduced APC pool, decreased fat mass, and hypertrophied adipocytes. ChIP-Seq and RNA-seq analyses show that PATZ1 supports adipogenesis by interacting with transcriptional machinery at the promoter regions of key early adipogenic factors. Mass-spec results show that PATZ1 associates with GTF2I, with GTF2I modulating PATZ1’s function during differentiation. These findings underscore PATZ1’s regulatory role in adipocyte differentiation and adiposity, offering insights into adipose tissue development.3101 Biochemistry and Cell Biology (for-2020)3102 Bioinformatics and Computational Biology (for-2020)31 Biological Sciences (for-2020)Human Genome (rcdc)Stem Cell Research (rcdc)Stem Cell Research - Nonembryonic - Non-Human (rcdc)Biotechnology (rcdc)Diabetes (rcdc)Nutrition (rcdc)Obesity (rcdc)Genetics (rcdc)Stem Cell Research - Nonembryonic - Human (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)7 Affordable and Clean Energy (sdg)Animals (mesh)Female (mesh)Humans (mesh)Male (mesh)Mice (mesh)3T3-L1 Cells (mesh)Adipocytes (mesh)Adipogenesis (mesh)Adipose TissueWhite (mesh)Cell Differentiation (mesh)Gene Expression Regulation (mesh)MiceInbred C57BL (mesh)Promoter RegionsGenetic (mesh)Transcription Factors (mesh)Repressor Proteins (mesh)Kruppel-Like Transcription Factors (mesh)Neoplasm Proteins (mesh)3T3-L1 Cells (mesh)Adipocytes (mesh)Animals (mesh)MiceInbred C57BL (mesh)Humans (mesh)Mice (mesh)Neoplasm Proteins (mesh)Transcription Factors (mesh)Repressor Proteins (mesh)Cell Differentiation (mesh)Gene Expression Regulation (mesh)Female (mesh)Male (mesh)Adipogenesis (mesh)Kruppel-Like Transcription Factors (mesh)Adipose TissueWhite (mesh)Promoter RegionsGenetic (mesh)Animals (mesh)Female (mesh)Humans (mesh)Male (mesh)Mice (mesh)3T3-L1 Cells (mesh)Adipocytes (mesh)Adipogenesis (mesh)Adipose TissueWhite (mesh)Cell Differentiation (mesh)Gene Expression Regulation (mesh)MiceInbred C57BL (mesh)Promoter RegionsGenetic (mesh)Transcription Factors (mesh)Repressor Proteins (mesh)Kruppel-Like Transcription Factors (mesh)Neoplasm Proteins (mesh)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/9tx7920rhttps://escholarship.org/content/qt9tx7920r/qt9tx7920r.pdfinfo:doi/10.1038/s41467-024-52917-yarticleNature Communications, vol 15, iss 18533oai:escholarship.org:ark:/13030/qt58j8v2zt2026-08-09T00:51:49Zqt58j8v2ztBuilding an Ethical and Trustworthy Biomedical AI Ecosystem for the Translational and Clinical Integration of Foundation ModelsSankar, Baradwaj SimhaGilliland, DestinyRincon, JackHermjakob, HenningYan, YuAdam, IrsyadLemaster, GwynethWang, DeanWatson, KarolBui, AlexWang, WeiPing, Peipei2024-10-01Foundation Models (FMs) are gaining increasing attention in the biomedical artificial intelligence (AI) ecosystem due to their ability to represent and contextualize multimodal biomedical data. These capabilities make FMs a valuable tool for a variety of tasks, including biomedical reasoning, hypothesis generation, and interpreting complex imaging data. In this review paper, we address the unique challenges associated with establishing an ethical and trustworthy biomedical AI ecosystem, with a particular focus on the development of FMs and their downstream applications. We explore strategies that can be implemented throughout the biomedical AI pipeline to effectively tackle these challenges, ensuring that these FMs are translated responsibly into clinical and translational settings. Additionally, we emphasize the importance of key stewardship and co-design principles that not only ensure robust regulation but also guarantee that the interests of all stakeholders-especially those involved in or affected by these clinical and translational applications-are adequately represented. We aim to empower the biomedical AI community to harness these models responsibly and effectively. As we navigate this exciting frontier, our collective commitment to ethical stewardship, co-design, and responsible translation will be instrumental in ensuring that the evolution of FMs truly enhances patient care and medical decision-making, ultimately leading to a more equitable and trustworthy biomedical AI ecosystem.40 Engineering (for-2020)4003 Biomedical Engineering (for-2020)Data Science (rcdc)Machine Learning and Artificial Intelligence (rcdc)Bioengineering (rcdc)Networking and Information Technology R&D (NITRD) (rcdc)Generic health relevance (hrcs-hc)Mental health (hrcs-hc)biomedical AIFoundation ModelsAI ecosystemAI lifecyleclinical integrationethical AItrustworthy AIAI governance and regulationstakeholder engagementAI ecosystemAI governance and regulationAI lifecyleFoundation Modelsbiomedical AIclinical integrationethical AIstakeholder engagementtrustworthy AI4003 Biomedical engineering (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/58j8v2zthttps://escholarship.org/content/qt58j8v2zt/qt58j8v2zt.pdfinfo:doi/10.3390/bioengineering11100984articleBioengineering, vol 11, iss 10984oai:escholarship.org:ark:/13030/qt8w11m1fp2026-08-08T23:13:27Zqt8w11m1fpEarly prediction of end-stage kidney disease using electronic health record data: a machine learning approach with a 2-year horizonPetousis, PanayiotisWilson, James MGelvezon, Alex VAlam, ShafiulJain, AnkurPrichard, LauraElashoff, David ARaja, NaveenBui, Alex AT2024-01-04Objectives: In the United States, end-stage kidney disease (ESKD) is responsible for high mortality and significant healthcare costs, with the number of cases sharply increasing in the past 2 decades. In this study, we aimed to reduce these impacts by developing an ESKD model for predicting its occurrence in a 2-year period.
Materials and Methods: We developed a machine learning (ML) pipeline to test different models for the prediction of ESKD. The electronic health record was used to capture several kidney disease-related variables. Various imputation methods, feature selection, and sampling approaches were tested. We compared the performance of multiple ML models using area under the ROC curve (AUCROC), area under the Precision-Recall curve (PR-AUC), and Brier scores for discrimination, precision, and calibration, respectively. Explainability methods were applied to the final model.
Results: Our best model was a gradient-boosting machine with feature selection and imputation methods as additional components. The model exhibited an AUCROC of 0.97, a PR-AUC of 0.33, and a Brier score of 0.002 on a holdout test set. A chart review analysis by expert physicians indicated clinical utility.
Discussion and Conclusion: An ESKD prediction model can identify individuals at risk for ESKD and has been successfully deployed within our health system.4203 Health Services and Systems (for-2020)42 Health Sciences (for-2020)Kidney Disease (rcdc)Data Science (rcdc)Bioengineering (rcdc)Precision Medicine (rcdc)Machine Learning and Artificial Intelligence (rcdc)Social Determinants of Health (rcdc)Networking and Information Technology R&D (NITRD) (rcdc)3 Good Health and Well Being (sdg)machine learning deploymentearly prediction ESKD modelelectronic health recordend-stage kidney disease (ESKD)early prediction ESKD modelelectronic health recordend-stage kidney disease (ESKD)machine learning deployment4203 Health services and systems (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/8w11m1fphttps://escholarship.org/content/qt8w11m1fp/qt8w11m1fp.pdfinfo:doi/10.1093/jamiaopen/ooae015articleJAMIA Open, vol 7, iss 1ooae015oai:escholarship.org:ark:/13030/qt2s73j3rq2026-08-08T23:00:00Zqt2s73j3rqA conserved mechanism for JNK-mediated loss of Notch function in advanced prostate cancerWang, Cheng-WeiClémot, MarieHashimoto, TakaoDiaz, Johnny AGoins, Lauren MGoldstein, Andrew SNagaraj, RaghavendraBanerjee, Utpal2023-11-07Dysregulated Notch signaling is a common feature of cancer; however, its effects on tumor initiation and progression are highly variable, with Notch having either oncogenic or tumor-suppressive functions in various cancers. To better understand the mechanisms that regulate Notch function in cancer, we studied Notch signaling in a Drosophila tumor model, prostate cancer-derived cell lines, and tissue samples from patients with advanced prostate cancer. We demonstrated that increased activity of the Src-JNK pathway in tumors inactivated Notch signaling because of JNK pathway-mediated inhibition of the expression of the gene encoding the Notch S2 cleavage protease, Kuzbanian, which is critical for Notch activity. Consequently, inactive Notch accumulated in cells, where it was unable to transcribe genes encoding its target proteins, many of which have tumor-suppressive activities. These findings suggest that Src-JNK activity in tumors predicts Notch activity status and that suppressing Src-JNK signaling could restore Notch function in tumors, offering opportunities for diagnosis and targeted therapies for a subset of patients with advanced prostate cancer.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Aging (rcdc)Urologic Diseases (rcdc)Prostate Cancer (rcdc)Cancer (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Cancer (hrcs-hc)Animals (mesh)Male (mesh)Humans (mesh)Drosophila Proteins (mesh)ReceptorsNotch (mesh)Drosophila (mesh)Signal Transduction (mesh)Prostatic Neoplasms (mesh)Animals (mesh)Humans (mesh)Drosophila (mesh)Prostatic Neoplasms (mesh)Drosophila Proteins (mesh)Signal Transduction (mesh)Male (mesh)ReceptorsNotch (mesh)Animals (mesh)Male (mesh)Humans (mesh)Drosophila Proteins (mesh)ReceptorsNotch (mesh)Drosophila (mesh)Signal Transduction (mesh)Prostatic Neoplasms (mesh)0601 Biochemistry and Cell Biology (for)3101 Biochemistry and cell biology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2s73j3rqhttps://escholarship.org/content/qt2s73j3rq/qt2s73j3rq.pdfinfo:doi/10.1126/scisignal.abo5213articleScience Signaling, vol 16, iss 810eabo5213 - eabo5213oai:escholarship.org:ark:/13030/qt8t20g57w2026-08-08T22:56:11Zqt8t20g57wAlveolar macrophage lipid burden correlates with clinical improvement in patients with pulmonary alveolar proteinosisLee, ElinorWilliams, Kevin JMcCarthy, CormacBridges, James PRedente, Elizabeth Fde Aguiar Vallim, Thomas QBarrington, Robert AWang, TishaTarling, Elizabeth J2024-02-01Pulmonary alveolar proteinosis (PAP) is a life-threatening, rare lung syndrome for which there is no cure and no approved therapies. PAP is a disease of lipid accumulation characterized by alveolar macrophage foam cell formation. While much is known about the clinical presentation, there is a paucity of information regarding temporal changes in lipids throughout the course of disease. Our objectives were to define the detailed lipid composition of alveolar macrophages in PAP patients at the time of diagnosis and during treatment. We performed comprehensive mass spectrometry to profile the lipid signature of alveolar macrophages obtained from three independent mouse models of PAP and from PAP and non-PAP patients. Additionally, we quantified changes in macrophage-associated lipids during clinical treatment of PAP patients. We found remarkable variations in lipid composition in PAP patients, which were consistent with data from three independent mouse models. Detailed lipidomic analysis revealed that the overall alveolar macrophage lipid burden inversely correlated with clinical improvement and response to therapy in PAP patients. Specifically, as PAP patients experienced clinical improvement, there was a notable decrease in the total lipid content of alveolar macrophages. This crucial observation suggests that the levels of these macrophage-associated lipids can be utilized to assess the efficacy of treatment. These findings provide valuable insights into the dysregulated lipid metabolism associated with PAP, offering the potential for lipid profiling to serve as a means of monitoring therapeutic interventions in PAP patients.32 Biomedical and Clinical Sciences (for-2020)3202 Clinical Sciences (for-2020)Clinical Research (rcdc)Lung (rcdc)Rare Diseases (rcdc)Orphan Drug (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Respiratory (hrcs-hc)Animals (mesh)Mice (mesh)Humans (mesh)Pulmonary Alveolar Proteinosis (mesh)MacrophagesAlveolar (mesh)Lung (mesh)Macrophages (mesh)Lipids (mesh)Cholesterolfoam cellslipidomicslipidsphospholipidspulmonary surfactantpulmonary alveolar proteinosisalveolar macrophagesLung (mesh)Macrophages (mesh)MacrophagesAlveolar (mesh)Animals (mesh)Humans (mesh)Mice (mesh)Pulmonary Alveolar Proteinosis (mesh)Lipids (mesh)Cholesterolalveolar macrophagesfoam cellslipidomicslipidsphospholipidspulmonary alveolar proteinosispulmonary surfactantAnimals (mesh)Mice (mesh)Humans (mesh)Pulmonary Alveolar Proteinosis (mesh)MacrophagesAlveolar (mesh)Lung (mesh)Macrophages (mesh)Lipids (mesh)0601 Biochemistry and Cell Biology (for)1101 Medical Biochemistry and Metabolomics (for)Biochemistry & Molecular Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)3205 Medical biochemistry and metabolomics (for-2020)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/8t20g57whttps://escholarship.org/content/qt8t20g57w/qt8t20g57w.pdfinfo:doi/10.1016/j.jlr.2024.100496articleJournal of Lipid Research, vol 65, iss 2100496oai:escholarship.org:ark:/13030/qt5cf8z1wj2026-08-08T21:33:54Zqt5cf8z1wjHypertriglyceridemia in Apoa5–/– mice results from reduced amounts of lipoprotein lipase in the capillary lumenYang, YeBeigneux, Anne PSong, WenxinNguyen, Le PhuongJung, HyesooTu, YipingWeston, Thomas ATran, Caitlyn MXie, KatherineYu, Rachel GTran, Anh PMiyashita, KazuyaNakajima, KatsuyukiMurakami, MasamiChen, Yan QZhen, Eugene YKim, Joonyoung RKim, Paul HBirrane, GabrielTontonoz, PeterPloug, MichaelKonrad, Robert JFong, Loren GYoung, Stephen G2023-12-01Why apolipoprotein AV (APOA5) deficiency causes hypertriglyceridemia has remained unclear, but we have suspected that the underlying cause is reduced amounts of lipoprotein lipase (LPL) in capillaries. By routine immunohistochemistry, we observed reduced LPL staining of heart and brown adipose tissue (BAT) capillaries in Apoa5-/- mice. Also, after an intravenous injection of LPL-, CD31-, and GPIHBP1-specific mAbs, the binding of LPL Abs to heart and BAT capillaries (relative to CD31 or GPIHBP1 Abs) was reduced in Apoa5-/- mice. LPL levels in the postheparin plasma were also lower in Apoa5-/- mice. We suspected that a recent biochemical observation - that APOA5 binds to the ANGPTL3/8 complex and suppresses its capacity to inhibit LPL catalytic activity - could be related to the low intracapillary LPL levels in Apoa5-/- mice. We showed that an ANGPTL3/8-specific mAb (IBA490) and APOA5 normalized plasma triglyceride (TG) levels and intracapillary LPL levels in Apoa5-/- mice. We also showed that ANGPTL3/8 detached LPL from heparan sulfate proteoglycans and GPIHBP1 on the surface of cells and that the LPL detachment was blocked by IBA490 and APOA5. Our studies explain the hypertriglyceridemia in Apoa5-/- mice and further illuminate the molecular mechanisms that regulate plasma TG metabolism.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Biotechnology (rcdc)Heart Disease (rcdc)Cardiovascular (rcdc)Animals (mesh)Mice (mesh)Capillaries (mesh)Hypertriglyceridemia (mesh)Lipoprotein Lipase (mesh)ReceptorsLipoprotein (mesh)Triglycerides (mesh)Apolipoprotein A-V (mesh)Vascular biologyCapillaries (mesh)Animals (mesh)Mice (mesh)Hypertriglyceridemia (mesh)Lipoprotein Lipase (mesh)Triglycerides (mesh)ReceptorsLipoprotein (mesh)Apolipoprotein A-V (mesh)Endothelial cellsLipoproteinsMetabolismMouse modelsVascular BiologyAnimals (mesh)Mice (mesh)Capillaries (mesh)Hypertriglyceridemia (mesh)Lipoprotein Lipase (mesh)ReceptorsLipoprotein (mesh)Triglycerides (mesh)Apolipoprotein A-V (mesh)11 Medical and Health Sciences (for)Immunology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/5cf8z1wjhttps://escholarship.org/content/qt5cf8z1wj/qt5cf8z1wj.pdfinfo:doi/10.1172/jci172600articleJournal of Clinical Investigation, vol 133, iss 23e172600oai:escholarship.org:ark:/13030/qt6bc5h2522026-08-08T21:33:46Zqt6bc5h252Pan-cancer landscape of epigenetic factor expression predicts tumor outcomeCheng, Michael WMitra, MithunColler, Hilary A2023-11-16Oncogenic pathways that drive cancer progression reflect both genetic changes and epigenetic regulation. Here we stratified primary tumors from each of 24 TCGA adult cancer types based on the gene expression patterns of epigenetic factors (epifactors). The tumors for five cancer types (ACC, KIRC, LGG, LIHC, and LUAD) separated into two robust clusters that were better than grade or epithelial-to-mesenchymal transition in predicting clinical outcomes. The majority of epifactors that drove the clustering were also individually prognostic. A pan-cancer machine learning model deploying epifactor expression data for these five cancer types successfully separated the patients into poor and better outcome groups. Single-cell analysis of adult and pediatric tumors revealed that expression patterns associated with poor or worse outcomes were present in individual cells within tumors. Our study provides an epigenetic map of cancer types and lays a foundation for discovering pan-cancer targetable epifactors.31 Biological Sciences (for-2020)32 Biomedical and Clinical Sciences (for-2020)3211 Oncology and Carcinogenesis (for-2020)Cancer Genomics (rcdc)Networking and Information Technology R&D (NITRD) (rcdc)Machine Learning and Artificial Intelligence (rcdc)Biotechnology (rcdc)Cancer (rcdc)Human Genome (rcdc)Rare Diseases (rcdc)Genetics (rcdc)Cancer (hrcs-hc)3 Good Health and Well Being (sdg)Adult (mesh)Child (mesh)Humans (mesh)EpigenesisGenetic (mesh)Neoplasms (mesh)Cluster Analysis (mesh)Epithelial-Mesenchymal Transition (mesh)Machine Learning (mesh)Humans (mesh)Neoplasms (mesh)Cluster Analysis (mesh)EpigenesisGenetic (mesh)Adult (mesh)Child (mesh)Epithelial-Mesenchymal Transition (mesh)Machine Learning (mesh)Adult (mesh)Child (mesh)Humans (mesh)EpigenesisGenetic (mesh)Neoplasms (mesh)Cluster Analysis (mesh)Epithelial-Mesenchymal Transition (mesh)Machine Learning (mesh)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/6bc5h252https://escholarship.org/content/qt6bc5h252/qt6bc5h252.pdfinfo:doi/10.1038/s42003-023-05459-warticleCommunications Biology, vol 6, iss 11138oai:escholarship.org:ark:/13030/qt4h84b6ws2026-08-08T21:22:50Zqt4h84b6wsWild-type C-Raf gene dosage and dimerization drive prostate cancer metastasisTa, LisaTsai, Brandon LDeng, WeixianSha, JihuiVaruzhanyan, GrigorTran, WendyWohlschlegel, James ACarr-Ascher, Janai RWitte, Owen N2023-12-01Mutated Ras and Raf kinases are well-known to promote cancer metastasis via flux through the Ras/Raf/MEK/ERK (mitogen-activated protein kinase [MAPK]) pathway. A role for non-mutated Raf in metastasis is also emerging, but the key mechanisms remain unclear. Elevated expression of any of the three wild-type Raf family members (C, A, or B) can drive metastasis. We utilized an in vivo model to show that wild-type C-Raf overexpression can promote metastasis of immortalized prostate cells in a gene dosage-dependent manner. Analysis of the transcriptomic and phosphoproteomic landscape indicated that C-Raf-driven metastasis is accompanied by upregulated MAPK signaling. Use of C-Raf mutants demonstrated that the dimerization domain, but not its kinase activity, is essential for metastasis. Endogenous Raf monomer knockouts revealed that C-Raf's ability to form dimers with endogenous Raf molecules is important for promoting metastasis. These data identify wild-type C-Raf heterodimer signaling as a potential target for treating metastatic disease.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)3211 Oncology and Carcinogenesis (for-2020)31 Biological Sciences (for-2020)Prostate Cancer (rcdc)Genetics (rcdc)Biotechnology (rcdc)Urologic Diseases (rcdc)Cancer (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Cancer (hrcs-hc)BiochemistryCancerMolecular biologyProteomicsTranscriptomicsapplication/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/4h84b6wshttps://escholarship.org/content/qt4h84b6ws/qt4h84b6ws.pdfinfo:doi/10.1016/j.isci.2023.108480articleiScience, vol 26, iss 12108480oai:escholarship.org:ark:/13030/qt9gr5s14f2026-08-08T21:08:07Zqt9gr5s14fComposition and in situ structure of the Methanospirillum hungatei cell envelope and surface layerWang, HuiZhang, JiayanLiao, ShiqingHenstra, Anne MLeon, DeborahErde, JonathanLoo, Joseph AOgorzalek Loo, Rachel RZhou, Z HongGunsalus, Robert P2024-12-13Archaea share genomic similarities with Eukarya and cellular architectural similarities with Bacteria, though archaeal and bacterial surface layers (S-layers) differ. Using cellular cryo-electron tomography, we visualized the S-layer lattice surrounding Methanospirillum hungatei, a methanogenic archaeon. Though more compact than known structures, M. hungatei's S-layer is a flexible hexagonal lattice of dome-shaped tiles, uniformly spaced from both the overlying cell sheath and the underlying cell membrane. Subtomogram averaging resolved the S-layer hexamer tile at 6.4-angstrom resolution. By fitting an AlphaFold model into hexamer tiles in flat and curved conformations, we uncover intra- and intertile interactions that contribute to the S-layer's cylindrical and flexible architecture, along with a spacer extension for cell membrane attachment. M. hungatei cell's end plug structure, likely composed of S-layer isoforms, further highlights the uniqueness of this archaeal cell. These structural features offer advantages for methane release and reflect divergent evolutionary adaptations to environmental pressures during early microbial emergence.3107 Microbiology (for-2020)31 Biological Sciences (for-2020)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Methanospirillum (mesh)Cell Membrane (mesh)Cryoelectron Microscopy (mesh)ModelsMolecular (mesh)Electron Microscope Tomography (mesh)Cell Membrane (mesh)Methanospirillum (mesh)Cryoelectron Microscopy (mesh)ModelsMolecular (mesh)Electron Microscope Tomography (mesh)Methanospirillum (mesh)Cell Membrane (mesh)Cryoelectron Microscopy (mesh)ModelsMolecular (mesh)Electron Microscope Tomography (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/9gr5s14fhttps://escholarship.org/content/qt9gr5s14f/qt9gr5s14f.pdfinfo:doi/10.1126/sciadv.adr8596articleScience Advances, vol 10, iss 50eadr8596oai:escholarship.org:ark:/13030/qt6nv0q8832026-08-08T20:50:45Zqt6nv0q883De novo determination of mosquitocidal Cry11Aa and Cry11Ba structures from naturally-occurring nanocrystalsTetreau, GuillaumeSawaya, Michael RDe Zitter, ElkeAndreeva, Elena ABanneville, Anne-SophieSchibrowsky, Natalie ACoquelle, NicolasBrewster, Aaron SGrünbein, Marie LuiseKovacs, Gabriela NassHunter, Mark SKloos, MarcoSierra, Raymond GSchiro, GiorgioQiao, PeiStricker, MyriamBideshi, DennisYoung, Iris DZala, NinonEngilberge, SylvainGorel, AlexanderSignor, LucaTeulon, Jean-MarieHilpert, MarioFoucar, LutzBielecki, JohanBean, Richardde Wijn, RaphaelSato, TokushiKirkwood, HenryLetrun, RomainBatyuk, AlexanderSnigireva, IrinaFenel, DaphnaSchubert, RobinCanfield, Ethan JAlba, Mario MLaporte, FrédéricDesprés, LaurenceBacia, MariaRoux, AmandineChapelle, ChristianRiobé, FrançoisMaury, OlivierLing, Wai LiBoutet, SébastienMancuso, AdrianGutsche, IrinaGirard, EricBarends, Thomas RMPellequer, Jean-LucPark, Hyun-WooLaganowsky, Arthur DRodriguez, JoseBurghammer, ManfredShoeman, Robert LDoak, R BruceWeik, MartinSauter, Nicholas KFederici, BrianCascio, DuilioSchlichting, IlmeColletier, Jacques-Philippe2022-07-28Cry11Aa and Cry11Ba are the two most potent toxins produced by mosquitocidal Bacillus thuringiensis subsp. israelensis and jegathesan, respectively. The toxins naturally crystallize within the host; however, the crystals are too small for structure determination at synchrotron sources. Therefore, we applied serial femtosecond crystallography at X-ray free electron lasers to in vivo-grown nanocrystals of these toxins. The structure of Cry11Aa was determined de novo using the single-wavelength anomalous dispersion method, which in turn enabled the determination of the Cry11Ba structure by molecular replacement. The two structures reveal a new pattern for in vivo crystallization of Cry toxins, whereby each of their three domains packs with a symmetrically identical domain, and a cleavable crystal packing motif is located within the protoxin rather than at the termini. The diversity of in vivo crystallization patterns suggests explanations for their varied levels of toxicity and rational approaches to improve these toxins for mosquito control.3402 Inorganic Chemistry (for-2020)3101 Biochemistry and Cell Biology (for-2020)34 Chemical Sciences (for-2020)31 Biological Sciences (for-2020)Animals (mesh)Bacillus thuringiensis (mesh)Bacterial Proteins (mesh)Endotoxins (mesh)Hemolysin Proteins (mesh)Larva (mesh)Mosquito Control (mesh)Nanoparticles (mesh)Animals (mesh)Bacillus thuringiensis (mesh)Bacterial Proteins (mesh)Endotoxins (mesh)Mosquito Control (mesh)Larva (mesh)Hemolysin Proteins (mesh)Nanoparticles (mesh)Animals (mesh)Bacillus thuringiensis (mesh)Bacterial Proteins (mesh)Endotoxins (mesh)Hemolysin Proteins (mesh)Larva (mesh)Mosquito Control (mesh)Nanoparticles (mesh)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6nv0q883https://escholarship.org/content/qt6nv0q883/qt6nv0q883.pdfinfo:doi/10.1038/s41467-022-31746-xarticleNature Communications, vol 13, iss 14376oai:escholarship.org:ark:/13030/qt2s59s0px2026-08-08T19:28:59Zqt2s59s0pxIron-regulated assembly of the cytosolic iron–sulfur cluster biogenesis machineryFan, XiaoruiBarshop, William DVashisht, Ajay APandey, VijayaLeal, StephanieRayatpisheh, ShimaJami-Alahmadi, YasamanSha, JihuiWohlschlegel, James A2022-07-01The cytosolic iron-sulfur (Fe-S) cluster assembly (CIA) pathway delivers Fe-S clusters to nuclear and cytosolic Fe-S proteins involved in essential cellular functions. Although the delivery process is regulated by the availability of iron and oxygen, it remains unclear how CIA components orchestrate the cluster transfer under varying cellular environments. Here, we utilized a targeted proteomics assay for monitoring CIA factors and substrates to characterize the CIA machinery. We find that nucleotide-binding protein 1 (NUBP1/NBP35), cytosolic iron-sulfur assembly component 3 (CIAO3/NARFL), and CIA substrates associate with nucleotide-binding protein 2 (NUBP2/CFD1), a component of the CIA scaffold complex. NUBP2 also weakly associates with the CIA targeting complex (MMS19, CIAO1, and CIAO2B) indicating the possible existence of a higher order complex. Interactions between CIAO3 and the CIA scaffold complex are strengthened upon iron supplementation or low oxygen tension, while iron chelation and reactive oxygen species weaken CIAO3 interactions with CIA components. We further demonstrate that CIAO3 mutants defective in Fe-S cluster binding fail to integrate into the higher order complexes. However, these mutants exhibit stronger associations with CIA substrates under conditions in which the association with the CIA targeting complex is reduced suggesting that CIAO3 and CIA substrates may associate in complexes independently of the CIA targeting complex. Together, our data suggest that CIA components potentially form a metabolon whose assembly is regulated by environmental cues and requires Fe-S cluster incorporation in CIAO3. These findings provide additional evidence that the CIA pathway adapts to changes in cellular environment through complex reorganization.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Generic health relevance (hrcs-hc)Cytosol (mesh)GTP-Binding Proteins (mesh)Intracellular Signaling Peptides and Proteins (mesh)Iron (mesh)Iron-Sulfur Proteins (mesh)Oxygen (mesh)Reactive Oxygen Species (mesh)Sulfur (mesh)Cytosol (mesh)Oxygen (mesh)Sulfur (mesh)Iron (mesh)Reactive Oxygen Species (mesh)GTP-Binding Proteins (mesh)Intracellular Signaling Peptides and Proteins (mesh)Iron-Sulfur Proteins (mesh)cytosolic iron–sulfur cluster assembly (CIA)iron–sulfur proteinmetalloproteinprotein–protein interactionproteomicsredox regulationCytosol (mesh)GTP-Binding Proteins (mesh)Intracellular Signaling Peptides and Proteins (mesh)Iron (mesh)Iron-Sulfur Proteins (mesh)Oxygen (mesh)Reactive Oxygen Species (mesh)Sulfur (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biochemistry & Molecular Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/2s59s0pxhttps://escholarship.org/content/qt2s59s0px/qt2s59s0px.pdfinfo:doi/10.1016/j.jbc.2022.102094articleJournal of Biological Chemistry, vol 298, iss 7102094oai:escholarship.org:ark:/13030/qt9xs7544n2026-08-08T19:17:31Zqt9xs7544nPressure-Driven Mitochondrial Transfer Pipeline Generates Mammalian Cells of Desired Genetic Combinations and FatesPatananan, Alexander NSercel, Alexander JWu, Ting-HsiangAhsan, Fasih MTorres, AlejandroKennedy, Stephanie ALVandiver, AmyCollier, Amanda JMehrabi, ArtinVan Lew, JonZakin, LiseRodriguez, NoeSixto, MarcosTadros, WaelLazar, AdamSieling, Peter ANguyen, Thang LDawson, Emma RBraas, DanielGolovato, JustinCisneros, LuisVaske, CharlesPlath, KathrinRabizadeh, ShahroozNiazi, Kayvan RChiou, Pei-YuTeitell, Michael A2020-12-01Generating mammalian cells with desired mitochondrial DNA (mtDNA) sequences is enabling for studies of mitochondria, disease modeling, and potential regenerative therapies. MitoPunch, a high-throughput mitochondrial transfer device, produces cells with specific mtDNA-nuclear DNA (nDNA) combinations by transferring isolated mitochondria from mouse or human cells into primary or immortal mtDNA-deficient (ρ0) cells. Stable isolated mitochondrial recipient (SIMR) cells isolated in restrictive media permanently retain donor mtDNA and reacquire respiration. However, SIMR fibroblasts maintain a ρ0-like cell metabolome and transcriptome despite growth in restrictive media. We reprogrammed non-immortal SIMR fibroblasts into induced pluripotent stem cells (iPSCs) with subsequent differentiation into diverse functional cell types, including mesenchymal stem cells (MSCs), adipocytes, osteoblasts, and chondrocytes. Remarkably, after reprogramming and differentiation, SIMR fibroblasts molecularly and phenotypically resemble unmanipulated control fibroblasts carried through the same protocol. Thus, our MitoPunch "pipeline" enables the production of SIMR cells with unique mtDNA-nDNA combinations for additional studies and applications in multiple cell types.3101 Biochemistry and Cell Biology (for-2020)3105 Genetics (for-2020)31 Biological Sciences (for-2020)Stem Cell Research - Nonembryonic - Human (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell (rcdc)Genetics (rcdc)Stem Cell Research (rcdc)Regenerative Medicine (rcdc)Stem Cell Research - Nonembryonic - Non-Human (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell - Human (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell - Non-Human (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Generic health relevance (hrcs-hc)Animals (mesh)Cell Differentiation (mesh)Cell Line (mesh)Cellular Reprogramming (mesh)DNAMitochondrial (mesh)Fibroblasts (mesh)Gene Transfer Techniques (mesh)HEK293 Cells (mesh)High-Throughput Screening Assays (mesh)Humans (mesh)Induced Pluripotent Stem Cells (mesh)Metabolome (mesh)Mice (mesh)MiceInbred C57BL (mesh)Mitochondria (mesh)Transcriptome (mesh)Cell Line (mesh)Mitochondria (mesh)Fibroblasts (mesh)Animals (mesh)MiceInbred C57BL (mesh)Humans (mesh)Mice (mesh)DNAMitochondrial (mesh)Gene Transfer Techniques (mesh)Cell Differentiation (mesh)Metabolome (mesh)Induced Pluripotent Stem Cells (mesh)High-Throughput Screening Assays (mesh)HEK293 Cells (mesh)Transcriptome (mesh)Cellular Reprogramming (mesh)cell engineeringdifferentiationMitoPunchmitochondrial transplantationmitochondrial replacementmitonuclear communicationisolated mitochondriamitochondrial transfermtDNAreprogrammingAnimals (mesh)Cell Differentiation (mesh)Cell Line (mesh)Cellular Reprogramming (mesh)DNAMitochondrial (mesh)Fibroblasts (mesh)Gene Transfer Techniques (mesh)HEK293 Cells (mesh)High-Throughput Screening Assays (mesh)Humans (mesh)Induced Pluripotent Stem Cells (mesh)Metabolome (mesh)Mice (mesh)MiceInbred C57BL (mesh)Mitochondria (mesh)Transcriptome (mesh)0601 Biochemistry and Cell Biology (for)1116 Medical Physiology (for)31 Biological sciences (for-2020)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/9xs7544nhttps://escholarship.org/content/qt9xs7544n/qt9xs7544n.pdfinfo:doi/10.1016/j.celrep.2020.108562articleCell Reports, vol 33, iss 13108562oai:escholarship.org:ark:/13030/qt2r12j56b2026-08-08T19:08:23Zqt2r12j56bChromGene: gene-based modeling of epigenomic dataJaroszewicz, ArturErnst, Jason2023-09-07Various computational approaches have been developed to annotate epigenomes on a per-position basis by modeling combinatorial and spatial patterns within epigenomic data. However, such annotations are less suitable for gene-based analyses. We present ChromGene, a method based on a mixture of learned hidden Markov models, to annotate genes based on multiple epigenomic maps across the gene body and flanks. We provide ChromGene assignments for over 100 cell and tissue types. We characterize the mixture components in terms of gene expression, constraint, and other gene annotations. The ChromGene method and annotations will provide a useful resource for gene-based epigenomic analyses.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)Human Genome (rcdc)Genetics (rcdc)Epigenomics (mesh)Epigenome (mesh)Histocompatibility Testing (mesh)Learning (mesh)Molecular Sequence Annotation (mesh)ChromatinMachine learningHidden Markov modelsHistone modificationsEpigenomicsHistocompatibility Testing (mesh)Learning (mesh)Epigenomics (mesh)Molecular Sequence Annotation (mesh)Epigenome (mesh)ChromatinEpigenomicsHidden Markov modelsHistone modificationsMachine learningEpigenomics (mesh)Epigenome (mesh)Histocompatibility Testing (mesh)Learning (mesh)Molecular Sequence Annotation (mesh)05 Environmental Sciences (for)06 Biological Sciences (for)08 Information and Computing Sciences (for)Bioinformatics (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/2r12j56bhttps://escholarship.org/content/qt2r12j56b/qt2r12j56b.pdfinfo:doi/10.1186/s13059-023-03041-5articleGenome Biology, vol 24, iss 1203oai:escholarship.org:ark:/13030/qt9nh2d4t32026-08-07T03:30:08Zqt9nh2d4t3The cardiomyocyte disrupts pyrimidine biosynthesis in non-myocytes to regulate heart repairLi, ShenYokota, TomohiroWang, PingHoeve, Johanna tenMa, FeiyangLe, Thuc MAbt, Evan RZhou, YonggangWu, RimaoNanthavongdouangsy, MaxineRodriguez, AbrahamWang, YijieLin, Yen-JuMuranaka, HayatoSharpley, MarkBraddock, Demetrios TMacRae, Vicky EBanerjee, UtpalChiou, Pei-YuSeldin, MarcusHuang, DianTeitell, MichaelGertsman, IlyaJung, MichaelBensinger, Steven JDamoiseaux, RobertFaull, KymPellegrini, MatteoLusis, AldonsGraeber, Thomas GRadu, Caius GDeb, Arjun2022-01-18Various populations of cells are recruited to the heart after cardiac injury, but little is known about whether cardiomyocytes directly regulate heart repair. Using a murine model of ischemic cardiac injury, we demonstrate that cardiomyocytes play a pivotal role in heart repair by regulating nucleotide metabolism and fates of nonmyocytes. Cardiac injury induced the expression of the ectonucleotidase ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1), which hydrolyzes extracellular ATP to form AMP. In response to AMP, cardiomyocytes released adenine and specific ribonucleosides that disrupted pyrimidine biosynthesis at the orotidine monophosphate (OMP) synthesis step and induced genotoxic stress and p53-mediated cell death of cycling nonmyocytes. As nonmyocytes are critical for heart repair, we showed that rescue of pyrimidine biosynthesis by administration of uridine or by genetic targeting of the ENPP1/AMP pathway enhanced repair after cardiac injury. We identified ENPP1 inhibitors using small molecule screening and showed that systemic administration of an ENPP1 inhibitor after heart injury rescued pyrimidine biosynthesis in nonmyocyte cells and augmented cardiac repair and postinfarct heart function. These observations demonstrate that the cardiac muscle cell regulates pyrimidine metabolism in nonmuscle cells by releasing adenine and specific nucleosides after heart injury and provide insight into how intercellular regulation of pyrimidine biosynthesis can be targeted and monitored for augmenting tissue repair.3101 Biochemistry and Cell Biology (for-2020)3208 Medical Physiology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Regenerative Medicine (rcdc)Heart Disease (rcdc)Cardiovascular (rcdc)Genetics (rcdc)Heart Disease - Coronary Heart Disease (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Cardiovascular (hrcs-hc)Adenosine Monophosphate (mesh)Adenosine Triphosphate (mesh)Animals (mesh)Heart Injuries (mesh)Mice (mesh)Myocardium (mesh)MyocytesCardiac (mesh)Phosphoric Diester Hydrolases (mesh)Pyrimidines (mesh)Pyrophosphatases (mesh)Regeneration (mesh)Signal Transduction (mesh)Myocardium (mesh)MyocytesCardiac (mesh)Animals (mesh)Mice (mesh)Heart Injuries (mesh)Pyrimidines (mesh)Pyrophosphatases (mesh)Phosphoric Diester Hydrolases (mesh)Adenosine Monophosphate (mesh)Adenosine Triphosphate (mesh)Regeneration (mesh)Signal Transduction (mesh)CardiologyCardiovascular diseaseAdenosine Monophosphate (mesh)Adenosine Triphosphate (mesh)Animals (mesh)Heart Injuries (mesh)Mice (mesh)Myocardium (mesh)MyocytesCardiac (mesh)Phosphoric Diester Hydrolases (mesh)Pyrimidines (mesh)Pyrophosphatases (mesh)Regeneration (mesh)Signal Transduction (mesh)11 Medical and Health Sciences (for)Immunology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/9nh2d4t3https://escholarship.org/content/qt9nh2d4t3/qt9nh2d4t3.pdfinfo:doi/10.1172/jci149711articleJournal of Clinical Investigation, vol 132, iss 2e149711oai:escholarship.org:ark:/13030/qt0k9088962026-08-06T21:22:54Zqt0k908896Members of the KCTD family are major regulators of cAMP signalingMuntean, Brian SMarwari, SubhiLi, XiaonaSloan, Douglas CYoung, Brian DWohlschlegel, James AMartemyanov, Kirill A2022-01-05Cyclic adenosine monophosphate (cAMP) is a pivotal second messenger with an essential role in neuronal function. cAMP synthesis by adenylyl cyclases (AC) is controlled by G protein-coupled receptor (GPCR) signaling systems. However, the network of molecular players involved in the process is incompletely defined. Here, we used CRISPR/Cas9-based screening to identify that members of the potassium channel tetradimerization domain (KCTD) family are major regulators of cAMP signaling. Focusing on striatal neurons, we show that the dominant isoform KCTD5 exerts its effects through an unusual mechanism that modulates the influx of Zn2+ via the Zip14 transporter to exert unique allosteric effects on AC. We further show that KCTD5 controls the amplitude and sensitivity of stimulatory GPCR inputs to cAMP production by Gβγ-mediated AC regulation. Finally, we report that KCTD5 haploinsufficiency in mice leads to motor deficits that can be reversed by chelating Zn2+ Together, our findings uncover KCTD proteins as major regulators of neuronal cAMP signaling via diverse mechanisms.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Neurosciences (rcdc)2.1 Biological and endogenous factors (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)Neurological (hrcs-hc)Allosteric Regulation (mesh)Animals (mesh)BehaviorAnimal (mesh)CRISPR-Cas Systems (mesh)Cation Transport Proteins (mesh)Corpus Striatum (mesh)Cyclic AMP (mesh)Humans (mesh)Mice (mesh)Neurons (mesh)Potassium Channels (mesh)ReceptorsG-Protein-Coupled (mesh)Signal Transduction (mesh)cAMPGPCRneuronstriatumzincCorpus Striatum (mesh)Neurons (mesh)Animals (mesh)Humans (mesh)Mice (mesh)Potassium Channels (mesh)Cation Transport Proteins (mesh)ReceptorsG-Protein-Coupled (mesh)Cyclic AMP (mesh)BehaviorAnimal (mesh)Signal Transduction (mesh)Allosteric Regulation (mesh)CRISPR-Cas Systems (mesh)GPCRcAMPneuronstriatumzincAllosteric Regulation (mesh)Animals (mesh)BehaviorAnimal (mesh)CRISPR-Cas Systems (mesh)Cation Transport Proteins (mesh)Corpus Striatum (mesh)Cyclic AMP (mesh)Humans (mesh)Mice (mesh)Neurons (mesh)Potassium Channels (mesh)ReceptorsG-Protein-Coupled (mesh)Signal Transduction (mesh)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/0k908896https://escholarship.org/content/qt0k908896/qt0k908896.pdfinfo:doi/10.1073/pnas.2119237119articleProceedings of the National Academy of Sciences of the United States of America, vol 119, iss 1e2119237119oai:escholarship.org:ark:/13030/qt7gn0w60g2026-08-06T21:22:20Zqt7gn0w60gA Novel Toxoplasma Inner Membrane Complex Suture-Associated Protein Regulates Suture Protein Targeting and Colocalizes with Membrane Trafficking MachineryChern, Jessica HPasquarelli, Rebecca RMoon, Andy SChen, Allan LSha, JihuiWohlschlegel, James ABradley, Peter JKoshy, Anita A2021-10-26The cytoskeleton of Toxoplasma gondii is composed of the inner membrane complex (IMC) and an array of underlying microtubules that provide support at the periphery of the parasite. Specific subregions of the IMC carry out distinct roles in replication, motility, and host cell invasion. Building on our previous in vivo biotinylation (BioID) experiments of the IMC, we identified here a novel protein that localizes to discrete puncta that are embedded in the parasite's cytoskeleton along the IMC sutures. Gene knockout analysis showed that loss of the protein results in defects in cytoskeletal suture protein targeting, cytoskeletal integrity, parasite morphology, and host cell invasion. We then used deletion analyses to identify a domain in the N terminus of the protein that is critical for both localization and function. Finally, we used the protein as bait for in vivo biotinylation, which identified several other proteins that colocalize in similar spot-like patterns. These putative interactors include several proteins that are implicated in membrane trafficking and are also associated with the cytoskeleton. Together, these data reveal an unexpected link between the IMC sutures and membrane trafficking elements of the parasite and suggest that the suture puncta are likely a portal for trafficking cargo across the IMC. IMPORTANCE The inner membrane complex (IMC) is a peripheral membrane and cytoskeletal system that is organized into intriguing rectangular plates at the periphery of the parasite. The IMC plates are delimited by an array of IMC suture proteins that are tethered to both the membrane and the cytoskeleton and are thought to provide structure to the organelle. Here, we identified a protein that forms discrete puncta that are embedded in the IMC sutures, and we show that it is important for the proper sorting of a group of IMC suture proteins as well as maintaining parasite shape and IMC cytoskeletal integrity. Intriguingly, proximity labeling experiments identified several proteins that are involved in membrane trafficking or endocytosis, suggesting that the IMC puncta provide a gateway for transporting molecules across the structure.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Biodefense (rcdc)Emerging Infectious Diseases (rcdc)Infectious Diseases (rcdc)2.1 Biological and endogenous factors (hrcs-rac)2.2 Factors relating to the physical environment (hrcs-rac)Infection (hrcs-hc)Cell Membrane (mesh)CellsCultured (mesh)Cytoskeletal Proteins (mesh)Cytoskeleton (mesh)Fibroblasts (mesh)Foreskin (mesh)Humans (mesh)Male (mesh)Membrane Proteins (mesh)Protein Transport (mesh)Protozoan Proteins (mesh)Toxoplasma (mesh)inner membrane complexToxoplasma gondiidynamin-related proteinCellsCultured (mesh)Cell Membrane (mesh)Cytoskeleton (mesh)Fibroblasts (mesh)Humans (mesh)Toxoplasma (mesh)Cytoskeletal Proteins (mesh)Membrane Proteins (mesh)Protozoan Proteins (mesh)Protein Transport (mesh)Male (mesh)Foreskin (mesh)ApicomplexaBioIDToxoplasma gondiidynamin-related proteininner membrane complexCell Membrane (mesh)CellsCultured (mesh)Cytoskeletal Proteins (mesh)Cytoskeleton (mesh)Fibroblasts (mesh)Foreskin (mesh)Humans (mesh)Male (mesh)Membrane Proteins (mesh)Protein Transport (mesh)Protozoan Proteins (mesh)Toxoplasma (mesh)0605 Microbiology (for)3101 Biochemistry and cell biology (for-2020)3107 Microbiology (for-2020)3207 Medical microbiology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/7gn0w60ghttps://escholarship.org/content/qt7gn0w60g/qt7gn0w60g.pdfinfo:doi/10.1128/mbio.02455-21articlemBio, vol 12, iss 510.1128/mbio.02455 - 10.1128/mbio.02421oai:escholarship.org:ark:/13030/qt5zq7s0222026-08-06T21:21:30Zqt5zq7s022A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports.Pelletier, Alexander RSteinecke, DylanSigdel, DibakarAdam, IrsyadCaufield, J HarryGuevara-Gonzalez, VladimirRamirez, JosephVerma, AarushiBali, KaitlynDowns, KatherineWang, WeiBui, AlexPing, Peipei2023-10-01The rapidly increasing and vast quantities of biomedical reports, each containing numerous entities and rich information, represent a rich resource for biomedical text-mining applications. These tools enable investigators to integrate, conceptualize, and translate these discoveries to uncover new insights into disease pathology and therapeutics. In this protocol, we present CaseOLAP LIFT, a new computational pipeline to investigate cellular components and their disease associations by extracting user-selected information from text datasets (e.g., biomedical literature). The software identifies sub-cellular proteins and their functional partners within disease-relevant documents. Additional disease-relevant documents are identified via the software's label imputation method. To contextualize the resulting protein-disease associations and to integrate information from multiple relevant biomedical resources, a knowledge graph is automatically constructed for further analyses. We present one use case with a corpus of ~34 million text documents downloaded online to provide an example of elucidating the role of mitochondrial proteins in distinct cardiovascular disease phenotypes using this method. Furthermore, a deep learning model was applied to the resulting knowledge graph to predict previously unreported relationships between proteins and disease, resulting in 1,583 associations with predicted probabilities >0.90 and with an area under the receiver operating characteristic curve (AUROC) of 0.91 on the test set. This software features a highly customizable and automated workflow, with a broad scope of raw data available for analysis; therefore, using this method, protein-disease associations can be identified with enhanced reliability within a text corpus.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)Networking and Information Technology R&D (NITRD) (rcdc)Machine Learning and Artificial Intelligence (rcdc)1.4 Methodologies and measurements (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)3 Good Health and Well Being (sdg)Pattern RecognitionAutomated (mesh)Reproducibility of Results (mesh)Software (mesh)Data Mining (mesh)Reproducibility of Results (mesh)Software (mesh)Pattern RecognitionAutomated (mesh)Data Mining (mesh)Pattern RecognitionAutomated (mesh)Reproducibility of Results (mesh)Software (mesh)Data Mining (mesh)0601 Biochemistry and Cell Biology (for)1701 Psychology (for)1702 Cognitive Sciences (for)3101 Biochemistry and cell biology (for-2020)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/5zq7s022info:doi/10.3791/65084articleJournal of Visualized Experiments, vol 2023, iss 200oai:escholarship.org:ark:/13030/qt39c3933x2026-08-06T21:04:23Zqt39c3933xAim32 is a dual-localized 2Fe-2S mitochondrial protein that functions in redox quality controlZhang, DanyunDailey, Owen RSimon, Daniel JRoca-Datzer, KamilahJami-Alahmadi, YasamanHennen, Mikayla SWohlschlegel, James AKoehler, Carla MDabir, Deepa V2021-10-01Yeast is a facultative anaerobe and uses diverse electron acceptors to maintain redox-regulated import of cysteine-rich precursors via the mitochondrial intermembrane space assembly (MIA) pathway. With the growing diversity of substrates utilizing the MIA pathway, understanding the capacity of the intermembrane space (IMS) to handle different types of stress is crucial. We used MS to identify additional proteins that interacted with the sulfhydryl oxidase Erv1 of the MIA pathway. Altered inheritance of mitochondria 32 (Aim32), a thioredoxin-like [2Fe-2S] ferredoxin protein, was identified as an Erv1-binding protein. Detailed localization studies showed that Aim32 resided in both the mitochondrial matrix and IMS. Aim32 interacted with additional proteins including redox protein Osm1 and protein import components Tim17, Tim23, and Tim22. Deletion of Aim32 or mutation of conserved cysteine residues that coordinate the Fe-S center in Aim32 resulted in an increased accumulation of proteins with aberrant disulfide linkages. In addition, the steady-state level of assembled TIM22, TIM23, and Oxa1 protein import complexes was decreased. Aim32 also bound to several mitochondrial proteins under nonreducing conditions, suggesting a function in maintaining the redox status of proteins by potentially targeting cysteine residues that may be sensitive to oxidation. Finally, Aim32 was essential for growth in conditions of stress such as elevated temperature and hydroxyurea, and under anaerobic conditions. These studies suggest that the Fe-S protein Aim32 has a potential role in general redox homeostasis in the matrix and IMS. Thus, Aim32 may be poised as a sensor or regulator in quality control for a broad range of mitochondrial proteins.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Electron Transport Complex IV (mesh)Ferredoxins (mesh)Membrane Transport Proteins (mesh)Mitochondrial Membrane Transport Proteins (mesh)Mitochondrial Precursor Protein Import Complex Proteins (mesh)Mitochondrial Proteins (mesh)Mutation (mesh)Nuclear Proteins (mesh)Oxidation-Reduction (mesh)Oxidoreductases Acting on Sulfur Group Donors (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)Saccharomyces cerevisiae (mesh)Electron Transport Complex IV (mesh)Ferredoxins (mesh)Membrane Transport Proteins (mesh)Saccharomyces cerevisiae Proteins (mesh)Mitochondrial Membrane Transport Proteins (mesh)Mitochondrial Proteins (mesh)Nuclear Proteins (mesh)Oxidation-Reduction (mesh)Mutation (mesh)Oxidoreductases Acting on Sulfur Group Donors (mesh)Mitochondrial Precursor Protein Import Complex Proteins (mesh)disulfidemitochondriamitochondrial transportprotein importredox regulationthiolthioredoxinElectron Transport Complex IV (mesh)Ferredoxins (mesh)Membrane Transport Proteins (mesh)Mitochondrial Membrane Transport Proteins (mesh)Mitochondrial Precursor Protein Import Complex Proteins (mesh)Mitochondrial Proteins (mesh)Mutation (mesh)Nuclear Proteins (mesh)Oxidation-Reduction (mesh)Oxidoreductases Acting on Sulfur Group Donors (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biochemistry & Molecular Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/39c3933xhttps://escholarship.org/content/qt39c3933x/qt39c3933x.pdfinfo:doi/10.1016/j.jbc.2021.101135articleJournal of Biological Chemistry, vol 297, iss 4101135oai:escholarship.org:ark:/13030/qt3qn7x0232026-08-06T20:14:31Zqt3qn7x023Specific Disruption of Hippocampal Mossy Fiber Synapses in a Mouse Model of Familial Alzheimer's DiseaseWilke, Scott ARaam, TaraAntonios, Joseph KBushong, Eric AKoo, Edward HEllisman, Mark HGhosh, AnirvanFerreira, Sergio T2014-01-13The earliest stages of Alzheimer's disease (AD) are characterized by deficits in memory and cognition indicating hippocampal pathology. While it is now recognized that synapse dysfunction precedes the hallmark pathological findings of AD, it is unclear if specific hippocampal synapses are particularly vulnerable. Since the mossy fiber (MF) synapse between dentate gyrus (DG) and CA3 regions underlies critical functions disrupted in AD, we utilized serial block-face electron microscopy (SBEM) to analyze MF microcircuitry in a mouse model of familial Alzheimer's disease (FAD). FAD mutant MF terminal complexes were severely disrupted compared to control - they were smaller, contacted fewer postsynaptic spines and had greater numbers of presynaptic filopodial processes. Multi-headed CA3 dendritic spines in the FAD mutant condition were reduced in complexity and had significantly smaller sites of synaptic contact. Significantly, there was no change in the volume of classical dendritic spines at neighboring inputs to CA3 neurons suggesting input-specific defects in the early course of AD related pathology. These data indicate a specific vulnerability of the DG-CA3 network in AD pathogenesis and demonstrate the utility of SBEM to assess circuit specific alterations in mouse models of human disease.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Neurodegenerative (rcdc)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)Brain Disorders (rcdc)Alzheimer's Disease (rcdc)Neurosciences (rcdc)Aging (rcdc)Dementia (rcdc)Acquired Cognitive Impairment (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Neurological (hrcs-hc)Alzheimer Disease (mesh)Animals (mesh)Dendritic Spines (mesh)Disease ModelsAnimal (mesh)Female (mesh)Humans (mesh)Mice (mesh)Mossy FibersHippocampal (mesh)Mutation (mesh)Synapses (mesh)Mossy FibersHippocampal (mesh)Dendritic Spines (mesh)Synapses (mesh)Animals (mesh)Humans (mesh)Mice (mesh)Alzheimer Disease (mesh)Disease ModelsAnimal (mesh)Mutation (mesh)Female (mesh)Alzheimer Disease (mesh)Animals (mesh)Dendritic Spines (mesh)Disease ModelsAnimal (mesh)Female (mesh)Humans (mesh)Mice (mesh)Mossy FibersHippocampal (mesh)Mutation (mesh)Synapses (mesh)General Science & Technology (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/3qn7x023https://escholarship.org/content/qt3qn7x023/qt3qn7x023.pdfinfo:doi/10.1371/journal.pone.0084349articlePLOS ONE, vol 9, iss 1e84349oai:escholarship.org:ark:/13030/qt0v82v2dv2026-08-06T19:37:52Zqt0v82v2dvIntegrated Transcriptome and Proteome Analyses Reveal the Regulatory Role of miR-146a in Human Limbal Epithelium via Notch SignalingPoe, Adam JKulkarni, MangeshLeszczynska, AleksandraTang, JieShah, RuchiJami-Alahmadi, YasamanWang, JasonKramerov, Andrei AWohlschlegel, JamesPunj, VasuLjubimov, Alexander VSaghizadeh, Mehrnoosh2020-10-01MiR-146a is upregulated in the stem cell-enriched limbal region vs. central human cornea and can mediate corneal epithelial wound healing. The aim of this study was to identify miR-146a targets in human primary limbal epithelial cells (LECs) using genomic and proteomic analyses. RNA-seq combined with quantitative proteomics based on multiplexed isobaric tandem mass tag labeling was performed in LECs transfected with miR-146a mimic vs. mimic control. Western blot and immunostaining were used to confirm the expression of some targeted genes/proteins. A total of 251 differentially expressed mRNAs and 163 proteins were identified. We found that miR-146a regulates the expression of multiple genes in different pathways, such as the Notch system. In LECs and organ-cultured corneas, miR-146a increased Notch-1 expression possibly by downregulating its inhibitor Numb, but decreased Notch-2. Integrated transcriptome and proteome analyses revealed the regulatory role of miR-146a in several other processes, including anchoring junctions, TNF-α, Hedgehog signaling, adherens junctions, TGF-β, mTORC2, and epidermal growth factor receptor (EGFR) signaling, which mediate wound healing, inflammation, and stem cell maintenance and differentiation. Our results provide insights into the regulatory network of miR-146a and its role in fine-tuning of Notch-1 and Notch-2 expressions in limbal epithelium, which could be a balancing factor in stem cell maintenance and differentiation.31 Biological Sciences (for-2020)32 Biomedical and Clinical Sciences (for-2020)Human Genome (rcdc)Stem Cell Research (rcdc)Wound Healing and Care (rcdc)Stem Cell Research - Nonembryonic - Human (rcdc)Genetics (rcdc)Eye Disease and Disorders of Vision (rcdc)Regenerative Medicine (rcdc)Biotechnology (rcdc)Stem Cell Research - Nonembryonic - Non-Human (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Eye (hrcs-hc)Cell Differentiation (mesh)Cell Proliferation (mesh)Cornea (mesh)Epithelial Cells (mesh)Epithelium (mesh)ErbB Receptors (mesh)Extremities (mesh)Gene Expression Regulation (mesh)Hedgehog Proteins (mesh)Humans (mesh)MicroRNAs (mesh)Proteome (mesh)ReceptorsNotch (mesh)Signal Transduction (mesh)Transcriptome (mesh)Tumor Necrosis Factor-alpha (mesh)Wound Healing (mesh)corneamiRNAmiR-146aNotchNumblimbal stem cellsproteomicstranscriptomicRNA-seqExtremities (mesh)Cornea (mesh)Epithelium (mesh)Epithelial Cells (mesh)Humans (mesh)Tumor Necrosis Factor-alpha (mesh)Proteome (mesh)MicroRNAs (mesh)Wound Healing (mesh)Signal Transduction (mesh)Cell Differentiation (mesh)Cell Proliferation (mesh)Gene Expression Regulation (mesh)ReceptorsNotch (mesh)Hedgehog Proteins (mesh)Transcriptome (mesh)ErbB Receptors (mesh)NotchNumbRNA-seqcornealimbal stem cellsmiR-146amiRNAproteomicstranscriptomicCell Differentiation (mesh)Cell Proliferation (mesh)Cornea (mesh)Epithelial Cells (mesh)Epithelium (mesh)ErbB Receptors (mesh)Extremities (mesh)Gene Expression Regulation (mesh)Hedgehog Proteins (mesh)Humans (mesh)MicroRNAs (mesh)Proteome (mesh)ReceptorsNotch (mesh)Signal Transduction (mesh)Transcriptome (mesh)Tumor Necrosis Factor-alpha (mesh)Wound Healing (mesh)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/0v82v2dvhttps://escholarship.org/content/qt0v82v2dv/qt0v82v2dv.pdfinfo:doi/10.3390/cells9102175articleCells, vol 9, iss 102175oai:escholarship.org:ark:/13030/qt0vd319c32026-08-06T19:37:45Zqt0vd319c3A genetic model for in vivo proximity labelling of the mammalian secretomeYang, RuiMeyer, Amanda SDroujinine, Ilia AUdeshi, Namrata DHu, YanhuiGuo, JinjinMcMahon, Jill ACarey, Dominique KXu, CharlesFang, QiaoSha, JihuiQin, ShishangRocco, DavidWohlschlegel, JamesTing, Alice YCarr, Steven APerrimon, NorbertMcMahon, Andrew P2022-08-01Organ functions are highly specialized and interdependent. Secreted factors regulate organ development and mediate homeostasis through serum trafficking and inter-organ communication. Enzyme-catalysed proximity labelling enables the identification of proteins within a specific cellular compartment. Here, we report a BirA*G3 mouse strain that enables CRE-dependent promiscuous biotinylation of proteins trafficking through the endoplasmic reticulum. When broadly activated throughout the mouse, widespread labelling of proteins was observed within the secretory pathway. Streptavidin affinity purification and peptide mapping by quantitative mass spectrometry (MS) proteomics revealed organ-specific secretory profiles and serum trafficking. As expected, secretory proteomes were highly enriched for signal peptide-containing proteins, highlighting both conventional and non-conventional secretory processes, and ectodomain shedding. Lower-abundance proteins with hormone-like properties were recovered and validated using orthogonal approaches. Hepatocyte-specific activation of BirA*G3 highlighted liver-specific biotinylated secretome profiles. The BirA*G3 mouse model demonstrates enhanced labelling efficiency and tissue specificity over viral transduction approaches and will facilitate a deeper understanding of secretory protein interplay in development, and in healthy and diseased adult states.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Digestive Diseases (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Animals (mesh)Biotinylation (mesh)Mammals (mesh)Mass Spectrometry (mesh)Mice (mesh)ModelsGenetic (mesh)Proteomics (mesh)Secretome (mesh)proximity-labellingBirATurboIDsecretomeinter-organ communicationserum proteinsAnimals (mesh)Mammals (mesh)Mice (mesh)Biotinylation (mesh)Proteomics (mesh)ModelsGenetic (mesh)Mass Spectrometry (mesh)Secretome (mesh)BirATurboIDinter-organ communicationproximity-labellingsecretomeserum proteinsAnimals (mesh)Biotinylation (mesh)Mammals (mesh)Mass Spectrometry (mesh)Mice (mesh)ModelsGenetic (mesh)Proteomics (mesh)Secretome (mesh)0601 Biochemistry and Cell Biology (for)0605 Microbiology (for)1107 Immunology (for)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/0vd319c3https://escholarship.org/content/qt0vd319c3/qt0vd319c3.pdfinfo:doi/10.1098/rsob.220149articleOpen Biology, vol 12, iss 8220149oai:escholarship.org:ark:/13030/qt1c5080822026-08-06T19:37:37Zqt1c508082RGS10 physically and functionally interacts with STIM2 and requires store-operated calcium entry to regulate pro-inflammatory gene expression in microgliaWendimu, MenbereAlqinyah, MohammedVella, StephenDean, PhillipAlmutairi, FarisRivera, Roseanne DavilaRayatpisheh, ShimaWohlschlegel, JamesMoreno, SilviaHooks, Shelley B2021-07-01Chronic activation of microglia is a driving factor in the progression of neuroinflammatory diseases, and mechanisms that regulate microglial inflammatory signaling are potential targets for novel therapeutics. Regulator of G protein Signaling 10 is the most abundant RGS protein in microglia, where it suppresses inflammatory gene expression and reduces microglia-mediated neurotoxicity. In particular, microglial RGS10 downregulates the expression of pro-inflammatory mediators including cyclooxygenase 2 (COX-2) following stimulation with lipopolysaccharide (LPS). However, the mechanism by which RGS10 affects inflammatory signaling is unknown and is independent of its canonical G protein targeted mechanism. Here, we sought to identify non-canonical RGS10 interacting partners that mediate its anti-inflammatory mechanism. Through RGS10 co-immunoprecipitation coupled with mass spectrometry, we identified STIM2, an endoplasmic reticulum (ER) localized calcium sensor and a component of the store-operated calcium entry (SOCE) machinery, as a novel RGS10 interacting protein in microglia. Direct immunoprecipitation experiments confirmed RGS10-STIM2 interaction in multiple microglia and macrophage cell lines, as well as in primary cells, with no interaction observed with the homologue STIM1. We further determined that STIM2, Orai channels, and the calcium-dependent phosphatase calcineurin are essential for LPS-induced COX-2 production in microglia, and this pathway is required for the inhibitory effect of RGS10 on COX-2. Additionally, our data demonstrated that RGS10 suppresses SOCE triggered by ER calcium depletion and that ER calcium depletion, which induces SOCE, amplifies pro-inflammatory genes. In addition to COX-2, we also show that RGS10 suppresses the expression of pro-inflammatory cytokines in microglia in response to thrombin and LPS stimulation, and all of these effects require SOCE. Collectively, the physical and functional links between RGS10 and STIM2 suggest a complex regulatory network connecting RGS10, SOCE, and pro-inflammatory gene expression in microglia, with broad implications in the pathogenesis and treatment of chronic neuroinflammation.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Neurosciences (rcdc)2.1 Biological and endogenous factors (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)Animals (mesh)Calcium (mesh)Calcium Channels (mesh)Calcium Signaling (mesh)Gene Expression Regulation (mesh)Inflammation (mesh)Mice (mesh)Microglia (mesh)RAW 264.7 Cells (mesh)RGS Proteins (mesh)Stromal Interaction Molecule 2 (mesh)Regulator of G protein signaling (RGS)10MicrogliaNeuroinflammationStore-operated calcium entry (SOCE)Toll-like receptor (TLR)Stromal interaction molecule (STIM)2Cyclooxygenase (COX)-2Microglia (mesh)Animals (mesh)Mice (mesh)Inflammation (mesh)Calcium (mesh)RGS Proteins (mesh)Calcium Channels (mesh)Calcium Signaling (mesh)Gene Expression Regulation (mesh)RAW 264.7 Cells (mesh)Stromal Interaction Molecule 2 (mesh)Cyclooxygenase (COX)-2MicrogliaNeuroinflammationRegulator of G protein signaling (RGS)10Store-operated calcium entry (SOCE)Stromal interaction molecule (STIM)2Toll-like receptor (TLR)Animals (mesh)Calcium (mesh)Calcium Channels (mesh)Calcium Signaling (mesh)Gene Expression Regulation (mesh)Inflammation (mesh)Mice (mesh)Microglia (mesh)RAW 264.7 Cells (mesh)RGS Proteins (mesh)Stromal Interaction Molecule 2 (mesh)0601 Biochemistry and Cell Biology (for)1116 Medical Physiology (for)Biochemistry & Molecular Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1c508082https://escholarship.org/content/qt1c508082/qt1c508082.pdfinfo:doi/10.1016/j.cellsig.2021.109974articleCellular Signalling, vol 83109974oai:escholarship.org:ark:/13030/qt9zv8n3xc2026-08-06T19:20:56Zqt9zv8n3xcLipin 1 modulates mRNA splicing during fasting adaptation in liverWang, HuanChan, Tracey WVashisht, Ajay ADrew, Brian GCalkin, Anna CHarris, Thurl EWohlschlegel, James AXiao, XinshuReue, Karen2021-09-08Lipin 1 regulates cellular lipid homeostasis through roles in glycerolipid synthesis (through phosphatidic acid phosphatase activity) and transcriptional coactivation. Lipin 1-deficient individuals exhibit episodic disease symptoms that are triggered by metabolic stress, such as stress caused by prolonged fasting. We sought to identify critical lipin 1 activities during fasting. We determined that lipin 1 deficiency induces widespread alternative mRNA splicing in liver during fasting, much of which is normalized by refeeding. The role of lipin 1 in mRNA splicing was largely independent of its enzymatic function. We identified interactions between lipin 1 and spliceosome proteins, as well as a requirement for lipin 1 to maintain homeostatic levels of spliceosome small nuclear RNAs and specific RNA splicing factors. In fasted Lpin1-/- liver, we identified a correspondence between alternative splicing of phospholipid biosynthetic enzymes and dysregulated phospholipid levels; splicing patterns and phospholipid levels were partly normalized by feeding. Thus, lipin 1 influences hepatic lipid metabolism through mRNA splicing, as well as through enzymatic and transcriptional activities, and fasting exacerbates the deleterious effects of lipin 1 deficiency on metabolic homeostasis.32 Biomedical and Clinical Sciences (for-2020)42 Health Sciences (for-2020)Nutrition (rcdc)Digestive Diseases (rcdc)Genetics (rcdc)Liver Disease (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Oral and gastrointestinal (hrcs-hc)Generic health relevance (hrcs-hc)AdaptationPhysiological (mesh)Alternative Splicing (mesh)Animals (mesh)CellsCultured (mesh)Fasting (mesh)Female (mesh)Humans (mesh)Lipid Metabolism (mesh)Liver (mesh)Male (mesh)Mice (mesh)MiceInbred BALB C (mesh)ModelsAnimal (mesh)Phosphatidate Phosphatase (mesh)RNA Splicing (mesh)RNAMessenger (mesh)Transcription Factors (mesh)Liver (mesh)CellsCultured (mesh)Animals (mesh)MiceInbred BALB C (mesh)Humans (mesh)Mice (mesh)Phosphatidate Phosphatase (mesh)Transcription Factors (mesh)RNAMessenger (mesh)Fasting (mesh)ModelsAnimal (mesh)AdaptationPhysiological (mesh)RNA Splicing (mesh)Alternative Splicing (mesh)Female (mesh)Male (mesh)Lipid Metabolism (mesh)Genetic diseasesMetabolismMolecular biologyMouse modelsAdaptationPhysiological (mesh)Alternative Splicing (mesh)Animals (mesh)CellsCultured (mesh)Fasting (mesh)Female (mesh)Humans (mesh)Lipid Metabolism (mesh)Liver (mesh)Male (mesh)Mice (mesh)MiceInbred BALB C (mesh)ModelsAnimal (mesh)Phosphatidate Phosphatase (mesh)RNA Splicing (mesh)RNAMessenger (mesh)Transcription Factors (mesh)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/9zv8n3xchttps://escholarship.org/content/qt9zv8n3xc/qt9zv8n3xc.pdfinfo:doi/10.1172/jci.insight.150114articleJCI Insight, vol 6, iss 17e150114oai:escholarship.org:ark:/13030/qt9s65x11w2026-08-06T17:50:09Zqt9s65x11wParent‐Reported Usability of a Patient Portal‐Based Asthma Care Tool for Parents of Children With AsthmaRoss, MKClark, EJChan, WKafashzadeh, DRadparvar, IGao, EGomez, ATran, MSim, MSRong, GFriedman, SSzilagyi, PGRyan, GBui, AAT2025-02-01INTRODUCTION: This study evaluates our new EHR-integrated patient portal for asthma care (PAC) management module for parents of children with asthma. The module includes a previsit asthma intake questionnaire via the portal. The parent answers are integrated into the provider's clinic progress note to support clinical decision-making. Our goals were to measure the functionality and usability of the PAC module and to understand facilitators and barriers to its use for parents.
METHODS: Parents of children ages 0-11 years old (n = 45) completed the PAC module's asthma intake questionnaires prior to their upcoming pediatric pulmonology clinic visit. To assess functionality, provider progress notes were manually reviewed to measure the amount of key asthma-related data captured. Differences in percent data captured with and without the PAC module were compared. Electronic surveys capture demographics, usability data (the System Usability Scale [SUS]), and open-ended experiential feedback about the module. Analysis included descriptive statistics for demographics and usability, as well as the constant comparative method for open-ended feedback.
RESULTS: The PAC module at this early stage of design significantly improved the capture of key asthma data in physician notes, increasing from 77% to 92% (p < 0.001). The average SUS score (83.8) indicated high usability. Favorable aspects of the module that were identified included time savings and ease of use.
CONCLUSION: Our PAC module enhanced data capture of key asthma management elements and demonstrated high parental usability. We will continue to refine the module through an iterative approach based on end-user feedback, with future expansion planned for broader patient populations.3213 Paediatrics (for-2020)32 Biomedical and Clinical Sciences (for-2020)3201 Cardiovascular Medicine and Haematology (for-2020)Lung (rcdc)Patient Safety (rcdc)Clinical Research (rcdc)Pediatric Research Initiative (rcdc)Asthma (rcdc)Respiratory (hrcs-hc)3 Good Health and Well Being (sdg)Humans (mesh)Asthma (mesh)Parents (mesh)Child (mesh)ChildPreschool (mesh)Male (mesh)Infant (mesh)Female (mesh)Patient Portals (mesh)Surveys and Questionnaires (mesh)Electronic Health Records (mesh)InfantNewborn (mesh)Adult (mesh)electronic health recordpatient participationpatient portalspediatric asthmaHumans (mesh)Asthma (mesh)Parents (mesh)Adult (mesh)Child (mesh)ChildPreschool (mesh)Infant (mesh)InfantNewborn (mesh)Female (mesh)Male (mesh)Electronic Health Records (mesh)Surveys and Questionnaires (mesh)Patient Portals (mesh)electronic health recordpatient participationpatient portalspediatric asthmaHumans (mesh)Asthma (mesh)Parents (mesh)Child (mesh)ChildPreschool (mesh)Male (mesh)Infant (mesh)Female (mesh)Patient Portals (mesh)Surveys and Questionnaires (mesh)Electronic Health Records (mesh)InfantNewborn (mesh)Adult (mesh)1114 Paediatrics and Reproductive Medicine (for)Respiratory System (science-metrix)3201 Cardiovascular medicine and haematology (for-2020)3213 Paediatrics (for-2020)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/9s65x11whttps://escholarship.org/content/qt9s65x11w/qt9s65x11w.pdfinfo:doi/10.1002/ppul.27509articlePediatric Pulmonology, vol 60, iss 2e27509oai:escholarship.org:ark:/13030/qt2b7761cb2026-08-06T17:31:38Zqt2b7761cbCoordinated histone methylation loss and MYC activation promote translational capacity under amino acid restrictionCheng, ChenSu, TrentMorselli, MarcoKurdistani, Siavash K2025-06-16BackgroundCells adapt to nutrient fluctuations through both signaling and epigenetic mechanisms. While amino acid (AA) deprivation is known to suppress protein synthesis via mTORC1 inactivation, the epigenetic pathways that support cellular adaptation and recovery remain poorly understood. We investigated how chromatin and transcriptional changes contribute to maintaining translational capacity during AA restriction and priming cells for growth upon AA repletion.MethodsHuman cells were cultured under amino acid-replete or -depleted conditions, and global histone methylation levels were assessed by Western blotting and ChIP-seq. RNA-seq and chromatin-associated RNA-seq (chromRNA-seq) were used to evaluate gene expression and transcriptional output. Ribosome profiling and [35S]-methionine/cysteine or O-propargyl-puromycin (OPP) incorporation assays measured protein synthesis. Functional contributions of SETD8 and MYC were tested through knockdown and overexpression experiments.ResultsAA deprivation induced a selective, genome-wide loss of H4K20me1, particularly from gene bodies, and led to increased MYC expression and binding at promoter regions. These changes were most pronounced at genes encoding ribosomal proteins and translation initiation factors. Although overall protein synthesis declined during AA restriction, these cells showed increased translational capacity evidenced by accumulation of monomeric ribosomes and enhanced translation upon AA repletion. Loss of H4K20me1 was independent of mTORC1 signaling and partly driven by SETD8 protein downregulation. While MYC overexpression alone was insufficient to upregulate translation-related genes, its combination with SETD8 knockdown in nutrient-rich conditions was both necessary and sufficient to induce expression of these genes and enhance protein synthesis.ConclusionsOur findings reveal a chromatin-based mechanism by which cells integrate metabolic status with transcriptional regulation to adapt to amino acid limitation. Loss of H4K20me1 and increased MYC activity act in parallel to prime the translational machinery during AA deprivation, enabling rapid recovery of protein synthesis upon nutrient restoration. This mechanism may help explain how cells maintain competitive growth potential under fluctuating nutrient conditions and has implications for understanding MYC-driven cancer progression.3205 Medical Biochemistry and Metabolomics (for-2020)32 Biomedical and Clinical Sciences (for-2020)3211 Oncology and Carcinogenesis (for-2020)Genetics (rcdc)Nutrition (rcdc)Human Genome (rcdc)Biotechnology (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Cancer (hrcs-hc)Epigenetic adaptationTranslational capacityAmino acid restrictionHistone modificationsMYCCancerAmino acid restrictionCancerEpigenetic adaptationH4K20me1Histone modificationsMYCTranslational capacity3205 Medical biochemistry and metabolomics (for-2020)3211 Oncology and carcinogenesis (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/2b7761cbhttps://escholarship.org/content/qt2b7761cb/qt2b7761cb.pdfinfo:doi/10.1186/s40170-025-00399-xarticleCancer & Metabolism, vol 13, iss 129oai:escholarship.org:ark:/13030/qt11g0x9q42026-08-06T16:34:26Zqt11g0x9q4Deciphering the impact of genomic variation on functionEngreitz, Jesse MLawson, Heather ASingh, HarinderStarita, Lea MHon, Gary CCarter, HannahSahni, NidhiReddy, Timothy ELin, XihongLi, YunMunshi, Nikhil VChahrour, Maria HBoyle, Alan PHitz, Benjamin CMortazavi, AliCraven, MarkMohlke, Karen LPinello, LucaWang, TingBly, ZoCalluori, StephanieGilchrist, Daniel AHutter, Carolyn MMorris, Stephanie ASamer, Ella K2024-09-05Our genomes influence nearly every aspect of human biology—from molecular and cellular functions to phenotypes in health and disease. Studying the differences in DNA sequence between individuals (genomic variation) could reveal previously unknown mechanisms of human biology, uncover the basis of genetic predispositions to diseases, and guide the development of new diagnostic tools and therapeutic agents. Yet, understanding how genomic variation alters genome function to influence phenotype has proved challenging. To unlock these insights, we need a systematic and comprehensive catalogue of genome function and the molecular and cellular effects of genomic variants. Towards this goal, the Impact of Genomic Variation on Function (IGVF) Consortium will combine approaches in single-cell mapping, genomic perturbations and predictive modelling to investigate the relationships among genomic variation, genome function and phenotypes. IGVF will create maps across hundreds of cell types and states describing how coding variants alter protein activity, how noncoding variants change the regulation of gene expression, and how such effects connect through gene-regulatory and protein-interaction networks. These experimental data, computational predictions and accompanying standards and pipelines will be integrated into an open resource that will catalyse community efforts to explore how our genomes influence biology and disease across populations.3101 Biochemistry and Cell Biology (for-2020)3102 Bioinformatics and Computational Biology (for-2020)3105 Genetics (for-2020)31 Biological Sciences (for-2020)Biotechnology (rcdc)Genetics (rcdc)Human Genome (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Generic health relevance (hrcs-hc)Humans (mesh)Cells (mesh)Computer Simulation (mesh)Gene Expression Regulation (mesh)Gene Regulatory Networks (mesh)Genetic Association Studies (mesh)Genetic Predisposition to Disease (mesh)Genetic Variation (mesh)GenomeHuman (mesh)Genomics (mesh)ModelsGenetic (mesh)Phenotype (mesh)Protein Interaction Maps (mesh)Single-Cell Analysis (mesh)IGVF ConsortiumCells (mesh)Humans (mesh)Genetic Predisposition to Disease (mesh)Genomics (mesh)Gene Expression Regulation (mesh)Phenotype (mesh)GenomeHuman (mesh)ModelsGenetic (mesh)Computer Simulation (mesh)Gene Regulatory Networks (mesh)Genetic Variation (mesh)Genetic Association Studies (mesh)Single-Cell Analysis (mesh)Protein Interaction Maps (mesh)Humans (mesh)Cells (mesh)Computer Simulation (mesh)Gene Expression Regulation (mesh)Gene Regulatory Networks (mesh)Genetic Association Studies (mesh)Genetic Predisposition to Disease (mesh)Genetic Variation (mesh)GenomeHuman (mesh)Genomics (mesh)ModelsGenetic (mesh)Phenotype (mesh)Protein Interaction Maps (mesh)Single-Cell Analysis (mesh)General Science & Technology (science-metrix)CC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/11g0x9q4info:doi/10.1038/s41586-024-07510-0articleNature, vol 633, iss 802847 - 57oai:escholarship.org:ark:/13030/qt7q45s22x2026-08-06T16:16:26Zqt7q45s22xSE(3)-equivariant ternary complex prediction towards target protein degradationXue, FangleiZhang, MeihanLi, ShuqiGao, XinyuWohlschlegel, James AHuang, WenbingYang, YiDeng, Weixian2025-07-01Targeted protein degradation (TPD) has rapidly emerged as a powerful modality for drugging previously “undruggable” proteins. TPD employs small molecules like PROTACs and molecular glue degraders (MGD) to induce target protein degradation via the formation of a ternary complex with an E3 ligase. However, the rational design of these degraders is severely hindered by the difficulty of obtaining these ternary structures. Here we introduce DeepTernary, a novel end-to-end deep learning approach using an SE(3)-equivariant encoder and a query-based decoder to accurately and rapidly predict these critical structures. Trained on carefully curated TernaryDB, DeepTernary achieves state-of-the-art performance on PROTAC benchmarks without prior exposure to known PROTACs and shows notable prediction capability on the more challenging MGD benchmark with a blind docking protocol. Remarkably, the buried surface areas calculated from predicted structures correlate with experimental degradation potency metrics. Overall, DeepTernary offers a powerful tool for the development of targeted protein degraders.3404 Medicinal and Biomolecular Chemistry (for-2020)34 Chemical Sciences (for-2020)Machine Learning and Artificial Intelligence (rcdc)Biotechnology (rcdc)Proteolysis (mesh)Proteins (mesh)Ubiquitin-Protein Ligases (mesh)Deep Learning (mesh)Humans (mesh)Molecular Docking Simulation (mesh)46 Information and Computing Sciences (for-2020)3404 Medicinal and Biomolecular Chemistry (for-2020)34 Chemical Sciences (for-2020)Biotechnology (rcdc)Machine Learning and Artificial Intelligence (rcdc)Networking and Information Technology R&D (NITRD) (rcdc)3404 Medicinal and Biomolecular Chemistry (for-2020)34 Chemical Sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/7q45s22xhttps://escholarship.org/content/qt7q45s22x/qt7q45s22x.pdfinfo:doi/10.1038/s41467-025-61272-5articleNature Communications, vol 16, iss 15514oai:escholarship.org:ark:/13030/qt94x6112j2026-08-06T12:52:32Zqt94x6112jMOTS-c modulates skeletal muscle function by directly binding and activating CK2Kumagai, HiroshiKim, Su-JeongMiller, BrendanZempo, HirofumiTanisawa, KumpeiNatsume, ToshiharuLee, Shin HyungWan, JunxiangLeelaprachakul, NaphadaKumagai, Michi EmmaRamirez, RicardoMehta, Hemal HCao, KevinOh, Tae JungWohlschlegel, James ASha, JihuiNishida, YuichiroFuku, NoriyukiDobashi, ShoheiMiyamoto-Mikami, EriTakaragawa, MizukiFuku, MizuhoYoshihara, ToshinoriNaito, HisashiKawakami, RyokoTorii, SuguruMidorikawa, TaishiOka, KoichiroHara, MegumiIwasaka, ChiharuYamada, YosukeHigaki, YasukiTanaka, KeitaroYen, KelvinCohen, Pinchas2024-11-01MOTS-c is a mitochondrial microprotein that improves metabolism. Here, we demonstrate CK2 is a direct and functional target of MOTS-c. MOTS-c directly binds to CK2 and activates it in cell-free systems. MOTS-c administration to mice prevented skeletal muscle atrophy and enhanced muscle glucose uptake, which were blunted by suppressing CK2 activity. Interestingly, the effects of MOTS-c are tissue-specific. Systemically administered MOTS-c binds to CK2 in fat and muscle, yet stimulates CK2 activity in muscle while suppressing it in fat by differentially modifying CK2-interacting proteins. Notably, a naturally occurring MOTS-c variant, K14Q MOTS-c, has reduced binding to CK2 and does not activate it or elicit its effects. Male K14Q MOTS-c carriers exhibited a higher risk of sarcopenia and type 2 diabetes (T2D) in an age- and physical-activity-dependent manner, whereas females had an age-specific reduced risk of T2D. Altogether, these findings provide evidence that CK2 is required for MOTS-c effects.3101 Biochemistry and Cell Biology (for-2020)42 Health Sciences (for-2020)31 Biological Sciences (for-2020)Diabetes (rcdc)Aging (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Musculoskeletal (hrcs-hc)Metabolic and endocrine (hrcs-hc)Physiologycell biologyapplication/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/94x6112jhttps://escholarship.org/content/qt94x6112j/qt94x6112j.pdfinfo:doi/10.1016/j.isci.2024.111212articleiScience, vol 27, iss 11111212oai:escholarship.org:ark:/13030/qt0fh0h1942026-08-06T11:33:30Zqt0fh0h194Double assurance in the induction of axial development by egg dorsal determinants in Xenopus embryosAzbazdar, YagmurDe Robertis, Edward M2025-02-18We recently reported that microinjection of Xenopus nodal-related (xnr) mRNAs into β-catenin-depleted Xenopus embryos rescued a complete dorsal axis. Xnrs mediate the signal of the Nieuwkoop center that induces the Spemann-Mangold organizer in the overlying mesoderm, a process inhibited by the Nodal antagonist Cerberus-short (CerS). However, β-catenin also induces a second signaling center in the dorsal prospective ectoderm, designated the Blastula Chordin and Noggin Expression (BCNE) center, in which the homeobox gene siamois (sia) plays a major role. In this study, we asked whether the Xnrs and Sia depend on each other or function on parallel pathways. Expression of both genes induced β-catenin-depleted embryos to form complete axes with heads and eyes via the activation of similar sets of downstream organizer-specific genes. Xnrs did not activate siamois, and, conversely, Sia did not activate xnrs, although both were induced by β-catenin stabilization. Depletion with morpholinos revealed a robust role for the downstream target Chordin. Remarkably, Chordin depletion prevented all ectopic effects resulting from microinjection of the mRNA encoding the maternal cytoplasmic determinant Huluwa, including the radial expansion of brain tissue and the ectopic expression of the ventral gene sizzled. The main conclusion was that the BCNE and Nieuwkoop centers provide a double assurance mechanism for axial formation by independently activating similar downstream transcriptional target gene repertoires. We suggest that Siamois likely evolved from an ancestral Mix-type homeodomain protein called Sebox as a Xenopus-specific adaptation for the rapid differentiation of the anterior neural plate in the ectoderm.3215 Reproductive Medicine (for-2020)32 Biomedical and Clinical Sciences (for-2020)Genetics (rcdc)Pediatric Research Initiative (rcdc)Neurosciences (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Animals (mesh)Xenopus Proteins (mesh)Xenopus laevis (mesh)Gene Expression RegulationDevelopmental (mesh)beta Catenin (mesh)Homeodomain Proteins (mesh)Body Patterning (mesh)Glycoproteins (mesh)Carrier Proteins (mesh)EmbryoNonmammalian (mesh)Nodal Protein (mesh)Signal Transduction (mesh)Ovum (mesh)Intercellular Signaling Peptides and Proteins (mesh)Noggin Protein (mesh)HuluwacateninChordinNodalSiamoisOvum (mesh)EmbryoNonmammalian (mesh)Animals (mesh)Xenopus laevis (mesh)Glycoproteins (mesh)Intercellular Signaling Peptides and Proteins (mesh)Xenopus Proteins (mesh)Carrier Proteins (mesh)Homeodomain Proteins (mesh)Signal Transduction (mesh)Gene Expression RegulationDevelopmental (mesh)Body Patterning (mesh)beta Catenin (mesh)Nodal Protein (mesh)Noggin Protein (mesh)ChordinHuluwaNodalSiamoisβ-cateninAnimals (mesh)Xenopus Proteins (mesh)Xenopus laevis (mesh)Gene Expression RegulationDevelopmental (mesh)beta Catenin (mesh)Homeodomain Proteins (mesh)Body Patterning (mesh)Glycoproteins (mesh)Carrier Proteins (mesh)EmbryoNonmammalian (mesh)Nodal Protein (mesh)Signal Transduction (mesh)Ovum (mesh)Intercellular Signaling Peptides and Proteins (mesh)Noggin Protein (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/0fh0h194https://escholarship.org/content/qt0fh0h194/qt0fh0h194.pdfinfo:doi/10.1073/pnas.2421772122articleProceedings of the National Academy of Sciences of the United States of America, vol 122, iss 7e2421772122oai:escholarship.org:ark:/13030/qt9nf8q0sh2026-08-06T11:33:06Zqt9nf8q0shHistone H3 cysteine 110 enhances iron metabolism and modulates replicative life span in Saccharomyces cerevisiaeCheng, ChenMcCauley, Brenna SMatulionis, NedasVogelauer, MariaCamacho, DimitriosChristofk, Heather RDang, WeiweiIrwin, Nicholas ATKurdistani, Siavash K2025-04-11The discovery of histone H3 copper reductase activity provides a novel metabolic framework for understanding the functions of core histone residues, which, unlike N-terminal residues, have remained largely unexplored. We previously demonstrated that histone H3 cysteine 110 (H3C110) contributes to cupric (Cu2+) ion binding and its reduction to the cuprous (Cu1+) form. However, this residue is absent in Saccharomyces cerevisiae, raising questions about its evolutionary and functional significance. Here, we report that H3C110 has been lost in many fungal lineages despite near-universal conservation across eukaryotes. Introduction of H3C110 into S. cerevisiae increased intracellular Cu1+ levels and ameliorated the iron homeostasis defects caused by inactivation of the Cup1 metallothionein or glutathione depletion. Enhanced histone copper reductase activity also extended replicative life span under oxidative growth conditions but reduced it under fermentative conditions. Our findings suggest that a trade-off between histone copper reductase activity, iron metabolism, and life span may underlie the loss or retention of H3C110 across eukaryotes.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Nutrition (rcdc)Generic health relevance (hrcs-hc)Saccharomyces cerevisiae (mesh)Iron (mesh)Histones (mesh)Cysteine (mesh)Saccharomyces cerevisiae Proteins (mesh)Copper (mesh)Homeostasis (mesh)Saccharomyces cerevisiae (mesh)Copper (mesh)Iron (mesh)Cysteine (mesh)Saccharomyces cerevisiae Proteins (mesh)Histones (mesh)Homeostasis (mesh)Saccharomyces cerevisiae (mesh)Iron (mesh)Histones (mesh)Cysteine (mesh)Saccharomyces cerevisiae Proteins (mesh)Copper (mesh)Homeostasis (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/9nf8q0shhttps://escholarship.org/content/qt9nf8q0sh/qt9nf8q0sh.pdfinfo:doi/10.1126/sciadv.adv4082articleScience Advances, vol 11, iss 15eadv4082oai:escholarship.org:ark:/13030/qt36v4s1vn2026-08-03T22:09:01Zqt36v4s1vnA synthetic coolant (WS-23) in disposable electronic cigarettes impairs cytoskeletal function in EpiAirway microtissues exposed at the air liquid interfaceWong, ManMartinez, TeresaTran, MonaZuvia, CoriGadkari, AlisaOmaiye, Esther ELuo, WentaiMcWhirter, Kevin JSha, JihuiKassem, AhmadWohlschlegel, JamesTalbot, Prue2023-10-07The design of popular disposable electronic cigarettes (ECs) was analyzed, and the concentrations of WS-23, a synthetic coolant, in EC fluids were determined for 22 devices from 4 different brands. All products contained WS-23 in concentrations that ranged from 1.0 to 40.1 mg/mL (mean = 21.4 ± 9.2 mg/mL). To determine the effects of WS-23 on human bronchial epithelium in isolation of other chemicals, we exposed EpiAirway 3-D microtissues to WS-23 at the air liquid interface (ALI) using a cloud chamber that generated aerosols without heating. Proteomics analysis of exposed tissues revealed that the cytoskeleton was a major target of WS-23. BEAS-2B cells were exposed to WS-23 in submerged culture to validate the main results from proteomics. F-actin, which was visualized with phalloidin, decreased concentration dependently in WS-23 treated BEAS-2B cells, and cells became immotile in concentrations above 1.5 mg/mL. Gap closure, which depends on both cell proliferation and migration, was inhibited by 0.45 mg/mL of WS-23. These data show that WS-23 is being added to popular EC fluids at concentrations that can impair processes dependent on the actin cytoskeleton and disturb homeostasis of the bronchial epithelium. The unregulated use of WS-23 in EC products may harm human health.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Humans (mesh)Electronic Nicotine Delivery Systems (mesh)Aerosols (mesh)Cytoskeleton (mesh)Cytoskeleton (mesh)Humans (mesh)Aerosols (mesh)Electronic Nicotine Delivery Systems (mesh)Humans (mesh)Electronic Nicotine Delivery Systems (mesh)Aerosols (mesh)Cytoskeleton (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/36v4s1vnhttps://escholarship.org/content/qt36v4s1vn/qt36v4s1vn.pdfinfo:doi/10.1038/s41598-023-43948-4articleScientific Reports, vol 13, iss 116906oai:escholarship.org:ark:/13030/qt0s3616zd2026-08-03T21:32:37Zqt0s3616zdTranscriptional drifts associated with environmental changes in endothelial cellsAfshar, YaldaMa, FeyiangQuach, AustinJeong, AnhyoSunshine, Hannah LFreitas, VanessaJami-Alahmadi, YasamanHelaers, RaphaelLi, XinminPellegrini, MatteoWohlschlegel, James ARomanoski, Casey EVikkula, MiikkaIruela-Arispe, M Luisa2023-03-27Environmental cues, such as physical forces and heterotypic cell interactions play a critical role in cell function, yet their collective contributions to transcriptional changes are unclear. Focusing on human endothelial cells, we performed broad individual sample analysis to identify transcriptional drifts associated with environmental changes that were independent of genetic background. Global gene expression profiling by RNA sequencing and protein expression by liquid chromatography-mass spectrometry directed proteomics distinguished endothelial cells in vivo from genetically matched culture (in vitro) samples. Over 43% of the transcriptome was significantly changed by the in vitro environment. Subjecting cultured cells to long-term shear stress significantly rescued the expression of approximately 17% of genes. Inclusion of heterotypic interactions by co-culture of endothelial cells with smooth muscle cells normalized approximately 9% of the original in vivo signature. We also identified novel flow dependent genes, as well as genes that necessitate heterotypic cell interactions to mimic the in vivo transcriptome. Our findings highlight specific genes and pathways that rely on contextual information for adequate expression from those that are agnostic of such environmental cues.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Cancer (rcdc)Biotechnology (rcdc)Cancer Genomics (rcdc)Human Genome (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Humans (mesh)Endothelial Cells (mesh)Endothelium (mesh)Gene Expression Profiling (mesh)CellsCultured (mesh)Coculture Techniques (mesh)endothelial cellvascular biologymolecular biologyHumanEndothelium (mesh)CellsCultured (mesh)Endothelial Cells (mesh)Humans (mesh)Coculture Techniques (mesh)Gene Expression Profiling (mesh)cell biologydevelopmental biologyendothelial cellhumanmolecular biologyvascular biologyHumans (mesh)Endothelial Cells (mesh)Endothelium (mesh)Gene Expression Profiling (mesh)CellsCultured (mesh)Coculture Techniques (mesh)0601 Biochemistry and Cell Biology (for)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/0s3616zdhttps://escholarship.org/content/qt0s3616zd/qt0s3616zd.pdfinfo:doi/10.7554/elife.81370articleELIFE, vol 12e81370oai:escholarship.org:ark:/13030/qt2pq7b3mk2026-08-03T21:00:23Zqt2pq7b3mkFAM111A induces nuclear dysfunction in disease and viral restrictionNie, MinghuaOravcová, MartinaJami-Alahmadi, YasamanWohlschlegel, James ALazzerini-Denchi, ErosBoddy, Michael N2021-02-03Mutations in the nuclear trypsin-like serine protease FAM111A cause Kenny–Caffey syndrome (KCS2) with hypoparathyroidism and skeletal dysplasia or perinatally lethal osteocraniostenosis (OCS). In addition, FAM111A was identified as a restriction factor for certain host range mutants of the SV40 polyomavirus and VACV orthopoxvirus. However, because FAM111A function is poorly characterized, its roles in restricting viral replication and the etiology of KCS2 and OCS remain undefined. We find that FAM111A KCS2 and OCS patient mutants are hyperactive and cytotoxic, inducing apoptosis-like phenotypes such as disruption of nuclear structure and pore distribution, in a protease-dependent manner. Moreover, wild-type FAM111A activity causes similar nuclear phenotypes, including the loss of nuclear barrier function, when SV40 host range mutants attempt to replicate in restrictive cells. Interestingly, pan-caspase inhibitors do not block these FAM111A-induced phenotypes, implying it acts independently or upstream of caspases. In this regard, we identify nucleoporins and the associated GANP transcription/replication factor as FAM111A interactors and candidate targets. Overall, we reveal a potentially unifying mechanism through which deregulated FAM111A activity restricts viral replication and causes KCS2 and OCS.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Infectious Diseases (rcdc)Emerging Infectious Diseases (rcdc)Rare Diseases (rcdc)Genetics (rcdc)Biodefense (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Bone DiseasesDevelopmental (mesh)Cell Nucleus (mesh)Craniofacial Abnormalities (mesh)Humans (mesh)HyperostosisCorticalCongenital (mesh)Hypoparathyroidism (mesh)ReceptorsVirus (mesh)Simian virus 40 (mesh)Virus Replication (mesh)FAM111AKenny–Caffey syndromenuclear pore complexOsteocraniostenosisrestriction of polyomavirus replicationCell Nucleus (mesh)Humans (mesh)Simian virus 40 (mesh)Bone DiseasesDevelopmental (mesh)HyperostosisCorticalCongenital (mesh)Craniofacial Abnormalities (mesh)Hypoparathyroidism (mesh)ReceptorsVirus (mesh)Virus Replication (mesh)FAM111AKenny-Caffey syndromeOsteocraniostenosisnuclear pore complexrestriction of polyomavirus replicationBone DiseasesDevelopmental (mesh)Cell Nucleus (mesh)Craniofacial Abnormalities (mesh)Humans (mesh)HyperostosisCorticalCongenital (mesh)Hypoparathyroidism (mesh)ReceptorsVirus (mesh)Simian virus 40 (mesh)Virus Replication (mesh)0601 Biochemistry and Cell Biology (for)Developmental Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2pq7b3mkhttps://escholarship.org/content/qt2pq7b3mk/qt2pq7b3mk.pdfinfo:doi/10.15252/embr.202050803articleEMBO Reports, vol 22, iss 2embr202050803oai:escholarship.org:ark:/13030/qt2r7881gt2026-08-03T17:59:26Zqt2r7881gtAPEX2 Proximity Proteomics Resolves Flagellum Subdomains and Identifies Flagellum Tip-Specific Proteins in Trypanosoma bruceiVélez-Ramírez, Daniel EShimogawa, Michelle MRay, Sunayan SLopez, AndrewRayatpisheh, ShimaLangousis, GerasimosGallagher-Jones, MarcusDean, SamuelWohlschlegel, James AHill, Kent LPhillips, Margaret2021-02-24Trypanosoma brucei is the protozoan parasite responsible for sleeping sickness, a lethal vector-borne disease. T. brucei has a single flagellum (cilium) that plays critical roles in transmission and pathogenesis. An emerging concept is that the flagellum is organized into subdomains, each having specialized composition and function. The overall flagellum proteome has been well studied, but a critical knowledge gap is the protein composition of individual subdomains. We have tested whether APEX-based proximity proteomics could be used to examine the protein composition of T. brucei flagellum subdomains. As APEX-based labeling has not previously been described in T. brucei, we first fused APEX2 to the DRC1 subunit of the nexin-dynein regulatory complex, a well-characterized axonemal complex. We found that DRC1-APEX2 directs flagellum-specific biotinylation, and purification of biotinylated proteins yields a DRC1 "proximity proteome" having good overlap with published proteomes obtained from purified axonemes. Having validated the use of APEX2 in T. brucei, we next attempted to distinguish flagellar subdomains by fusing APEX2 to a flagellar membrane protein that is restricted to the flagellum tip, AC1, and another one that is excluded from the tip, FS179. Fluorescence microscopy demonstrated subdomain-specific biotinylation, and principal-component analysis showed distinct profiles between AC1-APEX2 and FS179-APEX2. Comparing these two profiles allowed us to identify an AC1 proximity proteome that is enriched for tip proteins, including proteins involved in signaling. Our results demonstrate that APEX2-based proximity proteomics is effective in T. brucei and can be used to resolve the proteome composition of flagellum subdomains that cannot themselves be readily purified.IMPORTANCE Sleeping sickness is a neglected tropical disease caused by the protozoan parasite Trypanosoma brucei The disease disrupts the sleep-wake cycle, leading to coma and death if left untreated. T. brucei motility, transmission, and virulence depend on its flagellum (cilium), which consists of several different specialized subdomains. Given the essential and multifunctional role of the T. brucei flagellum, there is need for approaches that enable proteomic analysis of individual subdomains. Our work establishes that APEX2 proximity labeling can, indeed, be implemented in the biochemical environment of T. brucei and has allowed identification of proximity proteomes for different flagellar subdomains that cannot be purified. This capacity opens the possibility to study the composition and function of other compartments. We expect this approach may be extended to other eukaryotic pathogens and will enhance the utility of T. brucei as a model organism to study ciliopathies, heritable human diseases in which cilium function is impaired.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Vector-Borne Diseases (rcdc)Rare Diseases (rcdc)Infectious Diseases (rcdc)Biotechnology (rcdc)2.2 Factors relating to the physical environment (hrcs-rac)Infection (hrcs-hc)3 Good Health and Well Being (sdg)DNA-(Apurinic or Apyrimidinic Site) Lyase (mesh)Endonucleases (mesh)Flagella (mesh)Humans (mesh)Multifunctional Enzymes (mesh)Proteome (mesh)Proteomics (mesh)Protozoan Proteins (mesh)Signal Transduction (mesh)Trypanosoma brucei brucei (mesh)TrypanosomasignalingflagellaFlagella (mesh)Humans (mesh)Trypanosoma brucei brucei (mesh)DNA-(Apurinic or Apyrimidinic Site) Lyase (mesh)Endonucleases (mesh)Proteome (mesh)Protozoan Proteins (mesh)Proteomics (mesh)Signal Transduction (mesh)Multifunctional Enzymes (mesh)Trypanosomacell signalingflagellaDNA-(Apurinic or Apyrimidinic Site) Lyase (mesh)Endonucleases (mesh)Flagella (mesh)Humans (mesh)Multifunctional Enzymes (mesh)Proteome (mesh)Proteomics (mesh)Protozoan Proteins (mesh)Signal Transduction (mesh)Trypanosoma brucei brucei (mesh)1107 Immunology (for)Immunology (science-metrix)Microbiology (science-metrix)3204 Immunology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/2r7881gthttps://escholarship.org/content/qt2r7881gt/qt2r7881gt.pdfinfo:doi/10.1128/msphere.01090-20articlemSphere, vol 6, iss 110.1128/msphere.01090 - 10.1128/msphere.01020oai:escholarship.org:ark:/13030/qt33c3f7v82026-08-03T17:39:10Zqt33c3f7v8The plant mobile domain proteins MAIN and MAIL1 interact with the phosphatase PP7L to regulate gene expression and silence transposable elements in Arabidopsis thalianaNicolau, MelodyPicault, NathalieDescombin, JulieJami-Alahmadi, YasamanFeng, SuhuaBucher, EtienneJacobsen, Steven EDeragon, Jean-MarcWohlschlegel, JamesMoissiard, GuillaumeKöhler, Claudia2020-04-01Transposable elements (TEs) are DNA repeats that must remain silenced to ensure cell integrity. Several epigenetic pathways including DNA methylation and histone modifications are involved in the silencing of TEs, and in the regulation of gene expression. In Arabidopsis thaliana, the TE-derived plant mobile domain (PMD) proteins have been involved in TE silencing, genome stability, and control of developmental processes. Using a forward genetic screen, we found that the PMD protein MAINTENANCE OF MERISTEMS (MAIN) acts synergistically and redundantly with DNA methylation to silence TEs. We found that MAIN and its close homolog MAIN-LIKE 1 (MAIL1) interact together, as well as with the phosphoprotein phosphatase (PPP) PP7-like (PP7L). Remarkably, main, mail1, pp7l single and mail1 pp7l double mutants display similar developmental phenotypes, and share common subsets of upregulated TEs and misregulated genes. Finally, phylogenetic analyses of PMD and PP7-type PPP domains among the Eudicot lineage suggest neo-association processes between the two protein domains to potentially generate new protein function. We propose that, through this interaction, the PMD and PPP domains may constitute a functional protein module required for the proper expression of a common set of genes, and for silencing of TEs.3101 Biochemistry and Cell Biology (for-2020)3102 Bioinformatics and Computational Biology (for-2020)3105 Genetics (for-2020)31 Biological Sciences (for-2020)Human Genome (rcdc)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Arabidopsis (mesh)Arabidopsis Proteins (mesh)DNA Methylation (mesh)DNA Transposable Elements (mesh)EpigenesisGenetic (mesh)Gene Expression RegulationPlant (mesh)Gene Silencing (mesh)Heterochromatin (mesh)Mutation (mesh)Nuclear Proteins (mesh)Phosphoprotein Phosphatases (mesh)Protein Binding (mesh)Protein Domains (mesh)Repressor Proteins (mesh)Heterochromatin (mesh)Arabidopsis (mesh)Nuclear Proteins (mesh)Arabidopsis Proteins (mesh)Repressor Proteins (mesh)DNA Transposable Elements (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Gene Expression RegulationPlant (mesh)Gene Silencing (mesh)Protein Binding (mesh)Mutation (mesh)Phosphoprotein Phosphatases (mesh)Protein Domains (mesh)Arabidopsis (mesh)Arabidopsis Proteins (mesh)DNA Methylation (mesh)DNA Transposable Elements (mesh)EpigenesisGenetic (mesh)Gene Expression RegulationPlant (mesh)Gene Silencing (mesh)Heterochromatin (mesh)Mutation (mesh)Nuclear Proteins (mesh)Phosphoprotein Phosphatases (mesh)Protein Binding (mesh)Protein Domains (mesh)Repressor Proteins (mesh)0604 Genetics (for)Developmental Biology (science-metrix)3105 Genetics (for-2020)application/pdfhttps://creativecommons.org/publicdomain/zero/1.0/eScholarship, University of Californiahttps://escholarship.org/uc/item/33c3f7v8https://escholarship.org/content/qt33c3f7v8/qt33c3f7v8.pdfinfo:doi/10.1371/journal.pgen.1008324articlePLOS Genetics, vol 16, iss 4e1008324oai:escholarship.org:ark:/13030/qt9m5387j82026-07-26T17:23:59Zqt9m5387j8BRD2 inhibition blocks SARS-CoV-2 infection by reducing transcription of the host cell receptor ACE2Samelson, Avi JTran, Quang DinhRobinot, RémyCarrau, LuciaRezelj, Veronica VKain, Alice MacChen, MerissaRamadoss, Gokul NGuo, XiaoyanLim, Shion ALui, IreneNuñez, James KRockwood, Sarah JWang, JianhuiLiu, NaCarlson-Stevermer, JaredOki, JenniferMaures, TravisHolden, KevinWeissman, Jonathan SWells, James AConklin, Bruce RTenOever, Benjamin RChakrabarti, Lisa AVignuzzi, MarcoTian, RuilinKampmann, Martin2022-01-01SARS-CoV-2 infection of human cells is initiated by the binding of the viral Spike protein to its cell-surface receptor ACE2. We conducted a targeted CRISPRi screen to uncover druggable pathways controlling Spike protein binding to human cells. Here we show that the protein BRD2 is required for ACE2 transcription in human lung epithelial cells and cardiomyocytes, and BRD2 inhibitors currently evaluated in clinical trials potently block endogenous ACE2 expression and SARS-CoV-2 infection of human cells, including those of human nasal epithelia. Moreover, pharmacological BRD2 inhibition with the drug ABBV-744 inhibited SARS-CoV-2 replication in Syrian hamsters. We also found that BRD2 controls transcription of several other genes induced upon SARS-CoV-2 infection, including the interferon response, which in turn regulates the antiviral response. Together, our results pinpoint BRD2 as a potent and essential regulator of the host response to SARS-CoV-2 infection and highlight the potential of BRD2 as a therapeutic target for COVID-19.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Emerging Infectious Diseases (rcdc)Coronaviruses (rcdc)Lung (rcdc)Biodefense (rcdc)Coronaviruses Therapeutics and Interventions (rcdc)Infectious Diseases (rcdc)Genetics (rcdc)2.1 Biological and endogenous factors (hrcs-rac)5.1 Pharmaceuticals (hrcs-rac)Infection (hrcs-hc)3 Good Health and Well Being (sdg)Angiotensin-Converting Enzyme 2 (mesh)Antiviral Agents (mesh)COVID-19 (mesh)Cell Line (mesh)Epithelial Cells (mesh)Humans (mesh)Membrane Glycoproteins (mesh)SARS-CoV-2 (mesh)Transcription Factors (mesh)COVID-19 Drug Treatment (mesh)Bromodomain Containing Proteins (mesh)Cell Line (mesh)Epithelial Cells (mesh)Humans (mesh)Membrane Glycoproteins (mesh)Transcription Factors (mesh)Antiviral Agents (mesh)COVID-19 (mesh)Angiotensin-Converting Enzyme 2 (mesh)SARS-CoV-2 (mesh)COVID-19 Drug Treatment (mesh)Bromodomain Containing Proteins (mesh)Angiotensin-Converting Enzyme 2 (mesh)Antiviral Agents (mesh)COVID-19 (mesh)Cell Line (mesh)Epithelial Cells (mesh)Humans (mesh)Membrane Glycoproteins (mesh)SARS-CoV-2 (mesh)Transcription Factors (mesh)COVID-19 Drug Treatment (mesh)Bromodomain Containing Proteins (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9m5387j8https://escholarship.org/content/qt9m5387j8/qt9m5387j8.pdfinfo:doi/10.1038/s41556-021-00821-8articleNature Cell Biology, vol 24, iss 124 - 34oai:escholarship.org:ark:/13030/qt0g55k1vv2026-07-21T14:49:02Zqt0g55k1vvAssociating growth factor secretions and transcriptomes of single cells in nanovials using SEC-seqUdani, ShreyaLangerman, JustinKoo, DoyeonBaghdasarian, SevanaCheng, BrianKang, SimranSoemardy, Citradewide Rutte, JosephPlath, KathrinDi Carlo, Dino2024-03-01Cells secrete numerous bioactive molecules that are essential for the function of healthy organisms. However, scalable methods are needed to link individual cell secretions to their transcriptional state over time. Here, by developing and using secretion-encoded single-cell sequencing (SEC-seq), which exploits hydrogel particles with subnanolitre cavities (nanovials) to capture individual cells and their secretions, we simultaneously measured the secretion of vascular endothelial growth factor A (VEGF-A) and the transcriptome for thousands of individual mesenchymal stromal cells. Our data indicate that VEGF-A secretion is heterogeneous across the cell population and is poorly correlated with the VEGFA transcript level. The highest VEGF-A secretion occurs in a subpopulation of mesenchymal stromal cells characterized by a unique gene expression signature comprising a surface marker, interleukin-13 receptor subunit alpha 2 (IL13RA2), which allowed the enrichment of this subpopulation. SEC-seq enables the identification of gene signatures linked to specific secretory states, facilitating mechanistic studies, the isolation of secretory subpopulations and the development of means to modulate cellular secretion.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Human Genome (rcdc)Vascular Endothelial Growth Factor A (mesh)Transcriptome (mesh)Mesenchymal Stem Cells (mesh)Mesenchymal Stem Cells (mesh)Vascular Endothelial Growth Factor A (mesh)Transcriptome (mesh)Vascular Endothelial Growth Factor A (mesh)Transcriptome (mesh)Mesenchymal Stem Cells (mesh)Nanoscience & Nanotechnology (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0g55k1vvhttps://escholarship.org/content/qt0g55k1vv/qt0g55k1vv.pdfinfo:doi/10.1038/s41565-023-01560-7articleNature Nanotechnology, vol 19, iss 3354 - 363oai:escholarship.org:ark:/13030/qt8kj286zq2026-07-19T05:19:52Zqt8kj286zqIdentification of neural oscillations and epileptiform changes in human brain organoidsSamarasinghe, Ranmal AMiranda, Osvaldo AButh, Jessie EMitchell, SimonFerando, IsabellaWatanabe, MomokoAllison, Thomas FKurdian, ArinnaeFotion, Namie NGandal, Michael JGolshani, PeymanPlath, KathrinLowry, William EParent, Jack MMody, IstvanNovitch, Bennett G2021-10-01Brain organoids represent a powerful tool for studying human neurological diseases, particularly those that affect brain growth and structure. However, many diseases manifest with clear evidence of physiological and network abnormality in the absence of anatomical changes, raising the question of whether organoids possess sufficient neural network complexity to model these conditions. Here, we explore the network-level functions of brain organoids using calcium sensor imaging and extracellular recording approaches that together reveal the existence of complex network dynamics reminiscent of intact brain preparations. We demonstrate highly abnormal and epileptiform-like activity in organoids derived from induced pluripotent stem cells from individuals with Rett syndrome, accompanied by transcriptomic differences revealed by single-cell analyses. We also rescue key physiological activities with an unconventional neuroregulatory drug, pifithrin-α. Together, these findings provide an essential foundation for the utilization of brain organoids to study intact and disordered human brain network formation and illustrate their utility in therapeutic discovery.5202 Biological Psychology (for-2020)32 Biomedical and Clinical Sciences (for-2020)3209 Neurosciences (for-2020)52 Psychology (for-2020)Bioengineering (rcdc)Neurosciences (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell - Human (rcdc)Stem Cell Research (rcdc)Brain Disorders (rcdc)Mental Health (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Neurological (hrcs-hc)3 Good Health and Well Being (sdg)Adult (mesh)Benzothiazoles (mesh)Brain (mesh)Calcium Signaling (mesh)ChildPreschool (mesh)Epilepsy (mesh)Female (mesh)Humans (mesh)Induced Pluripotent Stem Cells (mesh)Methyl-CpG-Binding Protein 2 (mesh)Nerve Net (mesh)Neurogenesis (mesh)Neuroimaging (mesh)Neurons (mesh)Rett Syndrome (mesh)Single-Cell Analysis (mesh)Synapses (mesh)Toluene (mesh)Transcriptome (mesh)Brain (mesh)Nerve Net (mesh)Neurons (mesh)Synapses (mesh)Humans (mesh)Epilepsy (mesh)Rett Syndrome (mesh)Toluene (mesh)Calcium Signaling (mesh)Adult (mesh)ChildPreschool (mesh)Female (mesh)Methyl-CpG-Binding Protein 2 (mesh)Benzothiazoles (mesh)Neurogenesis (mesh)Induced Pluripotent Stem Cells (mesh)Single-Cell Analysis (mesh)Neuroimaging (mesh)Transcriptome (mesh)Adult (mesh)Benzothiazoles (mesh)Brain (mesh)Calcium Signaling (mesh)ChildPreschool (mesh)Epilepsy (mesh)Female (mesh)Humans (mesh)Induced Pluripotent Stem Cells (mesh)Methyl-CpG-Binding Protein 2 (mesh)Nerve Net (mesh)Neurogenesis (mesh)Neuroimaging (mesh)Neurons (mesh)Rett Syndrome (mesh)Single-Cell Analysis (mesh)Synapses (mesh)Toluene (mesh)Transcriptome (mesh)1109 Neurosciences (for)1701 Psychology (for)1702 Cognitive Sciences (for)Neurology & Neurosurgery (science-metrix)3209 Neurosciences (for-2020)5202 Biological psychology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8kj286zqhttps://escholarship.org/content/qt8kj286zq/qt8kj286zq.pdfinfo:doi/10.1038/s41593-021-00906-5articleNature Neuroscience, vol 24, iss 101488 - 1500oai:escholarship.org:ark:/13030/qt6v3762j62026-07-18T21:40:08Zqt6v3762j6Defining the nature of human pluripotent stem cell-derived interneurons via single-cell analysisAllison, ThomasLangerman, JustinSabri, ShanOtero-Garcia, MarcosLund, AndrewHuang, JohnWei, XiaofeiSamarasinghe, Ranmal APolioudakis, DamonMody, IstvanCobos, InmaNovitch, Bennett GGeschwind, Daniel HPlath, KathrinLowry, William E2021-10-01The specification of inhibitory neurons has been described for the mouse and human brain, and many studies have shown that pluripotent stem cells (PSCs) can be used to create interneurons in vitro. It is unclear whether in vitro methods to produce human interneurons generate all the subtypes found in brain, and how similar in vitro and in vivo interneurons are. We applied single-nuclei and single-cell transcriptomics to model interneuron development from human cortex and interneurons derived from PSCs. We provide a direct comparison of various in vitro interneuron derivation methods to determine the homogeneity achieved. We find that PSC-derived interneurons capture stages of development prior to mid-gestation, and represent a minority of potential subtypes found in brain. Comparison with those found in fetal or adult brain highlighted decreased expression of synapse-related genes. These analyses highlight the potential to tailor the method of generation to drive formation of particular subtypes.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Stem Cell Research - Embryonic - Human (rcdc)Genetics (rcdc)Neurosciences (rcdc)Human Fetal Tissue (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell - Human (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell (rcdc)Regenerative Medicine (rcdc)Stem Cell Research - Nonembryonic - Human (rcdc)Stem Cell Research (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Generic health relevance (hrcs-hc)Neurological (hrcs-hc)Cell Differentiation (mesh)Cellular Reprogramming Techniques (mesh)Humans (mesh)Interneurons (mesh)Neural Stem Cells (mesh)Pluripotent Stem Cells (mesh)Single-Cell Analysis (mesh)Transcription Factors (mesh)Transcriptome (mesh)Interneurons (mesh)Pluripotent Stem Cells (mesh)Humans (mesh)Transcription Factors (mesh)Cell Differentiation (mesh)Neural Stem Cells (mesh)Single-Cell Analysis (mesh)Transcriptome (mesh)Cellular Reprogramming Techniques (mesh)human brain interneuronneuronal specificationpluripotent stem cellsingle nuclei transcriptomicstranscriptional factor programmingCell Differentiation (mesh)Cellular Reprogramming Techniques (mesh)Humans (mesh)Interneurons (mesh)Neural Stem Cells (mesh)Pluripotent Stem Cells (mesh)Single-Cell Analysis (mesh)Transcription Factors (mesh)Transcriptome (mesh)0601 Biochemistry and Cell Biology (for)1103 Clinical Sciences (for)3101 Biochemistry and cell biology (for-2020)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/6v3762j6https://escholarship.org/content/qt6v3762j6/qt6v3762j6.pdfinfo:doi/10.1016/j.stemcr.2021.08.006articleStem Cell Reports, vol 16, iss 102548 - 2564oai:escholarship.org:ark:/13030/qt9vk8b4x42026-07-09T18:34:55Zqt9vk8b4x4Clinical phenomapping and outcomes after heart transplantationBakir, MaralJackson, Nicholas JHan, Simon XBui, AlexChang, EleanorLiem, David AArdehali, AbbasArdehali, RezaBaas, Arnold SPress, Marcella CalfonCruz, DanielDeng, Mario CDePasquale, Eugene CFonarow, Gregg CKhuu, TamKwon, Murray HKubak, Bernard MNsair, AliPhung, Jennifer LReed, Elaine FSchaenman, Joanna MShemin, Richard JZhang, Qiuheng JTseng, Chi-HongCadeiras, Martin2018-08-01BACKGROUND: Survival after heart transplantation (HTx) is limited by complications related to alloreactivity, immune suppression, and adverse effects of pharmacologic therapies. We hypothesize that time-dependent phenomapping of clinical and molecular data sets is a valuable approach to clinical assessments and guiding medical management to improve outcomes.
METHODS: We analyzed clinical, therapeutic, biomarker, and outcome data from 94 adult HTx patients and 1,557 clinical encounters performed between January 2010 and April 2013. Multivariate analyses were used to evaluate the association between immunosuppression therapy, biomarkers, and the combined clinical end point of death, allograft loss, retransplantation, and rejection. Data were analyzed by K-means clustering (K = 2) to identify patterns of similar combined immunosuppression management, and percentile slopes were computed to examine the changes in dosages over time. Findings were correlated with clinical parameters, human leucocyte antigen antibody titers, and peripheral blood mononuclear cell gene expression of the AlloMap (CareDx, Inc., Brisbane, CA) test genes. An intragraft, heart tissue gene coexpression network analysis was performed.
RESULTS: Unsupervised cluster analysis of immunosuppressive therapies identified 2 groups, 1 characterized by a steeper immunosuppression minimization, associated with a higher likelihood for the combined end point, and the other by a less pronounced change. A time-dependent phenomap suggested that patients in the group with higher event rates had increased human leukocyte antigen class I and II antibody titers, higher expression of the FLT3 AlloMap gene, and lower expression of the MARCH8 and WDR40A AlloMap genes. Intramyocardial biomarker-related coexpression network analysis of the FLT3 gene showed an immune system-related network underlying this biomarker.
CONCLUSIONS: Time-dependent precision phenotyping is a mechanistically insightful, data-driven approach to characterize patterns of clinical care and identify ways to improve clinical management and outcomes.32 Biomedical and Clinical Sciences (for-2020)3204 Immunology (for-2020)Organ Transplantation (rcdc)Genetics (rcdc)Clinical Research (rcdc)Transplantation (rcdc)4.1 Discovery and preclinical testing of markers and technologies (hrcs-rac)Inflammatory and immune system (hrcs-hc)3 Good Health and Well Being (sdg)Adult (mesh)Aged (mesh)Female (mesh)Follow-Up Studies (mesh)Genetic Markers (mesh)Graft Rejection (mesh)Heart Transplantation (mesh)Humans (mesh)Immunosuppressive Agents (mesh)Male (mesh)Middle Aged (mesh)Phenotype (mesh)Precision Medicine (mesh)Risk Factors (mesh)T-Lymphocytes (mesh)Ubiquitin-Protein Ligases (mesh)fms-Like Tyrosine Kinase 3 (mesh)heart transplantationphenomappingimmunosuppressionbiomarkersallograftrejectionT-Lymphocytes (mesh)Humans (mesh)Ubiquitin-Protein Ligases (mesh)Immunosuppressive Agents (mesh)Genetic Markers (mesh)Heart Transplantation (mesh)Risk Factors (mesh)Follow-Up Studies (mesh)Graft Rejection (mesh)Phenotype (mesh)Adult (mesh)Aged (mesh)Middle Aged (mesh)Female (mesh)Male (mesh)fms-Like Tyrosine Kinase 3 (mesh)Precision Medicine (mesh)allograftbiomarkersheart transplantationimmunosuppressionphenomappingrejectionAdult (mesh)Aged (mesh)Female (mesh)Follow-Up Studies (mesh)Genetic Markers (mesh)Graft Rejection (mesh)Heart Transplantation (mesh)Humans (mesh)Immunosuppressive Agents (mesh)Male (mesh)Middle Aged (mesh)Phenotype (mesh)Precision Medicine (mesh)Risk Factors (mesh)T-Lymphocytes (mesh)Ubiquitin-Protein Ligases (mesh)fms-Like Tyrosine Kinase 3 (mesh)1102 Cardiorespiratory Medicine and Haematology (for)Surgery (science-metrix)3201 Cardiovascular medicine and haematology (for-2020)3202 Clinical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9vk8b4x4https://escholarship.org/content/qt9vk8b4x4/qt9vk8b4x4.pdfinfo:doi/10.1016/j.healun.2018.03.006articleThe Journal of Heart and Lung Transplantation, vol 37, iss 8956 - 966oai:escholarship.org:ark:/13030/qt8tv510rn2026-07-04T16:26:08Zqt8tv510rnNoggin depletion in adipocytes promotes obesity in miceBlázquez-Medela, Ana MJumabay, MedetRajbhandari, PrashantSallam, TamerGuo, YinaYao, JiayiVergnes, LaurentReue, KarenZhang, LiYao, YuchengFogelman, Alan MTontonoz, PeterLusis, Aldons JWu, XiujuBoström, Kristina I2019-07-01OBJECTIVE: Obesity has increased to pandemic levels and enhanced understanding of adipose regulation is required for new treatment strategies. Although bone morphogenetic proteins (BMPs) influence adipogenesis, the effect of BMP antagonists such as Noggin is largely unknown. The aim of the study was to define the role of Noggin, an extracellular BMP inhibitor, in adipogenesis.
METHODS: We generated adipose-derived progenitor cells and a mouse model with adipocyte-specific Noggin deletion using the AdiponectinCre transgenic mouse, and determined the adipose phenotype of Noggin-deficiency.
RESULTS: Our studies showed that Noggin is expressed in progenitor cells but declines in adipocytes, possibly allowing for lipid accumulation. Correspondingly, adipocyte-specific Noggin deletion in vivo promoted age-related obesity in both genders with no change in food intake. Although the loss of Noggin caused white adipose tissue hypertrophy, and whitening and impaired function in brown adipose tissue in both genders, there were clear gender differences with the females being most affected. The females had suppressed expression of brown adipose markers and thermogenic genes including peroxisome proliferator activated receptor gamma coactivator 1 alpha (PGC1alpha) and uncoupling protein 1 (UCP1) as well as genes associated with adipogenesis and lipid metabolism. The males, on the other hand, had early changes in a few BAT markers and thermogenic genes, but the main changes were in the genes associated with adipogenesis and lipid metabolism. Further characterization revealed that both genders had reductions in VO2, VCO2, and RER, whereas females also had reduced heat production. Noggin was also reduced in diet-induced obesity in inbred mice consistent with the obesity phenotype of the Noggin-deficient mice.
CONCLUSIONS: BMP signaling regulates female and male adipogenesis through different metabolic pathways. Modulation of adipose tissue metabolism by select BMP antagonists may be a strategy for long-term regulation of age-related weight gain and obesity.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Stem Cell Research - Nonembryonic - Non-Human (rcdc)Stem Cell Research (rcdc)Nutrition (rcdc)Diabetes (rcdc)Women's Health (rcdc)Obesity (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Metabolic and endocrine (hrcs-hc)Adipocytes (mesh)Adipogenesis (mesh)Adipose Tissue (mesh)Adipose TissueBrown (mesh)Adipose TissueWhite (mesh)Animals (mesh)Bone Morphogenetic Proteins (mesh)Carrier Proteins (mesh)Disease ModelsAnimal (mesh)Eating (mesh)Female (mesh)Gene Deletion (mesh)Gene Expression Regulation (mesh)Genetic Association Studies (mesh)Lipid Accumulation Product (mesh)Lipid Metabolism (mesh)Male (mesh)Mice (mesh)MiceObese (mesh)MiceTransgenic (mesh)Obesity (mesh)Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha (mesh)Signal Transduction (mesh)Thermogenesis (mesh)Transcriptome (mesh)Uncoupling Protein 1 (mesh)Noggin Protein (mesh)NogginBone morphogenetic proteinAdipocyteAdipogenesisObesityAdipose Tissue (mesh)Adipocytes (mesh)Animals (mesh)MiceTransgenic (mesh)Mice (mesh)MiceObese (mesh)Obesity (mesh)Disease ModelsAnimal (mesh)Carrier Proteins (mesh)Bone Morphogenetic Proteins (mesh)Signal Transduction (mesh)Gene Expression Regulation (mesh)Gene Deletion (mesh)Thermogenesis (mesh)Eating (mesh)Female (mesh)Male (mesh)Adipogenesis (mesh)Lipid Metabolism (mesh)Adipose TissueBrown (mesh)Adipose TissueWhite (mesh)Genetic Association Studies (mesh)Transcriptome (mesh)Lipid Accumulation Product (mesh)Uncoupling Protein 1 (mesh)Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha (mesh)Noggin Protein (mesh)AdipocyteAdipogenesisBone morphogenetic proteinNogginObesityAdipocytes (mesh)Adipogenesis (mesh)Adipose Tissue (mesh)Adipose TissueBrown (mesh)Adipose TissueWhite (mesh)Animals (mesh)Bone Morphogenetic Proteins (mesh)Carrier Proteins (mesh)Disease ModelsAnimal (mesh)Eating (mesh)Female (mesh)Gene Deletion (mesh)Gene Expression Regulation (mesh)Genetic Association Studies (mesh)Lipid Accumulation Product (mesh)Lipid Metabolism (mesh)Male (mesh)Mice (mesh)MiceObese (mesh)MiceTransgenic (mesh)Obesity (mesh)Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha (mesh)Signal Transduction (mesh)Thermogenesis (mesh)Transcriptome (mesh)Uncoupling Protein 1 (mesh)Noggin Protein (mesh)0601 Biochemistry and Cell Biology (for)0606 Physiology (for)3101 Biochemistry and cell biology (for-2020)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/8tv510rnhttps://escholarship.org/content/qt8tv510rn/qt8tv510rn.pdfinfo:doi/10.1016/j.molmet.2019.04.004articleMolecular Metabolism, vol 2550 - 63oai:escholarship.org:ark:/13030/qt1vb3501q2026-07-02T04:14:04Zqt1vb3501qThe rippled β-sheet layer configuration—a novel supramolecular architecture based on predictions by Pauling and CoreyHazari, AmarukaSawaya, Michael RVlahakis, NikoJohnstone, Timothy CBoyer, DavidRodriguez, JoseEisenberg, DavidRaskatov, Jevgenij A2022-08-10The rippled β-sheet is a peptidic structural motif related to but distinct from the pleated β-sheet. Both motifs were predicted in the 1950s by Pauling and Corey. The pleated β-sheet was since observed in countless proteins and peptides and is considered common textbook knowledge. Conversely, the rippled β-sheet only gained a meaningful experimental foundation in the past decade, and the first crystal structural study of rippled β-sheets was published as recently as this year. Noteworthy, the crystallized assembly stopped at the rippled β-dimer stage. It did not form the extended, periodic rippled β-sheet layer topography hypothesized by Pauling and Corey, thus calling the validity of their prediction into question. NMR work conducted since moreover shows that certain model peptides rather form pleated and not rippled β-sheets in solution. To determine whether the periodic rippled β-sheet layer configuration is viable, the field urgently needs crystal structures. Here we report on crystal structures of two racemic and one quasi-racemic aggregating peptide systems, all of which yield periodic rippled antiparallel β-sheet layers that are in excellent agreement with the predictions by Pauling and Corey. Our study establishes the rippled β-sheet layer configuration as a motif with general features and opens the road to structure-based design of unique supramolecular architectures.3403 Macromolecular and Materials Chemistry (for-2020)34 Chemical Sciences (for-2020)03 Chemical Sciences (for)34 Chemical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1vb3501qhttps://escholarship.org/content/qt1vb3501q/qt1vb3501q.pdfinfo:doi/10.1039/d2sc02531karticleChemical Science, vol 13, iss 318947 - 8952oai:escholarship.org:ark:/13030/qt2z8359hb2026-06-24T03:35:10Zqt2z8359hbp21+TREM2+ senescent macrophages fuel inflammaging and metabolic dysfunction-associated steatotic liver diseaseSalladay-Perez, Ivan AAvila, ItzetlEstrada, LizethAlexandru, Andreea CPonce, CristianDhingra, AnikaTorres, GrasielaDeng, Christina YHegde, RonakGensheimer, JuliaKale, AbhijitHeckenbach, IndraHui, SimonEdillor, ChantleSoto, Jose ANapior, Alexander JLittle, IsaiahLarsen, MarkRose, JacobFarahi, LiaLopez Gonzalez, Edwin DJKrieger, Matthew RChowdhury, KushanSharma, MridulJiang, YumingWilliams, KevinScheibye-Knudsen, MortenKoehler, Carla MMeyer, Jesse GMack, Julia JBrenner, CharlesBensinger, Steven JLagger, Cyrilde Magalhães, João PedroSchilling, BirgitSingh, RajatVerdin, EricLusis, Aldons JCovarrubias, Anthony J2026-04-01Cellular senescence drives chronic sterile inflammation during aging via the senescence-associated secretory phenotype, yet the senescent cell types responsible are poorly defined. Macrophages share multiple features of senescence, including inflammatory secretion, yet whether macrophages can adopt a senescent state remains unclear. Here we identify p21⁺Trem2⁺ senescent macrophages as a major source of inflammaging, using primary mouse and human macrophage models of DNA damage and cholesterol-induced senescence characterized by multi-omic profiling. We found that senescent macrophages exhibit a distinctive p21-TREM2 expression profile and senescence-associated secretory phenotype, driven in part by type I interferon signaling via cytosolic mitochondrial DNA. We also found that senescent macrophage accumulation occurs in aging, metabolic dysfunction-associated steatotic liver disease mouse livers, and is enriched in human cirrhotic liver tissue. Finally, senolytic treatment targeting senescent macrophages reduced liver inflammation and steatosis in both aged mice and mice with metabolic dysfunction-associated steatotic liver disease. These findings establish macrophage senescence as a central driver of chronic inflammation in aging and metabolic liver disease, and a tractable therapeutic target.32 Biomedical and Clinical Sciences (for-2020)3202 Clinical Sciences (for-2020)Genetics (rcdc)Chronic Liver Disease and Cirrhosis (rcdc)Aging (rcdc)Digestive Diseases (rcdc)Liver Disease (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Inflammatory and immune system (hrcs-hc)Oral and gastrointestinal (hrcs-hc)3 Good Health and Well Being (sdg)Animals (mesh)Macrophages (mesh)Humans (mesh)Cellular Senescence (mesh)Mice (mesh)Inflammation (mesh)Fatty Liver (mesh)Aging (mesh)Cyclin-Dependent Kinase Inhibitor p21 (mesh)Male (mesh)MiceInbred C57BL (mesh)DNA Damage (mesh)Liver (mesh)Liver (mesh)Macrophages (mesh)Animals (mesh)MiceInbred C57BL (mesh)Humans (mesh)Mice (mesh)Fatty Liver (mesh)DNA Damage (mesh)Inflammation (mesh)Aging (mesh)Male (mesh)Cyclin-Dependent Kinase Inhibitor p21 (mesh)Cellular Senescence (mesh)Animals (mesh)Macrophages (mesh)Humans (mesh)Cellular Senescence (mesh)Mice (mesh)Inflammation (mesh)Fatty Liver (mesh)Aging (mesh)Cyclin-Dependent Kinase Inhibitor p21 (mesh)Male (mesh)MiceInbred C57BL (mesh)DNA Damage (mesh)Liver (mesh)3202 Clinical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/2z8359hbhttps://escholarship.org/content/qt2z8359hb/qt2z8359hb.pdfinfo:doi/10.1038/s43587-026-01101-6articleNature Aging, vol 6, iss 4792 - 815oai:escholarship.org:ark:/13030/qt9q6606322026-06-23T20:50:33Zqt9q660632Porcupine inhibition disrupts mitochondrial function and homeostasis in WNT ligand-addicted pancreatic cancerAguilera, Kristina YLe, ThucRiahi, RanaLay, Anna RHinz, StefanSaadat, Edris AVashisht, Ajay AWohlschlegel, JamesDonahue, Timothy RRadu, Caius GDawson, David W2022-06-01WNT signaling promotes pancreatic ductal adenocarcinoma (PDAC) through diverse effects on proliferation, differentiation, survival, and stemness. A subset of PDAC with inactivating mutations in ring finger protein 43 (RNF43) show growth dependency on autocrine WNT ligand signaling and are susceptible to agents that block WNT ligand acylation by Porcupine O-acyltransferase, which is required for proper WNT ligand processing and secretion. For this study, global transcriptomic, proteomic, and metabolomic analyses were performed to explore the therapeutic response of RNF43-mutant PDAC to the Porcupine inhibitor (PORCNi) LGK974. LGK974 disrupted cellular bioenergetics and mitochondrial function through actions that included rapid mitochondrial depolarization, reduced mitochondrial content, and inhibition of oxidative phosphorylation and tricarboxylic acid cycle. LGK974 also broadly altered transcriptional activity, downregulating genes involved in cell cycle, nucleotide metabolism, and ribosomal biogenesis and upregulating genes involved in epithelial-mesenchymal transition, hypoxia, endocytosis, and lysosomes. Autophagy and lysosomal activity were augmented in response to LGK974, which synergistically inhibited tumor cell viability in combination with chloroquine. Autocrine WNT ligand signaling dictates metabolic dependencies in RNF43-mutant PDAC through a combination of transcription dependent and independent effects linked to mitochondrial health and function. Metabolic adaptations to mitochondrial damage and bioenergetic stress represent potential targetable liabilities in combination with PORCNi for the treatment of WNT ligand-addicted PDAC.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Cancer (rcdc)Rare Diseases (rcdc)Digestive Diseases (rcdc)Pancreatic Cancer (rcdc)5.1 Pharmaceuticals (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Cancer (hrcs-hc)3 Good Health and Well Being (sdg)Acyltransferases (mesh)CarcinomaPancreatic Ductal (mesh)Cell LineTumor (mesh)Cell Proliferation (mesh)Homeostasis (mesh)Humans (mesh)Ligands (mesh)Membrane Proteins (mesh)Mitochondria (mesh)Pancreatic Neoplasms (mesh)Proteomics (mesh)Wnt Signaling Pathway (mesh)Cell LineTumor (mesh)Mitochondria (mesh)Humans (mesh)CarcinomaPancreatic Ductal (mesh)Pancreatic Neoplasms (mesh)Acyltransferases (mesh)Membrane Proteins (mesh)Ligands (mesh)Proteomics (mesh)Cell Proliferation (mesh)Homeostasis (mesh)Wnt Signaling Pathway (mesh)Acyltransferases (mesh)CarcinomaPancreatic Ductal (mesh)Cell LineTumor (mesh)Cell Proliferation (mesh)Homeostasis (mesh)Humans (mesh)Ligands (mesh)Membrane Proteins (mesh)Mitochondria (mesh)Pancreatic Neoplasms (mesh)Proteomics (mesh)Wnt Signaling Pathway (mesh)1112 Oncology and Carcinogenesis (for)1115 Pharmacology and Pharmaceutical Sciences (for)Oncology & Carcinogenesis (science-metrix)3101 Biochemistry and cell biology (for-2020)3211 Oncology and carcinogenesis (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9q660632https://escholarship.org/content/qt9q660632/qt9q660632.pdfinfo:doi/10.1158/1535-7163.mct-21-0623articleMolecular Cancer Therapeutics, vol 21, iss 6936 - 947oai:escholarship.org:ark:/13030/qt1wv9x4002026-06-23T17:08:35Zqt1wv9x400A neurovascular progenitor sits at the nexus of glioblastoma lineage trajectoriesFazzari, ElisaAzizad, Daria JYu, KwanhaGe, WeihongLi, Matthew XNano, Patricia RBaisiwala, ShivaniMartija, AntoniKan, Ryan LCaston, JaelaDiafos, Loukas NTum, Hong ATse, ChristopherBayley, Nicholas AHaka, VjolaCadet, DimitriPerryman, TravisSoto, Jose AWick, BrittneyVeerappa, AvinashGuda, ChittibabuPowers, Lauren WJain, VaibhavAksu, MichaelEverson, Richard GBergsneider, MarvinRaleigh, David RGregory, Simon GCrouch, Elizabeth EPatel, Kunal SLiau, Linda MNathanson, David ADeneen, BenjaminBhaduri, Aparna2024-07-24Glioblastoma (GBM) is the deadliest form of primary brain tumor with limited treatment options. Recent studies have profiled GBM tumor heterogeneity, revealing numerous axes of variation that explain the molecular and spatial features of the tumor. Here, we seek to bridge descriptive characterization of GBM cell type heterogeneity with the functional role of individual populations within the tumor. Our lens leverages a gene program-centric meta-atlas of published transcriptomic studies to identify commonalities between diverse tumors and cell types in order to decipher the mechanisms that drive them. This approach led to the discovery of a tumor-derived stem cell population with mixed vascular and neural stem cell features, termed a neurovascular progenitor (NVP). Following in situ validation and molecular characterization of NVP cells in GBM patient samples, we characterized their function in vivo. Genetic depletion of NVP cells resulted in altered tumor cell composition, fewer cycling cells, and extended survival, underscoring their critical functional role. Clonal analysis of primary patient tumors in a human organoid tumor transplantation system demonstrated that the NVP has dual potency, generating both neuronal and vascular tumor cells. Although NVP cells comprise a small fraction of the tumor, these clonal analyses demonstrated that they strongly contribute to the total number of cycling cells in the tumor and generate a defined subset of the whole tumor. This study represents a paradigm by which cell type-specific interrogation of tumor populations can be used to study functional heterogeneity and therapeutically targetable vulnerabilities of GBM.32 Biomedical and Clinical Sciences (for-2020)3211 Oncology and Carcinogenesis (for-2020)Genetics (rcdc)Stem Cell Research (rcdc)Cancer Genomics (rcdc)Cancer (rcdc)Human Genome (rcdc)Rare Diseases (rcdc)Neurosciences (rcdc)Stem Cell Research - Nonembryonic - Non-Human (rcdc)Orphan Drug (rcdc)Stem Cell Research - Nonembryonic - Human (rcdc)Brain Cancer (rcdc)Brain Disorders (rcdc)Cancer (hrcs-hc)application/pdfCC-BY-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/1wv9x400https://escholarship.org/content/qt1wv9x400/qt1wv9x400.pdfinfo:doi/10.1101/2024.07.24.604840articlebioRxiv, vol 5, iss 08-012024.07.24.604840oai:escholarship.org:ark:/13030/qt1dw233qz2026-06-17T12:42:34Zqt1dw233qzDual Knockout Models of the Spatially and Functionally Conserved rgra and rgrb Zebrafish Genes Reveal the Requirement of RGR for the Integrity of Cone‐Mediated Photopic Vision, the Photopic Visual Cycle and Bruch's Membrane MorphologyRuddin, GraceMcCann, TessKaylor, Joanna JFox, Michelle MFehilly, John DWard, RebeccaFaulkner, AdamMoran, Ailís LWynne, KieranRadu, Roxana AMonaghan, Michael GThorpe, Stephen DTravis, Gabriel HKennedy, Breandán N2026-05-31The retinal G protein-coupled receptor (RGR) is a visual cycle photoisomerase that photopically regenerates 11-cis-retinal (11cRAL). It plays a crucial role in sustaining vision. Here, we investigated the in vivo role of RGR in the cone photoreceptor-dominant, zebrafish retina, focusing predominantly on how visual function is impacted in the absence of RGR. There are two zebrafish RGR paralogs, rgra and rgrb, both with predominant expression in retinal pigment epithelium (RPE) and Müller glia cells. Under standard light rearing conditions, bespoke rgrb-/-; rgra-/- double knockout zebrafish present with a ~21% reduction in optokinetic response (OKR) saccades per minute relative to wild-type (WT). This impaired visual behavior worsens in higher photopic conditions ranging from 20 000-81 000 lx. In contrast, no significant OKR defect is observed under dark-adapted conditions, consolidating the light-dependent role of RGR in vision. Retinoid profiling of rgrb-/-; rgra-/- zebrafish larvae demonstrated significant decreases in 11cRAL levels under standard and brighter light rearing conditions. Proteomic profiling validated the successful generation of rgrb-/-; rgra-/- zebrafish and revealed an unanticipated upregulation in ocular extracellular matrix proteins. From polarized light microscopy, increased collagen fiber abundance with dysregulated organization in Bruch's membrane at the interface between the retina and choroid was observed. These novel findings demonstrate the role of RGR in sustaining visual function under cone-mediated photopic conditions, a concomitant deficit in the photopic visual cycle and a novel role in maintaining the integrity of Bruch's membrane.32 Biomedical and Clinical Sciences (for-2020)3212 Ophthalmology and Optometry (for-2020)Eye Disease and Disorders of Vision (rcdc)Neurosciences (rcdc)Eye (hrcs-hc)Animals (mesh)Zebrafish (mesh)Retinal Cone Photoreceptor Cells (mesh)Zebrafish Proteins (mesh)Bruch Membrane (mesh)ReceptorsG-Protein-Coupled (mesh)Color Vision (mesh)Gene Knockout Techniques (mesh)Retinal Pigment Epithelium (mesh)Eye Proteins (mesh)Bruch's membranePhotoisomeraseretinoidsRGRvisionzebrafishBruch Membrane (mesh)Animals (mesh)Zebrafish (mesh)Eye Proteins (mesh)Zebrafish Proteins (mesh)ReceptorsG-Protein-Coupled (mesh)Retinal Cone Photoreceptor Cells (mesh)Retinal Pigment Epithelium (mesh)Color Vision (mesh)Gene Knockout Techniques (mesh)Bruch's membranePhotoisomeraseRGRretinoidsvisionzebrafishAnimals (mesh)Zebrafish (mesh)Retinal Cone Photoreceptor Cells (mesh)Zebrafish Proteins (mesh)Bruch Membrane (mesh)ReceptorsG-Protein-Coupled (mesh)Color Vision (mesh)Gene Knockout Techniques (mesh)Retinal Pigment Epithelium (mesh)Eye Proteins (mesh)0601 Biochemistry and Cell Biology (for)0606 Physiology (for)1116 Medical Physiology (for)Biochemistry & Molecular Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)3208 Medical physiology (for-2020)application/pdfCC-BY-NCeScholarship, University of Californiahttps://escholarship.org/uc/item/1dw233qzhttps://escholarship.org/content/qt1dw233qz/qt1dw233qz.pdfinfo:doi/10.1096/fj.202504935rarticleThe FASEB Journal, vol 40, iss 10e71877oai:escholarship.org:ark:/13030/qt4kv549d82026-06-17T12:23:52Zqt4kv549d8FXR activation protects against NAFLD via bile-acid-dependent reductions in lipid absorptionClifford, Bethan LSedgeman, Leslie RWilliams, Kevin JMorand, PaulineCheng, AngelaJarrett, Kelsey EChan, Alvin PBrearley-Sholto, Madelaine CWahlström, AnnikaAshby, Julianne WBarshop, WilliamWohlschlegel, JamesCalkin, Anna CLiu, YingyingThorell, AndersMeikle, Peter JDrew, Brian GMack, Julia JMarschall, Hanns-UlrichTarling, Elizabeth JEdwards, Peter Ade Aguiar Vallim, Thomas Q2021-08-01FXR agonists are used to treat non-alcoholic fatty liver disease (NAFLD), in part because they reduce hepatic lipids. Here, we show that FXR activation with the FXR agonist GSK2324 controls hepatic lipids via reduced absorption and selective decreases in fatty acid synthesis. Using comprehensive lipidomic analyses, we show that FXR activation in mice or humans specifically reduces hepatic levels of mono- and polyunsaturated fatty acids (MUFA and PUFA). Decreases in MUFA are due to FXR-dependent repression of Scd1, Dgat2, and Lpin1 expression, which is independent of SHP and SREBP1c. FXR-dependent decreases in PUFAs are mediated by decreases in lipid absorption. Replenishing bile acids in the diet prevented decreased lipid absorption in GSK2324-treated mice, suggesting that FXR reduces absorption via decreased bile acids. We used tissue-specific FXR KO mice to show that hepatic FXR controls lipogenic genes, whereas intestinal FXR controls lipid absorption. Together, our studies establish two distinct pathways by which FXR regulates hepatic lipids.3205 Medical Biochemistry and Metabolomics (for-2020)32 Biomedical and Clinical Sciences (for-2020)Nutrition (rcdc)Digestive Diseases (rcdc)Liver Disease (rcdc)Prevention (rcdc)Chronic Liver Disease and Cirrhosis (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Metabolic and endocrine (hrcs-hc)Oral and gastrointestinal (hrcs-hc)Animals (mesh)Bile (mesh)Bile Acids and Salts (mesh)Humans (mesh)Lipids (mesh)Liver (mesh)Mice (mesh)MiceInbred C57BL (mesh)Non-alcoholic Fatty Liver Disease (mesh)Phosphatidate Phosphatase (mesh)ReceptorsCytoplasmic and Nuclear (mesh)ReceptorFarnesoid X-Activated (mesh)Liver (mesh)Bile (mesh)Animals (mesh)MiceInbred C57BL (mesh)Humans (mesh)Mice (mesh)Bile Acids and Salts (mesh)Phosphatidate Phosphatase (mesh)Lipids (mesh)ReceptorsCytoplasmic and Nuclear (mesh)Non-alcoholic Fatty Liver Disease (mesh)ReceptorFarnesoid X-Activated (mesh)FXRNAFLDbile acidsintestinal lipid absorptionAnimals (mesh)Bile (mesh)Bile Acids and Salts (mesh)Humans (mesh)Lipids (mesh)Liver (mesh)Mice (mesh)MiceInbred C57BL (mesh)Non-alcoholic Fatty Liver Disease (mesh)Phosphatidate Phosphatase (mesh)ReceptorsCytoplasmic and Nuclear (mesh)ReceptorFarnesoid X-Activated (mesh)0601 Biochemistry and Cell Biology (for)1101 Medical Biochemistry and Metabolomics (for)Endocrinology & Metabolism (science-metrix)3101 Biochemistry and cell biology (for-2020)3205 Medical biochemistry and metabolomics (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4kv549d8https://escholarship.org/content/qt4kv549d8/qt4kv549d8.pdfinfo:doi/10.1016/j.cmet.2021.06.012articleCell Metabolism, vol 33, iss 81671 - 1684.e4oai:escholarship.org:ark:/13030/qt9p24x9622026-06-17T07:56:23Zqt9p24x962CIPHER: An end-to-end framework for designing optimized aggregated spatial transcriptomics experiments.Hemminger, ZacharyDe Ocampo, HaleyXie, FangmingZhai, ZhiqianLi, JingyiWollman, Roy2026-06-01MotivationMost imaging-based spatial transcriptomics methods measure individual genes, which limits scalability and typically requires integration with scRNA-seq to recover full cellular states. Recent approaches such as CISI, FISHnCHIPs, and ATLAS address this limitation by measuring aggregate transcriptional signatures, where multiple genes are pooled into each channel to increase throughput. While aggregate measurements improve scalability, they shift the problem from gene selection to feature design. For effective integration with scRNA-seq, these signatures must be not only discriminative in transcriptional space but also straightforward to measure, with balanced signal, sufficient dynamic range, and robustness to experimental noise. By optimizing decoding accuracy in isolation, existing methods leave substantial performance on the table.ResultsWe present CIPHER (Cell Identity Projection using Hybridization Encoding Rules), a neural-network framework that jointly optimizes the experimental encoding matrix, i.e., the way that genes are aggregated to signatures, and the downstream cell embedding. CIPHER integrates the physical limits of imaging assays directly into its loss function, shaping the latent space to maximize discriminability while maintaining robustness to measurement noise and signal constraints. Using a large-scale mouse brain scRNA-seq reference, we show that CIPHER-designed encodings yield latent spaces with improved cell-type separability, uniform signal utilization, and greater resilience to hybridization variability, resulting in higher decoding accuracy from both simulated and experimental data.ConclusionCIPHER formulates aggregate signature design as a joint optimization problem over decoding accuracy and experimental measurability. This enables systematic, scRNA-seq-aligned feature design for scalable spatial transcriptomics based on aggregate measurements.AvailabilityCode and documentation are available at https://github.com/wollmanlab/Design/.AnimalsMiceGene Expression ProfilingComputational BiologyAlgorithmsSoftwareTranscriptomeSingle-Cell Gene Expression AnalysisSpatial Transcriptomicsapplication/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/9p24x962https://escholarship.org/content/qt9p24x962/qt9p24x962.pdfinfo:doi/10.1371/journal.pcbi.1014362articlePLoS Computational Biology, vol 22, iss 6oai:escholarship.org:ark:/13030/qt1bq243pb2026-06-14T06:49:49Zqt1bq243pbSingle-cell analysis of the developing human testis reveals somatic niche cell specification and fetal germline stem cell establishmentGuo, JingtaoSosa, EnriqueChitiashvili, TsotneNie, XichenRojas, Ernesto JavierOliver, ElizabethConnect, DonorPlath, KathrinHotaling, James MStukenborg, Jan-BerndClark, Amander TCairns, Bradley R2021-04-01Human testis development in prenatal life involves complex changes in germline and somatic cell identity. To better understand, we profiled and analyzed ∼32,500 single-cell transcriptomes of testicular cells from embryonic, fetal, and infant stages. Our data show that at 6-7 weeks postfertilization, as the testicular cords are established, the Sertoli and interstitial cells originate from a common heterogeneous progenitor pool, which then resolves into fetal Sertoli cells (expressing tube-forming genes) or interstitial cells (including Leydig-lineage cells expressing steroidogenesis genes). Almost 10 weeks later, beginning at 14-16 weeks postfertilization, the male primordial germ cells exit mitosis, downregulate pluripotent transcription factors, and transition into cells that strongly resemble the state 0 spermatogonia originally defined in the infant and adult testes. Therefore, we called these fetal spermatogonia "state f0." Overall, we reveal multiple insights into the coordinated and temporal development of the embryonic, fetal, and postnatal male germline together with the somatic niche.3101 Biochemistry and Cell Biology (for-2020)3215 Reproductive Medicine (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Pediatric Research Initiative (rcdc)Urologic Diseases (rcdc)Stem Cell Research (rcdc)Stem Cell Research - Nonembryonic - Non-Human (rcdc)Contraception/Reproduction (rcdc)Genetics (rcdc)Stem Cell Research - Embryonic - Non-Human (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Adult (mesh)Female (mesh)Humans (mesh)Male (mesh)Pregnancy (mesh)Sertoli Cells (mesh)Single-Cell Analysis (mesh)Spermatogonia (mesh)Stem Cells (mesh)Testis (mesh)DonorConnectTestis (mesh)Sertoli Cells (mesh)Spermatogonia (mesh)Stem Cells (mesh)Humans (mesh)Pregnancy (mesh)Adult (mesh)Female (mesh)Male (mesh)Single-Cell Analysis (mesh)Leydig cellSertoli cellfetal testis developmentinterstitial cellprimordial germ cellsingle-cell RNA sequencingspermatogonial stem cellAdult (mesh)Female (mesh)Humans (mesh)Male (mesh)Pregnancy (mesh)Sertoli Cells (mesh)Single-Cell Analysis (mesh)Spermatogonia (mesh)Stem Cells (mesh)Testis (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1bq243pbhttps://escholarship.org/content/qt1bq243pb/qt1bq243pb.pdfinfo:doi/10.1016/j.stem.2020.12.004articleCell Stem Cell, vol 28, iss 4764 - 778.e4oai:escholarship.org:ark:/13030/qt3261z1v52026-06-13T11:44:45Zqt3261z1v5JAKMIP1, a Novel Regulator of Neuronal Translation, Modulates Synaptic Function and Autistic-like Behaviors in MouseBerg, Jamee MLee, ChanghoonChen, LeslieGalvan, LaurieCepeda, CarlosChen, Jane YPeñagarikano, OlgaStein, Jason LLi, AlvinOguro-Ando, AsamiMiller, Jeremy AVashisht, Ajay AStarks, Mary EKite, Elyse PTam, EricGdalyahu, AmosAl-Sharif, Noor BBurkett, Zachary DWhite, Stephanie AFears, Scott CLevine, Michael SWohlschlegel, James AGeschwind, Daniel H2015-12-01Autism spectrum disorder (ASD) is a heritable, common neurodevelopmental disorder with diverse genetic causes. Several studies have implicated protein synthesis as one among several of its potential convergent mechanisms. We originally identified Janus kinase and microtubule-interacting protein 1 (JAKMIP1) as differentially expressed in patients with distinct syndromic forms of ASD, fragile X syndrome, and 15q duplication syndrome. Here, we provide multiple lines of evidence that JAKMIP1 is a component of polyribosomes and an RNP translational regulatory complex that includes fragile X mental retardation protein, DEAD box helicase 5, and the poly(A) binding protein cytoplasmic 1. JAKMIP1 loss dysregulates neuronal translation during synaptic development, affecting glutamatergic NMDAR signaling, and results in social deficits, stereotyped activity, abnormal postnatal vocalizations, and other autistic-like behaviors in the mouse. These findings define an important and novel role for JAKMIP1 in neural development and further highlight pathways regulating mRNA translation during synaptogenesis in the genesis of neurodevelopmental disorders.5202 Biological Psychology (for-2020)52 Psychology (for-2020)Mental Health (rcdc)Pediatric Research Initiative (rcdc)Genetics (rcdc)Brain Disorders (rcdc)Neurosciences (rcdc)Intellectual and Developmental Disabilities (IDD) (rcdc)Fragile X Syndrome (rcdc)Rare Diseases (rcdc)Autism (rcdc)Basic Behavioral and Social Science (rcdc)Behavioral and Social Science (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Neurological (hrcs-hc)Mental health (hrcs-hc)Adaptor ProteinsSignal Transducing (mesh)Animals (mesh)Autism Spectrum Disorder (mesh)Gene Regulatory Networks (mesh)Male (mesh)Mice (mesh)MiceInbred C57BL (mesh)MiceKnockout (mesh)Neurons (mesh)Protein Biosynthesis (mesh)Proteomics (mesh)RNA-Binding Proteins (mesh)Synapses (mesh)Neurons (mesh)Synapses (mesh)Animals (mesh)MiceInbred C57BL (mesh)MiceKnockout (mesh)Mice (mesh)Adaptor ProteinsSignal Transducing (mesh)RNA-Binding Proteins (mesh)Proteomics (mesh)Protein Biosynthesis (mesh)Male (mesh)Gene Regulatory Networks (mesh)Autism Spectrum Disorder (mesh)Adaptor ProteinsSignal Transducing (mesh)Animals (mesh)Autism Spectrum Disorder (mesh)Gene Regulatory Networks (mesh)Male (mesh)Mice (mesh)MiceInbred C57BL (mesh)MiceKnockout (mesh)Neurons (mesh)Protein Biosynthesis (mesh)Proteomics (mesh)RNA-Binding Proteins (mesh)Synapses (mesh)1109 Neurosciences (for)1701 Psychology (for)1702 Cognitive Sciences (for)Neurology & Neurosurgery (science-metrix)3209 Neurosciences (for-2020)5202 Biological psychology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3261z1v5https://escholarship.org/content/qt3261z1v5/qt3261z1v5.pdfinfo:doi/10.1016/j.neuron.2015.10.031articleNeuron, vol 88, iss 61173 - 1191oai:escholarship.org:ark:/13030/qt40k4w7jn2026-06-13T08:28:41Zqt40k4w7jnDefining STING–sterol interactions with chemoproteomicsFord, IanVillanueva, MirandaLee, Min SubZhou, Quan DYuen, ConstanceDamoiseaux, RobertBensinger, Steven JBackus, Keriann M2025-08-27Stimulator of interferon genes (STING) is an intracellular pattern recognition receptor that plays a key role in responding to cytosolic DNA and cyclic dinucleotides. STING activity is tightly regulated to avoid aberrant STING activity, excessive type I IFN responses, and resultant autoinflammatory disease. As such understanding the molecular events regulating STING activity is critical. Recent work has revealed cellular cholesterol metabolism also functions to modulate STING activity, although the molecular events linking cholesterol homeostasis with STING remain incompletely understood. Here we pair genetic and chemoproteomic approaches to inform the mechanisms governing cholesterol modulation of STING activity. Using gain- and loss-of-function systems, we find that markedly increasing SCAP-SREBP2 processing and resultant cholesterol synthesis has little impact on STING activity. In contrast, we find that genetic deletion of Srebf2 increased basal and ligand inducible type I IFN responses. Thus, STING can function in the absence of the SCAP-SREBP2 protein apparatus. Through activity-based protein profiling with three distinct sterol-mimetic probes, we provide direct evidence for STING-sterol binding. We also find that the mitochondrial protein VDAC1 co-purifies with STING and binds to sterol-mimetic probes. We also show that STING's subcellular localization is responsive to modulation of cellular sterol content. Our findings support a model where sterol synthesis in the ER regulates STING activity, aligning with recent studies indicating that cholesterol-mediated retention of STING in the endoplasmic reticulum occurs through cholesterol recognition amino acid consensus (CARC) motifs in STING.3404 Medicinal and Biomolecular Chemistry (for-2020)34 Chemical Sciences (for-2020)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Generic health relevance (hrcs-hc)3404 Medicinal and biomolecular chemistry (for-2020)application/pdfCC-BY-NCeScholarship, University of Californiahttps://escholarship.org/uc/item/40k4w7jnhttps://escholarship.org/content/qt40k4w7jn/qt40k4w7jn.pdfinfo:doi/10.1039/d5cb00171darticleRSC Chemical Biology, vol 6, iss 91451 - 1464oai:escholarship.org:ark:/13030/qt9d7003c92026-06-05T01:52:40Zqt9d7003c9An HK2 Antisense Oligonucleotide Induces Synthetic Lethality in HK1−HK2+ Multiple MyelomaXu, ShiliZhou, TianyuanDoh, Hanna MTrinh, K RyanCatapang, ArtLee, Jason TBraas, DanielBayley, Nicholas AYamada, Reiko EVasuthasawat, AlexSasine, Joshua PTimmerman, John MLarson, Sarah MKim, YoungsooMacLeod, A RobertMorrison, Sherie LHerschman, Harvey R2019-05-15Although the majority of adult tissues express only hexokinase 1 (HK1) for glycolysis, most cancers express hexokinase 2 (HK2) and many coexpress HK1 and HK2. In contrast to HK1+HK2+ cancers, HK1-HK2+ cancer subsets are sensitive to cytostasis induced by HK2shRNA knockdown and are also sensitive to synthetic lethality in response to the combination of HK2shRNA knockdown, an oxidative phosphorylation (OXPHOS) inhibitor diphenyleneiodonium (DPI), and a fatty acid oxidation (FAO) inhibitor perhexiline (PER). The majority of human multiple myeloma cell lines are HK1-HK2+. Here we describe an antisense oligonucleotide (ASO) directed against human HK2 (HK2-ASO1), which suppressed HK2 expression in human multiple myeloma cell cultures and human multiple myeloma mouse xenograft models. The HK2-ASO1/DPI/PER triple-combination achieved synthetic lethality in multiple myeloma cells in culture and prevented HK1-HK2+ multiple myeloma tumor xenograft progression. DPI was replaceable by the FDA-approved OXPHOS inhibitor metformin (MET), both for synthetic lethality in culture and for inhibition of tumor xenograft progression. In addition, we used an ASO targeting murine HK2 (mHK2-ASO1) to validate the safety of mHK2-ASO1/MET/PER combination therapy in mice bearing murine multiple myeloma tumors. HK2-ASO1 is the first agent that shows selective HK2 inhibition and therapeutic efficacy in cell culture and in animal models, supporting clinical development of this synthetically lethal combination as a therapy for HK1-HK2+ multiple myeloma. SIGNIFICANCE: A first-in-class HK2 antisense oligonucleotide suppresses HK2 expression in cell culture and in in vivo, presenting an effective, tolerated combination therapy for preventing progression of HK1-HK2+ multiple myeloma tumors. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/79/10/2748/F1.large.jpg.32 Biomedical and Clinical Sciences (for-2020)3211 Oncology and Carcinogenesis (for-2020)Rare Diseases (rcdc)Cancer (rcdc)Biotechnology (rcdc)Hematology (rcdc)Orphan Drug (rcdc)5.1 Pharmaceuticals (hrcs-rac)Cancer (hrcs-hc)Animals (mesh)Cell LineTumor (mesh)Cell Proliferation (mesh)Hexokinase (mesh)Humans (mesh)Mice (mesh)Multiple Myeloma (mesh)OligonucleotidesAntisense (mesh)Synthetic Lethal Mutations (mesh)Xenograft Model Antitumor Assays (mesh)Cell LineTumor (mesh)Animals (mesh)Humans (mesh)Mice (mesh)Multiple Myeloma (mesh)Hexokinase (mesh)OligonucleotidesAntisense (mesh)Xenograft Model Antitumor Assays (mesh)Cell Proliferation (mesh)Synthetic Lethal Mutations (mesh)Animals (mesh)Cell LineTumor (mesh)Cell Proliferation (mesh)Hexokinase (mesh)Humans (mesh)Mice (mesh)Multiple Myeloma (mesh)OligonucleotidesAntisense (mesh)Synthetic Lethal Mutations (mesh)Xenograft Model Antitumor Assays (mesh)1112 Oncology and Carcinogenesis (for)Oncology & Carcinogenesis (science-metrix)3101 Biochemistry and cell biology (for-2020)3211 Oncology and carcinogenesis (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9d7003c9https://escholarship.org/content/qt9d7003c9/qt9d7003c9.pdfinfo:doi/10.1158/0008-5472.can-18-2799articleCancer Research, vol 79, iss 102748 - 2760oai:escholarship.org:ark:/13030/qt7b47k3442026-05-30T17:27:54Zqt7b47k344Progesterone Receptor in the Vascular Endothelium Triggers Physiological Uterine Permeability PreimplantationGoddard, Lauren MMurphy, Thomas JOrg, TönisEnciso, Josephine MHashimoto-Partyka, Minako KWarren, Carmen MDomigan, Courtney KMcDonald, Austin IHe, HuanhuanSanchez, Lauren AAllen, Nancy COrsenigo, FabrizioChao, Lily CDejana, ElisabettaTontonoz, PeterMikkola, Hanna KAIruela-Arispe, M Luisa2014-01-01Vascular permeability is frequently associated with inflammation and is triggered by a cohort of secreted permeability factors such as vascular endothelial growth factor (VEGF). Here, we show that the physiological vascular permeability that precedes implantation is directly controlled by progesterone receptor (PR) and is independent of VEGF. Global or endothelial-specific deletion of PR blocks physiological vascular permeability in the uterus, whereas misexpression of PR in the endothelium of other organs results in ectopic vascular leakage. Integration of an endothelial genome-wide transcriptional profile with chromatin immunoprecipitation sequencing revealed that PR induces an NR4A1 (Nur77/TR3)-dependent transcriptional program that broadly regulates vascular permeability in response to progesterone. Silencing of NR4A1 blocks PR-mediated permeability responses, indicating a direct link between PR and NR4A1. This program triggers concurrent suppression of several junctional proteins and leads to an effective, timely, and venous-specific regulation of vascular barrier function that is critical for embryo implantation.3215 Reproductive Medicine (for-2020)32 Biomedical and Clinical Sciences (for-2020)Contraception/Reproduction (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Cardiovascular (hrcs-hc)Animals (mesh)Capillary Permeability (mesh)Endometrium (mesh)EndotheliumVascular (mesh)Female (mesh)Gene Expression Regulation (mesh)Humans (mesh)Mice (mesh)Nuclear Receptor Subfamily 4Group AMember 1 (mesh)Uterus (mesh)Uterus (mesh)Endometrium (mesh)EndotheliumVascular (mesh)Animals (mesh)Humans (mesh)Mice (mesh)Gene Expression Regulation (mesh)Capillary Permeability (mesh)Female (mesh)Nuclear Receptor Subfamily 4Group AMember 1 (mesh)Animals (mesh)Capillary Permeability (mesh)Endometrium (mesh)EndotheliumVascular (mesh)Female (mesh)Gene Expression Regulation (mesh)Humans (mesh)Mice (mesh)Nuclear Receptor Subfamily 4Group AMember 1 (mesh)Uterus (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7b47k344https://escholarship.org/content/qt7b47k344/qt7b47k344.pdfinfo:doi/10.1016/j.cell.2013.12.025articleCell, vol 156, iss 3549 - 562oai:escholarship.org:ark:/13030/qt18f9f0h72026-05-25T18:44:05Zqt18f9f0h7D-loop Dynamics and Near-Atomic-Resolution Cryo-EM Structure of Phalloidin-Bound F-ActinDas, SanchaitaGe, PengDurer, Zeynep A OztugGrintsevich, Elena EZhou, Z HongReisler, Emil2020-05-01Detailed molecular information on G-actin assembly into filaments (F-actin), and their structure, dynamics, and interactions, is essential for understanding their cellular functions. Previous studies indicate that a flexible DNase I binding loop (D-loop, residues 40-50) plays a major role in actin's conformational dynamics. Phalloidin, a "gold standard" for actin filament staining, stabilizes them and affects the D-loop. Using disulfide crosslinking in yeast actin D-loop mutant Q41C/V45C, light-scattering measurements, and cryoelectron microscopy reconstructions, we probed the constraints of D-loop dynamics and its contribution to F-actin formation/stability. Our data support a model of residues 41-45 distances that facilitate G- to F-actin transition. We report also a 3.3-Å resolution structure of phalloidin-bound F-actin in the ADP-Pi-like (ADP-BeFx) state. This shows the phalloidin-binding site on F-actin and how the relative movement between its two protofilaments is restricted by it. Together, our results provide molecular details of F-actin structure and D-loop dynamics.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Bioengineering (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Actins (mesh)Cross-Linking Reagents (mesh)Cryoelectron Microscopy (mesh)Deoxyribonuclease I (mesh)Disulfides (mesh)ModelsMolecular (mesh)Mutation (mesh)Phalloidine (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae (mesh)Disulfides (mesh)Phalloidine (mesh)Actins (mesh)Deoxyribonuclease I (mesh)Cross-Linking Reagents (mesh)Cryoelectron Microscopy (mesh)Mutation (mesh)ModelsMolecular (mesh)D-loop dynamicsF-actin structurechemical crosslinkinghigh-resolution cryo-EMActins (mesh)Cross-Linking Reagents (mesh)Cryoelectron Microscopy (mesh)Deoxyribonuclease I (mesh)Disulfides (mesh)ModelsMolecular (mesh)Mutation (mesh)Phalloidine (mesh)Saccharomyces cerevisiae (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)08 Information and Computing Sciences (for)Biophysics (science-metrix)31 Biological sciences (for-2020)34 Chemical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/18f9f0h7https://escholarship.org/content/qt18f9f0h7/qt18f9f0h7.pdfinfo:doi/10.1016/j.str.2020.04.004articleStructure, vol 28, iss 5586 - 593.e3oai:escholarship.org:ark:/13030/qt7fj7q33g2026-05-25T16:33:51Zqt7fj7q33gStructural mechanism of a Rag GTPase activation checkpoint by the lysosomal folliculin complexLawrence, Rosalie EFromm, Simon AFu, YangxueYokom, Adam LKim, JinThelen, Ashley MYoung, Lindsey NLim, Chun-YanSamelson, Avi JHurley, James HZoncu, Roberto2019-11-22The tumor suppressor folliculin (FLCN) enables nutrient-dependent activation of the mechanistic target of rapamycin complex 1 (mTORC1) protein kinase via its guanosine triphosphatase (GTPase) activating protein (GAP) activity toward the GTPase RagC. Concomitant with mTORC1 inactivation by starvation, FLCN relocalizes from the cytosol to lysosomes. To determine the lysosomal function of FLCN, we reconstituted the human lysosomal FLCN complex (LFC) containing FLCN, its partner FLCN-interacting protein 2 (FNIP2), and the RagAGDP:RagCGTP GTPases as they exist in the starved state with their lysosomal anchor Ragulator complex and determined its cryo-electron microscopy structure to 3.6 angstroms. The RagC-GAP activity of FLCN was inhibited within the LFC, owing to displacement of a catalytically required arginine in FLCN from the RagC nucleotide. Disassembly of the LFC and release of the RagC-GAP activity of FLCN enabled mTORC1-dependent regulation of the master regulator of lysosomal biogenesis, transcription factor E3, implicating the LFC as a checkpoint in mTORC1 signaling.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Generic health relevance (hrcs-hc)Basic Helix-Loop-Helix Leucine Zipper Transcription Factors (mesh)Carrier Proteins (mesh)Cell Nucleus (mesh)Cryoelectron Microscopy (mesh)Cytoplasm (mesh)GTPase-Activating Proteins (mesh)Guanosine Diphosphate (mesh)Humans (mesh)Lysosomes (mesh)Mechanistic Target of Rapamycin Complex 1 (mesh)ModelsMolecular (mesh)Monomeric GTP-Binding Proteins (mesh)Multiprotein Complexes (mesh)Protein Conformation (mesh)Protein Domains (mesh)Protein Multimerization (mesh)Proto-Oncogene Proteins (mesh)Signal Transduction (mesh)Tumor Suppressor Proteins (mesh)Cell Nucleus (mesh)Cytoplasm (mesh)Lysosomes (mesh)Humans (mesh)Multiprotein Complexes (mesh)Monomeric GTP-Binding Proteins (mesh)GTPase-Activating Proteins (mesh)Carrier Proteins (mesh)Proto-Oncogene Proteins (mesh)Tumor Suppressor Proteins (mesh)Guanosine Diphosphate (mesh)Cryoelectron Microscopy (mesh)Signal Transduction (mesh)Protein Conformation (mesh)ModelsMolecular (mesh)Basic Helix-Loop-Helix Leucine Zipper Transcription Factors (mesh)Protein Multimerization (mesh)Protein Domains (mesh)Mechanistic Target of Rapamycin Complex 1 (mesh)Basic Helix-Loop-Helix Leucine Zipper Transcription Factors (mesh)Carrier Proteins (mesh)Cell Nucleus (mesh)Cryoelectron Microscopy (mesh)Cytoplasm (mesh)GTPase-Activating Proteins (mesh)Guanosine Diphosphate (mesh)Humans (mesh)Lysosomes (mesh)Mechanistic Target of Rapamycin Complex 1 (mesh)ModelsMolecular (mesh)Monomeric GTP-Binding Proteins (mesh)Multiprotein Complexes (mesh)Protein Conformation (mesh)Protein Domains (mesh)Protein Multimerization (mesh)Proto-Oncogene Proteins (mesh)Signal Transduction (mesh)Tumor Suppressor Proteins (mesh)General Science & Technology (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7fj7q33ghttps://escholarship.org/content/qt7fj7q33g/qt7fj7q33g.pdfinfo:doi/10.1126/science.aax0364articleScience, vol 366, iss 6468971 - 977oai:escholarship.org:ark:/13030/qt90r900bq2026-05-23T22:49:29Zqt90r900bqThe BAF and PRC2 Complex Subunits Dpf2 and Eed Antagonistically Converge on Tbx3 to Control ESC DifferentiationZhang, WenshengChronis, ConstantinosChen, XiZhang, HeyaoSpalinskas, RapolasPardo, MercedesChen, LiangliangWu, GuangmingZhu, ZhexinYu, YongYu, LuChoudhary, JyotiNichols, JenniferParast, Mana MGreber, BorisSahlén, PelinPlath, Kathrin2019-01-01BAF complexes are composed of different subunits with varying functional and developmental roles, although many subunits have not been examined in depth. Here we show that the Baf45 subunit Dpf2 maintains pluripotency and ESC differentiation potential. Dpf2 co-occupies enhancers with Oct4, Sox2, p300, and the BAF subunit Brg1, and deleting Dpf2 perturbs ESC self-renewal, induces repression of Tbx3, and impairs mesendodermal differentiation without dramatically altering Brg1 localization. Mesendodermal differentiation can be rescued by restoring Tbx3 expression, whose distal enhancer is positively regulated by Dpf2-dependent H3K27ac maintenance and recruitment of pluripotency TFs and Brg1. In contrast, the PRC2 subunit Eed binds an intragenic Tbx3 enhancer to oppose Dpf2-dependent Tbx3 expression and mesendodermal differentiation. The PRC2 subunit Ezh2 likewise opposes Dpf2-dependent differentiation through a distinct mechanism involving Nanog repression. Together, these findings delineate distinct mechanistic roles for specific BAF and PRC2 subunits during ESC differentiation.3208 Medical Physiology (for-2020)32 Biomedical and Clinical Sciences (for-2020)Stem Cell Research - Embryonic - Non-Human (rcdc)Stem Cell Research (rcdc)Animals (mesh)Apoptosis (mesh)Cell Cycle (mesh)Cell Differentiation (mesh)DNA-Binding Proteins (mesh)Embryonic Stem Cells (mesh)Histones (mesh)Mice (mesh)MiceKnockout (mesh)Nanog Homeobox Protein (mesh)Polycomb Repressive Complex 2 (mesh)Protein Subunits (mesh)T-Box Domain Proteins (mesh)Transcription Factors (mesh)Animals (mesh)MiceKnockout (mesh)Mice (mesh)DNA-Binding Proteins (mesh)T-Box Domain Proteins (mesh)Histones (mesh)Protein Subunits (mesh)Transcription Factors (mesh)Cell Cycle (mesh)Apoptosis (mesh)Cell Differentiation (mesh)Embryonic Stem Cells (mesh)Polycomb Repressive Complex 2 (mesh)Nanog Homeobox Protein (mesh)BAF complexPRC2 complexcell fate decisiondifferentiationembryonic stem cellsenhancershistone modificationpluripotencyself-renewalAnimals (mesh)Apoptosis (mesh)Cell Cycle (mesh)Cell Differentiation (mesh)DNA-Binding Proteins (mesh)Embryonic Stem Cells (mesh)Histones (mesh)Mice (mesh)MiceKnockout (mesh)Nanog Homeobox Protein (mesh)Polycomb Repressive Complex 2 (mesh)Protein Subunits (mesh)T-Box Domain Proteins (mesh)Transcription Factors (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/90r900bqinfo:doi/10.1016/j.stem.2018.12.001articleCell Stem Cell, vol 24, iss 1138 - 152.e8oai:escholarship.org:ark:/13030/qt8kw5z8s72026-05-22T00:36:49Zqt8kw5z8s7Rapid degradation of mutant SLC25A46 by the ubiquitin-proteasome system results in MFN1/2-mediated hyperfusion of mitochondriaSteffen, JanosVashisht, Ajay AWan, JijunJen, Joanna CClaypool, Steven MWohlschlegel, James AKoehler, Carla MFox, Thomas D2017-03-01SCL25A46 is a mitochondrial carrier protein that surprisingly localizes to the outer membrane and is distantly related to Ugo1. Here we show that a subset of SLC25A46 interacts with mitochondrial dynamics components and the MICOS complex. Decreased expression of SLC25A46 results in increased stability and oligomerization of MFN1 and MFN2 on mitochondria, promoting mitochondrial hyperfusion. A mutation at L341P causes rapid degradation of SLC25A46, which manifests as a rare disease, pontocerebellar hypoplasia. The E3 ubiquitin ligases MULAN and MARCH5 coordinate ubiquitylation of SLC25A46 L341P, leading to degradation by organized activities of P97 and the proteasome. Whereas outer mitochondrial membrane-associated degradation is typically associated with apoptosis or a specialized type of autophagy termed mitophagy, SLC25A46 degradation operates independently of activation of outer membrane stress pathways. Thus SLC25A46 is a new component in mitochondrial dynamics that serves as a regulator for MFN1/2 oligomerization. Moreover, SLC25A46 is selectively degraded from the outer membrane independently of mitophagy and apoptosis, providing a framework for mechanistic studies in the proteolysis of outer membrane proteins.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Generic health relevance (hrcs-hc)Apoptosis (mesh)Autophagy (mesh)GTP Phosphohydrolases (mesh)HEK293 Cells (mesh)HeLa Cells (mesh)Humans (mesh)Mitochondria (mesh)Mitochondrial Dynamics (mesh)Mitochondrial Membrane Transport Proteins (mesh)Mitochondrial Membranes (mesh)Mitochondrial Proteins (mesh)Phosphate Transport Proteins (mesh)Proteasome Endopeptidase Complex (mesh)Proteolysis (mesh)Ubiquitin (mesh)Ubiquitin-Protein Ligases (mesh)Ubiquitination (mesh)Hela Cells (mesh)Mitochondria (mesh)Humans (mesh)Proteasome Endopeptidase Complex (mesh)GTP Phosphohydrolases (mesh)Ubiquitin-Protein Ligases (mesh)Phosphate Transport Proteins (mesh)Mitochondrial Membrane Transport Proteins (mesh)Mitochondrial Proteins (mesh)Ubiquitin (mesh)Apoptosis (mesh)Autophagy (mesh)Mitochondrial Membranes (mesh)Ubiquitination (mesh)HEK293 Cells (mesh)Proteolysis (mesh)Mitochondrial Dynamics (mesh)Apoptosis (mesh)Autophagy (mesh)GTP Phosphohydrolases (mesh)HEK293 Cells (mesh)HeLa Cells (mesh)Humans (mesh)Mitochondria (mesh)Mitochondrial Dynamics (mesh)Mitochondrial Membrane Transport Proteins (mesh)Mitochondrial Membranes (mesh)Mitochondrial Proteins (mesh)Phosphate Transport Proteins (mesh)Proteasome Endopeptidase Complex (mesh)Proteolysis (mesh)Ubiquitin (mesh)Ubiquitin-Protein Ligases (mesh)Ubiquitination (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8kw5z8s7https://escholarship.org/content/qt8kw5z8s7/qt8kw5z8s7.pdfinfo:doi/10.1091/mbc.e16-07-0545articleMolecular Biology of the Cell, vol 28, iss 5600 - 612oai:escholarship.org:ark:/13030/qt61c3v6b72026-05-22T00:19:04Zqt61c3v6b7Interferon-mediated reprogramming of membrane cholesterol to evade bacterial toxinsZhou, Quan DChi, XunLee, Min SubHsieh, Wei YuanMkrtchyan, Jonathan JFeng, An-ChiehHe, CuiwenYork, Autumn GBui, Viet LKronenberger, Eliza BFerrari, AlessandraXiao, XuDaly, Allison ETarling, Elizabeth JDamoiseaux, RobertScumpia, Philip OSmale, Stephen TWilliams, Kevin JTontonoz, PeterBensinger, Steven J2020-07-01Plasma membranes of animal cells are enriched for cholesterol. Cholesterol-dependent cytolysins (CDCs) are pore-forming toxins secreted by bacteria that target membrane cholesterol for their effector function. Phagocytes are essential for clearance of CDC-producing bacteria; however, the mechanisms by which these cells evade the deleterious effects of CDCs are largely unknown. Here, we report that interferon (IFN) signals convey resistance to CDC-induced pores on macrophages and neutrophils. We traced IFN-mediated resistance to CDCs to the rapid modulation of a specific pool of cholesterol in the plasma membrane of macrophages without changes to total cholesterol levels. Resistance to CDC-induced pore formation requires the production of the oxysterol 25-hydroxycholesterol (25HC), inhibition of cholesterol synthesis and redistribution of cholesterol to an esterified cholesterol pool. Accordingly, blocking the ability of IFN to reprogram cholesterol metabolism abrogates cellular protection and renders mice more susceptible to CDC-induced tissue damage. These studies illuminate targeted regulation of membrane cholesterol content as a host defense strategy.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)2.1 Biological and endogenous factors (hrcs-rac)Animals (mesh)Bacteria (mesh)Bacterial Infections (mesh)Bacterial Proteins (mesh)Bacterial Toxins (mesh)Cell Membrane (mesh)Cell Membrane Permeability (mesh)CellsCultured (mesh)Disease ModelsAnimal (mesh)Disease Susceptibility (mesh)Female (mesh)Host Microbial Interactions (mesh)Humans (mesh)Hydroxycholesterols (mesh)Interferons (mesh)Intravital Microscopy (mesh)Male (mesh)Mice (mesh)MiceTransgenic (mesh)Phagocytes (mesh)Primary Cell Culture (mesh)Steroid Hydroxylases (mesh)Streptolysins (mesh)CellsCultured (mesh)Cell Membrane (mesh)Phagocytes (mesh)Animals (mesh)MiceTransgenic (mesh)Humans (mesh)Mice (mesh)Bacteria (mesh)Bacterial Infections (mesh)Disease ModelsAnimal (mesh)Disease Susceptibility (mesh)Hydroxycholesterols (mesh)Steroid Hydroxylases (mesh)Bacterial Proteins (mesh)Interferons (mesh)Bacterial Toxins (mesh)Streptolysins (mesh)Cell Membrane Permeability (mesh)Female (mesh)Male (mesh)Primary Cell Culture (mesh)Intravital Microscopy (mesh)Host Microbial Interactions (mesh)Animals (mesh)Bacteria (mesh)Bacterial Infections (mesh)Bacterial Proteins (mesh)Bacterial Toxins (mesh)Cell Membrane (mesh)Cell Membrane Permeability (mesh)CellsCultured (mesh)Disease ModelsAnimal (mesh)Disease Susceptibility (mesh)Female (mesh)Host Microbial Interactions (mesh)Humans (mesh)Hydroxycholesterols (mesh)Interferons (mesh)Intravital Microscopy (mesh)Male (mesh)Mice (mesh)MiceTransgenic (mesh)Phagocytes (mesh)Primary Cell Culture (mesh)Steroid Hydroxylases (mesh)Streptolysins (mesh)1107 Immunology (for)Immunology (science-metrix)3101 Biochemistry and cell biology (for-2020)3204 Immunology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/61c3v6b7https://escholarship.org/content/qt61c3v6b7/qt61c3v6b7.pdfinfo:doi/10.1038/s41590-020-0695-4articleNature Immunology, vol 21, iss 7746 - 755oai:escholarship.org:ark:/13030/qt4ph3v4th2026-05-21T16:48:00Zqt4ph3v4thEstrogen receptor α protects pancreatic β-cells from apoptosis by preserving mitochondrial function and suppressing endoplasmic reticulum stressZhou, ZhenqiRibas, VicentRajbhandari, PrashantDrew, Brian GMoore, Timothy MFluitt, Amy HReddish, Britany RWhitney, Kate AGeorgia, SentaVergnes, LaurentReue, KarenLiesa, MarcShirihai, Orianvan der Bliek, Alexander MChi, Nai-WenMahata, Sushil KTiano, Joseph PHewitt, Sylvia CTontonoz, PeterKorach, Kenneth SMauvais-Jarvis, FranckHevener, Andrea L2018-03-01Estrogen receptor α (ERα) action plays an important role in pancreatic β-cell function and survival; thus, it is considered a potential therapeutic target for the treatment of type 2 diabetes in women. However, the mechanisms underlying the protective effects of ERα remain unclear. Because ERα regulates mitochondrial metabolism in other cell types, we hypothesized that ERα may act to preserve insulin secretion and promote β-cell survival by regulating mitochondrial-endoplasmic reticulum (EndoRetic) function. We tested this hypothesis using pancreatic islet-specific ERα knockout (PERαKO) mice and Min6 β-cells in culture with Esr1 knockdown (KD). We found that Esr1-KD promoted reactive oxygen species production that associated with reduced fission/fusion dynamics and impaired mitophagy. Electron microscopy showed mitochondrial enlargement and a pro-fusion phenotype. Mitochondrial cristae and endoplasmic reticulum were dilated in Esr1-KD compared with ERα replete Min6 β-cells. Increased expression of Oma1 and Chop was paralleled by increased oxygen consumption and apoptosis susceptibility in ERα-KD cells. In contrast, ERα overexpression and ligand activation reduced both Chop and Oma1 expression, likely by ERα binding to consensus estrogen-response element sites in the Oma1 and Chop promoters. Together, our findings suggest that ERα promotes β-cell survival and insulin secretion through maintenance of mitochondrial fission/fusion-mitophagy dynamics and EndoRetic function, in part by Oma1 and Chop repression.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Diabetes (rcdc)Estrogen (rcdc)2.1 Biological and endogenous factors (hrcs-rac)5.1 Pharmaceuticals (hrcs-rac)Metabolic and endocrine (hrcs-hc)Animals (mesh)Apoptosis (mesh)Cell Survival (mesh)Endoplasmic Reticulum Stress (mesh)Estrogen Receptor alpha (mesh)Female (mesh)Insulin (mesh)Insulin-Secreting Cells (mesh)Metalloproteases (mesh)Mice (mesh)MiceKnockout (mesh)Mitochondria (mesh)Mitochondrial Proteins (mesh)Mitophagy (mesh)Reactive Oxygen Species (mesh)Transcription Factor CHOP (mesh)Mitochondria (mesh)Animals (mesh)MiceKnockout (mesh)Mice (mesh)Reactive Oxygen Species (mesh)Insulin (mesh)Metalloproteases (mesh)Mitochondrial Proteins (mesh)Estrogen Receptor alpha (mesh)Apoptosis (mesh)Cell Survival (mesh)Female (mesh)Insulin-Secreting Cells (mesh)Transcription Factor CHOP (mesh)Endoplasmic Reticulum Stress (mesh)Mitophagy (mesh)apoptosisendoplasmic reticulum stress (ER stress)estrogen actionestrogen receptorinsulin secretionmitochondrial dynamicsmitochondrial metabolismAnimals (mesh)Apoptosis (mesh)Cell Survival (mesh)Endoplasmic Reticulum Stress (mesh)Estrogen Receptor alpha (mesh)Female (mesh)Insulin (mesh)Insulin-Secreting Cells (mesh)Metalloproteases (mesh)Mice (mesh)MiceKnockout (mesh)Mitochondria (mesh)Mitochondrial Proteins (mesh)Mitophagy (mesh)Reactive Oxygen Species (mesh)Transcription Factor CHOP (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biochemistry & Molecular Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/4ph3v4thhttps://escholarship.org/content/qt4ph3v4th/qt4ph3v4th.pdfinfo:doi/10.1074/jbc.m117.805069articleJournal of Biological Chemistry, vol 293, iss 134735 - 4751oai:escholarship.org:ark:/13030/qt6r50s7q82026-05-20T04:45:07Zqt6r50s7q8Atomic-level evidence for packing and positional amyloid polymorphism by segment from TDP-43 RRM2Guenther, Elizabeth LGe, PengTrinh, HamiltonSawaya, Michael RCascio, DuilioBoyer, David RGonen, TamirZhou, Z HongEisenberg, David S2018-04-01Proteins in the fibrous amyloid state are a major hallmark of neurodegenerative disease. Understanding the multiple conformations, or polymorphs, of amyloid proteins at the molecular level is a challenge of amyloid research. Here, we detail the wide range of polymorphs formed by a segment of human TAR DNA-binding protein 43 (TDP-43) as a model for the polymorphic capabilities of pathological amyloid aggregation. Using X-ray diffraction, microelectron diffraction (MicroED) and single-particle cryo-EM, we show that the 247DLIIKGISVHI257 segment from the second RNA-recognition motif (RRM2) forms an array of amyloid polymorphs. These associations include seven distinct interfaces displaying five different symmetry classes of steric zippers. Additionally, we find that this segment can adopt three different backbone conformations that contribute to its polymorphic capabilities. The polymorphic nature of this segment illustrates at the molecular level how amyloid proteins can form diverse fibril structures.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)Aging (rcdc)Alzheimer's Disease (rcdc)Acquired Cognitive Impairment (rcdc)Rare Diseases (rcdc)Brain Disorders (rcdc)Neurodegenerative (rcdc)Neurosciences (rcdc)Dementia (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Generic health relevance (hrcs-hc)Amino Acid Motifs (mesh)Amyloid (mesh)Amyloidogenic Proteins (mesh)Cryoelectron Microscopy (mesh)Crystallization (mesh)DNA-Binding Proteins (mesh)Humans (mesh)MicroscopyElectronTransmission (mesh)Neurodegenerative Diseases (mesh)Peptides (mesh)PolymorphismGenetic (mesh)X-Ray Diffraction (mesh)Humans (mesh)Neurodegenerative Diseases (mesh)Amyloid (mesh)Peptides (mesh)DNA-Binding Proteins (mesh)Cryoelectron Microscopy (mesh)MicroscopyElectronTransmission (mesh)Crystallization (mesh)X-Ray Diffraction (mesh)Amino Acid Motifs (mesh)PolymorphismGenetic (mesh)Amyloidogenic Proteins (mesh)Amino Acid Motifs (mesh)Amyloid (mesh)Amyloidogenic Proteins (mesh)Cryoelectron Microscopy (mesh)Crystallization (mesh)DNA-Binding Proteins (mesh)Humans (mesh)MicroscopyElectronTransmission (mesh)Neurodegenerative Diseases (mesh)Peptides (mesh)PolymorphismGenetic (mesh)X-Ray Diffraction (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biophysics (science-metrix)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6r50s7q8https://escholarship.org/content/qt6r50s7q8/qt6r50s7q8.pdfinfo:doi/10.1038/s41594-018-0045-5articleNature Structural & Molecular Biology, vol 25, iss 4311 - 319oai:escholarship.org:ark:/13030/qt8b78337f2026-05-18T18:12:59Zqt8b78337fThe histone H3-H4 tetramer is a copper reductase enzymeAttar, NarsisCampos, Oscar AVogelauer, MariaCheng, ChenXue, YongSchmollinger, StefanSalwinski, LukaszMallipeddi, Nathan VBoone, Brandon AYen, LindaYang, SichenZikovich, ShannonDardine, JadeCarey, Michael FMerchant, Sabeeha SKurdistani, Siavash K2020-07-03Eukaryotic histone H3-H4 tetramers contain a putative copper (Cu2+) binding site at the H3-H3' dimerization interface with unknown function. The coincident emergence of eukaryotes with global oxygenation, which challenged cellular copper utilization, raised the possibility that histones may function in cellular copper homeostasis. We report that the recombinant Xenopus laevis H3-H4 tetramer is an oxidoreductase enzyme that binds Cu2+ and catalyzes its reduction to Cu1+ in vitro. Loss- and gain-of-function mutations of the putative active site residues correspondingly altered copper binding and the enzymatic activity, as well as intracellular Cu1+ abundance and copper-dependent mitochondrial respiration and Sod1 function in the yeast Saccharomyces cerevisiae The histone H3-H4 tetramer, therefore, has a role other than chromatin compaction or epigenetic regulation and generates biousable Cu1+ ions in eukaryotes.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Animals (mesh)Biocatalysis (mesh)Catalytic Domain (mesh)Copper (mesh)Gain of Function Mutation (mesh)Histones (mesh)Mitochondria (mesh)Nuclear Proteins (mesh)Oxidoreductases (mesh)Protein Multimerization (mesh)Recombinant Proteins (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)Superoxide Dismutase-1 (mesh)Transcription Factors (mesh)Xenopus laevis (mesh)Mitochondria (mesh)Animals (mesh)Xenopus laevis (mesh)Saccharomyces cerevisiae (mesh)Copper (mesh)Oxidoreductases (mesh)Saccharomyces cerevisiae Proteins (mesh)Nuclear Proteins (mesh)Histones (mesh)Recombinant Proteins (mesh)Transcription Factors (mesh)Catalytic Domain (mesh)Biocatalysis (mesh)Protein Multimerization (mesh)Superoxide Dismutase-1 (mesh)Gain of Function Mutation (mesh)Animals (mesh)Biocatalysis (mesh)Catalytic Domain (mesh)Copper (mesh)Gain of Function Mutation (mesh)Histones (mesh)Mitochondria (mesh)Nuclear Proteins (mesh)Oxidoreductases (mesh)Protein Multimerization (mesh)Recombinant Proteins (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)Superoxide Dismutase-1 (mesh)Transcription Factors (mesh)Xenopus laevis (mesh)General Science & Technology (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8b78337fhttps://escholarship.org/content/qt8b78337f/qt8b78337f.pdfinfo:doi/10.1126/science.aba8740articleScience, vol 369, iss 649959 - 64oai:escholarship.org:ark:/13030/qt1qb664jb2026-05-18T16:48:55Zqt1qb664jbThe α-synuclein hereditary mutation E46K unlocks a more stable, pathogenic fibril structureBoyer, David RLi, BinsenSun, ChuanqiFan, WeijiaZhou, KangHughes, Michael PSawaya, Michael RJiang, LinEisenberg, David S2020-02-18Aggregation of α-synuclein is a defining molecular feature of Parkinson's disease, Lewy body dementia, and multiple systems atrophy. Hereditary mutations in α-synuclein are linked to both Parkinson's disease and Lewy body dementia; in particular, patients bearing the E46K disease mutation manifest a clinical picture of parkinsonism and Lewy body dementia, and E46K creates more pathogenic fibrils in vitro. Understanding the effect of these hereditary mutations on α-synuclein fibril structure is fundamental to α-synuclein biology. We therefore determined the cryo-electron microscopy (cryo-EM) structure of α-synuclein fibrils containing the hereditary E46K mutation. The 2.5-Å structure reveals a symmetric double protofilament in which the molecules adopt a vastly rearranged, lower energy fold compared to wild-type fibrils. We propose that the E46K misfolding pathway avoids electrostatic repulsion between K46 and K80, a residue pair which form the E46-K80 salt bridge in the wild-type fibril structure. We hypothesize that, under our conditions, the wild-type fold does not reach this deeper energy well of the E46K fold because the E46-K80 salt bridge diverts α-synuclein into a kinetic trap-a shallower, more accessible energy minimum. The E46K mutation apparently unlocks a more stable and pathogenic fibril structure.3101 Biochemistry and Cell Biology (for-2020)51 Physical Sciences (for-2020)31 Biological Sciences (for-2020)Brain Disorders (rcdc)Parkinson's Disease (rcdc)Dementia (rcdc)Genetics (rcdc)Neurosciences (rcdc)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)Aging (rcdc)Alzheimer's Disease Related Dementias (ADRD) (rcdc)Lewy Body Dementia (rcdc)Acquired Cognitive Impairment (rcdc)Neurodegenerative (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Neurological (hrcs-hc)Amino Acid Motifs (mesh)Cryoelectron Microscopy (mesh)Humans (mesh)Lewy Body Disease (mesh)MutationMissense (mesh)Parkinson Disease (mesh)Protein Folding (mesh)alpha-Synuclein (mesh)alpha-synucleinParkinson's diseaseLewy body dementiacryo-EMhereditary mutationsHumans (mesh)Lewy Body Disease (mesh)Parkinson Disease (mesh)Cryoelectron Microscopy (mesh)Amino Acid Motifs (mesh)Protein Folding (mesh)MutationMissense (mesh)alpha-Synuclein (mesh)Lewy body dementiaParkinson’s diseasecryo-EMhereditary mutationsα-synucleinAmino Acid Motifs (mesh)Cryoelectron Microscopy (mesh)Humans (mesh)Lewy Body Disease (mesh)MutationMissense (mesh)Parkinson Disease (mesh)Protein Folding (mesh)alpha-Synuclein (mesh)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1qb664jbhttps://escholarship.org/content/qt1qb664jb/qt1qb664jb.pdfinfo:doi/10.1073/pnas.1917914117articleProceedings of the National Academy of Sciences of the United States of America, vol 117, iss 73592 - 3602oai:escholarship.org:ark:/13030/qt4qm0t5cd2026-05-18T15:54:49Zqt4qm0t5cdStructures of fibrils formed by α-synuclein hereditary disease mutant H50Q reveal new polymorphsBoyer, David RLi, BinsenSun, ChuanqiFan, WeijiaSawaya, Michael RJiang, LinEisenberg, David S2019-11-01Deposits of amyloid fibrils of α-synuclein are the histological hallmarks of Parkinson’s disease, dementia with Lewy bodies and multiple system atrophy, with hereditary mutations in α-synuclein linked to the first two of these conditions. Seeing the changes to the structures of amyloid fibrils bearing these mutations may help to understand these diseases. To this end, we determined the cryo-EM structures of α-synuclein fibrils containing the H50Q hereditary mutation. We find that the H50Q mutation results in two previously unobserved polymorphs of α-synuclein: narrow and wide fibrils, formed from either one or two protofilaments, respectively. These structures recapitulate conserved features of the wild-type fold but reveal new structural elements, including a previously unobserved hydrogen-bond network and surprising new protofilament arrangements. The structures of the H50Q polymorphs help to rationalize the faster aggregation kinetics, higher seeding capacity in biosensor cells and greater cytotoxicity that we observe for H50Q compared to wild-type α-synuclein.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)Dementia (rcdc)Aging (rcdc)Neurodegenerative (rcdc)Acquired Cognitive Impairment (rcdc)Alzheimer's Disease Related Dementias (ADRD) (rcdc)Genetics (rcdc)Lewy Body Dementia (rcdc)Neurosciences (rcdc)Brain Disorders (rcdc)Parkinson's Disease (rcdc)Rare Diseases (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Neurological (hrcs-hc)Amino Acid Sequence (mesh)Amyloid (mesh)Cryoelectron Microscopy (mesh)HEK293 Cells (mesh)Humans (mesh)ModelsMolecular (mesh)Parkinson Disease (mesh)Point Mutation (mesh)Protein AggregationPathological (mesh)Protein Conformation (mesh)alpha-Synuclein (mesh)Humans (mesh)Parkinson Disease (mesh)Amyloid (mesh)Cryoelectron Microscopy (mesh)Amino Acid Sequence (mesh)Protein Conformation (mesh)Point Mutation (mesh)ModelsMolecular (mesh)alpha-Synuclein (mesh)HEK293 Cells (mesh)Protein AggregationPathological (mesh)Amino Acid Sequence (mesh)Amyloid (mesh)Cryoelectron Microscopy (mesh)HEK293 Cells (mesh)Humans (mesh)ModelsMolecular (mesh)Parkinson Disease (mesh)Point Mutation (mesh)Protein AggregationPathological (mesh)Protein Conformation (mesh)alpha-Synuclein (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biophysics (science-metrix)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4qm0t5cdhttps://escholarship.org/content/qt4qm0t5cd/qt4qm0t5cd.pdfinfo:doi/10.1038/s41594-019-0322-yarticleNature Structural & Molecular Biology, vol 26, iss 111044 - 1052oai:escholarship.org:ark:/13030/qt7fg0g9np2026-05-18T14:29:26Zqt7fg0g9npA Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestationPolioudakis, Damonde la Torre-Ubieta, LuisLangerman, JustinElkins, Andrew GShi, XuStein, Jason LVuong, Celine KNichterwitz, SusanneGevorgian, MelindaOpland, Carli KLu, DaningConnell, WilliamRuzzo, Elizabeth KLowe, Jennifer KHadzic, TarikHinz, Flora ISabri, ShanLowry, William EGerstein, Mark BPlath, KathrinGeschwind, Daniel H2019-09-01We performed RNA sequencing on 40,000 cells to create a high-resolution single-cell gene expression atlas of developing human cortex, providing the first single-cell characterization of previously uncharacterized cell types, including human subplate neurons, comparisons with bulk tissue, and systematic analyses of technical factors. These data permit deconvolution of regulatory networks connecting regulatory elements and transcriptional drivers to single-cell gene expression programs, significantly extending our understanding of human neurogenesis, cortical evolution, and the cellular basis of neuropsychiatric disease. We tie cell-cycle progression with early cell fate decisions during neurogenesis, demonstrating that differentiation occurs on a transcriptomic continuum; rather than only expressing a few transcription factors that drive cell fates, differentiating cells express broad, mixed cell-type transcriptomes before telophase. By mapping neuropsychiatric disease genes to cell types, we implicate dysregulation of specific cell types in ASD, ID, and epilepsy. We developed CoDEx, an online portal to facilitate data access and browsing.5202 Biological Psychology (for-2020)32 Biomedical and Clinical Sciences (for-2020)3209 Neurosciences (for-2020)52 Psychology (for-2020)Neurosciences (rcdc)Human Genome (rcdc)Genetics (rcdc)Brain Disorders (rcdc)Mental Health (rcdc)Stem Cell Research (rcdc)Stem Cell Research - Nonembryonic - Human (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Autism Spectrum Disorder (mesh)Cell Cycle (mesh)Cerebral Cortex (mesh)DatabasesGenetic (mesh)Ependymoglial Cells (mesh)Epilepsy (mesh)Female (mesh)Gene Expression Profiling (mesh)Gene Expression RegulationDevelopmental (mesh)Gene Regulatory Networks (mesh)Gestational Age (mesh)Humans (mesh)Intellectual Disability (mesh)Interneurons (mesh)Neocortex (mesh)Neural Stem Cells (mesh)Neurogenesis (mesh)Neurons (mesh)Pregnancy (mesh)Pregnancy TrimesterSecond (mesh)RNA-Seq (mesh)Single-Cell Analysis (mesh)Telophase (mesh)Cerebral Cortex (mesh)Neocortex (mesh)Neurons (mesh)Interneurons (mesh)Humans (mesh)Epilepsy (mesh)Gene Expression Profiling (mesh)Cell Cycle (mesh)Telophase (mesh)Gene Expression RegulationDevelopmental (mesh)Gestational Age (mesh)Pregnancy (mesh)Pregnancy TrimesterSecond (mesh)DatabasesGenetic (mesh)Female (mesh)Gene Regulatory Networks (mesh)Neurogenesis (mesh)Neural Stem Cells (mesh)Single-Cell Analysis (mesh)Intellectual Disability (mesh)Ependymoglial Cells (mesh)Autism Spectrum Disorder (mesh)RNA-Seq (mesh)autismcortical developmentdifferentiationepilepsyevolutionhumanintellectual disabilityneurogenesisschizophreniasubplateAutism Spectrum Disorder (mesh)Cell Cycle (mesh)Cerebral Cortex (mesh)DatabasesGenetic (mesh)Ependymoglial Cells (mesh)Epilepsy (mesh)Female (mesh)Gene Expression Profiling (mesh)Gene Expression RegulationDevelopmental (mesh)Gene Regulatory Networks (mesh)Gestational Age (mesh)Humans (mesh)Intellectual Disability (mesh)Interneurons (mesh)Neocortex (mesh)Neural Stem Cells (mesh)Neurogenesis (mesh)Neurons (mesh)Pregnancy (mesh)Pregnancy TrimesterSecond (mesh)RNA-Seq (mesh)Single-Cell Analysis (mesh)Telophase (mesh)1109 Neurosciences (for)1701 Psychology (for)1702 Cognitive Sciences (for)Neurology & Neurosurgery (science-metrix)3209 Neurosciences (for-2020)5202 Biological psychology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7fg0g9nphttps://escholarship.org/content/qt7fg0g9np/qt7fg0g9np.pdfinfo:doi/10.1016/j.neuron.2019.06.011articleNeuron, vol 103, iss 5785 - 801.e8oai:escholarship.org:ark:/13030/qt8hf5g0sc2026-05-18T14:28:47Zqt8hf5g0scCryo-EM structures of four polymorphic TDP-43 amyloid coresCao, QinBoyer, David RSawaya, Michael RGe, PengEisenberg, David S2019-07-01The DNA and RNA processing protein TDP-43 undergoes both functional and pathogenic aggregation. Functional TDP-43 aggregates form reversible, transient species such as nuclear bodies, stress granules, and myo-granules. Pathogenic, irreversible TDP-43 aggregates form in amyotrophic lateral sclerosis and other neurodegenerative conditions. Here we find the features of TDP-43 fibrils that confer both reversibility and irreversibility by determining structures of two segments reported to be the pathogenic cores of human TDP-43 aggregation: SegA (residues 311–360), which forms three polymorphs, all with dagger-shaped folds; and SegB A315E (residues 286–331 containing the amyotrophic lateral sclerosis hereditary mutation A315E), which forms R-shaped folds. Energetic analysis suggests that the dagger-shaped polymorphs represent irreversible fibril structures, whereas the SegB polymorph may participate in both reversible and irreversible fibrils. Our structures reveal the polymorphic nature of TDP-43 and suggest how the A315E mutation converts the R-shaped polymorph to an irreversible form that enhances pathology.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Neurosciences (rcdc)Brain Disorders (rcdc)Genetics (rcdc)ALS (rcdc)Rare Diseases (rcdc)Neurodegenerative (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Amino Acid Sequence (mesh)Amyloid (mesh)Cryoelectron Microscopy (mesh)DNA-Binding Proteins (mesh)Humans (mesh)ModelsMolecular (mesh)Point Mutation (mesh)Protein Aggregates (mesh)Protein AggregationPathological (mesh)Protein Conformation (mesh)Protein Folding (mesh)Protein Stability (mesh)Humans (mesh)Amyloid (mesh)DNA-Binding Proteins (mesh)Cryoelectron Microscopy (mesh)Amino Acid Sequence (mesh)Protein Conformation (mesh)Protein Folding (mesh)Point Mutation (mesh)ModelsMolecular (mesh)Protein Stability (mesh)Protein Aggregates (mesh)Protein AggregationPathological (mesh)Amino Acid Sequence (mesh)Amyloid (mesh)Cryoelectron Microscopy (mesh)DNA-Binding Proteins (mesh)Humans (mesh)ModelsMolecular (mesh)Point Mutation (mesh)Protein Aggregates (mesh)Protein AggregationPathological (mesh)Protein Conformation (mesh)Protein Folding (mesh)Protein Stability (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biophysics (science-metrix)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8hf5g0schttps://escholarship.org/content/qt8hf5g0sc/qt8hf5g0sc.pdfinfo:doi/10.1038/s41594-019-0248-4articleNature Structural & Molecular Biology, vol 26, iss 7619 - 627oai:escholarship.org:ark:/13030/qt2bf556pr2026-05-18T07:41:52Zqt2bf556prAtomic structures of TDP-43 LCD segments and insights into reversible or pathogenic aggregationGuenther, Elizabeth LCao, QinTrinh, HamiltonLu, JiahuiSawaya, Michael RCascio, DuilioBoyer, David RRodriguez, Jose AHughes, Michael PEisenberg, David S2018-06-01The normally soluble TAR DNA-binding protein 43 (TDP-43) is found aggregated both in reversible stress granules and in irreversible pathogenic amyloid. In TDP-43, the low-complexity domain (LCD) is believed to be involved in both types of aggregation. To uncover the structural origins of these two modes of β-sheet-rich aggregation, we have determined ten structures of segments of the LCD of human TDP-43. Six of these segments form steric zippers characteristic of the spines of pathogenic amyloid fibrils; four others form LARKS, the labile amyloid-like interactions characteristic of protein hydrogels and proteins found in membraneless organelles, including stress granules. Supporting a hypothetical pathway from reversible to irreversible amyloid aggregation, we found that familial ALS variants of TDP-43 convert LARKS to irreversible aggregates. Our structures suggest how TDP-43 adopts both reversible and irreversible β-sheet aggregates and the role of mutation in the possible transition of reversible to irreversible pathogenic aggregation.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Rare Diseases (rcdc)ALS (rcdc)Neurosciences (rcdc)Dementia (rcdc)Neurodegenerative (rcdc)Acquired Cognitive Impairment (rcdc)Aging (rcdc)Brain Disorders (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Amyotrophic Lateral Sclerosis (mesh)DNA-Binding Proteins (mesh)Humans (mesh)Mutation (mesh)Organelles (mesh)Protein Conformationbeta-Strand (mesh)Organelles (mesh)Humans (mesh)Amyotrophic Lateral Sclerosis (mesh)DNA-Binding Proteins (mesh)Mutation (mesh)Protein Conformationbeta-Strand (mesh)Amyotrophic Lateral Sclerosis (mesh)DNA-Binding Proteins (mesh)Humans (mesh)Mutation (mesh)Organelles (mesh)Protein Conformationbeta-Strand (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biophysics (science-metrix)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2bf556prhttps://escholarship.org/content/qt2bf556pr/qt2bf556pr.pdfinfo:doi/10.1038/s41594-018-0064-2articleNature Structural & Molecular Biology, vol 25, iss 6463 - 471oai:escholarship.org:ark:/13030/qt7sf6z8m72026-05-17T11:35:08Zqt7sf6z8m7Subcellular metal imaging identifies dynamic sites of Cu accumulation in ChlamydomonasHong-Hermesdorf, AnneMiethke, MarcusGallaher, Sean DKropat, JanetteDodani, Sheel CChan, JeffersonBarupala, DulminiDomaille, Dylan WShirasaki, Dyna ILoo, Joseph AWeber, Peter KPett-Ridge, JenniferStemmler, Timothy LChang, Christopher JMerchant, Sabeeha S2014-12-01A collection of chemical tools and spectroscopic techniques demonstrate that Zn availability influences Cu+ storage and localization in the green alga Chlamydomonas, with Zn limitation causing the accumulation of Cu+ in lysosome-related organelles.3404 Medicinal and Biomolecular Chemistry (for-2020)34 Chemical Sciences (for-2020)CationsDivalent (mesh)Chlamydomonas reinhardtii (mesh)Copper (mesh)Gene Expression Profiling (mesh)Homeostasis (mesh)Hydrogen-Ion Concentration (mesh)Isotope Labeling (mesh)Isotopes (mesh)Lysosomes (mesh)Molecular Imaging (mesh)Plastocyanin (mesh)Polyphosphates (mesh)Transcription Factors (mesh)Transcriptome (mesh)Zinc (mesh)Lysosomes (mesh)Chlamydomonas reinhardtii (mesh)Polyphosphates (mesh)CationsDivalent (mesh)Copper (mesh)Zinc (mesh)Isotopes (mesh)Plastocyanin (mesh)Transcription Factors (mesh)Gene Expression Profiling (mesh)Isotope Labeling (mesh)Homeostasis (mesh)Hydrogen-Ion Concentration (mesh)Molecular Imaging (mesh)Transcriptome (mesh)CationsDivalent (mesh)Chlamydomonas reinhardtii (mesh)Copper (mesh)Gene Expression Profiling (mesh)Homeostasis (mesh)Hydrogen-Ion Concentration (mesh)Isotope Labeling (mesh)Isotopes (mesh)Lysosomes (mesh)Molecular Imaging (mesh)Plastocyanin (mesh)Polyphosphates (mesh)Transcription Factors (mesh)Transcriptome (mesh)Zinc (mesh)LysosomesChlamydomonas reinhardtiiPolyphosphatesCationsDivalentCopperZincIsotopesPlastocyaninTranscription FactorsGene Expression ProfilingIsotope LabelingHomeostasisHydrogen-Ion ConcentrationMolecular ImagingTranscriptome0304 Medicinal and Biomolecular Chemistry (for)0601 Biochemistry and Cell Biology (for)Biochemistry & Molecular Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)3404 Medicinal and biomolecular chemistry (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7sf6z8m7https://escholarship.org/content/qt7sf6z8m7/qt7sf6z8m7.pdfinfo:doi/10.1038/nchembio.1662articleNature Chemical Biology, vol 10, iss 121034 - 1042oai:escholarship.org:ark:/13030/qt9rf7w7x92026-05-16T22:16:17Zqt9rf7w7x9Cryo-EM structure and inhibitor design of human IAPP (amylin) fibrilsCao, QinBoyer, David RSawaya, Michael RGe, PengEisenberg, David S2020-07-01Human islet amyloid polypeptide (hIAPP) functions as a glucose-regulating hormone but deposits as amyloid fibrils in more than 90% of patients with type II diabetes (T2D). Here we report the cryo-EM structure of recombinant full-length hIAPP fibrils. The fibril is composed of two symmetrically related protofilaments with ordered residues 14–37. Our hIAPP fibril structure (i) supports the previous hypothesis that residues 20–29 constitute the core of the hIAPP amyloid; (ii) suggests a molecular mechanism for the action of the hIAPP hereditary mutation S20G; (iii) explains why the six residue substitutions in rodent IAPP prevent aggregation; and (iv) suggests regions responsible for the observed hIAPP cross-seeding with β-amyloid. Furthermore, we performed structure-based inhibitor design to generate potential hIAPP aggregation inhibitors. Four of the designed peptides delay hIAPP aggregation in vitro, providing a starting point for the development of T2D therapeutics and proof of concept that the capping strategy can be used on full-length cryo-EM fibril structures.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Diabetes (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)5.1 Pharmaceuticals (hrcs-rac)Generic health relevance (hrcs-hc)Metabolic and endocrine (hrcs-hc)Amyloid (mesh)Animals (mesh)Cryoelectron Microscopy (mesh)Diabetes MellitusType 2 (mesh)Drug Design (mesh)Drug EvaluationPreclinical (mesh)Humans (mesh)Islet Amyloid Polypeptide (mesh)ModelsMolecular (mesh)Mutation (mesh)Peptides (mesh)Protein Conformation (mesh)Recombinant Proteins (mesh)Rodentia (mesh)Animals (mesh)Humans (mesh)Rodentia (mesh)Diabetes MellitusType 2 (mesh)Amyloid (mesh)Peptides (mesh)Recombinant Proteins (mesh)Cryoelectron Microscopy (mesh)Drug EvaluationPreclinical (mesh)Protein Conformation (mesh)Drug Design (mesh)Mutation (mesh)ModelsMolecular (mesh)Islet Amyloid Polypeptide (mesh)Amyloid (mesh)Animals (mesh)Cryoelectron Microscopy (mesh)Diabetes MellitusType 2 (mesh)Drug Design (mesh)Drug EvaluationPreclinical (mesh)Humans (mesh)Islet Amyloid Polypeptide (mesh)ModelsMolecular (mesh)Mutation (mesh)Peptides (mesh)Protein Conformation (mesh)Recombinant Proteins (mesh)Rodentia (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biophysics (science-metrix)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9rf7w7x9https://escholarship.org/content/qt9rf7w7x9/qt9rf7w7x9.pdfinfo:doi/10.1038/s41594-020-0435-3articleNature Structural & Molecular Biology, vol 27, iss 7653 - 659oai:escholarship.org:ark:/13030/qt66g278z42026-05-16T11:20:42Zqt66g278z4TGFβ superfamily signaling regulates the state of human stem cell pluripotency and capacity to create well-structured telencephalic organoidsWatanabe, MomokoButh, Jessie EHaney, Jillian RVishlaghi, NedaTurcios, FelixElahi, Lubayna SGu, WenPearson, Caroline AKurdian, ArinnaeBaliaouri, Natella VCollier, Amanda JMiranda, Osvaldo ADunn, NatassiaChen, DiSabri, Shande la Torre-Ubieta, LuisClark, Amander TPlath, KathrinChristofk, Heather RKornblum, Harley IGandal, Michael JNovitch, Bennett G2022-10-01Telencephalic organoids generated from human pluripotent stem cells (hPSCs) are a promising system for studying the distinct features of the developing human brain and the underlying causes of many neurological disorders. While organoid technology is steadily advancing, many challenges remain, including potential batch-to-batch and cell-line-to-cell-line variability, and structural inconsistency. Here, we demonstrate that a major contributor to cortical organoid quality is the way hPSCs are maintained prior to differentiation. Optimal results were achieved using particular fibroblast-feeder-supported hPSCs rather than feeder-independent cells, differences that were reflected in their transcriptomic states at the outset. Feeder-supported hPSCs displayed activation of diverse transforming growth factor β (TGFβ) superfamily signaling pathways and increased expression of genes connected to naive pluripotency. We further identified combinations of TGFβ-related growth factors that are necessary and together sufficient to impart broad telencephalic organoid competency to feeder-free hPSCs and enhance the formation of well-structured brain tissues suitable for disease modeling.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Stem Cell Research - Induced Pluripotent Stem Cell - Human (rcdc)Stem Cell Research - Embryonic - Human (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell (rcdc)Neurosciences (rcdc)Regenerative Medicine (rcdc)Stem Cell Research (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Neurological (hrcs-hc)Generic health relevance (hrcs-hc)Cell Differentiation (mesh)Humans (mesh)Organoids (mesh)Pluripotent Stem Cells (mesh)Telencephalon (mesh)Transforming Growth Factor beta (mesh)Telencephalon (mesh)Organoids (mesh)Pluripotent Stem Cells (mesh)Humans (mesh)Transforming Growth Factor beta (mesh)Cell Differentiation (mesh)brain organoidcerebral cortexchoroid plexusdifferentiationembryonic stem cellganglionic eminencehippocampusneural developmentneural stem cellneurogenesispluripotencypluripotent stem cellstem cell heterogeneityCell Differentiation (mesh)Humans (mesh)Organoids (mesh)Pluripotent Stem Cells (mesh)Telencephalon (mesh)Transforming Growth Factor beta (mesh)0601 Biochemistry and Cell Biology (for)1103 Clinical Sciences (for)3101 Biochemistry and cell biology (for-2020)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/66g278z4info:doi/10.1016/j.stemcr.2022.08.013articleStem Cell Reports, vol 17, iss 102220 - 2238oai:escholarship.org:ark:/13030/qt0mc9t6hr2026-05-16T05:22:50Zqt0mc9t6hrChromosome conformation elucidates regulatory relationships in developing human brainWon, Hyejungde la Torre-Ubieta, LuisStein, Jason LParikshak, Neelroop NHuang, JerryOpland, Carli KGandal, Michael JSutton, Gavin JHormozdiari, FarhadLu, DaningLee, ChanghoonEskin, EleazarVoineagu, IrinaErnst, JasonGeschwind, Daniel H2016-10-01Three-dimensional physical interactions within chromosomes dynamically regulate gene expression in a tissue-specific manner1,2,3. However, the 3D organization of chromosomes during human brain development and its role in regulating gene networks dysregulated in neurodevelopmental disorders, such as autism or schizophrenia4,5,6, are unknown. Here we generate high-resolution 3D maps of chromatin contacts during human corticogenesis, permitting large-scale annotation of previously uncharacterized regulatory relationships relevant to the evolution of human cognition and disease. Our analyses identify hundreds of genes that physically interact with enhancers gained on the human lineage, many of which are under purifying selection and associated with human cognitive function. We integrate chromatin contacts with non-coding variants identified in schizophrenia genome-wide association studies (GWAS), highlighting multiple candidate schizophrenia risk genes and pathways, including transcription factors involved in neurogenesis, and cholinergic signalling molecules, several of which are supported by independent expression quantitative trait loci and gene expression analyses. Genome editing in human neural progenitors suggests that one of these distal schizophrenia GWAS loci regulates FOXG1 expression, supporting its potential role as a schizophrenia risk gene. This work provides a framework for understanding the effect of non-coding regulatory elements on human brain development and the evolution of cognition, and highlights novel mechanisms underlying neuropsychiatric disorders.5202 Biological Psychology (for-2020)31 Biological Sciences (for-2020)3105 Genetics (for-2020)52 Psychology (for-2020)Stem Cell Research - Induced Pluripotent Stem Cell - Human (rcdc)Stem Cell Research (rcdc)Brain Disorders (rcdc)Genetics (rcdc)Stem Cell Research - Embryonic - Human (rcdc)Biotechnology (rcdc)Human Genome (rcdc)Serious Mental Illness (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell (rcdc)Mental Illness (rcdc)Neurosciences (rcdc)Schizophrenia (rcdc)Stem Cell Research - Nonembryonic - Human (rcdc)Mental Health (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Mental health (hrcs-hc)Brain (mesh)Chromatin (mesh)ChromosomesHuman (mesh)Cognition (mesh)Enhancer ElementsGenetic (mesh)EpigenesisGenetic (mesh)Forkhead Transcription Factors (mesh)Gene Expression RegulationDevelopmental (mesh)Genetic Predisposition to Disease (mesh)Genome-Wide Association Study (mesh)Humans (mesh)Nerve Tissue Proteins (mesh)Neural Stem Cells (mesh)Neurogenesis (mesh)Nucleic Acid Conformation (mesh)Organ Specificity (mesh)PolymorphismSingle Nucleotide (mesh)Promoter RegionsGenetic (mesh)Reproducibility of Results (mesh)Schizophrenia (mesh)Brain (mesh)ChromosomesHuman (mesh)Chromatin (mesh)Humans (mesh)Genetic Predisposition to Disease (mesh)Nerve Tissue Proteins (mesh)Reproducibility of Results (mesh)Cognition (mesh)Schizophrenia (mesh)Organ Specificity (mesh)EpigenesisGenetic (mesh)Gene Expression RegulationDevelopmental (mesh)Nucleic Acid Conformation (mesh)PolymorphismSingle Nucleotide (mesh)Forkhead Transcription Factors (mesh)Enhancer ElementsGenetic (mesh)Promoter RegionsGenetic (mesh)Genome-Wide Association Study (mesh)Neurogenesis (mesh)Neural Stem Cells (mesh)Brain (mesh)Chromatin (mesh)ChromosomesHuman (mesh)Cognition (mesh)Enhancer ElementsGenetic (mesh)EpigenesisGenetic (mesh)Forkhead Transcription Factors (mesh)Gene Expression RegulationDevelopmental (mesh)Genetic Predisposition to Disease (mesh)Genome-Wide Association Study (mesh)Humans (mesh)Nerve Tissue Proteins (mesh)Neural Stem Cells (mesh)Neurogenesis (mesh)Nucleic Acid Conformation (mesh)Organ Specificity (mesh)PolymorphismSingle Nucleotide (mesh)Promoter RegionsGenetic (mesh)Reproducibility of Results (mesh)Schizophrenia (mesh)General Science & Technology (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0mc9t6hrhttps://escholarship.org/content/qt0mc9t6hr/qt0mc9t6hr.pdfinfo:doi/10.1038/nature19847articleNature, vol 538, iss 7626523 - 527oai:escholarship.org:ark:/13030/qt6274g8m72026-05-15T22:54:46Zqt6274g8m7Damaging mutations in liver X receptor-α are hepatotoxic and implicate cholesterol sensing in liver healthLockhart, Sam MMuso, MilanZvetkova, IlonaLam, Brian YHFerrari, AlessandraSchoenmakers, ErikDuckett, KatieLeslie, JackCollins, AmyRomartínez-Alonso, BeatrizTadross, John AJia, RainaGardner, Eugene JKentistou, KatherineZhao, YajieDay, FelixMörseburg, AlexanderRainbow, KaraRimmington, DebraMastantuoni, MatteoHarrison, JamesNus, MeritxellGuma’a, KhalidSherratt-Mayhew, SamJiang, XiaoSmith, Katherine RPaul, Dirk SJenkins, BenjaminKoulman, AlbertPietzner, MaikLangenberg, ClaudiaWareham, NicholasYeo, Giles SChatterjee, KrishnaSchwabe, JohnOakley, FionaMann, Derek ATontonoz, PeterColl, Anthony POng, KenPerry, John RBO’Rahilly, Stephen2024-10-01Liver X receptor-α (LXRα) regulates cellular cholesterol abundance and potently activates hepatic lipogenesis. Here we show that at least 1 in 450 people in the UK Biobank carry functionally impaired mutations in LXRα, which is associated with biochemical evidence of hepatic dysfunction. On a western diet, male and female mice homozygous for a dominant negative mutation in LXRα have elevated liver cholesterol, diffuse cholesterol crystal accumulation and develop severe hepatitis and fibrosis, despite reduced liver triglyceride and no steatosis. This phenotype does not occur on low-cholesterol diets and can be prevented by hepatocyte-specific overexpression of LXRα. LXRα knockout mice exhibit a milder phenotype with regional variation in cholesterol crystal deposition and inflammation inversely correlating with steatosis. In summary, LXRα is necessary for the maintenance of hepatocyte health, likely due to regulation of cellular cholesterol content. The inverse association between steatosis and both inflammation and cholesterol crystallization may represent a protective action of hepatic lipogenesis in the context of excess hepatic cholesterol.3205 Medical Biochemistry and Metabolomics (for-2020)3208 Medical Physiology (for-2020)32 Biomedical and Clinical Sciences (for-2020)3210 Nutrition and Dietetics (for-2020)Liver Disease (rcdc)Chronic Liver Disease and Cirrhosis (rcdc)Hepatitis (rcdc)Digestive Diseases (rcdc)Genetics (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Oral and gastrointestinal (hrcs-hc)3 Good Health and Well Being (sdg)Animals (mesh)Liver X Receptors (mesh)Cholesterol (mesh)Humans (mesh)Mice (mesh)Liver (mesh)Male (mesh)Female (mesh)Mutation (mesh)MiceKnockout (mesh)Fatty Liver (mesh)Lipogenesis (mesh)Hepatocytes (mesh)Liver (mesh)Hepatocytes (mesh)Animals (mesh)MiceKnockout (mesh)Humans (mesh)Mice (mesh)Fatty Liver (mesh)Cholesterol (mesh)Mutation (mesh)Female (mesh)Male (mesh)Lipogenesis (mesh)Liver X Receptors (mesh)Animals (mesh)Liver X Receptors (mesh)Cholesterol (mesh)Humans (mesh)Mice (mesh)Liver (mesh)Male (mesh)Female (mesh)Mutation (mesh)MiceKnockout (mesh)Fatty Liver (mesh)Lipogenesis (mesh)Hepatocytes (mesh)3205 Medical biochemistry and metabolomics (for-2020)3208 Medical physiology (for-2020)3210 Nutrition and dietetics (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/6274g8m7https://escholarship.org/content/qt6274g8m7/qt6274g8m7.pdfinfo:doi/10.1038/s42255-024-01126-4articleNature Metabolism, vol 6, iss 101922 - 1938oai:escholarship.org:ark:/13030/qt89f233jn2026-05-07T20:18:43Zqt89f233jnThe transcription factor code in iPSC reprogrammingDeng, WeixianJacobson, ElsieCollier, Amanda JPlath, Kathrin2021-10-01Transcription factor (TF)-induced reprogramming of somatic cells across lineages and to induced pluripotent stem cells (iPSCs) has revealed a remarkable plasticity of differentiated cells and presents great opportunities for generating clinically relevant cell types for disease modeling and regenerative medicine. The understanding of iPSC reprogramming provides insights into the mechanisms that safeguard somatic cell identity, drive epigenetic reprogramming, and underlie cell fate specification in vivo. The combinatorial action of TFs has emerged as the key mechanism for the direct and indirect effects of reprogramming factors that induce the remodelling of the enhancer landscape. The interplay of TFs in iPSC reprogramming also yields trophectoderm- and extraembryonic endoderm-like cell populations, uncovering an intriguing plasticity of cell states and opening new avenues for exploring cell fate decisions during early embryogenesis.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Stem Cell Research - Induced Pluripotent Stem Cell - Human (rcdc)Human Genome (rcdc)Stem Cell Research - Embryonic - Human (rcdc)Genetics (rcdc)Stem Cell Research (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell - Non-Human (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell (rcdc)Regenerative Medicine (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Generic health relevance (hrcs-hc)Animals (mesh)Cellular Reprogramming (mesh)Embryonic Development (mesh)EpigenesisGenetic (mesh)Humans (mesh)Induced Pluripotent Stem Cells (mesh)Transcription Factors (mesh)Animals (mesh)Humans (mesh)Transcription Factors (mesh)EpigenesisGenetic (mesh)Embryonic Development (mesh)Induced Pluripotent Stem Cells (mesh)Cellular Reprogramming (mesh)Animals (mesh)Cellular Reprogramming (mesh)Embryonic Development (mesh)EpigenesisGenetic (mesh)Humans (mesh)Induced Pluripotent Stem Cells (mesh)Transcription Factors (mesh)0604 Genetics (for)Developmental Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)3105 Genetics (for-2020)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/89f233jnhttps://escholarship.org/content/qt89f233jn/qt89f233jn.pdfinfo:doi/10.1016/j.gde.2021.06.003articleCurrent Opinion in Genetics & Development, vol 7089 - 96oai:escholarship.org:ark:/13030/qt1r8691p92026-04-30T22:04:24Zqt1r8691p9Identification of Coq11, a New Coenzyme Q Biosynthetic Protein in the CoQ-Synthome in Saccharomyces cerevisiae *Allan, Christopher MAwad, Agape MJohnson, Jarrett SShirasaki, Dyna IWang, CharlesBlaby-Haas, Crysten EMerchant, Sabeeha SLoo, Joseph AClarke, Catherine F2015-03-01Coenzyme Q (Q or ubiquinone) is a redox active lipid composed of a fully substituted benzoquinone ring and a polyisoprenoid tail and is required for mitochondrial electron transport. In the yeast Saccharomyces cerevisiae, Q is synthesized by the products of 11 known genes, COQ1-COQ9, YAH1, and ARH1. The function of some of the Coq proteins remains unknown, and several steps in the Q biosynthetic pathway are not fully characterized. Several of the Coq proteins are associated in a macromolecular complex on the matrix face of the inner mitochondrial membrane, and this complex is required for efficient Q synthesis. Here, we further characterize this complex via immunoblotting and proteomic analysis of tandem affinity-purified tagged Coq proteins. We show that Coq8, a putative kinase required for the stability of the Q biosynthetic complex, is associated with a Coq6-containing complex. Additionally Q6 and late stage Q biosynthetic intermediates were also found to co-purify with the complex. A mitochondrial protein of unknown function, encoded by the YLR290C open reading frame, is also identified as a constituent of the complex and is shown to be required for efficient de novo Q biosynthesis. Given its effect on Q synthesis and its association with the biosynthetic complex, we propose that the open reading frame YLR290C be designated COQ11.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Complementary and Integrative Health (rcdc)ChromatographyLiquid (mesh)Proteomics (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)Tandem Mass Spectrometry (mesh)Ubiquinone (mesh)Mass Spectrometry (MS)Mitochondrial MetabolismProtein ComplexProteomicsSaccharomyces cerevisiaeUbiquinoneYeastQ Biosynthetic IntermediatesCoenzyme QImmunoprecipitationSaccharomyces cerevisiae (mesh)Ubiquinone (mesh)Saccharomyces cerevisiae Proteins (mesh)ChromatographyLiquid (mesh)Proteomics (mesh)Tandem Mass Spectrometry (mesh)Coenzyme QImmunoprecipitationMass Spectrometry (MS)Mitochondrial MetabolismProtein ComplexProteomicsQ Biosynthetic IntermediatesSaccharomyces cerevisiaeUbiquinoneYeastChromatographyLiquid (mesh)Proteomics (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)Tandem Mass Spectrometry (mesh)Ubiquinone (mesh)Saccharomyces cerevisiaeUbiquinoneSaccharomyces cerevisiae ProteinsChromatographyLiquidProteomicsTandem Mass Spectrometry03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biochemistry & Molecular Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/1r8691p9https://escholarship.org/content/qt1r8691p9/qt1r8691p9.pdfinfo:doi/10.1074/jbc.m114.633131articleJournal of Biological Chemistry, vol 290, iss 127517 - 7534oai:escholarship.org:ark:/13030/qt7pp441jk2026-04-29T05:25:50Zqt7pp441jkEndoplasmic reticulum–mitochondria junction is required for iron homeostasisXue, YongSchmollinger, StefanAttar, NarsisCampos, Oscar AVogelauer, MariaCarey, Michael FMerchant, Sabeeha SKurdistani, Siavash K2017-08-01The endoplasmic reticulum (ER)-mitochondria encounter structure (ERMES) is a protein complex that physically tethers the two organelles to each other and creates the physical basis for communication between them. ERMES functions in lipid exchange between the ER and mitochondria, protein import into mitochondria, and maintenance of mitochondrial morphology and genome. Here, we report that ERMES is also required for iron homeostasis. Loss of ERMES components activates an Aft1-dependent iron deficiency response even in iron-replete conditions, leading to accumulation of excess iron inside the cell. This function is independent of known ERMES roles in calcium regulation, phospholipid biosynthesis, or effects on mitochondrial morphology. A mutation in the vacuolar protein sorting 13 (VPS13) gene that rescues the glycolytic phenotype of ERMES mutants suppresses the iron deficiency response and iron accumulation. Our findings reveal that proper communication between the ER and mitochondria is required for appropriate maintenance of cellular iron levels.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Nutrition (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Generic health relevance (hrcs-hc)Metabolic and endocrine (hrcs-hc)Alleles (mesh)Amino Acid Substitution (mesh)Endoplasmic Reticulum (mesh)Energy Metabolism (mesh)Gene Deletion (mesh)Gene Expression RegulationFungal (mesh)Homeostasis (mesh)Iron (mesh)Membrane Proteins (mesh)Mitochondria (mesh)ModelsBiological (mesh)Point Mutation (mesh)Protein Transport (mesh)RNAFungal (mesh)RNAMessenger (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)Sequence AnalysisRNA (mesh)SpectrophotometryAtomic (mesh)Endoplasmic Reticulum (mesh)Mitochondria (mesh)Saccharomyces cerevisiae (mesh)Iron (mesh)Saccharomyces cerevisiae Proteins (mesh)Membrane Proteins (mesh)RNAFungal (mesh)RNAMessenger (mesh)SpectrophotometryAtomic (mesh)Amino Acid Substitution (mesh)Sequence AnalysisRNA (mesh)Gene Expression RegulationFungal (mesh)Gene Deletion (mesh)Protein Transport (mesh)Energy Metabolism (mesh)Homeostasis (mesh)Point Mutation (mesh)Alleles (mesh)ModelsBiological (mesh)endoplasmic reticulum (ER)iron metabolismmitochondriaprotein importrespirationAlleles (mesh)Amino Acid Substitution (mesh)Endoplasmic Reticulum (mesh)Energy Metabolism (mesh)Gene Deletion (mesh)Gene Expression RegulationFungal (mesh)Homeostasis (mesh)Iron (mesh)Membrane Proteins (mesh)Mitochondria (mesh)ModelsBiological (mesh)Point Mutation (mesh)Protein Transport (mesh)RNAFungal (mesh)RNAMessenger (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)Sequence AnalysisRNA (mesh)SpectrophotometryAtomic (mesh)Endoplasmic ReticulumMitochondriaSaccharomyces cerevisiaeIronSaccharomyces cerevisiae ProteinsMembrane ProteinsRNAFungalRNAMessengerSpectrophotometryAtomicAmino Acid SubstitutionSequence AnalysisRNAGene Expression RegulationFungalGene DeletionProtein TransportEnergy MetabolismHomeostasisPoint MutationAllelesModelsBiological03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biochemistry & Molecular Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/7pp441jkhttps://escholarship.org/content/qt7pp441jk/qt7pp441jk.pdfinfo:doi/10.1074/jbc.m117.784249articleJournal of Biological Chemistry, vol 292, iss 3213197 - 13204oai:escholarship.org:ark:/13030/qt0h0444hw2026-04-13T23:56:14Zqt0h0444hwH3K36 methylation maintains cell identity by regulating opposing lineage programmesHoetker, Michael SYagi, MasakiDi Stefano, BrunoLangerman, JustinCristea, SimonaWong, Lai PingHuebner, Aaron JCharlton, JocelynDeng, WeixianHaggerty, ChuckSadreyev, Ruslan IMeissner, AlexanderMichor, FranziskaPlath, KathrinHochedlinger, Konrad2023-08-01The epigenetic mechanisms that maintain differentiated cell states remain incompletely understood. Here we employed histone mutants to uncover a crucial role for H3K36 methylation in the maintenance of cell identities across diverse developmental contexts. Focusing on the experimental induction of pluripotency, we show that H3K36M-mediated depletion of H3K36 methylation endows fibroblasts with a plastic state poised to acquire pluripotency in nearly all cells. At a cellular level, H3K36M facilitates epithelial plasticity by rendering fibroblasts insensitive to TGFβ signals. At a molecular level, H3K36M enables the decommissioning of mesenchymal enhancers and the parallel activation of epithelial/stem cell enhancers. This enhancer rewiring is Tet dependent and redirects Sox2 from promiscuous somatic to pluripotency targets. Our findings reveal a previously unappreciated dual role for H3K36 methylation in the maintenance of cell identity by integrating a crucial developmental pathway into sustained expression of cell-type-specific programmes, and by opposing the expression of alternative lineage programmes through enhancer methylation.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Stem Cell Research - Nonembryonic - Non-Human (rcdc)Human Genome (rcdc)Genetics (rcdc)Stem Cell Research (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Methylation (mesh)Histones (mesh)Cell Differentiation (mesh)EpigenesisGenetic (mesh)Fibroblasts (mesh)Cell Lineage (mesh)Fibroblasts (mesh)Histones (mesh)Cell Differentiation (mesh)EpigenesisGenetic (mesh)Methylation (mesh)Cell Lineage (mesh)Methylation (mesh)Histones (mesh)Cell Differentiation (mesh)EpigenesisGenetic (mesh)Fibroblasts (mesh)Cell Lineage (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0h0444hwhttps://escholarship.org/content/qt0h0444hw/qt0h0444hw.pdfinfo:doi/10.1038/s41556-023-01191-zarticleNature Cell Biology, vol 25, iss 81121 - 1134oai:escholarship.org:ark:/13030/qt43k9p2pv2026-04-13T23:55:51Zqt43k9p2pvReduced MEK inhibition preserves genomic stability in naive human embryonic stem cellsDi Stefano, BrunoUeda, MaiSabri, ShanBrumbaugh, JustinHuebner, Aaron JSahakyan, AnnaClement, KendellClowers, Katie JErickson, Alison RShioda, KeikoGygi, Steven PGu, HongcangShioda, ToshiMeissner, AlexanderTakashima, YasuhiroPlath, KathrinHochedlinger, Konrad2018-09-01Human embryonic stem cells (hESCs) can be captured in a primed state in which they resemble the postimplantation epiblast, or in a naive state where they resemble the preimplantation epiblast. Naive-cell-specific culture conditions allow the study of preimplantation development ex vivo but reportedly lead to chromosomal abnormalities, which compromises their utility in research and potential therapeutic applications. Although MEK inhibition is essential for the naive state, here we show that reduced MEK inhibition facilitated the establishment and maintenance of naive hESCs that retained naive-cell-specific features, including global DNA hypomethylation, HERVK expression, and two active X chromosomes. We further show that hESCs cultured under these modified conditions proliferated more rapidly; accrued fewer chromosomal abnormalities; and displayed changes in the phosphorylation levels of MAPK components, regulators of DNA damage/repair, and cell cycle. We thus provide a simple modification to current methods that can enable robust growth and reduced genomic instability in naive hESCs.31 Biological Sciences (for-2020)Genetics (rcdc)Human Genome (rcdc)Stem Cell Research - Embryonic - Human (rcdc)Regenerative Medicine (rcdc)Stem Cell Research (rcdc)1.1 Normal biological development and functioning (hrcs-rac)DNA Methylation (mesh)Embryonic Stem Cells (mesh)Genomic Instability (mesh)Humans (mesh)MAP Kinase Kinase Kinases (mesh)Protein Kinase Inhibitors (mesh)Proteome (mesh)Transcriptome (mesh)Humans (mesh)Genomic Instability (mesh)MAP Kinase Kinase Kinases (mesh)Proteome (mesh)Protein Kinase Inhibitors (mesh)DNA Methylation (mesh)Embryonic Stem Cells (mesh)Transcriptome (mesh)DNA Methylation (mesh)Embryonic Stem Cells (mesh)Genomic Instability (mesh)Humans (mesh)MAP Kinase Kinase Kinases (mesh)Protein Kinase Inhibitors (mesh)Proteome (mesh)Transcriptome (mesh)06 Biological Sciences (for)10 Technology (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/43k9p2pvhttps://escholarship.org/content/qt43k9p2pv/qt43k9p2pv.pdfinfo:doi/10.1038/s41592-018-0104-1articleNature Methods, vol 15, iss 9732 - 740oai:escholarship.org:ark:/13030/qt31v6j2m82026-04-11T16:58:44Zqt31v6j2m8Peptide Length and Leaving-Group Sterics Influence Potency of Peptide Phosphonate Protease InhibitorsBrown, Christopher MRay, ManishaEroy-Reveles, Aura AEgea, PascalTajon, CherylCraik, Charles S2011-01-01The ability to follow enzyme activity in a cellular context represents a challenging technological frontier that impacts fields ranging from disease pathogenesis to epigenetics. Activity-based probes (ABPs) label the active form of an enzyme via covalent modification of catalytic residues. Here we present an analysis of parameters influencing potency of peptide phosphonate ABPs for trypsin-fold S1A proteases, an abundant and important class of enzymes with similar substrate specificities. We find that peptide length and stability influence potency more than sequence composition and present structural evidence that steric interactions at the prime-side of the substrate-binding cleft affect potency in a protease-dependent manner. We introduce guidelines for the design of peptide phosphonate ABPs and demonstrate their utility in a live-cell labeling application that specifically targets active S1A proteases at the cell surface of cancer cells.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Cancer (rcdc)Catalytic Domain (mesh)Cell LineTumor (mesh)Drug Design (mesh)Humans (mesh)ModelsMolecular (mesh)Organophosphonates (mesh)Peptide Hydrolases (mesh)Peptides (mesh)Protease Inhibitors (mesh)Serine Endopeptidases (mesh)Serine Proteases (mesh)Staining and Labeling (mesh)Structure-Activity Relationship (mesh)Cell LineTumor (mesh)Humans (mesh)Peptide Hydrolases (mesh)Serine Endopeptidases (mesh)Peptides (mesh)Protease Inhibitors (mesh)Staining and Labeling (mesh)Catalytic Domain (mesh)Structure-Activity Relationship (mesh)Drug Design (mesh)ModelsMolecular (mesh)Serine Proteases (mesh)Organophosphonates (mesh)Catalytic Domain (mesh)Cell LineTumor (mesh)Drug Design (mesh)Humans (mesh)ModelsMolecular (mesh)Organophosphonates (mesh)Peptide Hydrolases (mesh)Peptides (mesh)Protease Inhibitors (mesh)Serine Endopeptidases (mesh)Serine Proteases (mesh)Staining and Labeling (mesh)Structure-Activity Relationship (mesh)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/31v6j2m8https://escholarship.org/content/qt31v6j2m8/qt31v6j2m8.pdfinfo:doi/10.1016/j.chembiol.2010.11.007articleCell Chemical Biology, vol 18, iss 148 - 57oai:escholarship.org:ark:/13030/qt6np322qt2026-04-01T08:11:34Zqt6np322qtKDM4B protects against obesity and metabolic dysfunctionCheng, YingduanYuan, QuanVergnes, LaurentRong, XinYoun, Ji YounLi, JiongYu, YongxinLiu, WeiCai, HuaLin, Jiandie DTontonoz, PeterHong, ChristineReue, KarenWang, Cun-Yu2018-06-12Although significant progress has been made in understanding epigenetic regulation of in vitro adipogenesis, the physiological functions of epigenetic regulators in metabolism and their roles in obesity remain largely elusive. Here, we report that KDM4B (lysine demethylase 4B) in adipose tissues plays a critical role in energy balance, oxidation, lipolysis, and thermogenesis. Loss of KDM4B in mice resulted in obesity associated with reduced energy expenditure and impaired adaptive thermogenesis. Obesity in KDM4B-deficient mice was accompanied by hyperlipidemia, insulin resistance, and pathological changes in the liver and pancreas. Adipocyte-specific deletion of Kdm4b revealed that the adipose tissues were the main sites for KDM4B antiobesity effects. KDM4B directly controlled the expression of multiple metabolic genes, including Ppargc1a and Ppara Collectively, our studies identify KDM4B as an essential epigenetic factor for the regulation of metabolic health and maintaining normal body weight in mice. KDM4B may provide a therapeutic target for treatment of obesity.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Liver Disease (rcdc)Diabetes (rcdc)Genetics (rcdc)Digestive Diseases (rcdc)Obesity (rcdc)Nutrition (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Metabolic and endocrine (hrcs-hc)Adipocytes (mesh)Adipogenesis (mesh)Adipose Tissue (mesh)Animals (mesh)Body Weight (mesh)DietHigh-Fat (mesh)Energy Metabolism (mesh)EpigenesisGenetic (mesh)Insulin Resistance (mesh)Jumonji Domain-Containing Histone Demethylases (mesh)Lipolysis (mesh)Metabolic Diseases (mesh)Mice (mesh)MiceInbred C57BL (mesh)Obesity (mesh)Oxidation-Reduction (mesh)Thermogenesis (mesh)obesityepigeneticsKDM4BmetabolismAdipose Tissue (mesh)Adipocytes (mesh)Animals (mesh)MiceInbred C57BL (mesh)Mice (mesh)Metabolic Diseases (mesh)Insulin Resistance (mesh)Obesity (mesh)Body Weight (mesh)EpigenesisGenetic (mesh)Energy Metabolism (mesh)Oxidation-Reduction (mesh)Lipolysis (mesh)Thermogenesis (mesh)Adipogenesis (mesh)Jumonji Domain-Containing Histone Demethylases (mesh)DietHigh-Fat (mesh)KDM4BepigeneticsmetabolismobesityAdipocytes (mesh)Adipogenesis (mesh)Adipose Tissue (mesh)Animals (mesh)Body Weight (mesh)DietHigh-Fat (mesh)Energy Metabolism (mesh)EpigenesisGenetic (mesh)Insulin Resistance (mesh)Jumonji Domain-Containing Histone Demethylases (mesh)Lipolysis (mesh)Metabolic Diseases (mesh)Mice (mesh)MiceInbred C57BL (mesh)Obesity (mesh)Oxidation-Reduction (mesh)Thermogenesis (mesh)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6np322qthttps://escholarship.org/content/qt6np322qt/qt6np322qt.pdfinfo:doi/10.1073/pnas.1721814115articleProceedings of the National Academy of Sciences of the United States of America, vol 115, iss 24e5566 - e5575oai:escholarship.org:ark:/13030/qt2476r14p2026-03-24T12:41:14Zqt2476r14pA protein assembly mediates Xist localization and gene silencingPandya-Jones, AmyMarkaki, YolandaSerizay, JacquesChitiashvili, TsotneMancia Leon, Walter RDamianov, AndreyChronis, ConstantinosPapp, BernadettChen, Chun-KanMcKee, RobinWang, Xiao-JunChau, AnthonySabri, ShanLeonhardt, HeinrichZheng, SikaGuttman, MitchellBlack, Douglas LPlath, Kathrin2020-11-05Nuclear compartments have diverse roles in regulating gene expression, yet the molecular forces and components that drive compartment formation remain largely unclear1. The long non-coding RNA Xist establishes an intra-chromosomal compartment by localizing at a high concentration in a territory spatially close to its transcription locus2 and binding diverse proteins3–5 to achieve X-chromosome inactivation (XCI)6,7. The XCI process therefore serves as a paradigm for understanding how RNA-mediated recruitment of various proteins induces a functional compartment. The properties of the inactive X (Xi)-compartment are known to change over time, because after initial Xist spreading and transcriptional shutoff a state is reached in which gene silencing remains stable even if Xist is turned off8. Here we show that the Xist RNA-binding proteins PTBP19, MATR310, TDP-4311 and CELF112 assemble on the multivalent E-repeat element of Xist7 and, via self-aggregation and heterotypic protein–protein interactions, form a condensate1 in the Xi. This condensate is required for gene silencing and for the anchoring of Xist to the Xi territory, and can be sustained in the absence of Xist. Notably, these E-repeat-binding proteins become essential coincident with transition to the Xist-independent XCI phase8, indicating that the condensate seeded by the E-repeat underlies the developmental switch from Xist-dependence to Xist-independence. Taken together, our data show that Xist forms the Xi compartment by seeding a heteromeric condensate that consists of ubiquitous RNA-binding proteins, revealing an unanticipated mechanism for heritable gene silencing.3101 Biochemistry and Cell Biology (for-2020)3102 Bioinformatics and Computational Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Human Genome (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Animals (mesh)CELF1 Protein (mesh)Cell Line (mesh)DNA-Binding Proteins (mesh)Female (mesh)Gene Silencing (mesh)Heterogeneous-Nuclear Ribonucleoproteins (mesh)Humans (mesh)In Situ HybridizationFluorescence (mesh)Male (mesh)Mice (mesh)Nuclear Matrix-Associated Proteins (mesh)Polypyrimidine Tract-Binding Protein (mesh)RNALong Noncoding (mesh)RNA-Binding Proteins (mesh)X Chromosome Inactivation (mesh)Cell Line (mesh)Animals (mesh)Humans (mesh)Mice (mesh)RNA-Binding Proteins (mesh)Polypyrimidine Tract-Binding Protein (mesh)Heterogeneous-Nuclear Ribonucleoproteins (mesh)DNA-Binding Proteins (mesh)Nuclear Matrix-Associated Proteins (mesh)In Situ HybridizationFluorescence (mesh)Gene Silencing (mesh)Female (mesh)Male (mesh)X Chromosome Inactivation (mesh)RNALong Noncoding (mesh)CELF1 Protein (mesh)Animals (mesh)CELF1 Protein (mesh)Cell Line (mesh)DNA-Binding Proteins (mesh)Female (mesh)Gene Silencing (mesh)Heterogeneous-Nuclear Ribonucleoproteins (mesh)Humans (mesh)In Situ HybridizationFluorescence (mesh)Male (mesh)Mice (mesh)Nuclear Matrix-Associated Proteins (mesh)Polypyrimidine Tract-Binding Protein (mesh)RNALong Noncoding (mesh)RNA-Binding Proteins (mesh)X Chromosome Inactivation (mesh)General Science & Technology (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2476r14phttps://escholarship.org/content/qt2476r14p/qt2476r14p.pdfinfo:doi/10.1038/s41586-020-2703-0articleNature, vol 587, iss 7832145 - 151oai:escholarship.org:ark:/13030/qt83x6f8xc2026-03-24T01:28:39Zqt83x6f8xcHIV-1 Tat recruits transcription elongation factors dispersed along a flexible AFF4 scaffoldChou, SeemayUpton, HeatherBao, KatherineSchulze-Gahmen, UrsulaSamelson, Avi JHe, NanhaiNowak, AnnaLu, HuasongKrogan, Nevan JZhou, QiangAlber, Tom2013-01-08The HIV-1 Tat protein stimulates viral gene expression by recruiting human transcription elongation complexes containing P-TEFb, AFF4, ELL2, and ENL or AF9 to the viral promoter, but the molecular organization of these complexes remains unknown. To establish the overall architecture of the HIV-1 Tat elongation complex, we mapped the binding sites that mediate complex assembly in vitro and in vivo. The AFF4 protein emerges as the central scaffold that recruits other factors through direct interactions with short hydrophobic regions along its structurally disordered axis. Direct binding partners CycT1, ELL2, and ENL or AF9 act as bridging components that link this complex to two major elongation factors, P-TEFb and the PAF complex. The unique scaffolding properties of AFF4 allow dynamic and flexible assembly of multiple elongation factors and connect the components not only to each other but also to a larger network of transcriptional regulators.3207 Medical Microbiology (for-2020)32 Biomedical and Clinical Sciences (for-2020)34 Chemical Sciences (for-2020)Genetics (rcdc)Infectious Diseases (rcdc)HIV/AIDS (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Infection (hrcs-hc)Binding Sites (mesh)BlottingWestern (mesh)Circular Dichroism (mesh)Cyclin T (mesh)Electrophoresis (mesh)Escherichia coli (mesh)Gene Expression RegulationViral (mesh)HIV-1 (mesh)HeLa Cells (mesh)Humans (mesh)Immunoprecipitation (mesh)Luciferases (mesh)Multiprotein Complexes (mesh)Positive Transcriptional Elongation Factor B (mesh)Repressor Proteins (mesh)Transcriptional Elongation Factors (mesh)tat Gene ProductsHuman Immunodeficiency Virus (mesh)paused RNA polymerase IIintrinsically disordered proteinssuper elongation complexMLL-fusion complexHela Cells (mesh)Humans (mesh)Escherichia coli (mesh)HIV-1 (mesh)Multiprotein Complexes (mesh)Luciferases (mesh)Repressor Proteins (mesh)Transcriptional Elongation Factors (mesh)Positive Transcriptional Elongation Factor B (mesh)BlottingWestern (mesh)Electrophoresis (mesh)Circular Dichroism (mesh)Immunoprecipitation (mesh)Gene Expression RegulationViral (mesh)Binding Sites (mesh)tat Gene ProductsHuman Immunodeficiency Virus (mesh)Cyclin T (mesh)Binding Sites (mesh)BlottingWestern (mesh)Circular Dichroism (mesh)Cyclin T (mesh)Electrophoresis (mesh)Escherichia coli (mesh)Gene Expression RegulationViral (mesh)HIV-1 (mesh)HeLa Cells (mesh)Humans (mesh)Immunoprecipitation (mesh)Luciferases (mesh)Multiprotein Complexes (mesh)Positive Transcriptional Elongation Factor B (mesh)Repressor Proteins (mesh)Transcriptional Elongation Factors (mesh)tat Gene ProductsHuman Immunodeficiency Virus (mesh)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/83x6f8xchttps://escholarship.org/content/qt83x6f8xc/qt83x6f8xc.pdfinfo:doi/10.1073/pnas.1216971110articleProceedings of the National Academy of Sciences of the United States of America, vol 110, iss 2e123 - e131oai:escholarship.org:ark:/13030/qt4ph8w0v12026-03-22T10:00:52Zqt4ph8w0v1Genome-wide programmable transcriptional memory by CRISPR-based epigenome editingNuñez, James KChen, JinPommier, Greg CCogan, J ZacheryReplogle, Joseph MAdriaens, CarmenRamadoss, Gokul NShi, QuanmingHung, King LSamelson, Avi JPogson, Angela NKim, James YSChung, AmandaLeonetti, Manuel DChang, Howard YKampmann, MartinBernstein, Bradley EHovestadt, VolkerGilbert, Luke AWeissman, Jonathan S2021-04-01A general approach for heritably altering gene expression has the potential to enable many discovery and therapeutic efforts. Here, we present CRISPRoff-a programmable epigenetic memory writer consisting of a single dead Cas9 fusion protein that establishes DNA methylation and repressive histone modifications. Transient CRISPRoff expression initiates highly specific DNA methylation and gene repression that is maintained through cell division and differentiation of stem cells to neurons. Pairing CRISPRoff with genome-wide screens and analysis of chromatin marks establishes rules for heritable gene silencing. We identify single guide RNAs (sgRNAs) capable of silencing the large majority of genes including those lacking canonical CpG islands (CGIs) and reveal a wide targeting window extending beyond annotated CGIs. The broad ability of CRISPRoff to initiate heritable gene silencing even outside of CGIs expands the canonical model of methylation-based silencing and enables diverse applications including genome-wide screens, multiplexed cell engineering, enhancer silencing, and mechanistic exploration of epigenetic inheritance.31 Biological Sciences (for-2020)3105 Genetics (for-2020)Human Genome (rcdc)Genetics (rcdc)Biotechnology (rcdc)Stem Cell Research (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Cancer (hrcs-hc)Generic health relevance (hrcs-hc)CRISPR-Cas Systems (mesh)Cell Differentiation (mesh)Cellular Reprogramming (mesh)CpG Islands (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Epigenome (mesh)Gene Editing (mesh)Gene Silencing (mesh)Histone Code (mesh)Humans (mesh)Induced Pluripotent Stem Cells (mesh)Neurons (mesh)Protein ProcessingPost-Translational (mesh)Neurons (mesh)Humans (mesh)Cell Differentiation (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Gene Silencing (mesh)Protein ProcessingPost-Translational (mesh)Histone Code (mesh)CpG Islands (mesh)Induced Pluripotent Stem Cells (mesh)CRISPR-Cas Systems (mesh)Cellular Reprogramming (mesh)Gene Editing (mesh)Epigenome (mesh)CRISPRDNA methylationcell therapydCas9epigeneticsCRISPR-Cas Systems (mesh)Cell Differentiation (mesh)Cellular Reprogramming (mesh)CpG Islands (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Epigenome (mesh)Gene Editing (mesh)Gene Silencing (mesh)Histone Code (mesh)Humans (mesh)Induced Pluripotent Stem Cells (mesh)Neurons (mesh)Protein ProcessingPost-Translational (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4ph8w0v1https://escholarship.org/content/qt4ph8w0v1/qt4ph8w0v1.pdfinfo:doi/10.1016/j.cell.2021.03.025articleCell, vol 184, iss 92503 - 2519.e17oai:escholarship.org:ark:/13030/qt9nw3t87q2026-03-21T02:23:03Zqt9nw3t87qDamage-induced phosphorylation of Sld3 is important to block late origin firingLopez-Mosqueda, JaimeMaas, Nancy LJonsson, Zophonias ODeFazio-Eli, Lisa GWohlschlegel, JamesToczyski, David P2010-09-01Stop at the intra-S checkpointTwo classes of kinases, CDK and DDK, facilitate the initiation of DNA replication in S phase. In two studies, the Diffley and Toczyski labs show that when damage is sensed, another kinase — the checkpoint kinase Rad53 — halts replication by inhibiting both the CDK and DDK pathways through the phosphorylation of Sld3 and Dbf4, respectively. These results reveal that regulation of the firing of origins is the means by which the intra-S checkpoint slows S phase.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)1.1 Normal biological development and functioning (hrcs-rac)Cell Cycle Proteins (mesh)Checkpoint Kinase 2 (mesh)DNA Damage (mesh)DNA Replication (mesh)DNA-Binding Proteins (mesh)Hydroxyurea (mesh)Phosphorylation (mesh)Protein Serine-Threonine Kinases (mesh)Rad52 DNA Repair and Recombination Protein (mesh)Replication Origin (mesh)S Phase (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)Time Factors (mesh)Saccharomyces cerevisiae (mesh)DNA Damage (mesh)Hydroxyurea (mesh)Cell Cycle Proteins (mesh)DNA-Binding Proteins (mesh)Saccharomyces cerevisiae Proteins (mesh)S Phase (mesh)DNA Replication (mesh)Phosphorylation (mesh)Replication Origin (mesh)Time Factors (mesh)Rad52 DNA Repair and Recombination Protein (mesh)Checkpoint Kinase 2 (mesh)Protein Serine-Threonine Kinases (mesh)Cell Cycle Proteins (mesh)Checkpoint Kinase 2 (mesh)DNA Damage (mesh)DNA Replication (mesh)DNA-Binding Proteins (mesh)Hydroxyurea (mesh)Phosphorylation (mesh)Protein Serine-Threonine Kinases (mesh)Rad52 DNA Repair and Recombination Protein (mesh)Replication Origin (mesh)S Phase (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)Time Factors (mesh)General Science & Technology (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9nw3t87qhttps://escholarship.org/content/qt9nw3t87q/qt9nw3t87q.pdfinfo:doi/10.1038/nature09377articleNature, vol 467, iss 7314479 - 483oai:escholarship.org:ark:/13030/qt4065n1rm2026-03-21T01:34:13Zqt4065n1rmGcn5 and Sirtuins Regulate Acetylation of the Ribosomal Protein Transcription Factor Ifh1Downey, MichaelKnight, BrittaVashisht, Ajay ASeller, Charles AWohlschlegel, James AShore, DavidToczyski, David P2013-09-01BACKGROUND: In eukaryotes, ribosome biosynthesis involves the coordination of ribosomal RNA and ribosomal protein (RP) production. In S. cerevisiae, the regulation of ribosome biosynthesis occurs largely at the level of transcription. The transcription factor Ifh1 binds at RP genes and promotes their transcription when growth conditions are favorable. Although Ifh1 recruitment to RP genes has been characterized, little is known about the regulation of promoter-bound Ifh1.
RESULTS: We used a novel whole-cell-extract screening approach to identify Spt7, a member of the SAGA transcription complex, and the RP transactivator Ifh1 as highly acetylated nonhistone species. We report that Ifh1 is modified by acetylation specifically in an N-terminal domain. These acetylations require the Gcn5 histone acetyltransferase and are reversed by the sirtuin deacetylases Hst1 and Sir2. Ifh1 acetylation is regulated by rapamycin treatment and stress and limits the ability of Ifh1 to act as a transactivator at RP genes.
CONCLUSIONS: Our data suggest a novel mechanism of regulation whereby Gcn5 functions to titrate the activity of Ifh1 following its recruitment to RP promoters to provide more than an all-or-nothing mode of transcriptional regulation. We provide insights into how the action of histone acetylation machineries converges with nutrient-sensing pathways to regulate important aspects of cell growth.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Biotechnology (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Acetylation (mesh)Histone Acetyltransferases (mesh)Ribosomal Proteins (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)Sirtuins (mesh)Trans-Activators (mesh)Transcription Factors (mesh)Saccharomyces cerevisiae (mesh)Sirtuins (mesh)Trans-Activators (mesh)Saccharomyces cerevisiae Proteins (mesh)Ribosomal Proteins (mesh)Transcription Factors (mesh)Acetylation (mesh)Histone Acetyltransferases (mesh)p300-CBP-Associated Factor (mesh)Acetylation (mesh)Histone Acetyltransferases (mesh)Ribosomal Proteins (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)Sirtuins (mesh)Trans-Activators (mesh)Transcription Factors (mesh)p300-CBP-Associated Factor (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)17 Psychology and Cognitive Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)52 Psychology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4065n1rmhttps://escholarship.org/content/qt4065n1rm/qt4065n1rm.pdfinfo:doi/10.1016/j.cub.2013.06.050articleCurrent Biology, vol 23, iss 171638 - 1648oai:escholarship.org:ark:/13030/qt4jb9p6qn2026-03-21T01:34:09Zqt4jb9p6qnHst3 is turned over by a replication stress-responsive SCFCdc4 phospho-degronEdenberg, Ellen RVashisht, Ajay ATopacio, Benjamin RWohlschlegel, James AToczyski, David P2014-04-22Hst3 is the histone deacetylase that removes histone H3K56 acetylation. H3K56 acetylation is a cell-cycle- and damage-regulated chromatin marker, and proper regulation of H3K56 acetylation is important for replication, genomic stability, chromatin assembly, and the response to and recovery from DNA damage. Understanding the regulation of enzymes that regulate H3K56 acetylation is of great interest, because the loss of H3K56 acetylation leads to genomic instability. HST3 is controlled at both the transcriptional and posttranscriptional level. Here, we show that Hst3 is targeted for turnover by the ubiquitin ligase SCF(Cdc4) after phosphorylation of a multisite degron. In addition, we find that Hst3 turnover increases in response to replication stress in a Rad53-dependent way. Turnover of Hst3 is promoted by Mck1 activity in both conditions. The Hst3 degron contains two canonical Cdc4 phospho-degrons, and the phosphorylation of each of these is required for efficient turnover both in an unperturbed cell cycle and in response to replication stress.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Acetylation (mesh)Cell Cycle Proteins (mesh)DNA Damage (mesh)DNA Replication (mesh)F-Box Proteins (mesh)Histone Deacetylases (mesh)Histones (mesh)Lysine (mesh)Phosphorylation (mesh)Proteolysis (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)StressPhysiological (mesh)Substrate Specificity (mesh)Ubiquitin-Protein Ligases (mesh)Saccharomyces cerevisiae (mesh)DNA Damage (mesh)Histone Deacetylases (mesh)Ubiquitin-Protein Ligases (mesh)Lysine (mesh)F-Box Proteins (mesh)Cell Cycle Proteins (mesh)Saccharomyces cerevisiae Proteins (mesh)Histones (mesh)DNA Replication (mesh)Substrate Specificity (mesh)Acetylation (mesh)Phosphorylation (mesh)StressPhysiological (mesh)Proteolysis (mesh)Acetylation (mesh)Cell Cycle Proteins (mesh)DNA Damage (mesh)DNA Replication (mesh)F-Box Proteins (mesh)Histone Deacetylases (mesh)Histones (mesh)Lysine (mesh)Phosphorylation (mesh)Proteolysis (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)StressPhysiological (mesh)Substrate Specificity (mesh)Ubiquitin-Protein Ligases (mesh)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4jb9p6qnhttps://escholarship.org/content/qt4jb9p6qn/qt4jb9p6qn.pdfinfo:doi/10.1073/pnas.1315325111articleProceedings of the National Academy of Sciences of the United States of America, vol 111, iss 165962 - 5967oai:escholarship.org:ark:/13030/qt4xd2r3sr2026-03-21T01:12:35Zqt4xd2r3srStructure of an Fab–Protease Complex Reveals a Highly Specific Non-canonical Mechanism of InhibitionFarady, Christopher JEgea, Pascal FSchneider, Eric LDarragh, Molly RCraik, Charles S2008-07-01The vast majority of protein protease inhibitors bind their targets in a substrate-like manner. This is a robust and efficient mechanism of inhibition but, due to the highly conserved architecture of protease active sites, these inhibitors often exhibit promiscuity. Inhibitors that show strict specificity for one protease usually achieve this selectivity by combining substrate-like binding in the active site with exosite binding on the protease surface. The development of new, specific inhibitors can be aided greatly by binding to non-conserved regions of proteases if potency can be maintained. Due to their ability to bind specifically to nearly any antigen, antibodies provide an excellent scaffold for creating inhibitors targeted to a single member of a family of highly homologous enzymes. The 2.2 A resolution crystal structure of an Fab antibody inhibitor in complex with the serine protease membrane-type serine protease 1 (MT-SP1/matriptase) reveals the molecular basis of its picomolar potency and specificity. The inhibitor has a distinct mechanism of inhibition; it gains potency and specificity through interactions with the protease surface loops, and inhibits by binding in the active site in a catalytically non-competent manner. In contrast to most naturally occurring protease inhibitors, which have diverse structures but converge to a similar inhibitory archetype, antibody inhibitors provide an opportunity to develop divergent mechanisms of inhibition from a single scaffold.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)1.1 Normal biological development and functioning (hrcs-rac)5.1 Pharmaceuticals (hrcs-rac)Inflammatory and immune system (hrcs-hc)Binding Sites (mesh)CrystallographyX-Ray (mesh)Humans (mesh)Immunoglobulin Fab Fragments (mesh)ModelsMolecular (mesh)Molecular Sequence Data (mesh)Protein Conformation (mesh)Serine Endopeptidases (mesh)Serine Proteinase Inhibitors (mesh)antibodyserine proteaseprotease inhibitorsubstrate specificitystructureHumans (mesh)Serine Endopeptidases (mesh)Serine Proteinase Inhibitors (mesh)CrystallographyX-Ray (mesh)Binding Sites (mesh)Protein Conformation (mesh)ModelsMolecular (mesh)Molecular Sequence Data (mesh)Immunoglobulin Fab Fragments (mesh)Binding Sites (mesh)CrystallographyX-Ray (mesh)Humans (mesh)Immunoglobulin Fab Fragments (mesh)ModelsMolecular (mesh)Molecular Sequence Data (mesh)Protein Conformation (mesh)Serine Endopeptidases (mesh)Serine Proteinase Inhibitors (mesh)0304 Medicinal and Biomolecular Chemistry (for)0601 Biochemistry and Cell Biology (for)0605 Microbiology (for)Biochemistry & Molecular Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)3107 Microbiology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4xd2r3srhttps://escholarship.org/content/qt4xd2r3sr/qt4xd2r3sr.pdfinfo:doi/10.1016/j.jmb.2008.05.009articleJournal of Molecular Biology, vol 380, iss 2351 - 360oai:escholarship.org:ark:/13030/qt7rx7g6rq2026-03-20T13:23:15Zqt7rx7g6rqComparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystalsWolff, Alexander MYoung, Iris DSierra, Raymond GBrewster, Aaron SMartynowycz, Michael WNango, ErikoSugahara, MichihiroNakane, TakanoriIto, KazutakaAquila, AndrewBhowmick, AsmitBiel, Justin TCarbajo, SergioCohen, Aina ECortez, SaulGonzalez, AnaHino, TomoyaIm, DohyunKoralek, Jake DKubo, MinoruLazarou, Tomas SNomura, TakashiOwada, ShigekiSamelson, Avi JTanaka, TomoyukiTanaka, RieThompson, Erin Mvan den Bedem, HenryWoldeyes, Rahel AYumoto, FumiakiZhao, WeiTono, KensukeBoutet, SebastienIwata, SoGonen, TamirSauter, Nicholas KFraser, James SThompson, Michael C2020-03-01Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods for obtaining structural information from crystals on the nanometre to micrometre scale. Despite the utility of these methods, their implementation can often be difficult, as they present many challenges that are not encountered in traditional macromolecular crystallography experiments. Here, XFEL serial crystallography experiments and MicroED experiments using batch-grown microcrystals of the enzyme cyclophilin A are described. The results provide a roadmap for researchers hoping to design macromolecular microcrystallography experiments, and they highlight the strengths and weaknesses of the two methods. Specifically, we focus on how the different physical conditions imposed by the sample-preparation and delivery methods required for each type of experiment affect the crystal structure of the enzyme.3402 Inorganic Chemistry (for-2020)34 Chemical Sciences (for-2020)Bioengineering (rcdc)1.4 Methodologies and measurements (hrcs-rac)microcrystalsbatch crystallizationserial crystallographyMicroEDMicroEDbatch crystallizationmicrocrystalsserial crystallography0202 AtomicMolecularNuclearParticle and Plasma Physics (for)0204 Condensed Matter Physics (for)0306 Physical Chemistry (incl. Structural) (for)3406 Physical chemistry (for-2020)5104 Condensed matter physics (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/7rx7g6rqhttps://escholarship.org/content/qt7rx7g6rq/qt7rx7g6rq.pdfinfo:doi/10.1107/s205225252000072xarticleIUCrJ, vol 7, iss Pt 2306 - 323oai:escholarship.org:ark:/13030/qt7mm460pr2026-03-20T10:16:10Zqt7mm460prAdenovirus E4ORF1-Induced MYC Activation Promotes Host Cell Anabolic Glucose Metabolism and Virus ReplicationThai, MinhGraham, Nicholas ABraas, DanielNehil, MichaelKomisopoulou, EvangeliaKurdistani, Siavash KMcCormick, FrankGraeber, Thomas GChristofk, Heather R2014-04-01Virus infections trigger metabolic changes in host cells that support the bioenergetic and biosynthetic demands of viral replication. Although recent studies have characterized virus-induced changes in host cell metabolism (Munger et al., 2008; Terry et al., 2012), the molecular mechanisms by which viruses reprogram cellular metabolism have remained elusive. Here, we show that the gene product of adenovirus E4ORF1 is necessary for adenovirus-induced upregulation of host cell glucose metabolism and sufficient to promote enhanced glycolysis in cultured epithelial cells by activation of MYC. E4ORF1 localizes to the nucleus, binds to MYC, and enhances MYC binding to glycolytic target genes, resulting in elevated expression of specific glycolytic enzymes. E4ORF1 activation of MYC promotes increased nucleotide biosynthesis from glucose intermediates and enables optimal adenovirus replication in primary lung epithelial cells. Our findings show how a viral protein exploits host cell machinery to reprogram cellular metabolism and promote optimal progeny virion generation.3207 Medical Microbiology (for-2020)3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Infectious Diseases (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Infection (hrcs-hc)Adenovirus E4 Proteins (mesh)CellsCultured (mesh)Chromatin Immunoprecipitation (mesh)Epithelial Cells (mesh)Glucose (mesh)HeLa Cells (mesh)Humans (mesh)Immunoblotting (mesh)Immunoprecipitation (mesh)Metabolic Networks and Pathways (mesh)ModelsBiological (mesh)Nucleotides (mesh)Protein Binding (mesh)Proto-Oncogene Proteins c-myc (mesh)Virus Replication (mesh)CellsCultured (mesh)Hela Cells (mesh)Epithelial Cells (mesh)Humans (mesh)Nucleotides (mesh)Glucose (mesh)Proto-Oncogene Proteins c-myc (mesh)Adenovirus E4 Proteins (mesh)Immunoblotting (mesh)Chromatin Immunoprecipitation (mesh)Immunoprecipitation (mesh)Virus Replication (mesh)Protein Binding (mesh)ModelsBiological (mesh)Metabolic Networks and Pathways (mesh)Adenovirus E4 Proteins (mesh)CellsCultured (mesh)Chromatin Immunoprecipitation (mesh)Epithelial Cells (mesh)Glucose (mesh)HeLa Cells (mesh)Humans (mesh)Immunoblotting (mesh)Immunoprecipitation (mesh)Metabolic Networks and Pathways (mesh)ModelsBiological (mesh)Nucleotides (mesh)Protein Binding (mesh)Proto-Oncogene Proteins c-myc (mesh)Virus Replication (mesh)0601 Biochemistry and Cell Biology (for)1101 Medical Biochemistry and Metabolomics (for)Endocrinology & Metabolism (science-metrix)3101 Biochemistry and cell biology (for-2020)3205 Medical biochemistry and metabolomics (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7mm460prhttps://escholarship.org/content/qt7mm460pr/qt7mm460pr.pdfinfo:doi/10.1016/j.cmet.2014.03.009articleCell Metabolism, vol 19, iss 4694 - 701oai:escholarship.org:ark:/13030/qt45j7875f2026-03-20T08:07:57Zqt45j7875fRad53 Downregulates Mitotic Gene Transcription by Inhibiting the Transcriptional Activator Ndd1Edenberg, Ellen RVashisht, AjayBenanti, Jennifer AWohlschlegel, JamesToczyski, David P2014-02-01The 33 genes in the Saccharomyces cerevisiae mitotic CLB2 transcription cluster have been known to be downregulated by the DNA damage checkpoint for many years. Here, we show that this is mediated by the checkpoint kinase Rad53 and the dedicated transcriptional activator of the cluster, Ndd1. Ndd1 is phosphorylated in response to DNA damage, which blocks recruitment to promoters and leads to the transcriptional downregulation of the CLB2 cluster. Finally, we show that downregulation of Ndd1 is an essential function of Rad53, as a hypomorphic ndd1 allele rescues RAD53 deletion.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Animals (mesh)Cell Cycle Proteins (mesh)Checkpoint Kinase 2 (mesh)DNA Damage (mesh)Down-Regulation (mesh)Gene Expression RegulationFungal (mesh)Humans (mesh)Mitosis (mesh)Promoter RegionsGenetic (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)Transcription Factors (mesh)TranscriptionGenetic (mesh)Animals (mesh)Humans (mesh)Saccharomyces cerevisiae (mesh)DNA Damage (mesh)Cell Cycle Proteins (mesh)Saccharomyces cerevisiae Proteins (mesh)Transcription Factors (mesh)Mitosis (mesh)TranscriptionGenetic (mesh)Down-Regulation (mesh)Gene Expression RegulationFungal (mesh)Promoter RegionsGenetic (mesh)Checkpoint Kinase 2 (mesh)Animals (mesh)Cell Cycle Proteins (mesh)Checkpoint Kinase 2 (mesh)DNA Damage (mesh)Down-Regulation (mesh)Gene Expression RegulationFungal (mesh)Humans (mesh)Mitosis (mesh)Promoter RegionsGenetic (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)Transcription Factors (mesh)TranscriptionGenetic (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/45j7875fhttps://escholarship.org/content/qt45j7875f/qt45j7875f.pdfinfo:doi/10.1128/mcb.01056-13articleMolecular and Cellular Biology, vol 34, iss 4725 - 738oai:escholarship.org:ark:/13030/qt0wz968xz2026-03-14T06:56:30Zqt0wz968xzAdenovirus E1A binding to DCAF10 targets proteasomal degradation of RUVBL1/2 AAA+ ATPases required for quaternary assembly of multiprotein machines, innate immunity, and responses to metabolic stressZemke, Nathan RHsu, EmilyBarshop, William DSha, JihuiWohlschlegel, James ABerk, Arnold JBanks, Lawrence2023-12-21IMPORTANCE: Inactivation of EP300/CREBB paralogous cellular lysine acetyltransferases (KATs) during the early phase of infection is a consistent feature of DNA viruses. The cell responds by stabilizing transcription factor IRF3 which activates transcription of scores of interferon-stimulated genes (ISGs), inhibiting viral replication. Human respiratory adenoviruses counter this by assembling a CUL4-based ubiquitin ligase complex that polyubiquitinylates RUVBL1 and 2 inducing their proteasomal degradation. This inhibits accumulation of active IRF3 and the expression of anti-viral ISGs, allowing replication of the respiratory HAdVs in the face of inhibition of EP300/CBEBBP KAT activity by the N-terminal region of E1A.3207 Medical Microbiology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Biodefense (rcdc)Infectious Diseases (rcdc)2.1 Biological and endogenous factors (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)Humans (mesh)Adenovirus E1A Proteins (mesh)AdenovirusesHuman (mesh)ATPases Associated with Diverse Cellular Activities (mesh)Carrier Proteins (mesh)Cullin Proteins (mesh)DNA Helicases (mesh)ImmunityInnate (mesh)Interferons (mesh)Proteasome Endopeptidase Complex (mesh)Protein StructureQuaternary (mesh)StressPhysiological (mesh)Ubiquitin-Protein Ligase Complexes (mesh)Ubiquitination (mesh)Virus Replication (mesh)adenovirusE1AIRF3DCAF10CRL4innate immunityvirologyP300CBPHumans (mesh)AdenovirusesHuman (mesh)Proteasome Endopeptidase Complex (mesh)DNA Helicases (mesh)Ubiquitin-Protein Ligase Complexes (mesh)Cullin Proteins (mesh)Carrier Proteins (mesh)Adenovirus E1A Proteins (mesh)Interferons (mesh)Virus Replication (mesh)Protein StructureQuaternary (mesh)Interferon Regulatory Factor-3 (mesh)E1A-Associated p300 Protein (mesh)Ubiquitination (mesh)ImmunityInnate (mesh)StressPhysiological (mesh)ATPases Associated with Diverse Cellular Activities (mesh)CBPCRL4DCAF10E1AIRF3P300adenovirusinnate immunityvirologyHumans (mesh)Adenovirus E1A Proteins (mesh)AdenovirusesHuman (mesh)ATPases Associated with Diverse Cellular Activities (mesh)Carrier Proteins (mesh)Cullin Proteins (mesh)DNA Helicases (mesh)ImmunityInnate (mesh)Interferons (mesh)Proteasome Endopeptidase Complex (mesh)Protein StructureQuaternary (mesh)StressPhysiological (mesh)Ubiquitin-Protein Ligase Complexes (mesh)Ubiquitination (mesh)Virus Replication (mesh)E1A-Associated p300 Protein (mesh)Interferon Regulatory Factor-3 (mesh)06 Biological Sciences (for)07 Agricultural and Veterinary Sciences (for)11 Medical and Health Sciences (for)Virology (science-metrix)30 Agriculturalveterinary and food sciences (for-2020)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0wz968xzhttps://escholarship.org/content/qt0wz968xz/qt0wz968xz.pdfinfo:doi/10.1128/jvi.00993-23articleJournal of Virology, vol 97, iss 12e00993 - e00923oai:escholarship.org:ark:/13030/qt81p7p4952026-03-13T06:30:06Zqt81p7p495Epigenome-wide association in adipose tissue from the METSIM cohortOrozco, Luz DFarrell, ColinHale, ChristopherRubbi, LiudmillaRinaldi, ArturoCivelek, MetePan, CalvinLam, LarryMontoya, DennisEdillor, ChantleSeldin, MarcusBoehnke, MichaelMohlke, Karen LJacobsen, SteveKuusisto, JohannaLaakso, MarkkuLusis, Aldons JPellegrini, Matteo2018-05-15Most epigenome-wide association studies to date have been conducted in blood. However, metabolic syndrome is mediated by a dysregulation of adiposity and therefore it is critical to study adipose tissue in order to understand the effects of this syndrome on epigenomes. To determine if natural variation in DNA methylation was associated with metabolic syndrome traits, we profiled global methylation levels in subcutaneous abdominal adipose tissue. We measured association between 32 clinical traits related to diabetes and obesity in 201 people from the Metabolic Syndrome in Men cohort. We performed epigenome-wide association studies between DNA methylation levels and traits, and identified associations for 13 clinical traits in 21 loci. We prioritized candidate genes in these loci using expression quantitative trait loci, and identified 18 high confidence candidate genes, including known and novel genes associated with diabetes and obesity traits. Using methylation deconvolution, we examined which cell types may be mediating the associations, and concluded that most of the loci we identified were specific to adipocytes. We determined whether the abundance of cell types varies with metabolic traits, and found that macrophages increased in abundance with the severity of metabolic syndrome traits. Finally, we developed a DNA methylation-based biomarker to assess type 2 diabetes risk in adipose tissue. In conclusion, our results demonstrate that profiling DNA methylation in adipose tissue is a powerful tool for understanding the molecular effects of metabolic syndrome on adipose tissue, and can be used in conjunction with traditional genetic analyses to further characterize this disorder.31 Biological Sciences (for-2020)3105 Genetics (for-2020)Genetics (rcdc)Diabetes (rcdc)Prevention (rcdc)Biotechnology (rcdc)Nutrition (rcdc)Clinical Research (rcdc)Obesity (rcdc)Human Genome (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Metabolic and endocrine (hrcs-hc)Cardiovascular (hrcs-hc)Stroke (hrcs-hc)Cancer (hrcs-hc)Adipose Tissue (mesh)Adult (mesh)Aged (mesh)Biopsy (mesh)Body Mass Index (mesh)CpG Islands (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Gene Expression Regulation (mesh)GenomeHuman (mesh)Genome-Wide Association Study (mesh)Humans (mesh)Male (mesh)Metabolic Syndrome (mesh)Middle Aged (mesh)Obesity (mesh)Quantitative Trait Loci (mesh)Adipose Tissue (mesh)Humans (mesh)Obesity (mesh)Biopsy (mesh)Body Mass Index (mesh)DNA Methylation (mesh)Gene Expression Regulation (mesh)EpigenesisGenetic (mesh)CpG Islands (mesh)Quantitative Trait Loci (mesh)GenomeHuman (mesh)Adult (mesh)Aged (mesh)Middle Aged (mesh)Male (mesh)Genome-Wide Association Study (mesh)Metabolic Syndrome (mesh)Adipose Tissue (mesh)Adult (mesh)Aged (mesh)Biopsy (mesh)Body Mass Index (mesh)CpG Islands (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Gene Expression Regulation (mesh)GenomeHuman (mesh)Genome-Wide Association Study (mesh)Humans (mesh)Male (mesh)Metabolic Syndrome (mesh)Middle Aged (mesh)Obesity (mesh)Quantitative Trait Loci (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Genetics & Heredity (science-metrix)3105 Genetics (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/81p7p495https://escholarship.org/content/qt81p7p495/qt81p7p495.pdfinfo:doi/10.1093/hmg/ddy093articleHuman Molecular Genetics, vol 27, iss 101830 - 1846oai:escholarship.org:ark:/13030/qt78f1w3s72026-03-12T13:28:06Zqt78f1w3s7The persistence of potential: The life of Sir John B. Gurdon.Melton, Douglas ADe Robertis, Edward M2026-03-10The death of Sir John Bertrand Gurdon in October 2025 marks the passing of one of the most influential biologists of the modern era. A developmental biologist, Sir Gurdon's best-known experiments were performed with frog eggs and nuclear transfer, leading to discoveries that transformed our understanding of how genes control animal development and established the principles that underpin animal cloning, nuclear reprogramming, and regenerative medicine. These classical experiments paved the way for advances in induced pluripotent stem cells and energized thinking of new ways to treat diseases with cellular therapies. Sir John Gurdon's legacy endures through his transformative discoveries, institutional leadership, and the scientists he inspired.3206 Medical Biotechnology (for-2020)32 Biomedical and Clinical Sciences (for-2020)50 Philosophy and Religious Studies (for-2020)5002 History and Philosophy Of Specific Fields (for-2020)Stem Cell Research (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell - Human (rcdc)Biotechnology (rcdc)Regenerative Medicine (rcdc)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/78f1w3s7https://escholarship.org/content/qt78f1w3s7/qt78f1w3s7.pdfinfo:doi/10.1073/pnas.2600791123articleProceedings of the National Academy of Sciences of the United States of America, vol 123, iss 10e2600791123oai:escholarship.org:ark:/13030/qt9pr0595n2026-03-02T19:06:07Zqt9pr0595nComprehensive analysis of single cell ATAC-seq data with SnapATACFang, RongxinPreissl, SebastianLi, YangHou, XiaomengLucero, JacintaWang, XinxinMotamedi, AmirShiau, Andrew KZhou, XinzhuXie, FangmingMukamel, Eran AZhang, KaiZhang, YanxiaoBehrens, M MargaritaEcker, Joseph RRen, Bing2021-01-01Identification of the cis-regulatory elements controlling cell-type specific gene expression patterns is essential for understanding the origin of cellular diversity. Conventional assays to map regulatory elements via open chromatin analysis of primary tissues is hindered by sample heterogeneity. Single cell analysis of accessible chromatin (scATAC-seq) can overcome this limitation. However, the high-level noise of each single cell profile and the large volume of data pose unique computational challenges. Here, we introduce SnapATAC, a software package for analyzing scATAC-seq datasets. SnapATAC dissects cellular heterogeneity in an unbiased manner and map the trajectories of cellular states. Using the Nyström method, SnapATAC can process data from up to a million cells. Furthermore, SnapATAC incorporates existing tools into a comprehensive package for analyzing single cell ATAC-seq dataset. As demonstration of its utility, SnapATAC is applied to 55,592 single-nucleus ATAC-seq profiles from the mouse secondary motor cortex. The analysis reveals ~370,000 candidate regulatory elements in 31 distinct cell populations in this brain region and inferred candidate cell-type specific transcriptional regulators.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)3105 Genetics (for-2020)Genetics (rcdc)Human Genome (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Animals (mesh)Chromatin (mesh)Chromatin Immunoprecipitation Sequencing (mesh)Computational Biology (mesh)Epigenomics (mesh)Male (mesh)Mice (mesh)MiceInbred C57BL (mesh)Motor Cortex (mesh)Sequence AnalysisDNA (mesh)Single-Cell Analysis (mesh)Motor Cortex (mesh)Chromatin (mesh)Animals (mesh)MiceInbred C57BL (mesh)Mice (mesh)Sequence AnalysisDNA (mesh)Computational Biology (mesh)Male (mesh)Epigenomics (mesh)Single-Cell Analysis (mesh)Chromatin Immunoprecipitation Sequencing (mesh)Animals (mesh)Chromatin (mesh)Chromatin Immunoprecipitation Sequencing (mesh)Computational Biology (mesh)Epigenomics (mesh)Male (mesh)Mice (mesh)MiceInbred C57BL (mesh)Motor Cortex (mesh)Sequence AnalysisDNA (mesh)Single-Cell Analysis (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/9pr0595nhttps://escholarship.org/content/qt9pr0595n/qt9pr0595n.pdfinfo:doi/10.1038/s41467-021-21583-9articleNature Communications, vol 12, iss 11337oai:escholarship.org:ark:/13030/qt7vp3j2wn2026-03-02T16:20:58Zqt7vp3j2wnThe expanding amyloid family: Structure, stability, function, and pathogenesisSawaya, Michael RHughes, Michael PRodriguez, Jose ARiek, RolandEisenberg, David S2021-09-01The hidden world of amyloid biology has suddenly snapped into atomic-level focus, revealing over 80 amyloid protein fibrils, both pathogenic and functional. Unlike globular proteins, amyloid proteins flatten and stack into unbranched fibrils. Stranger still, a single protein sequence can adopt wildly different two-dimensional conformations, yielding distinct fibril polymorphs. Thus, an amyloid protein may define distinct diseases depending on its conformation. At the heart of this conformational variability lies structural frustrations. In functional amyloids, evolution tunes frustration levels to achieve either stability or sensitivity according to the fibril's biological function, accounting for the vast versatility of the amyloid fibril scaffold.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Acquired Cognitive Impairment (rcdc)Neurodegenerative (rcdc)Dementia (rcdc)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)Brain Disorders (rcdc)Neurosciences (rcdc)Aging (rcdc)Alzheimer's Disease (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Amyloidogenic Proteins (mesh)Animals (mesh)Disease (mesh)EvolutionMolecular (mesh)Humans (mesh)PolymorphismGenetic (mesh)Protein Folding (mesh)Protein Stability (mesh)Animals (mesh)Humans (mesh)Disease (mesh)EvolutionMolecular (mesh)Protein Folding (mesh)PolymorphismGenetic (mesh)Protein Stability (mesh)Amyloidogenic Proteins (mesh)Amyloidogenic Proteins (mesh)Animals (mesh)Disease (mesh)EvolutionMolecular (mesh)Humans (mesh)PolymorphismGenetic (mesh)Protein Folding (mesh)Protein Stability (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7vp3j2wnhttps://escholarship.org/content/qt7vp3j2wn/qt7vp3j2wn.pdfinfo:doi/10.1016/j.cell.2021.08.013articleCell, vol 184, iss 194857 - 4873oai:escholarship.org:ark:/13030/qt0q46x1dm2026-03-02T15:12:59Zqt0q46x1dmAccurate design of megadalton-scale two-component icosahedral protein complexesBale, Jacob BGonen, ShaneLiu, YuxiSheffler, WilliamEllis, DanielThomas, ChantzCascio, DuilioYeates, Todd OGonen, TamirKing, Neil PBaker, David2016-07-22Nature provides many examples of self- and co-assembling protein-based molecular machines, including icosahedral protein cages that serve as scaffolds, enzymes, and compartments for essential biochemical reactions and icosahedral virus capsids, which encapsidate and protect viral genomes and mediate entry into host cells. Inspired by these natural materials, we report the computational design and experimental characterization of co-assembling, two-component, 120-subunit icosahedral protein nanostructures with molecular weights (1.8 to 2.8 megadaltons) and dimensions (24 to 40 nanometers in diameter) comparable to those of small viral capsids. Electron microscopy, small-angle x-ray scattering, and x-ray crystallography show that 10 designs spanning three distinct icosahedral architectures form materials closely matching the design models. In vitro assembly of icosahedral complexes from independently purified components occurs rapidly, at rates comparable to those of viral capsids, and enables controlled packaging of molecular cargo through charge complementarity. The ability to design megadalton-scale materials with atomic-level accuracy and controllable assembly opens the door to a new generation of genetically programmable protein-based molecular machines.Macromolecular and Materials ChemistryChemical SciencesInfectious DiseasesGeneric health relevanceCapsidCrystallographyX-RayGenomeViralMicroscopyElectronModelsMolecularMolecular WeightMultiprotein ComplexesNanostructuresProtein EngineeringProtein SubunitsScatteringSmall AngleViral ProteinsX-Ray DiffractionGeneral Science & Technologyapplication/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0q46x1dmhttps://escholarship.org/content/qt0q46x1dm/qt0q46x1dm.pdfinfo:doi/10.1126/science.aaf8818articleScience, vol 353, iss 6297389 - 394oai:escholarship.org:ark:/13030/qt1qk3t54m2026-03-02T14:30:20Zqt1qk3t54mAn Updated Structure of Oxybutynin HydrochlorideLin, JieyeBu, GuanhongUnge, JohanGonen, Tamir2024-10-01Oxybutynin (Ditropan), a widely distributed muscarinic antagonist for treating the overactive bladder, has been awaiting a definitive crystal structure for ≈50 years due to the sample and technique limitations. Past reports used powder X-ray diffraction (PXRD) to shed light on the possible packing of the molecule however their model showed some inconsistencies when compared with the 2D chemical structure. These are largely attributed to X-ray-induced photoreduction. Here microcrystal electron diffraction (MicroED) is used to successfully unveil the experimental 3D structure of oxybutynin hydrochloride showing marked improvement over the reported PXRD structure. Using the improved model, molecular docking is applied to investigate the binding mechanism between M3 muscarinic receptor (M3R) and (R)-oxybutynin, revealing essential contacts/residues and conformational changes within the protein pocket. A possible universal conformation is proposed for M3R antagonists, which is valuable for future drug development and optimization. This study underscores the immense potential of MicroED as a complementary technique for elucidating unknown pharmaceutical structures, as well as for protein-drug interactions.3101 Biochemistry and Cell Biology (for-2020)34 Chemical Sciences (for-2020)31 Biological Sciences (for-2020)5.1 Pharmaceuticals (hrcs-rac)Generic health relevance (hrcs-hc)Mandelic Acids (mesh)Molecular Docking Simulation (mesh)Muscarinic Antagonists (mesh)X-Ray Diffraction (mesh)ModelsMolecular (mesh)ReceptorMuscarinic M3 (mesh)microcrystal electron diffraction (MicroED)molecular dockingoxybutynin (Ditropan)protein-drug interactionsracemic crystalMandelic Acids (mesh)ReceptorMuscarinic M3 (mesh)Muscarinic Antagonists (mesh)X-Ray Diffraction (mesh)ModelsMolecular (mesh)Molecular Docking Simulation (mesh)microcrystal electron diffraction (MicroED)molecular dockingoxybutynin (Ditropan)protein‐drug interactionsracemic crystalMandelic Acids (mesh)Molecular Docking Simulation (mesh)Muscarinic Antagonists (mesh)X-Ray Diffraction (mesh)ModelsMolecular (mesh)ReceptorMuscarinic M3 (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/1qk3t54mhttps://escholarship.org/content/qt1qk3t54m/qt1qk3t54m.pdfinfo:doi/10.1002/advs.202406494articleAdvanced Science, vol 11, iss 402406494oai:escholarship.org:ark:/13030/qt2ct9q1382026-03-02T14:20:53Zqt2ct9q138Characterization of Molecular Tweezer Binding on α‑Synuclein with Native Top-Down Mass Spectrometry and Ion Mobility-Mass Spectrometry Reveals a Mechanism for Aggregation InhibitionLantz, CarterLopez, JaybreeGoring, Andrew KZenaidee, Muhammad ABiggs, KarlWhitelegge, Julian PLoo, Rachel R OgorzalekKlärner, Frank-GerritSchrader, ThomasBitan, GalLoo, Joseph A2023-12-06Parkinson's disease, a neurodegenerative disease that affects 15 million people worldwide, is characterized by deposition of α-synuclein into Lewy Bodies in brain neurons. Although this disease is prevalent worldwide, a therapy or cure has yet to be found. Several small compounds have been reported to disrupt fibril formation. Among these compounds is a molecular tweezer known as CLR01 that targets lysine and arginine residues. This study aims to characterize how CLR01 interacts with various proteoforms of α-synuclein and how the structure of α-synuclein is subsequently altered. Native mass spectrometry (nMS) measurements of α-synuclein/CLR01 complexes reveal that multiple CLR01 molecules can bind to α-synuclein proteoforms such as α-synuclein phosphorylated at Ser-129 and α-synuclein bound with copper and manganese ions. The binding of one CLR01 molecule shifts the ability for α-synuclein to bind other ligands. Electron capture dissociation (ECD) with Fourier transform-ion cyclotron resonance (FT-ICR) top-down (TD) mass spectrometry of α-synuclein/CLR01 complexes pinpoints the locations of the modifications on each proteoform and reveals that CLR01 binds to the N-terminal region of α-synuclein. CLR01 binding compacts the gas-phase structure of α-synuclein, as shown by ion mobility-mass spectrometry (IM-MS). These data suggest that when multiple CLR01 molecules bind, the N-terminus of α-synuclein shifts toward a more compact state. This compaction suggests a mechanism for CLR01 halting the formation of oligomers and fibrils involved in many neurodegenerative diseases.3401 Analytical Chemistry (for-2020)34 Chemical Sciences (for-2020)3406 Physical Chemistry (for-2020)Aging (rcdc)Bioengineering (rcdc)Parkinson's Disease (rcdc)Neurosciences (rcdc)Neurodegenerative (rcdc)Brain Disorders (rcdc)Dementia (rcdc)Acquired Cognitive Impairment (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Neurological (hrcs-hc)Humans (mesh)alpha-Synuclein (mesh)Neurodegenerative Diseases (mesh)Mass Spectrometry (mesh)Parkinson Disease (mesh)Brain (mesh)Native Mass SpectrometryTop-Down Mass SpectrometryIon-Mobility Mass SpectrometryProteoformalpha-SynucleinBrain (mesh)Humans (mesh)Parkinson Disease (mesh)Neurodegenerative Diseases (mesh)alpha-Synuclein (mesh)Mass Spectrometry (mesh)Ion-Mobility Mass SpectrometryNative Mass SpectrometryProteoformTop-Down Mass Spectrometryα-SynucleinHumans (mesh)alpha-Synuclein (mesh)Neurodegenerative Diseases (mesh)Mass Spectrometry (mesh)Parkinson Disease (mesh)Brain (mesh)0301 Analytical Chemistry (for)0304 Medicinal and Biomolecular Chemistry (for)0306 Physical Chemistry (incl. Structural) (for)Analytical Chemistry (science-metrix)3401 Analytical chemistry (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2ct9q138https://escholarship.org/content/qt2ct9q138/qt2ct9q138.pdfinfo:doi/10.1021/jasms.3c00281articleJournal of The American Society for Mass Spectrometry, vol 34, iss 122739 - 2747oai:escholarship.org:ark:/13030/qt38x6955x2026-03-02T14:15:43Zqt38x6955xDetection of Lipid-Bound Bacteriorhodopsin Trimer Complex Directly from Purple Membrane by Native Mass SpectrometryLe, JessieLoo, Joseph A2023-12-06Native mass spectrometry (MS) was used to detect the membrane protein, bacteriorhodopsin (bR), in its 27 kDa monomeric form and trimeric assemblies directly from lipid-containing purple membranes (PMs) from the halophilic archaeon, Halobacterium salinarum. Trimer bR ion populations bound to lipid molecules were detected with n-octyl β-d-glucopyranoside as the solubilizing detergent; the use of octyl tetraethylene glycol monooctyl ether or n-dodecyl-β-d-maltopyranoside resulted in only detection of monomeric bR. The archaeal lipids phosphotidylglycerolphosphate methyl ester and 3-HSO3-Galp-β1,6-Manp-α1,2-Glcp-α1,1-sn-2,3-diphytanylglycerol were the only lipids in the PMs found to bind to bR, consistent with previous high-resolution structural studies. Removal of the lipids from the sample resulted in the detection of only the bR monomer, highlighting the importance of specific lipids for stabilizing the bR trimer. To the best of our knowledge, this is the first report of the detection of the bR trimer with resolved lipid-bound species by MS.3401 Analytical Chemistry (for-2020)34 Chemical Sciences (for-2020)3406 Physical Chemistry (for-2020)Purple Membrane (mesh)Bacteriorhodopsins (mesh)Halobacterium salinarum (mesh)Mass Spectrometry (mesh)Lipids (mesh)Purple Membrane (mesh)Halobacterium salinarum (mesh)Lipids (mesh)Bacteriorhodopsins (mesh)Mass Spectrometry (mesh)Purple Membrane (mesh)Bacteriorhodopsins (mesh)Halobacterium salinarum (mesh)Mass Spectrometry (mesh)Lipids (mesh)0301 Analytical Chemistry (for)0304 Medicinal and Biomolecular Chemistry (for)0306 Physical Chemistry (incl. Structural) (for)Analytical Chemistry (science-metrix)3401 Analytical chemistry (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/38x6955xhttps://escholarship.org/content/qt38x6955x/qt38x6955x.pdfinfo:doi/10.1021/jasms.3c00314articleJournal of The American Society for Mass Spectrometry, vol 34, iss 122620 - 2624oai:escholarship.org:ark:/13030/qt3n81k2qz2026-03-02T11:23:22Zqt3n81k2qzThe transcription factor NF-κB orchestrates nucleosome remodeling during the primary response to Toll-like receptor 4 signalingFeng, An-ChiehThomas, Brandon JPurbey, Prabhat Kde Melo, Filipe MenegattiLiu, XinDaly, Allison ESun, FeiLo, Jerry Hung-HaoCheng, LijingCarey, Michael FScumpia, Philip OSmale, Stephen T2024-03-01Inducible nucleosome remodeling at hundreds of latent enhancers and several promoters shapes the transcriptional response to Toll-like receptor 4 (TLR4) signaling in macrophages. We aimed to define the identities of the transcription factors that promote TLR-induced remodeling. An analysis strategy based on ATAC-seq and single-cell ATAC-seq that enriched for genomic regions most likely to undergo remodeling revealed that the transcription factor nuclear factor κB (NF-κB) bound to all high-confidence peaks marking remodeling during the primary response to the TLR4 ligand, lipid A. Deletion of NF-κB subunits RelA and c-Rel resulted in the loss of remodeling at high-confidence ATAC-seq peaks, and CRISPR-Cas9 mutagenesis of NF-κB-binding motifs impaired remodeling. Remodeling selectivity at defined regions was conferred by collaboration with other inducible factors, including IRF3- and MAP-kinase-induced factors. Thus, NF-κB is unique among TLR4-activated transcription factors in its broad contribution to inducible nucleosome remodeling, alongside its ability to activate poised enhancers and promoters assembled into open chromatin.32 Biomedical and Clinical Sciences (for-2020)3204 Immunology (for-2020)Human Genome (rcdc)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)NF-kappa B (mesh)Toll-Like Receptor 4 (mesh)Nucleosomes (mesh)Signal Transduction (mesh)Gene Expression Regulation (mesh)Transcription Factor RelA (mesh)Nucleosomes (mesh)NF-kappa B (mesh)Signal Transduction (mesh)Gene Expression Regulation (mesh)Toll-Like Receptor 4 (mesh)Transcription Factor RelA (mesh)IRF3NF-κBchromatinmacrophagesnucleosome remodelingtranscriptionNF-kappa B (mesh)Toll-Like Receptor 4 (mesh)Nucleosomes (mesh)Signal Transduction (mesh)Gene Expression Regulation (mesh)Transcription Factor RelA (mesh)1107 Immunology (for)Immunology (science-metrix)3204 Immunology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/3n81k2qzhttps://escholarship.org/content/qt3n81k2qz/qt3n81k2qz.pdfinfo:doi/10.1016/j.immuni.2024.02.004articleImmunity, vol 57, iss 3462 - 477.e9oai:escholarship.org:ark:/13030/qt3bn8q7tk2026-01-25T02:23:58Zqt3bn8q7tkDNA methylation networks underlying mammalian traitsHaghani, AminLi, Caesar ZRobeck, Todd RZhang, JoshuaLu, Ake TAblaeva, JuliaAcosta-Rodríguez, Victoria AAdams, Danielle MAlagaili, Abdulaziz NAlmunia, JavierAloysius, AjoyAmor, Nabil MSArdehali, RezaArneson, AdrianaBaker, C ScottBanks, GarethBelov, KatherineBennett, Nigel CBlack, PeterBlumstein, Daniel TBors, Eleanor KBreeze, Charles EBrooke, Robert TBrown, Janine LCarter, GeraldCaulton, AlexCavin, Julie MChakrabarti, LisaChatzistamou, IouliaChavez, Andreas SChen, HaoCheng, KaiyangChiavellini, PriscilaChoi, Oi-WaClarke, ShannonCook, Joseph ACooper, Lisa NCossette, Marie-LaurenceDay, JoannaDeYoung, JosephDirocco, StacyDold, ChristopherDunnum, Jonathan LEhmke, Erin EEmmons, Candice KEmmrich, StephanErbay, EbruErlacher-Reid, ClaireFaulkes, Chris GFei, ZheFerguson, Steven HFinno, Carrie JFlower, Jennifer EGaillard, Jean-MichelGarde, EvaGerber, LiviaGladyshev, Vadim NGoya, Rodolfo GGrant, Matthew JGreen, Carla BHanson, M BradleyHart, Daniel WHaulena, MartinHerrick, KelseyHogan, Andrew NHogg, Carolyn JHore, Timothy AHuang, TaoshengIzpisua Belmonte, Juan CarlosJasinska, Anna JJones, GarethJourdain, EveKashpur, OlgaKatcher, HaroldKatsumata, EtsukoKaza, VimalaKiaris, HippokratisKobor, Michael SKordowitzki, PawelKoski, William RKrützen, MichaelKwon, Soo BinLarison, BrendaLee, Sang-GooLehmann, MarianneLemaître, Jean-FrançoisLevine, Andrew JLi, XinminLi, CunLim, Andrea RLin, David TSLindemann, Dana MLiphardt, Schuyler WLittle, Thomas JMacoretta, NicholasMaddox, DeweyMatkin, Craig OMattison, Julie AMcClure, MatthewMergl, June2023-08-11Using DNA methylation profiles (n = 15,456) from 348 mammalian species, we constructed phyloepigenetic trees that bear marked similarities to traditional phylogenetic ones. Using unsupervised clustering across all samples, we identified 55 distinct cytosine modules, of which 30 are related to traits such as maximum life span, adult weight, age, sex, and human mortality risk. Maximum life span is associated with methylation levels in HOXL subclass homeobox genes and developmental processes and is potentially regulated by pluripotency transcription factors. The methylation state of some modules responds to perturbations such as caloric restriction, ablation of growth hormone receptors, consumption of high-fat diets, and expression of Yamanaka factors. This study reveals an intertwined evolution of the genome and epigenome that mediates the biological characteristics and traits of different mammalian species.31 Biological Sciences (for-2020)3105 Genetics (for-2020)Human Genome (rcdc)Genetics (rcdc)Aging (rcdc)Generic health relevance (hrcs-hc)Adult (mesh)Animals (mesh)Humans (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Epigenome (mesh)Genome (mesh)Mammals (mesh)Phylogeny (mesh)Animals (mesh)Mammals (mesh)Humans (mesh)Phylogeny (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Genome (mesh)Adult (mesh)Epigenome (mesh)Adult (mesh)Animals (mesh)Humans (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Epigenome (mesh)Genome (mesh)Mammals (mesh)Phylogeny (mesh)General Science & Technology (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3bn8q7tkhttps://escholarship.org/content/qt3bn8q7tk/qt3bn8q7tk.pdfinfo:doi/10.1126/science.abq5693articleScience, vol 381, iss 6658eabq5693oai:escholarship.org:ark:/13030/qt7z52x8272026-01-23T20:08:36Zqt7z52x827Author Correction: Universal DNA methylation age across mammalian tissuesLu, ATFei, ZHaghani, ARobeck, TRZoller, JALi, CZLowe, RYan, QZhang, JVu, HAblaeva, JAcosta-Rodriguez, VAAdams, DMAlmunia, JAloysius, AArdehali, RArneson, ABaker, CSBanks, GBelov, KBennett, NCBlack, PBlumstein, DTBors, EKBreeze, CEBrooke, RTBrown, JLCarter, GGCaulton, ACavin, JMChakrabarti, LChatzistamou, IChen, HCheng, KChiavellini, PChoi, OWClarke, SMCooper, LNCossette, MLDay, JDeYoung, JDiRocco, SDold, CEhmke, EEEmmons, CKEmmrich, SErbay, EErlacher-Reid, CFaulkes, CGFerguson, SHFinno, CJFlower, JEGaillard, JMGarde, EGerber, LGladyshev, VNGorbunova, VGoya, RGGrant, MJGreen, CBHales, ENHanson, MBHart, DWHaulena, MHerrick, KHogan, ANHogg, CJHore, TAHuang, TIzpisua Belmonte, JCJasinska, AJJones, GJourdain, EKashpur, OKatcher, HKatsumata, EKaza, VKiaris, HKobor, MSKordowitzki, PKoski, WRKrützen, MKwon, SBLarison, BLee, SGLehmann, MLemaitre, JFLevine, AJLi, CLi, XLim, ARLin, DTSLindemann, DMLittle, TJMacoretta, NMaddox, DMatkin, COMattison, JAMcClure, MMergl, J2023-11-01Correction to: Nature Aging, published online 10 August 2023. In the version of Supplementary Data initially published with this article, data were missing from Table S1.13 (Updated AnAge version in Class Mammalia), which now appear in an updated Supplementary Data file in the online version of the article.32 Biomedical and Clinical Sciences (for-2020)3202 Clinical Sciences (for-2020)3202 Clinical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/7z52x827https://escholarship.org/content/qt7z52x827/qt7z52x827.pdfinfo:doi/10.1038/s43587-023-00499-7articleNature Aging, vol 3, iss 111462 - 1462oai:escholarship.org:ark:/13030/qt5jw702382026-01-23T20:08:31Zqt5jw70238Universal DNA methylation age across mammalian tissuesLu, ATFei, ZHaghani, ARobeck, TRZoller, JALi, CZLowe, RYan, QZhang, JVu, HAblaeva, JAcosta-Rodriguez, VAAdams, DMAlmunia, JAloysius, AArdehali, RArneson, ABaker, CSBanks, GBelov, KBennett, NCBlack, PBlumstein, DTBors, EKBreeze, CEBrooke, RTBrown, JLCarter, GGCaulton, ACavin, JMChakrabarti, LChatzistamou, IChen, HCheng, KChiavellini, PChoi, OWClarke, SMCooper, LNCossette, MLDay, JDeYoung, JDiRocco, SDold, CEhmke, EEEmmons, CKEmmrich, SErbay, EErlacher-Reid, CFaulkes, CGFerguson, SHFinno, CJFlower, JEGaillard, JMGarde, EGerber, LGladyshev, VNGorbunova, VGoya, RGGrant, MJGreen, CBHales, ENHanson, MBHart, DWHaulena, MHerrick, KHogan, ANHogg, CJHore, TAHuang, TIzpisua Belmonte, JCJasinska, AJJones, GJourdain, EKashpur, OKatcher, HKatsumata, EKaza, VKiaris, HKobor, MSKordowitzki, PKoski, WRKrützen, MKwon, SBLarison, BLee, SGLehmann, MLemaitre, JFLevine, AJLi, CLi, XLim, ARLin, DTSLindemann, DMLittle, TJMacoretta, NMaddox, DMatkin, COMattison, JAMcClure, MMergl, J2023-09-01Aging, often considered a result of random cellular damage, can be accurately estimated using DNA methylation profiles, the foundation of pan-tissue epigenetic clocks. Here, we demonstrate the development of universal pan-mammalian clocks, using 11,754 methylation arrays from our Mammalian Methylation Consortium, which encompass 59 tissue types across 185 mammalian species. These predictive models estimate mammalian tissue age with high accuracy (r > 0.96). Age deviations correlate with human mortality risk, mouse somatotropic axis mutations and caloric restriction. We identified specific cytosines with methylation levels that change with age across numerous species. These sites, highly enriched in polycomb repressive complex 2-binding locations, are near genes implicated in mammalian development, cancer, obesity and longevity. Our findings offer new evidence suggesting that aging is evolutionarily conserved and intertwined with developmental processes across all mammals.32 Biomedical and Clinical Sciences (for-2020)3202 Clinical Sciences (for-2020)Genetics (rcdc)Aging (rcdc)Generic health relevance (hrcs-hc)Humans (mesh)Mice (mesh)Animals (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Aging (mesh)Longevity (mesh)Mammals (mesh)Animals (mesh)Mammals (mesh)Humans (mesh)Mice (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Aging (mesh)Longevity (mesh)Humans (mesh)Mice (mesh)Animals (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Aging (mesh)Longevity (mesh)Mammals (mesh)3202 Clinical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/5jw70238https://escholarship.org/content/qt5jw70238/qt5jw70238.pdfinfo:doi/10.1038/s43587-023-00462-6articleNature Aging, vol 3, iss 91144 - 1166oai:escholarship.org:ark:/13030/qt0dg0x3wj2026-01-22T18:35:26Zqt0dg0x3wjDeep-coverage whole genome sequences and blood lipids among 16,324 individualsNatarajan, PradeepPeloso, Gina MZekavat, Seyedeh MaryamMontasser, MayGanna, AndreaChaffin, MarkKhera, Amit VZhou, WeiBloom, Jonathan MEngreitz, Jesse MErnst, JasonO’Connell, Jeffrey RRuotsalainen, Sanni EAlver, MarisManichaikul, AniJohnson, W CraigPerry, James APoterba, TimothySeed, CottonSurakka, Ida LEsko, TonuRipatti, SamuliSalomaa, VeikkoCorrea, AdolfoVasan, Ramachandran SKellis, ManolisNeale, Benjamin MLander, Eric SAbecasis, GoncaloMitchell, BraxtonRich, Stephen SWilson, James GCupples, L AdrienneRotter, Jerome IWiller, Cristen JKathiresan, SekarNHLBI TOPMed Lipids Working Group2018-01-01Large-scale deep-coverage whole-genome sequencing (WGS) is now feasible and offers potential advantages for locus discovery. We perform WGS in 16,324 participants from four ancestries at mean depth >29X and analyze genotypes with four quantitative traits—plasma total cholesterol, low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol, and triglycerides. Common variant association yields known loci except for few variants previously poorly imputed. Rare coding variant association yields known Mendelian dyslipidemia genes but rare non-coding variant association detects no signals. A high 2M-SNP LDL-C polygenic score (top 5th percentile) confers similar effect size to a monogenic mutation (~30 mg/dl higher for each); however, among those with severe hypercholesterolemia, 23% have a high polygenic score and only 2% carry a monogenic mutation. At these sample sizes and for these phenotypes, the incremental value of WGS for discovery is limited but WGS permits simultaneous assessment of monogenic and polygenic models to severe hypercholesterolemia.4202 Epidemiology (for-2020)31 Biological Sciences (for-2020)42 Health Sciences (for-2020)3105 Genetics (for-2020)Human Genome (rcdc)Cardiovascular (rcdc)Biotechnology (rcdc)Atherosclerosis (rcdc)Genetics (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Cardiovascular (hrcs-hc)Base Sequence (mesh)CholesterolLDL (mesh)Gene Frequency (mesh)GenomeHuman (mesh)Genome-Wide Association Study (mesh)High-Throughput Nucleotide Sequencing (mesh)Humans (mesh)Lipids (mesh)ModelsGenetic (mesh)Mutation (mesh)NHLBI TOPMed Lipids Working GroupHumans (mesh)Lipids (mesh)Base Sequence (mesh)Gene Frequency (mesh)Mutation (mesh)GenomeHuman (mesh)ModelsGenetic (mesh)CholesterolLDL (mesh)Genome-Wide Association Study (mesh)High-Throughput Nucleotide Sequencing (mesh)Base Sequence (mesh)CholesterolLDL (mesh)Gene Frequency (mesh)GenomeHuman (mesh)Genome-Wide Association Study (mesh)High-Throughput Nucleotide Sequencing (mesh)Humans (mesh)Lipids (mesh)ModelsGenetic (mesh)Mutation (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/0dg0x3wjhttps://escholarship.org/content/qt0dg0x3wj/qt0dg0x3wj.pdfinfo:doi/10.1038/s41467-018-05747-8articleNature Communications, vol 9, iss 13391oai:escholarship.org:ark:/13030/qt4cz3d7122026-01-20T18:10:20Zqt4cz3d712Cryo-EM structures of the D290V mutant of the hnRNPA2 low-complexity domain suggests how D290V affects phase separation and aggregationLu, JiahuiGe, PengSawaya, Michael RHughes, Michael PBoyer, David RCao, QinAbskharon, RomanyCascio, DuilioTayeb-Fligelman, EinavEisenberg, David S2024-02-01Heterogeneous nuclear ribonucleoprotein A2 (hnRNPA2) is a human ribonucleoprotein that transports RNA to designated locations for translation via its ability to phase separate. Its mutated form, D290V, is implicated in multisystem proteinopathy known to afflict two families, mainly with myopathy and Paget's disease of bone. Here, we investigate this mutant form of hnRNPA2 by determining cryo-EM structures of the recombinant D290V low complexity domain. We find that the mutant form of hnRNPA2 differs from the WT fibrils in four ways. In contrast to the WT fibrils, the PY-nuclear localization signals in the fibril cores of all three mutant polymorphs are less accessible to chaperones. Also, the mutant fibrils are more stable than WT fibrils as judged by phase separation, thermal stability, and energetic calculations. Similar to other pathogenic amyloids, the mutant fibrils are polymorphic. Thus, these structures offer evidence to explain how a D-to-V missense mutation diverts the assembly of reversible, functional amyloid-like fibrils into the assembly of pathogenic amyloid, and may shed light on analogous conversions occurring in other ribonucleoproteins that lead to neurological diseases such as amyotrophic lateral sclerosis and frontotemporal dementia.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Neurosciences (rcdc)Rare Diseases (rcdc)Brain Disorders (rcdc)Aging (rcdc)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)Dementia (rcdc)Neurodegenerative (rcdc)Acquired Cognitive Impairment (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Neurological (hrcs-hc)Humans (mesh)Cryoelectron Microscopy (mesh)Phase Separation (mesh)Protein Domains (mesh)Mutation (mesh)Hydrogen-Ion Concentration (mesh)ModelsMolecular (mesh)Protein Stability (mesh)Protein StructureTertiary (mesh)Heterogeneous-Nuclear Ribonucleoprotein Group A-B (mesh)Humans (mesh)Heterogeneous-Nuclear Ribonucleoprotein Group A-B (mesh)Cryoelectron Microscopy (mesh)Protein StructureTertiary (mesh)Mutation (mesh)Hydrogen-Ion Concentration (mesh)ModelsMolecular (mesh)Protein Stability (mesh)Protein Domains (mesh)Phase Separation (mesh)Alzheimer's diseaseLARKSamyloidcondensatecryoEMlow complexity domainmembraneless organellemultisystem proteinopathynuclear localization signalphase separationpolymorphprotein aggregationribonucleoprotein A2Humans (mesh)Cryoelectron Microscopy (mesh)Phase Separation (mesh)Protein Domains (mesh)Mutation (mesh)Hydrogen-Ion Concentration (mesh)ModelsMolecular (mesh)Protein Stability (mesh)Protein StructureTertiary (mesh)Heterogeneous-Nuclear Ribonucleoprotein Group A-B (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biochemistry & Molecular Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/4cz3d712https://escholarship.org/content/qt4cz3d712/qt4cz3d712.pdfinfo:doi/10.1016/j.jbc.2023.105531articleJournal of Biological Chemistry, vol 300, iss 2105531oai:escholarship.org:ark:/13030/qt0hc7t5dm2026-01-20T09:55:05Zqt0hc7t5dmAmyloid fibrils in FTLD-TDP are composed of TMEM106B and not TDP-43Jiang, Yi XiaoCao, QinSawaya, Michael RAbskharon, RomanyGe, PengDeTure, MichaelDickson, Dennis WFu, Janine YOgorzalek Loo, Rachel RLoo, Joseph AEisenberg, David S2022-05-12Frontotemporal lobar degeneration (FTLD) is the third most common neurodegenerative condition after Alzheimer’s and Parkinson’s diseases1. FTLD typically presents in 45 to 64 year olds with behavioural changes or progressive decline of language skills2. The subtype FTLD-TDP is characterized by certain clinical symptoms and pathological neuronal inclusions with TAR DNA-binding protein (TDP-43) immunoreactivity3. Here we extracted amyloid fibrils from brains of four patients representing four of the five FTLD-TDP subclasses, and determined their structures by cryo-electron microscopy. Unexpectedly, all amyloid fibrils examined were composed of a 135-residue carboxy-terminal fragment of transmembrane protein 106B (TMEM106B), a lysosomal membrane protein previously implicated as a genetic risk factor for FTLD-TDP4. In addition to TMEM106B fibrils, we detected abundant non-fibrillar aggregated TDP-43 by immunogold labelling. Our observations confirm that FTLD-TDP is associated with amyloid fibrils, and that the fibrils are formed by TMEM106B rather than TDP-43.3101 Biochemistry and Cell Biology (for-2020)51 Physical Sciences (for-2020)31 Biological Sciences (for-2020)Aging (rcdc)Alzheimer's Disease (rcdc)Prevention (rcdc)Frontotemporal Dementia (FTD) (rcdc)Acquired Cognitive Impairment (rcdc)Brain Disorders (rcdc)Alzheimer's Disease Related Dementias (ADRD) (rcdc)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)Neurosciences (rcdc)Neurodegenerative (rcdc)Dementia (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Neurological (hrcs-hc)Amyloid (mesh)Cryoelectron Microscopy (mesh)DNA-Binding Proteins (mesh)Frontotemporal Lobar Degeneration (mesh)Humans (mesh)Membrane Proteins (mesh)Nerve Tissue Proteins (mesh)Humans (mesh)Amyloid (mesh)DNA-Binding Proteins (mesh)Membrane Proteins (mesh)Nerve Tissue Proteins (mesh)Cryoelectron Microscopy (mesh)Frontotemporal Lobar Degeneration (mesh)Amyloid (mesh)Cryoelectron Microscopy (mesh)DNA-Binding Proteins (mesh)Frontotemporal Lobar Degeneration (mesh)Humans (mesh)Membrane Proteins (mesh)Nerve Tissue Proteins (mesh)General Science & Technology (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0hc7t5dmhttps://escholarship.org/content/qt0hc7t5dm/qt0hc7t5dm.pdfinfo:doi/10.1038/s41586-022-04670-9articleNature, vol 605, iss 7909304 - 309oai:escholarship.org:ark:/13030/qt353610g52026-01-20T00:12:25Zqt353610g5Action of a minimal contractile bactericidal nanomachineGe, PengScholl, DeanProkhorov, Nikolai SAvaylon, JaycobShneider, Mikhail MBrowning, ChristopherButh, Sergey APlattner, MichelChakraborty, UrmiDing, KeLeiman, Petr GMiller, Jeff FZhou, Z Hong2020-04-30R-type bacteriocins are minimal contractile nanomachines that hold promise as precision antibiotics1–4. Each bactericidal complex uses a collar to bridge a hollow tube with a contractile sheath loaded in a metastable state by a baseplate scaffold1,2. Fine-tuning of such nucleic acid-free protein machines for precision medicine calls for an atomic description of the entire complex and contraction mechanism, which is not available from baseplate structures of the (DNA-containing) T4 bacteriophage5. Here we report the atomic model of the complete R2 pyocin in its pre-contraction and post-contraction states, each containing 384 subunits of 11 unique atomic models of 10 gene products. Comparison of these structures suggests the following sequence of events during pyocin contraction: tail fibres trigger lateral dissociation of baseplate triplexes; the dissociation then initiates a cascade of events leading to sheath contraction; and this contraction converts chemical energy into mechanical force to drive the iron-tipped tube across the bacterial cell surface, killing the bacterium.31 Biological Sciences (for-2020)34 Chemical Sciences (for-2020)3406 Physical Chemistry (for-2020)Genetics (rcdc)Bioengineering (rcdc)Bacteriophage T4 (mesh)Cryoelectron Microscopy (mesh)CrystallographyX-Ray (mesh)GenesBacterial (mesh)ModelsMolecular (mesh)Protein Subunits (mesh)Pseudomonas aeruginosa (mesh)Pyocins (mesh)Substrate Specificity (mesh)Type VI Secretion Systems (mesh)Pseudomonas aeruginosa (mesh)Bacteriophage T4 (mesh)Pyocins (mesh)Protein Subunits (mesh)Cryoelectron Microscopy (mesh)CrystallographyX-Ray (mesh)Substrate Specificity (mesh)GenesBacterial (mesh)ModelsMolecular (mesh)Type VI Secretion Systems (mesh)Bacteriophage T4 (mesh)Cryoelectron Microscopy (mesh)CrystallographyX-Ray (mesh)GenesBacterial (mesh)ModelsMolecular (mesh)Protein Subunits (mesh)Pseudomonas aeruginosa (mesh)Pyocins (mesh)Substrate Specificity (mesh)Type VI Secretion Systems (mesh)General Science & Technology (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/353610g5https://escholarship.org/content/qt353610g5/qt353610g5.pdfinfo:doi/10.1038/s41586-020-2186-zarticleNature, vol 580, iss 7805658 - 662oai:escholarship.org:ark:/13030/qt5bh746kp2026-01-20T00:11:05Zqt5bh746kpCryo-EM structure of a human prion fibril with a hydrophobic, protease-resistant coreGlynn, CalinaSawaya, Michael RGe, PengGallagher-Jones, MarcusShort, Connor WBowman, RonquiajahApostol, MarcinZhou, Z HongEisenberg, David SRodriguez, Jose A2020-05-01Self-templating assemblies of the human prion protein are clinically associated with transmissible spongiform encephalopathies. Here we present the cryo-EM structure of a denaturant- and protease-resistant fibril formed in vitro spontaneously by a 9.7-kDa unglycosylated fragment of the human prion protein. This human prion fibril contains two protofilaments intertwined with screw symmetry and linked by a tightly packed hydrophobic interface. Each protofilament consists of an extended beta arch formed by residues 106 to 145 of the prion protein, a hydrophobic and highly fibrillogenic disease-associated segment. Such structures of prion polymorphs serve as blueprints on which to evaluate the potential impact of sequence variants on prion disease.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Brain Disorders (rcdc)Transmissible Spongiform Encephalopathy (TSE) (rcdc)Emerging Infectious Diseases (rcdc)Neurodegenerative (rcdc)Rare Diseases (rcdc)Infectious Diseases (rcdc)Neurosciences (rcdc)Biodefense (rcdc)Amyloid (mesh)Animals (mesh)Cryoelectron Microscopy (mesh)CrystallographyX-Ray (mesh)Humans (mesh)Hydrophobic and Hydrophilic Interactions (mesh)Mammals (mesh)ModelsMolecular (mesh)Peptide Fragments (mesh)Peptide Hydrolases (mesh)Prion Diseases (mesh)Prions (mesh)Protein Stability (mesh)Recombinant Proteins (mesh)Animals (mesh)Mammals (mesh)Humans (mesh)Prion Diseases (mesh)Amyloid (mesh)Peptide Hydrolases (mesh)Peptide Fragments (mesh)Prions (mesh)Recombinant Proteins (mesh)Cryoelectron Microscopy (mesh)CrystallographyX-Ray (mesh)ModelsMolecular (mesh)Protein Stability (mesh)Hydrophobic and Hydrophilic Interactions (mesh)Amyloid (mesh)Animals (mesh)Cryoelectron Microscopy (mesh)CrystallographyX-Ray (mesh)Humans (mesh)Hydrophobic and Hydrophilic Interactions (mesh)Mammals (mesh)ModelsMolecular (mesh)Peptide Fragments (mesh)Peptide Hydrolases (mesh)Prion Diseases (mesh)Prions (mesh)Protein Stability (mesh)Recombinant Proteins (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biophysics (science-metrix)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5bh746kphttps://escholarship.org/content/qt5bh746kp/qt5bh746kp.pdfinfo:doi/10.1038/s41594-020-0403-yarticleNature Structural & Molecular Biology, vol 27, iss 5417 - 423oai:escholarship.org:ark:/13030/qt0bp4c3jz2026-01-19T21:19:17Zqt0bp4c3jzExpression-Based Cell Lineage Analysis in Drosophila Through a Course-Based Research Experience for Early UndergraduatesOlson, John MEvans, Cory JNgo, Kathy TKim, Hee JongNguyen, Joseph DuyGurley, Kayla GHTa, TrucPatel, VijayHan, LisaTruong-N, Khoa TLiang, LettyChu, Maggie KLam, HiuAhn, Hannah GBanerjee, Abhik KumarChoi, In YoungKelley, Ross GMoridzadeh, NaseemKhan, Awais MKhan, OmairLee, SzuyaoJohnson, Elizabeth BTigranyan, AnnieWang, JayGandhi, Anand DPadhiar, Manish MCalvopina, Joseph HarganSumra, KirandeepOu, KristyWu, Jessie CDickan, Joseph NAhmadi, Sabrena MAllen, Donald NMai, Van ThanhAnsari, SaifYeh, GeorgeYoon, EarlGon, KimberlyYu, John YHe, JohnnyZaretsky, Jesse MLee, Noemi EKuoy, EdwardPatananan, Alexander NSitz, DanielTran, PhuongThaoDo, Minh-TuAkhave, Samira JAlvarez, Silverio DAsem, BobbyAsem, NedaAzarian, Nicole ABabaesfahani, ArezouBahrami, AhmadBhamra, ManjeetBhargava, RaginiBhatia, RakeshBhatia, SubirBumacod, NicholasCaine, Jonathan JCaldwell, Thomas ACalica, Nicole ACalonico, Elise MChan, CarmanChan, Helen H-LChang, AlbertChang, ChiaenChang, DanielChang, Jennifer SCharania, NaumanChen, Jasmine YChen, KevinChen, LuChen, YuyuCheung, Derek JCheung, Jesse JChew, Jessica JChew, Nicole BChien, Cheng-An TonyChin, Alana MChin, Chee JiaCho, YounghoChou, Man TingChow, Ke-Huan KChu, CarolynChu, Derrick MChu, VirginiaChuang, KatherineChugh, Arunit SinghCubberly, Mark RDaniel, Michael GuillermoDatta, SangitaDhaliwal, RajDinh, JennyDixit, DhavalDowling, EmmylouFeng, MelindaFrom, Christopher MFurukawa, DaisukeGaddipati, Himaja2019-11-01A variety of genetic techniques have been devised to determine cell lineage relationships during tissue development. Some of these systems monitor cell lineages spatially and/or temporally without regard to gene expression by the cells, whereas others correlate gene expression with the lineage under study. The GAL4 Technique for Real-time and Clonal Expression (G-TRACE) system allows for rapid, fluorescent protein-based visualization of both current and past GAL4 expression patterns and is therefore amenable to genome-wide expression-based lineage screens. Here we describe the results from such a screen, performed by undergraduate students of the University of California, Los Angeles (UCLA) Undergraduate Research Consortium for Functional Genomics (URCFG) and high school summer scholars as part of a discovery-based education program. The results of the screen, which reveal novel expression-based lineage patterns within the brain, the imaginal disc epithelia, and the hematopoietic lymph gland, have been compiled into the G-TRACE Expression Database (GED), an online resource for use by the Drosophila research community. The impact of this discovery-based research experience on student learning gains was assessed independently and shown to be greater than that of similar programs conducted elsewhere. Furthermore, students participating in the URCFG showed considerably higher STEM retention rates than UCLA STEM students that did not participate in the URCFG, as well as STEM students nationwide.31 Biological Sciences (for-2020)3105 Genetics (for-2020)Human Genome (rcdc)Genetics (rcdc)Biotechnology (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Animals (mesh)Brain (mesh)Cell Lineage (mesh)Drosophila (mesh)Eye (mesh)Gene Expression (mesh)Lymphatic System (mesh)Research (mesh)Students (mesh)Universities (mesh)WingsAnimal (mesh)G-TRACEgene expressioneducationSTEMCUREEye (mesh)Brain (mesh)Lymphatic System (mesh)Animals (mesh)Drosophila (mesh)Gene Expression (mesh)Cell Lineage (mesh)Research (mesh)Students (mesh)Universities (mesh)WingsAnimal (mesh)CUREG-TRACESTEMeducationgene expressionAnimals (mesh)Brain (mesh)Cell Lineage (mesh)Drosophila (mesh)Eye (mesh)Gene Expression (mesh)Lymphatic System (mesh)Research (mesh)Students (mesh)Universities (mesh)WingsAnimal (mesh)0604 Genetics (for)3101 Biochemistry and cell biology (for-2020)3105 Genetics (for-2020)4905 Statistics (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/0bp4c3jzhttps://escholarship.org/content/qt0bp4c3jz/qt0bp4c3jz.pdfinfo:doi/10.1534/g3.119.400541articleG3: Genes, Genomes, Genetics, vol 9, iss 113791 - 3800oai:escholarship.org:ark:/13030/qt3v12v0142026-01-19T17:14:01Zqt3v12v014Atomic structure of the translation regulatory protein NS1 of bluetongue virusKerviel, AdelineGe, PengLai, MasonJih, JonathanBoyce, MarkZhang, XingZhou, Z HongRoy, Polly2019-05-01Bluetongue virus (BTV) non-structural protein 1 (NS1) regulates viral protein synthesis and exists as tubular and non-tubular forms in infected cells, but how tubules assemble and how protein synthesis is regulated are unknown. Here, we report near-atomic resolution structures of two NS1 tubular forms determined by cryo-electron microscopy. The two tubular forms are different helical assemblies of the same NS1 monomer, consisting of an amino-terminal foot, a head and body domains connected to an extended carboxy-terminal arm, which wraps atop the head domain of another NS1 subunit through hydrophobic interactions. Deletion of the C terminus prevents tubule formation but not viral replication, suggesting an active non-tubular form. Two zinc-finger-like motifs are present in each NS1 monomer, and tubules are disrupted by divalent cation chelation and restored by cation addition, including Zn2+, suggesting a regulatory role of divalent cations in tubule formation. In vitro luciferase assays show that the NS1 non-tubular form upregulates BTV mRNA translation, whereas zinc-finger disruption decreases viral mRNA translation, tubule formation and virus replication, confirming a functional role for the zinc-fingers. Thus, the non-tubular form of NS1 is sufficient for viral protein synthesis and infectious virus replication, and the regulatory mechanism involved operates through divalent cation-dependent conversion between the non-tubular and tubular forms.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)2.1 Biological and endogenous factors (hrcs-rac)3 Good Health and Well Being (sdg)Animals (mesh)Bluetongue (mesh)Bluetongue virus (mesh)Cell Line (mesh)Cricetinae (mesh)Protein Biosynthesis (mesh)Protein Domains (mesh)Viral Nonstructural Proteins (mesh)Virus Replication (mesh)Zinc (mesh)Zinc Fingers (mesh)Cell Line (mesh)Animals (mesh)Bluetongue virus (mesh)Bluetongue (mesh)Zinc (mesh)Viral Nonstructural Proteins (mesh)Virus Replication (mesh)Protein Biosynthesis (mesh)Zinc Fingers (mesh)Cricetinae (mesh)Protein Domains (mesh)Animals (mesh)Bluetongue (mesh)Bluetongue virus (mesh)Cell Line (mesh)Cricetinae (mesh)Protein Biosynthesis (mesh)Protein Domains (mesh)Viral Nonstructural Proteins (mesh)Virus Replication (mesh)Zinc (mesh)Zinc Fingers (mesh)0605 Microbiology (for)1108 Medical Microbiology (for)3107 Microbiology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3v12v014https://escholarship.org/content/qt3v12v014/qt3v12v014.pdfinfo:doi/10.1038/s41564-019-0369-xarticleNature Microbiology, vol 4, iss 5837 - 845oai:escholarship.org:ark:/13030/qt76f912gh2026-01-19T03:04:31Zqt76f912ghIn vivo genetic dissection of tumor growth and the Warburg effectWang, Cheng-WeiPurkayastha, ArunimaJones, Kevin TThaker, Shivani KBanerjee, Utpal2016-01-01A well-characterized metabolic landmark for aggressive cancers is the reprogramming from oxidative phosphorylation to aerobic glycolysis, referred to as the Warburg effect. Models mimicking this process are often incomplete due to genetic complexities of tumors and cell lines containing unmapped collaborating mutations. In order to establish a system where individual components of oncogenic signals and metabolic pathways can be readily elucidated, we induced a glycolytic tumor in the Drosophila wing imaginal disc by activating the oncogene PDGF/VEGF-receptor (Pvr). This causes activation of multiple oncogenic pathways including Ras, PI3K/Akt, Raf/ERK, Src and JNK. Together this network of genes stabilizes Hifα (Sima) that in turn, transcriptionally up-regulates many genes encoding glycolytic enzymes. Collectively, this network of genes also causes inhibition of pyruvate dehydrogenase (PDH) activity resulting in diminished ox-phos levels. The high ROS produced during this process functions as a feedback signal to consolidate this metabolic reprogramming.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Cancer (rcdc)Genetics (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Cancer (hrcs-hc)Animals (mesh)DNA-Binding Proteins (mesh)Disease ModelsAnimal (mesh)Drosophila (mesh)Drosophila Proteins (mesh)Gene Expression RegulationNeoplastic (mesh)Gene Regulatory Networks (mesh)Glycolysis (mesh)Neoplasms (mesh)Oxidative Phosphorylation (mesh)Pyruvate Dehydrogenase Complex (mesh)Animals (mesh)Drosophila (mesh)Neoplasms (mesh)Disease ModelsAnimal (mesh)Pyruvate Dehydrogenase Complex (mesh)DNA-Binding Proteins (mesh)Drosophila Proteins (mesh)Gene Expression RegulationNeoplastic (mesh)Oxidative Phosphorylation (mesh)Glycolysis (mesh)Gene Regulatory Networks (mesh)D. melanogasterLDHPvrcancercell biologydevelopmental biologyhypoxia-inducible factormetabolismstem cellswarburg effectAnimals (mesh)DNA-Binding Proteins (mesh)Disease ModelsAnimal (mesh)Drosophila (mesh)Drosophila Proteins (mesh)Gene Expression RegulationNeoplastic (mesh)Gene Regulatory Networks (mesh)Glycolysis (mesh)Neoplasms (mesh)Oxidative Phosphorylation (mesh)Pyruvate Dehydrogenase Complex (mesh)0601 Biochemistry and Cell Biology (for)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/76f912ghhttps://escholarship.org/content/qt76f912gh/qt76f912gh.pdfinfo:doi/10.7554/elife.18126articleeLife, vol 5, iss Septembere18126oai:escholarship.org:ark:/13030/qt1gq577rg2026-01-18T14:16:51Zqt1gq577rgAtomic structures of a bactericidal contractile nanotube in its pre- and postcontraction statesGe, PengScholl, DeanLeiman, Petr GYu, XuekuiMiller, Jeff FZhou, Z Hong2015-05-01Cryo-EM structures of the pre- and postcontraction states of Pseudomonas aeruginosa R-type pyocins provide details of the conformational changes between the tube and sheath that take place during contraction.3207 Medical Microbiology (for-2020)32 Biomedical and Clinical Sciences (for-2020)Anti-Bacterial Agents (mesh)Bacterial Proteins (mesh)Bacterial Secretion Systems (mesh)Bacteriophages (mesh)Cell Membrane (mesh)Contractile Proteins (mesh)CrystallographyX-Ray (mesh)MicroscopyElectron (mesh)ModelsMolecular (mesh)Nanotubes (mesh)Protein StructureSecondary (mesh)Pseudomonas aeruginosa (mesh)Pyocins (mesh)Cell Membrane (mesh)Pseudomonas aeruginosa (mesh)Bacteriophages (mesh)Bacterial Proteins (mesh)Pyocins (mesh)Contractile Proteins (mesh)Anti-Bacterial Agents (mesh)MicroscopyElectron (mesh)CrystallographyX-Ray (mesh)Protein StructureSecondary (mesh)ModelsMolecular (mesh)Nanotubes (mesh)Bacterial Secretion Systems (mesh)Anti-Bacterial Agents (mesh)Bacterial Proteins (mesh)Bacterial Secretion Systems (mesh)Bacteriophages (mesh)Cell Membrane (mesh)Contractile Proteins (mesh)CrystallographyX-Ray (mesh)MicroscopyElectron (mesh)ModelsMolecular (mesh)Nanotubes (mesh)Protein StructureSecondary (mesh)Pseudomonas aeruginosa (mesh)Pyocins (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biophysics (science-metrix)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1gq577rghttps://escholarship.org/content/qt1gq577rg/qt1gq577rg.pdfinfo:doi/10.1038/nsmb.2995articleNature Structural & Molecular Biology, vol 22, iss 5377 - 382oai:escholarship.org:ark:/13030/qt5vm7444q2026-01-18T14:00:36Zqt5vm7444qAtomic Structure of T6SS Reveals Interlaced Array Essential to FunctionClemens, Daniel LGe, PengLee, Bai-YuHorwitz, Marcus AZhou, Z Hong2015-02-01Type VI secretion systems (T6SSs) are newly identified contractile nanomachines that translocate effector proteins across bacterial membranes. The Francisella pathogenicity island, required for bacterial phagosome escape, intracellular replication, and virulence, was presumed to encode a T6SS-like apparatus. Here, we experimentally confirm the identity of this T6SS and, by cryo electron microscopy (cryoEM), show the structure of its post-contraction sheath at 3.7 Å resolution. We demonstrate the assembly of this T6SS by IglA/IglB and secretion of its putative effector proteins in response to environmental stimuli. The sheath has a quaternary structure with handedness opposite that of contracted sheath of T4 phage tail and is organized in an interlaced two-dimensional array by means of β sheet augmentation. By structure-based mutagenesis, we show that this interlacing is essential to secretion, phagosomal escape, and intracellular replication. Our atomic model of the T6SS will facilitate design of drugs targeting this highly prevalent secretion apparatus.3107 Microbiology (for-2020)31 Biological Sciences (for-2020)Infectious Diseases (rcdc)Infection (hrcs-hc)Bacterial Proteins (mesh)Bacterial Secretion Systems (mesh)Bacteriophage T4 (mesh)Bacteriophages (mesh)Cryoelectron Microscopy (mesh)Francisella (mesh)ModelsMolecular (mesh)Protein StructureSecondary (mesh)Francisella (mesh)Bacteriophages (mesh)Bacteriophage T4 (mesh)Bacterial Proteins (mesh)Cryoelectron Microscopy (mesh)Protein StructureSecondary (mesh)ModelsMolecular (mesh)Bacterial Secretion Systems (mesh)Bacterial Proteins (mesh)Bacterial Secretion Systems (mesh)Bacteriophage T4 (mesh)Bacteriophages (mesh)Cryoelectron Microscopy (mesh)Francisella (mesh)ModelsMolecular (mesh)Protein StructureSecondary (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5vm7444qhttps://escholarship.org/content/qt5vm7444q/qt5vm7444q.pdfinfo:doi/10.1016/j.cell.2015.02.005articleCell, vol 160, iss 5940 - 951oai:escholarship.org:ark:/13030/qt5bf3w5kq2026-01-18T12:52:41Zqt5bf3w5kqCryo-EM reveals different coronin binding modes for ADP– and ADP–BeFx actin filamentsGe, PengDurer, Zeynep A OztugKudryashov, DmitriZhou, Z HongReisler, Emil2014-12-01Cryo-EM analyses of coronin in complex with F-actin in its ADP-bound or ADP–BeFx–bound state and fitting of atomic models explain the nucleotide-dependent effects of coronin on cofilin-assisted remodeling of F-actin.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)2.1 Biological and endogenous factors (hrcs-rac)Generic health relevance (hrcs-hc)Actin Cytoskeleton (mesh)Actins (mesh)Adenosine Diphosphate (mesh)Amino Acid Sequence (mesh)Animals (mesh)Beryllium (mesh)Cryoelectron Microscopy (mesh)Fluorides (mesh)Microfilament Proteins (mesh)ModelsMolecular (mesh)Protein Binding (mesh)Protein StructureTertiary (mesh)Rabbits (mesh)Saccharomyces cerevisiae (mesh)Animals (mesh)Rabbits (mesh)Saccharomyces cerevisiae (mesh)Fluorides (mesh)Beryllium (mesh)Microfilament Proteins (mesh)Actins (mesh)Adenosine Diphosphate (mesh)Cryoelectron Microscopy (mesh)Amino Acid Sequence (mesh)Protein StructureTertiary (mesh)Protein Binding (mesh)ModelsMolecular (mesh)Actin Cytoskeleton (mesh)Actin Cytoskeleton (mesh)Actins (mesh)Adenosine Diphosphate (mesh)Amino Acid Sequence (mesh)Animals (mesh)Beryllium (mesh)Cryoelectron Microscopy (mesh)Fluorides (mesh)Microfilament Proteins (mesh)ModelsMolecular (mesh)Protein Binding (mesh)Protein StructureTertiary (mesh)Rabbits (mesh)Saccharomyces cerevisiae (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biophysics (science-metrix)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5bf3w5kqhttps://escholarship.org/content/qt5bf3w5kq/qt5bf3w5kq.pdfinfo:doi/10.1038/nsmb.2907articleNature Structural & Molecular Biology, vol 21, iss 121075 - 1081oai:escholarship.org:ark:/13030/qt6qx1g1bh2026-01-18T08:35:09Zqt6qx1g1bhAn unanticipated architecture of the 750-kDa α6β6 holoenzyme of 3-methylcrotonyl-CoA carboxylaseHuang, Christine SGe, PengZhou, Z HongTong, Liang2012-01-01The crystal structure of Pseudomonas aeruginosa 3-methylcrotonyl-CoA carboxylase is determined and found to be markedly different from that of propionyl-CoA carboxylase.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Binding Sites (mesh)Biocatalysis (mesh)Carbon-Carbon Ligases (mesh)Coenzyme A (mesh)CrystallographyX-Ray (mesh)Disease (mesh)Holoenzymes (mesh)Humans (mesh)Methylmalonyl-CoA Decarboxylase (mesh)ModelsMolecular (mesh)Mutation (mesh)Protein Binding (mesh)Protein StructureTertiary (mesh)Protein Subunits (mesh)Pseudomonas aeruginosa (mesh)Humans (mesh)Pseudomonas aeruginosa (mesh)Disease (mesh)Coenzyme A (mesh)Holoenzymes (mesh)Carbon-Carbon Ligases (mesh)Methylmalonyl-CoA Decarboxylase (mesh)Protein Subunits (mesh)CrystallographyX-Ray (mesh)Binding Sites (mesh)Protein StructureTertiary (mesh)Protein Binding (mesh)Mutation (mesh)ModelsMolecular (mesh)Biocatalysis (mesh)Binding Sites (mesh)Biocatalysis (mesh)Carbon-Carbon Ligases (mesh)Coenzyme A (mesh)CrystallographyX-Ray (mesh)Disease (mesh)Holoenzymes (mesh)Humans (mesh)Methylmalonyl-CoA Decarboxylase (mesh)ModelsMolecular (mesh)Mutation (mesh)Protein Binding (mesh)Protein StructureTertiary (mesh)Protein Subunits (mesh)Pseudomonas aeruginosa (mesh)General Science & Technology (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6qx1g1bhhttps://escholarship.org/content/qt6qx1g1bh/qt6qx1g1bh.pdfinfo:doi/10.1038/nature10691articleNature, vol 481, iss 7380219 - 223oai:escholarship.org:ark:/13030/qt2fk1r5962026-01-18T05:58:58Zqt2fk1r596INF2-Mediated Severing through Actin Filament Encirclement and DisruptionGurel, Pinar SGe, PengGrintsevich, Elena EShu, RuiBlanchoin, LaurentZhou, Z HongReisler, EmilHiggs, Henry N2014-01-01BACKGROUND: INF2 is a formin protein with the unique ability to accelerate both actin polymerization and depolymerization, the latter requiring filament severing. Mutations in INF2 lead to the kidney disease focal segmental glomerulosclerosis (FSGS) and the neurological disorder Charcot-Marie Tooth disease (CMTD).
RESULTS: Here, we compare the severing mechanism of INF2 with that of the well-studied severing protein cofilin. INF2, like cofilin, binds stoichiometrically to filament sides and severs in a manner that requires phosphate release from the filament. In contrast to cofilin, however, INF2 binds ADP and ADP-Pi filaments equally well. Furthermore, two-color total internal reflection fluorescence (TIRF) microscopy reveals that a low number of INF2 molecules, as few as a single INF2 dimer, are capable of severing, while measurable cofilin-mediated severing requires more extensive binding. Hence, INF2 is a more potent severing protein than cofilin. While a construct containing the FH1 and FH2 domains alone has some severing activity, addition of the C-terminal region increases severing potency by 40-fold, and we show that the WH2-resembling DAD motif is responsible for this increase. Helical 3D reconstruction from electron micrographs at 20 Å resolution provides a structure of filament-bound INF2, showing that the FH2 domain encircles the filament.
CONCLUSIONS: We propose a severing model in which FH2 binding and phosphate release causes local filament deformation, allowing the DAD to bind adjacent actin protomers, further disrupting filament structure.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Kidney Disease (rcdc)Neurosciences (rcdc)Peripheral Neuropathy (rcdc)Charcot-Marie-Tooth Disease (rcdc)Rare Diseases (rcdc)Neurodegenerative (rcdc)Actin Cytoskeleton (mesh)Animals (mesh)Microfilament Proteins (mesh)MicroscopyElectron (mesh)ModelsMolecular (mesh)Protein Binding (mesh)Protein StructureQuaternary (mesh)Protein StructureTertiary (mesh)Rabbits (mesh)Animals (mesh)Rabbits (mesh)Microfilament Proteins (mesh)MicroscopyElectron (mesh)Protein StructureQuaternary (mesh)Protein StructureTertiary (mesh)Protein Binding (mesh)ModelsMolecular (mesh)Actin Cytoskeleton (mesh)Actin Cytoskeleton (mesh)Animals (mesh)Microfilament Proteins (mesh)MicroscopyElectron (mesh)ModelsMolecular (mesh)Protein Binding (mesh)Protein StructureQuaternary (mesh)Protein StructureTertiary (mesh)Rabbits (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)17 Psychology and Cognitive Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)52 Psychology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2fk1r596https://escholarship.org/content/qt2fk1r596/qt2fk1r596.pdfinfo:doi/10.1016/j.cub.2013.12.018articleCurrent Biology, vol 24, iss 2156 - 164oai:escholarship.org:ark:/13030/qt0zt7k9bp2026-01-18T04:01:39Zqt0zt7k9bpCryo-EM structure of the mature dengue virus at 3.5-Å resolutionZhang, XiaokangGe, PengYu, XuekuiBrannan, Jennifer MBi, GuoqiangZhang, QinfenSchein, StanZhou, Z Hong2013-01-01Dengue virus has two membrane proteins, E and M, which undergo dramatic structural changes during the life cycle of the virus. The 3.5-Å cryo-EM structure of the mature prefusion Dengue virion reveals the detailed interactions between E and M, providing insight into how conformational changes are triggered.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)Infectious Diseases (rcdc)Emerging Infectious Diseases (rcdc)Biodefense (rcdc)Rare Diseases (rcdc)Vector-Borne Diseases (rcdc)2.2 Factors relating to the physical environment (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Infection (hrcs-hc)3 Good Health and Well Being (sdg)Aedes (mesh)Animals (mesh)Cell Line (mesh)Cryoelectron Microscopy (mesh)CrystallographyX-Ray (mesh)Dengue Virus (mesh)Hydrogen-Ion Concentration (mesh)Hydrophobic and Hydrophilic Interactions (mesh)Membrane Proteins (mesh)Protein Conformation (mesh)Viral Envelope Proteins (mesh)Viral Matrix Proteins (mesh)Virus Attachment (mesh)trans-Golgi Network (mesh)Cell Line (mesh)trans-Golgi Network (mesh)Animals (mesh)Aedes (mesh)Dengue Virus (mesh)Membrane Proteins (mesh)Viral Envelope Proteins (mesh)Viral Matrix Proteins (mesh)Cryoelectron Microscopy (mesh)CrystallographyX-Ray (mesh)Protein Conformation (mesh)Hydrogen-Ion Concentration (mesh)Virus Attachment (mesh)Hydrophobic and Hydrophilic Interactions (mesh)Aedes (mesh)Animals (mesh)Cell Line (mesh)Cryoelectron Microscopy (mesh)CrystallographyX-Ray (mesh)Dengue Virus (mesh)Hydrogen-Ion Concentration (mesh)Hydrophobic and Hydrophilic Interactions (mesh)Membrane Proteins (mesh)Protein Conformation (mesh)Viral Envelope Proteins (mesh)Viral Matrix Proteins (mesh)Virus Attachment (mesh)trans-Golgi Network (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biophysics (science-metrix)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0zt7k9bphttps://escholarship.org/content/qt0zt7k9bp/qt0zt7k9bp.pdfinfo:doi/10.1038/nsmb.2463articleNature Structural & Molecular Biology, vol 20, iss 1105 - 110oai:escholarship.org:ark:/13030/qt8hx7x3g92026-01-17T17:15:30Zqt8hx7x3g9Wnt, GSK3, and MacropinocytosisTejeda-Muñoz, NydiaDe Robertis, Edward M2022-01-01Here we review the regulation of macropinocytosis by Wnt growth factor signaling. Canonical Wnt signaling is normally thought of as a regulator of nuclear β-catenin, but emerging results indicate that there is much more than β-catenin to the Wnt pathway. Macropinocytosis is transiently regulated by EGF-RTK-Ras-PI3K signaling. Recent studies show that Wnt signaling provides for sustained acquisition of nutrients by macropinocytosis. Endocytosis of Wnt-Lrp6-Fz receptor complexes triggers the sequestration of GSK3 and components of the cytosolic destruction complex such as Axin1 inside multivesicular bodies (MVBs) through the action of the ESCRT machinery. Wnt macropinocytosis can be induced both by the transcriptional loop of stabilized β-catenin, and by the inhibition of GSK3 even in the absence of new protein synthesis. The cell is poised for macropinocytosis, and all it requires for triggering of Pak1 and the actin machinery is the inhibition of GSK3. Striking lysosomal acidification, which requires macropinocytosis, is induced by GSK3 chemical inhibitors or Wnt protein. Wnt-induced macropinocytosis requires the ESCRT machinery that forms MVBs. In cancer cells, mutations in the tumor suppressors APC and Axin1 result in extensive macropinocytosis, which can be reversed by restoring wild-type protein. In basal cellular conditions, GSK3 functions to constitutively repress macropinocytosis.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Cancer (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Cancer (hrcs-hc)Generic health relevance (hrcs-hc)Endosomal Sorting Complexes Required for Transport (mesh)Glycogen Synthase Kinase 3 (mesh)Phosphatidylinositol 3-Kinases (mesh)Wnt Proteins (mesh)Wnt Signaling Pathway (mesh)Glycogen Synthase Kinase 3 (mesh)Wnt Proteins (mesh)Endosomal Sorting Complexes Required for Transport (mesh)Phosphatidylinositol 3-Kinases (mesh)Wnt Signaling Pathway (mesh)Colorectal cancerESCRTEndocytosisGSK3Hepatocellular carcinomaLysosome regulationMacropinocytosisMultivesicular bodiesWnt-STOPEndosomal Sorting Complexes Required for Transport (mesh)Glycogen Synthase Kinase 3 (mesh)Phosphatidylinositol 3-Kinases (mesh)Wnt Proteins (mesh)Wnt Signaling Pathway (mesh)3101 Biochemistry and cell biology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/8hx7x3g9https://escholarship.org/content/qt8hx7x3g9/qt8hx7x3g9.pdfinfo:doi/10.1007/978-3-030-94004-1_9articleSubcellular Biochemistry, vol 98169 - 187oai:escholarship.org:ark:/13030/qt9p31j09v2026-01-17T16:41:28Zqt9p31j09vDifferential Metabolic Reprogramming by Zika Virus Promotes Cell Death in Human versus Mosquito CellsThaker, Shivani KChapa, TravisGarcia, GustavoGong, DanyangSchmid, Ernst WArumugaswami, VaithilingarajaSun, RenChristofk, Heather R2019-05-01Zika virus is a pathogen that poses serious consequences, including congenital microcephaly. Although many viruses reprogram host cell metabolism, whether Zika virus alters cellular metabolism and the functional consequences of Zika-induced metabolic changes remain unknown. Here, we show that Zika virus infection differentially reprograms glucose metabolism in human versus C6/36 mosquito cells by increasing glucose use in the tricarboxylic acid cycle in human cells versus increasing glucose use in the pentose phosphate pathway in mosquito cells. Infection of human cells selectively depletes nucleotide triphosphate levels, leading to elevated AMP/ATP ratios, AMP-activated protein kinase (AMPK) phosphorylation, and caspase-mediated cell death. AMPK is also phosphorylated in Zika virus-infected mouse brain. Inhibiting AMPK in human cells decreases Zika virus-mediated cell death, whereas activating AMPK in mosquito cells promotes Zika virus-mediated cell death. These findings suggest that the differential metabolic reprogramming during Zika virus infection of human versus mosquito cells determines whether cell death occurs.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Orphan Drug (rcdc)Rare Diseases (rcdc)Infectious Diseases (rcdc)Vector-Borne Diseases (rcdc)Biodefense (rcdc)Emerging Infectious Diseases (rcdc)2.1 Biological and endogenous factors (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)Infection (hrcs-hc)3 Good Health and Well Being (sdg)AMP-Activated Protein Kinases (mesh)Aedes (mesh)Animals (mesh)Cell Death (mesh)Chlorocebus aethiops (mesh)Citric Acid Cycle (mesh)Epithelial Cells (mesh)Fibroblasts (mesh)Foreskin (mesh)Glucose (mesh)Humans (mesh)Male (mesh)Mice (mesh)MiceKnockout (mesh)Pentose Phosphate Pathway (mesh)Phosphorylation (mesh)ReceptorInterferon alpha-beta (mesh)Retinal Pigment Epithelium (mesh)Vero Cells (mesh)Zika Virus (mesh)Zika Virus Infection (mesh)Vero Cells (mesh)Fibroblasts (mesh)Epithelial Cells (mesh)Animals (mesh)MiceKnockout (mesh)Humans (mesh)Mice (mesh)Aedes (mesh)Glucose (mesh)Cell Death (mesh)Citric Acid Cycle (mesh)Phosphorylation (mesh)Male (mesh)Pentose Phosphate Pathway (mesh)ReceptorInterferon alpha-beta (mesh)Foreskin (mesh)Retinal Pigment Epithelium (mesh)AMP-Activated Protein Kinases (mesh)Zika Virus (mesh)Zika Virus Infection (mesh)Chlorocebus aethiops (mesh)AMPKZika virusapoptosisvirus metabolismAMP-Activated Protein Kinases (mesh)Aedes (mesh)Animals (mesh)Cell Death (mesh)Chlorocebus aethiops (mesh)Citric Acid Cycle (mesh)Epithelial Cells (mesh)Fibroblasts (mesh)Foreskin (mesh)Glucose (mesh)Humans (mesh)Male (mesh)Mice (mesh)MiceKnockout (mesh)Pentose Phosphate Pathway (mesh)Phosphorylation (mesh)ReceptorInterferon alpha-beta (mesh)Retinal Pigment Epithelium (mesh)Vero Cells (mesh)Zika Virus (mesh)Zika Virus Infection (mesh)0601 Biochemistry and Cell Biology (for)1101 Medical Biochemistry and Metabolomics (for)Endocrinology & Metabolism (science-metrix)3101 Biochemistry and cell biology (for-2020)3205 Medical biochemistry and metabolomics (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9p31j09vhttps://escholarship.org/content/qt9p31j09v/qt9p31j09v.pdfinfo:doi/10.1016/j.cmet.2019.01.024articleCell Metabolism, vol 29, iss 51206 - 1216.e4oai:escholarship.org:ark:/13030/qt361217752026-01-17T11:34:59Zqt36121775Electron Cryo-microscopy Structure of Ebola Virus Nucleoprotein Reveals a Mechanism for Nucleocapsid-like AssemblySu, ZhaomingWu, ChaoShi, LiuqingLuthra, PriyaPintilie, Grigore DJohnson, BritneyPorter, Justin RGe, PengChen, MuyuanLiu, GaiFrederick, Thomas EBinning, Jennifer MBowman, Gregory RZhou, Z HongBasler, Christopher FGross, Michael LLeung, Daisy WChiu, WahAmarasinghe, Gaya K2018-02-01Ebola virus nucleoprotein (eNP) assembles into higher-ordered structures that form the viral nucleocapsid (NC) and serve as the scaffold for viral RNA synthesis. However, molecular insights into the NC assembly process are lacking. Using a hybrid approach, we characterized the NC-like assembly of eNP, identified novel regulatory elements, and described how these elements impact function. We generated a three-dimensional structure of the eNP NC-like assembly at 5.8 Å using electron cryo-microscopy and identified a new regulatory role for eNP helices α22-α23. Biochemical, biophysical, and mutational analyses revealed that inter-eNP contacts within α22-α23 are critical for viral NC assembly and regulate viral RNA synthesis. These observations suggest that the N terminus and α22-α23 of eNP function as context-dependent regulatory modules (CDRMs). Our current study provides a framework for a structural mechanism for NC-like assembly and a new therapeutic target.31 Biological Sciences (for-2020)Infectious Diseases (rcdc)Rare Diseases (rcdc)Emerging Infectious Diseases (rcdc)Genetics (rcdc)3 Good Health and Well Being (sdg)Cryoelectron Microscopy (mesh)Ebolavirus (mesh)ModelsBiological (mesh)Mutant Proteins (mesh)Mutation (mesh)Nucleocapsid (mesh)Nucleoproteins (mesh)Protein Multimerization (mesh)Protein StructureSecondary (mesh)Protein Subunits (mesh)RNAViral (mesh)Virus Assembly (mesh)Nucleocapsid (mesh)Nucleoproteins (mesh)Protein Subunits (mesh)RNAViral (mesh)Cryoelectron Microscopy (mesh)Virus Assembly (mesh)Protein StructureSecondary (mesh)Mutation (mesh)ModelsBiological (mesh)Mutant Proteins (mesh)Ebolavirus (mesh)Protein Multimerization (mesh)Ebola viruscryo-EMnucleocapsidnucleoproteinviral RNA synthesisCryoelectron Microscopy (mesh)Ebolavirus (mesh)ModelsBiological (mesh)Mutant Proteins (mesh)Mutation (mesh)Nucleocapsid (mesh)Nucleoproteins (mesh)Protein Multimerization (mesh)Protein StructureSecondary (mesh)Protein Subunits (mesh)RNAViral (mesh)Virus Assembly (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/36121775https://escholarship.org/content/qt36121775/qt36121775.pdfinfo:doi/10.1016/j.cell.2018.02.009articleCell, vol 172, iss 5966 - 978.e12oai:escholarship.org:ark:/13030/qt9hs2f5v52026-01-17T11:34:56Zqt9hs2f5v5Chaperone fusion proteins aid entropy-driven maturation of class II viral fusion proteinsGe, PengZhou, Z Hong2014-02-01Class II viral fusion proteins are present on the envelope of flaviviruses and togaviruses, viruses that often cause tropical and subtropical diseases. These proteins use a second membrane protein as a molecular chaperone to assist their folding and to ensure proper function during viral assembly, maturation, and infection. Recent progress in structural studies of dengue viruses has revealed how the chaperone pre-membrane (prM) protein guides viral maturation and how pH is sensed in both the maturation and infection processes. Drastic conformation changes and reorganization of these viral membrane proteins occur during the transition from their metastable to stable structural states in a unidirectional, entropy-driven process.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Infectious Diseases (rcdc)Biodefense (rcdc)Emerging Infectious Diseases (rcdc)Rare Diseases (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.2 Factors relating to the physical environment (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Infection (hrcs-hc)3 Good Health and Well Being (sdg)Dengue Virus (mesh)Entropy (mesh)Hydrogen-Ion Concentration (mesh)Molecular Chaperones (mesh)Protein Conformation (mesh)Protein Folding (mesh)Viral Envelope Proteins (mesh)Viral Fusion Proteins (mesh)cryo-electron microscopyflavivirustogavirusbio-threat agentenveloped virusesstructuresDengue Virus (mesh)Molecular Chaperones (mesh)Viral Envelope Proteins (mesh)Viral Fusion Proteins (mesh)Protein Conformation (mesh)Protein Folding (mesh)Hydrogen-Ion Concentration (mesh)Entropy (mesh)bio-threat agentcryo-electron microscopyenveloped virusesflavivirusstructurestogavirusDengue Virus (mesh)Entropy (mesh)Hydrogen-Ion Concentration (mesh)Molecular Chaperones (mesh)Protein Conformation (mesh)Protein Folding (mesh)Viral Envelope Proteins (mesh)Viral Fusion Proteins (mesh)0605 Microbiology (for)1108 Medical Microbiology (for)Microbiology (science-metrix)3101 Biochemistry and cell biology (for-2020)3107 Microbiology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9hs2f5v5https://escholarship.org/content/qt9hs2f5v5/qt9hs2f5v5.pdfinfo:doi/10.1016/j.tim.2013.11.006articleTrends in Microbiology, vol 22, iss 2100 - 106oai:escholarship.org:ark:/13030/qt68r712d82026-01-15T09:36:39Zqt68r712d8Revealing Ligand Binding Sites and Quantifying Subunit Variants of Noncovalent Protein Complexes in a Single Native Top-Down FTICR MS ExperimentLi, HuilinWongkongkathep, PiriyaVan Orden, Steve LOgorzalek Loo, Rachel RLoo, Joseph A2014-12-01Abstract“Native” mass spectrometry (MS) has been proven to be increasingly useful for structural biology studies of macromolecular assemblies. Using horse liver alcohol dehydrogenase (hADH) and yeast alcohol dehydrogenase (yADH) as examples, we demonstrate that rich information can be obtained in a single native top-down MS experiment using Fourier transform ion cyclotron mass spectrometry (FTICR MS). Beyond measuring the molecular weights of the protein complexes, isotopic mass resolution was achieved for yeast ADH tetramer (147 kDa) with an average resolving power of 412,700 at m/z 5466 in absorption mode, and the mass reflects that each subunit binds to two zinc atoms. The N-terminal 89 amino acid residues were sequenced in a top-down electron capture dissociation (ECD) experiment, along with the identifications of the zinc binding site at Cys46 and a point mutation (V58T). With the combination of various activation/dissociation techniques, including ECD, in-source dissociation (ISD), collisionally activated dissociation (CAD), and infrared multiphoton dissociation (IRMPD), 40% of the yADH sequence was derived directly from the native tetramer complex. For hADH, native top-down ECD-MS shows that both E and S subunits are present in the hADH sample, with a relative ratio of 4:1. Native top-down ISD of the hADH dimer shows that each subunit (E and S chains) binds not only to two zinc atoms, but also the NAD/NADH ligand, with a higher NAD/NADH binding preference for the S chain relative to the E chain. In total, 32% sequence coverage was achieved for both E and S chains.Figureᅟ3401 Analytical Chemistry (for-2020)34 Chemical Sciences (for-2020)3406 Physical Chemistry (for-2020)1.1 Normal biological development and functioning (hrcs-rac)Alcohol Dehydrogenase (mesh)Amino Acid Sequence (mesh)Animals (mesh)Binding Sites (mesh)Horses (mesh)Ligands (mesh)Liver (mesh)Mass Spectrometry (mesh)Molecular Sequence Data (mesh)Protein Binding (mesh)Proteins (mesh)Proteomics (mesh)Alcohol dehydrogenaseTop-down mass spectrometryNative mass spectrometryFourier transform ion cyclotron resonance mass spectrometryElectron capture dissociationLiver (mesh)Animals (mesh)Horses (mesh)Alcohol Dehydrogenase (mesh)Proteins (mesh)Ligands (mesh)Proteomics (mesh)Binding Sites (mesh)Amino Acid Sequence (mesh)Protein Binding (mesh)Molecular Sequence Data (mesh)Mass Spectrometry (mesh)Alcohol Dehydrogenase (mesh)Amino Acid Sequence (mesh)Animals (mesh)Binding Sites (mesh)Horses (mesh)Ligands (mesh)Liver (mesh)Mass Spectrometry (mesh)Molecular Sequence Data (mesh)Protein Binding (mesh)Proteins (mesh)Proteomics (mesh)0301 Analytical Chemistry (for)0304 Medicinal and Biomolecular Chemistry (for)0306 Physical Chemistry (incl. Structural) (for)Analytical Chemistry (science-metrix)3401 Analytical chemistry (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/68r712d8https://escholarship.org/content/qt68r712d8/qt68r712d8.pdfinfo:doi/10.1007/s13361-014-0928-6articleJournal of the American Society for Mass Spectrometry, vol 25, iss 122060 - 2068oai:escholarship.org:ark:/13030/qt4mx2r10v2026-01-14T05:52:56Zqt4mx2r10vAn integrated encyclopedia of DNA elements in the human genomeDunham, IanKundaje, AnshulAldred, Shelley FCollins, Patrick JDavis, Carrie ADoyle, FrancisEpstein, Charles BFrietze, SethHarrow, JenniferKaul, RajinderKhatun, JainabLajoie, Bryan RLandt, Stephen GLee, Bum-KyuPauli, FlorenciaRosenbloom, Kate RSabo, PeterSafi, AlexiasSanyal, AmartyaShoresh, NoamSimon, Jeremy MSong, LingyunTrinklein, Nathan DAltshuler, Robert CBirney, EwanBrown, James BCheng, ChaoDjebali, SarahDong, XianjunDunham, IanErnst, JasonFurey, Terrence SGerstein, MarkGiardine, BelindaGreven, MelissaHardison, Ross CHarris, Robert SHerrero, JavierHoffman, Michael MIyer, SowmyaKellis, ManolisKhatun, JainabKheradpour, PouyaKundaje, AnshulLassmann, TimoLi, QunhuaLin, XinyingMarinov, Georgi KMerkel, AngelikaMortazavi, AliParker, Stephen CJReddy, Timothy ERozowsky, JoelSchlesinger, FelixThurman, Robert EWang, JieWard, Lucas DWhitfield, Troy WWilder, Steven PWu, WeishengXi, Hualin SYip, Kevin YZhuang, JialiBernstein, Bradley EBirney, EwanDunham, IanGreen, Eric DGunter, ChrisSnyder, MichaelPazin, Michael JLowdon, Rebecca FDillon, Laura ALAdams, Leslie BKelly, Caroline JZhang, JuliaWexler, Judith RGreen, Eric DGood, Peter JFeingold, Elise ABernstein, Bradley EBirney, EwanCrawford, Gregory EDekker, JobElnitski, LauraFarnham, Peggy JGerstein, MarkGiddings, Morgan CGingeras, Thomas RGreen, Eric DGuigó, RodericHardison, Ross CHubbard, Timothy JKellis, ManolisKent, W JamesLieb, Jason DMargulies, Elliott HMyers, Richard MSnyder, MichaelStamatoyannopoulos, John ATenenbaum, Scott A2012-09-01The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)3105 Genetics (for-2020)Genetics (rcdc)Biotechnology (rcdc)Human Genome (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Alleles (mesh)Animals (mesh)Binding Sites (mesh)Chromatin (mesh)Chromatin Immunoprecipitation (mesh)ChromosomesHuman (mesh)DNA (mesh)DNA Footprinting (mesh)DNA Methylation (mesh)DNA-Binding Proteins (mesh)Deoxyribonuclease I (mesh)Encyclopedias as Topic (mesh)Exons (mesh)Genetic Predisposition to Disease (mesh)Genetic Variation (mesh)GenomeHuman (mesh)Genome-Wide Association Study (mesh)Genomics (mesh)Histones (mesh)Humans (mesh)Mammals (mesh)Molecular Sequence Annotation (mesh)Neoplasms (mesh)PolymorphismSingle Nucleotide (mesh)Promoter RegionsGenetic (mesh)Proteins (mesh)Regulatory SequencesNucleic Acid (mesh)Sequence AnalysisRNA (mesh)Transcription Factors (mesh)TranscriptionGenetic (mesh)ENCODE Project ConsortiumChromosomesHuman (mesh)Chromatin (mesh)Animals (mesh)Mammals (mesh)Humans (mesh)Neoplasms (mesh)Genetic Predisposition to Disease (mesh)Deoxyribonuclease I (mesh)Proteins (mesh)DNA-Binding Proteins (mesh)Histones (mesh)Transcription Factors (mesh)DNA (mesh)Chromatin Immunoprecipitation (mesh)DNA Footprinting (mesh)Sequence AnalysisRNA (mesh)Genomics (mesh)DNA Methylation (mesh)TranscriptionGenetic (mesh)Binding Sites (mesh)Regulatory SequencesNucleic Acid (mesh)PolymorphismSingle Nucleotide (mesh)Alleles (mesh)GenomeHuman (mesh)Exons (mesh)Encyclopedias as Topic (mesh)Promoter RegionsGenetic (mesh)Genetic Variation (mesh)Genome-Wide Association Study (mesh)Molecular Sequence Annotation (mesh)Alleles (mesh)Animals (mesh)Binding Sites (mesh)Chromatin (mesh)Chromatin Immunoprecipitation (mesh)ChromosomesHuman (mesh)DNA (mesh)DNA Footprinting (mesh)DNA Methylation (mesh)DNA-Binding Proteins (mesh)Deoxyribonuclease I (mesh)Encyclopedias as Topic (mesh)Exons (mesh)Genetic Predisposition to Disease (mesh)Genetic Variation (mesh)GenomeHuman (mesh)Genome-Wide Association Study (mesh)Genomics (mesh)Histones (mesh)Humans (mesh)Mammals (mesh)Molecular Sequence Annotation (mesh)Neoplasms (mesh)PolymorphismSingle Nucleotide (mesh)Promoter RegionsGenetic (mesh)Proteins (mesh)Regulatory SequencesNucleic Acid (mesh)Sequence AnalysisRNA (mesh)Transcription Factors (mesh)TranscriptionGenetic (mesh)General Science & Technology (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/4mx2r10vhttps://escholarship.org/content/qt4mx2r10v/qt4mx2r10v.pdfinfo:doi/10.1038/nature11247articleNature, vol 489, iss 741457 - 74oai:escholarship.org:ark:/13030/qt1z03r1jd2026-01-14T03:20:17Zqt1z03r1jdA transcriptomic and epigenomic cell atlas of the mouse primary motor cortexYao, ZizhenLiu, HanqingXie, FangmingFischer, StephanAdkins, Ricky SAldridge, Andrew IAment, Seth ABartlett, AnnaBehrens, M MargaritaVan den Berge, KoenBertagnolli, Darrende Bézieux, Hector RouxBiancalani, TommasoBooeshaghi, A SinaBravo, Héctor CorradaCasper, TamaraColantuoni, CarloCrabtree, JonathanCreasy, HeatherCrichton, KirstenCrow, MeganDee, NickDougherty, Elizabeth LDoyle, Wayne IDudoit, SandrineFang, RongxinFelix, VictorFong, OliviaGiglio, MichelleGoldy, JeffHawrylycz, MikeHerb, Brian RHertzano, RonnaHou, XiaomengHu, QiwenKancherla, JayaramKroll, MatthewLathia, KananLi, Yang EricLucero, Jacinta DLuo, ChongyuanMahurkar, AnupMcMillen, DelissaNadaf, Naeem MNery, Joseph RNguyen, Thuc NghiNiu, Sheng-YongNtranos, VasilisOrvis, JoshuaOsteen, Julia KPham, ThanhPinto-Duarte, AntonioPoirion, OlivierPreissl, SebastianPurdom, ElizabethRimorin, ChristineRisso, DavideRivkin, Angeline CSmith, KimberlyStreet, KellySulc, JosefSvensson, ValentineTieu, MichaelTorkelson, AmyTung, HermanVaishnav, Eeshit DhavalVanderburg, Charles Rvan Velthoven, CindyWang, XinxinWhite, Owen RHuang, Z JoshKharchenko, Peter VPachter, LiorNgai, JohnRegev, AvivTasic, BosiljkaWelch, Joshua DGillis, JesseMacosko, Evan ZRen, BingEcker, Joseph RZeng, HongkuiMukamel, Eran A2021-10-07Single-cell transcriptomics can provide quantitative molecular signatures for large, unbiased samples of the diverse cell types in the brain1–3. With the proliferation of multi-omics datasets, a major challenge is to validate and integrate results into a biological understanding of cell-type organization. Here we generated transcriptomes and epigenomes from more than 500,000 individual cells in the mouse primary motor cortex, a structure that has an evolutionarily conserved role in locomotion. We developed computational and statistical methods to integrate multimodal data and quantitatively validate cell-type reproducibility. The resulting reference atlas—containing over 56 neuronal cell types that are highly replicable across analysis methods, sequencing technologies and modalities—is a comprehensive molecular and genomic account of the diverse neuronal and non-neuronal cell types in the mouse primary motor cortex. The atlas includes a population of excitatory neurons that resemble pyramidal cells in layer 4 in other cortical regions4. We further discovered thousands of concordant marker genes and gene regulatory elements for these cell types. Our results highlight the complex molecular regulation of cell types in the brain and will directly enable the design of reagents to target specific cell types in the mouse primary motor cortex for functional analysis.3101 Biochemistry and Cell Biology (for-2020)3102 Bioinformatics and Computational Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)3105 Genetics (for-2020)Neurosciences (rcdc)Genetics (rcdc)Human Genome (rcdc)Bioengineering (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Neurological (hrcs-hc)Animals (mesh)Atlases as Topic (mesh)Datasets as Topic (mesh)EpigenesisGenetic (mesh)Epigenomics (mesh)Female (mesh)Gene Expression Profiling (mesh)Male (mesh)Mice (mesh)Motor Cortex (mesh)Neurons (mesh)Organ Specificity (mesh)Reproducibility of Results (mesh)Single-Cell Analysis (mesh)Transcriptome (mesh)Motor Cortex (mesh)Neurons (mesh)Animals (mesh)Mice (mesh)Reproducibility of Results (mesh)Gene Expression Profiling (mesh)Organ Specificity (mesh)EpigenesisGenetic (mesh)Female (mesh)Male (mesh)Atlases as Topic (mesh)Epigenomics (mesh)Single-Cell Analysis (mesh)Transcriptome (mesh)Datasets as Topic (mesh)Animals (mesh)Atlases as Topic (mesh)Datasets as Topic (mesh)EpigenesisGenetic (mesh)Epigenomics (mesh)Female (mesh)Gene Expression Profiling (mesh)Male (mesh)Mice (mesh)Motor Cortex (mesh)Neurons (mesh)Organ Specificity (mesh)Reproducibility of Results (mesh)Single-Cell Analysis (mesh)Transcriptome (mesh)General Science & Technology (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/1z03r1jdhttps://escholarship.org/content/qt1z03r1jd/qt1z03r1jd.pdfinfo:doi/10.1038/s41586-021-03500-8articleNature, vol 598, iss 7879103 - 110oai:escholarship.org:ark:/13030/qt1h9004pq2026-01-13T14:55:10Zqt1h9004pqA robust approach for MicroED sample preparation of lipidic cubic phase embedded membrane protein crystalsMartynowycz, Michael WShiriaeva, AnnaClabbers, Max TBNicolas, William JWeaver, Sara JHattne, JohanGonen, Tamir2023-01-01Crystallizing G protein-coupled receptors (GPCRs) in lipidic cubic phase (LCP) often yields crystals suited for the cryogenic electron microscopy (cryoEM) method microcrystal electron diffraction (MicroED). However, sample preparation is challenging. Embedded crystals cannot be targeted topologically. Here, we use an integrated fluorescence light microscope (iFLM) inside of a focused ion beam and scanning electron microscope (FIB-SEM) to identify fluorescently labeled GPCR crystals. Crystals are targeted using the iFLM and LCP is milled using a plasma focused ion beam (pFIB). The optimal ion source for preparing biological lamellae is identified using standard crystals of proteinase K. Lamellae prepared using either argon or xenon produced the highest quality data and structures. MicroED data are collected from the milled lamellae and the structures are determined. This study outlines a robust approach to identify and mill membrane protein crystals for MicroED and demonstrates plasma ion-beam milling is a powerful tool for preparing biological lamellae.3101 Biochemistry and Cell Biology (for-2020)34 Chemical Sciences (for-2020)31 Biological Sciences (for-2020)Membrane Proteins (mesh)Electrons (mesh)Cryoelectron Microscopy (mesh)Endopeptidase K (mesh)Lipids (mesh)Endopeptidase K (mesh)Lipids (mesh)Membrane Proteins (mesh)Cryoelectron Microscopy (mesh)Electrons (mesh)Membrane Proteins (mesh)Electrons (mesh)Cryoelectron Microscopy (mesh)Endopeptidase K (mesh)Lipids (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/1h9004pqhttps://escholarship.org/content/qt1h9004pq/qt1h9004pq.pdfinfo:doi/10.1038/s41467-023-36733-4articleNature Communications, vol 14, iss 11086oai:escholarship.org:ark:/13030/qt6644r2j82026-01-11T06:01:04Zqt6644r2j8Age-associated DNA methylation changes in Xenopus frogsMorselli, MarcoBennett, RonanShaidani, Nikko-IdeenHorb, MarkoPeshkin, LeonidPellegrini, Matteo2023-12-31Age-associated changes in DNA methylation have been characterized across various animals, but not yet in amphibians, which are of particular interest because they include widely studied model organisms. In this study, we present clear evidence that the aquatic vertebrate species Xenopus tropicalis displays patterns of age-associated changes in DNA methylation. We have generated whole-genome bisulfite sequencing (WGBS) profiles from skin samples of nine frogs representing young, mature, and old adults and characterized the gene- and chromosome-scale DNA methylation changes with age. Many of the methylation features and changes we observe are consistent with what is known in mammalian species, suggesting that the mechanism of age-related changes is conserved. Moreover, we selected a few thousand age-associated CpG sites to build an assay based on targeted DNA methylation analysis (TBSseq) to expand our findings in future studies involving larger cohorts of individuals. Preliminary results of a pilot TBSeq experiment recapitulate the findings obtained with WGBS setting the basis for the development of an epigenetic clock assay. The results of this study will allow us to leverage the unique resources available for Xenopus to study how DNA methylation relates to other hallmarks of ageing.31 Biological Sciences (for-2020)3105 Genetics (for-2020)Aging (rcdc)Human Genome (rcdc)Genetics (rcdc)Generic health relevance (hrcs-hc)Animals (mesh)DNA Methylation (mesh)Xenopus laevis (mesh)Xenopus (mesh)CpG Islands (mesh)Whole Genome Sequencing (mesh)Sulfites (mesh)Sequence AnalysisDNA (mesh)Mammals (mesh)Epigenetic clockXenopuswhole-genome bisulfite sequencingDNA methylationtargeted bisulfite sequencingAnimals (mesh)Xenopus (mesh)Xenopus laevis (mesh)Mammals (mesh)Sulfites (mesh)Sequence AnalysisDNA (mesh)DNA Methylation (mesh)CpG Islands (mesh)Whole Genome Sequencing (mesh)DNA methylationEpigenetic clockXenopustargeted bisulfite sequencingwhole-genome bisulfite sequencingAnimals (mesh)DNA Methylation (mesh)Xenopus laevis (mesh)Xenopus (mesh)CpG Islands (mesh)Whole Genome Sequencing (mesh)Sulfites (mesh)Sequence AnalysisDNA (mesh)Mammals (mesh)0601 Biochemistry and Cell Biology (for)0604 Genetics (for)1101 Medical Biochemistry and Metabolomics (for)Developmental Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)3105 Genetics (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/6644r2j8https://escholarship.org/content/qt6644r2j8/qt6644r2j8.pdfinfo:doi/10.1080/15592294.2023.2201517articleEpigenetics, vol 18, iss 12201517oai:escholarship.org:ark:/13030/qt08s1516k2026-01-08T21:21:52Zqt08s1516kUpdate to Our Reader, Reviewer, and Author CommunitiesApril 2020Burrows, Cynthia JWang, ShuKim, Hyun JaeMeyer, Gerald JSchanze, KirkLee, T RandallLutkenhaus, Jodie LKaplan, DavidJones, ChristopherBertozzi, CarolynKiessling, LauraMulcahy, Mary BethLindsley, Craig WFinn, MGBlum, Joel DKamat, PrashantAldrich, Courtney CRowan, StuartLiu, BinLiotta, DennisWeiss, Paul SZhang, DeqingGanesh, Krishna NSexton, PatrickAtwater, Harry AGooding, J JustinAllen, David TVoigt, Christopher ASweedler, JonathanSchepartz, AlannaRotello, VincentLecommandoux, SébastienSturla, Shana JHammes-Schiffer, SharonBuriak, JillianSteed, Jonathan WWu, HongweiZimmerman, JulieBrooks, BryanSavage, PhillipTolman, WilliamHofmann, Thomas FBrennecke, Joan FHolme, Thomas AMerz, Kenneth MScuseria, GustavoJorgensen, WilliamGeorg, Gunda IWang, ShaomengProteau, PhilipYates, John RStang, PeterWalker, Gilbert CHillmyer, MarcTaylor, Lynne SOdom, Teri WCarreira, ErickRossen, KaiChirik, PaulMiller, Scott JMcCoy, AnneShea, Joan-EmmaZanni, MartinMurphy, CatherineScholes, GregoryLoo, Joseph A2020-05-2734 Chemical Sciences (for-2020)03 Chemical Sciences (for)34 Chemical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/08s1516khttps://escholarship.org/content/qt08s1516k/qt08s1516k.pdfinfo:doi/10.1021/acscentsci.0c00471articleACS Central Science, vol 6, iss 5589 - 590oai:escholarship.org:ark:/13030/qt2sc094kc2026-01-08T21:21:46Zqt2sc094kcUpdate to Our Reader, Reviewer, and Author CommunitiesApril 2020Burrows, Cynthia JWang, ShuKim, Hyun JaeMeyer, Gerald JSchanze, KirkLee, T RandallLutkenhaus, Jodie LKaplan, DavidJones, ChristopherBertozzi, CarolynKiessling, LauraMulcahy, Mary BethLindsley, Craig WFinn, MGBlum, Joel DKamat, PrashantAldrich, Courtney CRowan, StuartLiu, BinLiotta, DennisWeiss, Paul SZhang, DeqingGanesh, Krishna NSexton, PatrickAtwater, Harry AGooding, J JustinAllen, David TVoigt, Christopher ASweedler, JonathanSchepartz, AlannaRotello, VincentLecommandoux, SébastienSturla, Shana JHammes-Schiffer, SharonBuriak, JillianSteed, Jonathan WWu, HongweiZimmerman, JulieBrooks, BryanSavage, PhillipTolman, WilliamHofmann, Thomas FBrennecke, Joan FHolme, Thomas AMerz, Kenneth MScuseria, GustavoJorgensen, WilliamGeorg, Gunda IWang, ShaomengProteau, PhilipYates, John RStang, PeterWalker, Gilbert CHillmyer, MarcTaylor, Lynne SOdom, Teri WCarreira, ErickRossen, KaiChirik, PaulMiller, Scott JMcCoy, AnneShea, Joan-EmmaZanni, MartinMurphy, CatherineScholes, GregoryLoo, Joseph A2020-05-053403 Macromolecular and Materials Chemistry (for-2020)34 Chemical Sciences (for-2020)3406 Physical Chemistry (for-2020)40 Engineering (for-2020)4004 Chemical Engineering (for-2020)0904 Chemical Engineering (for)0912 Materials Engineering (for)3403 Macromolecular and materials chemistry (for-2020)3406 Physical chemistry (for-2020)4004 Chemical engineering (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2sc094kchttps://escholarship.org/content/qt2sc094kc/qt2sc094kc.pdfinfo:doi/10.1021/acsomega.0c01788articleACS Omega, vol 5, iss 179624 - 9625oai:escholarship.org:ark:/13030/qt5w7737zh2026-01-08T19:13:17Zqt5w7737zhBottom-up structural proteomics: cryoEM of protein complexes enriched from the cellular milieuHo, Chi-MinLi, XiaorunLai, MasonTerwilliger, Thomas CBeck, Josh RWohlschlegel, JamesGoldberg, Daniel EFitzpatrick, Anthony WPZhou, Z Hong2020-01-01X-ray crystallography often requires non-native constructs involving mutations or truncations, and is challenged by membrane proteins and large multicomponent complexes. We present here a bottom-up endogenous structural proteomics approach whereby near-atomic-resolution cryo electron microscopy (cryoEM) maps are reconstructed ab initio from unidentified protein complexes enriched directly from the endogenous cellular milieu, followed by identification and atomic modeling of the proteins. The proteins in each complex are identified using cryoID, a program we developed to identify proteins in ab initio cryoEM maps. As a proof of principle, we applied this approach to the malaria-causing parasite Plasmodium falciparum, an organism that has resisted conventional structural-biology approaches, to obtain atomic models of multiple protein complexes implicated in intraerythrocytic survival of the parasite. Our approach is broadly applicable for determining structures of undiscovered protein complexes enriched directly from endogenous sources.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Malaria (rcdc)Bioengineering (rcdc)Vector-Borne Diseases (rcdc)Rare Diseases (rcdc)Biotechnology (rcdc)Infectious Diseases (rcdc)Generic health relevance (hrcs-hc)Infection (hrcs-hc)3 Good Health and Well Being (sdg)Amyloid Precursor Protein Secretases (mesh)Cryoelectron Microscopy (mesh)Erythrocytes (mesh)Humans (mesh)Image ProcessingComputer-Assisted (mesh)MalariaFalciparum (mesh)Mass Spectrometry (mesh)ModelsMolecular (mesh)Multiprotein Complexes (mesh)Plasmodium falciparum (mesh)Protein Conformation (mesh)Proteomics (mesh)Protozoan Proteins (mesh)Erythrocytes (mesh)Humans (mesh)Plasmodium falciparum (mesh)MalariaFalciparum (mesh)Multiprotein Complexes (mesh)Protozoan Proteins (mesh)Cryoelectron Microscopy (mesh)Proteomics (mesh)Protein Conformation (mesh)ModelsMolecular (mesh)Image ProcessingComputer-Assisted (mesh)Amyloid Precursor Protein Secretases (mesh)Mass Spectrometry (mesh)Amyloid Precursor Protein Secretases (mesh)Cryoelectron Microscopy (mesh)Erythrocytes (mesh)Humans (mesh)Image ProcessingComputer-Assisted (mesh)MalariaFalciparum (mesh)Mass Spectrometry (mesh)ModelsMolecular (mesh)Multiprotein Complexes (mesh)Plasmodium falciparum (mesh)Protein Conformation (mesh)Proteomics (mesh)Protozoan Proteins (mesh)06 Biological Sciences (for)10 Technology (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5w7737zhhttps://escholarship.org/content/qt5w7737zh/qt5w7737zh.pdfinfo:doi/10.1038/s41592-019-0637-yarticleNature Methods, vol 17, iss 179 - 85oai:escholarship.org:ark:/13030/qt66g062112026-01-06T11:40:55Zqt66g06211Malaria parasite translocon structure and mechanism of effector exportHo, Chi-MinBeck, Josh RLai, MasonCui, YanxiangGoldberg, Daniel EEgea, Pascal FZhou, Z Hong2018-09-06The putative Plasmodium translocon of exported proteins (PTEX) is essential for transport of malarial effector proteins across a parasite-encasing vacuolar membrane into host erythrocytes, but the mechanism of this process remains unknown. Here we show that PTEX is a bona fide translocon by determining structures of the PTEX core complex at near-atomic resolution using cryo-electron microscopy. We isolated the endogenous PTEX core complex containing EXP2, PTEX150 and HSP101 from Plasmodium falciparum in the ‘engaged’ and ‘resetting’ states of endogenous cargo translocation using epitope tags inserted using the CRISPR–Cas9 system. In the structures, EXP2 and PTEX150 interdigitate to form a static, funnel-shaped pseudo-seven-fold-symmetric protein-conducting channel spanning the vacuolar membrane. The spiral-shaped AAA+ HSP101 hexamer is tethered above this funnel, and undergoes pronounced compaction that allows three of six tyrosine-bearing pore loops lining the HSP101 channel to dissociate from the cargo, resetting the translocon for the next threading cycle. Our work reveals the mechanism of P. falciparum effector export, and will inform structure-based design of drugs targeting this unique translocon.3101 Biochemistry and Cell Biology (for-2020)3207 Medical Microbiology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Malaria (rcdc)Infectious Diseases (rcdc)Rare Diseases (rcdc)Vector-Borne Diseases (rcdc)2.2 Factors relating to the physical environment (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Infection (hrcs-hc)3 Good Health and Well Being (sdg)Animals (mesh)Cryoelectron Microscopy (mesh)Erythrocytes (mesh)MalariaFalciparum (mesh)ModelsBiological (mesh)ModelsMolecular (mesh)Molecular Targeted Therapy (mesh)Movement (mesh)Plasmodium falciparum (mesh)Protein Binding (mesh)Protein Multimerization (mesh)Protein StructureQuaternary (mesh)Protein Transport (mesh)Protozoan Proteins (mesh)Vacuoles (mesh)Erythrocytes (mesh)Vacuoles (mesh)Animals (mesh)Plasmodium falciparum (mesh)MalariaFalciparum (mesh)Protozoan Proteins (mesh)Cryoelectron Microscopy (mesh)Protein StructureQuaternary (mesh)Protein Binding (mesh)Protein Transport (mesh)Movement (mesh)ModelsBiological (mesh)ModelsMolecular (mesh)Protein Multimerization (mesh)Molecular Targeted Therapy (mesh)Animals (mesh)Cryoelectron Microscopy (mesh)Erythrocytes (mesh)MalariaFalciparum (mesh)ModelsBiological (mesh)ModelsMolecular (mesh)Molecular Targeted Therapy (mesh)Movement (mesh)Plasmodium falciparum (mesh)Protein Binding (mesh)Protein Multimerization (mesh)Protein StructureQuaternary (mesh)Protein Transport (mesh)Protozoan Proteins (mesh)Vacuoles (mesh)General Science & Technology (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/66g06211https://escholarship.org/content/qt66g06211/qt66g06211.pdfinfo:doi/10.1038/s41586-018-0469-4articleNature, vol 561, iss 772170 - 75oai:escholarship.org:ark:/13030/qt5sm387vh2026-01-05T17:16:48Zqt5sm387vhGenetics of single-cell protein abundance variation in large yeast populationsAlbert, Frank WTreusch, SebastianShockley, Arthur HBloom, Joshua SKruglyak, Leonid2014-02-01A new method for identifying genetic loci that influence protein expression in budding yeast reveals considerable complexity in how genetic variation shapes the proteome.3101 Biochemistry and Cell Biology (for-2020)3105 Genetics (for-2020)31 Biological Sciences (for-2020)Human Genome (rcdc)Biotechnology (rcdc)Genetics (rcdc)Generic health relevance (hrcs-hc)Gene Expression Profiling (mesh)Gene Expression RegulationFungal (mesh)Gene Frequency (mesh)Gene Regulatory Networks (mesh)GenesFungal (mesh)Genetic Variation (mesh)GenomeFungal (mesh)Genotype (mesh)Green Fluorescent Proteins (mesh)Multigene Family (mesh)Proteomics (mesh)Quantitative Trait Loci (mesh)RNAFungal (mesh)RNAMessenger (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)Sequence AnalysisDNA (mesh)Single-Cell Analysis (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)Green Fluorescent Proteins (mesh)RNAFungal (mesh)RNAMessenger (mesh)Gene Expression Profiling (mesh)Sequence AnalysisDNA (mesh)Proteomics (mesh)Gene Expression RegulationFungal (mesh)Gene Frequency (mesh)Genotype (mesh)GenesFungal (mesh)GenomeFungal (mesh)Multigene Family (mesh)Quantitative Trait Loci (mesh)Gene Regulatory Networks (mesh)Genetic Variation (mesh)Single-Cell Analysis (mesh)Gene Expression Profiling (mesh)Gene Expression RegulationFungal (mesh)Gene Frequency (mesh)Gene Regulatory Networks (mesh)GenesFungal (mesh)Genetic Variation (mesh)GenomeFungal (mesh)Genotype (mesh)Green Fluorescent Proteins (mesh)Multigene Family (mesh)Proteomics (mesh)Quantitative Trait Loci (mesh)RNAFungal (mesh)RNAMessenger (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)Sequence AnalysisDNA (mesh)Single-Cell Analysis (mesh)q-bio.GNq-bio.GNGeneral Science & Technology (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5sm387vhhttps://escholarship.org/content/qt5sm387vh/qt5sm387vh.pdfinfo:doi/10.1038/nature12904articleNature, vol 506, iss 7489494 - 497oai:escholarship.org:ark:/13030/qt8vx864sw2026-01-05T17:16:43Zqt8vx864swFinding the sources of missing heritability in a yeast crossBloom, Joshua SEhrenreich, Ian MLoo, Wesley TLite, Thúy-Lan VõKruglyak, Leonid2013-02-14In a cross between two yeast strains, detected loci are found to explain nearly the entire additive contribution to heritable variation for a number of quantitative traits.31 Biological Sciences (for-2020)3105 Genetics (for-2020)Human Genome (rcdc)Genetics (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Generic health relevance (hrcs-hc)CrossesGenetic (mesh)Humans (mesh)ModelsGenetic (mesh)Phenotype (mesh)Quantitative Trait Loci (mesh)Quantitative TraitHeritable (mesh)Saccharomyces cerevisiae (mesh)Humans (mesh)Saccharomyces cerevisiae (mesh)CrossesGenetic (mesh)Quantitative TraitHeritable (mesh)Phenotype (mesh)Quantitative Trait Loci (mesh)ModelsGenetic (mesh)CrossesGenetic (mesh)Humans (mesh)ModelsGenetic (mesh)Phenotype (mesh)Quantitative Trait Loci (mesh)Quantitative TraitHeritable (mesh)Saccharomyces cerevisiae (mesh)q-bio.GNq-bio.GNGeneral Science & Technology (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8vx864swhttps://escholarship.org/content/qt8vx864sw/qt8vx864sw.pdfinfo:doi/10.1038/nature11867articleNature, vol 494, iss 7436234 - 237oai:escholarship.org:ark:/13030/qt29k3w68p2026-01-05T09:55:56Zqt29k3w68pCommon Variants at 9p21 and 8q22 Are Associated with Increased Susceptibility to Optic Nerve Degeneration in GlaucomaWiggs, Janey LYaspan, Brian LHauser, Michael AKang, Jae HAllingham, R RandOlson, Lana MAbdrabou, WaelFan, Bao JWang, Dan YBrodeur, WendyBudenz, Donald LCaprioli, JosephCrenshaw, AndrewCrooks, KristyDelBono, ElizabethDoheny, Kimberly FFriedman, David SGaasterland, DouglasGaasterland, TerryLaurie, CathyLee, Richard KLichter, Paul RLoomis, StephanieLiu, YutaoMedeiros, Felipe AMcCarty, CathyMirel, DanielMoroi, Sayoko EMusch, David CRealini, AnthonyRozsa, Frank WSchuman, Joel SScott, KathleenSingh, KuldevStein, Joshua DTrager, Edward HVanVeldhuisen, PaulVollrath, DouglasWollstein, GadiYoneyama, SachikoZhang, KangWeinreb, Robert NErnst, JasonKellis, ManolisMasuda, TomohiroZack, DonRichards, Julia EPericak-Vance, MargaretPasquale, Louis RHaines, Jonathan LBarsh, Gregory S2012-01-01Optic nerve degeneration caused by glaucoma is a leading cause of blindness worldwide. Patients affected by the normal-pressure form of glaucoma are more likely to harbor risk alleles for glaucoma-related optic nerve disease. We have performed a meta-analysis of two independent genome-wide association studies for primary open angle glaucoma (POAG) followed by a normal-pressure glaucoma (NPG, defined by intraocular pressure (IOP) less than 22 mmHg) subgroup analysis. The single-nucleotide polymorphisms that showed the most significant associations were tested for association with a second form of glaucoma, exfoliation-syndrome glaucoma. The overall meta-analysis of the GLAUGEN and NEIGHBOR dataset results (3,146 cases and 3,487 controls) identified significant associations between two loci and POAG: the CDKN2BAS region on 9p21 (rs2157719 [G], OR = 0.69 [95%CI 0.63-0.75], p = 1.86×10⁻¹⁸), and the SIX1/SIX6 region on chromosome 14q23 (rs10483727 [A], OR = 1.32 [95%CI 1.21-1.43], p = 3.87×10⁻¹¹). In sub-group analysis two loci were significantly associated with NPG: 9p21 containing the CDKN2BAS gene (rs2157719 [G], OR = 0.58 [95% CI 0.50-0.67], p = 1.17×10⁻¹²) and a probable regulatory region on 8q22 (rs284489 [G], OR = 0.62 [95% CI 0.53-0.72], p = 8.88×10⁻¹⁰). Both NPG loci were also nominally associated with a second type of glaucoma, exfoliation syndrome glaucoma (rs2157719 [G], OR = 0.59 [95% CI 0.41-0.87], p = 0.004 and rs284489 [G], OR = 0.76 [95% CI 0.54-1.06], p = 0.021), suggesting that these loci might contribute more generally to optic nerve degeneration in glaucoma. Because both loci influence transforming growth factor beta (TGF-beta) signaling, we performed a genomic pathway analysis that showed an association between the TGF-beta pathway and NPG (permuted p = 0.009). These results suggest that neuro-protective therapies targeting TGF-beta signaling could be effective for multiple forms of glaucoma.31 Biological Sciences (for-2020)3105 Genetics (for-2020)Eye Disease and Disorders of Vision (rcdc)Genetics (rcdc)Neurosciences (rcdc)Human Genome (rcdc)Aging (rcdc)Neurodegenerative (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Eye (hrcs-hc)Alleles (mesh)ChromosomesHumanPair 8 (mesh)ChromosomesHumanPair 9 (mesh)Exfoliation Syndrome (mesh)Genome-Wide Association Study (mesh)GlaucomaOpen-Angle (mesh)Homeodomain Proteins (mesh)Humans (mesh)Nerve Degeneration (mesh)Optic Nerve (mesh)PolymorphismSingle Nucleotide (mesh)RNALong Noncoding (mesh)RNAUntranslated (mesh)Transforming Growth Factor beta (mesh)Optic Nerve (mesh)ChromosomesHumanPair 8 (mesh)ChromosomesHumanPair 9 (mesh)Humans (mesh)GlaucomaOpen-Angle (mesh)Exfoliation Syndrome (mesh)Nerve Degeneration (mesh)Transforming Growth Factor beta (mesh)Homeodomain Proteins (mesh)RNAUntranslated (mesh)PolymorphismSingle Nucleotide (mesh)Alleles (mesh)Genome-Wide Association Study (mesh)RNALong Noncoding (mesh)Alleles (mesh)ChromosomesHumanPair 8 (mesh)ChromosomesHumanPair 9 (mesh)Exfoliation Syndrome (mesh)Genome-Wide Association Study (mesh)GlaucomaOpen-Angle (mesh)Homeodomain Proteins (mesh)Humans (mesh)Nerve Degeneration (mesh)Optic Nerve (mesh)PolymorphismSingle Nucleotide (mesh)RNALong Noncoding (mesh)RNAUntranslated (mesh)Transforming Growth Factor beta (mesh)0604 Genetics (for)Developmental Biology (science-metrix)3105 Genetics (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/29k3w68phttps://escholarship.org/content/qt29k3w68p/qt29k3w68p.pdfinfo:doi/10.1371/journal.pgen.1002654articlePLOS Genetics, vol 8, iss 4e1002654oai:escholarship.org:ark:/13030/qt27r7h8s42026-01-04T14:11:50Zqt27r7h8s4Wearable microneedle-based electrochemical aptamer biosensing for precision dosing of drugs with narrow therapeutic windowsLin, ShuyuCheng, XuanbingZhu, JialunWang, BoJelinek, DavidZhao, YichaoWu, Tsung-YuHorrillo, AbrahamTan, JiaweiYeung, JustinYan, WenzhongForman, SarahColler, Hilary AMilla, CarlosEmaminejad, Sam2022-09-23Therapeutic drug monitoring is essential for dosing pharmaceuticals with narrow therapeutic windows. Nevertheless, standard methods are imprecise and involve invasive/resource-intensive procedures with long turnaround times. Overcoming these limitations, we present a microneedle-based electrochemical aptamer biosensing patch (μNEAB-patch) that minimally invasively probes the interstitial fluid (ISF) and renders correlated, continuous, and real-time measurements of the circulating drugs' pharmacokinetics. The μNEAB-patch is created following an introduced low-cost fabrication scheme, which transforms a shortened clinical-grade needle into a high-quality gold nanoparticle-based substrate for robust aptamer immobilization and efficient electrochemical signal retrieval. This enables the reliable in vivo detection of a wide library of ISF analytes-especially those with nonexistent natural recognition elements. Accordingly, we developed μNEABs targeting various drugs, including antibiotics with narrow therapeutic windows (tobramycin and vancomycin). Through in vivo animal studies, we demonstrated the strong correlation between the ISF/circulating drug levels and the device's potential clinical use for timely prediction of total drug exposure.3214 Pharmacology and Pharmaceutical Sciences (for-2020)46 Information and Computing Sciences (for-2020)32 Biomedical and Clinical Sciences (for-2020)Biotechnology (rcdc)Bioengineering (rcdc)Nanotechnology (rcdc)5.1 Pharmaceuticals (hrcs-rac)4.1 Discovery and preclinical testing of markers and technologies (hrcs-rac)3 Good Health and Well Being (sdg)application/pdfCC-BY-NCeScholarship, University of Californiahttps://escholarship.org/uc/item/27r7h8s4https://escholarship.org/content/qt27r7h8s4/qt27r7h8s4.pdfinfo:doi/10.1126/sciadv.abq4539articleScience Advances, vol 8, iss 38eabq4539oai:escholarship.org:ark:/13030/qt80j7540x2026-01-04T09:59:41Zqt80j7540xProspecting for natural products by genome mining and microcrystal electron diffractionKim, Lee JoonOhashi, MasaoZhang, ZhuanTan, DanAsay, MatthewCascio, DuilioRodriguez, José ATang, YiNelson, Hosea M2021-08-01More than 60% of pharmaceuticals are related to natural products (NPs), chemicals produced by living organisms. Despite this, the rate of NP discovery has slowed over the past few decades. In many cases the rate-limiting step in NP discovery is structural characterization. Here we report the use of microcrystal electron diffraction (MicroED), an emerging cryogenic electron microscopy (CryoEM) method, in combination with genome mining to accelerate NP discovery and structural elucidation. As proof of principle we rapidly determine the structure of a new 2-pyridone NP, Py-469, and revise the structure of fischerin, an NP isolated more than 25 years ago, with potent cytotoxicity but hitherto ambiguous structural assignment. This study serves as a powerful demonstration of the synergy of MicroED and synthetic biology in NP discovery, technologies that when taken together will ultimately accelerate the rate at which new drugs are discovered.3402 Inorganic Chemistry (for-2020)34 Chemical Sciences (for-2020)31 Biological Sciences (for-2020)Generic health relevance (hrcs-hc)Biological Products (mesh)Cryoelectron Microscopy (mesh)ModelsMolecular (mesh)Molecular Conformation (mesh)Biological Products (mesh)Cryoelectron Microscopy (mesh)Molecular Conformation (mesh)ModelsMolecular (mesh)Biological Products (mesh)Cryoelectron Microscopy (mesh)ModelsMolecular (mesh)Molecular Conformation (mesh)0304 Medicinal and Biomolecular Chemistry (for)0601 Biochemistry and Cell Biology (for)Biochemistry & Molecular Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)3404 Medicinal and biomolecular chemistry (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/80j7540xhttps://escholarship.org/content/qt80j7540x/qt80j7540x.pdfinfo:doi/10.1038/s41589-021-00834-2articleNature Chemical Biology, vol 17, iss 8872 - 877oai:escholarship.org:ark:/13030/qt8cs8z9p32026-01-04T07:03:24Zqt8cs8z9p3Improving the solubility of pseudo-hydrophobic chemicals through co-crystal formulationJanilkarn-Urena, IsisTse, AmandaLin, JieyeTafolla-Aguirre, BlissIdrissova, AlinaZhang, MindySkinner, Samantha GMostowfi, NaderKim, JinahKalapatapu, NikhilaChang, XinminEfthymiou, ChristinaWilliams, Christopher KMagaki, Shino DVinters, Harry VGonen, TamirAhmed, S KaleemGukasyan, Hovhannes JDavies, Daryl LSeidler, Paul MBahar, Ivet2024-12-23Natural products are ligands and in vitro inhibitors of Alzheimer's disease (AD) tau. Dihydromyricetin (DHM) bears chemical similarity to known natural product tau inhibitors. Despite having signature polyphenolic character, DHM is ostensibly hydrophobic owing to intermolecular hydrogen bonds that shield hydrophilic phenols. Our research shows DHM becomes ionized at near-neutral pH, allowing the formulation of salts with transformed solubility. The MicroED co-crystal structure with trolamine reveals DHM salts as metastable co-crystalline solids with unlocked hydrogen bonding and a thermodynamic bent to solubilize in water. All co-crystal formulations show better inhibitory activity against AD tau than the nonsalt form, with efficacies correlating to enhanced solubilities. In vitro and in vivo pharmacokinetic measures demonstrate that DHM co-crystals display enhanced absorption and distribution with altered rates of elimination, suggesting that co-crystal formulations could be strategically used to fine-tune delivery properties. These results underscore the role of structural chemistry in guiding the selection of solubilizing agents for chemical formulation. We propose DHM co-crystals are appropriate formulations for research as dietary supplements to promote healthy aging by combating protein misfolding, although central nervous system (CNS) delivery remains a major limitation. DHM may be a suitable backbone for medicinal chemistry and possible development of pharmaceuticals with enhanced CNS exposure.3402 Inorganic Chemistry (for-2020)34 Chemical Sciences (for-2020)Aging (rcdc)Alzheimer's Disease (rcdc)Neurodegenerative (rcdc)Acquired Cognitive Impairment (rcdc)Neurosciences (rcdc)Brain Disorders (rcdc)Dementia (rcdc)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/8cs8z9p3https://escholarship.org/content/qt8cs8z9p3/qt8cs8z9p3.pdfinfo:doi/10.1093/pnasnexus/pgaf007articlePNAS Nexus, vol 4, iss 1pgaf007oai:escholarship.org:ark:/13030/qt9jr5g1hb2026-01-04T02:58:43Zqt9jr5g1hbRobust enhancer-gene regulation identified by single-cell transcriptomes and epigenomesXie, FangmingArmand, Ethan JYao, ZizhenLiu, HanqingBartlett, AnnaBehrens, M MargaritaLi, Yang EricLucero, Jacinta DLuo, ChongyuanNery, Joseph RPinto-Duarte, AntonioPoirion, Olivier BPreissl, SebastianRivkin, Angeline CTasic, BosiljkaZeng, HongkuiRen, BingEcker, Joseph RMukamel, Eran A2023-07-01Single-cell sequencing could help to solve the fundamental challenge of linking millions of cell-type-specific enhancers with their target genes. However, this task is confounded by patterns of gene co-expression in much the same way that genetic correlation due to linkage disequilibrium confounds fine-mapping in genome-wide association studies (GWAS). We developed a non-parametric permutation-based procedure to establish stringent statistical criteria to control the risk of false-positive associations in enhancer-gene association studies (EGAS). We applied our procedure to large-scale transcriptome and epigenome data from multiple tissues and species, including the mouse and human brain, to predict enhancer-gene associations genome wide. We tested the functional validity of our predictions by comparing them with chromatin conformation data and causal enhancer perturbation experiments. Our study shows how controlling for gene co-expression enables robust enhancer-gene linkage using single-cell sequencing data.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)3105 Genetics (for-2020)4202 Epidemiology (for-2020)42 Health Sciences (for-2020)Cancer Genomics (rcdc)Cancer (rcdc)Genetics (rcdc)Biotechnology (rcdc)Human Genome (rcdc)2.1 Biological and endogenous factors (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)DNA methylationbrainchromatin accessibilityenhancerepigenomeapplication/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/9jr5g1hbhttps://escholarship.org/content/qt9jr5g1hb/qt9jr5g1hb.pdfinfo:doi/10.1016/j.xgen.2023.100342articleCell Genomics, vol 3, iss 7100342oai:escholarship.org:ark:/13030/qt1wc6w7gj2026-01-04T00:27:21Zqt1wc6w7gjA PPARγ/long noncoding RNA axis regulates adipose thermoneutral remodeling in miceZhang, ZhengyiCui, YaSu, VivienWang, DanTol, Marcus JCheng, LijingWu, XiaohuiKim, JasonRajbhandari, PrashantZhang, SichengLi, WeiTontonoz, PeterVillanueva, Claudio JSallam, Tamer2023-11-01Interplay between energy-storing white adipose cells and thermogenic beige adipocytes contributes to obesity and insulin resistance. Irrespective of specialized niche, adipocytes require the activity of the nuclear receptor PPARγ for proper function. Exposure to cold or adrenergic signaling enriches thermogenic cells though multiple pathways that act synergistically with PPARγ; however, the molecular mechanisms by which PPARγ licenses white adipose tissue to preferentially adopt a thermogenic or white adipose fate in response to dietary cues or thermoneutral conditions are not fully elucidated. Here, we show that a PPARγ/long noncoding RNA (lncRNA) axis integrates canonical and noncanonical thermogenesis to restrain white adipose tissue heat dissipation during thermoneutrality and diet-induced obesity. Pharmacologic inhibition or genetic deletion of the lncRNA Lexis enhances uncoupling protein 1-dependent (UCP1-dependent) and -independent thermogenesis. Adipose-specific deletion of Lexis counteracted diet-induced obesity, improved insulin sensitivity, and enhanced energy expenditure. Single-nuclei transcriptomics revealed that Lexis regulates a distinct population of thermogenic adipocytes. We systematically map Lexis motif preferences and show that it regulates the thermogenic program through the activity of the metabolic GWAS gene and WNT modulator TCF7L2. Collectively, our studies uncover a new mode of crosstalk between PPARγ and WNT that preserves white adipose tissue plasticity.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Nutrition (rcdc)Obesity (rcdc)Diabetes (rcdc)Genetics (rcdc)Human Genome (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Metabolic and endocrine (hrcs-hc)2 Zero Hunger (sdg)Animals (mesh)Mice (mesh)Adipocytes (mesh)Adipose TissueBrown (mesh)Adipose TissueWhite (mesh)Insulin Resistance (mesh)Obesity (mesh)PPAR gamma (mesh)RNALong Noncoding (mesh)Thermogenesis (mesh)Uncoupling Protein 1 (mesh)Adipocytes (mesh)Animals (mesh)Mice (mesh)Insulin Resistance (mesh)Obesity (mesh)PPAR gamma (mesh)Thermogenesis (mesh)Adipose TissueBrown (mesh)Adipose TissueWhite (mesh)RNALong Noncoding (mesh)Uncoupling Protein 1 (mesh)Adipose tissueCardiologyMetabolismMolecular geneticsNoncoding RNAsAnimals (mesh)Mice (mesh)Adipocytes (mesh)Adipose TissueBrown (mesh)Adipose TissueWhite (mesh)Insulin Resistance (mesh)Obesity (mesh)PPAR gamma (mesh)RNALong Noncoding (mesh)Thermogenesis (mesh)Uncoupling Protein 1 (mesh)11 Medical and Health Sciences (for)Immunology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/1wc6w7gjhttps://escholarship.org/content/qt1wc6w7gj/qt1wc6w7gj.pdfinfo:doi/10.1172/jci170072articleJournal of Clinical Investigation, vol 133, iss 21e170072oai:escholarship.org:ark:/13030/qt25w8x7042026-01-03T19:25:41Zqt25w8x704Structure-based design of nanobodies that inhibit seeding of Alzheimer’s patient–extracted tau fibrilsAbskharon, RomanyPan, HopeSawaya, Michael RSeidler, Paul MOlivares, Eileen JChen, YuMurray, Kevin AZhang, JeffreyLantz, CarterBentzel, MeganBoyer, David RCascio, DuilioNguyen, Binh AHou, KeCheng, XinyiPardon, ElsWilliams, Christopher KNana, Alissa LVinters, Harry VSpina, SalvatoreGrinberg, Lea TSeeley, William WSteyaert, JanGlabe, Charles GLoo, Rachel R OgorzalekLoo, Joseph AEisenberg, David S2023-10-10Despite much effort, antibody therapies for Alzheimer's disease (AD) have shown limited efficacy. Challenges to the rational design of effective antibodies include the difficulty of achieving specific affinity to critical targets, poor expression, and antibody aggregation caused by buried charges and unstructured loops. To overcome these challenges, we grafted previously determined sequences of fibril-capping amyloid inhibitors onto a camel heavy chain antibody scaffold. These sequences were designed to cap fibrils of tau, known to form the neurofibrillary tangles of AD, thereby preventing fibril elongation. The nanobodies grafted with capping inhibitors blocked tau aggregation in biosensor cells seeded with postmortem brain extracts from AD and progressive supranuclear palsy (PSP) patients. The tau capping nanobody inhibitors also blocked seeding by recombinant tau oligomers. Another challenge to the design of effective antibodies is their poor blood-brain barrier (BBB) penetration. In this study, we also designed a bispecific nanobody composed of a nanobody that targets a receptor on the BBB and a tau capping nanobody inhibitor, conjoined by a flexible linker. We provide evidence that the bispecific nanobody improved BBB penetration over the tau capping inhibitor alone after intravenous administration in mice. Our results suggest that the design of synthetic antibodies that target sequences that drive protein aggregation may be a promising approach to inhibit the prion-like seeding of tau and other proteins involved in AD and related proteinopathies.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Acquired Cognitive Impairment (rcdc)Neurodegenerative (rcdc)Brain Disorders (rcdc)Immunization (rcdc)Aging (rcdc)Neurosciences (rcdc)Alzheimer's Disease Related Dementias (ADRD) (rcdc)Dementia (rcdc)Biotechnology (rcdc)Rare Diseases (rcdc)Alzheimer's Disease (rcdc)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)5.1 Pharmaceuticals (hrcs-rac)Neurological (hrcs-hc)Humans (mesh)Animals (mesh)Mice (mesh)Alzheimer Disease (mesh)tau Proteins (mesh)Single-Domain Antibodies (mesh)Neurofibrillary Tangles (mesh)Supranuclear PalsyProgressive (mesh)Antibodies (mesh)Brain (mesh)nanobodyamyloidtauprion-like spreadingsynthetic antibodyBrain (mesh)Neurofibrillary Tangles (mesh)Animals (mesh)Humans (mesh)Mice (mesh)Supranuclear PalsyProgressive (mesh)Alzheimer Disease (mesh)tau Proteins (mesh)Antibodies (mesh)Single-Domain Antibodies (mesh)amyloidnanobodyprion-like spreadingsynthetic antibodytauHumans (mesh)Animals (mesh)Mice (mesh)Alzheimer Disease (mesh)tau Proteins (mesh)Single-Domain Antibodies (mesh)Neurofibrillary Tangles (mesh)Supranuclear PalsyProgressive (mesh)Antibodies (mesh)Brain (mesh)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/25w8x704https://escholarship.org/content/qt25w8x704/qt25w8x704.pdfinfo:doi/10.1073/pnas.2300258120articleProceedings of the National Academy of Sciences of the United States of America, vol 120, iss 41e2300258120oai:escholarship.org:ark:/13030/qt69k286p72026-01-03T14:54:51Zqt69k286p7Eliminating the missing cone challenge through innovative approachesGillman, CodyBu, GuanhongDanelius, EmmaHattne, JohanNannenga, Brent LGonen, Tamir2024-06-01Microcrystal electron diffraction (MicroED) has emerged as a powerful technique for unraveling molecular structures from microcrystals too small for X-ray diffraction. However, a significant hurdle arises with plate-like crystals that consistently orient themselves flat on the electron microscopy grid. If the normal of the plate correlates with the axes of the crystal lattice, the crystal orientations accessible for measurement are restricted because the crystal cannot be arbitrarily rotated. This limits the information that can be acquired, resulting in a missing cone of information. We recently introduced a novel crystallization strategy called suspended drop crystallization and proposed that crystals in a suspended drop could effectively address the challenge of preferred crystal orientation. Here we demonstrate the success of the suspended drop approach in eliminating the missing cone in two samples that crystallize as thin plates: bovine liver catalase and the SARS‑CoV‑2 main protease (Mpro). This innovative solution proves indispensable for crystals exhibiting systematic preferred orientations, unlocking new possibilities for structure determination by MicroED.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Microcrystal electron diffractionMicroEDCryo-EMFIB millingCryogenic freezingPlasma FIB/SEMpFIBSuspended dropMissing coneCryo-EMCryogenic freezingFIB millingMicroEDMicrocrystal electron diffractionMissing conePlasma FIB/SEMSuspended droppFIB3101 Biochemistry and cell biology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/69k286p7https://escholarship.org/content/qt69k286p7/qt69k286p7.pdfinfo:doi/10.1016/j.yjsbx.2024.100102articleJournal of Structural Biology X, vol 9100102oai:escholarship.org:ark:/13030/qt2mj8h4cj2026-01-03T14:10:19Zqt2mj8h4cjVirtually the Same? Evaluating the Effectiveness of Remote Undergraduate Research ExperiencesHess, Riley AErickson, Olivia ACole, Rebecca BIsaacs, Jared MAlvarez-Clare, SilviaArnold, JonathanAugustus-Wallace, AllisonAyoob, Joseph CBerkowitz, AlanBranchaw, JanetBurgio, Kevin RCannon, Charles HCeballos, Ruben MichaelCohen, C SarahColler, HilaryDisney, JaneDoze, Van AEggers, Margaret JFerguson, Edwin LGray, Jeffrey JGreenberg, Jean THoffmann, AlexanderJensen-Ryan, DanielleKao, Robert MKeene, Alex CKowalko, Johanna ELopez, Steven AMathis, CamilleMinkara, MonaMurren, Courtney JOndrechen, Mary JoOrdoñez, PatriciaOsano, AnnePadilla-Crespo, ElizabethPalchoudhury, SoubantikaQin, HongRamírez-Lugo, JuanReithel, JenniferShaw, Colin ASmith, AmberSmith, Rosemary JTsien, FernDolan, Erin LFrantz, Kyle2023-06-01In-person undergraduate research experiences (UREs) promote students' integration into careers in life science research. In 2020, the COVID-19 pandemic prompted institutions hosting summer URE programs to offer them remotely, raising questions about whether undergraduates who participate in remote research can experience scientific integration and whether they might perceive doing research less favorably (i.e., not beneficial or too costly). To address these questions, we examined indicators of scientific integration and perceptions of the benefits and costs of doing research among students who participated in remote life science URE programs in Summer 2020. We found that students experienced gains in scientific self-efficacy pre- to post-URE, similar to results reported for in-person UREs. We also found that students experienced gains in scientific identity, graduate and career intentions, and perceptions of the benefits of doing research only if they started their remote UREs at lower levels on these variables. Collectively, students did not change in their perceptions of the costs of doing research despite the challenges of working remotely. Yet students who started with low cost perceptions increased in these perceptions. These findings indicate that remote UREs can support students' self-efficacy development, but may otherwise be limited in their potential to promote scientific integration.3901 Curriculum and Pedagogy (for-2020)39 Education (for-2020)Humans (mesh)Students (mesh)Pandemics (mesh)COVID-19 (mesh)Humans (mesh)Students (mesh)Pandemics (mesh)COVID-19 (mesh)Humans (mesh)Students (mesh)Pandemics (mesh)COVID-19 (mesh)1302 Curriculum and Pedagogy (for)Education (science-metrix)3901 Curriculum and pedagogy (for-2020)application/pdfCC-BY-NC-SAeScholarship, University of Californiahttps://escholarship.org/uc/item/2mj8h4cjhttps://escholarship.org/content/qt2mj8h4cj/qt2mj8h4cj.pdfinfo:doi/10.1187/cbe.22-01-0001articleCBE—Life Sciences Education, vol 22, iss 2ar25oai:escholarship.org:ark:/13030/qt21c9989z2026-01-03T12:49:21Zqt21c9989zAn LXR-Cholesterol Axis Creates a Metabolic Co-Dependency for Brain CancersVilla, Genaro RHulce, Jonathan JZanca, CiroBi, JunfengIkegami, ShiroCahill, Gabrielle LGu, YuchaoLum, Kenneth MMasui, KentaYang, HuijunRong, XinHong, CynthiaTurner, Kristen MLiu, FengHon, Gary CJenkins, DavidMartini, MichaelArmando, Aaron MQuehenberger, OswaldCloughesy, Timothy FFurnari, Frank BCavenee, Webster KTontonoz, PeterGahman, Timothy CShiau, Andrew KCravatt, Benjamin FMischel, Paul S2016-11-01Small-molecule inhibitors targeting growth factor receptors have failed to show efficacy for brain cancers, potentially due to their inability to achieve sufficient drug levels in the CNS. Targeting non-oncogene tumor co-dependencies provides an alternative approach, particularly if drugs with high brain penetration can be identified. Here we demonstrate that the highly lethal brain cancer glioblastoma (GBM) is remarkably dependent on cholesterol for survival, rendering these tumors sensitive to Liver X receptor (LXR) agonist-dependent cell death. We show that LXR-623, a clinically viable, highly brain-penetrant LXRα-partial/LXRβ-full agonist selectively kills GBM cells in an LXRβ- and cholesterol-dependent fashion, causing tumor regression and prolonged survival in mouse models. Thus, a metabolic co-dependency provides a pharmacological means to kill growth factor-activated cancers in the CNS.32 Biomedical and Clinical Sciences (for-2020)3211 Oncology and Carcinogenesis (for-2020)Brain Cancer (rcdc)Digestive Diseases (rcdc)Cancer (rcdc)Orphan Drug (rcdc)Neurosciences (rcdc)Liver Disease (rcdc)Rare Diseases (rcdc)Brain Disorders (rcdc)5.1 Pharmaceuticals (hrcs-rac)Cancer (hrcs-hc)Animals (mesh)Brain Neoplasms (mesh)Cell LineTumor (mesh)Cell Proliferation (mesh)Cell Survival (mesh)Cholesterol (mesh)Female (mesh)Glioblastoma (mesh)Humans (mesh)Indazoles (mesh)Liver X Receptors (mesh)Mice (mesh)Treatment Outcome (mesh)Cell LineTumor (mesh)Animals (mesh)Humans (mesh)Mice (mesh)Glioblastoma (mesh)Brain Neoplasms (mesh)Indazoles (mesh)Cholesterol (mesh)Treatment Outcome (mesh)Cell Proliferation (mesh)Cell Survival (mesh)Female (mesh)Liver X Receptors (mesh)brain cancercholesterolglioblastomaliver X receptormetabolismoxysterolsAnimals (mesh)Brain Neoplasms (mesh)Cell LineTumor (mesh)Cell Proliferation (mesh)Cell Survival (mesh)Cholesterol (mesh)Female (mesh)Glioblastoma (mesh)Humans (mesh)Indazoles (mesh)Liver X Receptors (mesh)Mice (mesh)Treatment Outcome (mesh)1109 Neurosciences (for)1112 Oncology and Carcinogenesis (for)Oncology & Carcinogenesis (science-metrix)3101 Biochemistry and cell biology (for-2020)3211 Oncology and carcinogenesis (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/21c9989zhttps://escholarship.org/content/qt21c9989z/qt21c9989z.pdfinfo:doi/10.1016/j.ccell.2016.09.008articleCancer Cell, vol 30, iss 5683 - 693oai:escholarship.org:ark:/13030/qt2pk6r6c82026-01-03T11:46:44Zqt2pk6r6c8Dact-4 is a Xenopus laevis Spemann organizer gene related to the Dapper/Frodo antagonist of β-catenin family of proteinsColozza, GabrieleDe Robertis, Edward M2020-12-01Dact/Dapper/Frodo members belong to an evolutionarily conserved family of Dishevelled-binding proteins present in mammals, birds, amphibians and fishes that are involved in the regulation of Wnt and TGF-β signaling. In addition to the three established genes (Dact1-3) that compose the Dact family, a fourth paralogue group of related proteins has been recently identified and named Dact-4. Interestingly, Dact-4 is the most rapidly evolving gene of the entire family, as it displays very low homology with other Dact proteins and has lost key conserved domains. Dact-4 is not present in mammals, but weakly conserved homologs were found in reptiles and fishes. Recent RNAseq from our group identified new genes specifically expressed in the Xenopus laevis Spemann organizer. Among these, LOC100170590 mRNA encoded a protein sharing weak homology with a coelacanth Dact-like protein member. Here, by analyzing protein phylogeny and synteny, we show that this organizer gene corresponds to Dact-4. We report that Dact-4 is expressed in the Xenopus blastula pre-organizer region in addition to the gastrula organizer, as well as in placodes, eyes, neural tube, presomitic mesoderm and pronephros. Dact-4-Flag microinjection experiments suggest it is a nucleocytoplasmic protein, as are the other Dact paralogues.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Adaptor ProteinsSignal Transducing (mesh)Animals (mesh)EvolutionMolecular (mesh)OrganizersEmbryonic (mesh)Phylogeny (mesh)Sequence HomologyAmino Acid (mesh)Synteny (mesh)Xenopus Proteins (mesh)Xenopus laevis (mesh)beta Catenin (mesh)Spemann organizerDact-4DapperFrodoWhole-genome duplicationsOrganizersEmbryonic (mesh)Animals (mesh)Xenopus laevis (mesh)Adaptor ProteinsSignal Transducing (mesh)Xenopus Proteins (mesh)EvolutionMolecular (mesh)Phylogeny (mesh)Sequence HomologyAmino Acid (mesh)Synteny (mesh)beta Catenin (mesh)Dact-4DapperFrodoSpemann organizerWhole-genome duplicationsAdaptor ProteinsSignal Transducing (mesh)Animals (mesh)EvolutionMolecular (mesh)OrganizersEmbryonic (mesh)Phylogeny (mesh)Sequence HomologyAmino Acid (mesh)Synteny (mesh)Xenopus Proteins (mesh)Xenopus laevis (mesh)beta Catenin (mesh)0604 Genetics (for)1103 Clinical Sciences (for)Developmental Biology (science-metrix)3105 Genetics (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/2pk6r6c8https://escholarship.org/content/qt2pk6r6c8/qt2pk6r6c8.pdfinfo:doi/10.1016/j.gep.2020.119153articleGene Expression Patterns, vol 38119153oai:escholarship.org:ark:/13030/qt2120303x2026-01-03T02:26:57Zqt2120303x2-Hydroxyglutarate Inhibits ATP Synthase and mTOR SignalingFu, XudongChin, Randall MVergnes, LaurentHwang, HeejunDeng, GangXing, YanpengPai, Melody YLi, SichenTa, LisaFazlollahi, FarbodChen, ChuoPrins, Robert MTeitell, Michael ANathanson, David ALai, AlbertFaull, Kym FJiang, MeishengClarke, Steven GCloughesy, Timothy FGraeber, Thomas GBraas, DanielChristofk, Heather RJung, Michael EReue, KarenHuang, Jing2015-09-01We discovered recently that the central metabolite α-ketoglutarate (α-KG) extends the lifespan of C. elegans through inhibition of ATP synthase and TOR signaling. Here we find, unexpectedly, that (R)-2-hydroxyglutarate ((R)-2HG), an oncometabolite that interferes with various α-KG-mediated processes, similarly extends worm lifespan. (R)-2HG accumulates in human cancers carrying neomorphic mutations in the isocitrate dehydrogenase (IDH) 1 and 2 genes. We show that, like α-KG, both (R)-2HG and (S)-2HG bind and inhibit ATP synthase and inhibit mTOR signaling. These effects are mirrored in IDH1 mutant cells, suggesting a growth-suppressive function of (R)-2HG. Consistently, inhibition of ATP synthase by 2-HG or α-KG in glioblastoma cells is sufficient for growth arrest and tumor cell killing under conditions of glucose limitation, e.g., when ketone bodies (instead of glucose) are supplied for energy. These findings inform therapeutic strategies and open avenues for investigating the roles of 2-HG and metabolites in biology and disease.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Brain Cancer (rcdc)Rare Diseases (rcdc)Genetics (rcdc)Brain Disorders (rcdc)Cancer (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Adenosine Triphosphatases (mesh)Animals (mesh)Caenorhabditis elegans (mesh)Cell Proliferation (mesh)Glioblastoma (mesh)Glutarates (mesh)Humans (mesh)Isocitrate Dehydrogenase (mesh)Longevity (mesh)Mutation (mesh)Signal Transduction (mesh)TOR Serine-Threonine Kinases (mesh)Animals (mesh)Humans (mesh)Caenorhabditis elegans (mesh)Glioblastoma (mesh)Glutarates (mesh)Isocitrate Dehydrogenase (mesh)Signal Transduction (mesh)Cell Proliferation (mesh)Longevity (mesh)Mutation (mesh)Adenosine Triphosphatases (mesh)TOR Serine-Threonine Kinases (mesh)Adenosine Triphosphatases (mesh)Animals (mesh)Caenorhabditis elegans (mesh)Cell Proliferation (mesh)Glioblastoma (mesh)Glutarates (mesh)Humans (mesh)Isocitrate Dehydrogenase (mesh)Longevity (mesh)Mutation (mesh)Signal Transduction (mesh)TOR Serine-Threonine Kinases (mesh)0601 Biochemistry and Cell Biology (for)1101 Medical Biochemistry and Metabolomics (for)Endocrinology & Metabolism (science-metrix)3101 Biochemistry and cell biology (for-2020)3205 Medical biochemistry and metabolomics (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2120303xhttps://escholarship.org/content/qt2120303x/qt2120303x.pdfinfo:doi/10.1016/j.cmet.2015.06.009articleCell Metabolism, vol 22, iss 3508 - 515oai:escholarship.org:ark:/13030/qt7gr0686g2026-01-03T01:46:12Zqt7gr0686gDe novo phasing with X-ray laser reveals mosquito larvicide BinAB structureColletier, Jacques-PhilippeSawaya, Michael RGingery, MariRodriguez, Jose ACascio, DuilioBrewster, Aaron SMichels-Clark, TaraHice, Robert HCoquelle, NicolasBoutet, SébastienWilliams, Garth JMesserschmidt, MarcDePonte, Daniel PSierra, Raymond GLaksmono, HartawanKoglin, Jason EHunter, Mark SPark, Hyun-WooUervirojnangkoorn, MonarinBideshi, Dennis KBrunger, Axel TFederici, Brian ASauter, Nicholas KEisenberg, David S2016-11-03BinAB is a naturally occurring paracrystalline larvicide distributed worldwide to combat the devastating diseases borne by mosquitoes. These crystals are composed of homologous molecules, BinA and BinB, which play distinct roles in the multi-step intoxication process, transforming from harmless, robust crystals, to soluble protoxin heterodimers, to internalized mature toxin, and finally to toxic oligomeric pores. The small size of the crystals—50 unit cells per edge, on average—has impeded structural characterization by conventional means. Here we report the structure of Lysinibacillus sphaericus BinAB solved de novo by serial-femtosecond crystallography at an X-ray free-electron laser. The structure reveals tyrosine- and carboxylate-mediated contacts acting as pH switches to release soluble protoxin in the alkaline larval midgut. An enormous heterodimeric interface appears to be responsible for anchoring BinA to receptor-bound BinB for co-internalization. Remarkably, this interface is largely composed of propeptides, suggesting that proteolytic maturation would trigger dissociation of the heterodimer and progression to pore formation.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Infectious Diseases (rcdc)Animals (mesh)Bacillus (mesh)Bacterial Toxins (mesh)Binding Sites (mesh)Crystallization (mesh)CrystallographyX-Ray (mesh)Culicidae (mesh)Hydrogen-Ion Concentration (mesh)Insecticides (mesh)Larva (mesh)Lasers (mesh)ModelsMolecular (mesh)Protein Multimerization (mesh)Proteolysis (mesh)Tyrosine (mesh)Animals (mesh)Culicidae (mesh)Bacillus (mesh)Tyrosine (mesh)Bacterial Toxins (mesh)Insecticides (mesh)Crystallization (mesh)CrystallographyX-Ray (mesh)Lasers (mesh)Binding Sites (mesh)Larva (mesh)Hydrogen-Ion Concentration (mesh)ModelsMolecular (mesh)Protein Multimerization (mesh)Proteolysis (mesh)Animals (mesh)Bacillus (mesh)Bacterial Toxins (mesh)Binding Sites (mesh)Crystallization (mesh)CrystallographyX-Ray (mesh)Culicidae (mesh)Hydrogen-Ion Concentration (mesh)Insecticides (mesh)Larva (mesh)Lasers (mesh)ModelsMolecular (mesh)Protein Multimerization (mesh)Proteolysis (mesh)Tyrosine (mesh)General Science & Technology (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7gr0686ghttps://escholarship.org/content/qt7gr0686g/qt7gr0686g.pdfinfo:doi/10.1038/nature19825articleNature, vol 539, iss 762743 - 47oai:escholarship.org:ark:/13030/qt2rv6q3mh2026-01-02T18:14:22Zqt2rv6q3mhEvo-Devo of Urbilateria and its larval formsDe Robertis, Edward MTejeda-Muñoz, Nydia2022-07-01Developmental biology has contributed greatly to evolutionary biology in the past century. With the discovery that vertebrates share Hox genes with Drosophila in 1984, it became apparent that all animals evolved from variations of an ancestral embryonic patterning genetic tool-kit. In the dorsal-ventral (D-V) axis, a fundamental experiment was the Spemann-Mangold organizer transplant performed in 1924. Almost a century later, D-V genes have been subjected to saturating molecular screens in Xenopus and extensive genetic screens in zebrafish. A network of secreted growth factor antagonists has emerged, and we review here in detail the Chordin/Tolloid/BMP pathway. Chordin establishes a morphogen gradient spanning the entire embryo that was present even in the cnidarian Nematostella. This ancient system was present in Urbilateria, the last common ancestor of the protostome and deuterostome bilateral animals. We suggest that Urbilateria had a complex life cycle with an adult benthic form on the sea bottom, and also a primary larval pelagic or planktonic phase to disperse the species in the marine milieu. Larvae with two rows of cilia beating in opposite directions to entrap food particles, an apical sensory organ, and a rudimentary eye, are present in many protostome and deuterostome phyla. Although the larval phase has been lost multiple times in evolution, and larvae can adopt traits present in their adult forms, the simplest explanation is that Urbilateria had a pelago-benthic life cycle. The use of conserved developmental patterning systems likely placed evolutionary constraints in the animal forms that evolved by natural selection.31 Biological Sciences (for-2020)3103 Ecology (for-2020)3105 Genetics (for-2020)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Animals (mesh)Body Patterning (mesh)Drosophila (mesh)GenesHomeobox (mesh)Larva (mesh)OrganizersEmbryonic (mesh)Zebrafish (mesh)Hox genesChordinTolloidTrochophore larvaCNS evolutionEvolutionary constraintsOrganizersEmbryonic (mesh)Animals (mesh)Zebrafish (mesh)Drosophila (mesh)Body Patterning (mesh)Larva (mesh)GenesHomeobox (mesh)CNS evolutionChordinEvolutionary constraintsHox genesTolloidTrochophore larvaAnimals (mesh)Body Patterning (mesh)Drosophila (mesh)GenesHomeobox (mesh)Larva (mesh)OrganizersEmbryonic (mesh)Zebrafish (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/2rv6q3mhhttps://escholarship.org/content/qt2rv6q3mh/qt2rv6q3mh.pdfinfo:doi/10.1016/j.ydbio.2022.04.003articleDevelopmental Biology, vol 48710 - 20oai:escholarship.org:ark:/13030/qt6s4867562026-01-02T17:39:07Zqt6s486756Author Correction: Atomic structures of TDP-43 LCD segments and insights into reversible or pathogenic aggregationGuenther, Elizabeth LCao, QinTrinh, HamiltonLu, JiahuiSawaya, Michael RCascio, DuilioBoyer, David RRodriguez, Jose AHughes, Michael PEisenberg, David S2019-10-01An amendment to this paper has been published and can be accessed via a link at the top of the paper.31 Biological Sciences (for-2020)32 Biomedical and Clinical Sciences (for-2020)34 Chemical Sciences (for-2020)Rare Diseases (rcdc)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biophysics (science-metrix)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6s486756https://escholarship.org/content/qt6s486756/qt6s486756.pdfinfo:doi/10.1038/s41594-019-0316-9articleNature Structural & Molecular Biology, vol 26, iss 10988 - 988oai:escholarship.org:ark:/13030/qt4866j6tp2026-01-02T16:38:15Zqt4866j6tpUpdate to Our Reader, Reviewer, and Author CommunitiesApril 2020Burrows, Cynthia JWang, ShuKim, Hyun JaeMeyer, Gerald JSchanze, KirkLee, T RandallLutkenhaus, Jodie LKaplan, DavidJones, ChristopherBertozzi, CarolynKiessling, LauraMulcahy, Mary BethLindsley, Craig WFinn, MGBlum, Joel DKamat, PrashantAldrich, Courtney CRowan, StuartLiu, BinLiotta, DennisWeiss, Paul SZhang, DeqingGanesh, Krishna NSexton, PatrickAtwater, Harry AGooding, J JustinAllen, David TVoigt, Christopher ASweedler, JonathanSchepartz, AlannaRotello, VincentLecommandoux, SébastienSturla, Shana JHammes-Schiffer, SharonBuriak, JillianSteed, Jonathan WWu, HongweiZimmerman, JulieBrooks, BryanSavage, PhillipTolman, WilliamHofmann, Thomas FBrennecke, Joan FHolme, Thomas AMerz, Kenneth MScuseria, GustavoJorgensen, WilliamGeorg, Gunda IWang, ShaomengProteau, PhilipYates, John RStang, PeterWalker, Gilbert CHillmyer, MarcTaylor, Lynne SOdom, Teri WCarreira, ErickRossen, KaiChirik, PaulMiller, Scott JMcCoy, AnneShea, Joan-EmmaZanni, MartinMurphy, CatherineScholes, GregoryLoo, Joseph A2020-05-0640 Engineering (for-2020)34 Chemical Sciences (for-2020)03 Chemical Sciences (for)General Chemistry (science-metrix)34 Chemical sciences (for-2020)40 Engineering (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4866j6tphttps://escholarship.org/content/qt4866j6tp/qt4866j6tp.pdfinfo:doi/10.1021/jacs.0c04253articleJournal of the American Chemical Society, vol 142, iss 188059 - 8060oai:escholarship.org:ark:/13030/qt7h56d5qz2026-01-02T16:01:47Zqt7h56d5qzNew astroglial injury-defined biomarkers for neurotrauma assessmentHalford, JuliaShen, SeanItamura, KyoheiLevine, JaclynnChong, Albert CCzerwieniec, GreggGlenn, Thomas CHovda, David AVespa, PaulBullock, RossDietrich, W DaltonMondello, StefaniaLoo, Joseph AWanner, Ina-Beate2017-10-01Traumatic brain injury (TBI) is an expanding public health epidemic with pathophysiology that is difficult to diagnose and thus treat. TBI biomarkers should assess patients across severities and reveal pathophysiology, but currently, their kinetics and specificity are unclear. No single ideal TBI biomarker exists. We identified new candidates from a TBI CSF proteome by selecting trauma-released, astrocyte-enriched proteins including aldolase C (ALDOC), its 38kD breakdown product (BDP), brain lipid binding protein (BLBP), astrocytic phosphoprotein (PEA15), glutamine synthetase (GS) and new 18-25kD-GFAP-BDPs. Their levels increased over four orders of magnitude in severe TBI CSF. First post-injury week, ALDOC levels were markedly high and stable. Short-lived BLBP and PEA15 related to injury progression. ALDOC, BLBP and PEA15 appeared hyper-acutely and were similarly robust in severe and mild TBI blood; 25kD-GFAP-BDP appeared overnight after TBI and was rarely present after mild TBI. Using a human culture trauma model, we investigated biomarker kinetics. Wounded (mechanoporated) astrocytes released ALDOC, BLBP and PEA15 acutely. Delayed cell death corresponded with GFAP release and proteolysis into small GFAP-BDPs. Associating biomarkers with cellular injury stages produced astroglial injury-defined (AID) biomarkers that facilitate TBI assessment, as neurological deficits are rooted not only in death of CNS cells, but also in their functional compromise.32 Biomedical and Clinical Sciences (for-2020)3209 Neurosciences (for-2020)3202 Clinical Sciences (for-2020)Brain Disorders (rcdc)Traumatic Brain Injury (TBI) (rcdc)Traumatic Head and Spine Injury (rcdc)Neurosciences (rcdc)Physical Injury - Accidents and Adverse Effects (rcdc)4.1 Discovery and preclinical testing of markers and technologies (hrcs-rac)Injuries and accidents (hrcs-hc)Apoptosis Regulatory Proteins (mesh)Astrocytes (mesh)Biomarkers (mesh)Brain Concussion (mesh)Brain InjuriesTraumatic (mesh)CellsCultured (mesh)Fatty Acid-Binding Protein 7 (mesh)Fructose-Bisphosphate Aldolase (mesh)Humans (mesh)Intracellular Signaling Peptides and Proteins (mesh)Kinetics (mesh)Phosphoproteins (mesh)Proteome (mesh)Tumor Suppressor Proteins (mesh)Astrocytesbrain traumaproteomicscell culturecerebrospinal fluidexploratory factor analysisAstrocytes (mesh)CellsCultured (mesh)Humans (mesh)Brain Concussion (mesh)Fructose-Bisphosphate Aldolase (mesh)Intracellular Signaling Peptides and Proteins (mesh)Tumor Suppressor Proteins (mesh)Phosphoproteins (mesh)Proteome (mesh)Kinetics (mesh)Apoptosis Regulatory Proteins (mesh)Biomarkers (mesh)Fatty Acid-Binding Protein 7 (mesh)Brain InjuriesTraumatic (mesh)Astrocytesbrain traumacell culturecerebrospinal fluidexploratory factor analysisproteomicsApoptosis Regulatory Proteins (mesh)Astrocytes (mesh)Biomarkers (mesh)Brain Concussion (mesh)Brain InjuriesTraumatic (mesh)CellsCultured (mesh)Fatty Acid-Binding Protein 7 (mesh)Fructose-Bisphosphate Aldolase (mesh)Humans (mesh)Intracellular Signaling Peptides and Proteins (mesh)Kinetics (mesh)Phosphoproteins (mesh)Proteome (mesh)Tumor Suppressor Proteins (mesh)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7h56d5qzhttps://escholarship.org/content/qt7h56d5qz/qt7h56d5qz.pdfinfo:doi/10.1177/0271678x17724681articleJournal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism, vol 37, iss 103278 - 3299oai:escholarship.org:ark:/13030/qt5d39j3wm2026-01-02T14:10:43Zqt5d39j3wmMassively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samplesBloom, Joshua SSathe, LailaMunugala, ChetanJones, Eric MGasperini, MollyLubock, Nathan BYarza, FaunaThompson, Erin MKovary, Kyle MPark, JiminMarquette, DawnKay, StephaniaLucas, MarkLove, TreQuanSina Booeshaghi, ABrandenberg, Oliver FGuo, LonghuaBoocock, JamesHochman, MylesSimpkins, Scott WLin, IsabellaLaPierre, NathanHong, DukeZhang, YiOland, GabrielChoe, Bianca JudyChandrasekaran, SukanthaHilt, Evann EButte, Manish JDamoiseaux, RobertKravit, CliffordCooper, Aaron RYin, YiPachter, LiorGarner, Omai BFlint, JonathanEskin, EleazarLuo, ChongyuanKosuri, SriramKruglyak, LeonidArboleda, Valerie A2021-07-01Frequent and widespread testing of members of the population who are asymptomatic for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for the mitigation of the transmission of the virus. Despite the recent increases in testing capacity, tests based on quantitative polymerase chain reaction (qPCR) assays cannot be easily deployed at the scale required for population-wide screening. Here, we show that next-generation sequencing of pooled samples tagged with sample-specific molecular barcodes enables the testing of thousands of nasal or saliva samples for SARS-CoV-2 RNA in a single run without the need for RNA extraction. The assay, which we named SwabSeq, incorporates a synthetic RNA standard that facilitates end-point quantification and the calling of true negatives, and that reduces the requirements for automation, purification and sample-to-sample normalization. We used SwabSeq to perform 80,000 tests, with an analytical sensitivity and specificity comparable to or better than traditional qPCR tests, in less than two months with turnaround times of less than 24 h. SwabSeq could be rapidly adapted for the detection of other pathogens.40 Engineering (for-2020)4003 Biomedical Engineering (for-2020)Emerging Infectious Diseases (rcdc)Coronaviruses Diagnostics and Prognostics (rcdc)Genetics (rcdc)Infectious Diseases (rcdc)Coronaviruses (rcdc)Biotechnology (rcdc)High-Throughput Nucleotide Sequencing (mesh)Humans (mesh)RNAViral (mesh)SARS-CoV-2 (mesh)Saliva (mesh)Sensitivity and Specificity (mesh)Saliva (mesh)Humans (mesh)RNAViral (mesh)Sensitivity and Specificity (mesh)High-Throughput Nucleotide Sequencing (mesh)SARS-CoV-2 (mesh)High-Throughput Nucleotide Sequencing (mesh)Humans (mesh)RNAViral (mesh)SARS-CoV-2 (mesh)Saliva (mesh)Sensitivity and Specificity (mesh)4003 Biomedical engineering (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/5d39j3wmhttps://escholarship.org/content/qt5d39j3wm/qt5d39j3wm.pdfinfo:doi/10.1038/s41551-021-00754-5articleNature Biomedical Engineering, vol 5, iss 7657 - 665oai:escholarship.org:ark:/13030/qt0gj472gj2026-01-02T12:37:21Zqt0gj472gjThe ASM Journals Committee Values the Contributions of Black MicrobiologistsSchloss, Patrick DJunior, MelissaAlvania, RebeccaArias, Cesar ABaumler, AndreasCasadevall, ArturoDetweiler, CorrellaDrake, HaroldGilbert, JackImperiale, Michael JLovett, SusanMaloy, StanleyMcAdam, Alexander JNewton, Irene LGSadowsky, Michael JSandri-Goldin, Rozanne MSilhavy, Thomas JTontonoz, PeterYoung, Jo-Anne HCameron, Craig ECann, IsaacFuller, A OvetaKozik, Ariangela J2020-08-263107 Microbiology (for-2020)31 Biological Sciences (for-2020)Black or African American (mesh)Humans (mesh)Laboratory Personnel (mesh)Microbiology (mesh)Periodicals as Topic (mesh)Research (mesh)3107 Microbiology (for-2020)31 Biological Sciences (for-2020)Black or African American (mesh)Biomedical Research (mesh)COVID-19 (mesh)Editorial Policies (mesh)Healthcare Disparities (mesh)Humans (mesh)Microbiology (mesh)Racism (mesh)United States (mesh)Humans (mesh)Microbiology (mesh)Research (mesh)Laboratory Personnel (mesh)Periodicals as Topic (mesh)Black or African American (mesh)Black or African American (mesh)Humans (mesh)Laboratory Personnel (mesh)Microbiology (mesh)Periodicals as Topic (mesh)Research (mesh)1107 Immunology (for)Immunology (science-metrix)Microbiology (science-metrix)3204 Immunology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0gj472gjhttps://escholarship.org/content/qt0gj472gj/qt0gj472gj.pdfinfo:doi/10.1128/msphere.00719-20articlemSphere, vol 5, iss 410.1128/msphere.00719 - 10.1128/msphere.00720oai:escholarship.org:ark:/13030/qt68v9p9j12026-01-02T12:19:37Zqt68v9p9j1Oxidized phospholipids cause changes in jejunum mucus that induce dysbiosis and systemic inflammationMukherjee, PallaviChattopadhyay, ArnabGrijalva, VictorDorreh, NasrinLagishetty, VenuJacobs, Jonathan PClifford, Bethan LVallim, ThomasMack, Julia JNavab, MohamadReddy, Srinivasa TFogelman, Alan M2022-01-01We previously reported that adding a concentrate of transgenic tomatoes expressing the apoA-I mimetic peptide 6F (Tg6F) to a Western diet (WD) ameliorated systemic inflammation. To determine the mechanism(s) responsible for these observations, Ldlr-/- mice were fed chow, a WD, or WD plus Tg6F. We found that a WD altered the taxonomic composition of bacteria in jejunum mucus. For example, Akkermansia muciniphila virtually disappeared, while overall bacteria numbers and lipopolysaccharide (LPS) levels increased. In addition, gut permeability increased, as did the content of reactive oxygen species and oxidized phospholipids in jejunum mucus in WD-fed mice. Moreover, gene expression in the jejunum decreased for multiple peptides and proteins that are secreted into the mucous layer of the jejunum that act to limit bacteria numbers and their interaction with enterocytes including regenerating islet-derived proteins, defensins, mucin 2, surfactant A, and apoA-I. Following WD, gene expression also decreased for Il36γ, Il23, and Il22, cytokines critical for antimicrobial activity. WD decreased expression of both Atoh1 and Gfi1, genes required for the formation of goblet and Paneth cells, and immunohistochemistry revealed decreased numbers of goblet and Paneth cells. Adding Tg6F ameliorated these WD-mediated changes. Adding oxidized phospholipids ex vivo to the jejunum from mice fed a chow diet reproduced the changes in gene expression in vivo that occurred when the mice were fed WD and were prevented with addition of 6F peptide. We conclude that Tg6F ameliorates the WD-mediated increase in oxidized phospholipids that cause changes in jejunum mucus, which induce dysbiosis and systemic inflammation.3107 Microbiology (for-2020)31 Biological Sciences (for-2020)32 Biomedical and Clinical Sciences (for-2020)Biotechnology (rcdc)Nutrition (rcdc)Microbiome (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Animals (mesh)Mice (mesh)Jejunum (mesh)Inflammation (mesh)Dysbiosis (mesh)Oxidation-Reduction (mesh)Phospholipids (mesh)Mucus (mesh)Male (mesh)Apolipoprotein A-I (apoA-I) mimetic peptidesatherosclerosisregenerating islet-derived family members 3 alpha (Reg3a)3 beta (Reg3b)and 3 gamma (Reg3g)lipopolysaccharide (LPS)mucin 2 (Muc2)surfactant AInterleukins 36 (IL-36)23 (IL-23)and 22 (IL-22)Paneth cellsgoblet cellsAkkermansia muciniphilaJejunum (mesh)Mucus (mesh)Animals (mesh)Mice (mesh)Inflammation (mesh)Phospholipids (mesh)Oxidation-Reduction (mesh)Male (mesh)Dysbiosis (mesh)Akkermansia muciniphilaApolipoprotein A-I (apoA-I) mimetic peptidesInterleukins 36 (IL-36)23 (IL-23)and 22 (IL-22)Paneth cellsatherosclerosisgoblet cellslipopolysaccharide (LPS)mucin 2 (Muc2)regenerating islet-derived family members 3 alpha (Reg3a)3 beta (Reg3b)and 3 gamma (Reg3g)surfactant AAnimals (mesh)Mice (mesh)Jejunum (mesh)Inflammation (mesh)Dysbiosis (mesh)Oxidation-Reduction (mesh)Phospholipids (mesh)Mucus (mesh)Male (mesh)0601 Biochemistry and Cell Biology (for)1101 Medical Biochemistry and Metabolomics (for)Biochemistry & Molecular Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)3205 Medical biochemistry and metabolomics (for-2020)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/68v9p9j1https://escholarship.org/content/qt68v9p9j1/qt68v9p9j1.pdfinfo:doi/10.1016/j.jlr.2021.100153articleJournal of Lipid Research, vol 63, iss 1100153oai:escholarship.org:ark:/13030/qt6z47571v2026-01-02T11:46:27Zqt6z47571vMultiplexed CuAAC Suzuki–Miyaura Labeling for Tandem Activity-Based Chemoproteomic ProfilingCao, JianBoatner, Lisa MDesai, Heta SBurton, Nikolas RArmenta, ErnestChan, Neil JCastellón, José OBackus, Keriann M2021-02-02Mass-spectrometry-based chemoproteomics has enabled the rapid and proteome-wide discovery of functional and potentially 'druggable' hotspots in proteins. While numerous transformations are now available, chemoproteomic studies still rely overwhelmingly on copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) or 'click' chemistry. The absence of bio-orthogonal chemistries that are functionally equivalent and complementary to CuAAC for chemoproteomic applications has hindered the development of multiplexed chemoproteomic platforms capable of assaying multiple amino acid side chains in parallel. Here, we identify and optimize Suzuki-Miyaura cross-coupling conditions for activity-based protein profiling and mass-spectrometry-based chemoproteomics, including for target deconvolution and labeling site identification. Uniquely enabled by the observed orthogonality of palladium-catalyzed cross-coupling and CuAAC, we combine both reactions to achieve dual labeling. Multiplexed targeted deconvolution identified the protein targets of bifunctional cysteine- and lysine-reactive probes.3401 Analytical Chemistry (for-2020)3405 Organic Chemistry (for-2020)34 Chemical Sciences (for-2020)Alkynes (mesh)Azides (mesh)Catalysis (mesh)Click Chemistry (mesh)Copper (mesh)Cycloaddition Reaction (mesh)HEK293 Cells (mesh)Humans (mesh)Molecular Structure (mesh)Proteomics (mesh)Humans (mesh)Copper (mesh)Azides (mesh)Alkynes (mesh)Proteomics (mesh)Molecular Structure (mesh)Catalysis (mesh)HEK293 Cells (mesh)Click Chemistry (mesh)Cycloaddition Reaction (mesh)Alkynes (mesh)Azides (mesh)Catalysis (mesh)Click Chemistry (mesh)Copper (mesh)Cycloaddition Reaction (mesh)HEK293 Cells (mesh)Humans (mesh)Molecular Structure (mesh)Proteomics (mesh)0301 Analytical Chemistry (for)0399 Other Chemical Sciences (for)Analytical Chemistry (science-metrix)3205 Medical biochemistry and metabolomics (for-2020)3401 Analytical chemistry (for-2020)4004 Chemical engineering (for-2020)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/6z47571vinfo:doi/10.1021/acs.analchem.0c04726articleAnalytical Chemistry, vol 93, iss 42610 - 2618oai:escholarship.org:ark:/13030/qt7dg6p3mn2026-01-02T10:59:07Zqt7dg6p3mnEndothelial NOTCH1 is suppressed by circulating lipids and antagonizes inflammation during atherosclerosisBriot, AnaïsCivelek, MeteSeki, AtsukoHoi, KarenMack, Julia JLee, Stephen DKim, JasonHong, CynthiaYu, JingjingFishbein, Gregory AVakili, LadanFogelman, Alan MFishbein, Michael CLusis, Aldons JTontonoz, PeterNavab, MohamadBerliner, Judith AIruela-Arispe, M Luisa2015-11-16Although much progress has been made in identifying the mechanisms that trigger endothelial activation and inflammatory cell recruitment during atherosclerosis, less is known about the intrinsic pathways that counteract these events. Here we identified NOTCH1 as an antagonist of endothelial cell (EC) activation. NOTCH1 was constitutively expressed by adult arterial endothelium, but levels were significantly reduced by high-fat diet. Furthermore, treatment of human aortic ECs (HAECs) with inflammatory lipids (oxidized 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine [Ox-PAPC]) and proinflammatory cytokines (TNF and IL1β) decreased Notch1 expression and signaling in vitro through a mechanism that requires STAT3 activation. Reduction of NOTCH1 in HAECs by siRNA, in the absence of inflammatory lipids or cytokines, increased inflammatory molecules and binding of monocytes. Conversely, some of the effects mediated by Ox-PAPC were reversed by increased NOTCH1 signaling, suggesting a link between lipid-mediated inflammation and Notch1. Interestingly, reduction of NOTCH1 by Ox-PAPC in HAECs was associated with a genetic variant previously correlated to high-density lipoprotein in a human genome-wide association study. Finally, endothelial Notch1 heterozygous mice showed higher diet-induced atherosclerosis. Based on these findings, we propose that reduction of endothelial NOTCH1 is a predisposing factor in the onset of vascular inflammation and initiation of atherosclerosis.32 Biomedical and Clinical Sciences (for-2020)Biotechnology (rcdc)Human Genome (rcdc)Cardiovascular (rcdc)Atherosclerosis (rcdc)Genetics (rcdc)Prevention (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Cardiovascular (hrcs-hc)Adult (mesh)Animals (mesh)Atherosclerosis (mesh)Cell LineTumor (mesh)CellsCultured (mesh)DietHigh-Fat (mesh)Endothelial Cells (mesh)Female (mesh)Humans (mesh)Inflammation (mesh)Interleukin-1beta (mesh)Lipids (mesh)Male (mesh)MiceInbred C57BL (mesh)MiceKnockout (mesh)MiceTransgenic (mesh)MicroscopyConfocal (mesh)Oligonucleotide Array Sequence Analysis (mesh)Phosphatidylcholines (mesh)RNA Interference (mesh)ReceptorNotch1 (mesh)Reverse Transcriptase Polymerase Chain Reaction (mesh)Transcriptome (mesh)Tumor Necrosis Factor-alpha (mesh)CellsCultured (mesh)Cell LineTumor (mesh)Endothelial Cells (mesh)Animals (mesh)MiceInbred C57BL (mesh)MiceTransgenic (mesh)MiceKnockout (mesh)Humans (mesh)Inflammation (mesh)Lipids (mesh)Phosphatidylcholines (mesh)Tumor Necrosis Factor-alpha (mesh)MicroscopyConfocal (mesh)Oligonucleotide Array Sequence Analysis (mesh)Reverse Transcriptase Polymerase Chain Reaction (mesh)RNA Interference (mesh)Adult (mesh)Female (mesh)Male (mesh)Atherosclerosis (mesh)ReceptorNotch1 (mesh)Interleukin-1beta (mesh)Transcriptome (mesh)DietHigh-Fat (mesh)Adult (mesh)Animals (mesh)Atherosclerosis (mesh)Cell LineTumor (mesh)CellsCultured (mesh)DietHigh-Fat (mesh)Endothelial Cells (mesh)Female (mesh)Humans (mesh)Inflammation (mesh)Interleukin-1beta (mesh)Lipids (mesh)Male (mesh)MiceInbred C57BL (mesh)MiceKnockout (mesh)MiceTransgenic (mesh)MicroscopyConfocal (mesh)Oligonucleotide Array Sequence Analysis (mesh)Phosphatidylcholines (mesh)RNA Interference (mesh)ReceptorNotch1 (mesh)Reverse Transcriptase Polymerase Chain Reaction (mesh)Transcriptome (mesh)Tumor Necrosis Factor-alpha (mesh)11 Medical and Health Sciences (for)Immunology (science-metrix)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7dg6p3mnhttps://escholarship.org/content/qt7dg6p3mn/qt7dg6p3mn.pdfinfo:doi/10.1084/jem.20150603articleJournal of Experimental Medicine, vol 212, iss 122147 - 2163oai:escholarship.org:ark:/13030/qt9r6053cj2026-01-02T10:25:39Zqt9r6053cjThe lipoprotein lipase that is shuttled into capillaries by GPIHBP1 enters the glycocalyx where it mediates lipoprotein processingSong, WenxinBeigneux, Anne PWeston, Thomas AChen, KaiYang, YeNguyen, Le PhuongGuagliardo, PaulJung, HyesooTran, Anh PTu, YipingTran, CaitlynBirrane, GabrielMiyashita, KazuyaNakajima, KatsuyukiMurakami, MasamiTontonoz, PeterJiang, HaiboPloug, MichaelFong, Loren GYoung, Stephen G2023-10-31Lipoprotein lipase (LPL), the enzyme that carries out the lipolytic processing of triglyceride-rich lipoproteins (TRLs), is synthesized by adipocytes and myocytes and secreted into the interstitial spaces. The LPL is then bound by GPIHBP1, a GPI-anchored protein of endothelial cells (ECs), and transported across ECs to the capillary lumen. The assumption has been that the LPL that is moved into capillaries remains attached to GPIHBP1 and that GPIHBP1 serves as a platform for TRL processing. In the current studies, we examined the validity of that assumption. We found that an LPL-specific monoclonal antibody (mAb), 88B8, which lacks the ability to detect GPIHBP1-bound LPL, binds avidly to LPL within capillaries. We further demonstrated, by confocal microscopy, immunogold electron microscopy, and nanoscale secondary ion mass spectrometry analyses, that the LPL detected by mAb 88B8 is located within the EC glycocalyx, distant from the GPIHBP1 on the EC plasma membrane. The LPL within the glycocalyx mediates the margination of TRLs along capillaries and is active in TRL processing, resulting in the delivery of lipoprotein-derived lipids to immediately adjacent parenchymal cells. Thus, the LPL that GPIHBP1 transports into capillaries can detach and move into the EC glycocalyx, where it functions in the intravascular processing of TRLs.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Biotechnology (rcdc)AntibodiesMonoclonal (mesh)Capillaries (mesh)Endothelial Cells (mesh)Glycocalyx (mesh)Lipoprotein Lipase (mesh)Lipoproteins (mesh)ReceptorsLipoprotein (mesh)Triglycerides (mesh)Humans (mesh)Animals (mesh)triglyceridesGPIHBP1lipoprotein lipaseendothelial cellsCapillaries (mesh)Glycocalyx (mesh)Endothelial Cells (mesh)Animals (mesh)Humans (mesh)Lipoprotein Lipase (mesh)Triglycerides (mesh)Lipoproteins (mesh)ReceptorsLipoprotein (mesh)AntibodiesMonoclonal (mesh)GPIHBP1endothelial cellslipoprotein lipasetriglyceridesAntibodiesMonoclonal (mesh)Capillaries (mesh)Endothelial Cells (mesh)Glycocalyx (mesh)Lipoprotein Lipase (mesh)Lipoproteins (mesh)ReceptorsLipoprotein (mesh)Triglycerides (mesh)Humans (mesh)Animals (mesh)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/9r6053cjhttps://escholarship.org/content/qt9r6053cj/qt9r6053cj.pdfinfo:doi/10.1073/pnas.2313825120articleProceedings of the National Academy of Sciences of the United States of America, vol 120, iss 44e2313825120oai:escholarship.org:ark:/13030/qt13z9t5zn2026-01-02T09:57:37Zqt13z9t5znCryoEM structure of the low-complexity domain of hnRNPA2 and its conversion to pathogenic amyloidLu, JiahuiCao, QinHughes, Michael PSawaya, Michael RBoyer, David RCascio, DuilioEisenberg, David S2020-01-01AbstracthnRNPA2 is a human ribonucleoprotein (RNP) involved in RNA metabolism. It forms fibrils both under cellular stress and in mutated form in neurodegenerative conditions. Previous work established that the C-terminal low-complexity domain (LCD) of hnRNPA2 fibrillizes under stress, and missense mutations in this domain are found in the disease multisystem proteinopathy (MSP). However, little is known at the atomic level about the hnRNPA2 LCD structure that is involved in those processes and how disease mutations cause structural change. Here we present the cryo-electron microscopy (cryoEM) structure of the hnRNPA2 LCD fibril core and demonstrate its capability to form a reversible hydrogel in vitro containing amyloid-like fibrils. Whereas these fibrils, like pathogenic amyloid, are formed from protein chains stacked into β-sheets by backbone hydrogen bonds, they display distinct structural differences: the chains are kinked, enabling non-covalent cross-linking of fibrils and disfavoring formation of pathogenic steric zippers. Both reversibility and energetic calculations suggest these fibrils are less stable than pathogenic amyloid. Moreover, the crystal structure of the disease-mutation-containing segment (D290V) of hnRNPA2 suggests that the replacement fundamentally alters the fibril structure to a more stable energetic state. These findings illuminate how molecular interactions promote protein fibril networks and how mutation can transform fibril structure from functional to a pathogenic form.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Neurodegenerative (rcdc)Rare Diseases (rcdc)Neurosciences (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Generic health relevance (hrcs-hc)Amyloid (mesh)Cryoelectron Microscopy (mesh)Heterogeneous-Nuclear Ribonucleoprotein Group A-B (mesh)Humans (mesh)Hydrogels (mesh)RNA-Binding Proteins (mesh)Humans (mesh)Amyloid (mesh)RNA-Binding Proteins (mesh)Heterogeneous-Nuclear Ribonucleoprotein Group A-B (mesh)Hydrogels (mesh)Cryoelectron Microscopy (mesh)Amyloid (mesh)Cryoelectron Microscopy (mesh)Heterogeneous-Nuclear Ribonucleoprotein Group A-B (mesh)Humans (mesh)Hydrogels (mesh)RNA-Binding Proteins (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/13z9t5znhttps://escholarship.org/content/qt13z9t5zn/qt13z9t5zn.pdfinfo:doi/10.1038/s41467-020-17905-yarticleNature Communications, vol 11, iss 14090oai:escholarship.org:ark:/13030/qt3hv8h8m82026-01-02T08:50:51Zqt3hv8h8m8A pair of peptides inhibits seeding of the hormone transporter transthyretin into amyloid fibrilsSaelices, LorenaNguyen, Binh AChung, KevinWang, YifeiOrtega, AlfredoLee, Ji HCoelho, TeresaBijzet, JohanBenson, Merrill DEisenberg, David S2019-04-01The tetrameric protein transthyretin is a transporter of retinol and thyroxine in blood, cerebrospinal fluid, and the eye, and is secreted by the liver, choroid plexus, and retinal epithelium, respectively. Systemic amyloid deposition of aggregated transthyretin causes hereditary and sporadic amyloidoses. A common treatment of patients with hereditary transthyretin amyloidosis is liver transplantation. However, this procedure, which replaces the patient's variant transthyretin with the WT protein, can fail to stop subsequent cardiac deposition, ultimately requiring heart transplantation. We recently showed that preformed amyloid fibrils present in the heart at the time of surgery can template or seed further amyloid aggregation of native transthyretin. Here we assess possible interventions to halt this seeding, using biochemical and EM assays. We found that chemical or mutational stabilization of the transthyretin tetramer does not hinder amyloid seeding. In contrast, binding of the peptide inhibitor TabFH2 to ex vivo fibrils efficiently inhibits amyloid seeding by impeding self-association of the amyloid-driving strands F and H in a tissue-independent manner. Our findings point to inhibition of amyloid seeding by peptide inhibitors as a potential therapeutic approach.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Rare Diseases (rcdc)Heart Disease (rcdc)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)Neurosciences (rcdc)Cardiovascular (rcdc)Digestive Diseases (rcdc)Neurodegenerative (rcdc)Brain Disorders (rcdc)Aging (rcdc)Alzheimer's Disease (rcdc)Acquired Cognitive Impairment (rcdc)Liver Disease (rcdc)Dementia (rcdc)Aged (mesh)Aged80 and over (mesh)Amyloid (mesh)Amyloid NeuropathiesFamilial (mesh)Female (mesh)Humans (mesh)Male (mesh)Middle Aged (mesh)Peptides (mesh)Prealbumin (mesh)Protein Aggregates (mesh)amyloidprotein aggregationinhibition mechanismagingdrug discoverypeptidesamyloidosisinhibitionpeptideseedingtransthyretinHumans (mesh)Amyloid NeuropathiesFamilial (mesh)Amyloid (mesh)Peptides (mesh)Prealbumin (mesh)Aged (mesh)Aged80 and over (mesh)Middle Aged (mesh)Female (mesh)Male (mesh)Protein Aggregates (mesh)agingamyloidamyloidosisdrug discoveryinhibitioninhibition mechanismpeptidepeptidesprotein aggregationseedingtransthyretinAged (mesh)Aged80 and over (mesh)Amyloid (mesh)Amyloid NeuropathiesFamilial (mesh)Female (mesh)Humans (mesh)Male (mesh)Middle Aged (mesh)Peptides (mesh)Prealbumin (mesh)Protein Aggregates (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biochemistry & Molecular Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/3hv8h8m8https://escholarship.org/content/qt3hv8h8m8/qt3hv8h8m8.pdfinfo:doi/10.1074/jbc.ra118.005257articleJournal of Biological Chemistry, vol 294, iss 156130 - 6141oai:escholarship.org:ark:/13030/qt59m0r68j2026-01-02T03:28:01Zqt59m0r68jNear-atomic cryo-EM imaging of a small protein displayed on a designed scaffolding systemLiu, YuxiGonen, ShaneGonen, TamirYeates, Todd O2018-03-27Current single-particle cryo-electron microscopy (cryo-EM) techniques can produce images of large protein assemblies and macromolecular complexes at atomic level detail without the need for crystal growth. However, proteins of smaller size, typical of those found throughout the cell, are not presently amenable to detailed structural elucidation by cryo-EM. Here we use protein design to create a modular, symmetrical scaffolding system to make protein molecules of typical size suitable for cryo-EM. Using a rigid continuous alpha helical linker, we connect a small 17-kDa protein (DARPin) to a protein subunit that was designed to self-assemble into a cage with cubic symmetry. We show that the resulting construct is amenable to structural analysis by single-particle cryo-EM, allowing us to identify and solve the structure of the attached small protein at near-atomic detail, ranging from 3.5- to 5-Å resolution. The result demonstrates that proteins considerably smaller than the theoretical limit of 50 kDa for cryo-EM can be visualized clearly when arrayed in a rigid fashion on a symmetric designed protein scaffold. Furthermore, because the amino acid sequence of a DARPin can be chosen to confer tight binding to various other protein or nucleic acid molecules, the system provides a future route for imaging diverse macromolecules, potentially broadening the application of cryo-EM to proteins of typical size in the cell.3101 Biochemistry and Cell Biology (for-2020)51 Physical Sciences (for-2020)31 Biological Sciences (for-2020)Biotechnology (rcdc)Bioengineering (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Cryoelectron Microscopy (mesh)CrystallographyX-Ray (mesh)Macromolecular Substances (mesh)ModelsMolecular (mesh)Protein Conformation (mesh)Proteins (mesh)cryo-electron microscopyprotein designDARPinprotein cageprotein scaffoldMacromolecular Substances (mesh)Proteins (mesh)Cryoelectron Microscopy (mesh)CrystallographyX-Ray (mesh)Protein Conformation (mesh)ModelsMolecular (mesh)DARPincryo-electron microscopyprotein cageprotein designprotein scaffoldCryoelectron Microscopy (mesh)CrystallographyX-Ray (mesh)Macromolecular Substances (mesh)ModelsMolecular (mesh)Protein Conformation (mesh)Proteins (mesh)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/59m0r68jhttps://escholarship.org/content/qt59m0r68j/qt59m0r68j.pdfinfo:doi/10.1073/pnas.1718825115articleProceedings of the National Academy of Sciences of the United States of America, vol 115, iss 133362 - 3367oai:escholarship.org:ark:/13030/qt5br2076m2026-01-02T03:23:26Zqt5br2076mStructure-based inhibitors of tau aggregationSeidler, PMBoyer, DRRodriguez, JASawaya, MRCascio, DMurray, KGonen, TEisenberg, DS2018-02-01Aggregated tau protein is associated with over 20 neurological disorders, which include Alzheimer's disease. Previous work has shown that tau's sequence segments VQIINK and VQIVYK drive its aggregation, but inhibitors based on the structure of the VQIVYK segment only partially inhibit full-length tau aggregation and are ineffective at inhibiting seeding by full-length fibrils. Here we show that the VQIINK segment is the more powerful driver of tau aggregation. Two structures of this segment determined by the cryo-electron microscopy method micro-electron diffraction explain its dominant influence on tau aggregation. Of practical significance, the structures lead to the design of inhibitors that not only inhibit tau aggregation but also inhibit the ability of exogenous full-length tau fibrils to seed intracellular tau in HEK293 biosensor cells into amyloid. We also raise the possibility that the two VQIINK structures represent amyloid polymorphs of tau that may account for a subset of prion-like strains of tau.34 Chemical Sciences (for-2020)Neurosciences (rcdc)Alzheimer's Disease (rcdc)Neurodegenerative (rcdc)Aging (rcdc)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)Brain Disorders (rcdc)Dementia (rcdc)Acquired Cognitive Impairment (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Neurological (hrcs-hc)HEK293 Cells (mesh)Humans (mesh)ModelsMolecular (mesh)Peptide Fragments (mesh)Protein Aggregates (mesh)Protein AggregationPathological (mesh)tau Proteins (mesh)Humans (mesh)Peptide Fragments (mesh)tau Proteins (mesh)ModelsMolecular (mesh)HEK293 Cells (mesh)Protein Aggregates (mesh)Protein AggregationPathological (mesh)HEK293 Cells (mesh)Humans (mesh)ModelsMolecular (mesh)Peptide Fragments (mesh)Protein Aggregates (mesh)Protein AggregationPathological (mesh)tau Proteins (mesh)03 Chemical Sciences (for)Organic Chemistry (science-metrix)34 Chemical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5br2076mhttps://escholarship.org/content/qt5br2076m/qt5br2076m.pdfinfo:doi/10.1038/nchem.2889articleNature Chemistry, vol 10, iss 2170 - 176oai:escholarship.org:ark:/13030/qt5q44w5f92026-01-02T03:07:15Zqt5q44w5f9The l-isoaspartate modification within protein fragments in the aging lens can promote protein aggregationWarmack, Rebeccah AShawa, HarrisonLiu, KateLopez, KatiaLoo, Joseph AHorwitz, JosephClarke, Steven G2019-08-01Transparency in the lens is accomplished by the dense packing and short-range order interactions of the crystallin proteins in fiber cells lacking organelles. These features are accompanied by a lack of protein turnover, leaving lens proteins susceptible to a number of damaging modifications and aggregation. The loss of lens transparency is attributed in part to such aggregation during aging. Among the damaging post-translational modifications that accumulate in long-lived proteins, isomerization at aspartate residues has been shown to be extensive throughout the crystallins. In this study of the human lens, we localize the accumulation of l-isoaspartate within water-soluble protein extracts primarily to crystallin peptides in high-molecular weight aggregates and show with MS that these peptides are from a variety of crystallins. To investigate the consequences of aspartate isomerization, we investigated two αA crystallin peptides 52LFRTVLDSGISEVR65 and 89VQDDFVEIH98, identified within this study, with the l-isoaspartate modification introduced at Asp58 and Asp91, respectively. Importantly, whereas both peptides modestly increase protein precipitation, the native 52LFRTVLDSGISEVR65 peptide shows higher aggregation propensity. In contrast, the introduction of l-isoaspartate within a previously identified anti-chaperone peptide from water-insoluble aggregates, αA crystallin 66SDRDKFVIFL(isoAsp)VKHF80, results in enhanced amyloid formation in vitro The modification of this peptide also increases aggregation of the lens chaperone αB crystallin. These findings may represent multiple pathways within the lens wherein the isomerization of aspartate residues in crystallin peptides differentially results in peptides associating with water-soluble or water-insoluble aggregates. Here the eye lens serves as a model for the cleavage and modification of long-lived proteins within other aging tissues.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Aging (rcdc)Eye Disease and Disorders of Vision (rcdc)5.1 Pharmaceuticals (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)Amino Acid Sequence (mesh)ChromatographyHigh Pressure Liquid (mesh)Crystallins (mesh)Humans (mesh)Isoaspartic Acid (mesh)Isomerism (mesh)LensCrystalline (mesh)Mass Spectrometry (mesh)Peptides (mesh)Protein Aggregates (mesh)Protein D-Aspartate-L-Isoaspartate Methyltransferase (mesh)Recombinant Proteins (mesh)alpha-Crystallin A Chain (mesh)alpha-Crystallin B Chain (mesh)lenspost-translational modification (PTM)agingprotein degradationprotein aggregationL-isoaspartateLensCrystalline (mesh)Humans (mesh)Protein D-Aspartate-L-Isoaspartate Methyltransferase (mesh)Isoaspartic Acid (mesh)Peptides (mesh)Crystallins (mesh)alpha-Crystallin A Chain (mesh)alpha-Crystallin B Chain (mesh)Recombinant Proteins (mesh)ChromatographyHigh Pressure Liquid (mesh)Amino Acid Sequence (mesh)Isomerism (mesh)Mass Spectrometry (mesh)Protein Aggregates (mesh)L-isoaspartateaginglenspost-translational modification (PTM)protein aggregationprotein degradationAmino Acid Sequence (mesh)ChromatographyHigh Pressure Liquid (mesh)Crystallins (mesh)Humans (mesh)Isoaspartic Acid (mesh)Isomerism (mesh)LensCrystalline (mesh)Mass Spectrometry (mesh)Peptides (mesh)Protein Aggregates (mesh)Protein D-Aspartate-L-Isoaspartate Methyltransferase (mesh)Recombinant Proteins (mesh)alpha-Crystallin A Chain (mesh)alpha-Crystallin B Chain (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biochemistry & Molecular Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/5q44w5f9https://escholarship.org/content/qt5q44w5f9/qt5q44w5f9.pdfinfo:doi/10.1074/jbc.ra119.009052articleJournal of Biological Chemistry, vol 294, iss 3212203 - 12219oai:escholarship.org:ark:/13030/qt0643h16r2026-01-02T02:08:42Zqt0643h16rSmall molecules disaggregate alpha-synuclein and prevent seeding from patient brain-derived fibrilsMurray, Kevin AHu, Carolyn JPan, HopeLu, JiahuiAbskharon, RomanyBowler, Jeannette TRosenberg, Gregory MWilliams, Christopher KElezi, GazmendBalbirnie, MelindaFaull, Kym FVinters, Harry VSeidler, Paul MEisenberg, David S2023-02-14The amyloid aggregation of alpha-synuclein within the brain is associated with the pathogenesis of Parkinson's disease (PD) and other related synucleinopathies, including multiple system atrophy (MSA). Alpha-synuclein aggregates are a major therapeutic target for treatment of these diseases. We identify two small molecules capable of disassembling preformed alpha-synuclein fibrils. The compounds, termed CNS-11 and CNS-11g, disaggregate recombinant alpha-synuclein fibrils in vitro, prevent the intracellular seeded aggregation of alpha-synuclein fibrils, and mitigate alpha-synuclein fibril cytotoxicity in neuronal cells. Furthermore, we demonstrate that both compounds disassemble fibrils extracted from MSA patient brains and prevent their intracellular seeding. They also reduce in vivo alpha-synuclein aggregates in C. elegans. Both compounds also penetrate brain tissue in mice. A molecular dynamics-based computational model suggests the compounds may exert their disaggregating effects on the N terminus of the fibril core. These compounds appear to be promising therapeutic leads for targeting alpha-synuclein for the treatment of synucleinopathies.32 Biomedical and Clinical Sciences (for-2020)3404 Medicinal and Biomolecular Chemistry (for-2020)34 Chemical Sciences (for-2020)Parkinson's Disease (rcdc)Neurodegenerative (rcdc)Aging (rcdc)Acquired Cognitive Impairment (rcdc)Brain Disorders (rcdc)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)Prevention (rcdc)Dementia (rcdc)Neurosciences (rcdc)5.1 Pharmaceuticals (hrcs-rac)Neurological (hrcs-hc)Mice (mesh)Animals (mesh)alpha-Synuclein (mesh)Synucleinopathies (mesh)Caenorhabditis elegans (mesh)Parkinson Disease (mesh)Multiple System Atrophy (mesh)Brain (mesh)Amyloid (mesh)Parkinson'samyloiddisaggregationmultiple system atrophyBrain (mesh)Animals (mesh)Mice (mesh)Caenorhabditis elegans (mesh)Multiple System Atrophy (mesh)Parkinson Disease (mesh)Amyloid (mesh)alpha-Synuclein (mesh)Synucleinopathies (mesh)Parkinson'samyloiddisaggregationmultiple system atrophyMice (mesh)Animals (mesh)alpha-Synuclein (mesh)Synucleinopathies (mesh)Caenorhabditis elegans (mesh)Parkinson Disease (mesh)Multiple System Atrophy (mesh)Brain (mesh)Amyloid (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/0643h16rhttps://escholarship.org/content/qt0643h16r/qt0643h16r.pdfinfo:doi/10.1073/pnas.2217835120articleProceedings of the National Academy of Sciences of the United States of America, vol 120, iss 7e2217835120oai:escholarship.org:ark:/13030/qt3j0844hx2026-01-02T02:08:12Zqt3j0844hxTunable Amine‐Reactive Electrophiles for Selective Profiling of LysineTang, Kuei‐ChienCao, JianBoatner, Lisa MLi, LinweiFarhi, JonathanHouk, Kendall NSpangle, JenniferBackus, Keriann MRaj, Monika2022-01-26Proteome profiling by activated esters identified >9000 ligandable lysines but they are limited as covalent inhibitors due to poor hydrolytic stability. Here we report our efforts to design and discover a new series of tunable amine-reactive electrophiles (TAREs) for selective and robust labeling of lysine. The major challenges in developing selective probes for lysine are the high nucleophilicity of cysteines and poor hydrolytic stability. Our work circumvents these challenges by a unique design of the TAREs that form stable adducts with lysine and on reaction with cysteine generate another reactive electrophiles for lysine. We highlight that TAREs exhibit substantially high hydrolytic stability as compared to the activated esters and are non-cytotoxic thus have the potential to act as covalent ligands. We applied these alternative TAREs for the intracellular labeling of proteins in different cell lines, and for the selective identification of lysines in the human proteome on a global scale.34 Chemical Sciences (for-2020)Lysine (mesh)Amines (mesh)Humans (mesh)Proteome (mesh)Molecular Structure (mesh)bioconjugationchemoselectivemass sensitivity boostersprotein labelingtracelessbioconjugationchemoselectivemass sensitivity boostersprotein labelingtracelessHumans (mesh)Amines (mesh)Lysine (mesh)Proteome (mesh)Molecular Structure (mesh)bioconjugationchemoselectivemass sensitivity boostersprotein labelingtracelessLysine (mesh)Amines (mesh)Humans (mesh)Proteome (mesh)Molecular Structure (mesh)03 Chemical Sciences (for)Organic Chemistry (science-metrix)34 Chemical sciences (for-2020)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/3j0844hxinfo:doi/10.1002/anie.202112107articleAngewandte Chemie International Edition, vol 61, iss 5e202112107oai:escholarship.org:ark:/13030/qt5v00z3sf2026-01-02T02:07:59Zqt5v00z3sfAtlas of fetal metabolism during mid-to-late gestation and diabetic pregnancyPerez-Ramirez, Cesar ANakano, HarukoLaw, Richard CMatulionis, NedasThompson, JenniferPfeiffer, AndrewPark, Junyoung ONakano, AtsushiChristofk, Heather R2024-01-01Mounting evidence suggests metabolism instructs stem cell fate decisions. However, how fetal metabolism changes during development and how altered maternal metabolism shapes fetal metabolism remain unexplored. We present a descriptive atlas of in vivo fetal murine metabolism during mid-to-late gestation in normal and diabetic pregnancy. Using 13C-glucose and liquid chromatography-mass spectrometry (LC-MS), we profiled the metabolism of fetal brains, hearts, livers, and placentas harvested from pregnant dams between embryonic days (E)10.5 and 18.5. Our analysis revealed metabolic features specific to a hyperglycemic environment and signatures that may denote developmental transitions during euglycemic development. We observed sorbitol accumulation in fetal tissues and altered neurotransmitter levels in fetal brains isolated from hyperglycemic dams. Tracing 13C-glucose revealed disparate fetal nutrient sourcing depending on maternal glycemic states. Regardless of glycemic state, histidine-derived metabolites accumulated in late-stage fetal tissues. Our rich dataset presents a comprehensive overview of in vivo fetal tissue metabolism and alterations due to maternal hyperglycemia.3215 Reproductive Medicine (for-2020)32 Biomedical and Clinical Sciences (for-2020)Pediatric (rcdc)Perinatal Period - Conditions Originating in Perinatal Period (rcdc)Diabetes (rcdc)Women's Health (rcdc)Nutrition (rcdc)Pregnancy (rcdc)Reproductive health and childbirth (hrcs-hc)3 Good Health and Well Being (sdg)Animals (mesh)Female (mesh)Mice (mesh)Pregnancy (mesh)Diabetes Mellitus (mesh)Fetus (mesh)Glucose (mesh)Placenta (mesh)DiabetesGestational (mesh)Fetus (mesh)Placenta (mesh)Animals (mesh)Mice (mesh)DiabetesGestational (mesh)Diabetes Mellitus (mesh)Glucose (mesh)Pregnancy (mesh)Female (mesh)developmentdiabetesfetal metabolismisotope tracingmetabolismmetabolomicspregnancyAnimals (mesh)Female (mesh)Mice (mesh)Pregnancy (mesh)Diabetes Mellitus (mesh)Fetus (mesh)Glucose (mesh)Placenta (mesh)DiabetesGestational (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/5v00z3sfhttps://escholarship.org/content/qt5v00z3sf/qt5v00z3sf.pdfinfo:doi/10.1016/j.cell.2023.11.011articleCell, vol 187, iss 1204 - 215.e14oai:escholarship.org:ark:/13030/qt333013t92026-01-02T01:55:17Zqt333013t9Resistance-gene-directed discovery of a natural-product herbicide with a new mode of actionYan, YanLiu, QikunZang, XinYuan, ShuguangBat-Erdene, UndramaaNguyen, CalvinGan, JianhuaZhou, JiahaiJacobsen, Steven ETang, Yi2018-07-01Bioactive natural products have evolved to inhibit specific cellular targets and have served as lead molecules for health and agricultural applications for the past century1–3. The post-genomics era has brought a renaissance in the discovery of natural products using synthetic-biology tools4–6. However, compared to traditional bioactivity-guided approaches, genome mining of natural products with specific and potent biological activities remains challenging4. Here we present the discovery and validation of a potent herbicide that targets a critical metabolic enzyme that is required for plant survival. Our approach is based on the co-clustering of a self-resistance gene in the natural-product biosynthesis gene cluster7–9, which provides insight into the potential biological activity of the encoded compound. We targeted dihydroxy-acid dehydratase in the branched-chain amino acid biosynthetic pathway in plants; the last step in this pathway is often targeted for herbicide development10. We show that the fungal sesquiterpenoid aspterric acid, which was discovered using the method described above, is a sub-micromolar inhibitor of dihydroxy-acid dehydratase that is effective as a herbicide in spray applications. The self-resistance gene astD was validated to be insensitive to aspterric acid and was deployed as a transgene in the establishment of plants that are resistant to aspterric acid. This herbicide-resistance gene combination complements the urgent ongoing efforts to overcome weed resistance11. Our discovery demonstrates the potential of using a resistance-gene-directed approach in the discovery of bioactive natural products.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Biotechnology (rcdc)Complementary and Integrative Health (rcdc)5.1 Pharmaceuticals (hrcs-rac)Arabidopsis (mesh)Biological Products (mesh)Enzyme Inhibitors (mesh)Herbicide Resistance (mesh)Herbicides (mesh)Heterocyclic Compounds3-Ring (mesh)Hydro-Lyases (mesh)ModelsMolecular (mesh)Multigene Family (mesh)Plant Growth Regulators (mesh)PlantsGenetically Modified (mesh)Transgenes (mesh)PlantsGenetically Modified (mesh)Arabidopsis (mesh)Heterocyclic Compounds3-Ring (mesh)Hydro-Lyases (mesh)Plant Growth Regulators (mesh)Biological Products (mesh)Enzyme Inhibitors (mesh)Herbicides (mesh)Multigene Family (mesh)Transgenes (mesh)ModelsMolecular (mesh)Herbicide Resistance (mesh)Arabidopsis (mesh)Biological Products (mesh)Enzyme Inhibitors (mesh)Herbicide Resistance (mesh)Herbicides (mesh)Heterocyclic Compounds3-Ring (mesh)Hydro-Lyases (mesh)ModelsMolecular (mesh)Multigene Family (mesh)Plant Growth Regulators (mesh)PlantsGenetically Modified (mesh)Transgenes (mesh)General Science & Technology (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/333013t9https://escholarship.org/content/qt333013t9/qt333013t9.pdfinfo:doi/10.1038/s41586-018-0319-4articleNature, vol 559, iss 7714415 - 418oai:escholarship.org:ark:/13030/qt3w7727492026-01-02T01:45:50Zqt3w772749Obese Skeletal Muscle-Expressed Interferon Regulatory Factor 4 Transcriptionally Regulates Mitochondrial Branched-Chain Aminotransferase Reprogramming Metabolome.Yao, TingYan, HongmeiZhu, XiaopengZhang, QiongyueKong, XingyuGuo, ShanshanFeng, YonghaoWang, HuiHua, YinghuiZhang, JingMittelman, Steven DTontonoz, PeterZhou, ZhenqiLiu, TieminKong, Xingxing2022-11-01In addition to the significant role in physical activity, skeletal muscle also contributes to health through the storage and use of macronutrients associated with energy homeostasis. However, the mechanisms of regulating integrated metabolism in skeletal muscle are not well-defined. Here, we compared the skeletal muscle transcriptome from obese and lean control subjects in different species (human and mouse) and found that interferon regulatory factor 4 (IRF4), an inflammation-immune transcription factor, conservatively increased in obese subjects. Thus, we investigated whether IRF4 gain of function in the skeletal muscle predisposed to obesity and insulin resistance. Conversely, mice with specific IRF4 loss in skeletal muscle showed protection against the metabolic effects of high-fat diet, increased branched-chain amino acids (BCAA) level of serum and muscle, and reprogrammed metabolome in serum. Mechanistically, IRF4 could transcriptionally upregulate mitochondrial branched-chain aminotransferase (BCATm) expression; subsequently, the enhanced BCATm could counteract the effects caused by IRF4 deletion. Furthermore, we demonstrated that IRF4 ablation in skeletal muscle enhanced mitochondrial activity, BCAA, and fatty acid oxidation in a BCATm-dependent manner. Taken together, these studies, for the first time, established IRF4 as a novel metabolic driver of macronutrients via BCATm in skeletal muscle in terms of diet-induced obesity.3208 Medical Physiology (for-2020)32 Biomedical and Clinical Sciences (for-2020)Obesity (rcdc)Diabetes (rcdc)Physical Activity (rcdc)Nutrition (rcdc)2.1 Biological and endogenous factors (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)Musculoskeletal (hrcs-hc)Metabolic and endocrine (hrcs-hc)Animals (mesh)Humans (mesh)Mice (mesh)Amino AcidsBranched-Chain (mesh)Fatty Acids (mesh)Interferon Regulatory Factors (mesh)Metabolome (mesh)MuscleSkeletal (mesh)Obesity (mesh)MuscleSkeletal (mesh)Animals (mesh)Humans (mesh)Mice (mesh)Obesity (mesh)Fatty Acids (mesh)Amino AcidsBranched-Chain (mesh)Interferon Regulatory Factors (mesh)Metabolome (mesh)Animals (mesh)Humans (mesh)Mice (mesh)Amino AcidsBranched-Chain (mesh)Fatty Acids (mesh)Interferon Regulatory Factors (mesh)Metabolome (mesh)MuscleSkeletal (mesh)Obesity (mesh)11 Medical and Health Sciences (for)Endocrinology & Metabolism (science-metrix)32 Biomedical and clinical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3w772749https://escholarship.org/content/qt3w772749/qt3w772749.pdfinfo:doi/10.2337/db22-0260articleDiabetes, vol 71, iss 112256 - 2271oai:escholarship.org:ark:/13030/qt011168j92026-01-02T01:44:37Zqt011168j9Protein Labeling via a Specific Lysine-Isopeptide Bond Using the Pilin Polymerizing Sortase from Corynebacterium diphtheriaeMcConnell, Scott AAmer, Brendan RMuroski, JohnFu, JanineChang, ChungyuLoo, Rachel R OgorzalekLoo, Joseph AOsipiuk, JerzyTon-That, HungClubb, Robert T2018-07-11Proteins that are site-specifically modified with peptides and chemicals can be used as novel therapeutics, imaging tools, diagnostic reagents and materials. However, there are few enzyme-catalyzed methods currently available to selectively conjugate peptides to internal sites within proteins. Here we show that a pilus-specific sortase enzyme from Corynebacterium diphtheriae (CdSrtA) can be used to attach a peptide to a protein via a specific lysine-isopeptide bond. Using rational mutagenesis we created CdSrtA3M, a highly activated cysteine transpeptidase that catalyzes in vitro isopeptide bond formation. CdSrtA3M mediates bioconjugation to a specific lysine residue within a fused domain derived from the corynebacterial SpaA protein. Peptide modification yields greater than >95% can be achieved. We demonstrate that CdSrtA3M can be used in concert with the Staphylococcus aureus SrtA enzyme, enabling dual, orthogonal protein labeling via lysine-isopeptide and backbone-peptide bonds.40 Engineering (for-2020)34 Chemical Sciences (for-2020)Biotechnology (rcdc)Aminoacyltransferases (mesh)Bacterial Proteins (mesh)Corynebacterium diphtheriae (mesh)Cysteine Endopeptidases (mesh)Fimbriae Proteins (mesh)Fluorescent Dyes (mesh)Lysine (mesh)ModelsMolecular (mesh)Peptides (mesh)Polymerization (mesh)Staining and Labeling (mesh)Staphylococcus aureus (mesh)Corynebacterium diphtheriae (mesh)Staphylococcus aureus (mesh)Cysteine Endopeptidases (mesh)Aminoacyltransferases (mesh)Lysine (mesh)Peptides (mesh)Bacterial Proteins (mesh)Fimbriae Proteins (mesh)Fluorescent Dyes (mesh)Staining and Labeling (mesh)ModelsMolecular (mesh)Polymerization (mesh)Aminoacyltransferases (mesh)Bacterial Proteins (mesh)Corynebacterium diphtheriae (mesh)Cysteine Endopeptidases (mesh)Fimbriae Proteins (mesh)Fluorescent Dyes (mesh)Lysine (mesh)ModelsMolecular (mesh)Peptides (mesh)Polymerization (mesh)Staining and Labeling (mesh)Staphylococcus aureus (mesh)03 Chemical Sciences (for)General Chemistry (science-metrix)34 Chemical sciences (for-2020)40 Engineering (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/011168j9https://escholarship.org/content/qt011168j9/qt011168j9.pdfinfo:doi/10.1021/jacs.8b05200articleJournal of the American Chemical Society, vol 140, iss 278420 - 8423oai:escholarship.org:ark:/13030/qt6474m4372026-01-02T01:27:28Zqt6474m437Structure and noncanonical Cdk8 activation mechanism within an Argonaute-containing Mediator kinase moduleLi, Yi-ChuanChao, Ti-ChunKim, Hee JongCholko, TimothyChen, Shin-FuLi, GuojieSnyder, LauraNakanishi, KotaroChang, Chia-EnMurakami, KenjiGarcia, Benjamin ABoyer, Thomas GTsai, Kuang-Lei2021-01-15The Cdk8 kinase module (CKM) in Mediator, comprising Med13, Med12, CycC, and Cdk8, regulates RNA polymerase II transcription through kinase-dependent and -independent functions. Numerous pathogenic mutations causative for neurodevelopmental disorders and cancer congregate in CKM subunits. However, the structure of the intact CKM and the mechanism by which Cdk8 is non-canonically activated and functionally affected by oncogenic CKM alterations are poorly understood. Here, we report a cryo-electron microscopy structure of Saccharomyces cerevisiae CKM that redefines prior CKM structural models and explains the mechanism of Med12-dependent Cdk8 activation. Med12 interacts extensively with CycC and activates Cdk8 by stabilizing its activation (T-)loop through conserved Med12 residues recurrently mutated in human tumors. Unexpectedly, Med13 has a characteristic Argonaute-like bi-lobal architecture. These findings not only provide a structural basis for understanding CKM function and pathological dysfunction, but also further impute a previously unknown regulatory mechanism of Mediator in transcriptional modulation through its Med13 Argonaute-like features.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)2.1 Biological and endogenous factors (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)application/pdfCC-BY-NCeScholarship, University of Californiahttps://escholarship.org/uc/item/6474m437https://escholarship.org/content/qt6474m437/qt6474m437.pdfinfo:doi/10.1126/sciadv.abd4484articleScience Advances, vol 7, iss 3eabd4484oai:escholarship.org:ark:/13030/qt3d77c8fb2026-01-02T00:35:51Zqt3d77c8fbInsight into the molecular basis of substrate recognition by the wall teichoic acid glycosyltransferase TagAMartinez, Orlando EMahoney, Brendan JGoring, Andrew KYi, Sung-WookTran, Denise PCascio, DuilioPhillips, Martin LMuthana, Musleh MChen, XiJung, Michael ELoo, Joseph AClubb, Robert T2022-02-01Wall teichoic acid (WTA) polymers are covalently affixed to the Gram-positive bacterial cell wall and have important functions in cell elongation, cell morphology, biofilm formation, and β-lactam antibiotic resistance. The first committed step in WTA biosynthesis is catalyzed by the TagA glycosyltransferase (also called TarA), a peripheral membrane protein that produces the conserved linkage unit, which joins WTA to the cell wall peptidoglycan. TagA contains a conserved GT26 core domain followed by a C-terminal polypeptide tail that is important for catalysis and membrane binding. Here, we report the crystal structure of the Thermoanaerobacter italicus TagA enzyme bound to UDP-N-acetyl-d-mannosamine, revealing the molecular basis of substrate binding. Native MS experiments support the model that only monomeric TagA is enzymatically active and that it is stabilized by membrane binding. Molecular dynamics simulations and enzyme activity measurements indicate that the C-terminal polypeptide tail facilitates catalysis by encapsulating the UDP-N-acetyl-d-mannosamine substrate, presenting three highly conserved arginine residues to the active site that are important for catalysis (R214, R221, and R224). From these data, we present a mechanistic model of catalysis that ascribes functions for these residues. This work could facilitate the development of new antimicrobial compounds that disrupt WTA biosynthesis in pathogenic bacteria.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Antimicrobial Resistance (rcdc)Infectious Diseases (rcdc)Infection (hrcs-hc)Bacterial Proteins (mesh)Cell Wall (mesh)Glycosyltransferases (mesh)Lipoproteins (mesh)Staphylococcus aureus (mesh)Substrate Specificity (mesh)Teichoic Acids (mesh)Uridine Diphosphate (mesh)Cell Wall (mesh)Staphylococcus aureus (mesh)Glycosyltransferases (mesh)Teichoic Acids (mesh)Lipoproteins (mesh)Bacterial Proteins (mesh)Uridine Diphosphate (mesh)Substrate Specificity (mesh)MSNMRTagAThermoanaerobacter italicusX-ray crystallographyglycosyltransferasemethicillin-resistant Staphylococcus aureusmolecular dynamicsperipheral membrane proteinteichoic acidBacterial Proteins (mesh)Cell Wall (mesh)Glycosyltransferases (mesh)Lipoproteins (mesh)Staphylococcus aureus (mesh)Substrate Specificity (mesh)Teichoic Acids (mesh)Uridine Diphosphate (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biochemistry & Molecular Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/3d77c8fbhttps://escholarship.org/content/qt3d77c8fb/qt3d77c8fb.pdfinfo:doi/10.1016/j.jbc.2021.101464articleJournal of Biological Chemistry, vol 298, iss 2101464oai:escholarship.org:ark:/13030/qt61t760z32026-01-02T00:16:38Zqt61t760z3Rod Photoreceptors Avoid Saturation in Bright Light by the Movement of the G Protein TransducinFrederiksen, RikardMorshedian, AlaTripathy, Sonia AXu, TongzhouTravis, Gabriel HFain, Gordon LSampath, Alapakkam P2021-04-14Rod photoreceptors can be saturated by exposure to bright background light, so that no flash superimposed on the background can elicit a detectable response. This phenomenon, called increment saturation, was first demonstrated psychophysically by Aguilar and Stiles and has since been shown in many studies to occur in single rods. Recent experiments indicate, however, that rods may be able to avoid saturation under some conditions of illumination. We now show in ex vivo electroretinogram and single-cell recordings that in continuous and prolonged exposure even to very bright light, the rods of mice from both sexes recover as much as 15% of their dark current and that responses can persist for hours. In parallel to recovery of outer segment current is an ∼10-fold increase in the sensitivity of rod photoresponses. This recovery is decreased in transgenic mice with reduced light-dependent translocation of the G protein transducin. The reduction in outer-segment transducin together with a novel mechanism of visual-pigment regeneration within the rod itself enable rods to remain responsive over the whole of the physiological range of vision. In this way, rods are able to avoid an extended period of transduction channel closure, which is known to cause photoreceptor degeneration.SIGNIFICANCE STATEMENT Rods are initially saturated in bright light so that no flash superimposed on the background can elicit a detectable response. Frederiksen and colleagues show in whole retina and single-cell recordings that, if the background light is prolonged, rods slowly recover and can continue to produce significant responses over the entire physiological range of vision. Response recovery occurs by translocation of the G protein transducin from the rod outer to the inner segment, together with a novel mechanism of visual-pigment regeneration within the rod itself. Avoidance of saturation in bright light may be one of the principal mechanisms the retina uses to keep rod outer-segment channels from ever closing for too long a time, which is known to produce photoreceptor degeneration.32 Biomedical and Clinical Sciences (for-2020)3212 Ophthalmology and Optometry (for-2020)Neurosciences (rcdc)Eye Disease and Disorders of Vision (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Eye (hrcs-hc)Animals (mesh)Electroretinography (mesh)Female (mesh)Light (mesh)Male (mesh)Mice (mesh)Protein Transport (mesh)Retinal Rod Photoreceptor Cells (mesh)Single-Cell Analysis (mesh)Transducin (mesh)VisionOcular (mesh)adaptationG proteinretinarod photoreceptorsaturationvisual pigmentAnimals (mesh)Mice (mesh)Transducin (mesh)Electroretinography (mesh)Protein Transport (mesh)Light (mesh)Female (mesh)Male (mesh)VisionOcular (mesh)Retinal Rod Photoreceptor Cells (mesh)Single-Cell Analysis (mesh)G proteinadaptationretinarod photoreceptorsaturationvisual pigmentAnimals (mesh)Electroretinography (mesh)Female (mesh)Light (mesh)Male (mesh)Mice (mesh)Protein Transport (mesh)Retinal Rod Photoreceptor Cells (mesh)Single-Cell Analysis (mesh)Transducin (mesh)VisionOcular (mesh)11 Medical and Health Sciences (for)17 Psychology and Cognitive Sciences (for)Neurology & Neurosurgery (science-metrix)3209 Neurosciences (for-2020)application/pdfCC-BY-NC-SAeScholarship, University of Californiahttps://escholarship.org/uc/item/61t760z3https://escholarship.org/content/qt61t760z3/qt61t760z3.pdfinfo:doi/10.1523/jneurosci.2817-20.2021articleJournal of Neuroscience, vol 41, iss 153320 - 3330oai:escholarship.org:ark:/13030/qt24n8r9jt2026-01-01T19:47:18Zqt24n8r9jtThe impact of ageing on lipid-mediated regulation of adult stem cell behavior and tissue homeostasisSênos Demarco, RafaelClémot, MarieJones, D Leanne2020-07-01Adult stem cells sustain tissue homeostasis throughout life and provide an important reservoir of cells capable of tissue repair in response to stress and tissue damage. Age-related changes to stem cells and/or the specialized niches that house them have been shown to negatively impact stem cell maintenance and activity. In addition, metabolic inputs have surfaced as another crucial layer in the control of stem cell behavior (Chandel et al., 2016; Folmes and Terzic, 2016; Ito and Suda, 2014; Mana et al., 2017; Shyh-Chang and Ng, 2017). Here, we will present a brief review of how lipid metabolism influences adult stem cell behavior under homeostatic conditions and speculate on how changes in lipid metabolism may impact stem cell ageing. This review considers the future of lipid metabolism research in stem cells, with the long-term goal of identifying mechanisms that could be targeted to counter or slow the age-related decline in stem cell function.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Stem Cell Research (rcdc)Regenerative Medicine (rcdc)Stem Cell Research - Nonembryonic - Non-Human (rcdc)Aging (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Generic health relevance (hrcs-hc)Adult Stem Cells (mesh)Aging (mesh)Animals (mesh)Cellular Senescence (mesh)Humans (mesh)Lipid Metabolism (mesh)LipidMetabolismFatty acidsStem cellsNicheAnimals (mesh)Humans (mesh)Aging (mesh)Lipid Metabolism (mesh)Adult Stem Cells (mesh)Cellular Senescence (mesh)Fatty acidsLipidMetabolismNicheStem cellsAdult Stem Cells (mesh)Aging (mesh)Animals (mesh)Cellular Senescence (mesh)Humans (mesh)Lipid Metabolism (mesh)1103 Clinical Sciences (for)Gerontology (science-metrix)3101 Biochemistry and cell biology (for-2020)3202 Clinical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/24n8r9jthttps://escholarship.org/content/qt24n8r9jt/qt24n8r9jt.pdfinfo:doi/10.1016/j.mad.2020.111278articleMechanisms of Ageing and Development, vol 189111278oai:escholarship.org:ark:/13030/qt8m2074hh2026-01-01T15:30:13Zqt8m2074hhThe molecular tweezer CLR01 inhibits aberrant superoxide dismutase 1 (SOD1) self-assembly in vitro and in the G93A-SOD1 mouse model of ALSMalik, RavinderMeng, HelenWongkongkathep, PiriyaCorrales, Christian ISepanj, NikiAtlasi, Ryan SKlärner, Frank-GerritSchrader, ThomasSpencer, Melissa JLoo, Joseph AWiedau, MartinaBitan, Gal2019-03-01Mutations in superoxide dismutase 1 (SOD1) cause 15-20% of familial amyotrophic lateral sclerosis (fALS) cases. The resulting amino acid substitutions destabilize SOD1's protein structure, leading to its self-assembly into neurotoxic oligomers and aggregates, a process hypothesized to cause the characteristic motor-neuron degeneration in affected individuals. Currently, effective disease-modifying therapy is not available for ALS. Molecular tweezers prevent formation of toxic protein assemblies, yet their protective action has not been tested previously on SOD1 or in the context of ALS. Here, we tested the molecular tweezer CLR01-a broad-spectrum inhibitor of the self-assembly and toxicity of amyloid proteins-as a potential therapeutic agent for ALS. Using recombinant WT and mutant SOD1, we found that CLR01 inhibited the aggregation of all tested SOD1 forms in vitro Next, we examined whether CLR01 could prevent the formation of misfolded SOD1 in the G93A-SOD1 mouse model of ALS and whether such inhibition would have a beneficial therapeutic effect. CLR01 treatment decreased misfolded SOD1 in the spinal cord significantly. However, these histological findings did not correlate with improvement of the disease phenotype. A small, dose-dependent decrease in disease duration was found in CLR01-treated mice, relative to vehicle-treated animals, yet motor function did not improve in any of the treatment groups. These results demonstrate that CLR01 can inhibit SOD1 misfolding and aggregation both in vitro and in vivo, but raise the question whether such inhibition is sufficient for achieving a therapeutic effect. Additional studies in other less aggressive ALS models may be needed to determine the therapeutic potential of this approach.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Prevention (rcdc)Orphan Drug (rcdc)Brain Disorders (rcdc)Rare Diseases (rcdc)Neurosciences (rcdc)ALS (rcdc)Neurodegenerative (rcdc)5.1 Pharmaceuticals (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Neurological (hrcs-hc)Amino Acid Sequence (mesh)Amyotrophic Lateral Sclerosis (mesh)Animals (mesh)Binding Sites (mesh)Body Weight (mesh)Bridged-Ring Compounds (mesh)Disease ModelsAnimal (mesh)Mice (mesh)Muscle Strength (mesh)Mutation (mesh)Organophosphates (mesh)Protein Aggregates (mesh)Spinal Cord (mesh)Superoxide Dismutase-1 (mesh)Survival Analysis (mesh)superoxide dismutase (SOD)amyotrophic lateral sclerosis (ALS) (Lou Gehrig disease)protein aggregationmouseinhibitorneurodegenerationamyloidprotein misfoldingmolecular tweezermotor neuronSpinal Cord (mesh)Animals (mesh)Mice (mesh)Amyotrophic Lateral Sclerosis (mesh)Disease ModelsAnimal (mesh)Body Weight (mesh)Survival Analysis (mesh)Binding Sites (mesh)Amino Acid Sequence (mesh)Mutation (mesh)Muscle Strength (mesh)Organophosphates (mesh)Protein Aggregates (mesh)Bridged-Ring Compounds (mesh)Superoxide Dismutase-1 (mesh)amyloidamyotrophic lateral sclerosis (ALS) (Lou Gehrig disease)inhibitormolecular tweezermotor neuronmouseneurodegenerationprotein aggregationprotein misfoldingsuperoxide dismutase (SOD)Amino Acid Sequence (mesh)Amyotrophic Lateral Sclerosis (mesh)Animals (mesh)Binding Sites (mesh)Body Weight (mesh)Bridged-Ring Compounds (mesh)Disease ModelsAnimal (mesh)Mice (mesh)Muscle Strength (mesh)Mutation (mesh)Organophosphates (mesh)Protein Aggregates (mesh)Spinal Cord (mesh)Superoxide Dismutase-1 (mesh)Survival Analysis (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biochemistry & Molecular Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/8m2074hhhttps://escholarship.org/content/qt8m2074hh/qt8m2074hh.pdfinfo:doi/10.1074/jbc.ra118.005940articleJournal of Biological Chemistry, vol 294, iss 103501 - 3513oai:escholarship.org:ark:/13030/qt71b0j4nw2026-01-01T12:32:57Zqt71b0j4nwPolymorphic Structure Determination of the Macrocyclic Drug Paritaprevir by MicroEDBu, GuanhongDanelius, EmmaWieske, Lianne HEGonen, Tamir2024-05-01Paritaprevir is an orally bioavailable, macrocyclic drug used for treating chronic Hepatitis C virus (HCV) infection. Its structures have been elusive to the public until recently when one of the crystal forms is solved by microcrystal electron diffraction (MicroED). In this work, the MicroED structures of two distinct polymorphic crystal forms of paritaprevir are reported from the same experiment. The different polymorphs show conformational changes in the macrocyclic core, as well as the cyclopropyl sulfonamide and methyl pyrazinamide substituents. Molecular docking shows that one of the conformations fits well into the active site pocket of the HCV non-structural 3/4A (NS3/4A) serine protease target, and can interact with the pocket and catalytic triad via hydrophobic interactions and hydrogen bonds. These results can provide further insight for optimization of the binding of acyl sulfonamide inhibitors to the HCV NS3/4A serine protease. In addition, this also demonstrates the opportunity to derive different polymorphs and distinct macrocycle conformations from the same experiments using MicroED.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Digestive Diseases (rcdc)Infectious Diseases (rcdc)Sexually Transmitted Infections (rcdc)Liver Disease (rcdc)Hepatitis (rcdc)Emerging Infectious Diseases (rcdc)Chronic Liver Disease and Cirrhosis (rcdc)Hepatitis - C (rcdc)3 Good Health and Well Being (sdg)Sulfonamides (mesh)Cyclopropanes (mesh)LactamsMacrocyclic (mesh)Proline (mesh)Molecular Docking Simulation (mesh)Macrocyclic Compounds (mesh)Antiviral Agents (mesh)Hepacivirus (mesh)Viral Nonstructural Proteins (mesh)HCV proteasemacrocyclesMicroEDmolecular chameleonspolymorphismHepacivirus (mesh)LactamsMacrocyclic (mesh)Sulfonamides (mesh)Cyclopropanes (mesh)Macrocyclic Compounds (mesh)Proline (mesh)Viral Nonstructural Proteins (mesh)Antiviral Agents (mesh)Molecular Docking Simulation (mesh)HCV proteaseMicroEDmacrocyclesmolecular chameleonspolymorphismSulfonamides (mesh)Cyclopropanes (mesh)LactamsMacrocyclic (mesh)Proline (mesh)Molecular Docking Simulation (mesh)Macrocyclic Compounds (mesh)Antiviral Agents (mesh)Hepacivirus (mesh)Viral Nonstructural Proteins (mesh)3101 Biochemistry and cell biology (for-2020)3206 Medical biotechnology (for-2020)4003 Biomedical engineering (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/71b0j4nwhttps://escholarship.org/content/qt71b0j4nw/qt71b0j4nw.pdfinfo:doi/10.1002/adbi.202300570articleAdvanced Biology, vol 8, iss 5e2300570 - e2300570oai:escholarship.org:ark:/13030/qt9tv115kq2026-01-01T11:10:07Zqt9tv115kqCysDB: a human cysteine database based on experimental quantitative chemoproteomicsBoatner, Lisa MPalafox, Maria FSchweppe, Devin KBackus, Keriann M2023-06-01Cysteine chemoproteomics provides proteome-wide portraits of the ligandability or potential "druggability" for thousands of cysteine residues. Consequently, these studies are facilitating resources for closing the druggability gap, namely, achieving pharmacological manipulation of ∼96% of the human proteome that remains untargeted by U.S. Food and Drug Administration (FDA) approved small molecules. Recent interactive datasets have enabled users to interface more readily with cysteine chemoproteomics datasets. However, these resources remain limited to single studies and therefore do not provide a mechanism to perform cross-study analyses. Here we report CysDB as a curated community-wide repository of human cysteine chemoproteomics data derived from nine high-coverage studies. CysDB is publicly available at https://backuslab.shinyapps.io/cysdb/ and features measures of identification for 62,888 cysteines (24% of the cysteinome), as well as annotations of functionality, druggability, disease relevance, genetic variation, and structural features. Most importantly, we have designed CysDB to incorporate new datasets to further support the continued growth of the druggable cysteinome.3404 Medicinal and Biomolecular Chemistry (for-2020)34 Chemical Sciences (for-2020)Generic health relevance (hrcs-hc)Humans (mesh)Cysteine (mesh)Proteome (mesh)Humans (mesh)Cysteine (mesh)Proteome (mesh)Cysteinechemoproteomicscovalent probescysteinomedatabaseelectrophilic fragmentsligandabilitymulti-omicsHumans (mesh)Cysteine (mesh)Proteome (mesh)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9tv115kqhttps://escholarship.org/content/qt9tv115kq/qt9tv115kq.pdfinfo:doi/10.1016/j.chembiol.2023.04.004articleCell Chemical Biology, vol 30, iss 6683 - 698.e3oai:escholarship.org:ark:/13030/qt5qf0t0p22026-01-01T10:33:36Zqt5qf0t0p2Arabidopsis TRB proteins function in H3K4me3 demethylation by recruiting JMJ14Wang, MingZhong, ZhenhuiGallego-Bartolomé, JavierFeng, SuhuaShih, Yuan-HsinLiu, MukunZhou, JessicaRichey, John CurtisNg, CharmaineJami-Alahmadi, YasamanWohlschlegel, JamesWu, KeqiangJacobsen, Steven E2023-01-01Arabidopsis telomeric repeat binding factors (TRBs) can bind telomeric DNA sequences to protect telomeres from degradation. TRBs can also recruit Polycomb Repressive Complex 2 (PRC2) to deposit tri-methylation of H3 lysine 27 (H3K27me3) over certain target loci. Here, we demonstrate that TRBs also associate and colocalize with JUMONJI14 (JMJ14) and trigger H3K4me3 demethylation at some loci. The trb1/2/3 triple mutant and the jmj14-1 mutant show an increased level of H3K4me3 over TRB and JMJ14 binding sites, resulting in up-regulation of their target genes. Furthermore, tethering TRBs to the promoter region of genes with an artificial zinc finger (TRB-ZF) successfully triggers target gene silencing, as well as H3K27me3 deposition, and H3K4me3 removal. Interestingly, JMJ14 is predominantly recruited to ZF off-target sites with low levels of H3K4me3, which is accompanied with TRB-ZFs triggered H3K4me3 removal at these loci. These results suggest that TRB proteins coordinate PRC2 and JMJ14 activities to repress target genes via H3K27me3 deposition and H3K4me3 removal.31 Biological Sciences (for-2020)3105 Genetics (for-2020)Biotechnology (rcdc)Genetics (rcdc)Histones (mesh)Arabidopsis Proteins (mesh)Arabidopsis (mesh)Polycomb Repressive Complex 2 (mesh)Telomere-Binding Proteins (mesh)Demethylation (mesh)Gene Expression RegulationPlant (mesh)Polycomb-Group Proteins (mesh)Jumonji Domain-Containing Histone Demethylases (mesh)Arabidopsis (mesh)Telomere-Binding Proteins (mesh)Histones (mesh)Arabidopsis Proteins (mesh)Gene Expression RegulationPlant (mesh)Jumonji Domain-Containing Histone Demethylases (mesh)Polycomb-Group Proteins (mesh)Polycomb Repressive Complex 2 (mesh)Demethylation (mesh)Histones (mesh)Arabidopsis Proteins (mesh)Arabidopsis (mesh)Polycomb Repressive Complex 2 (mesh)Telomere-Binding Proteins (mesh)Demethylation (mesh)Gene Expression RegulationPlant (mesh)Polycomb-Group Proteins (mesh)Jumonji Domain-Containing Histone Demethylases (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/5qf0t0p2https://escholarship.org/content/qt5qf0t0p2/qt5qf0t0p2.pdfinfo:doi/10.1038/s41467-023-37263-9articleNature Communications, vol 14, iss 11736oai:escholarship.org:ark:/13030/qt1122r0tg2026-01-01T08:59:59Zqt1122r0tgDe novo designed protein inhibitors of amyloid aggregation and seedingMurray, Kevin AHu, Carolyn JGriner, Sarah LPan, HopeBowler, Jeannette TAbskharon, RomanyRosenberg, Gregory MCheng, XinyiSeidler, Paul MEisenberg, David S2022-08-23Neurodegenerative diseases are characterized by the pathologic accumulation of aggregated proteins. Known as amyloid, these fibrillar aggregates include proteins such as tau and amyloid-β (Aβ) in Alzheimer's disease (AD) and alpha-synuclein (αSyn) in Parkinson's disease (PD). The development and spread of amyloid fibrils within the brain correlates with disease onset and progression, and inhibiting amyloid formation is a possible route toward therapeutic development. Recent advances have enabled the determination of amyloid fibril structures to atomic-level resolution, improving the possibility of structure-based inhibitor design. In this work, we use these amyloid structures to design inhibitors that bind to the ends of fibrils, "capping" them so as to prevent further growth. Using de novo protein design, we develop a library of miniprotein inhibitors of 35 to 48 residues that target the amyloid structures of tau, Aβ, and αSyn. Biophysical characterization of top in silico designed inhibitors shows they form stable folds, have no sequence similarity to naturally occurring proteins, and specifically prevent the aggregation of their targeted amyloid-prone proteins in vitro. The inhibitors also prevent the seeded aggregation and toxicity of fibrils in cells. In vivo evaluation reveals their ability to reduce aggregation and rescue motor deficits in Caenorhabditis elegans models of PD and AD.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Alzheimer's Disease (rcdc)Prevention (rcdc)Brain Disorders (rcdc)Neurosciences (rcdc)Dementia (rcdc)Parkinson's Disease (rcdc)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)Acquired Cognitive Impairment (rcdc)Neurodegenerative (rcdc)Aging (rcdc)2.1 Biological and endogenous factors (hrcs-rac)5.1 Pharmaceuticals (hrcs-rac)Neurological (hrcs-hc)Alzheimer Disease (mesh)Amyloid (mesh)Amyloid beta-Peptides (mesh)Amyloidosis (mesh)Humans (mesh)Parkinson Disease (mesh)Protein AggregationPathological (mesh)alpha-Synuclein (mesh)tau Proteins (mesh)protein designamyloidtaualpha-synucleinamyloid-betaHumans (mesh)Parkinson Disease (mesh)Alzheimer Disease (mesh)Amyloidosis (mesh)Amyloid (mesh)tau Proteins (mesh)alpha-Synuclein (mesh)Amyloid beta-Peptides (mesh)Protein AggregationPathological (mesh)alpha-synucleinamyloidamyloid-betaprotein designtauAlzheimer Disease (mesh)Amyloid (mesh)Amyloid beta-Peptides (mesh)Amyloidosis (mesh)Humans (mesh)Parkinson Disease (mesh)Protein AggregationPathological (mesh)alpha-Synuclein (mesh)tau Proteins (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/1122r0tghttps://escholarship.org/content/qt1122r0tg/qt1122r0tg.pdfinfo:doi/10.1073/pnas.2206240119articleProceedings of the National Academy of Sciences of the United States of America, vol 119, iss 34e2206240119oai:escholarship.org:ark:/13030/qt82q3d98q2026-01-01T06:35:49Zqt82q3d98qVision-dependent specification of cell types and function in the developing cortexCheng, SarahButrus, SalwanTan, LimingXu, RunzheSagireddy, SrikantTrachtenberg, Joshua TShekhar, KarthikZipursky, S Lawrence2022-01-01The role of postnatal experience in sculpting cortical circuitry, while long appreciated, is poorly understood at the level of cell types. We explore this in the mouse primary visual cortex (V1) using single-nucleus RNA sequencing, visual deprivation, genetics, and functional imaging. We find that vision selectively drives the specification of glutamatergic cell types in upper layers (L) (L2/3/4), while deeper-layer glutamatergic, GABAergic, and non-neuronal cell types are established prior to eye opening. L2/3 cell types form an experience-dependent spatial continuum defined by the graded expression of ∼200 genes, including regulators of cell adhesion and synapse formation. One of these genes, Igsf9b, a vision-dependent gene encoding an inhibitory synaptic cell adhesion molecule, is required for the normal development of binocular responses in L2/3. In summary, vision preferentially regulates the development of upper-layer glutamatergic cell types through the regulation of cell-type-specific gene expression programs.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Neurosciences (rcdc)Eye Disease and Disorders of Vision (rcdc)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Eye (hrcs-hc)Animals (mesh)AnimalsNewborn (mesh)Biomarkers (mesh)Gene Expression Profiling (mesh)Gene Expression RegulationDevelopmental (mesh)Glutamic Acid (mesh)Male (mesh)Membrane Proteins (mesh)MiceInbred C57BL (mesh)Nerve Tissue Proteins (mesh)Neurons (mesh)RNA-Seq (mesh)Transcriptome (mesh)VisionBinocular (mesh)VisionOcular (mesh)Visual Cortex (mesh)gamma-Aminobutyric Acid (mesh)Mice (mesh)Visual Cortex (mesh)Neurons (mesh)Animals (mesh)MiceInbred C57BL (mesh)AnimalsNewborn (mesh)Mice (mesh)gamma-Aminobutyric Acid (mesh)Glutamic Acid (mesh)Membrane Proteins (mesh)Nerve Tissue Proteins (mesh)Gene Expression Profiling (mesh)Gene Expression RegulationDevelopmental (mesh)VisionBinocular (mesh)Male (mesh)VisionOcular (mesh)Transcriptome (mesh)Biomarkers (mesh)RNA-Seq (mesh)binocular visioncell typescritical periodinhibitory synapseslayer 2/3single-nucleus RNA-seqvisual cortexAnimals (mesh)AnimalsNewborn (mesh)Biomarkers (mesh)Gene Expression Profiling (mesh)Gene Expression RegulationDevelopmental (mesh)Glutamic Acid (mesh)Male (mesh)Membrane Proteins (mesh)MiceInbred C57BL (mesh)Nerve Tissue Proteins (mesh)Neurons (mesh)RNA-Seq (mesh)Transcriptome (mesh)VisionBinocular (mesh)VisionOcular (mesh)Visual Cortex (mesh)gamma-Aminobutyric Acid (mesh)Mice (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/82q3d98qhttps://escholarship.org/content/qt82q3d98q/qt82q3d98q.pdfinfo:doi/10.1016/j.cell.2021.12.022articleCell, vol 185, iss 2311 - 327.e24oai:escholarship.org:ark:/13030/qt0276k5kw2026-01-01T04:35:18Zqt0276k5kwCryo-EM structures of hIAPP fibrils seeded by patient-extracted fibrils reveal new polymorphs and conserved fibril coresCao, QinBoyer, David RSawaya, Michael RAbskharon, RomanySaelices, LorenaNguyen, Binh ALu, JiahuiMurray, Kevin AKandeel, FouadEisenberg, David S2021-09-01Amyloidosis of human islet amyloid polypeptide (hIAPP) is a pathological hallmark of type II diabetes (T2D), an epidemic afflicting nearly 10% of the world’s population. To visualize disease-relevant hIAPP fibrils, we extracted amyloid fibrils from islet cells of a T2D donor and amplified their quantity by seeding synthetic hIAPP. Cryo-EM studies revealed four fibril polymorphic atomic structures. Their resemblance to four unseeded hIAPP fibrils varies from nearly identical (TW3) to non-existent (TW2). The diverse repertoire of hIAPP polymorphs appears to arise from three distinct protofilament cores entwined in different combinations. The structural distinctiveness of TW1, TW2 and TW4 suggests they may be faithful replications of the pathogenic seeds. If so, the structures determined here provide the most direct view yet of hIAPP amyloid fibrils formed during T2D.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)2.1 Biological and endogenous factors (hrcs-rac)Metabolic and endocrine (hrcs-hc)Amino Acid Sequence (mesh)Amyloid (mesh)Congo Red (mesh)Cryoelectron Microscopy (mesh)Diabetes MellitusType 2 (mesh)Genotype (mesh)Humans (mesh)Islet Amyloid Polypeptide (mesh)Islets of Langerhans (mesh)ModelsMolecular (mesh)Polymerase Chain Reaction (mesh)Protein Aggregates (mesh)Protein Conformation (mesh)Recombinant Proteins (mesh)Sequence AnalysisDNA (mesh)Staining and Labeling (mesh)Islets of Langerhans (mesh)Humans (mesh)Diabetes MellitusType 2 (mesh)Congo Red (mesh)Amyloid (mesh)Recombinant Proteins (mesh)Cryoelectron Microscopy (mesh)Staining and Labeling (mesh)Polymerase Chain Reaction (mesh)Sequence AnalysisDNA (mesh)Amino Acid Sequence (mesh)Protein Conformation (mesh)Genotype (mesh)ModelsMolecular (mesh)Islet Amyloid Polypeptide (mesh)Protein Aggregates (mesh)Amino Acid Sequence (mesh)Amyloid (mesh)Congo Red (mesh)Cryoelectron Microscopy (mesh)Diabetes MellitusType 2 (mesh)Genotype (mesh)Humans (mesh)Islet Amyloid Polypeptide (mesh)Islets of Langerhans (mesh)ModelsMolecular (mesh)Polymerase Chain Reaction (mesh)Protein Aggregates (mesh)Protein Conformation (mesh)Recombinant Proteins (mesh)Sequence AnalysisDNA (mesh)Staining and Labeling (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biophysics (science-metrix)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0276k5kwhttps://escholarship.org/content/qt0276k5kw/qt0276k5kw.pdfinfo:doi/10.1038/s41594-021-00646-xarticleNature Structural & Molecular Biology, vol 28, iss 9724 - 730oai:escholarship.org:ark:/13030/qt794008rq2026-01-01T03:16:01Zqt794008rqAn amygdala-to-hypothalamus circuit for social rewardHu, Rongfeng KZuo, YanningLy, TruongWang, JunMeera, PratapWu, Ye EmilyHong, Weizhe2021-06-01Social interactions and relationships are often rewarding, but the neural mechanisms through which social interaction drives positive experience remain poorly understood. In this study, we developed an automated operant conditioning system to measure social reward in mice and found that adult mice of both sexes display robust reinforcement of social interaction. Through cell-type-specific manipulations, we identified a crucial role for GABAergic neurons in the medial amygdala (MeA) in promoting the positive reinforcement of social interaction. Moreover, MeA GABAergic neurons mediate social reinforcement behavior through their projections to the medial preoptic area (MPOA) and promote dopamine release in the nucleus accumbens. Finally, activation of this MeA-to-MPOA circuit can robustly overcome avoidance behavior. Together, these findings establish the MeA as a key node for regulating social reward in both sexes, providing new insights into the regulation of social reward beyond the classic mesolimbic reward system.5202 Biological Psychology (for-2020)3214 Pharmacology and Pharmaceutical Sciences (for-2020)32 Biomedical and Clinical Sciences (for-2020)52 Psychology (for-2020)Neurosciences (rcdc)Basic Behavioral and Social Science (rcdc)Behavioral and Social Science (rcdc)Mental Health (rcdc)Amygdala (mesh)Animals (mesh)ConditioningOperant (mesh)Female (mesh)Hypothalamus (mesh)Male (mesh)Mice (mesh)MiceInbred C57BL (mesh)MiceTransgenic (mesh)Nerve Net (mesh)Optogenetics (mesh)ReinforcementPsychology (mesh)Reward (mesh)Social Behavior (mesh)Amygdala (mesh)Hypothalamus (mesh)Nerve Net (mesh)Animals (mesh)MiceInbred C57BL (mesh)MiceTransgenic (mesh)Mice (mesh)Social Behavior (mesh)ConditioningOperant (mesh)Reward (mesh)Female (mesh)Male (mesh)Optogenetics (mesh)ReinforcementPsychology (mesh)Amygdala (mesh)Animals (mesh)ConditioningOperant (mesh)Female (mesh)Hypothalamus (mesh)Male (mesh)Mice (mesh)MiceInbred C57BL (mesh)MiceTransgenic (mesh)Nerve Net (mesh)Optogenetics (mesh)ReinforcementPsychology (mesh)Reward (mesh)Social Behavior (mesh)1109 Neurosciences (for)1701 Psychology (for)1702 Cognitive Sciences (for)Neurology & Neurosurgery (science-metrix)3209 Neurosciences (for-2020)5202 Biological psychology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/794008rqhttps://escholarship.org/content/qt794008rq/qt794008rq.pdfinfo:doi/10.1038/s41593-021-00828-2articleNature Neuroscience, vol 24, iss 6831 - 842oai:escholarship.org:ark:/13030/qt9bq5p9vz2026-01-01T01:13:22Zqt9bq5p9vzThe ASM Journals Committee Values the Contributions of Black MicrobiologistsSchloss, Patrick DJunior, MelissaAlvania, RebeccaArias, Cesar ABaumler, AndreasCasadevall, ArturoDetweiler, CorrellaDrake, HaroldGilbert, JackImperiale, Michael JLovett, SusanMaloy, StanleyMcAdam, Alexander JNewton, Irene LGSadowsky, MichaelSandri-Goldin, Rozanne MSilhavy, Thomas JTontonoz, PeterYoung, Jo-Anne HCameron, Craig ECann, IsaacFuller, A OvetaKozik, Ariangela J2020-01-013901 Curriculum and Pedagogy (for-2020)39 Education (for-2020)1302 Curriculum and Pedagogy (for)3901 Curriculum and pedagogy (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9bq5p9vzhttps://escholarship.org/content/qt9bq5p9vz/qt9bq5p9vz.pdfinfo:doi/10.1128/jmbe.v21i2.2227articleJournal of Microbiology and Biology Education, vol 21, iss 221.2.58oai:escholarship.org:ark:/13030/qt9285q4sj2026-01-01T01:04:58Zqt9285q4sjStructure Determination from Lipidic Cubic Phase Embedded Microcrystals by MicroEDZhu, LanBu, GuanhongJing, LiangShi, DanLee, Ming-YueGonen, TamirLiu, WeiNannenga, Brent L2020-10-01The lipidic cubic phase (LCP) technique has proved to facilitate the growth of high-quality crystals that are otherwise difficult to grow by other methods. However, the crystal size optimization process could be time and resource consuming, if it ever happens. Therefore, improved techniques for structure determination using these small crystals is an important strategy in diffraction technology development. Microcrystal electron diffraction (MicroED) is a technique that uses a cryo-transmission electron microscopy to collect electron diffraction data and determine high-resolution structures from very thin micro- and nanocrystals. In this work, we have used modified LCP and MicroED protocols to analyze crystals embedded in LCP converted by 2-methyl-2,4-pentanediol or lipase, including Proteinase K crystals grown in solution, cholesterol crystals, and human adenosine A2A receptor crystals grown in LCP. These results set the stage for the use of MicroED to analyze microcrystalline samples grown in LCP, especially for those highly challenging membrane protein targets.34 Chemical Sciences (for-2020)1.5 Resources and infrastructure (underpinning) (hrcs-rac)Cholesterol (mesh)Cryoelectron Microscopy (mesh)Crystallization (mesh)Endopeptidase K (mesh)Glycols (mesh)Lipids (mesh)MicroscopyElectronTransmission (mesh)Nanoparticles (mesh)ReceptorAdenosine A2A (mesh)Glycols (mesh)Cholesterol (mesh)Endopeptidase K (mesh)Lipids (mesh)ReceptorAdenosine A2A (mesh)Cryoelectron Microscopy (mesh)MicroscopyElectronTransmission (mesh)Crystallization (mesh)Nanoparticles (mesh)GPCRProteinase Kadditive phase conversioncholesterolcryo-electron microscopy (cryo-EM)lipase hydrolysislipidic cubic phase (LCP)membrane proteinmicrocrystal electron diffraction (MicroED)microcrystallographyCholesterol (mesh)Cryoelectron Microscopy (mesh)Crystallization (mesh)Endopeptidase K (mesh)Glycols (mesh)Lipids (mesh)MicroscopyElectronTransmission (mesh)Nanoparticles (mesh)ReceptorAdenosine A2A (mesh)Biophysics (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9285q4sjhttps://escholarship.org/content/qt9285q4sj/qt9285q4sj.pdfinfo:doi/10.1016/j.str.2020.07.006articleStructure, vol 28, iss 101149 - 1159.e4oai:escholarship.org:ark:/13030/qt21z0364r2026-01-01T00:35:17Zqt21z0364rKinetics and Optimization of the Lysine–Isopeptide Bond Forming Sortase Enzyme from Corynebacterium diphtheriaeSue, Christopher KMcConnell, Scott AEllis-Guardiola, KenMuroski, John MMcAllister, Rachel AYu, JustinAlvarez, Ana IChang, ChungyuLoo, Rachel R OgorzalekLoo, Joseph ATon-That, HungClubb, Robert T2020-06-17Site-specifically modified protein bioconjugates have important applications in biology, chemistry, and medicine. Functionalizing specific protein side chains with enzymes using mild reaction conditions is of significant interest, but remains challenging. Recently, the lysine-isopeptide bond forming activity of the sortase enzyme that builds surface pili in Corynebacterium diphtheriae (CdSrtA) has been reconstituted in vitro. A mutationally activated form of CdSrtA was shown to be a promising bioconjugating enzyme that can attach Leu-Pro-Leu-Thr-Gly peptide fluorophores to a specific lysine residue within the N-terminal domain of the SpaA protein (NSpaA), enabling the labeling of target proteins that are fused to NSpaA. Here we present a detailed analysis of the CdSrtA catalyzed protein labeling reaction. We show that the first step in catalysis is rate limiting, which is the formation of the CdSrtA-peptide thioacyl intermediate that subsequently reacts with a lysine ε-amine in NSpaA. This intermediate is surprisingly stable, limiting spurious proteolysis of the peptide substrate. We report the discovery of a new enzyme variant (CdSrtAΔ) that has significantly improved transpeptidation activity, because it completely lacks an inhibitory polypeptide appendage ("lid") that normally masks the active site. We show that the presence of the lid primarily impairs formation of the thioacyl intermediate and not the recognition of the NSpaA substrate. Quantitative measurements reveal that CdSrtAΔ generates its cross-linked product with a catalytic turnover number of 1.4 ± 0.004 h-1 and that it has apparent KM values of 0.16 ± 0.04 and 1.6 ± 0.3 mM for its NSpaA and peptide substrates, respectively. CdSrtAΔ is 7-fold more active than previously studied variants, labeling >90% of NSpaA with peptide within 6 h. The results of this study further improve the utility of CdSrtA as a protein labeling tool and provide insight into the enzyme catalyzed reaction that underpins protein labeling and pilus biogenesis.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Biocatalysis (mesh)Corynebacterium diphtheriae (mesh)Cysteine Endopeptidases (mesh)Kinetics (mesh)Lysine (mesh)Mutation (mesh)Peptides (mesh)Protein Domains (mesh)Corynebacterium diphtheriae (mesh)Cysteine Endopeptidases (mesh)Lysine (mesh)Peptides (mesh)Kinetics (mesh)Mutation (mesh)Biocatalysis (mesh)Protein Domains (mesh)Biocatalysis (mesh)Corynebacterium diphtheriae (mesh)Cysteine Endopeptidases (mesh)Kinetics (mesh)Lysine (mesh)Mutation (mesh)Peptides (mesh)Protein Domains (mesh)0304 Medicinal and Biomolecular Chemistry (for)0305 Organic Chemistry (for)0601 Biochemistry and Cell Biology (for)Organic Chemistry (science-metrix)3101 Biochemistry and cell biology (for-2020)3404 Medicinal and biomolecular chemistry (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/21z0364rhttps://escholarship.org/content/qt21z0364r/qt21z0364r.pdfinfo:doi/10.1021/acs.bioconjchem.0c00163articleBioconjugate Chemistry, vol 31, iss 61624 - 1634oai:escholarship.org:ark:/13030/qt8fx6077v2025-12-31T18:34:03Zqt8fx6077vAster Proteins Facilitate Nonvesicular Plasma Membrane to ER Cholesterol Transport in Mammalian CellsSandhu, JaspreetLi, ShiqianFairall, LouisePfisterer, Simon GGurnett, Jennifer EXiao, XuWeston, Thomas AVashi, DiptiFerrari, AlessandraOrozco, Jose LHartman, Celine LStrugatsky, DavidLee, Stephen DHe, CuiwenHong, CynthiaJiang, HaiboBentolila, Laurent AGatta, Alberto TLevine, Tim PFerng, AnnieLee, RichardFord, David AYoung, Stephen GIkonen, ElinaSchwabe, John WRTontonoz, Peter2018-10-01The mechanisms underlying sterol transport in mammalian cells are poorly understood. In particular, how cholesterol internalized from HDL is made available to the cell for storage or modification is unknown. Here, we describe three ER-resident proteins (Aster-A, -B, -C) that bind cholesterol and facilitate its removal from the plasma membrane. The crystal structure of the central domain of Aster-A broadly resembles the sterol-binding fold of mammalian StARD proteins, but sequence differences in the Aster pocket result in a distinct mode of ligand binding. The Aster N-terminal GRAM domain binds phosphatidylserine and mediates Aster recruitment to plasma membrane-ER contact sites in response to cholesterol accumulation in the plasma membrane. Mice lacking Aster-B are deficient in adrenal cholesterol ester storage and steroidogenesis because of an inability to transport cholesterol from SR-BI to the ER. These findings identify a nonvesicular pathway for plasma membrane to ER sterol trafficking in mammals.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)3T3 Cells (mesh)Animals (mesh)Biological Transport (mesh)CD36 Antigens (mesh)CHO Cells (mesh)Carrier Proteins (mesh)Cell Line (mesh)Cell Membrane (mesh)Cholesterol (mesh)CholesterolHDL (mesh)Cricetulus (mesh)Endoplasmic Reticulum (mesh)Humans (mesh)Membrane Proteins (mesh)Mice (mesh)MiceInbred C57BL (mesh)Mitochondrial Membranes (mesh)Sequence Alignment (mesh)Sterols (mesh)Cell Line (mesh)CHO Cells (mesh)3T3 Cells (mesh)Cell Membrane (mesh)Endoplasmic Reticulum (mesh)Animals (mesh)MiceInbred C57BL (mesh)Humans (mesh)Cricetulus (mesh)Mice (mesh)Cholesterol (mesh)Sterols (mesh)Carrier Proteins (mesh)Membrane Proteins (mesh)Sequence Alignment (mesh)Biological Transport (mesh)Mitochondrial Membranes (mesh)CholesterolHDL (mesh)CD36 Antigens (mesh)HDL metabolismLXRSR-BISREBPcholesterolmembrane contact sitesnonvesicular transportsteroidogenesis3T3 Cells (mesh)Animals (mesh)Biological Transport (mesh)CD36 Antigens (mesh)CHO Cells (mesh)Carrier Proteins (mesh)Cell Line (mesh)Cell Membrane (mesh)Cholesterol (mesh)CholesterolHDL (mesh)Cricetulus (mesh)Endoplasmic Reticulum (mesh)Humans (mesh)Membrane Proteins (mesh)Mice (mesh)MiceInbred C57BL (mesh)Mitochondrial Membranes (mesh)Sequence Alignment (mesh)Sterols (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8fx6077vhttps://escholarship.org/content/qt8fx6077v/qt8fx6077v.pdfinfo:doi/10.1016/j.cell.2018.08.033articleCell, vol 175, iss 2514 - 529.e20oai:escholarship.org:ark:/13030/qt4v90f19f2025-12-31T18:20:12Zqt4v90f19fMacrophages release plasma membrane-derived particles rich in accessible cholesterolHe, CuiwenHu, XuchenWeston, Thomas AJung, Rachel SSandhu, JaspreetHuang, SongHeizer, PatrickKim, JasonEllison, RochelleXu, JiakeKilburn, MatthewBensinger, Steven JRiezman, HowardTontonoz, PeterFong, Loren GJiang, HaiboYoung, Stephen G2018-09-04Macrophages are generally assumed to unload surplus cholesterol through direct interactions between ABC transporters on the plasma membrane and HDLs, but they have also been reported to release cholesterol-containing particles. How macrophage-derived particles are formed and released has not been clear. To understand the genesis of macrophage-derived particles, we imaged mouse macrophages by EM and nanoscale secondary ion mass spectrometry (nanoSIMS). By scanning EM, we found that large numbers of 20- to 120-nm particles are released from the fingerlike projections (filopodia) of macrophages. These particles attach to the substrate, forming a "lawn" of particles surrounding macrophages. By nanoSIMS imaging we showed that these particles are enriched in the mobile and metabolically active accessible pool of cholesterol (detectable by ALO-D4, a modified version of a cholesterol-binding cytolysin). The cholesterol content of macrophage-derived particles was increased by loading the cells with cholesterol or by adding LXR and RXR agonists to the cell-culture medium. Incubating macrophages with HDL reduced the cholesterol content of macrophage-derived particles. We propose that release of accessible cholesterol-rich particles from the macrophage plasma membrane could assist in disposing of surplus cholesterol and increase the efficiency of cholesterol movement to HDL.3206 Medical Biotechnology (for-2020)32 Biomedical and Clinical Sciences (for-2020)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Animals (mesh)Cell-Derived Microparticles (mesh)Cholesterol (mesh)LipoproteinsHDL (mesh)Macrophages (mesh)Mice (mesh)MiceKnockout (mesh)MicroscopyElectron (mesh)RAW 264.7 Cells (mesh)SpectrometryMassSecondary Ion (mesh)cholesterol effluxaccessible cholesterolnanoSIMSMacrophages (mesh)Animals (mesh)MiceKnockout (mesh)Mice (mesh)Cholesterol (mesh)LipoproteinsHDL (mesh)MicroscopyElectron (mesh)SpectrometryMassSecondary Ion (mesh)Cell-Derived Microparticles (mesh)RAW 264.7 Cells (mesh)accessible cholesterolcholesterol effluxnanoSIMSAnimals (mesh)Cell-Derived Microparticles (mesh)Cholesterol (mesh)LipoproteinsHDL (mesh)Macrophages (mesh)Mice (mesh)MiceKnockout (mesh)MicroscopyElectron (mesh)RAW 264.7 Cells (mesh)SpectrometryMassSecondary Ion (mesh)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4v90f19fhttps://escholarship.org/content/qt4v90f19f/qt4v90f19f.pdfinfo:doi/10.1073/pnas.1810724115articleProceedings of the National Academy of Sciences of the United States of America, vol 115, iss 36e8499 - e8508oai:escholarship.org:ark:/13030/qt5c79h4zj2025-12-31T17:54:45Zqt5c79h4zjDeep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestriesZekavat, Seyedeh MRuotsalainen, SanniHandsaker, Robert EAlver, MarisBloom, JonathanPoterba, TimothySeed, CottonErnst, JasonChaffin, MarkEngreitz, JessePeloso, Gina MManichaikul, AniYang, ChaojieRyan, Kathleen AFu, MaoJohnson, W CraigTsai, MichaelBudoff, MatthewVasan, Ramachandran SCupples, L AdrienneRotter, Jerome IRich, Stephen SPost, WendyMitchell, Braxton DCorrea, AdolfoMetspalu, AndresWilson, James GSalomaa, VeikkoKellis, ManolisDaly, Mark JNeale, Benjamin MMcCarroll, StevenSurakka, IdaEsko, TonuGanna, AndreaRipatti, SamuliKathiresan, SekarNatarajan, Pradeep2018-01-01Lipoprotein(a), Lp(a), is a modified low-density lipoprotein particle that contains apolipoprotein(a), encoded by LPA, and is a highly heritable, causal risk factor for cardiovascular diseases that varies in concentrations across ancestries. Here, we use deep-coverage whole genome sequencing in 8392 individuals of European and African ancestry to discover and interpret both single-nucleotide variants and copy number (CN) variation associated with Lp(a). We observe that genetic determinants between Europeans and Africans have several unique determinants. The common variant rs12740374 associated with Lp(a) cholesterol is an eQTL for SORT1 and independent of LDL cholesterol. Observed associations of aggregates of rare non-coding variants are largely explained by LPA structural variation, namely the LPA kringle IV 2 (KIV2)-CN. Finally, we find that LPA risk genotypes confer greater relative risk for incident atherosclerotic cardiovascular diseases compared to directly measured Lp(a), and are significantly associated with measures of subclinical atherosclerosis in African Americans.31 Biological Sciences (for-2020)3105 Genetics (for-2020)Cardiovascular (rcdc)Atherosclerosis (rcdc)Genetics (rcdc)Human Genome (rcdc)Prevention (rcdc)Biotechnology (rcdc)Heart Disease (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Cardiovascular (hrcs-hc)3 Good Health and Well Being (sdg)Adaptor ProteinsVesicular Transport (mesh)Black People (mesh)Cardiovascular Diseases (mesh)CholesterolLDL (mesh)DNA Copy Number Variations (mesh)Gene Expression (mesh)GenomeHuman (mesh)Genome-Wide Association Study (mesh)Humans (mesh)Lipoprotein(a) (mesh)PolymorphismSingle Nucleotide (mesh)Quantitative Trait Loci (mesh)Risk Factors (mesh)White People (mesh)Whole Genome Sequencing (mesh)Black or African American (mesh)NHLBI TOPMed Lipids Working GroupHumans (mesh)Cardiovascular Diseases (mesh)Lipoprotein(a) (mesh)Adaptor ProteinsVesicular Transport (mesh)Risk Factors (mesh)Gene Expression (mesh)PolymorphismSingle Nucleotide (mesh)Quantitative Trait Loci (mesh)GenomeHuman (mesh)CholesterolLDL (mesh)Genome-Wide Association Study (mesh)DNA Copy Number Variations (mesh)Whole Genome Sequencing (mesh)White People (mesh)Black or African American (mesh)Black People (mesh)Adaptor ProteinsVesicular Transport (mesh)Black People (mesh)Cardiovascular Diseases (mesh)CholesterolLDL (mesh)DNA Copy Number Variations (mesh)Gene Expression (mesh)GenomeHuman (mesh)Genome-Wide Association Study (mesh)Humans (mesh)Lipoprotein(a) (mesh)PolymorphismSingle Nucleotide (mesh)Quantitative Trait Loci (mesh)Risk Factors (mesh)White People (mesh)Whole Genome Sequencing (mesh)Black or African American (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/5c79h4zjhttps://escholarship.org/content/qt5c79h4zj/qt5c79h4zj.pdfinfo:doi/10.1038/s41467-018-04668-warticleNature Communications, vol 9, iss 12606oai:escholarship.org:ark:/13030/qt0pd0f1p02025-12-31T17:36:45Zqt0pd0f1p0In vitro reconstitution of sortase-catalyzed pilus polymerization reveals structural elements involved in pilin cross-linkingChang, ChungyuAmer, Brendan ROsipiuk, JerzyMcConnell, Scott AHuang, I-HsiuHsieh, VanFu, JanineNguyen, Hong HMuroski, JohnFlores, ErikaOgorzalek Loo, Rachel RLoo, Joseph APutkey, John AJoachimiak, AndrzejDas, AsisClubb, Robert TTon-That, Hung2018-06-12Covalently cross-linked pilus polymers displayed on the cell surface of Gram-positive bacteria are assembled by class C sortase enzymes. These pilus-specific transpeptidases located on the bacterial membrane catalyze a two-step protein ligation reaction, first cleaving the LPXTG motif of one pilin protomer to form an acyl-enzyme intermediate and then joining the terminal Thr to the nucleophilic Lys residue residing within the pilin motif of another pilin protomer. To date, the determinants of class C enzymes that uniquely enable them to construct pili remain unknown. Here, informed by high-resolution crystal structures of corynebacterial pilus-specific sortase (SrtA) and utilizing a structural variant of the enzyme (SrtA2M), whose catalytic pocket has been unmasked by activating mutations, we successfully reconstituted in vitro polymerization of the cognate major pilin (SpaA). Mass spectrometry, electron microscopy, and biochemical experiments authenticated that SrtA2M synthesizes pilus fibers with correct Lys-Thr isopeptide bonds linking individual pilins via a thioacyl intermediate. Structural modeling of the SpaA-SrtA-SpaA polymerization intermediate depicts SrtA2M sandwiched between the N- and C-terminal domains of SpaA harboring the reactive pilin and LPXTG motifs, respectively. Remarkably, the model uncovered a conserved TP(Y/L)XIN(S/T)H signature sequence following the catalytic Cys, in which the alanine substitutions abrogated cross-linking activity but not cleavage of LPXTG. These insights and our evidence that SrtA2M can terminate pilus polymerization by joining the terminal pilin SpaB to SpaA and catalyze ligation of isolated SpaA domains in vitro provide a facile and versatile platform for protein engineering and bio-conjugation that has major implications for biotechnology.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Infectious Diseases (rcdc)Biotechnology (rcdc)Aminoacyltransferases (mesh)Bacterial Proteins (mesh)Catalysis (mesh)Cell Wall (mesh)Corynebacterium (mesh)CrystallographyX-Ray (mesh)Cysteine Endopeptidases (mesh)Fimbriae Proteins (mesh)FimbriaeBacterial (mesh)Peptidyl Transferases (mesh)Polymerization (mesh)Corynebacterium diphtheriaesortasepilus polymerizationprotein ligationtranspeptidationFimbriaeBacterial (mesh)Cell Wall (mesh)Corynebacterium (mesh)Cysteine Endopeptidases (mesh)Aminoacyltransferases (mesh)Peptidyl Transferases (mesh)Bacterial Proteins (mesh)Fimbriae Proteins (mesh)CrystallographyX-Ray (mesh)Catalysis (mesh)Polymerization (mesh)Corynebacterium diphtheriaepilus polymerizationprotein ligationsortasetranspeptidationAminoacyltransferases (mesh)Bacterial Proteins (mesh)Catalysis (mesh)Cell Wall (mesh)Corynebacterium (mesh)CrystallographyX-Ray (mesh)Cysteine Endopeptidases (mesh)Fimbriae Proteins (mesh)FimbriaeBacterial (mesh)Peptidyl Transferases (mesh)Polymerization (mesh)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/0pd0f1p0https://escholarship.org/content/qt0pd0f1p0/qt0pd0f1p0.pdfinfo:doi/10.1073/pnas.1800954115articleProceedings of the National Academy of Sciences of the United States of America, vol 115, iss 24e5477 - e5486oai:escholarship.org:ark:/13030/qt2cd4k3zk2025-12-31T16:29:17Zqt2cd4k3zkAtomic structures of low-complexity protein segments reveal kinked β sheets that assemble networksHughes, Michael PSawaya, Michael RBoyer, David RGoldschmidt, LukaszRodriguez, Jose ACascio, DuilioChong, LisaGonen, TamirEisenberg, David S2018-02-09Subcellular membraneless assemblies are a reinvigorated area of study in biology, with spirited scientific discussions on the forces between the low-complexity protein domains within these assemblies. To illuminate these forces, we determined the atomic structures of five segments from protein low-complexity domains associated with membraneless assemblies. Their common structural feature is the stacking of segments into kinked β sheets that pair into protofilaments. Unlike steric zippers of amyloid fibrils, the kinked sheets interact weakly through polar atoms and aromatic side chains. By computationally threading the human proteome on our kinked structures, we identified hundreds of low-complexity segments potentially capable of forming such interactions. These segments are found in proteins as diverse as RNA binders, nuclear pore proteins, and keratins, which are known to form networks and localize to membraneless assemblies.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Generic health relevance (hrcs-hc)Humans (mesh)Protein Conformationbeta-Strand (mesh)Protein Interaction Domains and Motifs (mesh)Proteome (mesh)Humans (mesh)Proteome (mesh)Protein Interaction Domains and Motifs (mesh)Protein Conformationbeta-Strand (mesh)Humans (mesh)Protein Conformationbeta-Strand (mesh)Protein Interaction Domains and Motifs (mesh)Proteome (mesh)General Science & Technology (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2cd4k3zkhttps://escholarship.org/content/qt2cd4k3zk/qt2cd4k3zk.pdfinfo:doi/10.1126/science.aan6398articleScience, vol 359, iss 6376698 - 701oai:escholarship.org:ark:/13030/qt6fx7611c2025-12-31T16:24:25Zqt6fx7611cTranscriptional regulation of macrophage cholesterol efflux and atherogenesis by a long noncoding RNASallam, TamerJones, MariusThomas, Brandon JWu, XiaohuiGilliland, ThomasQian, KevinEskin, AsciaCasero, DavidZhang, ZhengyiSandhu, JaspreetSalisbury, DavidRajbhandari, PrashantCivelek, MeteHong, CynthiaIto, AyakaLiu, XinDaniel, BenceLusis, Aldons JWhitelegge, JulianNagy, LaszloCastrillo, AntonioSmale, StephenTontonoz, Peter2018-03-01The conserved long noncoding RNA MeXis has anti-atherosclerotic effects in mice by acting with the nuclear hormone receptor LXR in macrophages to promote cholesterol efflux.32 Biomedical and Clinical Sciences (for-2020)42 Health Sciences (for-2020)Atherosclerosis (rcdc)Cardiovascular (rcdc)Genetics (rcdc)2.1 Biological and endogenous factors (hrcs-rac)ATP Binding Cassette Transporter 1 (mesh)Animals (mesh)Atherosclerosis (mesh)Bone Marrow Cells (mesh)Cholesterol (mesh)DEAD-box RNA Helicases (mesh)Gene Expression Regulation (mesh)Humans (mesh)Liver X Receptors (mesh)Macrophages (mesh)Mice (mesh)Promoter RegionsGenetic (mesh)RNALong Noncoding (mesh)TranscriptionGenetic (mesh)Bone Marrow Cells (mesh)Macrophages (mesh)Animals (mesh)Humans (mesh)Mice (mesh)Cholesterol (mesh)TranscriptionGenetic (mesh)Gene Expression Regulation (mesh)Atherosclerosis (mesh)DEAD-box RNA Helicases (mesh)Promoter RegionsGenetic (mesh)ATP Binding Cassette Transporter 1 (mesh)RNALong Noncoding (mesh)Liver X Receptors (mesh)ATP Binding Cassette Transporter 1 (mesh)Animals (mesh)Atherosclerosis (mesh)Bone Marrow Cells (mesh)Cholesterol (mesh)DEAD-box RNA Helicases (mesh)Gene Expression Regulation (mesh)Humans (mesh)Liver X Receptors (mesh)Macrophages (mesh)Mice (mesh)Promoter RegionsGenetic (mesh)RNALong Noncoding (mesh)TranscriptionGenetic (mesh)11 Medical and Health Sciences (for)Immunology (science-metrix)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6fx7611chttps://escholarship.org/content/qt6fx7611c/qt6fx7611c.pdfinfo:doi/10.1038/nm.4479articleNature Medicine, vol 24, iss 3304 - 312oai:escholarship.org:ark:/13030/qt7c68m4pw2025-12-31T16:12:02Zqt7c68m4pwSub-ångström cryo-EM structure of a prion protofibril reveals a polar claspGallagher-Jones, MarcusGlynn, CalinaBoyer, David RMartynowycz, Michael WHernandez, EvelynMiao, JenniferZee, Chih-TeNovikova, Irina VGoldschmidt, LukaszMcFarlane, Heather THelguera, Gustavo FEvans, James ESawaya, Michael RCascio, DuilioEisenberg, David SGonen, TamirRodriguez, Jose A2018-02-01The atomic structure of the infectious, protease-resistant, β-sheet-rich and fibrillar mammalian prion remains unknown. Through the cryo-EM method MicroED, we reveal the sub-ångström-resolution structure of a protofibril formed by a wild-type segment from the β2–α2 loop of the bank vole prion protein. The structure of this protofibril reveals a stabilizing network of hydrogen bonds that link polar zippers within a sheet, producing motifs we have named ‘polar clasps’.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Neurosciences (rcdc)Infectious Diseases (rcdc)Neurodegenerative (rcdc)Transmissible Spongiform Encephalopathy (TSE) (rcdc)Brain Disorders (rcdc)Emerging Infectious Diseases (rcdc)Rare Diseases (rcdc)Neurological (hrcs-hc)3 Good Health and Well Being (sdg)Amyloid (mesh)Amyloidogenic Proteins (mesh)Animals (mesh)Carbamazepine (mesh)Cattle (mesh)Cricetinae (mesh)Cryoelectron Microscopy (mesh)Deer (mesh)Electrons (mesh)Humans (mesh)Hydrogen Bonding (mesh)Mice (mesh)Peptides (mesh)Phylogeny (mesh)Prions (mesh)Protein StructureSecondary (mesh)Proteome (mesh)Sheep (mesh)Surface Properties (mesh)X-Ray Diffraction (mesh)Animals (mesh)Cattle (mesh)Deer (mesh)Sheep (mesh)Humans (mesh)Mice (mesh)Carbamazepine (mesh)Amyloid (mesh)Peptides (mesh)Prions (mesh)Proteome (mesh)Cryoelectron Microscopy (mesh)X-Ray Diffraction (mesh)Phylogeny (mesh)Protein StructureSecondary (mesh)Hydrogen Bonding (mesh)Surface Properties (mesh)Electrons (mesh)Cricetinae (mesh)Amyloidogenic Proteins (mesh)Amyloid (mesh)Amyloidogenic Proteins (mesh)Animals (mesh)Carbamazepine (mesh)Cattle (mesh)Cricetinae (mesh)Cryoelectron Microscopy (mesh)Deer (mesh)Electrons (mesh)Humans (mesh)Hydrogen Bonding (mesh)Mice (mesh)Peptides (mesh)Phylogeny (mesh)Prions (mesh)Protein StructureSecondary (mesh)Proteome (mesh)Sheep (mesh)Surface Properties (mesh)X-Ray Diffraction (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biophysics (science-metrix)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7c68m4pwhttps://escholarship.org/content/qt7c68m4pw/qt7c68m4pw.pdfinfo:doi/10.1038/s41594-017-0018-0articleNature Structural & Molecular Biology, vol 25, iss 2131 - 134oai:escholarship.org:ark:/13030/qt12p6m0h72025-12-31T13:36:57Zqt12p6m0h7Copper-zinc superoxide dismutase is activated through a sulfenic acid intermediate at a copper ion entry siteFetherolf, Morgan MBoyd, Stefanie DTaylor, Alexander BKim, Hee JongWohlschlegel, James ABlackburn, Ninian JHart, P JohnWinge, Dennis RWinkler, Duane D2017-07-01Metallochaperones are a diverse family of trafficking molecules that provide metal ions to protein targets for use as cofactors. The copper chaperone for superoxide dismutase (Ccs1) activates immature copper-zinc superoxide dismutase (Sod1) by delivering copper and facilitating the oxidation of the Sod1 intramolecular disulfide bond. Here, we present structural, spectroscopic, and cell-based data supporting a novel copper-induced mechanism for Sod1 activation. Ccs1 binding exposes an electropositive cavity and proposed "entry site" for copper ion delivery on immature Sod1. Copper-mediated sulfenylation leads to a sulfenic acid intermediate that eventually resolves to form the Sod1 disulfide bond with concomitant release of copper into the Sod1 active site. Sod1 is the predominant disulfide bond-requiring enzyme in the cytoplasm, and this copper-induced mechanism of disulfide bond formation obviates the need for a thiol/disulfide oxidoreductase in that compartment.3101 Biochemistry and Cell Biology (for-2020)34 Chemical Sciences (for-2020)31 Biological Sciences (for-2020)2.1 Biological and endogenous factors (hrcs-rac)Amino Acid Substitution (mesh)Apoenzymes (mesh)Binding Sites (mesh)Copper (mesh)CrystallographyX-Ray (mesh)Cysteine (mesh)Cystine (mesh)Enzyme Activation (mesh)Enzyme Stability (mesh)Humans (mesh)Ligands (mesh)ModelsMolecular (mesh)Molecular Chaperones (mesh)MutagenesisSite-Directed (mesh)Mutation (mesh)Oxidation-Reduction (mesh)Protein Conformation (mesh)Protein Interaction Domains and Motifs (mesh)Protein ProcessingPost-Translational (mesh)Recombinant Proteins (mesh)Saccharomyces cerevisiae Proteins (mesh)Superoxide Dismutase (mesh)Humans (mesh)Cystine (mesh)Copper (mesh)Cysteine (mesh)Superoxide Dismutase (mesh)Apoenzymes (mesh)Saccharomyces cerevisiae Proteins (mesh)Molecular Chaperones (mesh)Recombinant Proteins (mesh)Ligands (mesh)CrystallographyX-Ray (mesh)Amino Acid Substitution (mesh)MutagenesisSite-Directed (mesh)Enzyme Stability (mesh)Protein ProcessingPost-Translational (mesh)Binding Sites (mesh)Enzyme Activation (mesh)Protein Conformation (mesh)Oxidation-Reduction (mesh)Mutation (mesh)ModelsMolecular (mesh)Protein Interaction Domains and Motifs (mesh)X-ray crystallographychaperonecopperenzyme activationmetalloenzymesuperoxide dismutase (SOD)Amino Acid Substitution (mesh)Apoenzymes (mesh)Binding Sites (mesh)Copper (mesh)CrystallographyX-Ray (mesh)Cysteine (mesh)Cystine (mesh)Enzyme Activation (mesh)Enzyme Stability (mesh)Humans (mesh)Ligands (mesh)ModelsMolecular (mesh)Molecular Chaperones (mesh)MutagenesisSite-Directed (mesh)Mutation (mesh)Oxidation-Reduction (mesh)Protein Conformation (mesh)Protein Interaction Domains and Motifs (mesh)Protein ProcessingPost-Translational (mesh)Recombinant Proteins (mesh)Saccharomyces cerevisiae Proteins (mesh)Superoxide Dismutase (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biochemistry & Molecular Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/12p6m0h7https://escholarship.org/content/qt12p6m0h7/qt12p6m0h7.pdfinfo:doi/10.1074/jbc.m117.775981articleJournal of Biological Chemistry, vol 292, iss 2912025 - 12040oai:escholarship.org:ark:/13030/qt9qt161892025-12-31T11:12:46Zqt9qt16189Sphingosine kinases regulate ER contacts with late endocytic organelles and cholesterol traffickingPalladino, Elisa NDBernas, TytusGreen, Christopher DWeigel, CynthiaSingh, Sandeep KSenkal, Can EMartello, AndreaKennelly, John PBieberich, ErhardTontonoz, PeterFord, David AMilstien, SheldonEden, Emily RSpiegel, Sarah2022-09-27Membrane contact sites (MCS), close membrane apposition between organelles, are platforms for interorganellar transfer of lipids including cholesterol, regulation of lipid homeostasis, and co-ordination of endocytic trafficking. Sphingosine kinases (SphKs), two isoenzymes that phosphorylate sphingosine to the bioactive sphingosine-1-phosphate (S1P), have been implicated in endocytic trafficking. However, the physiological functions of SphKs in regulation of membrane dynamics, lipid trafficking and MCS are not known. Here, we report that deletion of SphKs decreased S1P with concomitant increases in its precursors sphingosine and ceramide, and markedly reduced endoplasmic reticulum (ER) contacts with late endocytic organelles. Expression of enzymatically active SphK1, but not catalytically inactive, rescued the deficit of these MCS. Although free cholesterol accumulated in late endocytic organelles in SphK null cells, surprisingly however, cholesterol transport to the ER was not reduced. Importantly, deletion of SphKs promoted recruitment of the ER-resident cholesterol transfer protein Aster-B (also called GRAMD1B) to the plasma membrane (PM), consistent with higher accessible cholesterol and ceramide at the PM, to facilitate cholesterol transfer from the PM to the ER. In addition, ceramide enhanced in vitro binding of the Aster-B GRAM domain to phosphatidylserine and cholesterol liposomes. Our study revealed a previously unknown role for SphKs and sphingolipid metabolites in governing diverse MCS between the ER network and late endocytic organelles versus the PM to control the movement of cholesterol between distinct cell membranes.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Ceramides (mesh)Cholesterol (mesh)Endoplasmic Reticulum (mesh)Isoenzymes (mesh)Liposomes (mesh)Lysophospholipids (mesh)Phosphatidylserines (mesh)Sphingolipids (mesh)Sphingosine (mesh)Endoplasmic Reticulum (mesh)Sphingosine (mesh)Cholesterol (mesh)Isoenzymes (mesh)Ceramides (mesh)Phosphatidylserines (mesh)Lysophospholipids (mesh)Sphingolipids (mesh)Liposomes (mesh)Aster-B/GRAMD1bcholesterolmembrane contact sitessphingolipidssphingosine kinaseCeramides (mesh)Cholesterol (mesh)Endoplasmic Reticulum (mesh)Isoenzymes (mesh)Liposomes (mesh)Lysophospholipids (mesh)Phosphatidylserines (mesh)Sphingolipids (mesh)Sphingosine (mesh)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/9qt16189https://escholarship.org/content/qt9qt16189/qt9qt16189.pdfinfo:doi/10.1073/pnas.2204396119articleProceedings of the National Academy of Sciences of the United States of America, vol 119, iss 39e2204396119oai:escholarship.org:ark:/13030/qt1kg6n08c2025-12-31T00:38:31Zqt1kg6n08cThe metabolite α-ketoglutarate extends lifespan by inhibiting ATP synthase and TORChin, Randall MFu, XudongPai, Melody YVergnes, LaurentHwang, HeejunDeng, GangDiep, SimonLomenick, BrettMeli, Vijaykumar SMonsalve, Gabriela CHu, EileenWhelan, Stephen AWang, Jennifer XJung, GwanghyunSolis, Gregory MFazlollahi, FarbodKaweeteerawat, ChitradaQuach, AustinNili, MahtaKrall, Abby SGodwin, Hilary AChang, Helena RFaull, Kym FGuo, FengJiang, MeishengTrauger, Sunia ASaghatelian, AlanBraas, DanielChristofk, Heather RClarke, Catherine FTeitell, Michael APetrascheck, MichaelReue, KarenJung, Michael EFrand, Alison RHuang, Jing2014-06-01Ageing in the worm Caenorhabditis elegans is shown to be delayed by supplementation with α-ketoglutarate, an effect that is probably mediated by ATP synthase—which is identified as a direct target of α-ketoglutarate—and target of rapamycin (TOR).3205 Medical Biochemistry and Metabolomics (for-2020)31 Biological Sciences (for-2020)32 Biomedical and Clinical Sciences (for-2020)Animals (mesh)Caenorhabditis elegans (mesh)Cell Line (mesh)Enzyme Activation (mesh)Enzyme Inhibitors (mesh)Gene Knockdown Techniques (mesh)HEK293 Cells (mesh)Humans (mesh)Jurkat Cells (mesh)Ketoglutaric Acids (mesh)Longevity (mesh)Mice (mesh)Mitochondrial Proton-Translocating ATPases (mesh)Protein Binding (mesh)TOR Serine-Threonine Kinases (mesh)Cell Line (mesh)Jurkat Cells (mesh)Animals (mesh)Humans (mesh)Mice (mesh)Caenorhabditis elegans (mesh)Ketoglutaric Acids (mesh)Mitochondrial Proton-Translocating ATPases (mesh)Enzyme Inhibitors (mesh)Enzyme Activation (mesh)Protein Binding (mesh)Longevity (mesh)Gene Knockdown Techniques (mesh)HEK293 Cells (mesh)TOR Serine-Threonine Kinases (mesh)Animals (mesh)Caenorhabditis elegans (mesh)Cell Line (mesh)Enzyme Activation (mesh)Enzyme Inhibitors (mesh)Gene Knockdown Techniques (mesh)HEK293 Cells (mesh)Humans (mesh)Jurkat Cells (mesh)Ketoglutaric Acids (mesh)Longevity (mesh)Mice (mesh)Mitochondrial Proton-Translocating ATPases (mesh)Protein Binding (mesh)TOR Serine-Threonine Kinases (mesh)General Science & Technology (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1kg6n08chttps://escholarship.org/content/qt1kg6n08c/qt1kg6n08c.pdfinfo:doi/10.1038/nature13264articleNature, vol 510, iss 7505397 - 401oai:escholarship.org:ark:/13030/qt9b10d0s82025-12-31T00:11:04Zqt9b10d0s8Cofilin-Induced Changes in F‑Actin Detected via Cross-Linking with Benzophenone-4-maleimideChen, Christine KBenchaar, Sabrina APhan, MaiGrintsevich, Elena ELoo, Rachel R OgorzalekLoo, Joseph AReisler, Emil2013-08-13Cofilin is a member of the actin depolymerizing factor (ADF)/cofilin family of proteins. It plays a key role in actin dynamics by promoting disassembly and assembly of actin filaments. Upon its binding, cofilin has been shown to bridge two adjacent protomers in filamentous actin (F-actin) and promote the displacement and disordering of subdomain 2 of actin. Here, we present evidence for cofilin promoting a new structural change in the actin filament, as detected via a switch in cross-linking sites. Benzophenone-4-maleimide, which normally forms intramolecular cross-linking in F-actin, cross-links F-actin intermolecularly upon cofilin binding. We mapped the cross-linking sites and found that in the absence of cofilin intramolecular cross-linking occurred between residues Cys374 and Asp11. In contrast, cofilin shifts the cross-linking by this reagent to intermolecular, between residue Cys374, located within subdomain 1 of the upper protomer, and Met44, located in subdomain 2 of the lower protomer. The intermolecular cross-linking of F-actin slows the rate of cofilin dissociation from the filaments and decreases the effect of ionic strength on cofilin-actin binding. These results are consistent with a significant role of filament flexibility in cofilin-actin interactions.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Generic health relevance (hrcs-hc)Actin Depolymerizing Factors (mesh)Actins (mesh)Animals (mesh)Benzophenones (mesh)Binding Sites (mesh)Cross-Linking Reagents (mesh)Maleimides (mesh)ModelsMolecular (mesh)Protein Conformation (mesh)Rabbits (mesh)Animals (mesh)Rabbits (mesh)Maleimides (mesh)Benzophenones (mesh)Actins (mesh)Cross-Linking Reagents (mesh)Binding Sites (mesh)Protein Conformation (mesh)ModelsMolecular (mesh)Actin Depolymerizing Factors (mesh)Actin Depolymerizing Factors (mesh)Actins (mesh)Animals (mesh)Benzophenones (mesh)Binding Sites (mesh)Cross-Linking Reagents (mesh)Maleimides (mesh)ModelsMolecular (mesh)Protein Conformation (mesh)Rabbits (mesh)0304 Medicinal and Biomolecular Chemistry (for)0601 Biochemistry and Cell Biology (for)1101 Medical Biochemistry and Metabolomics (for)Biochemistry & Molecular Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)3205 Medical biochemistry and metabolomics (for-2020)3404 Medicinal and biomolecular chemistry (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9b10d0s8https://escholarship.org/content/qt9b10d0s8/qt9b10d0s8.pdfinfo:doi/10.1021/bi400715zarticleBiochemistry, vol 52, iss 325503 - 5509oai:escholarship.org:ark:/13030/qt6zc1f7qz2025-12-31T00:01:52Zqt6zc1f7qzBiomarkers to Predict Antidepressant ResponseLeuchter, Andrew FCook, Ian AHamilton, Steven PNarr, Katherine LToga, ArthurHunter, Aimee MFaull, KymWhitelegge, JulianAndrews, Anne MLoo, JosephWay, BaldwinNelson, Stanley FHorvath, StevenLebowitz, Barry D2010-12-01During the past several years, we have achieved a deeper understanding of the etiology/pathophysiology of major depressive disorder (MDD). However, this improved understanding has not translated to improved treatment outcome. Treatment often results in symptomatic improvement, but not full recovery. Clinical approaches are largely trial-and-error, and when the first treatment does not result in recovery for the patient, there is little proven scientific basis for choosing the next. One approach to enhancing treatment outcomes in MDD has been the use of standardized sequential treatment algorithms and measurement-based care. Such treatment algorithms stand in contrast to the personalized medicine approach, in which biomarkers would guide decision making. Incorporation of biomarker measurements into treatment algorithms could speed recovery from MDD by shortening or eliminating lengthy and ineffective trials. Recent research results suggest several classes of physiologic biomarkers may be useful for predicting response. These include brain structural or functional findings, as well as genomic, proteomic, and metabolomic measures. Recent data indicate that such measures, at baseline or early in the course of treatment, may constitute useful predictors of treatment outcome. Once such biomarkers are validated, they could form the basis of new paradigms for antidepressant treatment selection.5202 Biological Psychology (for-2020)32 Biomedical and Clinical Sciences (for-2020)3202 Clinical Sciences (for-2020)52 Psychology (for-2020)Bioengineering (rcdc)Clinical Research (rcdc)Mental Health (rcdc)Depression (rcdc)Precision Medicine (rcdc)Brain Disorders (rcdc)Mental Illness (rcdc)Clinical Trials and Supportive Activities (rcdc)Serious Mental Illness (rcdc)Major Depressive Disorder (rcdc)4.1 Discovery and preclinical testing of markers and technologies (hrcs-rac)4.2 Evaluation of markers and technologies (hrcs-rac)Mental health (hrcs-hc)3 Good Health and Well Being (sdg)Antidepressive Agents (mesh)Biomarkers (mesh)Depressive Disorder (mesh)Humans (mesh)Predictive Value of Tests (mesh)Treatment Outcome (mesh)BiomarkersMajor depressionPredicting treatment responseBrain imagingMagnetic resonance imaging (MRI)Quantitative electroencephalography (QEEG)CordanceAntidepressant Treatment Response (ATR) IndexPositron emission tomography (PET)PharmacogenomicsProteomicsMetabolomicsHumans (mesh)Antidepressive Agents (mesh)Treatment Outcome (mesh)Predictive Value of Tests (mesh)Depressive Disorder (mesh)Biomarkers (mesh)Antidepressive Agents (mesh)Biomarkers (mesh)Depressive Disorder (mesh)Humans (mesh)Predictive Value of Tests (mesh)Treatment Outcome (mesh)1103 Clinical Sciences (for)1109 Neurosciences (for)1701 Psychology (for)Psychiatry (science-metrix)3202 Clinical sciences (for-2020)5201 Applied and developmental psychology (for-2020)5203 Clinical and health psychology (for-2020)application/pdfCC-BY-NCeScholarship, University of Californiahttps://escholarship.org/uc/item/6zc1f7qzhttps://escholarship.org/content/qt6zc1f7qz/qt6zc1f7qz.pdfinfo:doi/10.1007/s11920-010-0160-4articleCurrent Psychiatry Reports, vol 12, iss 6553 - 562oai:escholarship.org:ark:/13030/qt77t5d3q42025-12-30T22:56:18Zqt77t5d3q4ABL fusion oncogene transformation and inhibitor sensitivity are mediated by the cellular regulator RIN1Thai, MTing, PYMcLaughlin, JCheng, DMüschen, MWitte, ONColicelli, J2011-02-01ABL gene translocations create constitutively active tyrosine kinases that are causative in chronic myeloid leukemia, acute lymphocytic leukemia and other hematopoietic malignancies. Consistent retention of ABL SH3/SH2 autoinhibitory domains, however, suggests that these leukemogenic tyrosine kinase fusion proteins remain subject to regulation. We resolve this paradox, demonstrating that BCR-ABL1 kinase activity is regulated by RIN1, an ABL SH3/SH2 binding protein. BCR-ABL1 activity was increased by RIN1 overexpression and decreased by RIN1 silencing. Moreover, Rin1−/− bone marrow cells were not transformed by BCR-ABL1, ETV6-ABL1 or BCR-ABL1T315I, a patient-derived drug-resistant mutant, as judged by growth factor independence. Rescue by ectopic RIN1 verified a cell autonomous mechanism of collaboration with BCR-ABL1 during transformation. Sensitivity to the ABL kinase inhibitor imatinib was increased by RIN1 silencing, consistent with RIN1 stabilization of an activated BCR-ABL1 conformation having reduced drug affinity. The dependence on activation by RIN1 to unleash full catalytic and cell transformation potential reveals a previously unknown vulnerability that could be exploited for treatment of leukemic cases driven by ABL translocations. The findings suggest that RIN1 targeting could be efficacious for imatinib-resistant disease and might complement ABL kinase inhibitors in first-line therapy.32 Biomedical and Clinical Sciences (for-2020)3201 Cardiovascular Medicine and Haematology (for-2020)3202 Clinical Sciences (for-2020)3211 Oncology and Carcinogenesis (for-2020)Pediatric Cancer (rcdc)Pediatric (rcdc)Hematology (rcdc)Cancer (rcdc)Orphan Drug (rcdc)Rare Diseases (rcdc)Childhood Leukemia (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Cancer (hrcs-hc)Animals (mesh)Benzamides (mesh)Cell TransformationNeoplastic (mesh)Fusion Proteinsbcr-abl (mesh)Genesabl (mesh)Humans (mesh)Imatinib Mesylate (mesh)Intracellular Signaling Peptides and Proteins (mesh)K562 Cells (mesh)Mice (mesh)Piperazines (mesh)Protein Kinase Inhibitors (mesh)Pyrimidines (mesh)TranslocationGenetic (mesh)src Homology Domains (mesh)BCR-ABL1RIN1RasCMLimatinibresistanceK562 Cells (mesh)Animals (mesh)Humans (mesh)Mice (mesh)Cell TransformationNeoplastic (mesh)TranslocationGenetic (mesh)Benzamides (mesh)Piperazines (mesh)Pyrimidines (mesh)Intracellular Signaling Peptides and Proteins (mesh)Fusion Proteinsbcr-abl (mesh)Protein Kinase Inhibitors (mesh)src Homology Domains (mesh)Genesabl (mesh)Imatinib Mesylate (mesh)Animals (mesh)Benzamides (mesh)Cell TransformationNeoplastic (mesh)Fusion Proteinsbcr-abl (mesh)Genesabl (mesh)Humans (mesh)Imatinib Mesylate (mesh)Intracellular Signaling Peptides and Proteins (mesh)K562 Cells (mesh)Mice (mesh)Piperazines (mesh)Protein Kinase Inhibitors (mesh)Pyrimidines (mesh)TranslocationGenetic (mesh)src Homology Domains (mesh)1103 Clinical Sciences (for)1112 Oncology and Carcinogenesis (for)Immunology (science-metrix)3201 Cardiovascular medicine and haematology (for-2020)3202 Clinical sciences (for-2020)3211 Oncology and carcinogenesis (for-2020)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/77t5d3q4https://escholarship.org/content/qt77t5d3q4/qt77t5d3q4.pdfinfo:doi/10.1038/leu.2010.268articleLeukemia, vol 25, iss 2290 - 300oai:escholarship.org:ark:/13030/qt6d3974112025-12-30T22:55:17Zqt6d397411Plants regenerated from tissue culture contain stable epigenome changes in riceStroud, HumeDing, BoSimon, Stacey AFeng, SuhuaBellizzi, MariaPellegrini, MatteoWang, Guo-LiangMeyers, Blake CJacobsen, Steven E2013-01-01Most transgenic crops are produced through tissue culture. The impact of utilizing such methods on the plant epigenome is poorly understood. Here we generated whole-genome, single-nucleotide resolution maps of DNA methylation in several regenerated rice lines. We found that all tested regenerated plants had significant losses of methylation compared to non-regenerated plants. Loss of methylation was largely stable across generations, and certain sites in the genome were particularly susceptible to loss of methylation. Loss of methylation at promoters was associated with deregulated expression of protein-coding genes. Analyses of callus and untransformed plants regenerated from callus indicated that loss of methylation is stochastically induced at the tissue culture step. These changes in methylation may explain a component of somaclonal variation, a phenomenon in which plants derived from tissue culture manifest phenotypic variability. DOI:http://dx.doi.org/10.7554/eLife.00354.001.31 Biological Sciences (for-2020)3105 Genetics (for-2020)Genetics (rcdc)Human Genome (rcdc)DNA Methylation (mesh)EpigenesisGenetic (mesh)Epigenomics (mesh)Gene Expression RegulationPlant (mesh)Genotype (mesh)Oryza (mesh)Phenotype (mesh)PlantsGenetically Modified (mesh)Promoter RegionsGenetic (mesh)Regeneration (mesh)Stochastic Processes (mesh)Time Factors (mesh)Tissue Culture Techniques (mesh)PlantsGenetically Modified (mesh)Tissue Culture Techniques (mesh)Stochastic Processes (mesh)Regeneration (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Gene Expression RegulationPlant (mesh)Genotype (mesh)Phenotype (mesh)Time Factors (mesh)Promoter RegionsGenetic (mesh)Epigenomics (mesh)Oryza (mesh)DNA methylationOtherRiceregenerationsmall RNAtissue cultureDNA Methylation (mesh)EpigenesisGenetic (mesh)Epigenomics (mesh)Gene Expression RegulationPlant (mesh)Genotype (mesh)Oryza (mesh)Phenotype (mesh)PlantsGenetically Modified (mesh)Promoter RegionsGenetic (mesh)Regeneration (mesh)Stochastic Processes (mesh)Time Factors (mesh)Tissue Culture Techniques (mesh)0601 Biochemistry and Cell Biology (for)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/6d397411https://escholarship.org/content/qt6d397411/qt6d397411.pdfinfo:doi/10.7554/elife.00354articleeLife, vol 2, iss 2e00354oai:escholarship.org:ark:/13030/qt8dj1x7nm2025-12-30T22:41:16Zqt8dj1x7nmTetramerization Reinforces the Dimer Interface of MnSODSheng, YueweiDurazo, ArmandoSchumacher, MikhailGralla, Edith ButlerCascio, DuilioCabelli, Diane EValentine, Joan SelverstoneSoares, Claudio M2013-01-01Two yeast manganese superoxide dismutases (MnSOD), one from Saccharomyces cerevisiae mitochondria (ScMnSOD) and the other from Candida albicans cytosol (CaMnSODc), have most biochemical and biophysical properties in common, yet ScMnSOD is a tetramer and CaMnSODc is a dimer or "loose tetramer" in solution. Although CaMnSODc was found to crystallize as a tetramer, there is no indication from the solution properties that the functionality of CaMnSODc in vivo depends upon the formation of the tetrameric structure. To elucidate further the functional significance of MnSOD quaternary structure, wild-type and mutant forms of ScMnSOD (K182R, A183P mutant) and CaMnSODc (K184R, L185P mutant) with the substitutions at dimer interfaces were analyzed with respect to their oligomeric states and resistance to pH, heat, and denaturant. Dimeric CaMnSODc was found to be significantly more subject to thermal or denaturant-induced unfolding than tetrameric ScMnSOD. The residue substitutions at dimer interfaces caused dimeric CaMnSODc but not tetrameric ScMnSOD to dissociate into monomers. We conclude that the tetrameric assembly strongly reinforces the dimer interface, which is critical for MnSOD activity.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Amino Acid Sequence (mesh)Candida albicans (mesh)Cytosol (mesh)Enzyme Activation (mesh)Enzyme Stability (mesh)Hot Temperature (mesh)Mitochondria (mesh)ModelsMolecular (mesh)Molecular Sequence Data (mesh)MutagenesisSite-Directed (mesh)Mutation (mesh)Protein Denaturation (mesh)Protein Multimerization (mesh)Protein StructureQuaternary (mesh)Saccharomyces cerevisiae (mesh)Superoxide Dismutase (mesh)Mitochondria (mesh)Cytosol (mesh)Saccharomyces cerevisiae (mesh)Candida albicans (mesh)Superoxide Dismutase (mesh)MutagenesisSite-Directed (mesh)Enzyme Stability (mesh)Enzyme Activation (mesh)Amino Acid Sequence (mesh)Protein StructureQuaternary (mesh)Protein Denaturation (mesh)Mutation (mesh)ModelsMolecular (mesh)Molecular Sequence Data (mesh)Hot Temperature (mesh)Protein Multimerization (mesh)Amino Acid Sequence (mesh)Candida albicans (mesh)Cytosol (mesh)Enzyme Activation (mesh)Enzyme Stability (mesh)Hot Temperature (mesh)Mitochondria (mesh)ModelsMolecular (mesh)Molecular Sequence Data (mesh)MutagenesisSite-Directed (mesh)Mutation (mesh)Protein Denaturation (mesh)Protein Multimerization (mesh)Protein StructureQuaternary (mesh)Saccharomyces cerevisiae (mesh)Superoxide Dismutase (mesh)General Science & Technology (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/8dj1x7nmhttps://escholarship.org/content/qt8dj1x7nm/qt8dj1x7nm.pdfinfo:doi/10.1371/journal.pone.0062446articlePLOS ONE, vol 8, iss 5e62446oai:escholarship.org:ark:/13030/qt3r60c0kf2025-12-30T22:01:35Zqt3r60c0kfCharacterization and Therapeutic Potential of Induced Pluripotent Stem Cell-Derived Cardiovascular Progenitor CellsNsair, AliSchenke-Layland, KatjaVan Handel, BenEvseenko, DenisKahn, MichaelZhao, PengMendelis, JosephHeydarkhan, SanazAwaji, ObinaVottler, MiriamGeist, SusanneChyu, JenniferGago-Lopez, NuriaCrooks, Gay MPlath, KathrinGoldhaber, JoshMikkola, Hanna KAMacLellan, W RobbPesce, Maurizio2012-01-01BACKGROUND: Cardiovascular progenitor cells (CPCs) have been identified within the developing mouse heart and differentiating pluripotent stem cells by intracellular transcription factors Nkx2.5 and Islet 1 (Isl1). Study of endogenous and induced pluripotent stem cell (iPSC)-derived CPCs has been limited due to the lack of specific cell surface markers to isolate them and conditions for their in vitro expansion that maintain their multipotency.
METHODOLOGY/PRINCIPAL FINDINGS: We sought to identify specific cell surface markers that label endogenous embryonic CPCs and validated these markers in iPSC-derived Isl1(+)/Nkx2.5(+) CPCs. We developed conditions that allow propagation and characterization of endogenous and iPSC-derived Isl1(+)/Nkx2.5(+) CPCs and protocols for their clonal expansion in vitro and transplantation in vivo. Transcriptome analysis of CPCs from differentiating mouse embryonic stem cells identified a panel of surface markers. Comparison of these markers as well as previously described surface markers revealed the combination of Flt1(+)/Flt4(+) best identified and facilitated enrichment for Isl1(+)/Nkx2.5(+) CPCs from embryonic hearts and differentiating iPSCs. Endogenous mouse and iPSC-derived Flt1(+)/Flt4(+) CPCs differentiated into all three cardiovascular lineages in vitro. Flt1(+)/Flt4(+) CPCs transplanted into left ventricles demonstrated robust engraftment and differentiation into mature cardiomyocytes (CMs).
CONCLUSION/SIGNIFICANCE: The cell surface marker combination of Flt1 and Flt4 specifically identify and enrich for an endogenous and iPSC-derived Isl1(+)/Nkx2.5(+) CPC with trilineage cardiovascular potential in vitro and robust ability for engraftment and differentiation into morphologically and electrophysiologically mature adult CMs in vivo post transplantation into adult hearts.3206 Medical Biotechnology (for-2020)32 Biomedical and Clinical Sciences (for-2020)Stem Cell Research (rcdc)Stem Cell Research - Embryonic - Non-Human (rcdc)Stem Cell Research - Nonembryonic - Non-Human (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell (rcdc)Regenerative Medicine (rcdc)Heart Disease (rcdc)Transplantation (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell - Human (rcdc)Cardiovascular (rcdc)Stem Cell Research - Nonembryonic - Human (rcdc)5.2 Cellular and gene therapies (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)Cardiovascular (hrcs-hc)Animals (mesh)Cell Differentiation (mesh)CellsCultured (mesh)EmbryoMammalian (mesh)Embryonic Stem Cells (mesh)Fibroblasts (mesh)Gene Expression RegulationDevelopmental (mesh)Green Fluorescent Proteins (mesh)Homeobox Protein Nkx-2.5 (mesh)Homeodomain Proteins (mesh)Immunohistochemistry (mesh)Induced Pluripotent Stem Cells (mesh)LIM-Homeodomain Proteins (mesh)Mice (mesh)MiceInbred C57BL (mesh)MiceTransgenic (mesh)MyocytesCardiac (mesh)Pluripotent Stem Cells (mesh)Reverse Transcriptase Polymerase Chain Reaction (mesh)Stem Cell Transplantation (mesh)Stem Cells (mesh)Transcription Factors (mesh)Transcriptome (mesh)Vascular Endothelial Growth Factor Receptor-1 (mesh)Vascular Endothelial Growth Factor Receptor-3 (mesh)CellsCultured (mesh)Fibroblasts (mesh)MyocytesCardiac (mesh)Stem Cells (mesh)Pluripotent Stem Cells (mesh)Animals (mesh)MiceInbred C57BL (mesh)MiceTransgenic (mesh)Mice (mesh)Vascular Endothelial Growth Factor Receptor-1 (mesh)Vascular Endothelial Growth Factor Receptor-3 (mesh)Homeodomain Proteins (mesh)Green Fluorescent Proteins (mesh)Transcription Factors (mesh)Stem Cell Transplantation (mesh)Immunohistochemistry (mesh)Reverse Transcriptase Polymerase Chain Reaction (mesh)Cell Differentiation (mesh)Gene Expression RegulationDevelopmental (mesh)Embryonic Stem Cells (mesh)EmbryoMammalian (mesh)Induced Pluripotent Stem Cells (mesh)LIM-Homeodomain Proteins (mesh)Transcriptome (mesh)Homeobox Protein Nkx-2.5 (mesh)Animals (mesh)Cell Differentiation (mesh)CellsCultured (mesh)EmbryoMammalian (mesh)Embryonic Stem Cells (mesh)Fibroblasts (mesh)Gene Expression RegulationDevelopmental (mesh)Green Fluorescent Proteins (mesh)Homeobox Protein Nkx-2.5 (mesh)Homeodomain Proteins (mesh)Immunohistochemistry (mesh)Induced Pluripotent Stem Cells (mesh)LIM-Homeodomain Proteins (mesh)Mice (mesh)MiceInbred C57BL (mesh)MiceTransgenic (mesh)MyocytesCardiac (mesh)Pluripotent Stem Cells (mesh)Reverse Transcriptase Polymerase Chain Reaction (mesh)Stem Cell Transplantation (mesh)Stem Cells (mesh)Transcription Factors (mesh)Transcriptome (mesh)Vascular Endothelial Growth Factor Receptor-1 (mesh)Vascular Endothelial Growth Factor Receptor-3 (mesh)General Science & Technology (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/3r60c0kfhttps://escholarship.org/content/qt3r60c0kf/qt3r60c0kf.pdfinfo:doi/10.1371/journal.pone.0045603articlePLOS ONE, vol 7, iss 10e45603oai:escholarship.org:ark:/13030/qt9b56v2cn2025-12-30T19:47:45Zqt9b56v2cnSingle-cell methylation analysis of brain tissue prioritizes mutations that alter transcriptionFlint, JonathanHeffel, Matthew GChen, ZeyuanMefford, JoelMarcus, EmilieChen, Patrick BErnst, JasonLuo, Chongyuan2023-12-01Relating genetic variants to behavior remains a fundamental challenge. To assess the utility of DNA methylation marks in discovering causative variants, we examined their relationship to genetic variation by generating single-nucleus methylomes from the hippocampus of eight inbred mouse strains. At CpG sequence densities under 40 CpG/Kb, cells compensate for loss of methylated sites by methylating additional sites to maintain methylation levels. At higher CpG sequence densities, the exact location of a methylated site becomes more important, suggesting that variants affecting methylation will have a greater effect when occurring in higher CpG densities than in lower. We found this to be true for a variant's effect on transcript abundance, indicating that candidate variants can be prioritized based on CpG sequence density. Our findings imply that DNA methylation influences the likelihood that mutations occur at specific sites in the genome, supporting the view that the distribution of mutations is not random.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)3105 Genetics (for-2020)Genetics (rcdc)Human Genome (rcdc)2.1 Biological and endogenous factors (hrcs-rac)hippocampusinbred mouse strainsmethylationvariant functionapplication/pdfCC-BY-NC-SAeScholarship, University of Californiahttps://escholarship.org/uc/item/9b56v2cnhttps://escholarship.org/content/qt9b56v2cn/qt9b56v2cn.pdfinfo:doi/10.1016/j.xgen.2023.100454articleCell Genomics, vol 3, iss 12100454oai:escholarship.org:ark:/13030/qt2mc7j5vs2025-12-30T19:00:16Zqt2mc7j5vsTandem metabolic reaction–based sensors unlock in vivo metabolomicsCheng, XuanbingLi, ZongqiZhu, JialunWang, JingyuHuang, RuyiYu, Lewis WLin, ShuyuForman, SarahGromilina, EvelinaPuri, SameeraPatel, PriteshBahramian, MohammadrezaTan, JiaweiHojaiji, HannanehJelinek, DavidVoisin, LaurentYu, Kristie BZhang, AoHo, ConnieLei, LeiColler, Hilary AHsiao, Elaine YReyes, Beck LMatsumoto, Joyce HLu, Daniel CLiu, ChongMilla, CarlosDavis, Ronald WEmaminejad, Sam2025-03-04Mimicking metabolic pathways on electrodes enables in vivo metabolite monitoring for decoding metabolism. Conventional in vivo sensors cannot accommodate underlying complex reactions involving multiple enzymes and cofactors, addressing only a fraction of enzymatic reactions for few metabolites. We devised a single-wall-carbon-nanotube-electrode architecture supporting tandem metabolic pathway-like reactions linkable to oxidoreductase-based electrochemical analysis, making a vast majority of metabolites detectable in vivo. This architecture robustly integrates cofactors, self-mediates reactions at maximum enzyme capacity, and facilitates metabolite intermediation/detection and interference inactivation through multifunctional enzymatic use. Accordingly, we developed sensors targeting 12 metabolites, with 100-fold-enhanced signal-to-noise ratio and days-long stability. Leveraging these sensors, we monitored trace endogenous metabolites in sweat/saliva for noninvasive health monitoring, and a bacterial metabolite in the brain, marking a key milestone for unraveling gut microbiota-brain axis dynamics.3401 Analytical Chemistry (for-2020)31 Biological Sciences (for-2020)32 Biomedical and Clinical Sciences (for-2020)34 Chemical Sciences (for-2020)3205 Medical Biochemistry and Metabolomics (for-2020)Bioengineering (rcdc)Metabolomics (mesh)Humans (mesh)Metabolic Networks and Pathways (mesh)NanotubesCarbon (mesh)Sweat (mesh)Gastrointestinal Microbiome (mesh)Brain (mesh)Electrodes (mesh)Biosensing Techniques (mesh)Metabolome (mesh)Electrochemical Techniques (mesh)wearable and implantable metabolite sensorscofactor- assisted enzymatic reactionsin vivo metabolomicsmicrobiomepersonalized medicineBrain (mesh)Sweat (mesh)Humans (mesh)NanotubesCarbon (mesh)Biosensing Techniques (mesh)Electrodes (mesh)Metabolic Networks and Pathways (mesh)Metabolomics (mesh)Metabolome (mesh)Electrochemical Techniques (mesh)Gastrointestinal Microbiome (mesh)cofactor-assisted enzymatic reactionsin vivo metabolomicsmicrobiomepersonalized medicinewearable and implantable metabolite sensorsMetabolomics (mesh)Humans (mesh)Metabolic Networks and Pathways (mesh)NanotubesCarbon (mesh)Sweat (mesh)Gastrointestinal Microbiome (mesh)Brain (mesh)Electrodes (mesh)Biosensing Techniques (mesh)Metabolome (mesh)Electrochemical Techniques (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/2mc7j5vshttps://escholarship.org/content/qt2mc7j5vs/qt2mc7j5vs.pdfinfo:doi/10.1073/pnas.2425526122articleProceedings of the National Academy of Sciences of the United States of America, vol 122, iss 9e2425526122oai:escholarship.org:ark:/13030/qt2qs1g1fm2025-12-30T15:41:23Zqt2qs1g1fmThe Number of X Chromosomes Causes Sex Differences in Adiposity in MiceChen, XuqiMcClusky, RebeccaChen, JennyBeaven, Simon WTontonoz, PeterArnold, Arthur PReue, KarenAttie, Alan2012-01-01Sexual dimorphism in body weight, fat distribution, and metabolic disease has been attributed largely to differential effects of male and female gonadal hormones. Here, we report that the number of X chromosomes within cells also contributes to these sex differences. We employed a unique mouse model, known as the "four core genotypes," to distinguish between effects of gonadal sex (testes or ovaries) and sex chromosomes (XX or XY). With this model, we produced gonadal male and female mice carrying XX or XY sex chromosome complements. Mice were gonadectomized to remove the acute effects of gonadal hormones and to uncover effects of sex chromosome complement on obesity. Mice with XX sex chromosomes (relative to XY), regardless of their type of gonad, had up to 2-fold increased adiposity and greater food intake during daylight hours, when mice are normally inactive. Mice with two X chromosomes also had accelerated weight gain on a high fat diet and developed fatty liver and elevated lipid and insulin levels. Further genetic studies with mice carrying XO and XXY chromosome complements revealed that the differences between XX and XY mice are attributable to dosage of the X chromosome, rather than effects of the Y chromosome. A subset of genes that escape X chromosome inactivation exhibited higher expression levels in adipose tissue and liver of XX compared to XY mice, and may contribute to the sex differences in obesity. Overall, our study is the first to identify sex chromosome complement, a factor distinguishing all male and female cells, as a cause of sex differences in obesity and metabolism.31 Biological Sciences (for-2020)3105 Genetics (for-2020)Genetics (rcdc)Women's Health (rcdc)Obesity (rcdc)Estrogen (rcdc)Nutrition (rcdc)Prevention (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Metabolic and endocrine (hrcs-hc)Oral and gastrointestinal (hrcs-hc)Cardiovascular (hrcs-hc)Reproductive health and childbirth (hrcs-hc)Adiposity (mesh)Animals (mesh)DietHigh-Fat (mesh)Female (mesh)Gonadal Hormones (mesh)Gonads (mesh)Insulin (mesh)Lipid Metabolism (mesh)Lipids (mesh)Male (mesh)Mice (mesh)Obesity (mesh)Sex Characteristics (mesh)Sex Determination Processes (mesh)Weight Gain (mesh)X Chromosome (mesh)Y Chromosome (mesh)Gonads (mesh)X Chromosome (mesh)Y Chromosome (mesh)Animals (mesh)Mice (mesh)Obesity (mesh)Weight Gain (mesh)Gonadal Hormones (mesh)Insulin (mesh)Lipids (mesh)Sex Characteristics (mesh)Female (mesh)Male (mesh)Adiposity (mesh)Lipid Metabolism (mesh)Sex Determination Processes (mesh)DietHigh-Fat (mesh)Adiposity (mesh)Animals (mesh)DietHigh-Fat (mesh)Female (mesh)Gonadal Hormones (mesh)Gonads (mesh)Insulin (mesh)Lipid Metabolism (mesh)Lipids (mesh)Male (mesh)Mice (mesh)Obesity (mesh)Sex Characteristics (mesh)Sex Determination Processes (mesh)Weight Gain (mesh)X Chromosome (mesh)Y Chromosome (mesh)0604 Genetics (for)Developmental Biology (science-metrix)3105 Genetics (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/2qs1g1fmhttps://escholarship.org/content/qt2qs1g1fm/qt2qs1g1fm.pdfinfo:doi/10.1371/journal.pgen.1002709articlePLOS Genetics, vol 8, iss 5e1002709oai:escholarship.org:ark:/13030/qt4gp4j5ck2025-12-30T12:57:01Zqt4gp4j5ckTaking the measure of MicroEDRodriguez, Jose AEisenberg, David SGonen, Tamir2017-10-01It is now possible to routinely determine atomic resolution structures by electron cryo-microscopy (cryoEM), facilitated in part by the method known as micro electron-diffraction (MicroED). Since its initial demonstration in 2013, MicroED has helped determine a variety of protein structures ranging in molecular weight from a few hundred Daltons to several hundred thousand Daltons. Some of these structures were novel while others were previously known. The resolutions of structures obtained thus far by MicroED range from 3.2Å to 1.0Å, with most better than 2.5Å. Crystals of various sizes and shapes, with different space group symmetries, and with a range of solvent content have all been studied by MicroED. The wide range of crystals explored to date presents the community with a landscape of opportunity for structure determination from nano crystals. Here we summarize the lessons we have learned during the first few years of MicroED, and from our attempts at the first ab initio structure determined by the method. We re-evaluate theoretical considerations in choosing the appropriate crystals for MicroED and for extracting the most meaning out of measured data. With more laboratories worldwide adopting the technique, we speculate what the first decade might hold for MicroED.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Amyloid (mesh)Cryoelectron Microscopy (mesh)Humans (mesh)Protein Conformation (mesh)Quantum Theory (mesh)Humans (mesh)Amyloid (mesh)Cryoelectron Microscopy (mesh)Protein Conformation (mesh)Quantum Theory (mesh)Amyloid (mesh)Cryoelectron Microscopy (mesh)Humans (mesh)Protein Conformation (mesh)Quantum Theory (mesh)0304 Medicinal and Biomolecular Chemistry (for)0601 Biochemistry and Cell Biology (for)Biophysics (science-metrix)3101 Biochemistry and cell biology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4gp4j5ckhttps://escholarship.org/content/qt4gp4j5ck/qt4gp4j5ck.pdfinfo:doi/10.1016/j.sbi.2017.06.004articleCurrent Opinion in Structural Biology, vol 4679 - 86oai:escholarship.org:ark:/13030/qt03p035b02025-12-30T11:45:24Zqt03p035b0TFAP2C regulates transcription in human naive pluripotency by opening enhancersPastor, William ALiu, WanluChen, DiHo, JamieKim, RachelHunt, Timothy JLukianchikov, AnastasiaLiu, XiaodongPolo, Jose MJacobsen, Steven EClark, Amander T2018-05-01Naive and primed pluripotent human embryonic stem cells bear transcriptional similarity to pre- and post-implantation epiblast and thus constitute a developmental model for understanding the pluripotent stages in human embryo development. To identify new transcription factors that differentially regulate the unique pluripotent stages, we mapped open chromatin using ATAC-seq and found enrichment of the activator protein-2 (AP2) transcription factor binding motif at naive-specific open chromatin. We determined that the AP2 family member TFAP2C is upregulated during primed to naive reversion and becomes widespread at naive-specific enhancers. TFAP2C functions to maintain pluripotency and repress neuroectodermal differentiation during the transition from primed to naive by facilitating the opening of enhancers proximal to pluripotency factors. Additionally, we identify a previously undiscovered naive-specific POU5F1(OCT4) enhancer enriched for TFAP2C binding. Taken together, TFAP2C establishes and maintains naive human pluripotency and regulates OCT4 expression by mechanisms that are distinct from mouse.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Stem Cell Research - Embryonic - Human (rcdc)Stem Cell Research (rcdc)Human Genome (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Animals (mesh)Binding Sites (mesh)Cell Lineage (mesh)CellsCultured (mesh)Chromatin (mesh)Chromatin Assembly and Disassembly (mesh)Enhancer ElementsGenetic (mesh)Gene Expression RegulationDevelopmental (mesh)Human Embryonic Stem Cells (mesh)Humans (mesh)Mice (mesh)Mouse Embryonic Stem Cells (mesh)Nucleotide Motifs (mesh)Octamer Transcription Factor-3 (mesh)Phenotype (mesh)Protein Binding (mesh)Signal Transduction (mesh)Species Specificity (mesh)Transcription Factor AP-2 (mesh)TranscriptionGenetic (mesh)CellsCultured (mesh)Chromatin (mesh)Animals (mesh)Humans (mesh)Mice (mesh)Signal Transduction (mesh)Chromatin Assembly and Disassembly (mesh)Species Specificity (mesh)TranscriptionGenetic (mesh)Gene Expression RegulationDevelopmental (mesh)Binding Sites (mesh)Protein Binding (mesh)Cell Lineage (mesh)Phenotype (mesh)Transcription Factor AP-2 (mesh)Octamer Transcription Factor-3 (mesh)Enhancer ElementsGenetic (mesh)Nucleotide Motifs (mesh)Human Embryonic Stem Cells (mesh)Mouse Embryonic Stem Cells (mesh)Animals (mesh)Binding Sites (mesh)Cell Lineage (mesh)CellsCultured (mesh)Chromatin (mesh)Chromatin Assembly and Disassembly (mesh)Enhancer ElementsGenetic (mesh)Gene Expression RegulationDevelopmental (mesh)Human Embryonic Stem Cells (mesh)Humans (mesh)Mice (mesh)Mouse Embryonic Stem Cells (mesh)Nucleotide Motifs (mesh)Octamer Transcription Factor-3 (mesh)Phenotype (mesh)Protein Binding (mesh)Signal Transduction (mesh)Species Specificity (mesh)Transcription Factor AP-2 (mesh)TranscriptionGenetic (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/03p035b0https://escholarship.org/content/qt03p035b0/qt03p035b0.pdfinfo:doi/10.1038/s41556-018-0089-0articleNature Cell Biology, vol 20, iss 5553 - 564oai:escholarship.org:ark:/13030/qt8k02r9342025-12-30T10:31:05Zqt8k02r934In Crystallo Selection to Establish New RNA Crystal ContactsShoffner, Grant MWang, RuixuanPodell, ElaineCech, Thomas RGuo, Feng2018-09-01Crystallography is a major technique for determining large RNA structures. Obtaining diffraction-quality crystals has been the bottleneck. Although several RNA crystallization methods have been developed, the field strongly needs additional approaches. Here we invented an in crystallo selection strategy for identifying mutations that enhance a target RNA's crystallizability. The strategy includes constructing an RNA pool containing random mutations, obtaining crystals, and amplifying the sequences enriched by crystallization. We demonstrated a proof-of-principle application to the P4-P6 domain from the Tetrahymena ribozyme. We further determined the structures of four selected mutants. All four establish new crystal lattice contacts while maintaining the native structure. Three mutants achieve this by relocating bulges and one by making a helix more flexible. In crystallo selection provides opportunities to improve crystals of RNAs or RNA-ligand complexes. Our results also suggest that mutants may be rationally designed for crystallization by "walking" a bulge along the RNA chain.3101 Biochemistry and Cell Biology (for-2020)3402 Inorganic Chemistry (for-2020)34 Chemical Sciences (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Crystallization (mesh)ModelsMolecular (mesh)Mutation (mesh)Nucleic Acid Conformation (mesh)RNA (mesh)RNACatalytic (mesh)RNAProtozoan (mesh)Sequence AnalysisRNA (mesh)Tetrahymena (mesh)Tetrahymena (mesh)RNACatalytic (mesh)RNA (mesh)RNAProtozoan (mesh)Crystallization (mesh)Sequence AnalysisRNA (mesh)Nucleic Acid Conformation (mesh)Mutation (mesh)ModelsMolecular (mesh)X-ray crystallographycrystal lattice contactsgroup I intronin vitro selectionstructural biologyCrystallization (mesh)ModelsMolecular (mesh)Mutation (mesh)Nucleic Acid Conformation (mesh)RNA (mesh)RNACatalytic (mesh)RNAProtozoan (mesh)Sequence AnalysisRNA (mesh)Tetrahymena (mesh)Biophysics (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8k02r934https://escholarship.org/content/qt8k02r934/qt8k02r934.pdfinfo:doi/10.1016/j.str.2018.05.005articleStructure, vol 26, iss 91275 - 1283.e3oai:escholarship.org:ark:/13030/qt8gh9h23v2025-12-30T10:14:35Zqt8gh9h23vMicroED Structure of Au146(p-MBA)57 at Subatomic Resolution Reveals a Twinned FCC ClusterVergara, SandraLukes, Dylan AMartynowycz, Michael WSantiago, UlisesPlascencia-Villa, GermánWeiss, Simon Cde la Cruz, M JasonBlack, David MAlvarez, Marcos MLópez-Lozano, XochitlBarnes, Christopher OLin, GuowuWeissker, Hans-ChristianWhetten, Robert LGonen, TamirYacaman, Miguel JoseCalero, Guillermo2017-11-16Solving the atomic structure of metallic clusters is fundamental to understanding their optical, electronic, and chemical properties. Herein we present the structure of the largest aqueous gold cluster, Au146(p-MBA)57 (p-MBA: para-mercaptobenzoic acid), solved by electron micro-diffraction (MicroED) to subatomic resolution (0.85 Å) and by X-ray diffraction at atomic resolution (1.3 Å). The 146 gold atoms may be decomposed into two constituent sets consisting of 119 core and 27 peripheral atoms. The core atoms are organized in a twinned FCC structure, whereas the surface gold atoms follow a C2 rotational symmetry about an axis bisecting the twinning plane. The protective layer of 57 p-MBAs fully encloses the cluster and comprises bridging, monomeric, and dimeric staple motifs. Au146(p-MBA)57 is the largest cluster observed exhibiting a bulk-like FCC structure as well as the smallest gold particle exhibiting a stacking fault.3402 Inorganic Chemistry (for-2020)34 Chemical Sciences (for-2020)51 Physical Sciences (for-2020)physics.atm-clusphysics.atm-cluscond-mat.mtrl-sci02 Physical Sciences (for)03 Chemical Sciences (for)34 Chemical sciences (for-2020)51 Physical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8gh9h23vhttps://escholarship.org/content/qt8gh9h23v/qt8gh9h23v.pdfinfo:doi/10.1021/acs.jpclett.7b02621articleThe Journal of Physical Chemistry Letters, vol 8, iss 225523 - 5530oai:escholarship.org:ark:/13030/qt2pr0p5dd2025-12-30T09:52:28Zqt2pr0p5ddStructure-based discovery of fiber-binding compounds that reduce the cytotoxicity of amyloid betaJiang, LinLiu, CongLeibly, DavidLandau, MeytalZhao, MingleiHughes, Michael PEisenberg, David S2013-01-01Amyloid protein aggregates are associated with dozens of devastating diseases including Alzheimer's, Parkinson's, ALS, and diabetes type 2. While structure-based discovery of compounds has been effective in combating numerous infectious and metabolic diseases, ignorance of amyloid structure has hindered similar approaches to amyloid disease. Here we show that knowledge of the atomic structure of one of the adhesive, steric-zipper segments of the amyloid-beta (Aβ) protein of Alzheimer's disease, when coupled with computational methods, identifies eight diverse but mainly flat compounds and three compound derivatives that reduce Aβ cytotoxicity against mammalian cells by up to 90%. Although these compounds bind to Aβ fibers, they do not reduce fiber formation of Aβ. Structure-activity relationship studies of the fiber-binding compounds and their derivatives suggest that compound binding increases fiber stability and decreases fiber toxicity, perhaps by shifting the equilibrium of Aβ from oligomers to fibers. DOI:http://dx.doi.org/10.7554/eLife.00857.001.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Acquired Cognitive Impairment (rcdc)Dementia (rcdc)Aging (rcdc)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)Brain Disorders (rcdc)Neurodegenerative (rcdc)Alzheimer's Disease (rcdc)Neurosciences (rcdc)Neurological (hrcs-hc)Alzheimer Disease (mesh)Amyloid beta-Peptides (mesh)Humans (mesh)Magnetic Resonance Spectroscopy (mesh)Molecular Structure (mesh)Protein Binding (mesh)Structure-Activity Relationship (mesh)Humans (mesh)Alzheimer Disease (mesh)Magnetic Resonance Spectroscopy (mesh)Molecular Structure (mesh)Protein Binding (mesh)Structure-Activity Relationship (mesh)Amyloid beta-Peptides (mesh)Alzheimer's diseaseOtheramyloid fibercomputational biologydrug discoveryligand dockingAlzheimer Disease (mesh)Amyloid beta-Peptides (mesh)Humans (mesh)Magnetic Resonance Spectroscopy (mesh)Molecular Structure (mesh)Protein Binding (mesh)Structure-Activity Relationship (mesh)0601 Biochemistry and Cell Biology (for)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/2pr0p5ddhttps://escholarship.org/content/qt2pr0p5dd/qt2pr0p5dd.pdfinfo:doi/10.7554/elife.00857articleeLife, vol 2, iss 2e00857oai:escholarship.org:ark:/13030/qt4r79p5wn2025-12-30T08:03:58Zqt4r79p5wnIdentification of the Major Expressed S‐Layer and Cell Surface‐Layer‐Related Proteins in the Model Methanogenic Archaea: Methanosarcina barkeri Fusaro and Methanosarcina acetivorans C2ARohlin, LarsLeon, Deborah RKim, UnmiLoo, Joseph ALoo, Rachel R OgorzalekGunsalus, Robert P2012-01-01Many archaeal cell envelopes contain a protein coat or sheath composed of one or more surface exposed proteins. These surface layer (S-layer) proteins contribute structural integrity and protect the lipid membrane from environmental challenges. To explore the species diversity of these layers in the Methanosarcinaceae, the major S-layer protein in Methanosarcina barkeri strain Fusaro was identified using proteomics. The Mbar_A1758 gene product was present in multiple forms with apparent sizes of 130, 120, and 100 kDa, consistent with post-translational modifications including signal peptide excision and protein glycosylation. A protein with features related to the surface layer proteins found in Methanosarcina acetivorans C2A and Methanosarcina mazei Goel was identified in the M. barkeri genome. These data reveal a distinct conserved protein signature with features and implied cell surface architecture in the Methanosarcinaceae that is absent in other archaea. Paralogous gene expression patterns in two Methanosarcina species revealed abundant expression of a single S-layer paralog in each strain. Respective promoter elements were identified and shown to be conserved in mRNA coding and upstream untranslated regions. Prior M. acetivorans genome annotations assigned S-layer or surface layer associated roles of eighty genes: however, of 68 examined none was significantly expressed relative to the experimentally determined S-layer gene.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)Biotechnology (rcdc)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)DNAArchaeal (mesh)Gene Expression (mesh)GenesArchaeal (mesh)GenomeArchaeal (mesh)Membrane Glycoproteins (mesh)Methanosarcina (mesh)Molecular Weight (mesh)Promoter RegionsGenetic (mesh)Protein ProcessingPost-Translational (mesh)Proteomics (mesh)Methanosarcina (mesh)Membrane Glycoproteins (mesh)DNAArchaeal (mesh)Proteomics (mesh)Gene Expression (mesh)Protein ProcessingPost-Translational (mesh)GenesArchaeal (mesh)GenomeArchaeal (mesh)Molecular Weight (mesh)Promoter RegionsGenetic (mesh)DNAArchaeal (mesh)Gene Expression (mesh)GenesArchaeal (mesh)GenomeArchaeal (mesh)Membrane Glycoproteins (mesh)Methanosarcina (mesh)Molecular Weight (mesh)Promoter RegionsGenetic (mesh)Protein ProcessingPost-Translational (mesh)Proteomics (mesh)0605 Microbiology (for)1108 Medical Microbiology (for)Microbiology (science-metrix)3107 Microbiology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/4r79p5wnhttps://escholarship.org/content/qt4r79p5wn/qt4r79p5wn.pdfinfo:doi/10.1155/2012/873589articleArchaea, vol 2012, iss 1873589oai:escholarship.org:ark:/13030/qt1hj8z0df2025-12-30T07:42:02Zqt1hj8z0dfCompositional Analysis of Complex Mixtures using Automatic MicroED Data CollectionUnge, JohanLin, JieyeWeaver, Sara JHer, Ampon SaeGonen, Tamir2024-06-01Quantitative analysis of complex mixtures, including compounds having similar chemical properties, is demonstrated using an automatic and high throughput approach to microcrystal electron diffraction (MicroED). Compositional analysis of organic and inorganic compounds can be accurately executed without the need of diffraction standards. Additionally, with sufficient statistics, small amounts of compounds in mixtures can be reliably detected. These compounds can be distinguished by their crystal structure properties prior to structure solution. In addition, if the crystals are of good quality, the crystal structures can be generated on the fly, providing a complete analysis of the sample. MicroED is an effective method for analyzing the structural properties of sub-micron crystals, which are frequently found in small-molecule powders. By developing and using an automatic and high throughput approach to MicroED, and with the use of SerialEM for data collection, data from thousands of crystals allow sufficient statistics to detect even small amounts of compounds reliably.3402 Inorganic Chemistry (for-2020)34 Chemical Sciences (for-2020)Biotechnology (rcdc)1.5 Resources and infrastructure (underpinning) (hrcs-rac)analyticalautomationcompositionCryoEMhigh-throughputmicrocrystal electron diffractionMicroEDCryoEMMicroEDanalyticalautomationcompositionhigh‐throughputmicrocrystal electron diffractionapplication/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/1hj8z0dfhttps://escholarship.org/content/qt1hj8z0df/qt1hj8z0df.pdfinfo:doi/10.1002/advs.202400081articleAdvanced Science, vol 11, iss 232400081oai:escholarship.org:ark:/13030/qt8w56h1s92025-12-30T07:31:46Zqt8w56h1s9Unraveling the Structure of Meclizine Dihydrochloride with MicroEDLin, JieyeUnge, JohanGonen, Tamir2024-02-01Meclizine (Antivert, Bonine) is a first-generation H1 antihistamine used in the treatment of motion sickness and vertigo. Despite its wide medical use for over 70 years, its crystal structure and the details of protein-drug interactions remained unknown. Single-crystal X-ray diffraction (SC-XRD) is previously unsuccessful for meclizine. Today, microcrystal electron diffraction (MicroED) enables the analysis of nano- or micro-sized crystals that are merely a billionth the size needed for SC-XRD directly from seemingly amorphous powder. In this study, MicroED to determine the 3D crystal structure of meclizine dihydrochloride is used. Two racemic enantiomers (R/S) are found in the unit cell, which is packed as repetitive double layers in the crystal lattice. The packing is made of multiple strong N-H-Cl- hydrogen bonding interactions and weak interactions like C-H-Cl- and pi-stacking. Molecular docking reveals the binding mechanism of meclizine to the histamine H1 receptor. A comparison of the docking complexes between histamine H1 receptor and meclizine or levocetirizine (a second-generation antihistamine) shows the conserved binding sites. This research illustrates the combined use of MicroED and molecular docking in unraveling elusive drug structures and protein-drug interactions for precision drug design and optimization.3402 Inorganic Chemistry (for-2020)34 Chemical Sciences (for-2020)Generic health relevance (hrcs-hc)Meclizine (mesh)Molecular Docking Simulation (mesh)Electrons (mesh)ReceptorsHistamine H1 (mesh)Proteins (mesh)Histamine Antagonists (mesh)Meclizine (AntivertBonine)Microcrystal electron diffraction (MicroED)Molecular dockingProtein-drug interactionsRacemic crystalMeclizine (mesh)Proteins (mesh)ReceptorsHistamine H1 (mesh)Histamine Antagonists (mesh)Electrons (mesh)Molecular Docking Simulation (mesh)Meclizine (AntivertBonine)Microcrystal electron diffraction (MicroED)Molecular dockingProtein-drug interactionsRacemic crystalMeclizine (mesh)Molecular Docking Simulation (mesh)Electrons (mesh)ReceptorsHistamine H1 (mesh)Proteins (mesh)Histamine Antagonists (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/8w56h1s9https://escholarship.org/content/qt8w56h1s9/qt8w56h1s9.pdfinfo:doi/10.1002/advs.202306435articleAdvanced Science, vol 11, iss 62306435oai:escholarship.org:ark:/13030/qt2jh1b4nh2025-12-30T07:27:51Zqt2jh1b4nhA Highly Ordered Nitroxide Side Chain for Distance Mapping and Monitoring Slow Structural Fluctuations in ProteinsChen, MengzhenKálai, TamásCascio, DuilioBridges, Michael DWhitelegge, Julian PElgeti, MatthiasHubbell, Wayne L2024-03-01Site-directed spin labeling electron paramagnetic resonance (SDSL-EPR) is an established tool for exploring protein structure and dynamics. Although nitroxide side chains attached to a single cysteine via a disulfide linkage are commonly employed in SDSL-EPR, their internal flexibility complicates applications to monitor slow internal motions in proteins and to structure determination by distance mapping. Moreover, the labile disulfide linkage prohibits the use of reducing agents often needed for protein stability. To enable the application of SDSL-EPR to the measurement of slow internal dynamics, new spin labels with hindered internal motion are desired. Here, we introduce a highly ordered nitroxide side chain, designated R9, attached at a single cysteine residue via a non-reducible thioether linkage. The reaction to introduce R9 is highly selective for solvent-exposed cysteine residues. Structures of R9 at two helical sites in T4 Lysozyme were determined by X-ray crystallography and the mobility in helical sequences was characterized by EPR spectral lineshape analysis, Saturation Transfer EPR, and Saturation Recovery EPR. In addition, interspin distance measurements between pairs of R9 residues are reported. Collectively, all data indicate that R9 will be useful for monitoring slow internal structural fluctuations, and applications to distance mapping via dipolar spectroscopy and relaxation enhancement methods are anticipated.34 Chemical Sciences (for-2020)3406 Physical Chemistry (for-2020)Bioengineering (rcdc)Generic health relevance (hrcs-hc)0202 AtomicMolecularNuclearParticle and Plasma Physics (for)0301 Analytical Chemistry (for)0306 Physical Chemistry (incl. Structural) (for)Chemical Physics (science-metrix)3406 Physical chemistry (for-2020)5106 Nuclear and plasma physics (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/2jh1b4nhhttps://escholarship.org/content/qt2jh1b4nh/qt2jh1b4nh.pdfinfo:doi/10.1007/s00723-023-01618-8articleApplied Magnetic Resonance, vol 55, iss 1-3251 - 277oai:escholarship.org:ark:/13030/qt4kg4k0352025-12-30T02:16:49Zqt4kg4k035Intrinsic electronic conductivity of individual atomically resolved amyloid crystals reveals micrometer-long hole hopping via tyrosinesShipps, CatharineKelly, H RayDahl, Peter JYi, Sophia MVu, DennisBoyer, DavidGlynn, CalinaSawaya, Michael REisenberg, DavidBatista, Victor SMalvankar, Nikhil S2021-01-12Proteins are commonly known to transfer electrons over distances limited to a few nanometers. However, many biological processes require electron transport over far longer distances. For example, soil and sediment bacteria transport electrons, over hundreds of micrometers to even centimeters, via putative filamentous proteins rich in aromatic residues. However, measurements of true protein conductivity have been hampered by artifacts due to large contact resistances between proteins and electrodes. Using individual amyloid protein crystals with atomic-resolution structures as a model system, we perform contact-free measurements of intrinsic electronic conductivity using a four-electrode approach. We find hole transport through micrometer-long stacked tyrosines at physiologically relevant potentials. Notably, the transport rate through tyrosines (105 s-1) is comparable to cytochromes. Our studies therefore show that amyloid proteins can efficiently transport charges, under ordinary thermal conditions, without any need for redox-active metal cofactors, large driving force, or photosensitizers to generate a high oxidation state for charge injection. By measuring conductivity as a function of molecular length, voltage, and temperature, while eliminating the dominant contribution of contact resistances, we show that a multistep hopping mechanism (composed of multiple tunneling steps), not single-step tunneling, explains the measured conductivity. Combined experimental and computational studies reveal that proton-coupled electron transfer confers conductivity; both the energetics of the proton acceptor, a neighboring glutamine, and its proximity to tyrosine influence the hole transport rate through a proton rocking mechanism. Surprisingly, conductivity increases 200-fold upon cooling due to higher availability of the proton acceptor by increased hydrogen bonding.3101 Biochemistry and Cell Biology (for-2020)51 Physical Sciences (for-2020)31 Biological Sciences (for-2020)Amyloidogenic Proteins (mesh)Cytochromes (mesh)Electric Conductivity (mesh)Electron Transport (mesh)Electrons (mesh)Hydrogen Bonding (mesh)ModelsBiological (mesh)Molecular Dynamics Simulation (mesh)Oxidation-Reduction (mesh)Proteins (mesh)Protons (mesh)Tyrosine (mesh)electron transportamyloidsprotein electronicsproton-coupled electron transfermolecular dynamicsProtons (mesh)Cytochromes (mesh)Tyrosine (mesh)Proteins (mesh)Electron Transport (mesh)Oxidation-Reduction (mesh)Electric Conductivity (mesh)Hydrogen Bonding (mesh)Electrons (mesh)ModelsBiological (mesh)Molecular Dynamics Simulation (mesh)Amyloidogenic Proteins (mesh)amyloidselectron transportmolecular dynamicsprotein electronicsproton-coupled electron transferAmyloidogenic Proteins (mesh)Cytochromes (mesh)Electric Conductivity (mesh)Electron Transport (mesh)Electrons (mesh)Hydrogen Bonding (mesh)ModelsBiological (mesh)Molecular Dynamics Simulation (mesh)Oxidation-Reduction (mesh)Proteins (mesh)Protons (mesh)Tyrosine (mesh)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4kg4k035https://escholarship.org/content/qt4kg4k035/qt4kg4k035.pdfinfo:doi/10.1073/pnas.2014139118articleProceedings of the National Academy of Sciences of the United States of America, vol 118, iss 2e2014139118oai:escholarship.org:ark:/13030/qt7m03r3mt2025-12-30T01:42:08Zqt7m03r3mtPPARα regulates ER–lipid droplet protein Calsyntenin-3β to promote ketogenesis in hepatocytesUchiyama, Lauren FNguyen, AlexanderQian, KevinCui, LiujuanPham, Khoi TXiao, XuGao, YajingShimanaka, YutaTol, Marcus JVergnes, LaurentReue, KarenTontonoz, Peter2025-04-29Ketogenesis requires fatty acid flux from intracellular (lipid droplets) and extrahepatic (adipose tissue) lipid stores to hepatocyte mitochondria. However, whether interorganelle contact sites regulate this process is unknown. Recent studies have revealed a role for Calsyntenin-3β (CLSTN3β), an endoplasmic reticulum-lipid droplet contact site protein, in the control of lipid utilization in adipose tissue. Here, we show that Clstn3b expression is induced in the liver by the nuclear receptor PPARα in settings of high lipid utilization, including fasting and ketogenic diet feeding. Hepatocyte-specific loss of CLSTN3β in mice impairs ketogenesis independent of changes in PPARα activation. Conversely, hepatic overexpression of CLSTN3β promotes ketogenesis in mice. Mechanistically, CLSTN3β affects LD-mitochondria crosstalk, as evidenced by changes in fatty acid oxidation, lipid-dependent mitochondrial respiration, and the mitochondrial integrated stress response. These findings define a function for CLSTN3β-dependent membrane contacts in hepatic lipid utilization and ketogenesis.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Digestive Diseases (rcdc)Nutrition (rcdc)Liver Disease (rcdc)2.1 Biological and endogenous factors (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)Metabolic and endocrine (hrcs-hc)Animals (mesh)Hepatocytes (mesh)PPAR alpha (mesh)Mice (mesh)Endoplasmic Reticulum (mesh)Lipid Droplets (mesh)Membrane Proteins (mesh)Liver (mesh)Male (mesh)Lipid Metabolism (mesh)Ketone Bodies (mesh)Mitochondria (mesh)MiceInbred C57BL (mesh)hepatocytelipid metabolismketogenesisketogenic dietLiver (mesh)Endoplasmic Reticulum (mesh)Mitochondria (mesh)Hepatocytes (mesh)Animals (mesh)MiceInbred C57BL (mesh)Mice (mesh)Ketone Bodies (mesh)Membrane Proteins (mesh)PPAR alpha (mesh)Male (mesh)Lipid Metabolism (mesh)Lipid Droplets (mesh)hepatocyteketogenesisketogenic dietlipid metabolismAnimals (mesh)Hepatocytes (mesh)PPAR alpha (mesh)Mice (mesh)Endoplasmic Reticulum (mesh)Lipid Droplets (mesh)Membrane Proteins (mesh)Liver (mesh)Male (mesh)Lipid Metabolism (mesh)Ketone Bodies (mesh)Mitochondria (mesh)MiceInbred C57BL (mesh)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7m03r3mthttps://escholarship.org/content/qt7m03r3mt/qt7m03r3mt.pdfinfo:doi/10.1073/pnas.2426338122articleProceedings of the National Academy of Sciences of the United States of America, vol 122, iss 17e2426338122oai:escholarship.org:ark:/13030/qt6vq1b3ps2025-12-30T01:32:06Zqt6vq1b3psSpatial profiling of the interplay between cell type- and vision-dependent transcriptomic programs in the visual cortexXie, FangmingJain, SaumyaXu, RunzheButrus, SalwanTan, ZhiqunXu, XiangminShekhar, KarthikZipursky, S Lawrence2025-02-18How early sensory experience during "critical periods" of postnatal life affects the organization of the mammalian neocortex at the resolution of neuronal cell types is poorly understood. We previously reported that the functional and molecular profiles of layer 2/3 (L2/3) cell types in the primary visual cortex (V1) are vision-dependent [S. Cheng et al., Cell 185, 311-327.e24 (2022)]. Here, we characterize the spatial organization of L2/3 cell types with and without visual experience. Spatial transcriptomic profiling based on 500 genes recapitulates the zonation of L2/3 cell types along the pial-ventricular axis in V1. By applying multitasking theory, we suggest that the spatial zonation of L2/3 cell types is linked to the continuous nature of their gene expression profiles, which can be represented as a 2D manifold bounded by three archetypal cell types. By comparing normally reared and dark reared L2/3 cells, we show that visual deprivation-induced transcriptomic changes comprise two independent gene programs. The first, induced specifically in the visual cortex, includes immediate-early genes and genes associated with metabolic processes. It manifests as a change in cell state that is orthogonal to cell-type-specific gene expression programs. By contrast, the second program impacts L2/3 cell-type identity, regulating a subset of cell-type-specific genes and shifting the distribution of cells within the L2/3 cell-type manifold. Through an integrated analysis of spatial transcriptomics with single-nucleus RNA-seq data, we describe how vision patterns cortical L2/3 cell types during the critical period.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)51 Physical Sciences (for-2020)Neurosciences (rcdc)Human Genome (rcdc)Eye Disease and Disorders of Vision (rcdc)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Animals (mesh)Transcriptome (mesh)Visual Cortex (mesh)Gene Expression Profiling (mesh)Neurons (mesh)Mice (mesh)VisionOcular (mesh)Primary Visual Cortex (mesh)cortex|transcriptomicsspatial transcriptomicsvisiongradientsVisual Cortex (mesh)Neurons (mesh)Animals (mesh)Mice (mesh)Gene Expression Profiling (mesh)VisionOcular (mesh)Transcriptome (mesh)Primary Visual Cortex (mesh)cortexgradientsspatial transcriptomicstranscriptomicsvisionAnimals (mesh)Transcriptome (mesh)Visual Cortex (mesh)Gene Expression Profiling (mesh)Neurons (mesh)Mice (mesh)VisionOcular (mesh)Primary Visual Cortex (mesh)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/6vq1b3pshttps://escholarship.org/content/qt6vq1b3ps/qt6vq1b3ps.pdfinfo:doi/10.1073/pnas.2421022122articleProceedings of the National Academy of Sciences of the United States of America, vol 122, iss 7e2421022122oai:escholarship.org:ark:/13030/qt4g6773bt2025-12-29T23:35:54Zqt4g6773btLoss of TLE3 promotes the mitochondrial program in beige adipocytes and improves glucose metabolismPearson, StephanieLoft, AnneRajbhandari, PrashantSimcox, JudithLee, SanghoonTontonoz, PeterMandrup, SusanneVillanueva, Claudio J2019-07-01Prolonged cold exposure stimulates the recruitment of beige adipocytes within white adipose tissue. Beige adipocytes depend on mitochondrial oxidative phosphorylation to drive thermogenesis. The transcriptional mechanisms that promote remodeling in adipose tissue during the cold are not well understood. Here we demonstrate that the transcriptional coregulator transducin-like enhancer of split 3 (TLE3) inhibits mitochondrial gene expression in beige adipocytes. Conditional deletion of TLE3 in adipocytes promotes mitochondrial oxidative metabolism and increases energy expenditure, thereby improving glucose control. Using chromatin immunoprecipitation and deep sequencing, we found that TLE3 occupies distal enhancers in proximity to nuclear-encoded mitochondrial genes and that many of these binding sites are also enriched for early B-cell factor (EBF) transcription factors. TLE3 interacts with EBF2 and blocks its ability to promote the thermogenic transcriptional program. Collectively, these studies demonstrate that TLE3 regulates thermogenic gene expression in beige adipocytes through inhibition of EBF2 transcriptional activity. Inhibition of TLE3 may provide a novel therapeutic approach for obesity and diabetes.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Obesity (rcdc)Genetics (rcdc)Nutrition (rcdc)Diabetes (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Metabolic and endocrine (hrcs-hc)AdipocytesBeige (mesh)Animals (mesh)Basic Helix-Loop-Helix Transcription Factors (mesh)CellsCultured (mesh)Co-Repressor Proteins (mesh)DietHigh-Fat (mesh)Energy Metabolism (mesh)Gene Deletion (mesh)Gene Expression Regulation (mesh)Genome-Wide Association Study (mesh)Glucose (mesh)Insulin Resistance (mesh)Male (mesh)Mice (mesh)MiceInbred C57BL (mesh)Mitochondria (mesh)Thermogenesis (mesh)adipocytesbeige adipocytesdevelopmentdiabetesmetabolismTLE3thermogenesisCellsCultured (mesh)Mitochondria (mesh)Animals (mesh)MiceInbred C57BL (mesh)Mice (mesh)Insulin Resistance (mesh)Glucose (mesh)Gene Expression Regulation (mesh)Gene Deletion (mesh)Energy Metabolism (mesh)Thermogenesis (mesh)Male (mesh)Basic Helix-Loop-Helix Transcription Factors (mesh)Genome-Wide Association Study (mesh)Co-Repressor Proteins (mesh)DietHigh-Fat (mesh)AdipocytesBeige (mesh)TLE3adipocytesbeige adipocytesdevelopmentdiabetesmetabolismthermogenesisAdipocytesBeige (mesh)Animals (mesh)Basic Helix-Loop-Helix Transcription Factors (mesh)CellsCultured (mesh)Co-Repressor Proteins (mesh)DietHigh-Fat (mesh)Energy Metabolism (mesh)Gene Deletion (mesh)Gene Expression Regulation (mesh)Genome-Wide Association Study (mesh)Glucose (mesh)Insulin Resistance (mesh)Male (mesh)Mice (mesh)MiceInbred C57BL (mesh)Mitochondria (mesh)Thermogenesis (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)17 Psychology and Cognitive Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)52 Psychology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4g6773bthttps://escholarship.org/content/qt4g6773bt/qt4g6773bt.pdfinfo:doi/10.1101/gad.321059.118articleGenes & Development, vol 33, iss 13-14747 - 762oai:escholarship.org:ark:/13030/qt35s312ff2025-12-29T22:36:35Zqt35s312ffAn activation-based high throughput screen identifies caspase-10 inhibitorsCastellón, José OYuen, ConstanceHan, BrandonAndrews, Katrina HOfori, SamuelJulio, Ashley RBoatner, Lisa MPalafox, Maria FPerumal, NitheshDamoiseaux, RobertBackus, Keriann M2025-04-02Caspases are a family of highly homologous cysteine proteases that play critical roles in inflammation and apoptosis. Small molecule inhibitors are useful tools for studying caspase biology, complementary to genetic approaches. However, achieving inhibitor selectivity for individual members of this highly homologous enzyme family remains a major challenge in developing such tool compounds. Prior studies have revealed that one strategy to tackle this selectivity gap is to target the precursor or zymogen forms of individual caspases, which share reduced structural homology when compared to active proteases. To establish a screening assay that favors the discovery of zymogen-directed caspase-10 selective inhibitors, we engineered a low-background and high-activity tobacco etch virus (TEV)-activated caspase-10 protein. We then subjected this turn-on protease to a high-throughput screen of approximately 100 000 compounds, with an average Z' value of 0.58 across all plates analyzed. Counter screening, including against TEV protease, delineated bona fide procaspase-10 inhibitors. Confirmatory studies identified a class of thiadiazine-containing compounds that undergo isomerization and oxidation to generate cysteine-reactive compounds with caspase-10 inhibitory activity. In parallel, mode-of-action studies revealed that pifithrin-μ (PFTμ), a reported TP53 inhibitor, also functions as a promiscuous caspase inhibitor. Both inhibitor classes showed preferential zymogen inhibition. Given the generalized utility of activation assays, we expect our screening platform to have widespread applications in identifying state-specific protease inhibitors.3404 Medicinal and Biomolecular Chemistry (for-2020)34 Chemical Sciences (for-2020)5.1 Pharmaceuticals (hrcs-rac)3404 Medicinal and biomolecular chemistry (for-2020)application/pdfCC-BY-NCeScholarship, University of Californiahttps://escholarship.org/uc/item/35s312ffhttps://escholarship.org/content/qt35s312ff/qt35s312ff.pdfinfo:doi/10.1039/d5cb00017carticleRSC Chemical Biology, vol 6, iss 4604 - 617oai:escholarship.org:ark:/13030/qt59j9f1pz2025-12-29T22:22:39Zqt59j9f1pzRefined Molecular Structure of Pig Pancreatic α-Amylase at 2·1 Å ResolutionLarson, Steven BGreenwood, AaronCascio, DuilioDay, JohnMcPherson, Alexander1994-02-01The structure of pig pancreatic alpha-amylase has been determined by X-ray diffraction analysis using multiple isomorphous replacement in a crystal of space group P2(1)2(1)2(1) (a = 70.6 A, b = 114.8 A, c = 118.8 A) containing nearly 75% solvent. The structure was refined by simulated annealing and Powell minimization, as monitored by 2Fo-Fc difference Fourier syntheses, to a conventional R of 0.168 at 2.1 A resolution. The final model consists of all 496 amino acid residues, a chloride and a calcium ion, 145 water molecules and an endogenous disaccharide molecule that contiguously links protein molecules related by the 2(1) crystallographic operator along x. The protein is composed of a large domain (amino acid residues 1 to 403) featuring a central alpha ta-barrel of eight parallel strands and connecting helices with a prominent excursion between strand beta 3 and helix alpha 3 (amino acid residues 100 to 168). The final 93 amino acid residues at the carboxyl terminus form a second small domain consisting of a compact Greek key beta-barrel. The domains are tightly associated through hydrophobic interfaces. The beta 3/alpha 3 excursion and portions of the central alpha/beta-barrel provide four protein ligands to the tightly bound Ca ion; three water molecules complete the coordination. The Cl- ion is bound within one end of the alpha/beta-barrel by two arginine residues in a manner suggesting a plausible mechanism for its allosteric activation of the enzyme. A crystalline complex of the pancreatic alpha-amylase with alpha-cyclodextrin, a cyclic substrate analog of six glucose residues, reveals, in difference Fourier maps, three unique binding sites. One of the alpha-cyclodextrin sites is near the center of the long polysaccharide binding cleft that traverses one end of the alpha/beta-barrel, another is at the extreme of this cleft. By symmetry this can also be considered as two half sites located at the extremes of the active site cleft. This latter alpha-cyclodextrin displaces the endogenous disaccharide when it binds and, along with the first sugar ring, delineates the extended starch binding site. The third alpha-cyclodextrin binds at an "accessory site" near the edge of the protein and is quite distant from the polysaccharide binding cleft. Its presence explains the multivalency of alpha-amylase binding to dextrins in solution. The extended active site cleft is formed by large, sweeping, connecting loops at one end of the alpha/beta-barrel. These include three sequence segments that are highly conserved among alpha-amylases.(ABSTRACT TRUNCATED AT 400 WORDS)3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Animals (mesh)Binding Sites (mesh)Calcium (mesh)Chlorides (mesh)Computer Graphics (mesh)Crystallization (mesh)CrystallographyX-Ray (mesh)Disaccharides (mesh)Hydrogen Bonding (mesh)ModelsMolecular (mesh)Pancreas (mesh)Protein Conformation (mesh)Protein StructureSecondary (mesh)Swine (mesh)alpha-Amylases (mesh)ALPHA-AMYLASEX-RAY STRUCTURECALCIUM IONALPHA/BETA-BARRELCHLORIDE IONPancreas (mesh)Animals (mesh)Swine (mesh)Chlorides (mesh)Calcium (mesh)Disaccharides (mesh)Crystallization (mesh)CrystallographyX-Ray (mesh)Binding Sites (mesh)Protein Conformation (mesh)Protein StructureSecondary (mesh)Hydrogen Bonding (mesh)ModelsMolecular (mesh)Computer Graphics (mesh)alpha-Amylases (mesh)Animals (mesh)Binding Sites (mesh)Calcium (mesh)Chlorides (mesh)Computer Graphics (mesh)Crystallization (mesh)CrystallographyX-Ray (mesh)Disaccharides (mesh)Hydrogen Bonding (mesh)ModelsMolecular (mesh)Pancreas (mesh)Protein Conformation (mesh)Protein StructureSecondary (mesh)Swine (mesh)alpha-Amylases (mesh)0304 Medicinal and Biomolecular Chemistry (for)0601 Biochemistry and Cell Biology (for)0605 Microbiology (for)Biochemistry & Molecular Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)3107 Microbiology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/59j9f1pzhttps://escholarship.org/content/qt59j9f1pz/qt59j9f1pz.pdfinfo:doi/10.1006/jmbi.1994.1107articleJournal of Molecular Biology, vol 235, iss 51560 - 1584oai:escholarship.org:ark:/13030/qt1kd335d12025-12-29T20:54:53Zqt1kd335d1The 2024 challenges in structural biology summitNannenga, Brent LGonen, Tamir2025-07-01In October 2024, the Challenges in Structural Biology Summit was held at the UCLA Lake Arrowhead Lodge. The meeting focused on new advancements and methods developments in structural biology. Here, we briefly summarize the 2024 Challenges in Structural Biology Summit.5107 Particle and High Energy Physics (for-2020)34 Chemical Sciences (for-2020)3406 Physical Chemistry (for-2020)51 Physical Sciences (for-2020)5104 Condensed Matter Physics (for-2020)3406 Physical chemistry (for-2020)5104 Condensed matter physics (for-2020)5107 Particle and high energy physics (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/1kd335d1https://escholarship.org/content/qt1kd335d1/qt1kd335d1.pdfinfo:doi/10.1063/4.0000752articleStructural Dynamics, vol 12, iss 4040901oai:escholarship.org:ark:/13030/qt3g79735q2025-12-29T18:44:56Zqt3g79735qMicroED Structures of Fluticasone Furoate and Fluticasone Propionate Provide New Insights into Their FunctionLin, JieyeUnge, JohanGonen, Tamir2025-03-05The detailed understanding of the conformational pathway of fluticasone, a widely prescribed medicine for allergic rhinitis, asthma, and chronic obstructive pulmonary disease (COPD), from formulation to its protein-bound state, has been limited due to a lack of access to its high-resolution structures. The three-dimensional (3D) structure of fluticasone furoate 1 remains unpublished, and the deposited structure of fluticasone propionate 2 could be further refined due to refinement against new data. We applied microcrystal electron diffraction (MicroED) to determine the 3D structures of 1 and 2 in their solid states. The preferred geometries in solution were predicted by using density functional theory (DFT) calculations. A comparative analysis of the structures of 1 and 2 across three states (in solid state, in solution, and protein-bound conformation) revealed the course of the conformational changes during the entire transition. Potential energy plots were calculated for the most dynamic bonds, uncovering their rotational barriers. This study underscores the combined use of MicroED and DFT calculations to provide a comprehensive understanding of conformational and energy changes during drug administration. The quantitative comparison also highlights the subtle structural differences that may lead to significant changes in the pharmaceutical properties.34 Chemical Sciences (for-2020)3406 Physical Chemistry (for-2020)2.1 Biological and endogenous factors (hrcs-rac)0302 Inorganic Chemistry (for)0306 Physical Chemistry (incl. Structural) (for)0912 Materials Engineering (for)Inorganic & Nuclear Chemistry (science-metrix)3402 Inorganic chemistry (for-2020)3406 Physical chemistry (for-2020)4016 Materials engineering (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/3g79735qhttps://escholarship.org/content/qt3g79735q/qt3g79735q.pdfinfo:doi/10.1021/acs.cgd.4c01683articleCrystal Growth & Design, vol 25, iss 51588 - 1596oai:escholarship.org:ark:/13030/qt9185g8gj2025-12-29T18:04:18Zqt9185g8gjHistone H3 lysine 4 methylation recruits DNA demethylases to enforce gene expression in ArabidopsisWang, MingHe, YanZhong, ZhenhuiPapikian, AshotWang, ShuyaGardiner, JasonGhoshal, BasudevFeng, SuhuaJami-Alahmadi, YasamanWohlschlegel, James AJacobsen, Steven E2025-02-01Patterning of DNA methylation in eukaryotic genomes is controlled by de novo methylation, maintenance mechanisms and demethylation pathways. In Arabidopsis thaliana, DNA demethylation enzymes are clearly important for shaping methylation patterns, but how they are regulated is poorly understood. Here we show that the targeting of histone H3 lysine four trimethylation (H3K4me3) with the catalytic domain of the SDG2 histone methyltransferase potently erased DNA methylation and gene silencing at FWA and also erased CG DNA methylation in many other regions of the Arabidopsis genome. This methylation erasure was completely blocked in the ros1 dml2 dml3 triple mutant lacking DNA demethylation enzymes, showing that H3K4me3 promotes the active removal of DNA methylation. Conversely, we found that the targeted removal of H3K4me3 increased the efficiency of targeted DNA methylation. These results highlight H3K4me3 as a potent anti-DNA methylation mark and also pave the way for development of more powerful epigenome engineering tools.3108 Plant Biology (for-2020)31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)3105 Genetics (for-2020)Human Genome (rcdc)Genetics (rcdc)Arabidopsis (mesh)Histones (mesh)DNA Methylation (mesh)Arabidopsis Proteins (mesh)Gene Expression RegulationPlant (mesh)Lysine (mesh)Methylation (mesh)Histone-Lysine N-Methyltransferase (mesh)Histone Demethylases (mesh)Arabidopsis (mesh)Histone-Lysine N-Methyltransferase (mesh)Lysine (mesh)Histones (mesh)Arabidopsis Proteins (mesh)DNA Methylation (mesh)Gene Expression RegulationPlant (mesh)Methylation (mesh)Histone Demethylases (mesh)Arabidopsis (mesh)Histones (mesh)DNA Methylation (mesh)Arabidopsis Proteins (mesh)Gene Expression RegulationPlant (mesh)Lysine (mesh)Methylation (mesh)Histone-Lysine N-Methyltransferase (mesh)Histone Demethylases (mesh)0607 Plant Biology (for)0703 Crop and Pasture Production (for)3103 Ecology (for-2020)3108 Plant biology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/9185g8gjhttps://escholarship.org/content/qt9185g8gj/qt9185g8gj.pdfinfo:doi/10.1038/s41477-025-01924-yarticleNature Plants, vol 11, iss 2206 - 217oai:escholarship.org:ark:/13030/qt1jm3x7902025-12-29T13:57:24Zqt1jm3x790RDH12 allows cone photoreceptors to regenerate opsin visual pigments from a chromophore precursor to escape competition with rodsKaylor, Joanna JFrederiksen, RikardBedrosian, Christina KHuang, MelodyStennis-Weatherspoon, DavidHuynh, TheodoreNgan, TiffanyMulamreddy, VarshaSampath, Alapakkam PFain, Gordon LTravis, Gabriel H2024-08-01Capture of a photon by an opsin visual pigment isomerizes its 11-cis-retinaldehyde (11cRAL) chromophore to all-trans-retinaldehyde (atRAL), which subsequently dissociates. To restore light sensitivity, the unliganded apo-opsin combines with another 11cRAL to make a new visual pigment. Two enzyme pathways supply chromophore to photoreceptors. The canonical visual cycle in retinal pigment epithelial cells supplies 11cRAL at low rates. The photic visual cycle in Müller cells supplies cones with 11-cis-retinol (11cROL) chromophore precursor at high rates. Although rods can only use 11cRAL to regenerate rhodopsin, cones can use 11cRAL or 11cROL to regenerate cone visual pigments. We performed a screen in zebrafish retinas and identified ZCRDH as a candidate for the enzyme that converts 11cROL to 11cRAL in cone inner segments. Retinoid analysis of eyes from Zcrdh-mutant zebrafish showed reduced 11cRAL and increased 11cROL levels, suggesting impaired conversion of 11cROL to 11cRAL. By microspectrophotometry, isolated Zcrdh-mutant cones lost the capacity to regenerate visual pigments from 11cROL. ZCRDH therefore possesses all predicted properties of the cone 11cROL dehydrogenase. The human protein most similar to ZCRDH is RDH12. By immunocytochemistry, ZCRDH was abundantly present in cone inner segments, similar to the reported distribution of RDH12. Finally, RDH12 was the only mammalian candidate protein to exhibit 11cROL-oxidase catalytic activity. These observations suggest that RDH12 in mammals is the functional ortholog of ZCRDH, which allows cones, but not rods, to regenerate visual pigments from 11cROL provided by Müller cells. This capacity permits cones to escape competition from rods for visual chromophore in daylight-exposed retinas.31 Biological Sciences (for-2020)32 Biomedical and Clinical Sciences (for-2020)3212 Ophthalmology and Optometry (for-2020)Eye Disease and Disorders of Vision (rcdc)Neurosciences (rcdc)Eye (hrcs-hc)Animals (mesh)Humans (mesh)Alcohol Oxidoreductases (mesh)Opsins (mesh)Retinal Cone Photoreceptor Cells (mesh)Retinal Pigments (mesh)Retinal Rod Photoreceptor Cells (mesh)Retinaldehyde (mesh)Zebrafish (mesh)Zebrafish Proteins (mesh)Animals (mesh)Zebrafish (mesh)Humans (mesh)Retinaldehyde (mesh)Alcohol Oxidoreductases (mesh)Retinal Pigments (mesh)Zebrafish Proteins (mesh)Retinal Rod Photoreceptor Cells (mesh)Retinal Cone Photoreceptor Cells (mesh)Opsins (mesh)RDH12cone photoreceptordehydrogenaseretinalvisionvisual cyclezebrafishAnimals (mesh)Humans (mesh)Alcohol Oxidoreductases (mesh)Opsins (mesh)Retinal Cone Photoreceptor Cells (mesh)Retinal Pigments (mesh)Retinal Rod Photoreceptor Cells (mesh)Retinaldehyde (mesh)Zebrafish (mesh)Zebrafish Proteins (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)17 Psychology and Cognitive Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)52 Psychology (for-2020)application/pdfCC-BY-NCeScholarship, University of Californiahttps://escholarship.org/uc/item/1jm3x790https://escholarship.org/content/qt1jm3x790/qt1jm3x790.pdfinfo:doi/10.1016/j.cub.2024.06.031articleCurrent Biology, vol 34, iss 153342 - 3353.e6oai:escholarship.org:ark:/13030/qt9ww4h6kp2025-12-29T13:56:53Zqt9ww4h6kpAre Internal Fragments Observable in Electron Based Top-Down Mass Spectrometry?Mikawy, Neven NRojas Ramírez, CarolinaDeFiglia, Steven ASzot, Carson WLe, JessieLantz, CarterWei, BenqianZenaidee, Muhammad ABlakney, Greg TNesvizhskii, Alexey ILoo, Joseph ARuotolo, Brandon TShabanowitz, JeffreyAnderson, Lissa CHåkansson, Kristina2024-09-01Protein tandem mass spectrometry (MS/MS) often generates sequence-informative fragments from backbone bond cleavages near the termini. This lack of fragmentation in the protein interior is particularly apparent in native top-down mass spectrometry (MS). Improved sequence coverage, critical for reliable annotation of posttranslational modifications and sequence variants, may be obtained from internal fragments generated by multiple backbone cleavage events. However, internal fragment assignments can be error prone due to isomeric/isobaric fragments from different parts of a protein sequence. Also, internal fragment generation propensity depends on the chosen MS/MS activation strategy. Here, we examine internal fragment formation in electron capture dissociation (ECD) and electron transfer dissociation (ETD) following native and denaturing MS, as well as LC/MS of several proteins. Experiments were undertaken on multiple instruments, including quadrupole time-of-flight, Orbitrap, and high-field Fourier-transform ion cyclotron resonance (FT-ICR) across four laboratories. ECD was performed at both ultrahigh vacuum and at similar pressure to ETD conditions. Two complementary software packages were used for data analysis. When feasible, ETD-higher energy collision dissociation MS3 was performed to validate/refute potential internal fragment assignments, including differentiating MS3 fragmentation behavior of radical versus even-electron primary fragments. We show that, under typical operating conditions, internal fragments cannot be confidently assigned in ECD or ETD. On the other hand, such fragments, along with some b-type terminal fragments (not typically observed in ECD/ETD spectra) appear at atypical ECD operating conditions, suggesting they originate from a separate ion-electron activation process. Furthermore, atypical fragment ion types, e.g., x ions, are observed at such conditions as well as upon EThcD, presumably due to vibrational activation of radical z-type ions.3401 Analytical Chemistry (for-2020)34 Chemical Sciences (for-2020)3406 Physical Chemistry (for-2020)Tandem Mass Spectrometry (mesh)Electrons (mesh)Amino Acid Sequence (mesh)Software (mesh)ChromatographyLiquid (mesh)Proteins (mesh)Peptide Fragments (mesh)Mass Spectrometry (mesh)Fourier Analysis (mesh)Peptide Fragments (mesh)Proteins (mesh)ChromatographyLiquid (mesh)Amino Acid Sequence (mesh)Fourier Analysis (mesh)Electrons (mesh)Software (mesh)Mass Spectrometry (mesh)Tandem Mass Spectrometry (mesh)electron capture dissociation (ECD)electron transfer dissociation (ETD)internal fragmentsnative mass spectrometrytop-down mass spectrometry (TD-MS)Tandem Mass Spectrometry (mesh)Electrons (mesh)Amino Acid Sequence (mesh)Software (mesh)ChromatographyLiquid (mesh)Proteins (mesh)Peptide Fragments (mesh)Mass Spectrometry (mesh)Fourier Analysis (mesh)Biochemistry & Molecular Biology (science-metrix)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/9ww4h6kphttps://escholarship.org/content/qt9ww4h6kp/qt9ww4h6kp.pdfinfo:doi/10.1016/j.mcpro.2024.100814articleMolecular & Cellular Proteomics, vol 23, iss 9100814oai:escholarship.org:ark:/13030/qt6bv8c5kb2025-12-29T11:03:48Zqt6bv8c5kbFunctionalizing tandem mass tags for streamlining click-based quantitative chemoproteomicsBurton, Nikolas RBackus, Keriann M2024-01-01Mapping the ligandability or potential druggability of all proteins in the human proteome is a central goal of mass spectrometry-based covalent chemoproteomics. Achieving this ambitious objective requires high throughput and high coverage sample preparation and liquid chromatography-tandem mass spectrometry analysis for hundreds to thousands of reactive compounds and chemical probes. Conducting chemoproteomic screens at this scale benefits from technical innovations that achieve increased sample throughput. Here we realize this vision by establishing the silane-based cleavable linkers for isotopically-labeled proteomics-tandem mass tag (sCIP-TMT) proteomic platform, which is distinguished by early sample pooling that increases sample preparation throughput. sCIP-TMT pairs a custom click-compatible sCIP capture reagent that is readily functionalized in high yield with commercially available TMT reagents. Synthesis and benchmarking of a 10-plex set of sCIP-TMT reveal a substantial decrease in sample preparation time together with high coverage and high accuracy quantification. By screening a focused set of four cysteine-reactive electrophiles, we demonstrate the utility of sCIP-TMT for chemoproteomic target hunting, identifying 789 total liganded cysteines. Distinguished by its compatibility with established enrichment and quantification protocols, we expect sCIP-TMT will readily translate to a wide range of covalent chemoproteomic applications.3401 Analytical Chemistry (for-2020)34 Chemical Sciences (for-2020)34 Chemical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/6bv8c5kbhttps://escholarship.org/content/qt6bv8c5kb/qt6bv8c5kb.pdfinfo:doi/10.1038/s42004-024-01162-xarticleCommunications Chemistry, vol 7, iss 180oai:escholarship.org:ark:/13030/qt6655r3x52025-12-29T10:42:54Zqt6655r3x5Reprogramming of the LXRα Transcriptome Sustains Macrophage Secondary Inflammatory Responsesde la Rosa, Juan VladimirTabraue, CarlosHuang, ZhiqiangOrizaola, Marta CMartin‐Rodríguez, PatriciaSteffensen, Knut RZapata, Juan ManuelBoscá, LisardoTontonoz, PeterAlemany, SusanaTreuter, EckardtCastrillo, Antonio2024-05-01Macrophages regulate essential aspects of innate immunity against pathogens. In response to microbial components, macrophages activate primary and secondary inflammatory gene programs crucial for host defense. The liver X receptors (LXRα, LXRβ) are ligand-dependent nuclear receptors that direct gene expression important for cholesterol metabolism and inflammation, but little is known about the individual roles of LXRα and LXRβ in antimicrobial responses. Here, the results demonstrate that induction of LXRα transcription by prolonged exposure to lipopolysaccharide (LPS) supports inflammatory gene expression in macrophages. LXRα transcription is induced by NF-κB and type-I interferon downstream of TLR4 activation. Moreover, LPS triggers a reprogramming of the LXRα cistrome that promotes cytokine and chemokine gene expression through direct LXRα binding to DNA consensus sequences within cis-regulatory regions including enhancers. LXRα-deficient macrophages present fewer binding of p65 NF-κB and reduced histone H3K27 acetylation at enhancers of secondary inflammatory response genes. Mice lacking LXRα in the hematopoietic compartment show impaired responses to bacterial endotoxin in peritonitis models, exhibiting reduced neutrophil infiltration and decreased expansion and inflammatory activation of recruited F4/80lo-MHC-IIhi peritoneal macrophages. Together, these results uncover a previously unrecognized function for LXRα-dependent transcriptional cis-activation of secondary inflammatory gene expression in macrophages and the host response to microbial ligands.3107 Microbiology (for-2020)31 Biological Sciences (for-2020)32 Biomedical and Clinical Sciences (for-2020)Emerging Infectious Diseases (rcdc)Biodefense (rcdc)Infectious Diseases (rcdc)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Infection (hrcs-hc)Inflammatory and immune system (hrcs-hc)Animals (mesh)Mice (mesh)Disease ModelsAnimal (mesh)Inflammation (mesh)Lipopolysaccharides (mesh)Liver X Receptors (mesh)Macrophages (mesh)MiceInbred C57BL (mesh)Transcriptome (mesh)gene expressioninflammationmacrophagenuclear receptor LXRMacrophages (mesh)Animals (mesh)MiceInbred C57BL (mesh)Mice (mesh)Disease ModelsAnimal (mesh)Inflammation (mesh)Lipopolysaccharides (mesh)Transcriptome (mesh)Liver X Receptors (mesh)gene expressioninflammationmacrophagenuclear receptor LXRAnimals (mesh)Mice (mesh)Disease ModelsAnimal (mesh)Inflammation (mesh)Lipopolysaccharides (mesh)Liver X Receptors (mesh)Macrophages (mesh)MiceInbred C57BL (mesh)Transcriptome (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/6655r3x5https://escholarship.org/content/qt6655r3x5/qt6655r3x5.pdfinfo:doi/10.1002/advs.202307201articleAdvanced Science, vol 11, iss 202307201oai:escholarship.org:ark:/13030/qt5xs2g4st2025-12-29T10:26:25Zqt5xs2g4stAlphaFold-assisted structure determination of a bacterial protein of unknown function using X-ray and electron crystallographyMiller, Justin EAgdanowski, Matthew PDolinsky, Joshua LSawaya, Michael RCascio, DuilioRodriguez, Jose AYeates, Todd O2024-04-01Macromolecular crystallography generally requires the recovery of missing phase information from diffraction data to reconstruct an electron-density map of the crystallized molecule. Most recent structures have been solved using molecular replacement as a phasing method, requiring an a priori structure that is closely related to the target protein to serve as a search model; when no such search model exists, molecular replacement is not possible. New advances in computational machine-learning methods, however, have resulted in major advances in protein structure predictions from sequence information. Methods that generate predicted structural models of sufficient accuracy provide a powerful approach to molecular replacement. Taking advantage of these advances, AlphaFold predictions were applied to enable structure determination of a bacterial protein of unknown function (UniProtKB Q63NT7, NCBI locus BPSS0212) based on diffraction data that had evaded phasing attempts using MIR and anomalous scattering methods. Using both X-ray and micro-electron (microED) diffraction data, it was possible to solve the structure of the main fragment of the protein using a predicted model of that domain as a starting point. The use of predicted structural models importantly expands the promise of electron diffraction, where structure determination relies critically on molecular replacement.3101 Biochemistry and Cell Biology (for-2020)34 Chemical Sciences (for-2020)31 Biological Sciences (for-2020)1.4 Methodologies and measurements (hrcs-rac)Generic health relevance (hrcs-hc)Bacterial Proteins (mesh)X-Rays (mesh)Electrons (mesh)Protein Conformation (mesh)CrystallographyX-Ray (mesh)electron diffractionprotein structure predictionAlphaFoldbacterial proteinsmolecular replacementBacterial Proteins (mesh)CrystallographyX-Ray (mesh)Protein Conformation (mesh)Electrons (mesh)X-Rays (mesh)AlphaFoldbacterial proteinselectron diffractionmolecular replacementprotein structure predictionBacterial Proteins (mesh)X-Rays (mesh)Electrons (mesh)Protein Conformation (mesh)CrystallographyX-Ray (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/5xs2g4sthttps://escholarship.org/content/qt5xs2g4st/qt5xs2g4st.pdfinfo:doi/10.1107/s205979832400072xarticleActa Crystallographica Section D, Structural Biology, vol 80, iss Pt 4270 - 278oai:escholarship.org:ark:/13030/qt70z6b7ff2025-12-29T09:59:59Zqt70z6b7ffNeural activity in cortico-basal ganglia circuits of juvenile songbirds encodes performance during goal-directed learningAchiro, Jennifer MShen, JohnBottjer, Sarah W2017-01-01Cortico-basal ganglia circuits are thought to mediate goal-directed learning by a process of outcome evaluation to gradually select appropriate motor actions. We investigated spiking activity in core and shell subregions of the cortical nucleus LMAN during development as juvenile zebra finches are actively engaged in evaluating feedback of self-generated behavior in relation to their memorized tutor song (the goal). Spiking patterns of single neurons in both core and shell subregions during singing correlated with acoustic similarity to tutor syllables, suggesting a process of outcome evaluation. Both core and shell neurons encoded tutor similarity via either increases or decreases in firing rate, although only shell neurons showed a significant association at the population level. Tutor similarity predicted firing rates most strongly during early stages of learning, and shell but not core neurons showed decreases in response variability across development, suggesting that the activity of shell neurons reflects the progression of learning.32 Biomedical and Clinical Sciences (for-2020)3209 Neurosciences (for-2020)Behavioral and Social Science (rcdc)Neurosciences (rcdc)Basic Behavioral and Social Science (rcdc)Action Potentials (mesh)Animals (mesh)Basal Ganglia (mesh)Cerebral Cortex (mesh)Electroencephalography (mesh)Finches (mesh)Learning (mesh)Neural Pathways (mesh)VocalizationAnimal (mesh)Basal Ganglia (mesh)Cerebral Cortex (mesh)Neural Pathways (mesh)Animals (mesh)Finches (mesh)Electroencephalography (mesh)VocalizationAnimal (mesh)Learning (mesh)Action Potentials (mesh)action selectionbasal ganglianeuroscienceoutcome evaluationprocedural learningreinforcement learningsongbirdAction Potentials (mesh)Animals (mesh)Basal Ganglia (mesh)Cerebral Cortex (mesh)Electroencephalography (mesh)Finches (mesh)Learning (mesh)Neural Pathways (mesh)VocalizationAnimal (mesh)0601 Biochemistry and Cell Biology (for)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/70z6b7ffhttps://escholarship.org/content/qt70z6b7ff/qt70z6b7ff.pdfinfo:doi/10.7554/elife.26973articleeLife, vol 6e26973oai:escholarship.org:ark:/13030/qt8qr1712g2025-12-29T09:21:21Zqt8qr1712gAging differentially alters the transcriptome and landscape of chromatin accessibility in the male and female mouse hippocampusAchiro, Jennifer MTao, YangGao, FuyingLin, Chia-HoWatanabe, MarikaNeumann, SylviaCoppola, GiovanniBlack, Douglas LMartin, Kelsey C2024-01-01Aging-related memory impairment and pathological memory disorders such as Alzheimer's disease differ between males and females, and yet little is known about how aging-related changes in the transcriptome and chromatin environment differ between sexes in the hippocampus. To investigate this question, we compared the chromatin accessibility landscape and gene expression/alternative splicing pattern of young adult and aged mouse hippocampus in both males and females using ATAC-seq and RNA-seq. We detected significant aging-dependent changes in the expression of genes involved in immune response and synaptic function and aging-dependent changes in the alternative splicing of myelin sheath genes. We found significant sex-bias in the expression and alternative splicing of hundreds of genes, including aging-dependent female-biased expression of myelin sheath genes and aging-dependent male-biased expression of genes involved in synaptic function. Aging was associated with increased chromatin accessibility in both male and female hippocampus, especially in repetitive elements, and with an increase in LINE-1 transcription. We detected significant sex-bias in chromatin accessibility in both autosomes and the X chromosome, with male-biased accessibility enriched at promoters and CpG-rich regions. Sex differences in gene expression and chromatin accessibility were amplified with aging, findings that may shed light on sex differences in aging-related and pathological memory loss.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)3105 Genetics (for-2020)Genetics (rcdc)Dementia (rcdc)Neurodegenerative (rcdc)Human Genome (rcdc)Acquired Cognitive Impairment (rcdc)Neurosciences (rcdc)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)Aging (rcdc)Brain Disorders (rcdc)Alzheimer's Disease (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Neurological (hrcs-hc)agingsex biashippocampusgene expressionalternative splicingATAC-seqchromatin accessibilityLINE-1ATAC-seqLINE-1agingalternative splicingchromatin accessibilitygene expressionhippocampussex bias1103 Clinical Sciences (for)1109 Neurosciences (for)3101 Biochemistry and cell biology (for-2020)3209 Neurosciences (for-2020)5202 Biological psychology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/8qr1712ghttps://escholarship.org/content/qt8qr1712g/qt8qr1712g.pdfinfo:doi/10.3389/fnmol.2024.1334862articleFrontiers in Molecular Neuroscience, vol 171334862oai:escholarship.org:ark:/13030/qt6vm0727s2025-12-29T08:38:00Zqt6vm0727sA Mouse Model with a Frameshift Mutation in the Nuclear Factor I/X (NFIX) Gene Has Phenotypic Features of Marshall Smith SyndromeKooblall, Kreepa GStevenson, MarkStewart, MichelleHarris, LachlanZalucki, OressiaDewhurst, HannahButterfield, NatalieLeng, HoufuHough, Tertius AMa, DaSiow, BernardPotter, PaulCox, Roger DBrown, Stephen DMHorwood, NicoleWright, BenjaminLockstone, HelenBuck, DavidVincent, Tonia LHannan, Fadil MBassett, JH DuncanWilliams, Graham RLines, Kate EPiper, MichaelWells, SaraTeboul, LydiaHennekam, Raoul CThakker, Rajesh V2023-06-01The nuclear factor I/X (NFIX) gene encodes a ubiquitously expressed transcription factor whose mutations lead to two allelic disorders characterized by developmental, skeletal, and neural abnormalities, namely, Malan syndrome (MAL) and Marshall-Smith syndrome (MSS). NFIX mutations associated with MAL mainly cluster in exon 2 and are cleared by nonsense-mediated decay (NMD) leading to NFIX haploinsufficiency, whereas NFIX mutations associated with MSS are clustered in exons 6-10 and escape NMD and result in the production of dominant-negative mutant NFIX proteins. Thus, different NFIX mutations have distinct consequences on NFIX expression. To elucidate the in vivo effects of MSS-associated NFIX exon 7 mutations, we used CRISPR-Cas9 to generate mouse models with exon 7 deletions that comprised: a frameshift deletion of two nucleotides (Nfix Del2); in-frame deletion of 24 nucleotides (Nfix Del24); and deletion of 140 nucleotides (Nfix Del140). Nfix +/Del2, Nfix +/Del24, Nfix +/Del140, Nfix Del24/Del24, and Nfix Del140/Del140 mice were viable, normal, and fertile, with no skeletal abnormalities, but Nfix Del2/Del2 mice had significantly reduced viability (p < 0.002) and died at 2-3 weeks of age. Nfix Del2 was not cleared by NMD, and NfixDel2/Del2 mice, when compared to Nfix +/+ and Nfix +/Del2 mice, had: growth retardation; short stature with kyphosis; reduced skull length; marked porosity of the vertebrae with decreased vertebral and femoral bone mineral content; and reduced caudal vertebrae height and femur length. Plasma biochemistry analysis revealed Nfix Del2/Del2 mice to have increased total alkaline phosphatase activity but decreased C-terminal telopeptide and procollagen-type-1-N-terminal propeptide concentrations compared to Nfix +/+ and Nfix +/Del2 mice. Nfix Del2/Del2 mice were also found to have enlarged cerebral cortices and ventricular areas but smaller dentate gyrus compared to Nfix +/+ mice. Thus, Nfix Del2/Del2 mice provide a model for studying the in vivo effects of NFIX mutants that escape NMD and result in developmental abnormalities of the skeletal and neural tissues that are associated with MSS. © 2023 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.3213 Paediatrics (for-2020)32 Biomedical and Clinical Sciences (for-2020)Genetics (rcdc)Rare Diseases (rcdc)Neurosciences (rcdc)2.1 Biological and endogenous factors (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)Musculoskeletal (hrcs-hc)NFIXkyphosisosteopeniabrain abnormalitiesframeshift mutationNFIXbrain abnormalitiesframeshift mutationkyphosisosteopenia32 Biomedical and clinical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/6vm0727shttps://escholarship.org/content/qt6vm0727s/qt6vm0727s.pdfinfo:doi/10.1002/jbm4.10739articleJBMR Plus, vol 7, iss 6e10739oai:escholarship.org:ark:/13030/qt87q7w0212025-12-29T08:37:57Zqt87q7w021Blocking glycosphingolipid production alters autophagy in osteoclasts and improves myeloma bone diseaseLeng, HoufuSimon, Anna KatharinaHorwood, Nicole J2024-04-02Glycosphingolipids (GSLs) are key constituents of membrane bilayers playing a role in structural integrity, cell signalling in microdomains, endosomes and lysosomes, and cell death pathways. Conversion of ceramide into GSLs is controlled by GCS (glucosylceramide synthase) and inhibitors of this enzyme for the treatment of lipid storage disorders and specific cancers. With a diverse range of functions attributed to GSLs, the ability of the GSC inhibitor, eliglustat, to reduce myeloma bone disease was investigated. In pre-clinical models of multiple myeloma, osteoclast-driven bone loss was reduced by eliglustat in a mechanistically separate manner to zoledronic acid, a bisphosphonate that prevents osteoclast-mediated bone destruction. Autophagic degradation of TNF receptor-associated factor 3 (TRAF3), a key step for osteoclast differentiation, was inhibited by eliglustat as evidenced by TRAF3 lysosomal and cytoplasmic accumulation. By altering GSL composition, eliglustat prevented lysosomal degradation whilst exogenous addition of missing GSLs rescued TRAF3 degradation to restore osteoclast formation in bone marrow cells from myeloma patients. This work highlights the clinical potential of eliglustat as a therapy for myeloma bone disease. Furthermore, using eliglustat as a lysosomal inhibitor in osteoclasts may widen its therapeutic uses to other bone disorders such as bone metastasis, osteoporosis and inflammatory bone loss.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Rare Diseases (rcdc)Osteoporosis (rcdc)Hematology (rcdc)2.1 Biological and endogenous factors (hrcs-rac)5.1 Pharmaceuticals (hrcs-rac)Cancer (hrcs-hc)Osteoclasts (mesh)Autophagy (mesh)Multiple Myeloma (mesh)Animals (mesh)Humans (mesh)Glycosphingolipids (mesh)Bone Diseases (mesh)Lysosomes (mesh)Mice (mesh)Pyrrolidines (mesh)Zoledronic Acid (mesh)Glucosyltransferases (mesh)AutophagyglycosphingolipidTRAF3osteoclastmultiple myelomaLysosomes (mesh)Osteoclasts (mesh)Animals (mesh)Humans (mesh)Mice (mesh)Multiple Myeloma (mesh)Bone Diseases (mesh)Pyrrolidines (mesh)Glucosyltransferases (mesh)Glycosphingolipids (mesh)Autophagy (mesh)Zoledronic Acid (mesh)AutophagyTRAF3glycosphingolipidmultiple myelomaosteoclastOsteoclasts (mesh)Autophagy (mesh)Multiple Myeloma (mesh)Animals (mesh)Humans (mesh)Glycosphingolipids (mesh)Bone Diseases (mesh)Lysosomes (mesh)Mice (mesh)Pyrrolidines (mesh)Zoledronic Acid (mesh)Glucosyltransferases (mesh)0601 Biochemistry and Cell Biology (for)Biochemistry & Molecular Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/87q7w021https://escholarship.org/content/qt87q7w021/qt87q7w021.pdfinfo:doi/10.1080/15548627.2023.2208931articleAutophagy, vol 20, iss 4930 - 932oai:escholarship.org:ark:/13030/qt4xq0f0tt2025-12-29T08:29:19Zqt4xq0f0ttMBD2 couples DNA methylation to transposable element silencing during male gametogenesisWang, ShuyaWang, MingIchino, LuciaBoone, Brandon AZhong, ZhenhuiPapareddy, Ranjith KLin, Evan KYun, JaewonFeng, SuhuaJacobsen, Steven E2024-01-01DNA methylation is an essential component of transposable element (TE) silencing, yet the mechanism by which methylation causes transcriptional repression remains poorly understood1–5. Here we study the Arabidopsis thaliana Methyl-CpG Binding Domain (MBD) proteins MBD1, MBD2 and MBD4 and show that MBD2 acts as a TE repressor during male gametogenesis. MBD2 bound chromatin regions containing high levels of CG methylation, and MBD2 was capable of silencing the FWA gene when tethered to its promoter. MBD2 loss caused activation at a small subset of TEs in the vegetative cell of mature pollen without affecting DNA methylation levels, demonstrating that MBD2-mediated silencing acts strictly downstream of DNA methylation. TE activation in mbd2 became more significant in the mbd5 mbd6 and adcp1 mutant backgrounds, suggesting that MBD2 acts redundantly with other silencing pathways to repress TEs. Overall, our study identifies MBD2 as a methyl reader that acts downstream of DNA methylation to silence TEs during male gametogenesis.31 Biological Sciences (for-2020)3105 Genetics (for-2020)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Cancer (hrcs-hc)DNA Methylation (mesh)DNA Transposable Elements (mesh)CpG Islands (mesh)Promoter RegionsGenetic (mesh)Gametogenesis (mesh)DNA Transposable Elements (mesh)Gametogenesis (mesh)DNA Methylation (mesh)CpG Islands (mesh)Promoter RegionsGenetic (mesh)DNA Methylation (mesh)DNA Transposable Elements (mesh)CpG Islands (mesh)Promoter RegionsGenetic (mesh)Gametogenesis (mesh)0607 Plant Biology (for)0703 Crop and Pasture Production (for)3103 Ecology (for-2020)3108 Plant biology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/4xq0f0tthttps://escholarship.org/content/qt4xq0f0tt/qt4xq0f0tt.pdfinfo:doi/10.1038/s41477-023-01599-3articleNature Plants, vol 10, iss 113 - 24oai:escholarship.org:ark:/13030/qt2qz526572025-12-29T07:55:51Zqt2qz52657Transcriptional and epigenetic dysregulation impairs generation of proliferative neural stem and progenitor cells during brain agingLi, MeiyangGuo, HongzhiCarey, MichaelHuang, Chengyang2024-01-01The decline in stem cell function during aging may affect the regenerative capacity of mammalian organisms; however, the gene regulatory mechanism underlying this decline remains unclear. Here we show that the aging of neural stem and progenitor cells (NSPCs) in the male mouse brain is characterized by a decrease in the generation efficacy of proliferative NSPCs rather than the changes in lineage specificity of NSPCs. We reveal that the downregulation of age-dependent genes in NSPCs drives cell aging by decreasing the population of actively proliferating NSPCs while increasing the expression of quiescence markers. We found that epigenetic deregulation of the MLL complex at promoters leads to transcriptional inactivation of age-dependent genes, highlighting the importance of the dynamic interaction between histone modifiers and gene regulatory elements in regulating transcriptional program of aging cells. Our study sheds light on the key intrinsic mechanisms driving stem cell aging through epigenetic regulators and identifies potential rejuvenation targets that could restore the function of aging stem cells.3206 Medical Biotechnology (for-2020)32 Biomedical and Clinical Sciences (for-2020)Genetics (rcdc)Stem Cell Research - Nonembryonic - Non-Human (rcdc)Stem Cell Research (rcdc)Aging (rcdc)Stem Cell Research - Nonembryonic - Human (rcdc)Neurosciences (rcdc)Regenerative Medicine (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Neurological (hrcs-hc)Animals (mesh)Mice (mesh)Male (mesh)Neural Stem Cells (mesh)Aging (mesh)Cellular Senescence (mesh)Brain (mesh)EpigenesisGenetic (mesh)Mammals (mesh)Brain (mesh)Animals (mesh)Mammals (mesh)Mice (mesh)EpigenesisGenetic (mesh)Aging (mesh)Male (mesh)Neural Stem Cells (mesh)Cellular Senescence (mesh)Animals (mesh)Mice (mesh)Male (mesh)Neural Stem Cells (mesh)Aging (mesh)Cellular Senescence (mesh)Brain (mesh)EpigenesisGenetic (mesh)Mammals (mesh)3202 Clinical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2qz52657https://escholarship.org/content/qt2qz52657/qt2qz52657.pdfinfo:doi/10.1038/s43587-023-00549-0articleNature Aging, vol 4, iss 162 - 79oai:escholarship.org:ark:/13030/qt8vg2414c2025-12-29T07:27:36Zqt8vg2414cProteostasis in T cell agingGressler, A ElisabethLeng, HoufuZinecker, HeidiSimon, Anna Katharina2023-11-01Aging leads to a decline in immune cell function, which leaves the organism vulnerable to infections and age-related multimorbidities. One major player of the adaptive immune response are T cells, and recent studies argue for a major role of disturbed proteostasis contributing to reduced function of these cells upon aging. Proteostasis refers to the state of a healthy, balanced proteome in the cell and is influenced by synthesis (translation), maintenance and quality control of proteins, as well as degradation of damaged or unwanted proteins by the proteasome, autophagy, lysosome and cytoplasmic enzymes. This review focuses on molecular processes impacting on proteostasis in T cells, and specifically functional or quantitative changes of each of these upon aging. Importantly, we describe the biological consequences of compromised proteostasis in T cells, which range from impaired T cell activation and function to enhancement of inflamm-aging by aged T cells. Finally, approaches to improve proteostasis and thus rejuvenate aged T cells through pharmacological or physical interventions are discussed.32 Biomedical and Clinical Sciences (for-2020)3204 Immunology (for-2020)Aging (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Generic health relevance (hrcs-hc)Humans (mesh)Aged (mesh)Proteostasis (mesh)T-Cell Senescence (mesh)Aging (mesh)Proteasome Endopeptidase Complex (mesh)Autophagy (mesh)ProteostasisT cellAgingTranslationDegradationInflamm-agingHumans (mesh)Proteasome Endopeptidase Complex (mesh)Aging (mesh)Aged (mesh)Autophagy (mesh)Proteostasis (mesh)T-Cell Senescence (mesh)AgingDegradationInflamm-agingProteostasisT cellTranslationHumans (mesh)Aged (mesh)Proteostasis (mesh)T-Cell Senescence (mesh)Aging (mesh)Proteasome Endopeptidase Complex (mesh)Autophagy (mesh)1107 Immunology (for)Immunology (science-metrix)3204 Immunology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/8vg2414chttps://escholarship.org/content/qt8vg2414c/qt8vg2414c.pdfinfo:doi/10.1016/j.smim.2023.101838articleSeminars in Immunology, vol 70101838oai:escholarship.org:ark:/13030/qt162319w12025-12-29T07:13:22Zqt162319w1Addition of exogenous diacylglycerol enhances Wnt/β-catenin signaling through stimulation of macropinocytosisAzbazdar, YagmurTejeda-Munoz, NydiaMonka, Julia CDayrit, AlexBinder, GraceOzhan, GunesDe Robertis, Edward M2023-10-01Activation of Wnt signaling triggers macropinocytosis and drives many tumors. We now report that the exogenous addition of the second messenger lipid sn-1,2 DAG to the culture medium rapidly induces macropinocytosis. This is accompanied by potentiation of the effects of added Wnt3a recombinant protein or the glycogen synthase kinase 3 (GSK3) inhibitor lithium chloride (LiCl, which mimics Wnt signaling) in luciferase transcriptional reporter assays. In a colorectal carcinoma cell line in which mutation of adenomatous polyposis coli (APC) causes constitutive Wnt signaling, DAG addition increased levels of nuclear β-catenin, and this increase was partially inhibited by an inhibitor of macropinocytosis. DAG also expanded multivesicular bodies marked by the tetraspan protein CD63. In an in vivo situation, microinjection of DAG induced Wnt-like twinned body axes when co-injected with small amounts of LiCl into Xenopus embryos. These results suggest that the DAG second messenger plays a role in Wnt-driven cancer progression.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Cancer (rcdc)Colo-Rectal Cancer (rcdc)Digestive Diseases (rcdc)BiomoleculesCancerPathophysiologyapplication/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/162319w1https://escholarship.org/content/qt162319w1/qt162319w1.pdfinfo:doi/10.1016/j.isci.2023.108075articleiScience, vol 26, iss 10108075oai:escholarship.org:ark:/13030/qt5fz8k8xt2025-12-29T07:11:55Zqt5fz8k8xtMetabolic sinkholes: Histones as methyl repositoriesKarimian, AnsarVogelauer, MariaKurdistani, Siavash K2023-01-01Perez and Sarkies uncover histones as methyl group repositories in normal and cancer human cells, shedding light on an intriguing function of histone methylation in optimizing the cellular methylation potential independently of gene regulation.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Cancer (rcdc)Genetics (rcdc)Biotechnology (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Cancer (hrcs-hc)Humans (mesh)Histones (mesh)Methylation (mesh)Gene Expression Regulation (mesh)Neoplasms (mesh)Histone Methyltransferases (mesh)Humans (mesh)Neoplasms (mesh)Histones (mesh)Gene Expression Regulation (mesh)Methylation (mesh)Histone Methyltransferases (mesh)Humans (mesh)Histones (mesh)Methylation (mesh)Gene Expression Regulation (mesh)Neoplasms (mesh)Histone Methyltransferases (mesh)06 Biological Sciences (for)07 Agricultural and Veterinary Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)30 Agriculturalveterinary and food sciences (for-2020)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/5fz8k8xthttps://escholarship.org/content/qt5fz8k8xt/qt5fz8k8xt.pdfinfo:doi/10.1371/journal.pbio.3002371articlePLOS Biology, vol 21, iss 10e3002371oai:escholarship.org:ark:/13030/qt6w98q56f2025-12-29T06:31:09Zqt6w98q56fThe early dorsal signal in vertebrate embryos requires endolysosomal membrane traffickingAzbazdar, YagmurDe Robertis, Edward M2024-01-01Fertilization triggers cytoplasmic movements in the frog egg that lead in mysterious ways to the stabilization of β-catenin on the dorsal side of the embryo. The novel Huluwa (Hwa) transmembrane protein, identified in China, is translated specifically in the dorsal side, acting as an egg cytoplasmic determinant essential for β-catenin stabilization. The Wnt signaling pathway requires macropinocytosis and the sequestration inside multivesicular bodies (MVBs, the precursors of endolysosomes) of Axin1 and Glycogen Synthase Kinase 3 (GSK3) that normally destroy β-catenin. In Xenopus, the Wnt-like activity of GSK3 inhibitors and of Hwa mRNA can be blocked by brief treatment with inhibitors of membrane trafficking or lysosomes at the 32-cell stage. In dorsal blastomeres, lysosomal cathepsin is activated and intriguing MVBs surrounded by electron dense vesicles are formed at the 64-cell stage. We conclude that membrane trafficking and lysosomal activity are critically important for the earliest asymmetries in vertebrate embryonic development.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Animals (mesh)beta Catenin (mesh)Glycogen Synthase Kinase 3 (mesh)Endosomes (mesh)Lysosomes (mesh)Xenopus laevis (mesh)cytoplasmic determinantsGBPgray crescentHuluwalysosomesmacropinocytosisSpemann organizerEndosomes (mesh)Lysosomes (mesh)Animals (mesh)Xenopus laevis (mesh)Glycogen Synthase Kinase 3 (mesh)beta Catenin (mesh)GBPHuluwaSpemann organizercytoplasmic determinantsgray crescentlysosomesmacropinocytosisAnimals (mesh)beta Catenin (mesh)Glycogen Synthase Kinase 3 (mesh)Endosomes (mesh)Lysosomes (mesh)Xenopus laevis (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)17 Psychology and Cognitive Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/6w98q56fhttps://escholarship.org/content/qt6w98q56f/qt6w98q56f.pdfinfo:doi/10.1002/bies.202300179articleBioEssays, vol 46, iss 1e2300179oai:escholarship.org:ark:/13030/qt9jh9b2wd2025-12-29T05:21:23Zqt9jh9b2wdUnexpected metabolic rewiring of CO2 fixation in H2-mediated materials–biology hybridsXie, YongchaoErşan, SevcanGuan, XunWang, JingyuSha, JihuiXu, ShuangningWohlschlegel, James APark, Junyoung OLiu, Chong2023-10-17A hybrid approach combining water-splitting electrochemistry and H2-oxidizing, CO2-fixing microorganisms offers a viable solution for producing value-added chemicals from sunlight, water, and air. The classic wisdom without thorough examination to date assumes that the electrochemistry in such a H2-mediated process is innocent of altering microbial behavior. Here, we report unexpected metabolic rewiring induced by water-splitting electrochemistry in H2-oxidizing acetogenic bacterium Sporomusa ovata that challenges such a classic view. We found that the planktonic S. ovata is more efficient in utilizing reducing equivalent for ATP generation in the materials-biology hybrids than cells grown with H2 supply, supported by our metabolomic and proteomic studies. The efficiency of utilizing reducing equivalents and fixing CO2 into acetate has increased from less than 80% of chemoautotrophy to more than 95% under electroautotrophic conditions. These observations unravel previously underappreciated materials' impact on microbial metabolism in seemingly simply H2-mediated charge transfer between biotic and abiotic components. Such a deeper understanding of the materials-biology interface will foster advanced design of hybrid systems for sustainable chemical transformation.31 Biological Sciences (for-2020)34 Chemical Sciences (for-2020)3406 Physical Chemistry (for-2020)Carbon Dioxide (mesh)Proteomics (mesh)Sunlight (mesh)Acetates (mesh)Water (mesh)materials-biology hybridCO2 fixationmetabolic rewiringproteomicsmetabolomicsCarbon Dioxide (mesh)Water (mesh)Acetates (mesh)Proteomics (mesh)Sunlight (mesh)CO2 fixationmaterials–biology hybridmetabolic rewiringmetabolomicsproteomicsCarbon Dioxide (mesh)Proteomics (mesh)Sunlight (mesh)Acetates (mesh)Water (mesh)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/9jh9b2wdhttps://escholarship.org/content/qt9jh9b2wd/qt9jh9b2wd.pdfinfo:doi/10.1073/pnas.2308373120articleProceedings of the National Academy of Sciences of the United States of America, vol 120, iss 42e2308373120oai:escholarship.org:ark:/13030/qt6216b9r42025-12-29T03:39:13Zqt6216b9r4Cellular acidosis triggers human MondoA transcriptional activity by driving mitochondrial ATP productionWilde, Blake RYe, ZhizhouLim, Tian-YehAyer, Donald E2019-01-01Human MondoA requires glucose as well as other modulatory signals to function in transcription. One such signal is acidosis, which increases MondoA activity and also drives a protective gene signature in breast cancer. How low pH controls MondoA transcriptional activity is unknown. We found that low pH medium increases mitochondrial ATP (mtATP), which is subsequently exported from the mitochondrial matrix. Mitochondria-bound hexokinase transfers a phosphate from mtATP to cytoplasmic glucose to generate glucose-6-phosphate (G6P), which is an established MondoA activator. The outer mitochondrial membrane localization of MondoA suggests that it is positioned to coordinate the adaptive transcriptional response to a cell's most abundant energy sources, cytoplasmic glucose and mtATP. In response to acidosis, MondoA shows preferential binding to just two targets, TXNIP and its paralog ARRDC4. Because these transcriptional targets are suppressors of glucose uptake, we propose that MondoA is critical for restoring metabolic homeostasis in response to high energy charge.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Breast Cancer (rcdc)Cancer (rcdc)Women's Health (rcdc)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Acidosis (mesh)Adenosine Triphosphate (mesh)Arrestins (mesh)Basic Helix-Loop-Helix Leucine Zipper Transcription Factors (mesh)Carrier Proteins (mesh)Enzyme Activators (mesh)Glucose-6-Phosphate (mesh)Hexokinase (mesh)Humans (mesh)Hydrogen-Ion Concentration (mesh)Phosphates (mesh)Protein Binding (mesh)TranscriptionGenetic (mesh)Humans (mesh)Acidosis (mesh)Phosphates (mesh)Hexokinase (mesh)Glucose-6-Phosphate (mesh)Carrier Proteins (mesh)Arrestins (mesh)Adenosine Triphosphate (mesh)Enzyme Activators (mesh)TranscriptionGenetic (mesh)Protein Binding (mesh)Hydrogen-Ion Concentration (mesh)Basic Helix-Loop-Helix Leucine Zipper Transcription Factors (mesh)MondoATXNIPacidosiscancer biologychromosomesgene expressionglucosehexokinasehumanmitochondrial ATPmouseAcidosis (mesh)Adenosine Triphosphate (mesh)Arrestins (mesh)Basic Helix-Loop-Helix Leucine Zipper Transcription Factors (mesh)Carrier Proteins (mesh)Enzyme Activators (mesh)Glucose-6-Phosphate (mesh)Hexokinase (mesh)Humans (mesh)Hydrogen-Ion Concentration (mesh)Phosphates (mesh)Protein Binding (mesh)TranscriptionGenetic (mesh)0601 Biochemistry and Cell Biology (for)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/6216b9r4https://escholarship.org/content/qt6216b9r4/qt6216b9r4.pdfinfo:doi/10.7554/elife.40199articleeLife, vol 8e40199oai:escholarship.org:ark:/13030/qt8fz156t22025-12-29T02:06:24Zqt8fz156t2Pan-primate studies of age and sexHorvath, SteveHaghani, AminZoller, Joseph ALu, Ake TErnst, JasonPellegrini, MatteoJasinska, Anna JMattison, Julie ASalmon, Adam BRaj, KenHorvath, MarkusPaul, Kimberly CRitz, Beate RRobeck, Todd RSpriggs, MariaEhmke, Erin EJenkins, SusanLi, CunNathanielsz, Peter W2023-12-01Age and sex have a profound effect on cytosine methylation levels in humans and many other species. Here we analyzed DNA methylation profiles of 2400 tissues derived from 37 primate species including 11 haplorhine species (baboons, marmosets, vervets, rhesus macaque, chimpanzees, gorillas, orangutan, humans) and 26 strepsirrhine species (suborders Lemuriformes and Lorisiformes). From these we present here, pan-primate epigenetic clocks which are highly accurate for all primates including humans (age correlation R = 0.98). We also carried out in-depth analysis of baboon DNA methylation profiles and generated five epigenetic clocks for baboons (Olive-yellow baboon hybrid), one of which, the pan-tissue epigenetic clock, was trained on seven tissue types (fetal cerebral cortex, adult cerebral cortex, cerebellum, adipose, heart, liver, and skeletal muscle) with ages ranging from late fetal life to 22.8 years of age. Using the primate data, we characterize the effect of age and sex on individual cytosines in highly conserved regions. We identify 11 sex-related CpGs on autosomes near genes (POU3F2, CDYL, MYCL, FBXL4, ZC3H10, ZXDC, RRAS, FAM217A, RBM39, GRIA2, UHRF2). Low overlap can be observed between age- and sex-related CpGs. Overall, this study advances our understanding of conserved age- and sex-related epigenetic changes in primates, and provides biomarkers of aging for all primates.31 Biological Sciences (for-2020)3105 Genetics (for-2020)Genetics (rcdc)Aging (rcdc)Human Genome (rcdc)Humans (mesh)Animals (mesh)Macaca mulatta (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Aging (mesh)Papio (mesh)Ubiquitin-Protein Ligases (mesh)Carrier Proteins (mesh)PrimateBaboonLemurStrepsirrhineDevelopmentEpigenetic clockDNA methylationAnimals (mesh)Macaca mulatta (mesh)Papio (mesh)Humans (mesh)Ubiquitin-Protein Ligases (mesh)Carrier Proteins (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Aging (mesh)BaboonDNA methylationDevelopmentEpigenetic clockLemurPrimateStrepsirrhineHumans (mesh)Animals (mesh)Macaca mulatta (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Aging (mesh)Papio (mesh)Ubiquitin-Protein Ligases (mesh)Carrier Proteins (mesh)3105 Genetics (for-2020)3202 Clinical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/8fz156t2https://escholarship.org/content/qt8fz156t2/qt8fz156t2.pdfinfo:doi/10.1007/s11357-023-00878-3articleGeroScience, vol 45, iss 63187 - 3209oai:escholarship.org:ark:/13030/qt8tb9t3592025-12-29T02:01:20Zqt8tb9t359Improving cassava bacterial blight resistance by editing the epigenomeVeley, Kira MElliott, KionaJensen, GregZhong, ZhenhuiFeng, SuhuaYoder, MarisaGilbert, Kerrigan BBerry, Jeffrey CLin, Zuh-Jyh DanielGhoshal, BasudevGallego-Bartolomé, JavierNorton, JoannaMotomura-Wages, SharonCarrington, James CJacobsen, Steven EBart, Rebecca S2023-01-01Pathogens rely on expression of host susceptibility (S) genes to promote infection and disease. As DNA methylation is an epigenetic modification that affects gene expression, blocking access to S genes through targeted methylation could increase disease resistance. Xanthomonas phaseoli pv. manihotis, the causal agent of cassava bacterial blight (CBB), uses transcription activator-like20 (TAL20) to induce expression of the S gene MeSWEET10a. In this work, we direct methylation to the TAL20 effector binding element within the MeSWEET10a promoter using a synthetic zinc-finger DNA binding domain fused to a component of the RNA-directed DNA methylation pathway. We demonstrate that this methylation prevents TAL20 binding, blocks transcriptional activation of MeSWEET10a in vivo and that these plants display decreased CBB symptoms while maintaining normal growth and development. This work therefore presents an epigenome editing approach useful for crop improvement.30 AgriculturalVeterinary and Food Sciences (for-2020)3108 Plant Biology (for-2020)31 Biological Sciences (for-2020)3008 Horticultural Production (for-2020)Human Genome (rcdc)Genetics (rcdc)Biotechnology (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Manihot (mesh)Epigenome (mesh)Xanthomonas (mesh)Disease Resistance (mesh)Transcription Factors (mesh)Plant Diseases (mesh)Xanthomonas (mesh)Manihot (mesh)Transcription Factors (mesh)Plant Diseases (mesh)Disease Resistance (mesh)Epigenome (mesh)Manihot (mesh)Epigenome (mesh)Xanthomonas (mesh)Disease Resistance (mesh)Transcription Factors (mesh)Plant Diseases (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/8tb9t359https://escholarship.org/content/qt8tb9t359/qt8tb9t359.pdfinfo:doi/10.1038/s41467-022-35675-7articleNature Communications, vol 14, iss 185oai:escholarship.org:ark:/13030/qt59q429kb2025-12-29T01:51:42Zqt59q429kbGPCR Agonist-to-Antagonist Conversion: Enabling the Design of Nucleoside Functional Switches for the A2A Adenosine ReceptorShiriaeva, AnnaPark, DaejinKim, GyudongLee, YoonjiHou, XiyanJarhad, Dnyandev BKim, GibaeYu, JinhaHyun, Young EumKim, WoomiGao, Zhan-GuoJacobson, Kenneth AHan, Gye WonStevens, Raymond CJeong, Lak ShinChoi, SunCherezov, Vadim2022-09-08Modulators of the G protein-coupled A2A adenosine receptor (A2AAR) have been considered promising agents to treat Parkinson's disease, inflammation, cancer, and central nervous system disorders. Herein, we demonstrate that a thiophene modification at the C8 position in the common adenine scaffold converted an A2AAR agonist into an antagonist. We synthesized and characterized a novel A2AAR antagonist, 2 (LJ-4517), with Ki = 18.3 nM. X-ray crystallographic structures of 2 in complex with two thermostabilized A2AAR constructs were solved at 2.05 and 2.80 Å resolutions. In contrast to A2AAR agonists, which simultaneously interact with both Ser2777.42 and His2787.43, 2 only transiently contacts His2787.43, which can be direct or water-mediated. The n-hexynyl group of 2 extends into an A2AAR exosite. Structural analysis revealed that the introduced thiophene modification restricted receptor conformational rearrangements required for subsequent activation. This approach can expand the repertoire of adenosine receptor antagonists that can be designed based on available agonist scaffolds.3214 Pharmacology and Pharmaceutical Sciences (for-2020)32 Biomedical and Clinical Sciences (for-2020)34 Chemical Sciences (for-2020)Neurosciences (rcdc)Adenosine A2 Receptor Antagonists (mesh)CrystallographyX-Ray (mesh)Molecular Conformation (mesh)Nucleosides (mesh)ReceptorAdenosine A2A (mesh)Thiophenes (mesh)Thiophenes (mesh)Nucleosides (mesh)ReceptorAdenosine A2A (mesh)CrystallographyX-Ray (mesh)Molecular Conformation (mesh)Adenosine A2 Receptor Antagonists (mesh)Adenosine A2 Receptor Antagonists (mesh)CrystallographyX-Ray (mesh)Molecular Conformation (mesh)Nucleosides (mesh)ReceptorAdenosine A2A (mesh)Thiophenes (mesh)0304 Medicinal and Biomolecular Chemistry (for)0305 Organic Chemistry (for)1115 Pharmacology and Pharmaceutical Sciences (for)Medicinal & Biomolecular Chemistry (science-metrix)3214 Pharmacology and pharmaceutical sciences (for-2020)3404 Medicinal and biomolecular chemistry (for-2020)3405 Organic chemistry (for-2020)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/59q429kbhttps://escholarship.org/content/qt59q429kb/qt59q429kb.pdfinfo:doi/10.1021/acs.jmedchem.2c00462articleJournal of Medicinal Chemistry, vol 65, iss 1711648 - 11657oai:escholarship.org:ark:/13030/qt8wb8q5k22025-12-29T01:36:38Zqt8wb8q5k2Astrocyte–neuron subproteomes and obsessive–compulsive disorder mechanismsSoto, Joselyn SJami-Alahmadi, YasamanChacon, JakelynMoye, Stefanie LDiaz-Castro, BlancaWohlschlegel, James AKhakh, Baljit S2023-04-27Astrocytes and neurons extensively interact in the brain. Identifying astrocyte and neuron proteomes is essential for elucidating the protein networks that dictate their respective contributions to physiology and disease. Here we used cell-specific and subcompartment-specific proximity-dependent biotinylation1 to study the proteomes of striatal astrocytes and neurons in vivo. We evaluated cytosolic and plasma membrane compartments for astrocytes and neurons to discover how these cells differ at the protein level in their signalling machinery. We also assessed subcellular compartments of astrocytes, including end feet and fine processes, to reveal their subproteomes and the molecular basis of essential astrocyte signalling and homeostatic functions. Notably, SAPAP3 (encoded by Dlgap3), which is associated with obsessive–compulsive disorder (OCD) and repetitive behaviours2–8, was detected at high levels in striatal astrocytes and was enriched within specific astrocyte subcompartments where it regulated actin cytoskeleton organization. Furthermore, genetic rescue experiments combined with behavioural analyses and molecular assessments in a mouse model of OCD4 lacking SAPAP3 revealed distinct contributions of astrocytic and neuronal SAPAP3 to repetitive and anxiety-related OCD-like phenotypes. Our data define how astrocytes and neurons differ at the protein level and in their major signalling pathways. Moreover, they reveal how astrocyte subproteomes vary between physiological subcompartments and how both astrocyte and neuronal SAPAP3 mechanisms contribute to OCD phenotypes in mice. Our data indicate that therapeutic strategies that target both astrocytes and neurons may be useful to explore in OCD and potentially other brain disorders.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Neurosciences (rcdc)Anxiety Disorders (rcdc)Mental Illness (rcdc)Brain Disorders (rcdc)Mental Health (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Mental health (hrcs-hc)Neurological (hrcs-hc)Animals (mesh)Mice (mesh)Astrocytes (mesh)Neurons (mesh)Obsessive-Compulsive Disorder (mesh)Proteome (mesh)Biotinylation (mesh)Cell Membrane (mesh)Signal Transduction (mesh)Cytosol (mesh)Homeostasis (mesh)Phenotype (mesh)Actin Cytoskeleton (mesh)Astrocytes (mesh)Neurons (mesh)Cell Membrane (mesh)Cytosol (mesh)Animals (mesh)Mice (mesh)Proteome (mesh)Biotinylation (mesh)Obsessive-Compulsive Disorder (mesh)Signal Transduction (mesh)Homeostasis (mesh)Phenotype (mesh)Actin Cytoskeleton (mesh)Animals (mesh)Mice (mesh)Astrocytes (mesh)Neurons (mesh)Obsessive-Compulsive Disorder (mesh)Proteome (mesh)Biotinylation (mesh)Cell Membrane (mesh)Signal Transduction (mesh)Cytosol (mesh)Homeostasis (mesh)Phenotype (mesh)Actin Cytoskeleton (mesh)General Science & Technology (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/8wb8q5k2https://escholarship.org/content/qt8wb8q5k2/qt8wb8q5k2.pdfinfo:doi/10.1038/s41586-023-05927-7articleNature, vol 616, iss 7958764 - 773oai:escholarship.org:ark:/13030/qt2ms7118k2025-12-28T23:59:00Zqt2ms7118kAdded Value of Internal Fragments for Top-Down Mass Spectrometry of Intact Monoclonal Antibodies and Antibody–Drug ConjugatesWei, BenqianLantz, CarterLiu, WeijingViner, RosaLoo, Rachel R OgorzalekCampuzano, Iain DGLoo, Joseph A2023-06-20Monoclonal antibodies (mAbs) and antibody-drug conjugates (ADCs) are two of the most important therapeutic drug classes that require extensive characterization, whereas their large size and structural complexity make them challenging to characterize and demand the use of advanced analytical methods. Top-down mass spectrometry (TD-MS) is an emerging technique that minimizes sample preparation and preserves endogenous post-translational modifications (PTMs); however, TD-MS of large proteins suffers from low fragmentation efficiency, limiting the sequence and structure information that can be obtained. Here, we show that including the assignment of internal fragments in native TD-MS of an intact mAb and an ADC can improve their molecular characterization. For the NIST mAb, internal fragments can access the sequence region constrained by disulfide bonds to increase the TD-MS sequence coverage to over 75%. Important PTM information, including intrachain disulfide connectivity and N-glycosylation sites, can be revealed after including internal fragments. For a heterogeneous lysine-linked ADC, we show that assigning internal fragments improves the identification of drug conjugation sites to achieve a coverage of 58% of all putative conjugation sites. This proof-of-principle study demonstrates the potential value of including internal fragments in native TD-MS of intact mAbs and ADCs, and this analytical strategy can be extended to bottom-up and middle-down MS approaches to achieve even more comprehensive characterization of important therapeutic molecules.3401 Analytical Chemistry (for-2020)34 Chemical Sciences (for-2020)Biotechnology (rcdc)Immunization (rcdc)5.1 Pharmaceuticals (hrcs-rac)Generic health relevance (hrcs-hc)AntibodiesMonoclonal (mesh)Humans (mesh)Glycosylation (mesh)Mass Spectrometry (mesh)Disulfides (mesh)Lysine (mesh)Humans (mesh)Disulfides (mesh)Lysine (mesh)AntibodiesMonoclonal (mesh)Glycosylation (mesh)Mass Spectrometry (mesh)AntibodiesMonoclonal (mesh)Humans (mesh)Glycosylation (mesh)Mass Spectrometry (mesh)Disulfides (mesh)Lysine (mesh)0301 Analytical Chemistry (for)0399 Other Chemical Sciences (for)Analytical Chemistry (science-metrix)3205 Medical biochemistry and metabolomics (for-2020)3401 Analytical chemistry (for-2020)4004 Chemical engineering (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2ms7118khttps://escholarship.org/content/qt2ms7118k/qt2ms7118k.pdfinfo:doi/10.1021/acs.analchem.3c01426articleAnalytical Chemistry, vol 95, iss 249347 - 9356oai:escholarship.org:ark:/13030/qt1wf306sz2025-12-28T22:06:28Zqt1wf306szLipid flipping in the omega-3 fatty-acid transporterNguyen, ChiLei, Hsiang-TingLai, Louis Tung FaatGallenito, Marc JMu, XuelangMatthies, DoreenGonen, Tamir2023-01-01Mfsd2a is the transporter for docosahexaenoic acid (DHA), an omega-3 fatty acid, across the blood brain barrier (BBB). Defects in Mfsd2a are linked to ailments from behavioral and motor dysfunctions to microcephaly. Mfsd2a transports long-chain unsaturated fatty-acids, including DHA and α-linolenic acid (ALA), that are attached to the zwitterionic lysophosphatidylcholine (LPC) headgroup. Even with the recently determined structures of Mfsd2a, the molecular details of how this transporter performs the energetically unfavorable task of translocating and flipping lysolipids across the lipid bilayer remains unclear. Here, we report five single-particle cryo-EM structures of Danio rerio Mfsd2a (drMfsd2a): in the inward-open conformation in the ligand-free state and displaying lipid-like densities modeled as ALA-LPC at four distinct positions. These Mfsd2a snapshots detail the flipping mechanism for lipid-LPC from outer to inner membrane leaflet and release for membrane integration on the cytoplasmic side. These results also map Mfsd2a mutants that disrupt lipid-LPC transport and are associated with disease.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Complementary and Integrative Health (rcdc)Nutrition (rcdc)Neurosciences (rcdc)Dietary Supplements (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Fatty AcidsOmega-3 (mesh)Symporters (mesh)Membrane Transport Proteins (mesh)Blood-Brain Barrier (mesh)Biological Transport (mesh)Docosahexaenoic Acids (mesh)Lysophosphatidylcholines (mesh)Blood-Brain Barrier (mesh)Fatty AcidsOmega-3 (mesh)Docosahexaenoic Acids (mesh)Lysophosphatidylcholines (mesh)Membrane Transport Proteins (mesh)Symporters (mesh)Biological Transport (mesh)Fatty AcidsOmega-3 (mesh)Symporters (mesh)Membrane Transport Proteins (mesh)Blood-Brain Barrier (mesh)Biological Transport (mesh)Docosahexaenoic Acids (mesh)Lysophosphatidylcholines (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/1wf306szhttps://escholarship.org/content/qt1wf306sz/qt1wf306sz.pdfinfo:doi/10.1038/s41467-023-37702-7articleNature Communications, vol 14, iss 12571oai:escholarship.org:ark:/13030/qt33m6d05h2025-12-28T21:02:53Zqt33m6d05hTXNIP loss expands Myc-dependent transcriptional programs by increasing Myc genomic bindingLim, Tian-YehWilde, Blake RThomas, Mallory LMurphy, Kristin EVahrenkamp, Jeffery MConway, Megan EVarley, Katherine EGertz, JasonAyer, Donald EEaves, Connie J2023-01-01The c-Myc protooncogene places a demand on glucose uptake to drive glucose-dependent biosynthetic pathways. To meet this demand, c-Myc protein (Myc henceforth) drives the expression of glucose transporters, glycolytic enzymes, and represses the expression of thioredoxin interacting protein (TXNIP), which is a potent negative regulator of glucose uptake. A Mychigh/TXNIPlow gene signature is clinically significant as it correlates with poor clinical prognosis in triple-negative breast cancer (TNBC) but not in other subtypes of breast cancer, suggesting a functional relationship between Myc and TXNIP. To better understand how TXNIP contributes to the aggressive behavior of TNBC, we generated TXNIP null MDA-MB-231 (231:TKO) cells for our study. We show that TXNIP loss drives a transcriptional program that resembles those driven by Myc and increases global Myc genome occupancy. TXNIP loss allows Myc to invade the promoters and enhancers of target genes that are potentially relevant to cell transformation. Together, these findings suggest that TXNIP is a broad repressor of Myc genomic binding. The increase in Myc genomic binding in the 231:TKO cells expands the Myc-dependent transcriptome we identified in parental MDA-MB-231 cells. This expansion of Myc-dependent transcription following TXNIP loss occurs without an apparent increase in Myc's intrinsic capacity to activate transcription and without increasing Myc levels. Together, our findings suggest that TXNIP loss mimics Myc overexpression, connecting Myc genomic binding and transcriptional programs to the nutrient and progrowth signals that control TXNIP expression.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)3211 Oncology and Carcinogenesis (for-2020)31 Biological Sciences (for-2020)Human Genome (rcdc)Cancer Genomics (rcdc)Cancer (rcdc)Breast Cancer (rcdc)Genetics (rcdc)Biotechnology (rcdc)Women's Health (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Generic health relevance (hrcs-hc)Cancer (hrcs-hc)Humans (mesh)Biological Transport (mesh)Carrier Proteins (mesh)Genomics (mesh)Glucose (mesh)Triple Negative Breast Neoplasms (mesh)Proto-Oncogene Proteins c-myc (mesh)Humans (mesh)Glucose (mesh)Carrier Proteins (mesh)Proto-Oncogene Proteins c-myc (mesh)Genomics (mesh)Biological Transport (mesh)Triple Negative Breast Neoplasms (mesh)Humans (mesh)Biological Transport (mesh)Carrier Proteins (mesh)Genomics (mesh)Glucose (mesh)Triple Negative Breast Neoplasms (mesh)Proto-Oncogene Proteins c-myc (mesh)06 Biological Sciences (for)07 Agricultural and Veterinary Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)30 Agriculturalveterinary and food sciences (for-2020)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/33m6d05hhttps://escholarship.org/content/qt33m6d05h/qt33m6d05h.pdfinfo:doi/10.1371/journal.pbio.3001778articlePLOS Biology, vol 21, iss 3e3001778oai:escholarship.org:ark:/13030/qt6n57d33z2025-12-28T19:35:19Zqt6n57d33zSynaptic gradients transform object location to actionDombrovski, MarkPeek, Martin YPark, Jin-YongVaccari, AndreaSumathipala, MarissaMorrow, CarmenBreads, PatrickZhao, ArthurKurmangaliyev, Yerbol ZSanfilippo, PieroRehan, AadilPolsky, JasonAlghailani, ShadaTenshaw, EmilyNamiki, ShigehiroZipursky, S LawrenceCard, Gwyneth M2023-01-19To survive, animals must convert sensory information into appropriate behaviours1,2. Vision is a common sense for locating ethologically relevant stimuli and guiding motor responses3–5. How circuitry converts object location in retinal coordinates to movement direction in body coordinates remains largely unknown. Here we show through behaviour, physiology, anatomy and connectomics in Drosophila that visuomotor transformation occurs by conversion of topographic maps formed by the dendrites of feature-detecting visual projection neurons (VPNs)6,7 into synaptic weight gradients of VPN outputs onto central brain neurons. We demonstrate how this gradient motif transforms the anteroposterior location of a visual looming stimulus into the fly’s directional escape. Specifically, we discover that two neurons postsynaptic to a looming-responsive VPN type promote opposite takeoff directions. Opposite synaptic weight gradients onto these neurons from looming VPNs in different visual field regions convert localized looming threats into correctly oriented escapes. For a second looming-responsive VPN type, we demonstrate graded responses along the dorsoventral axis. We show that this synaptic gradient motif generalizes across all 20 primary VPN cell types and most often arises without VPN axon topography. Synaptic gradients may thus be a general mechanism for conveying spatial features of sensory information into directed motor outputs.31 Biological Sciences (for-2020)32 Biomedical and Clinical Sciences (for-2020)46 Information and Computing Sciences (for-2020)3209 Neurosciences (for-2020)4611 Machine Learning (for-2020)Eye Disease and Disorders of Vision (rcdc)Neurosciences (rcdc)Neurological (hrcs-hc)Animals (mesh)Brain (mesh)Drosophila (mesh)Neurons (mesh)Visual Fields (mesh)Synapses (mesh)BehaviorAnimal (mesh)Axons (mesh)Psychomotor Performance (mesh)Dendrites (mesh)Escape Reaction (mesh)Brain (mesh)Neurons (mesh)Dendrites (mesh)Axons (mesh)Synapses (mesh)Animals (mesh)Drosophila (mesh)BehaviorAnimal (mesh)Escape Reaction (mesh)Psychomotor Performance (mesh)Visual Fields (mesh)Animals (mesh)Brain (mesh)Drosophila (mesh)Neurons (mesh)Visual Fields (mesh)Synapses (mesh)BehaviorAnimal (mesh)Axons (mesh)Psychomotor Performance (mesh)Dendrites (mesh)Escape Reaction (mesh)General Science & Technology (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/6n57d33zhttps://escholarship.org/content/qt6n57d33z/qt6n57d33z.pdfinfo:doi/10.1038/s41586-022-05562-8articleNature, vol 613, iss 7944534 - 542oai:escholarship.org:ark:/13030/qt2bk482vt2025-12-28T17:25:00Zqt2bk482vtMicroED in drug discoveryDanelius, EmmaPatel, KhushbooGonzalez, BrendaGonen, Tamir2023-04-01The cryo-electron microscopy (cryo-EM) method microcrystal electron diffraction (MicroED) was initially described in 2013 and has recently gained attention as an emerging technique for research in drug discovery. As compared to other methods in structural biology, MicroED provides many advantages deriving from the use of nanocrystalline material for the investigations. Here, we review the recent advancements in the field of MicroED and show important examples of small molecule, peptide and protein structures that has contributed to the current development of this method as an important tool for drug discovery.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Biotechnology (rcdc)Generic health relevance (hrcs-hc)Cryoelectron Microscopy (mesh)Electrons (mesh)ModelsMolecular (mesh)Proteins (mesh)Drug Discovery (mesh)Cr yo-EM MicroEDSmall molecule structuresNanocrystalsProtein-ligand structuresProteins (mesh)Cryoelectron Microscopy (mesh)Electrons (mesh)ModelsMolecular (mesh)Drug Discovery (mesh)Cryo-EMMicroEDNanocrystalsProtein-ligand structuresSmall molecule structuresCryoelectron Microscopy (mesh)Electrons (mesh)ModelsMolecular (mesh)Proteins (mesh)Drug Discovery (mesh)0304 Medicinal and Biomolecular Chemistry (for)0601 Biochemistry and Cell Biology (for)Biophysics (science-metrix)3101 Biochemistry and cell biology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/2bk482vthttps://escholarship.org/content/qt2bk482vt/qt2bk482vt.pdfinfo:doi/10.1016/j.sbi.2023.102549articleCurrent Opinion in Structural Biology, vol 79102549oai:escholarship.org:ark:/13030/qt4n14z8n92025-12-28T13:56:02Zqt4n14z8n9Single-nucleus RNA-seq reveals that MBD5, MBD6, and SILENZIO maintain silencing in the vegetative cell of developing pollenIchino, LuciaPicard, Colette LYun, JaewonChotai, MeeraWang, ShuyaLin, Evan KPapareddy, Ranjith KXue, YanJacobsen, Steven E2022-11-01Silencing of transposable elements (TEs) drives the evolution of numerous redundant mechanisms of transcriptional regulation. Arabidopsis MBD5, MBD6, and SILENZIO act as TE repressors downstream of DNA methylation. Here, we show, via single-nucleus RNA-seq of developing male gametophytes, that these repressors are critical for TE silencing in the pollen vegetative cell, a companion cell important for fertilization that undergoes chromatin decompaction. Instead, other silencing mutants (met1, ddm1, mom1, morc) show loss of silencing in all pollen nucleus types and somatic cells. We show that TEs repressed by MBD5/6 gain chromatin accessibility in wild-type vegetative nuclei despite remaining silent, suggesting that loss of DNA compaction makes them sensitive to loss of MBD5/6. Consistently, crossing mbd5/6 to histone 1 mutants, which have decondensed chromatin in leaves, reveals derepression of MBD5/6-dependent TEs in leaves. MBD5/6 and SILENZIO thus act as a silencing system particularly important when chromatin compaction is compromised.3101 Biochemistry and Cell Biology (for-2020)3102 Bioinformatics and Computational Biology (for-2020)3105 Genetics (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Human Genome (rcdc)Generic health relevance (hrcs-hc)RNA-Seq (mesh)Arabidopsis (mesh)Pollen (mesh)DNA Transposable Elements (mesh)Chromatin (mesh)Transcription Factors (mesh)DNA (Cytosine-5-)-Methyltransferases (mesh)Arabidopsis Proteins (mesh)DNA-Binding Proteins (mesh)Highlightsvegetative nucleiChromatin (mesh)Arabidopsis (mesh)Pollen (mesh)DNA-Binding Proteins (mesh)Arabidopsis Proteins (mesh)Transcription Factors (mesh)DNA Transposable Elements (mesh)DNA (Cytosine-5-)-Methyltransferases (mesh)RNA-Seq (mesh)ArabidopsisCP: Developmental biologyCP: PlantsDNA methylationMBDchromatinepigeneticsmale germlinemethyl readerspollensingle-cell analysistransposable elementsRNA-Seq (mesh)Arabidopsis (mesh)Pollen (mesh)DNA Transposable Elements (mesh)Chromatin (mesh)Transcription Factors (mesh)DNA (Cytosine-5-)-Methyltransferases (mesh)Arabidopsis Proteins (mesh)DNA-Binding Proteins (mesh)0601 Biochemistry and Cell Biology (for)1116 Medical Physiology (for)31 Biological sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/4n14z8n9https://escholarship.org/content/qt4n14z8n9/qt4n14z8n9.pdfinfo:doi/10.1016/j.celrep.2022.111699articleCell Reports, vol 41, iss 8111699oai:escholarship.org:ark:/13030/qt34g3z3q02025-12-28T10:21:11Zqt34g3z3q0Moving Lipids, by the NumbersEgea, Pascal F2022-01-01application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/34g3z3q0https://escholarship.org/content/qt34g3z3q0/qt34g3z3q0.pdfinfo:doi/10.1177/25152564221103080articleContact The Journal of Inter-Organelle Communication, vol 525152564221103080oai:escholarship.org:ark:/13030/qt5b94887z2025-12-28T09:05:12Zqt5b94887zLiver X receptors in lipid signalling and membrane homeostasisWang, BoTontonoz, Peter2018-08-01Liver X receptors α and β (LXRα and LXRβ) are nuclear receptors with pivotal roles in the transcriptional control of lipid metabolism. Transcriptional activity of LXRs is induced in response to elevated cellular levels of cholesterol. LXRs bind to and regulate the expression of genes that encode proteins involved in cholesterol absorption, transport, efflux, excretion and conversion to bile acids. The coordinated, tissue-specific actions of the LXR pathway maintain systemic cholesterol homeostasis and regulate immune and inflammatory responses. LXRs also regulate fatty acid metabolism by controlling the lipogenic transcription factor sterol regulatory element-binding protein 1c and regulate genes that encode proteins involved in fatty acid elongation and desaturation. LXRs exert important effects on the metabolism of phospholipids, which, along with cholesterol, are major constituents of cellular membranes. LXR activation preferentially drives the incorporation of polyunsaturated fatty acids into phospholipids by inducing transcription of the remodelling enzyme lysophosphatidylcholine acyltransferase 3. The ability of the LXR pathway to couple cellular sterol levels with the saturation of fatty acids in membrane phospholipids has implications for several physiological processes, including lipoprotein production, dietary lipid absorption and intestinal stem cell proliferation. Understanding how LXRs regulate membrane composition and function might provide new therapeutic insight into diseases associated with dysregulated lipid metabolism, including atherosclerosis, diabetes mellitus and cancer.32 Biomedical and Clinical Sciences (for-2020)3202 Clinical Sciences (for-2020)Nutrition (rcdc)Cardiovascular (rcdc)Digestive Diseases (rcdc)Genetics (rcdc)Atherosclerosis (rcdc)Liver Disease (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Animals (mesh)Cholesterol (mesh)Gene Expression Regulation (mesh)Homeostasis (mesh)Humans (mesh)Lipid Metabolism (mesh)Liver X Receptors (mesh)Needs Assessment (mesh)Signal Transduction (mesh)Translational ResearchBiomedical (mesh)Animals (mesh)Humans (mesh)Cholesterol (mesh)Signal Transduction (mesh)Gene Expression Regulation (mesh)Homeostasis (mesh)Needs Assessment (mesh)Lipid Metabolism (mesh)Liver X Receptors (mesh)Translational ResearchBiomedical (mesh)Animals (mesh)Cholesterol (mesh)Gene Expression Regulation (mesh)Homeostasis (mesh)Humans (mesh)Lipid Metabolism (mesh)Liver X Receptors (mesh)Needs Assessment (mesh)Signal Transduction (mesh)Translational ResearchBiomedical (mesh)Endocrinology & Metabolism (science-metrix)3202 Clinical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5b94887zhttps://escholarship.org/content/qt5b94887z/qt5b94887z.pdfinfo:doi/10.1038/s41574-018-0037-xarticleNature Reviews Endocrinology, vol 14, iss 8452 - 463oai:escholarship.org:ark:/13030/qt8df8v4sh2025-12-28T08:12:57Zqt8df8v4shNeural control of affiliative touch in prosocial interactionWu, Ye EmilyDang, JamesKingsbury, LyleZhang, MingminSun, FangmiaoHu, Rongfeng KHong, Weizhe2021-11-11The ability to help and care for others fosters social cohesiveness and is vital to the physical and emotional well-being of social species, including humans1–3. Affiliative social touch, such as allogrooming (grooming behaviour directed towards another individual), is a major type of prosocial behaviour that provides comfort to others1–6. Affiliative touch serves to establish and strengthen social bonds between animals and can help to console distressed conspecifics. However, the neural circuits that promote prosocial affiliative touch have remained unclear. Here we show that mice exhibit affiliative allogrooming behaviour towards distressed partners, providing a consoling effect. The increase in allogrooming occurs in response to different types of stressors and can be elicited by olfactory cues from distressed individuals. Using microendoscopic calcium imaging, we find that neural activity in the medial amygdala (MeA) responds differentially to naive and distressed conspecifics and encodes allogrooming behaviour. Through intersectional functional manipulations, we establish a direct causal role of the MeA in controlling affiliative allogrooming and identify a select, tachykinin-expressing subpopulation of MeA GABAergic (γ-aminobutyric-acid-expressing) neurons that promote this behaviour through their projections to the medial preoptic area. Together, our study demonstrates that mice display prosocial comforting behaviour and reveals a neural circuit mechanism that underlies the encoding and control of affiliative touch during prosocial interactions.31 Biological Sciences (for-2020)32 Biomedical and Clinical Sciences (for-2020)3209 Neurosciences (for-2020)Neurosciences (rcdc)Basic Behavioral and Social Science (rcdc)Behavioral and Social Science (rcdc)1.2 Psychological and socioeconomic processes (hrcs-rac)Neurological (hrcs-hc)Amygdala (mesh)Animals (mesh)Cooperative Behavior (mesh)Emotions (mesh)Female (mesh)Male (mesh)Mice (mesh)Neural Pathways (mesh)Neurons (mesh)Preoptic Area (mesh)Social Behavior (mesh)StressPsychological (mesh)Touch (mesh)Amygdala (mesh)Preoptic Area (mesh)Neural Pathways (mesh)Neurons (mesh)Animals (mesh)Mice (mesh)StressPsychological (mesh)Social Behavior (mesh)Cooperative Behavior (mesh)Emotions (mesh)Touch (mesh)Female (mesh)Male (mesh)Amygdala (mesh)Animals (mesh)Cooperative Behavior (mesh)Emotions (mesh)Female (mesh)Male (mesh)Mice (mesh)Neural Pathways (mesh)Neurons (mesh)Preoptic Area (mesh)Social Behavior (mesh)StressPsychological (mesh)Touch (mesh)General Science & Technology (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8df8v4shhttps://escholarship.org/content/qt8df8v4sh/qt8df8v4sh.pdfinfo:doi/10.1038/s41586-021-03962-warticleNature, vol 599, iss 7884262 - 267oai:escholarship.org:ark:/13030/qt9pj481082025-12-28T07:15:33Zqt9pj48108Ab initio phasing macromolecular structures using electron-counted MicroED dataMartynowycz, Michael WClabbers, Max TBHattne, JohanGonen, Tamir2022-06-01Structures of two globular proteins were determined ab initio using microcrystal electron diffraction (MicroED) data that were collected on a direct electron detector in counting mode. Microcrystals were identified using a scanning electron microscope (SEM) and thinned with a focused ion beam (FIB) to produce crystalline lamellae of ideal thickness. Continuous-rotation data were collected using an ultra-low exposure rate to enable electron counting in diffraction. For the first sample, triclinic lysozyme extending to a resolution of 0.87 Å, an ideal helical fragment of only three alanine residues provided initial phases. These phases were improved using density modification, allowing the entire atomic structure to be built automatically. A similar approach was successful on a second macromolecular sample, proteinase K, which is much larger and diffracted to a resolution of 1.5 Å. These results demonstrate that macromolecules can be determined to sub-ångström resolution by MicroED and that ab initio phasing can be successfully applied to counting data.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Biotechnology (rcdc)Bioengineering (rcdc)Electrons (mesh)Macromolecular Substances (mesh)Macromolecular Substances (mesh)Electrons (mesh)Electrons (mesh)Macromolecular Substances (mesh)06 Biological Sciences (for)10 Technology (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/9pj48108https://escholarship.org/content/qt9pj48108/qt9pj48108.pdfinfo:doi/10.1038/s41592-022-01485-4articleNature Methods, vol 19, iss 6724 - 729oai:escholarship.org:ark:/13030/qt7f44f3tp2025-12-28T06:36:46Zqt7f44f3tpBiocatalytic Carbene Transfer Using DiazirinesPorter, Nicholas JDanelius, EmmaGonen, TamirArnold, Frances H2022-05-25Biocatalytic carbene transfer from diazo compounds is a versatile strategy in asymmetric synthesis. However, the limited pool of stable diazo compounds constrains the variety of accessible products. To overcome this restriction, we have engineered variants of Aeropyrum pernix protoglobin (ApePgb) that use diazirines as carbene precursors. While the enhanced stability of diazirines relative to their diazo isomers enables access to a diverse array of carbenes, they have previously resisted catalytic activation. Our engineered ApePgb variants represent the first example of catalysts for selective carbene transfer from these species at room temperature. The structure of an ApePgb variant, determined by microcrystal electron diffraction (MicroED), reveals that evolution has enhanced access to the heme active site to facilitate this new-to-nature catalysis. Using readily prepared aryl diazirines as model substrates, we demonstrate the application of these highly stable carbene precursors in biocatalytic cyclopropanation, N-H insertion, and Si-H insertion reactions.3402 Inorganic Chemistry (for-2020)3405 Organic Chemistry (for-2020)34 Chemical Sciences (for-2020)Azo Compounds (mesh)Biocatalysis (mesh)Catalysis (mesh)Diazomethane (mesh)Methane (mesh)Azo Compounds (mesh)Diazomethane (mesh)Methane (mesh)Catalysis (mesh)Biocatalysis (mesh)Azo Compounds (mesh)Biocatalysis (mesh)Catalysis (mesh)Diazomethane (mesh)Methane (mesh)03 Chemical Sciences (for)General Chemistry (science-metrix)34 Chemical sciences (for-2020)40 Engineering (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7f44f3tphttps://escholarship.org/content/qt7f44f3tp/qt7f44f3tp.pdfinfo:doi/10.1021/jacs.2c02723articleJournal of the American Chemical Society, vol 144, iss 208892 - 8896oai:escholarship.org:ark:/13030/qt3tb646fs2025-12-28T05:48:29Zqt3tb646fsDawn and dusk peaks of outer segment phagocytosis, and visual cycle function require Rab28Moran, Ailís LCarter, Stephen PKaylor, Joanna JJiang, ZhichunBroekman, SanneDillon, Eugene TSánchez, Alicia GómezMinhas, Sajal Kvan Wijk, ErwinRadu, Roxana ATravis, Gabriel HCarey, MichelleBlacque, Oliver EKennedy, Breandán N2022-05-01RAB28 is a farnesylated, ciliary G-protein. Patient variants in RAB28 are causative of autosomal recessive cone-rod dystrophy (CRD), an inherited human blindness. In rodent and zebrafish models, the absence of Rab28 results in diminished dawn, photoreceptor, outer segment phagocytosis (OSP). Here, we demonstrate that Rab28 is also required for dusk peaks of OSP, but not for basal OSP levels. This study further elucidated the molecular mechanisms by which Rab28 controls OSP and inherited blindness. Proteomic profiling identified factors whose expression in the eye or whose expression at dawn and dusk peaks of OSP is dysregulated by loss of Rab28. Notably, transgenic overexpression of Rab28, solely in zebrafish cones, rescues the OSP defect in rab28 KO fish, suggesting rab28 gene replacement in cone photoreceptors is sufficient to regulate Rab28-OSP. Rab28 loss also perturbs function of the visual cycle as retinoid levels of 11-cRAL, 11cRP, and atRP are significantly reduced in larval and adult rab28 KO retinae (p < .05). These data give further understanding on the molecular mechanisms of RAB28-associated CRD, highlighting roles of Rab28 in both peaks of OSP, in vitamin A metabolism and in retinoid recycling.31 Biological Sciences (for-2020)32 Biomedical and Clinical Sciences (for-2020)3212 Ophthalmology and Optometry (for-2020)Neurosciences (rcdc)Rare Diseases (rcdc)Genetics (rcdc)Eye Disease and Disorders of Vision (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Eye (hrcs-hc)Animals (mesh)Blindness (mesh)Humans (mesh)Phagocytosis (mesh)Proteomics (mesh)Retinal Cone Photoreceptor Cells (mesh)Retinoids (mesh)Zebrafish (mesh)rab GTP-Binding Proteins (mesh)bisretinoidsciliaciliopathycone-rod dystrophyouter segmentphagocytosisRab28retinoidsvisual cyclezebrafishAnimals (mesh)Zebrafish (mesh)Humans (mesh)Blindness (mesh)Retinoids (mesh)rab GTP-Binding Proteins (mesh)Proteomics (mesh)Phagocytosis (mesh)Retinal Cone Photoreceptor Cells (mesh)Rab28bisretinoidsciliaciliopathycone-rod dystrophyouter segmentphagocytosisretinoidsvisual cyclezebrafishAnimals (mesh)Blindness (mesh)Humans (mesh)Phagocytosis (mesh)Proteomics (mesh)Retinal Cone Photoreceptor Cells (mesh)Retinoids (mesh)Zebrafish (mesh)rab GTP-Binding Proteins (mesh)0601 Biochemistry and Cell Biology (for)0606 Physiology (for)1116 Medical Physiology (for)Biochemistry & Molecular Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)3208 Medical physiology (for-2020)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/3tb646fshttps://escholarship.org/content/qt3tb646fs/qt3tb646fs.pdfinfo:doi/10.1096/fj.202101897rarticleThe FASEB Journal, vol 36, iss 5e22309oai:escholarship.org:ark:/13030/qt12v7k4712025-12-28T05:05:56Zqt12v7k471FH Variant Pathogenicity Promotes Purine Salvage Pathway Dependence in Kidney Cancer.Wilde, Blake RChakraborty, NishmaMatulionis, NedasHernandez, StephanieUeno, DaikiGee, Michayla EEsplin, Edward DOuyang, KarenNykamp, KeithShuch, BrianChristofk, Heather R2023-09-06Fumarate accumulation due to loss of fumarate hydratase (FH) drives cellular transformation. Germline FH alterations lead to hereditary leiomyomatosis and renal cell cancer (HLRCC) where patients are predisposed to an aggressive form of kidney cancer. There is an unmet need to classify FH variants by cancer-associated risk. We quantified catalytic efficiencies of 74 variants of uncertain significance. Over half were enzymatically inactive, which is strong evidence of pathogenicity. We next generated a panel of HLRCC cell lines expressing FH variants with a range of catalytic activities, then correlated fumarate levels with metabolic features. We found that fumarate accumulation blocks de novo purine biosynthesis, rendering FH-deficient cells reliant on purine salvage for proliferation. Genetic or pharmacologic inhibition of the purine salvage pathway reduced HLRCC tumor growth in vivo. These findings suggest the pathogenicity of patient-associated FH variants and reveal purine salvage as a targetable vulnerability in FH-deficient tumors.
SIGNIFICANCE: This study functionally characterizes patient-associated FH variants with unknown significance for pathogenicity. This study also reveals nucleotide salvage pathways as a targetable feature of FH-deficient cancers, which are shown to be sensitive to the purine salvage pathway inhibitor 6-mercaptopurine. This presents a new rapidly translatable treatment strategy for FH-deficient cancers. This article is featured in Selected Articles from This Issue, p. 1949.31 Biological Sciences (for-2020)32 Biomedical and Clinical Sciences (for-2020)3211 Oncology and Carcinogenesis (for-2020)Genetics (rcdc)Human Genome (rcdc)Cancer (rcdc)Kidney Disease (rcdc)Rare Diseases (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Cancer (hrcs-hc)Kidney Neoplasms (mesh)Fumarate Hydratase (mesh)Uterine Neoplasms (mesh)Neoplastic SyndromesHereditary (mesh)Leiomyomatosis (mesh)Virulence (mesh)CarcinomaRenal Cell (mesh)Humans (mesh)Skin Neoplasms (mesh)Purines (mesh)Humans (mesh)Leiomyomatosis (mesh)CarcinomaRenal Cell (mesh)Skin Neoplasms (mesh)Uterine Neoplasms (mesh)Kidney Neoplasms (mesh)Neoplastic SyndromesHereditary (mesh)Purines (mesh)Fumarate Hydratase (mesh)Virulence (mesh)Kidney Neoplasms (mesh)Fumarate Hydratase (mesh)Uterine Neoplasms (mesh)Neoplastic SyndromesHereditary (mesh)Leiomyomatosis (mesh)Virulence (mesh)CarcinomaRenal Cell (mesh)Humans (mesh)Skin Neoplasms (mesh)Purines (mesh)1112 Oncology and Carcinogenesis (for)3101 Biochemistry and cell biology (for-2020)3211 Oncology and carcinogenesis (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/12v7k471https://escholarship.org/content/qt12v7k471/qt12v7k471.pdfinfo:doi/10.1158/2159-8290.cd-22-0874articleCancer Discovery, vol 13, iss 92072 - 2089oai:escholarship.org:ark:/13030/qt2q99d6zj2025-12-28T05:00:23Zqt2q99d6zjCryo-EM structure of RNA-induced tau fibrils reveals a small C-terminal core that may nucleate fibril formationAbskharon, RomanySawaya, Michael RBoyer, David RCao, QinNguyen, Binh ACascio, DuilioEisenberg, David S2022-04-12In neurodegenerative diseases including Alzheimer’s and amyotrophic lateral sclerosis, proteins that bind RNA are found in aggregated forms in autopsied brains. Evidence suggests that RNA aids nucleation of these pathological aggregates; however, the mechanism has not been investigated at the level of atomic structure. Here, we present the 3.4-Å resolution structure of fibrils of full-length recombinant tau protein in the presence of RNA, determined by electron cryomicroscopy (cryo-EM). The structure reveals the familiar in-register cross-β amyloid scaffold but with a small fibril core spanning residues Glu391 to Ala426, a region disordered in the fuzzy coat in all previously studied tau polymorphs. RNA is bound on the fibril surface to the positively charged residues Arg406 and His407 and runs parallel to the fibril axis. The fibrils dissolve when RNase is added, showing that RNA is necessary for fibril integrity. While this structure cannot exist simultaneously with the tau fibril structures extracted from patients’ brains, it could conceivably account for the nucleating effects of RNA cofactors followed by remodeling as fibrils mature.3101 Biochemistry and Cell Biology (for-2020)51 Physical Sciences (for-2020)31 Biological Sciences (for-2020)Alzheimer's Disease (rcdc)Neurodegenerative (rcdc)Acquired Cognitive Impairment (rcdc)Dementia (rcdc)Genetics (rcdc)Brain Disorders (rcdc)Neurosciences (rcdc)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)Aging (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Neurological (hrcs-hc)Amyloid (mesh)Cryoelectron Microscopy (mesh)Humans (mesh)RNA (mesh)tau Proteins (mesh)tauamyloidRNAcryo-EMAlzheimer'sHumans (mesh)Amyloid (mesh)tau Proteins (mesh)RNA (mesh)Cryoelectron Microscopy (mesh)Alzheimer’sRNAamyloidcryo-EMtauAmyloid (mesh)Cryoelectron Microscopy (mesh)Humans (mesh)RNA (mesh)tau Proteins (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/2q99d6zjhttps://escholarship.org/content/qt2q99d6zj/qt2q99d6zj.pdfinfo:doi/10.1073/pnas.2119952119articleProceedings of the National Academy of Sciences of the United States of America, vol 119, iss 15e2119952119oai:escholarship.org:ark:/13030/qt4xw5v4c52025-12-28T04:06:07Zqt4xw5v4c5Electrostatic sheathing of lipoprotein lipase is essential for its movement across capillary endothelial cellsSong, WenxinBeigneux, Anne PWinther, Anne-Marie LKristensen, Kristian KGrønnemose, Anne LYang, YeTu, YipingMunguia, PriscillaMorales, JazminJung, Hyesoode Jong, Pieter JJung, Cris JMiyashita, KazuyaKimura, TakaoNakajima, KatsuyukiMurakami, MasamiBirrane, GabrielJiang, HaiboTontonoz, PeterPloug, MichaelFong, Loren GYoung, Stephen G2022-03-01GPIHBP1, an endothelial cell (EC) protein, captures lipoprotein lipase (LPL) within the interstitial spaces (where it is secreted by myocytes and adipocytes) and transports it across ECs to its site of action in the capillary lumen. GPIHBP1's 3-fingered LU domain is required for LPL binding, but the function of its acidic domain (AD) has remained unclear. We created mutant mice lacking the AD and found severe hypertriglyceridemia. As expected, the mutant GPIHBP1 retained the capacity to bind LPL. Unexpectedly, however, most of the GPIHBP1 and LPL in the mutant mice was located on the abluminal surface of ECs (explaining the hypertriglyceridemia). The GPIHBP1-bound LPL was trapped on the abluminal surface of ECs by electrostatic interactions between the large basic patch on the surface of LPL and negatively charged heparan sulfate proteoglycans (HSPGs) on the surface of ECs. GPIHBP1 trafficking across ECs in the mutant mice was normalized by disrupting LPL-HSPG electrostatic interactions with either heparin or an AD peptide. Thus, GPIHBP1's AD plays a crucial function in plasma triglyceride metabolism; it sheathes LPL's basic patch on the abluminal surface of ECs, thereby preventing LPL-HSPG interactions and freeing GPIHBP1-LPL complexes to move across ECs to the capillary lumen.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)2.1 Biological and endogenous factors (hrcs-rac)Animals (mesh)Capillaries (mesh)Endothelial Cells (mesh)Lipoprotein Lipase (mesh)Mice (mesh)ReceptorsLipoprotein (mesh)Static Electricity (mesh)Capillaries (mesh)Endothelial Cells (mesh)Animals (mesh)Mice (mesh)Lipoprotein Lipase (mesh)ReceptorsLipoprotein (mesh)Static Electricity (mesh)LipoproteinsMetabolismAnimals (mesh)Capillaries (mesh)Endothelial Cells (mesh)Lipoprotein Lipase (mesh)Mice (mesh)ReceptorsLipoprotein (mesh)Static Electricity (mesh)11 Medical and Health Sciences (for)Immunology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/4xw5v4c5https://escholarship.org/content/qt4xw5v4c5/qt4xw5v4c5.pdfinfo:doi/10.1172/jci157500articleJournal of Clinical Investigation, vol 132, iss 5e157500oai:escholarship.org:ark:/13030/qt6k65721j2025-12-28T04:01:49Zqt6k65721jEnhancing Cysteine Chemoproteomic Coverage through Systematic Assessment of Click Chemistry Product FragmentationYan, TianyangPalmer, Andrew BGeiszler, Daniel JPolasky, Daniel ABoatner, Lisa MBurton, Nikolas RArmenta, ErnestNesvizhskii, Alexey IBackus, Keriann M2022-03-08Mass spectrometry-based chemoproteomics has enabled functional analysis and small molecule screening at thousands of cysteine residues in parallel. Widely adopted chemoproteomic sample preparation workflows rely on the use of pan cysteine-reactive probes such as iodoacetamide alkyne combined with biotinylation via copper-catalyzed azide-alkyne cycloaddition (CuAAC) or "click chemistry" for cysteine capture. Despite considerable advances in both sample preparation and analytical platforms, current techniques only sample a small fraction of all cysteines encoded in the human proteome. Extending the recently introduced labile mode of the MSFragger search engine, here we report an in-depth analysis of cysteine biotinylation via click chemistry (CBCC) reagent gas-phase fragmentation during MS/MS analysis. We find that CBCC conjugates produce both known and novel diagnostic fragments and peptide remainder ions. Among these species, we identified a candidate signature ion for CBCC peptides, the cyclic oxonium-biotin fragment ion that is generated upon fragmentation of the N(triazole)-C(alkyl) bond. Guided by our empirical comparison of fragmentation patterns of six CBCC reagent combinations, we achieved enhanced coverage of cysteine-labeled peptides. Implementation of labile searches afforded unique PSMs and provides a roadmap for the utility of such searches in enhancing chemoproteomic peptide coverage.3401 Analytical Chemistry (for-2020)34 Chemical Sciences (for-2020)3405 Organic Chemistry (for-2020)3406 Physical Chemistry (for-2020)Generic health relevance (hrcs-hc)Alkynes (mesh)Azides (mesh)Catalysis (mesh)Click Chemistry (mesh)Copper (mesh)Cycloaddition Reaction (mesh)Cysteine (mesh)Humans (mesh)Tandem Mass Spectrometry (mesh)Humans (mesh)Copper (mesh)Azides (mesh)Alkynes (mesh)Cysteine (mesh)Catalysis (mesh)Tandem Mass Spectrometry (mesh)Click Chemistry (mesh)Cycloaddition Reaction (mesh)Alkynes (mesh)Azides (mesh)Catalysis (mesh)Click Chemistry (mesh)Copper (mesh)Cycloaddition Reaction (mesh)Cysteine (mesh)Humans (mesh)Tandem Mass Spectrometry (mesh)0301 Analytical Chemistry (for)0399 Other Chemical Sciences (for)Analytical Chemistry (science-metrix)3205 Medical biochemistry and metabolomics (for-2020)3401 Analytical chemistry (for-2020)4004 Chemical engineering (for-2020)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/6k65721jinfo:doi/10.1021/acs.analchem.1c04402articleAnalytical Chemistry, vol 94, iss 93800 - 3810oai:escholarship.org:ark:/13030/qt8883t6j92025-12-28T04:00:35Zqt8883t6j9Studying membrane proteins with MicroEDGallenito, Marc JGonen, Tamir2022-02-28The structural investigation of biological macromolecules is indispensable in understanding the molecular mechanisms underlying diseases. Several structural biology techniques have been introduced to unravel the structural facets of biomolecules. Among these, the electron cryomicroscopy (cryo-EM) method microcrystal electron diffraction (MicroED) has produced atomic resolution structures of important biological and small molecules. Since its inception in 2013, MicroED established a demonstrated ability for solving structures of difficult samples using vanishingly small crystals. However, membrane proteins remain the next big frontier for MicroED. The intrinsic properties of membrane proteins necessitate improved sample handling and imaging techniques to be developed and optimized for MicroED. Here, we summarize the milestones of electron crystallography of two-dimensional crystals leading to MicroED of three-dimensional crystals. Then, we focus on four different membrane protein families and discuss representatives from each family solved by MicroED.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)1.5 Resources and infrastructure (underpinning) (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Cryoelectron Microscopy (mesh)CrystallographyX-Ray (mesh)Electrons (mesh)Membrane Proteins (mesh)ModelsMolecular (mesh)Membrane Proteins (mesh)Cryoelectron Microscopy (mesh)CrystallographyX-Ray (mesh)Electrons (mesh)ModelsMolecular (mesh)MicroEDcryo-EMmicrocrystal electron diffractiontransmembrane proteinsCryoelectron Microscopy (mesh)CrystallographyX-Ray (mesh)Electrons (mesh)Membrane Proteins (mesh)ModelsMolecular (mesh)0601 Biochemistry and Cell Biology (for)1101 Medical Biochemistry and Metabolomics (for)Biochemistry & Molecular Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/8883t6j9https://escholarship.org/content/qt8883t6j9/qt8883t6j9.pdfinfo:doi/10.1042/bst20210911articleBiochemical Society Transactions, vol 50, iss 1231 - 239oai:escholarship.org:ark:/13030/qt5dw2f7d62025-12-28T03:50:46Zqt5dw2f7d6The Acyl-Proteome of Syntrophus aciditrophicus Reveals Metabolic Relationships in Benzoate DegradationMuroski, John MFu, Janine YNguyen, Hong HanhWofford, Neil QMouttaki, HousnaJames, Kimberly LMcInerney, Michael JGunsalus, Robert PLoo, Joseph ALoo, Rachel R Ogorzalek2022-04-01Syntrophus aciditrophicus is a model syntrophic bacterium that degrades fatty and aromatic acids into acetate, CO2, formate, and H2 that are utilized by methanogens and other hydrogen-consuming microbes. S. aciditrophicus benzoate degradation proceeds by a multistep pathway with many intermediate reactive acyl-coenzyme A species (RACS) that can potentially Nε-acylate lysine residues. Herein, we describe the identification and characterization of acyl-lysine modifications that correspond to RACS in the benzoate degradation pathway. The amounts of modified peptides are sufficient to analyze the post-translational modifications without antibody enrichment, enabling a range of acylations located, presumably, on the most extensively acylated proteins throughout the proteome to be studied. Seven types of acyl modifications were identified, six of which correspond directly to RACS that are intermediates in the benzoate degradation pathway including 3-hydroxypimeloylation, a modification first identified in this system. Indeed, benzoate-degrading enzymes are heavily represented among the acylated proteins. A total of 125 sites were identified in 60 proteins. Functional deacylase enzymes are present in the proteome, indicating a potential regulatory system/mechanism by which S. aciditrophicus modulates acylation. Uniquely, Nε-acyl-lysine RACS are highly abundant in these syntrophic bacteria, raising the compelling possibility that post-translational modifications modulate benzoate degradation in this and potentially other, syntrophic bacteria. Our results outline candidates for further study of how acylations impact syntrophic consortia.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Bacteria (mesh)Benzoates (mesh)Deltaproteobacteria (mesh)Lysine (mesh)Proteome (mesh)Bacteria (mesh)Deltaproteobacteria (mesh)Benzoates (mesh)Lysine (mesh)Proteome (mesh)Syntrophus aciditrophicuslysine acylationsirtuinssyntrophsBacteria (mesh)Benzoates (mesh)Deltaproteobacteria (mesh)Lysine (mesh)Proteome (mesh)Biochemistry & Molecular Biology (science-metrix)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/5dw2f7d6https://escholarship.org/content/qt5dw2f7d6/qt5dw2f7d6.pdfinfo:doi/10.1016/j.mcpro.2022.100215articleMolecular & Cellular Proteomics, vol 21, iss 4100215oai:escholarship.org:ark:/13030/qt4116h7ng2025-12-28T03:39:47Zqt4116h7ngA mammalian methylation array for profiling methylation levels at conserved sequencesArneson, AdrianaHaghani, AminThompson, Michael JPellegrini, MatteoKwon, Soo BinVu, HaMaciejewski, EmilyYao, MingjiaLi, Caesar ZLu, Ake TMorselli, MarcoRubbi, LiudmillaBarnes, BretHansen, Kasper DZhou, WandingBreeze, Charles EErnst, JasonHorvath, Steve2022-01-01Infinium methylation arrays are not available for the vast majority of non-human mammals. Moreover, even if species-specific arrays were available, probe differences between them would confound cross-species comparisons. To address these challenges, we developed the mammalian methylation array, a single custom array that measures up to 36k CpGs per species that are well conserved across many mammalian species. We designed a set of probes that can tolerate specific cross-species mutations. We annotate the array in over 200 species and report CpG island status and chromatin states in select species. Calibration experiments demonstrate the high fidelity in humans, rats, and mice. The mammalian methylation array has several strengths: it applies to all mammalian species even those that have not yet been sequenced, it provides deep coverage of conserved cytosines facilitating the development of epigenetic biomarkers, and it increases the probability that biological insights gained in one species will translate to others.31 Biological Sciences (for-2020)32 Biomedical and Clinical Sciences (for-2020)3105 Genetics (for-2020)Human Genome (rcdc)Genetics (rcdc)Generic health relevance (hrcs-hc)Animals (mesh)Biomarkers (mesh)Conserved Sequence (mesh)CpG Islands (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Humans (mesh)Mammals (mesh)Mice (mesh)Mutation (mesh)Protein ProcessingPost-Translational (mesh)Rats (mesh)Transcriptome (mesh)Animals (mesh)Mammals (mesh)Humans (mesh)Mice (mesh)Rats (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Protein ProcessingPost-Translational (mesh)CpG Islands (mesh)Conserved Sequence (mesh)Mutation (mesh)Transcriptome (mesh)Biomarkers (mesh)Animals (mesh)Biomarkers (mesh)Conserved Sequence (mesh)CpG Islands (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Humans (mesh)Mammals (mesh)Mice (mesh)Mutation (mesh)Protein ProcessingPost-Translational (mesh)Rats (mesh)Transcriptome (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/4116h7nghttps://escholarship.org/content/qt4116h7ng/qt4116h7ng.pdfinfo:doi/10.1038/s41467-022-28355-zarticleNature Communications, vol 13, iss 1783oai:escholarship.org:ark:/13030/qt2jx5j3d72025-12-28T01:38:42Zqt2jx5j3d7Atomic view of an amyloid dodecamer exhibiting selective cellular toxic vulnerability in acute brain slicesGray, Amber LHSawaya, Michael RAcharyya, DebalinaLou, JinchaoEdington, Emery MBest, Michael DProsser, Rebecca AEisenberg, David SD., Thanh2022-03-01Atomic structures of amyloid oligomers that capture the neurodegenerative disease pathology are essential to understand disease-state causes and finding cures. Here we investigate the G6W mutation of the cytotoxic, hexameric amyloid model KV11. The mutation results into an asymmetric dodecamer composed of a pair of 30° twisted antiparallel β-sheets. The complete break between adjacent β-strands is unprecedented among amyloid fibril crystal structures and supports that our structure is an oligomer. The poor shape complementarity between mated sheets reveals an interior channel for binding lipids, suggesting that the toxicity may be due to a perturbation of lipid transport rather than a direct disruption of membrane integrity. Viability assays on mouse suprachiasmatic nucleus, anterior hypothalamus, and cerebral cortex demonstrated selective regional vulnerability consistent with Alzheimer's disease. Neuropeptides released from the brain slices may provide clues to how G6W initiates cellular injury.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Brain Disorders (rcdc)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)Dementia (rcdc)Neurosciences (rcdc)Aging (rcdc)Neurodegenerative (rcdc)Alzheimer's Disease (rcdc)Acquired Cognitive Impairment (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Neurological (hrcs-hc)Alzheimer Disease (mesh)Amyloid (mesh)Amyloid beta-Peptides (mesh)Animals (mesh)Brain (mesh)Mice (mesh)ModelsMolecular (mesh)Neurodegenerative Diseases (mesh)Peptide Fragments (mesh)amyloid oligomersbrain slicesion-mobility mass spectrometrysuprachiasmatic nucleusX-ray crystallographyBrain (mesh)Animals (mesh)Mice (mesh)Alzheimer Disease (mesh)Neurodegenerative Diseases (mesh)Amyloid (mesh)Peptide Fragments (mesh)ModelsMolecular (mesh)Amyloid beta-Peptides (mesh)X-ray crystallographyamyloid oligomersbrain slicesion-mobility mass spectrometrysuprachiasmatic nucleusAlzheimer Disease (mesh)Amyloid (mesh)Amyloid beta-Peptides (mesh)Animals (mesh)Brain (mesh)Mice (mesh)ModelsMolecular (mesh)Neurodegenerative Diseases (mesh)Peptide Fragments (mesh)0601 Biochemistry and Cell Biology (for)0802 Computation Theory and Mathematics (for)0899 Other Information and Computing Sciences (for)Biophysics (science-metrix)3101 Biochemistry and cell biology (for-2020)3404 Medicinal and biomolecular chemistry (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2jx5j3d7https://escholarship.org/content/qt2jx5j3d7/qt2jx5j3d7.pdfinfo:doi/10.1002/pro.4268articleProtein Science, vol 31, iss 3716 - 727oai:escholarship.org:ark:/13030/qt6dj9b7cx2025-12-28T01:29:16Zqt6dj9b7cxIn Search of Small Molecules That Selectively Inhibit MBOAT4Murzinski, Emily SSaha, IshikaDing, HuiStrugatsky, DavidHollibaugh, Ryan ALiu, HaixiaTontonoz, PeterHarran, Patrick G2021-01-01Ghrelin is a 28-residue peptide hormone produced by stomach P/D1 cells located in oxyntic glands of the fundus mucosa. Post-translational octanoylation of its Ser-3 residue, catalyzed by MBOAT4 (aka ghrelin O-acyl transferase (GOAT)), is essential for the binding of the hormone to its receptor in target tissues. Physiological roles of acyl ghrelin include the regulation of food intake, growth hormone secretion from the pituitary, and inhibition of insulin secretion from the pancreas. Here, we describe a medicinal chemistry campaign that led to the identification of small lipopeptidomimetics that inhibit GOAT in vitro. These molecules compete directly for substrate binding. We further describe the synthesis of heterocyclic inhibitors that compete at the acyl coenzyme A binding site.3404 Medicinal and Biomolecular Chemistry (for-2020)3405 Organic Chemistry (for-2020)34 Chemical Sciences (for-2020)Nutrition (rcdc)Digestive Diseases (rcdc)Acyltransferases (mesh)Animals (mesh)Enzyme Inhibitors (mesh)Gastric Mucosa (mesh)Ghrelin (mesh)Lipoylation (mesh)Membrane Proteins (mesh)Mice (mesh)Peptidomimetics (mesh)ghrelin O-acyl transferaseMBOAT 4peptidomimeticGastric Mucosa (mesh)Animals (mesh)Mice (mesh)Acyltransferases (mesh)Membrane Proteins (mesh)Enzyme Inhibitors (mesh)Ghrelin (mesh)Lipoylation (mesh)Peptidomimetics (mesh)MBOAT 4ghrelin O-acyl transferasepeptidomimeticAcyltransferases (mesh)Animals (mesh)Enzyme Inhibitors (mesh)Gastric Mucosa (mesh)Ghrelin (mesh)Lipoylation (mesh)Membrane Proteins (mesh)Mice (mesh)Peptidomimetics (mesh)0304 Medicinal and Biomolecular Chemistry (for)0305 Organic Chemistry (for)0307 Theoretical and Computational Chemistry (for)Organic Chemistry (science-metrix)3404 Medicinal and biomolecular chemistry (for-2020)3405 Organic chemistry (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/6dj9b7cxhttps://escholarship.org/content/qt6dj9b7cx/qt6dj9b7cx.pdfinfo:doi/10.3390/molecules26247599articleMolecules, vol 26, iss 247599oai:escholarship.org:ark:/13030/qt2d92b2102025-12-28T01:19:13Zqt2d92b210Benchmarking the ideal sample thickness in cryo-EMMartynowycz, Michael WClabbers, Max TBUnge, JohanHattne, JohanGonen, Tamir2021-12-07The relationship between sample thickness and quality of data obtained is investigated by microcrystal electron diffraction (MicroED). Several electron microscopy (EM) grids containing proteinase K microcrystals of similar sizes from the same crystallization batch were prepared. Each grid was transferred into a focused ion beam and a scanning electron microscope in which the crystals were then systematically thinned into lamellae between 95- and 1,650-nm thick. MicroED data were collected at either 120-, 200-, or 300-kV accelerating voltages. Lamellae thicknesses were expressed in multiples of the corresponding inelastic mean free path to allow the results from different acceleration voltages to be compared. The quality of the data and subsequently determined structures were assessed using standard crystallographic measures. Structures were reliably determined with similar quality from crystalline lamellae up to twice the inelastic mean free path. Lower resolution diffraction was observed at three times the mean free path for all three accelerating voltages, but the data quality was insufficient to yield structures. Finally, no coherent diffraction was observed from lamellae thicker than four times the calculated inelastic mean free path. This study benchmarks the ideal specimen thickness with implications for all cryo-EM methods.51 Physical Sciences (for-2020)5104 Condensed Matter Physics (for-2020)Animals (mesh)Benchmarking (mesh)Cryoelectron Microscopy (mesh)Crystallization (mesh)Crystallography (mesh)Electrons (mesh)Humans (mesh)MicroscopyElectronScanning (mesh)MicroscopyElectronTransmission (mesh)ModelsMolecular (mesh)Specimen Handling (mesh)Cryo-EMMicroEDFIB millingelectron scatteringmean free pathAnimals (mesh)Humans (mesh)Cryoelectron Microscopy (mesh)MicroscopyElectronScanning (mesh)MicroscopyElectronTransmission (mesh)Specimen Handling (mesh)Crystallization (mesh)Crystallography (mesh)Electrons (mesh)ModelsMolecular (mesh)Benchmarking (mesh)Cryo-EMFIB millingMicroEDelectron scatteringmean free pathAnimals (mesh)Benchmarking (mesh)Cryoelectron Microscopy (mesh)Crystallization (mesh)Crystallography (mesh)Electrons (mesh)Humans (mesh)MicroscopyElectronScanning (mesh)MicroscopyElectronTransmission (mesh)ModelsMolecular (mesh)Specimen Handling (mesh)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/2d92b210https://escholarship.org/content/qt2d92b210/qt2d92b210.pdfinfo:doi/10.1073/pnas.2108884118articleProceedings of the National Academy of Sciences of the United States of America, vol 118, iss 49e2108884118oai:escholarship.org:ark:/13030/qt7p20896t2025-12-28T01:13:57Zqt7p20896tMechanisms of Non-Vesicular Exchange of Lipids at Membrane Contact Sites: Of Shuttles, Tunnels and, FunnelsEgea, Pascal F2021-01-01Eukaryotic cells are characterized by their exquisite compartmentalization resulting from a cornucopia of membrane-bound organelles. Each of these compartments hosts a flurry of biochemical reactions and supports biological functions such as genome storage, membrane protein and lipid biosynthesis/degradation and ATP synthesis, all essential to cellular life. Acting as hubs for the transfer of matter and signals between organelles and throughout the cell, membrane contacts sites (MCSs), sites of close apposition between membranes from different organelles, are essential to cellular homeostasis. One of the now well-acknowledged function of MCSs involves the non-vesicular trafficking of lipids; its characterization answered one long-standing question of eukaryotic cell biology revealing how some organelles receive and distribute their membrane lipids in absence of vesicular trafficking. The endoplasmic reticulum (ER) in synergy with the mitochondria, stands as the nexus for the biosynthesis and distribution of phospholipids (PLs) throughout the cell by contacting nearly all other organelle types. MCSs create and maintain lipid fluxes and gradients essential to the functional asymmetry and polarity of biological membranes throughout the cell. Membrane apposition is mediated by proteinaceous tethers some of which function as lipid transfer proteins (LTPs). We summarize here the current state of mechanistic knowledge of some of the major classes of LTPs and tethers based on the available atomic to near-atomic resolution structures of several "model" MCSs from yeast but also in Metazoans; we describe different models of lipid transfer at MCSs and analyze the determinants of their specificity and directionality. Each of these systems illustrate fundamental principles and mechanisms for the non-vesicular exchange of lipids between eukaryotic membrane-bound organelles essential to a wide range of cellular processes such as at PL biosynthesis and distribution, lipid storage, autophagy and organelle biogenesis.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)organellemembrane contact sitelipid transfer proteinlipid distributionmembrane asymmetrymitochondria-attached membraneslipid-dropletautophagyautophagylipid distributionlipid transfer proteinlipid-dropletmembrane asymmetrymembrane contact sitemitochondria-attached membranesorganelle31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7p20896thttps://escholarship.org/content/qt7p20896t/qt7p20896t.pdfinfo:doi/10.3389/fcell.2021.784367articleFrontiers in Cell and Developmental Biology, vol 9784367oai:escholarship.org:ark:/13030/qt0wd0m4n12025-12-28T00:21:12Zqt0wd0m4n1The Human Proteoform Project: Defining the human proteomeSmith, Lloyd MAgar, Jeffrey NChamot-Rooke, JuliaDanis, Paul OGe, YingLoo, Joseph APaša-Tolić, LjiljanaTsybin, Yury OKelleher, Neil LProteomics, The Consortium for Top-Down2021-11-12Proteins are the primary effectors of function in biology, and thus, complete knowledge of their structure and properties is fundamental to deciphering function in basic and translational research. The chemical diversity of proteins is expressed in their many proteoforms, which result from combinations of genetic polymorphisms, RNA splice variants, and posttranslational modifications. This knowledge is foundational for the biological complexes and networks that control biology yet remains largely unknown. We propose here an ambitious initiative to define the human proteome, that is, to generate a definitive reference set of the proteoforms produced from the genome. Several examples of the power and importance of proteoform-level knowledge in disease-based research are presented along with a call for improved technologies in a two-pronged strategy to the Human Proteoform Project.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)3105 Genetics (for-2020)Genetics (rcdc)Human Genome (rcdc)Biotechnology (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Generic health relevance (hrcs-hc)Consortium for Top-Down Proteomicsapplication/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/0wd0m4n1https://escholarship.org/content/qt0wd0m4n1/qt0wd0m4n1.pdfinfo:doi/10.1126/sciadv.abk0734articleScience Advances, vol 7, iss 46eabk0734oai:escholarship.org:ark:/13030/qt4872m5px2025-12-28T00:07:46Zqt4872m5pxIs There a Histone Code for Cellular Quiescence?Bonitto, KenyaSarathy, KirthanaAtai, KaiserMitra, MithunColler, Hilary A2021-01-01Many of the cells in our bodies are quiescent, that is, temporarily not dividing. Under certain physiological conditions such as during tissue repair and maintenance, quiescent cells receive the appropriate stimulus and are induced to enter the cell cycle. The ability of cells to successfully transition into and out of a quiescent state is crucial for many biological processes including wound healing, stem cell maintenance, and immunological responses. Across species and tissues, transcriptional, epigenetic, and chromosomal changes associated with the transition between proliferation and quiescence have been analyzed, and some consistent changes associated with quiescence have been identified. Histone modifications have been shown to play a role in chromatin packing and accessibility, nucleosome mobility, gene expression, and chromosome arrangement. In this review, we critically evaluate the role of different histone marks in these processes during quiescence entry and exit. We consider different model systems for quiescence, each of the most frequently monitored candidate histone marks, and the role of their writers, erasers and readers. We highlight data that support these marks contributing to the changes observed with quiescence. We specifically ask whether there is a quiescence histone "code," a mechanism whereby the language encoded by specific combinations of histone marks is read and relayed downstream to modulate cell state and function. We conclude by highlighting emerging technologies that can be applied to gain greater insight into the role of a histone code for quiescence.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Generic health relevance (hrcs-hc)histone post translational modificationquiescencehistone methylationhistone acetylationmetabolismhistone codehistone acetylationhistone codehistone methylationhistone post translational modificationmetabolismquiescence31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/4872m5pxhttps://escholarship.org/content/qt4872m5px/qt4872m5px.pdfinfo:doi/10.3389/fcell.2021.739780articleFrontiers in Cell and Developmental Biology, vol 9739780oai:escholarship.org:ark:/13030/qt79x1b6h62025-12-27T22:54:08Zqt79x1b6h6Comparative cellular analysis of motor cortex in human, marmoset and mouseBakken, Trygve EJorstad, Nikolas LHu, QiwenLake, Blue BTian, WeiKalmbach, Brian ECrow, MeganHodge, Rebecca DKrienen, Fenna MSorensen, Staci AEggermont, JeroenYao, ZizhenAevermann, Brian DAldridge, Andrew IBartlett, AnnaBertagnolli, DarrenCasper, TamaraCastanon, Rosa GCrichton, KirstenDaigle, Tanya LDalley, RachelDee, NickDembrow, NikolaiDiep, DinhDing, Song-LinDong, WeixiuFang, RongxinFischer, StephanGoldman, MelissaGoldy, JeffGraybuck, Lucas THerb, Brian RHou, XiaomengKancherla, JayaramKroll, MatthewLathia, Kananvan Lew, BaldurLi, Yang EricLiu, Christine SLiu, HanqingLucero, Jacinta DMahurkar, AnupMcMillen, DelissaMiller, Jeremy AMoussa, MarmarNery, Joseph RNicovich, Philip RNiu, Sheng-YongOrvis, JoshuaOsteen, Julia KOwen, ScottPalmer, Carter RPham, ThanhPlongthongkum, NonglukPoirion, OlivierReed, Nora MRimorin, ChristineRivkin, AngelineRomanow, William JSedeño-Cortés, Adriana ESiletti, KimberlySomasundaram, SarojaSulc, JosefTieu, MichaelTorkelson, AmyTung, HermanWang, XinxinXie, FangmingYanny, Anna MarieZhang, ReneeAment, Seth ABehrens, M MargaritaBravo, Hector CorradaChun, JeroldDobin, AlexanderGillis, JesseHertzano, RonnaHof, Patrick RHöllt, ThomasHorwitz, Gregory DKeene, C DirkKharchenko, Peter VKo, Andrew LLelieveldt, Boudewijn PLuo, ChongyuanMukamel, Eran APinto-Duarte, AntónioPreissl, SebastianRegev, AvivRen, BingScheuermann, Richard HSmith, KimberlySpain, William JWhite, Owen RKoch, ChristofHawrylycz, MichaelTasic, BosiljkaMacosko, Evan ZMcCarroll, Steven ATing, Jonathan T2021-10-07The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals1. Here, using high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmoset monkeys and mice, we demonstrate a broadly conserved cellular makeup of this region, with similarities that mirror evolutionary distance and are consistent between the transcriptome and epigenome. The core conserved molecular identities of neuronal and non-neuronal cell types allow us to generate a cross-species consensus classification of cell types, and to infer conserved properties of cell types across species. Despite the overall conservation, however, many species-dependent specializations are apparent, including differences in cell-type proportions, gene expression, DNA methylation and chromatin state. Few cell-type marker genes are conserved across species, revealing a short list of candidate genes and regulatory mechanisms that are responsible for conserved features of homologous cell types, such as the GABAergic chandelier cells. This consensus transcriptomic classification allows us to use patch–seq (a combination of whole-cell patch-clamp recordings, RNA sequencing and morphological characterization) to identify corticospinal Betz cells from layer 5 in non-human primates and humans, and to characterize their highly specialized physiology and anatomy. These findings highlight the robust molecular underpinnings of cell-type diversity in M1 across mammals, and point to the genes and regulatory pathways responsible for the functional identity of cell types and their species-specific adaptations.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)3105 Genetics (for-2020)Neurosciences (rcdc)Genetics (rcdc)Human Genome (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Neurological (hrcs-hc)Animals (mesh)Atlases as Topic (mesh)Callithrix (mesh)EpigenesisGenetic (mesh)Epigenomics (mesh)Female (mesh)GABAergic Neurons (mesh)Gene Expression Profiling (mesh)Glutamates (mesh)Humans (mesh)In Situ HybridizationFluorescence (mesh)Male (mesh)Mice (mesh)Middle Aged (mesh)Motor Cortex (mesh)Neurons (mesh)Organ Specificity (mesh)Phylogeny (mesh)Single-Cell Analysis (mesh)Species Specificity (mesh)Transcriptome (mesh)Motor Cortex (mesh)Neurons (mesh)Animals (mesh)Callithrix (mesh)Humans (mesh)Mice (mesh)Glutamates (mesh)In Situ HybridizationFluorescence (mesh)Gene Expression Profiling (mesh)Phylogeny (mesh)Organ Specificity (mesh)Species Specificity (mesh)EpigenesisGenetic (mesh)Middle Aged (mesh)Female (mesh)Male (mesh)Atlases as Topic (mesh)Epigenomics (mesh)Single-Cell Analysis (mesh)Transcriptome (mesh)GABAergic Neurons (mesh)Animals (mesh)Atlases as Topic (mesh)Callithrix (mesh)EpigenesisGenetic (mesh)Epigenomics (mesh)Female (mesh)GABAergic Neurons (mesh)Gene Expression Profiling (mesh)Glutamates (mesh)Humans (mesh)In Situ HybridizationFluorescence (mesh)Male (mesh)Mice (mesh)Middle Aged (mesh)Motor Cortex (mesh)Neurons (mesh)Organ Specificity (mesh)Phylogeny (mesh)Single-Cell Analysis (mesh)Species Specificity (mesh)Transcriptome (mesh)General Science & Technology (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/79x1b6h6https://escholarship.org/content/qt79x1b6h6/qt79x1b6h6.pdfinfo:doi/10.1038/s41586-021-03465-8articleNature, vol 598, iss 7879111 - 119oai:escholarship.org:ark:/13030/qt6x6354202025-12-27T22:19:04Zqt6x635420Prevalence and species distribution of the low-complexity, amyloid-like, reversible, kinked segment structural motif in amyloid-like fibrilsHughes, Michael PGoldschmidt, LukaszEisenberg, David S2021-10-01Membraneless organelles (MLOs) are vital and dynamic reaction centers in cells that compartmentalize the cytoplasm in the absence of a membrane. Multivalent interactions between protein low-complexity domains contribute to MLO organization. Previously, we used computational methods to identify structural motifs termed low-complexity amyloid-like reversible kinked segments (LARKS) that promote phase transition to form hydrogels and that are common in human proteins that participate in MLOs. Here, we searched for LARKS in the proteomes of six model organisms: Homo sapiens, Drosophila melanogaster, Plasmodium falciparum, Saccharomyces cerevisiae, Mycobacterium tuberculosis, and Escherichia coli to gain an understanding of the distribution of LARKS in the proteomes of various species. We found that LARKS are abundant in M. tuberculosis, D. melanogaster, and H. sapiens but not in S. cerevisiae or P. falciparum. LARKS have high glycine content, which enables kinks to form as exemplified by the known LARKS-rich amyloidogenic structures of TDP43, FUS, and hnRNPA2, three proteins that are known to participate in MLOs. These results support the idea of LARKS as an evolved structural motif. Based on these results, we also established the LARKSdb Web server, which permits users to search for LARKS in their protein sequences of interest.3101 Biochemistry and Cell Biology (for-2020)3102 Bioinformatics and Computational Biology (for-2020)31 Biological Sciences (for-2020)Infectious Diseases (rcdc)Tuberculosis (rcdc)Emerging Infectious Diseases (rcdc)Rare Diseases (rcdc)3 Good Health and Well Being (sdg)Amino Acid Motifs (mesh)Amyloid (mesh)Animals (mesh)Drosophila Proteins (mesh)Drosophila melanogaster (mesh)Humans (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)Animals (mesh)Humans (mesh)Drosophila melanogaster (mesh)Saccharomyces cerevisiae (mesh)Amyloid (mesh)Saccharomyces cerevisiae Proteins (mesh)Drosophila Proteins (mesh)Amino Acid Motifs (mesh)LARKSamyloidlow-complexity domainsmembraneless organellesphase-separationAmino Acid Motifs (mesh)Amyloid (mesh)Animals (mesh)Drosophila Proteins (mesh)Drosophila melanogaster (mesh)Humans (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biochemistry & Molecular Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/6x635420https://escholarship.org/content/qt6x635420/qt6x635420.pdfinfo:doi/10.1016/j.jbc.2021.101194articleJournal of Biological Chemistry, vol 297, iss 4101194oai:escholarship.org:ark:/13030/qt3qq5n0592025-12-27T21:41:41Zqt3qq5n059Metabolic plasticity drives development during mammalian embryogenesisSharpley, Mark SChi, FangtaoHoeve, Johanna TenBanerjee, Utpal2021-08-01Mammalian preimplantation embryos follow a stereotypic pattern of development from zygotes to blastocysts. Here, we use labeled nutrient isotopologue analysis of small numbers of embryos to track downstream metabolites. Combined with transcriptomic analysis, we assess the capacity of the embryo to reprogram its metabolism through development. Early embryonic metabolism is rigid in its nutrient requirements, sensitive to reductive stress and has a marked disequilibrium between two halves of the TCA cycle. Later, loss of maternal LDHB and transcription of zygotic products favors increased activity of bioenergetic shuttles, fatty-acid oxidation and equilibration of the TCA cycle. As metabolic plasticity peaks, blastocysts can develop without external nutrients. Normal developmental metabolism of the early embryo is distinct from cancer metabolism. However, similarities emerge upon reductive stress. Increased metabolic plasticity with maturation is due to changes in redox control mechanisms and to transcriptional reprogramming of later-stage embryos during homeostasis or upon adaptation to environmental changes.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Pediatric (rcdc)Nutrition (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)AdaptationPhysiological (mesh)Animals (mesh)Blastocyst (mesh)CellsCultured (mesh)Citric Acid Cycle (mesh)Glucose (mesh)Glutamine (mesh)Metabolome (mesh)Mice (mesh)MiceInbred C57BL (mesh)NAD (mesh)Oxidation-Reduction (mesh)Transcriptome (mesh)CellsCultured (mesh)Blastocyst (mesh)Animals (mesh)MiceInbred C57BL (mesh)Mice (mesh)NAD (mesh)Glucose (mesh)Glutamine (mesh)AdaptationPhysiological (mesh)Citric Acid Cycle (mesh)Oxidation-Reduction (mesh)Metabolome (mesh)Transcriptome (mesh)MYCNAD+/NADHdevelopmental metabolismembryometabolic plasticitymetabolic reprogrammingpreimplantationredoxreductive stresszygotic genome activationAdaptationPhysiological (mesh)Animals (mesh)Blastocyst (mesh)CellsCultured (mesh)Citric Acid Cycle (mesh)Glucose (mesh)Glutamine (mesh)Metabolome (mesh)Mice (mesh)MiceInbred C57BL (mesh)NAD (mesh)Oxidation-Reduction (mesh)Transcriptome (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3qq5n059https://escholarship.org/content/qt3qq5n059/qt3qq5n059.pdfinfo:doi/10.1016/j.devcel.2021.07.020articleDevelopmental Cell, vol 56, iss 162329 - 2347.e6oai:escholarship.org:ark:/13030/qt63v3d7k12025-12-27T21:19:14Zqt63v3d7k1Determining the Lipid-Binding Specificity of SMP Domains: An ERMES Subunit as a Case StudyAhYoung, Andrew PEgea, Pascal F2019-01-01Membrane contact sites between the endoplasmic reticulum (ER) and mitochondria function as a central hub for the exchange of phospholipids and calcium. The yeast Endoplasmic Reticulum–Mitochondrion Encounter Structure (ERMES) complex is composed of five subunits that tether the ER and mitochondria. Three ERMES subunits (i.e., Mdm12, Mmm1, and Mdm34) contain the synaptotagmin-like mitochondrial lipid-binding protein (SMP) domain. The SMP domain belongs to the tubular lipid-binding protein (TULIP) superfamily, which consists of ubiquitous lipid scavenging and transfer proteins. Herein, we describe the methods for expression and purification of recombinant Mdm12, a bona fide SMP-containing protein, together with the subsequent identification of its bound phospholipids by high-performance thin-layer chromatography (HPTLC) and the characterization of its lipid exchange and transfer functions using lipid displacement and liposome flotation in vitro assays with liposomes as model biological membranes. These methods can be applied to the study and characterization of novel lipid-binding and lipid-transfer proteins.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)1.1 Normal biological development and functioning (hrcs-rac)Bacteria (mesh)Biological Transport (mesh)Carrier Proteins (mesh)ChromatographyLiquid (mesh)ChromatographyThin Layer (mesh)Endoplasmic Reticulum (mesh)Gene Expression Regulation (mesh)Liposomes (mesh)Mitochondrial Proteins (mesh)Phospholipids (mesh)Protein Interaction Domains and Motifs (mesh)Protein Subunits (mesh)Recombinant Proteins (mesh)Structure-Activity Relationship (mesh)Yeasts (mesh)ERMESMdm12SMP domainLipid-transfer proteinPhospholipidMembrane contact sitesLiposomeHPTLCLipid displacementLiposome flotationEndoplasmic Reticulum (mesh)Bacteria (mesh)Yeasts (mesh)Phospholipids (mesh)Carrier Proteins (mesh)Mitochondrial Proteins (mesh)Protein Subunits (mesh)Recombinant Proteins (mesh)Liposomes (mesh)ChromatographyLiquid (mesh)ChromatographyThin Layer (mesh)Gene Expression Regulation (mesh)Structure-Activity Relationship (mesh)Biological Transport (mesh)Protein Interaction Domains and Motifs (mesh)ERMESHPTLCLipid displacementLipid-transfer proteinLiposomeLiposome flotationMdm12Membrane contact sitesPhospholipidSMP domainBacteria (mesh)Biological Transport (mesh)Carrier Proteins (mesh)ChromatographyLiquid (mesh)ChromatographyThin Layer (mesh)Endoplasmic Reticulum (mesh)Gene Expression Regulation (mesh)Liposomes (mesh)Mitochondrial Proteins (mesh)Phospholipids (mesh)Protein Interaction Domains and Motifs (mesh)Protein Subunits (mesh)Recombinant Proteins (mesh)Structure-Activity Relationship (mesh)Yeasts (mesh)0399 Other Chemical Sciences (for)0601 Biochemistry and Cell Biology (for)Developmental Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)3404 Medicinal and biomolecular chemistry (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/63v3d7k1https://escholarship.org/content/qt63v3d7k1/qt63v3d7k1.pdfinfo:doi/10.1007/978-1-4939-9136-5_16articleMethods in Molecular Biology, vol 1949213 - 235oai:escholarship.org:ark:/13030/qt4x6933x02025-12-27T21:19:04Zqt4x6933x0Crossing the Vacuolar Rubicon: Structural Insights into Effector Protein Trafficking in Apicomplexan ParasitesEgea, Pascal F2020-01-01Apicomplexans form a large phylum of parasitic protozoa, including the genera Plasmodium, Toxoplasma, and Cryptosporidium, the causative agents of malaria, toxoplasmosis, and cryptosporidiosis, respectively. They cause diseases not only in humans but also in animals, with dramatic consequences in agriculture. Most apicomplexans are vacuole-dwelling and obligate intracellular parasites; as they invade the host cell, they become encased in a parasitophorous vacuole (PV) derived from the host cellular membrane. This creates a parasite-host interface that acts as a protective barrier but also constitutes an obstacle through which the pathogen must import nutrients, eliminate wastes, and eventually break free upon egress. Completion of the parasitic life cycle requires intense remodeling of the infected host cell. Host cell subversion is mediated by a subset of essential effector parasitic proteins and virulence factors actively trafficked across the PV membrane. In the malaria parasite Plasmodium, a unique and highly specialized ATP-driven vacuolar secretion system, the Plasmodium translocon of exported proteins (PTEX), transports effector proteins across the vacuolar membrane. Its core is composed of the three essential proteins EXP2, PTEX150, and HSP101, and is supplemented by the two auxiliary proteins TRX2 and PTEX88. Many but not all secreted malarial effector proteins contain a vacuolar trafficking signal or Plasmodium export element (PEXEL) that requires processing by an endoplasmic reticulum protease, plasmepsin V, for proper export. Because vacuolar parasitic protein export is essential to parasite survival and virulence, this pathway is a promising target for the development of novel antimalarial therapeutics. This review summarizes the current state of structural and mechanistic knowledge on the Plasmodium parasitic vacuolar secretion and effector trafficking pathway, describing its most salient features and discussing the existing differences and commonalities with the vacuolar effector translocation MYR machinery recently described in Toxoplasma and other apicomplexans of significance to medical and veterinary sciences.31 Biological Sciences (for-2020)32 Biomedical and Clinical Sciences (for-2020)3101 Biochemistry and Cell Biology (for-2020)3107 Microbiology (for-2020)3207 Medical Microbiology (for-2020)Vector-Borne Diseases (rcdc)Foodborne Illness (rcdc)Malaria (rcdc)Biodefense (rcdc)Emerging Infectious Diseases (rcdc)Orphan Drug (rcdc)Rare Diseases (rcdc)Infectious Diseases (rcdc)2.2 Factors relating to the physical environment (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Infection (hrcs-hc)3 Good Health and Well Being (sdg)apicomplexaPlasmodiummalariaToxoplasmaPTEXMYRtranslocon-protein secretionparasitophorous vacuoleparasite-host interfaceeffectorvirulence factorpore-forming membrane proteinAAA plus chaperoneClpBHSP104thioredoxinproteaseanti-parasitic drugAAA+ chaperoneApicomplexaClpB/HSP104MYRPTEXPlasmodiumToxoplasmaanti-parasitic drugeffectormalariaparasite–host interfaceparasitophorous vacuolepore-forming membrane proteinproteasethioredoxintranslocon–protein secretionvirulence factor3107 Microbiology (for-2020)3207 Medical microbiology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4x6933x0https://escholarship.org/content/qt4x6933x0/qt4x6933x0.pdfinfo:doi/10.3390/microorganisms8060865articleMicroorganisms, vol 8, iss 6865oai:escholarship.org:ark:/13030/qt5ds8b5p62025-12-27T20:23:02Zqt5ds8b5p6Crosstalk between epitranscriptomic and epigenetic mechanisms in gene regulationKan, Ryan LChen, JianjunSallam, Tamer2022-02-01Epigenetic modifications occur on genomic DNA and histones to influence gene expression. More recently, the discovery that mRNA undergoes similar chemical modifications that powerfully impact transcript turnover and translation adds another layer of dynamic gene regulation. Central to precise and synchronized regulation of gene expression is intricate crosstalk between multiple checkpoints involved in transcript biosynthesis and processing. There are more than 100 internal modifications of RNA in mammalian cells. The most common is N6-methyladenosine (m6A) methylation. Although m6A is established to influence RNA stability dynamics and translation efficiency, rapidly accumulating evidence shows significant crosstalk between RNA methylation and histone/DNA epigenetic mechanisms. These interactions specify transcriptional outputs, translation, recruitment of chromatin modifiers, as well as the deployment of the m6A methyltransferase complex (MTC) at target sites. In this review, we dissect m6A-orchestrated feedback circuits that regulate histone modifications and the activity of regulatory RNAs, such as long noncoding (lnc)RNA and chromosome-associated regulatory RNA. Collectively, this body of evidence suggests that m6A acts as a versatile checkpoint that can couple different layers of gene regulation with one another.3101 Biochemistry and Cell Biology (for-2020)3105 Genetics (for-2020)31 Biological Sciences (for-2020)Human Genome (rcdc)Genetics (rcdc)Biotechnology (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Animals (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Gene Expression Regulation (mesh)Histones (mesh)Methylation (mesh)RNALong Noncoding (mesh)Animals (mesh)Histones (mesh)DNA Methylation (mesh)Gene Expression Regulation (mesh)EpigenesisGenetic (mesh)Methylation (mesh)RNALong Noncoding (mesh)RNA methylationRNA modificationepigeneticsgene regulationAnimals (mesh)DNA Methylation (mesh)EpigenesisGenetic (mesh)Gene Expression Regulation (mesh)Histones (mesh)Methylation (mesh)RNALong Noncoding (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/5ds8b5p6https://escholarship.org/content/qt5ds8b5p6/qt5ds8b5p6.pdfinfo:doi/10.1016/j.tig.2021.06.014articleTrends in Genetics, vol 38, iss 2182 - 193oai:escholarship.org:ark:/13030/qt2wg9k38h2025-12-27T18:32:18Zqt2wg9k38hCortical Representations of Conspecific Sex Shape Social BehaviorKingsbury, LyleHuang, ShanRaam, TaraYe, Letizia SWei, DonHu, Rongfeng KYe, LiHong, Weizhe2020-09-01A central question related to virtually all social decisions is how animals integrate sex-specific cues from conspecifics. Using microendoscopic calcium imaging in mice, we find that sex information is represented in the dorsal medial prefrontal cortex (dmPFC) across excitatory and inhibitory neurons. These cells form a distributed code that differentiates the sex of conspecifics and is strengthened with social experience. While males and females both represent sex in the dmPFC, male mice show stronger encoding of female cues, and the relative strength of these sex representations predicts sex preference behavior. Using activity-dependent optogenetic manipulations of natively active ensembles, we further show that these specific representations modulate preference behavior toward males and females. Together, these results define a functional role for native representations of sex in shaping social behavior and reveal a neural mechanism underlying male- versus female-directed sociality.5202 Biological Psychology (for-2020)32 Biomedical and Clinical Sciences (for-2020)3209 Neurosciences (for-2020)52 Psychology (for-2020)Women's Health (rcdc)Basic Behavioral and Social Science (rcdc)Neurosciences (rcdc)Behavioral and Social Science (rcdc)Mental Health (rcdc)1.2 Psychological and socioeconomic processes (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)Neurological (hrcs-hc)Animals (mesh)BehaviorAnimal (mesh)Cues (mesh)Female (mesh)Male (mesh)Mice (mesh)Neurons (mesh)Prefrontal Cortex (mesh)Sex Characteristics (mesh)Social Behavior (mesh)Prefrontal Cortex (mesh)Neurons (mesh)Animals (mesh)Mice (mesh)BehaviorAnimal (mesh)Social Behavior (mesh)Cues (mesh)Sex Characteristics (mesh)Female (mesh)Male (mesh)E-SAREFosPFCactivity-dependent labelingconspecificcorticalminiature microendoscopeneural encodingsexsocial behaviorAnimals (mesh)BehaviorAnimal (mesh)Cues (mesh)Female (mesh)Male (mesh)Mice (mesh)Neurons (mesh)Prefrontal Cortex (mesh)Sex Characteristics (mesh)Social Behavior (mesh)1109 Neurosciences (for)1701 Psychology (for)1702 Cognitive Sciences (for)Neurology & Neurosurgery (science-metrix)3209 Neurosciences (for-2020)5202 Biological psychology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2wg9k38hhttps://escholarship.org/content/qt2wg9k38h/qt2wg9k38h.pdfinfo:doi/10.1016/j.neuron.2020.06.020articleNeuron, vol 107, iss 5941 - 953.e7oai:escholarship.org:ark:/13030/qt09f2t96j2025-12-27T17:56:32Zqt09f2t96jAn Overview of Microcrystal Electron Diffraction (MicroED)Mu, XuelangGillman, CodyNguyen, ChiGonen, Tamir2021-06-20The bedrock of drug discovery and a key tool for understanding cellular function and drug mechanisms of action is the structure determination of chemical compounds, peptides, and proteins. The development of new structure characterization tools, particularly those that fill critical gaps in existing methods, presents important steps forward for structural biology and drug discovery. The emergence of microcrystal electron diffraction (MicroED) expands the application of cryo-electron microscopy to include samples ranging from small molecules and membrane proteins to even large protein complexes using crystals that are one-billionth the size of those required for X-ray crystallography. This review outlines the conception, achievements, and exciting future trajectories for MicroED, an important addition to the existing biophysical toolkit.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Biotechnology (rcdc)1.5 Resources and infrastructure (underpinning) (hrcs-rac)Generic health relevance (hrcs-hc)Cryoelectron Microscopy (mesh)Crystallization (mesh)Drug Discovery (mesh)Electrons (mesh)MicroscopyElectronTransmission (mesh)Nanoparticles (mesh)Proteins (mesh)Workflow (mesh)MicroEDmicrocrystal electron diffractioncryo-EMcryo-electron microscopystructurescrystallographyproteinsProteins (mesh)Cryoelectron Microscopy (mesh)MicroscopyElectronTransmission (mesh)Crystallization (mesh)Electrons (mesh)Nanoparticles (mesh)Drug Discovery (mesh)Workflow (mesh)MicroEDcryo-EMcryo–electron microscopycrystallographymicrocrystal electron diffractionproteinsstructuresCryoelectron Microscopy (mesh)Crystallization (mesh)Drug Discovery (mesh)Electrons (mesh)MicroscopyElectronTransmission (mesh)Nanoparticles (mesh)Proteins (mesh)Workflow (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biochemistry & Molecular Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/09f2t96jhttps://escholarship.org/content/qt09f2t96j/qt09f2t96j.pdfinfo:doi/10.1146/annurev-biochem-081720-020121articleAnnual Review of Biochemistry, vol 90, iss 1431 - 450oai:escholarship.org:ark:/13030/qt2s9253cj2025-12-27T17:35:31Zqt2s9253cjControl of the Serine Integrase Reaction: Roles of the Coiled-Coil and Helix E Regions in DNA Site Synapsis and RecombinationMandali, SridharJohnson, Reid CMetcalf, William W2021-07-22Bacteriophage serine integrases catalyze highly specific recombination reactions between defined DNA segments called att sites. These reactions are reversible depending upon the presence of a second phage-encoded directionality factor. The bipartite C-terminal DNA-binding region of integrases includes a recombinase domain (RD) connected to a zinc-binding domain (ZD), which contains a long flexible coiled-coil (CC) motif that extends away from the bound DNA. We directly show that the identities of the phage A118 integrase att sites are specified by the DNA spacing between the RD and ZD DNA recognition determinants, which in turn directs the relative trajectories of the CC motifs on each subunit of the att-bound integrase dimer. Recombination between compatible dimer-bound att sites requires minimal-length CC motifs and 14 residues surrounding the tip where the pairing of CC motifs between synapsing dimers occurs. Our alanine-scanning data suggest that molecular interactions between CC motif tips may differ in integrative (attP × attB) and excisive (attL × attR) recombination reactions. We identify mutations in 5 residues within the integrase oligomerization helix that control the remodeling of dimers into tetramers during synaptic complex formation. Whereas most of these gain-of-function mutants still require the CC motifs for synapsis, one mutant efficiently, but indiscriminately, forms synaptic complexes without the CC motifs. However, the CC motifs are still required for recombination, suggesting a function for the CC motifs after the initial assembly of the integrase synaptic tetramer. IMPORTANCE The robust and exquisitely regulated site-specific recombination reactions promoted by serine integrases are integral to the life cycle of temperate bacteriophage and, in the case of the A118 prophage, are an important virulence factor of Listeria monocytogenes. The properties of these recombinases have led to their repurposing into tools for genetic engineering and synthetic biology. In this report, we identify determinants regulating synaptic complex formation between correct DNA sites, including the DNA architecture responsible for specifying the identity of recombination sites, features of the unique coiled-coil structure on the integrase that are required to initiate synapsis, and amino acid residues on the integrase oligomerization helix that control the remodeling of synapsing dimers into a tetramer active for DNA strand exchange.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Biotechnology (rcdc)Genetics (rcdc)Amino Acid Motifs (mesh)Attachment SitesMicrobiological (mesh)Bacteriophages (mesh)Chromosome Pairing (mesh)Integrases (mesh)Listeria monocytogenes (mesh)Prophages (mesh)Protein Domains (mesh)RecombinationGenetic (mesh)Viral Proteins (mesh)Virus Integration (mesh)site-specific DNA recombinationserine recombinasesynaptic complexphage A118Listeria monocytogenesListeria monocytogenes (mesh)Bacteriophages (mesh)Prophages (mesh)Integrases (mesh)Viral Proteins (mesh)Virus Integration (mesh)Chromosome Pairing (mesh)RecombinationGenetic (mesh)Amino Acid Motifs (mesh)Attachment SitesMicrobiological (mesh)Protein Domains (mesh)Listeria monocytogenesphage A118serine recombinasesite-specific DNA recombinationsynaptic complexAmino Acid Motifs (mesh)Attachment SitesMicrobiological (mesh)Bacteriophages (mesh)Chromosome Pairing (mesh)Integrases (mesh)Listeria monocytogenes (mesh)Prophages (mesh)Protein Domains (mesh)RecombinationGenetic (mesh)Viral Proteins (mesh)Virus Integration (mesh)06 Biological Sciences (for)07 Agricultural and Veterinary Sciences (for)11 Medical and Health Sciences (for)Microbiology (science-metrix)30 Agriculturalveterinary and food sciences (for-2020)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2s9253cjhttps://escholarship.org/content/qt2s9253cj/qt2s9253cj.pdfinfo:doi/10.1128/jb.00703-20articleJournal of Bacteriology, vol 203, iss 1610.1128/jb.00703 - 10.1128/jb.00720oai:escholarship.org:ark:/13030/qt2744849d2025-12-27T17:35:23Zqt2744849dInternal Fragments Generated from Different Top-Down Mass Spectrometry Fragmentation Methods Extend Protein Sequence CoverageZenaidee, Muhammad AWei, BenqianLantz, CarterWu, Hoi TingLambeth, Tyler RDiedrich, Jolene KLoo, Rachel R OgorzalekJulian, Ryan RLoo, Joseph A2021-07-07Top-down mass spectrometry (TD-MS) of intact proteins results in fragment ions that can be correlated to the protein primary sequence. Fragments generated can either be terminal fragments that contain the N- or C-terminus or internal fragments that contain neither termini. Traditionally in TD-MS experiments, the generation of internal fragments has been avoided because of ambiguity in assigning these fragments. Here, we demonstrate that in TD-MS experiments internal fragments can be formed and assigned in collision-based, electron-based, and photon-based fragmentation methods and are rich with sequence information, allowing for a greater extent of the primary protein sequence to be explained. For the three test proteins cytochrome c, myoglobin, and carbonic anhydrase II, the inclusion of internal fragments in the analysis resulted in approximately 15-20% more sequence coverage, with no less than 85% sequence coverage obtained. Combining terminal fragment and internal fragment assignments results in near complete protein sequence coverage. Hence, by including both terminal and internal fragment assignments in TD-MS analysis, deep protein sequence analysis, allowing for the localization of modification sites more reliably, can be possible.3401 Analytical Chemistry (for-2020)34 Chemical Sciences (for-2020)3406 Physical Chemistry (for-2020)Mass Spectrometry (mesh)Peptide Fragments (mesh)Proteins (mesh)Sequence AnalysisProtein (mesh)top-down mass spectrometryelectron capture dissociationelectron ionization dissociationUVPDinternal fragmentsCADPeptide Fragments (mesh)Proteins (mesh)Sequence AnalysisProtein (mesh)Mass Spectrometry (mesh)CADUVPDelectron capture dissociationelectron ionization dissociationinternal fragmentstop-down mass spectrometryMass Spectrometry (mesh)Peptide Fragments (mesh)Proteins (mesh)Sequence AnalysisProtein (mesh)0301 Analytical Chemistry (for)0304 Medicinal and Biomolecular Chemistry (for)0306 Physical Chemistry (incl. Structural) (for)Analytical Chemistry (science-metrix)3401 Analytical chemistry (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2744849dhttps://escholarship.org/content/qt2744849d/qt2744849d.pdfinfo:doi/10.1021/jasms.1c00113articleJournal of The American Society for Mass Spectrometry, vol 32, iss 71752 - 1758oai:escholarship.org:ark:/13030/qt6pn0s1hw2025-12-27T17:31:43Zqt6pn0s1hwStructure of human factor VIIa–soluble tissue factor with calcium, magnesium and rubidiumVadivel, KanagasabaiSchmidt, Amy ECascio, DuilioPadmanabhan, KaillatheKrishnaswamy, SriramBrandstetter, HansBajaj, S Paul2021-06-01Coagulation factor VIIa (FVIIa) consists of a γ-carboxyglutamic acid (GLA) domain, two epidermal growth factor-like (EGF) domains and a protease domain. FVIIa binds three Mg2+ ions and four Ca2+ ions in the GLA domain, one Ca2+ ion in the EGF1 domain and one Ca2+ ion in the protease domain. Further, FVIIa contains an Na+ site in the protease domain. Since Na+ and water share the same number of electrons, Na+ sites in proteins are difficult to distinguish from waters in X-ray structures. Here, to verify the Na+ site in FVIIa, the structure of the FVIIa-soluble tissue factor (TF) complex was solved at 1.8 Å resolution containing Mg2+, Ca2+ and Rb+ ions. In this structure, Rb+ replaced two Ca2+ sites in the GLA domain and occupied three non-metal sites in the protease domain. However, Rb+ was not detected at the expected Na+ site. In kinetic experiments, Na+ increased the amidolytic activity of FVIIa towards the synthetic substrate S-2288 (H-D-Ile-Pro-Arg-p-nitroanilide) by ∼20-fold; however, in the presence of Ca2+, Na+ had a negligible effect. Ca2+ increased the hydrolytic activity of FVIIa towards S-2288 by ∼60-fold in the absence of Na+ and by ∼82-fold in the presence of Na+. In molecular-dynamics simulations, Na+ stabilized the two Na+-binding loops (the 184-loop and 220-loop) and the TF-binding region spanning residues 163-180. Ca2+ stabilized the Ca2+-binding loop (the 70-loop) and Na+-binding loops but not the TF-binding region. Na+ and Ca2+ together stabilized both the Na+-binding and Ca2+-binding loops and the TF-binding region. Previously, Rb+ has been used to define the Na+ site in thrombin; however, it was unsuccessful in detecting the Na+ site in FVIIa. A conceivable explanation for this observation is provided.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Binding Sites (mesh)Calcium (mesh)Factor VIIa (mesh)Humans (mesh)Magnesium (mesh)Protein Binding (mesh)Protein Domains (mesh)Recombinant Proteins (mesh)Rubidium (mesh)Structure-Activity Relationship (mesh)blood coagulation factor VIIarubidiumcalciummagnesiumsodiumHumans (mesh)Rubidium (mesh)Calcium (mesh)Magnesium (mesh)Factor VIIa (mesh)Recombinant Proteins (mesh)Binding Sites (mesh)Protein Binding (mesh)Structure-Activity Relationship (mesh)Protein Domains (mesh)blood coagulation factor VIIacalciummagnesiumrubidiumsodiumBinding Sites (mesh)Calcium (mesh)Factor VIIa (mesh)Humans (mesh)Magnesium (mesh)Protein Binding (mesh)Protein Domains (mesh)Recombinant Proteins (mesh)Rubidium (mesh)Structure-Activity Relationship (mesh)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6pn0s1hwhttps://escholarship.org/content/qt6pn0s1hw/qt6pn0s1hw.pdfinfo:doi/10.1107/s2059798321003922articleActa Crystallographica Section D, Structural Biology, vol 77, iss Pt 6809 - 819oai:escholarship.org:ark:/13030/qt9r79p4tz2025-12-27T17:26:05Zqt9r79p4tzSingle-nucleotide conservation state annotation of the SARS-CoV-2 genomeKwon, Soo BinErnst, Jason2021-01-01Given the global impact and severity of COVID-19, there is a pressing need for a better understanding of the SARS-CoV-2 genome and mutations. Multi-strain sequence alignments of coronaviruses (CoV) provide important information for interpreting the genome and its variation. We apply a comparative genomics method, ConsHMM, to the multi-strain alignments of CoV to annotate every base of the SARS-CoV-2 genome with conservation states based on sequence alignment patterns among CoV. The learned conservation states show distinct enrichment patterns for genes, protein domains, and other regions of interest. Certain states are strongly enriched or depleted of SARS-CoV-2 mutations, which can be used to predict potentially consequential mutations. We expect the conservation states to be a resource for interpreting the SARS-CoV-2 genome and mutations.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)3105 Genetics (for-2020)Genetics (rcdc)Human Genome (rcdc)Infectious Diseases (rcdc)Emerging Infectious Diseases (rcdc)Coronaviruses (rcdc)Animals (mesh)Base Sequence (mesh)COVID-19 (mesh)Conserved Sequence (mesh)EvolutionMolecular (mesh)GenomeViral (mesh)Genomics (mesh)Humans (mesh)Mutation (mesh)Nucleotides (mesh)SARS-CoV-2 (mesh)Sequence Alignment (mesh)Animals (mesh)Humans (mesh)Nucleotides (mesh)Sequence Alignment (mesh)Genomics (mesh)EvolutionMolecular (mesh)Base Sequence (mesh)Conserved Sequence (mesh)Mutation (mesh)GenomeViral (mesh)COVID-19 (mesh)SARS-CoV-2 (mesh)Animals (mesh)Base Sequence (mesh)COVID-19 (mesh)Conserved Sequence (mesh)EvolutionMolecular (mesh)GenomeViral (mesh)Genomics (mesh)Humans (mesh)Mutation (mesh)Nucleotides (mesh)SARS-CoV-2 (mesh)Sequence Alignment (mesh)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/9r79p4tzhttps://escholarship.org/content/qt9r79p4tz/qt9r79p4tz.pdfinfo:doi/10.1038/s42003-021-02231-warticleCommunications Biology, vol 4, iss 1698oai:escholarship.org:ark:/13030/qt0s50j8n82025-12-27T16:22:55Zqt0s50j8n8Learning a genome-wide score of human–mouse conservation at the functional genomics levelKwon, Soo BinErnst, Jason2021-01-01Identifying genomic regions with functional genomic properties that are conserved between human and mouse is an important challenge in the context of mouse model studies. To address this, we develop a method to learn a score of evidence of conservation at the functional genomics level by integrating information from a compendium of epigenomic, transcription factor binding, and transcriptomic data from human and mouse. The method, Learning Evidence of Conservation from Integrated Functional genomic annotations (LECIF), trains neural networks to generate this score for the human and mouse genomes. The resulting LECIF score highlights human and mouse regions with shared functional genomic properties and captures correspondence of biologically similar human and mouse annotations. Analysis with independent datasets shows the score also highlights loci associated with similar phenotypes in both species. LECIF will be a resource for mouse model studies by identifying loci whose functional genomic properties are likely conserved.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)3105 Genetics (for-2020)Genetics (rcdc)Human Genome (rcdc)Biotechnology (rcdc)Cancer (rcdc)Cancer Genomics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Animals (mesh)Computational Biology (mesh)DNA (mesh)Epigenomics (mesh)GenomeHuman (mesh)Genomics (mesh)Humans (mesh)Mice (mesh)Sequence AnalysisDNA (mesh)Sequence HomologyNucleic Acid (mesh)Transcriptome (mesh)Animals (mesh)Humans (mesh)Mice (mesh)DNA (mesh)Sequence AnalysisDNA (mesh)Computational Biology (mesh)Genomics (mesh)Sequence HomologyNucleic Acid (mesh)GenomeHuman (mesh)Epigenomics (mesh)Transcriptome (mesh)Animals (mesh)Computational Biology (mesh)DNA (mesh)Epigenomics (mesh)GenomeHuman (mesh)Genomics (mesh)Humans (mesh)Mice (mesh)Sequence AnalysisDNA (mesh)Sequence HomologyNucleic Acid (mesh)Transcriptome (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/0s50j8n8https://escholarship.org/content/qt0s50j8n8/qt0s50j8n8.pdfinfo:doi/10.1038/s41467-021-22653-8articleNature Communications, vol 12, iss 12495oai:escholarship.org:ark:/13030/qt88t137x02025-12-27T15:06:27Zqt88t137x0The return of quiescence metabolitesColler, Hilary A2021-04-01The transition of endothelial cells between quiescence and proliferation is essential for regulating the extent of the vasculature that supplies oxygen and nutrients to tissues. A study now shows that the FOXO1 transcription factor regulates endothelial cell proliferation by controlling levels of the metabolite 2-hydroxyglutarate.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Cell Division (mesh)Cell Division (mesh)Cell Division (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/88t137x0https://escholarship.org/content/qt88t137x0/qt88t137x0.pdfinfo:doi/10.1038/s41556-021-00640-xarticleNature Cell Biology, vol 23, iss 4303 - 304oai:escholarship.org:ark:/13030/qt5f73d0wn2025-12-27T14:42:11Zqt5f73d0wnMicrocrystal Electron Diffraction for Molecular Design of Functional Non-Fullerene Acceptor StructuresHalaby, SteveMartynowycz, Michael WZhu, ZiyueTretiak, SergeiZhugayevych, AndriyGonen, TamirSeifrid, Martin2021-02-09Understanding the relationship between molecular structure and solid-state arrangement informs about the design of new organic semiconductor (OSC) materials with improved optoelectronic properties. However, determining their atomic structure remains challenging. Here, we report the lattice organization of two non-fullerene acceptors (NFAs) determined using microcrystal electron diffraction (MicroED) from crystals not traceable by X-ray crystallography. The MicroED structure of o-IDTBR was determined from a powder without crystallization, and a new polymorph of ITIC-Th is identified with the most distorted backbone of any NFA. Electronic structure calculations elucidate the relationships between molecular structures, lattice arrangements, and charge-transport properties for a number of NFA lattices. The high dimensionality of the connectivity of the 3D wire mesh topology is the best for robust charge transport within NFA crystals. However, some examples suffer from uneven electronic coupling. MicroED combined with advanced electronic structure modeling is a powerful new approach for structure determination, exploring polymorphism and guiding the design of new OSCs and NFAs.3402 Inorganic Chemistry (for-2020)3403 Macromolecular and Materials Chemistry (for-2020)34 Chemical Sciences (for-2020)40 Engineering (for-2020)4016 Materials Engineering (for-2020)03 Chemical Sciences (for)09 Engineering (for)Materials (science-metrix)34 Chemical sciences (for-2020)40 Engineering (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5f73d0wnhttps://escholarship.org/content/qt5f73d0wn/qt5f73d0wn.pdfinfo:doi/10.1021/acs.chemmater.0c04111articleChemistry of Materials, vol 33, iss 3966 - 977oai:escholarship.org:ark:/13030/qt23s7b1402025-12-27T12:40:00Zqt23s7b140Lysophospholipid acylation modulates plasma membrane lipid organization and insulin sensitivity in skeletal muscleFerrara, Patrick JRong, XinMaschek, J AlanVerkerke, Anthony RPSiripoksup, PiyaratSong, HaoweiGreen, Thomas DKrishnan, Karthickeyan CJohnson, Jordan MTurk, JohnHoumard, Joseph ALusis, Aldons JDrummond, Micah JMcClung, Joseph MCox, James EShaikh, Saame RTontonoz, PeterHolland, William LFunai, Katsuhiko2021-04-15Aberrant lipid metabolism promotes the development of skeletal muscle insulin resistance, but the exact identity of lipid-mediated mechanisms relevant to human obesity remains unclear. A comprehensive lipidomic analysis of primary myocytes from individuals who were insulin-sensitive and lean (LN) or insulin-resistant with obesity (OB) revealed several species of lysophospholipids (lyso-PLs) that were differentially abundant. These changes coincided with greater expression of lysophosphatidylcholine acyltransferase 3 (LPCAT3), an enzyme involved in phospholipid transacylation (Lands cycle). Strikingly, mice with skeletal muscle-specific knockout of LPCAT3 (LPCAT3-MKO) exhibited greater muscle lysophosphatidylcholine/phosphatidylcholine, concomitant with improved skeletal muscle insulin sensitivity. Conversely, skeletal muscle-specific overexpression of LPCAT3 (LPCAT3-MKI) promoted glucose intolerance. The absence of LPCAT3 reduced phospholipid packing of cellular membranes and increased plasma membrane lipid clustering, suggesting that LPCAT3 affects insulin receptor phosphorylation by modulating plasma membrane lipid organization. In conclusion, obesity accelerates the skeletal muscle Lands cycle, whose consequence might induce the disruption of plasma membrane organization that suppresses muscle insulin action.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)42 Health Sciences (for-2020)4207 Sports Science and Exercise (for-2020)3208 Medical Physiology (for-2020)Diabetes (rcdc)Obesity (rcdc)Nutrition (rcdc)5.1 Pharmaceuticals (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)1-Acylglycerophosphocholine O-Acyltransferase (mesh)Acylation (mesh)Animals (mesh)Cell Membrane (mesh)CellsCultured (mesh)Humans (mesh)Insulin Resistance (mesh)Lipid Metabolism (mesh)Lysophospholipids (mesh)Mice (mesh)MiceKnockout (mesh)MuscleSkeletal (mesh)Phosphorylation (mesh)ReceptorInsulin (mesh)MuscleSkeletal (mesh)CellsCultured (mesh)Cell Membrane (mesh)Animals (mesh)MiceKnockout (mesh)Humans (mesh)Mice (mesh)Insulin Resistance (mesh)1-Acylglycerophosphocholine O-Acyltransferase (mesh)ReceptorInsulin (mesh)Lysophospholipids (mesh)Acylation (mesh)Phosphorylation (mesh)Lipid Metabolism (mesh)Insulin signalingMetabolismMuscle BiologySkeletal muscle1-Acylglycerophosphocholine O-Acyltransferase (mesh)Acylation (mesh)Animals (mesh)Cell Membrane (mesh)CellsCultured (mesh)Humans (mesh)Insulin Resistance (mesh)Lipid Metabolism (mesh)Lysophospholipids (mesh)Mice (mesh)MiceKnockout (mesh)MuscleSkeletal (mesh)Phosphorylation (mesh)ReceptorInsulin (mesh)11 Medical and Health Sciences (for)Immunology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/23s7b140https://escholarship.org/content/qt23s7b140/qt23s7b140.pdfinfo:doi/10.1172/jci135963articleJournal of Clinical Investigation, vol 131, iss 8135963oai:escholarship.org:ark:/13030/qt4qh5v71w2025-12-27T12:22:30Zqt4qh5v71wMethotrexate attenuates vascular inflammation through an adenosine-microRNA dependent pathwayYang, DafengHaemmig, StefanZhou, HaoyangPérez-Cremades, DanielSun, XinghuiChen, LeiLi, JieHaneo-Mejia, JorgeYang, TianlunHollan, IvanaFeinberg, Mark W2021-01-01Endothelial cell (EC) activation is an early hallmark in the pathogenesis of chronic vascular diseases. MicroRNA-181b (Mir181b) is an important anti-inflammatory mediator in the vascular endothelium affecting endotoxemia, atherosclerosis, and insulin resistance. Herein, we identify that the drug methotrexate (MTX) and its downstream metabolite adenosine exert anti-inflammatory effects in the vascular endothelium by targeting and activating Mir181b expression. Both systemic and endothelial-specific Mir181a2b2-deficient mice develop vascular inflammation, white adipose tissue (WAT) inflammation, and insulin resistance in a diet-induced obesity model. Moreover, MTX attenuated diet-induced WAT inflammation, insulin resistance, and EC activation in a Mir181a2b2-dependent manner. Mechanistically, MTX attenuated cytokine-induced EC activation through a unique adenosine-adenosine receptor A3-SMAD3/4-Mir181b signaling cascade. These findings establish an essential role of endothelial Mir181b in controlling vascular inflammation and that restoring Mir181b in ECs by high-dose MTX or adenosine signaling may provide a potential therapeutic opportunity for anti-inflammatory therapy.3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Atherosclerosis (rcdc)Nutrition (rcdc)Obesity (rcdc)Diabetes (rcdc)2.1 Biological and endogenous factors (hrcs-rac)5.1 Pharmaceuticals (hrcs-rac)Cardiovascular (hrcs-hc)Adenosine (mesh)Animals (mesh)Antirheumatic Agents (mesh)ArthritisRheumatoid (mesh)Female (mesh)Humans (mesh)Inflammation (mesh)Male (mesh)Methotrexate (mesh)Mice (mesh)MicroRNAs (mesh)Signal Transduction (mesh)Animals (mesh)Humans (mesh)Mice (mesh)ArthritisRheumatoid (mesh)Inflammation (mesh)Methotrexate (mesh)MicroRNAs (mesh)Adenosine (mesh)Antirheumatic Agents (mesh)Signal Transduction (mesh)Female (mesh)Male (mesh)adenosineendothelial cellshumanimmunologyinflammationmedicinemethotrexatemicroRNAmouseAdenosine (mesh)Animals (mesh)Antirheumatic Agents (mesh)ArthritisRheumatoid (mesh)Female (mesh)Humans (mesh)Inflammation (mesh)Male (mesh)Methotrexate (mesh)Mice (mesh)MicroRNAs (mesh)Signal Transduction (mesh)0601 Biochemistry and Cell Biology (for)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/4qh5v71whttps://escholarship.org/content/qt4qh5v71w/qt4qh5v71w.pdfinfo:doi/10.7554/elife.58064articleeLife, vol 10e58064oai:escholarship.org:ark:/13030/qt75q1084b2025-12-27T12:16:30Zqt75q1084bConsHMM Atlas: conservation state annotations for major genomes and human genetic variationArneson, AdrianaFelsheim, BrookeChien, JenniferErnst, Jason2020-12-17ConsHMM is a method recently introduced to annotate genomes into conservation states, which are defined based on the combinatorial and spatial patterns of which species align to and match a reference genome in a multi-species DNA sequence alignment. Previously, ConsHMM was only applied to a single genome for one multi-species sequence alignment. Here, we apply ConsHMM to produce 22 additional genome annotations covering human and seven other organisms for a variety of multi-species alignments. Additionally, we extend ConsHMM to generate allele-specific annotations, which we use to produce conservation state annotations for every possible single-nucleotide mutation in the human genome. Finally, we provide a web interface to interactively visualize parameters and annotation enrichments for ConsHMM models. These annotations and visualizations comprise the ConsHMM Atlas, which we expect will be a valuable resource for analyzing a variety of major genomes and genetic variation.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)3105 Genetics (for-2020)Human Genome (rcdc)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)3102 Bioinformatics and computational biology (for-2020)3105 Genetics (for-2020)application/pdfCC-BY-NCeScholarship, University of Californiahttps://escholarship.org/uc/item/75q1084bhttps://escholarship.org/content/qt75q1084b/qt75q1084b.pdfinfo:doi/10.1093/nargab/lqaa104articleNAR Genomics and Bioinformatics, vol 2, iss 4lqaa104oai:escholarship.org:ark:/13030/qt91m9t2g22025-12-27T10:38:04Zqt91m9t2g2DNA methylation-linked chromatin accessibility affects genomic architecture in ArabidopsisZhong, ZhenhuiFeng, SuhuaDuttke, Sascha HPotok, Magdalena EZhang, YiweiGallego-Bartolomé, JavierLiu, WanluJacobsen, Steven E2021-02-02DNA methylation is a major epigenetic modification found across species and has a profound impact on many biological processes. However, its influence on chromatin accessibility and higher-order genome organization remains unclear, particularly in plants. Here, we present genome-wide chromatin accessibility profiles of 18 Arabidopsis mutants that are deficient in CG, CHG, or CHH DNA methylation. We find that DNA methylation in all three sequence contexts impacts chromatin accessibility in heterochromatin. Many chromatin regions maintain inaccessibility when DNA methylation is lost in only one or two sequence contexts, and signatures of accessibility are particularly affected when DNA methylation is reduced in all contexts, suggesting an interplay between different types of DNA methylation. In addition, we found that increased chromatin accessibility was not always accompanied by increased transcription, suggesting that DNA methylation can directly impact chromatin structure by other mechanisms. We also observed that an increase in chromatin accessibility was accompanied by enhanced long-range chromatin interactions. Together, these results provide a valuable resource for chromatin architecture and DNA methylation analyses and uncover a pivotal role for methylation in the maintenance of heterochromatin inaccessibility.3108 Plant Biology (for-2020)31 Biological Sciences (for-2020)3105 Genetics (for-2020)Genetics (rcdc)Human Genome (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Arabidopsis (mesh)Chromatin (mesh)DNA Methylation (mesh)GenomePlant (mesh)Mutation (mesh)TranscriptionGenetic (mesh)DNA methylationepigeneticschromatin accessibilityChromatin (mesh)Arabidopsis (mesh)DNA Methylation (mesh)TranscriptionGenetic (mesh)Mutation (mesh)GenomePlant (mesh)DNA methylationchromatin accessibilityepigeneticsArabidopsis (mesh)Chromatin (mesh)DNA Methylation (mesh)GenomePlant (mesh)Mutation (mesh)TranscriptionGenetic (mesh)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/91m9t2g2https://escholarship.org/content/qt91m9t2g2/qt91m9t2g2.pdfinfo:doi/10.1073/pnas.2023347118articleProceedings of the National Academy of Sciences of the United States of America, vol 118, iss 5e2023347118oai:escholarship.org:ark:/13030/qt5pj5r6fv2025-12-27T08:07:11Zqt5pj5r6fvSelective Aster inhibitors distinguish vesicular and nonvesicular sterol transport mechanismsXiao, XuKim, YoungjaeRomartinez-Alonso, BeatrizSirvydis, KristupasOry, Daniel SSchwabe, John WRJung, Michael ETontonoz, Peter2021-01-12The Aster proteins (encoded by the Gramd1a-c genes) contain a ligand-binding fold structurally similar to a START domain and mediate nonvesicular plasma membrane (PM) to endoplasmic reticulum (ER) cholesterol transport. In an effort to develop small molecule modulators of Asters, we identified 20α-hydroxycholesterol (HC) and U18666A as lead compounds. Unfortunately, both 20α-HC and U18666A target other sterol homeostatic proteins, limiting their utility. 20α-HC inhibits sterol regulatory element-binding protein 2 (SREBP2) processing, and U18666A is an inhibitor of the vesicular trafficking protein Niemann-Pick C1 (NPC1). To develop potent and selective Aster inhibitors, we synthesized a series of compounds by modifying 20α-HC and U18666A. Among these, AI (Aster inhibitor)-1l, which has a longer side chain than 20α-HC, selectively bound to Aster-C. The crystal structure of Aster-C in complex with AI-1l suggests that sequence and flexibility differences in the loop that gates the binding cavity may account for the ligand specificity for Aster C. We further identified the U18666A analog AI-3d as a potent inhibitor of all three Aster proteins. AI-3d blocks the ability of Asters to bind and transfer cholesterol in vitro and in cells. Importantly, AI-3d also inhibits the movement of low-density lipoprotein (LDL) cholesterol to the ER, although AI-3d does not block NPC1. This finding positions the nonvesicular Aster pathway downstream of NPC1-dependent vesicular transport in the movement of LDL cholesterol to the ER. Selective Aster inhibitors represent useful chemical tools to distinguish vesicular and nonvesicular sterol transport mechanisms in mammalian cells.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Androstenes (mesh)Animals (mesh)Biological Transport (mesh)CHO Cells (mesh)Carrier Proteins (mesh)Cell Membrane (mesh)Cholesterol (mesh)CholesterolLDL (mesh)Cricetulus (mesh)Endoplasmic Reticulum (mesh)Humans (mesh)Hydroxycholesterols (mesh)Intracellular Signaling Peptides and Proteins (mesh)Membrane Glycoproteins (mesh)Membrane Proteins (mesh)Niemann-Pick C1 Protein (mesh)Sterol Regulatory Element Binding Protein 2 (mesh)Sterols (mesh)cholesterollipid transportlipid metabolismCHO Cells (mesh)Cell Membrane (mesh)Endoplasmic Reticulum (mesh)Animals (mesh)Humans (mesh)Cricetulus (mesh)Androstenes (mesh)Cholesterol (mesh)Hydroxycholesterols (mesh)Sterols (mesh)Intracellular Signaling Peptides and Proteins (mesh)Carrier Proteins (mesh)Membrane Glycoproteins (mesh)Membrane Proteins (mesh)Biological Transport (mesh)Sterol Regulatory Element Binding Protein 2 (mesh)CholesterolLDL (mesh)Niemann-Pick C1 Protein (mesh)cholesterollipid metabolismlipid transportAndrostenes (mesh)Animals (mesh)Biological Transport (mesh)CHO Cells (mesh)Carrier Proteins (mesh)Cell Membrane (mesh)Cholesterol (mesh)CholesterolLDL (mesh)Cricetulus (mesh)Endoplasmic Reticulum (mesh)Humans (mesh)Hydroxycholesterols (mesh)Intracellular Signaling Peptides and Proteins (mesh)Membrane Glycoproteins (mesh)Membrane Proteins (mesh)Niemann-Pick C1 Protein (mesh)Sterol Regulatory Element Binding Protein 2 (mesh)Sterols (mesh)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5pj5r6fvhttps://escholarship.org/content/qt5pj5r6fv/qt5pj5r6fv.pdfinfo:doi/10.1073/pnas.2024149118articleProceedings of the National Academy of Sciences of the United States of America, vol 118, iss 2e2024149118oai:escholarship.org:ark:/13030/qt3mc5h2382025-12-27T07:52:48Zqt3mc5h238Single-Cell Sequencing of Brain Cell Transcriptomes and EpigenomesArmand, Ethan JLi, JunhaoXie, FangmingLuo, ChongyuanMukamel, Eran A2021-01-01Single-cell sequencing technologies, including transcriptomic and epigenomic assays, are transforming our understanding of the cellular building blocks of neural circuits. By directly measuring multiple molecular signatures in thousands to millions of individual cells, single-cell sequencing methods can comprehensively characterize the diversity of brain cell types. These measurements uncover gene regulatory mechanisms that shape cellular identity and provide insight into developmental and evolutionary relationships between brain cell populations. Single-cell sequencing data can aid the design of tools for targeted functional studies of brain circuit components, linking molecular signatures with anatomy, connectivity, morphology, and physiology. Here, we discuss the fundamental principles of single-cell transcriptome and epigenome sequencing, integrative computational analysis of the data, and key applications in neuroscience.5202 Biological Psychology (for-2020)32 Biomedical and Clinical Sciences (for-2020)3209 Neurosciences (for-2020)52 Psychology (for-2020)Genetics (rcdc)Neurosciences (rcdc)Human Genome (rcdc)Mental Health (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Neurological (hrcs-hc)Generic health relevance (hrcs-hc)Brain (mesh)DNA Methylation (mesh)Epigenome (mesh)Epigenomics (mesh)Humans (mesh)Sequence AnalysisDNA (mesh)Sequence AnalysisRNA (mesh)Single-Cell Analysis (mesh)Transcriptome (mesh)Brain (mesh)Humans (mesh)Sequence AnalysisDNA (mesh)Sequence AnalysisRNA (mesh)DNA Methylation (mesh)Epigenomics (mesh)Single-Cell Analysis (mesh)Transcriptome (mesh)Epigenome (mesh)ATAC-seqDNA methylationcell statecell typeepigenomemulti-omicsopen chromatinsingle-cell sequencingspatial transcriptomicstranscriptomeBrain (mesh)DNA Methylation (mesh)Epigenome (mesh)Epigenomics (mesh)Humans (mesh)Sequence AnalysisDNA (mesh)Sequence AnalysisRNA (mesh)Single-Cell Analysis (mesh)Transcriptome (mesh)1109 Neurosciences (for)1701 Psychology (for)1702 Cognitive Sciences (for)Neurology & Neurosurgery (science-metrix)3209 Neurosciences (for-2020)5202 Biological psychology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3mc5h238https://escholarship.org/content/qt3mc5h238/qt3mc5h238.pdfinfo:doi/10.1016/j.neuron.2020.12.010articleNeuron, vol 109, iss 111 - 26oai:escholarship.org:ark:/13030/qt5845p3pd2025-12-27T06:43:19Zqt5845p3pdA conformational change in the N terminus of SLC38A9 signals mTORC1 activationLei, Hsiang-TingMu, XuelangHattne, JohanGonen, Tamir2021-05-01mTORC1 is a central hub that integrates environmental cues, such as cellular stresses and nutrient availability to modulate metabolism and cellular responses. Recently, SLC38A9, a lysosomal amino acid transporter, emerged as a sensor for luminal arginine and as an activator of mTORC1. The amino acid-mediated activation of mTORC1 is regulated by the N-terminal domain of SLC38A9. Here, we determined the crystal structure of zebrafish SLC38A9 (drSLC38A9) and found the N-terminal fragment inserted deep within the transporter, bound in the substrate-binding pocket where normally arginine would bind. This represents a significant conformational change of the N-terminal domain (N-plug) when compared with our recent arginine-bound structure of drSLC38A9. We propose a ball-and-chain model for mTORC1 activation, where N-plug insertion and Rag GTPase binding with SLC38A9 is regulated by luminal arginine levels. This work provides important insights into nutrient sensing by SLC38A9 to activate the mTORC1 pathways in response to dietary amino acids.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Nutrition (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Amino Acid Transport Systems (mesh)Animals (mesh)Mechanistic Target of Rapamycin Complex 1 (mesh)Molecular Dynamics Simulation (mesh)Protein Domains (mesh)Sf9 Cells (mesh)Signal Transduction (mesh)Spodoptera (mesh)Zebrafish (mesh)Zebrafish Proteins (mesh)Animals (mesh)Zebrafish (mesh)Spodoptera (mesh)Amino Acid Transport Systems (mesh)Zebrafish Proteins (mesh)Signal Transduction (mesh)Molecular Dynamics Simulation (mesh)Sf9 Cells (mesh)Protein Domains (mesh)Mechanistic Target of Rapamycin Complex 1 (mesh)SLC38A9arginine transportcrystallographymTORC1Amino Acid Transport Systems (mesh)Animals (mesh)Mechanistic Target of Rapamycin Complex 1 (mesh)Molecular Dynamics Simulation (mesh)Protein Domains (mesh)Sf9 Cells (mesh)Signal Transduction (mesh)Spodoptera (mesh)Zebrafish (mesh)Zebrafish Proteins (mesh)Biophysics (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/5845p3pdhttps://escholarship.org/content/qt5845p3pd/qt5845p3pd.pdfinfo:doi/10.1016/j.str.2020.11.014articleStructure, vol 29, iss 5426 - 432.e8oai:escholarship.org:ark:/13030/qt5fh9g38b2025-12-27T06:43:13Zqt5fh9g38bMicroED structure of lipid-embedded mammalian mitochondrial voltage-dependent anion channelMartynowycz, Michael WKhan, FarhaHattne, JohanAbramson, JeffGonen, Tamir2020-12-22A structure of the murine voltage-dependent anion channel (VDAC) was determined by microcrystal electron diffraction (MicroED). Microcrystals of an essential mutant of VDAC grew in a viscous bicelle suspension, making it unsuitable for conventional X-ray crystallography. Thin, plate-like crystals were identified using scanning-electron microscopy (SEM). Crystals were milled into thin lamellae using a focused-ion beam (FIB). MicroED data were collected from three crystal lamellae and merged for completeness. The refined structure revealed unmodeled densities between protein monomers, indicative of lipids that likely mediate contacts between the proteins in the crystal. This body of work demonstrates the effectiveness of milling membrane protein microcrystals grown in viscous media using a focused ion beam for subsequent structure determination by MicroED. This approach is well suited for samples that are intractable by X-ray crystallography. To our knowledge, the presented structure is a previously undescribed mutant of the membrane protein VDAC, crystallized in a lipid bicelle matrix and solved by MicroED.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Infectious Diseases (rcdc)Animals (mesh)Cryoelectron Microscopy (mesh)Crystallization (mesh)Lipids (mesh)Mice (mesh)MicroscopyElectronScanning (mesh)MicroscopyElectronTransmission (mesh)Mitochondrial Proteins (mesh)Protein Conformation (mesh)Voltage-Dependent Anion Channels (mesh)cryoEMMicroEDbicelle crystallizationFIB/SEMmicrocrystal electron diffractionAnimals (mesh)Mice (mesh)Lipids (mesh)Mitochondrial Proteins (mesh)Cryoelectron Microscopy (mesh)MicroscopyElectronScanning (mesh)MicroscopyElectronTransmission (mesh)Crystallization (mesh)Protein Conformation (mesh)Voltage-Dependent Anion Channels (mesh)FIB/SEMMicroEDbicelle crystallizationcryoEMmicrocrystal electron diffractionAnimals (mesh)Cryoelectron Microscopy (mesh)Crystallization (mesh)Lipids (mesh)Mice (mesh)MicroscopyElectronScanning (mesh)MicroscopyElectronTransmission (mesh)Mitochondrial Proteins (mesh)Protein Conformation (mesh)Voltage-Dependent Anion Channels (mesh)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5fh9g38bhttps://escholarship.org/content/qt5fh9g38b/qt5fh9g38b.pdfinfo:doi/10.1073/pnas.2020010117articleProceedings of the National Academy of Sciences of the United States of America, vol 117, iss 5132380 - 32385oai:escholarship.org:ark:/13030/qt6b64n0mj2025-12-27T06:20:04Zqt6b64n0mjChromatin and Nuclear Architecture in Stem CellsMeshorer, EranPlath, Kathrin2020-12-01Here we outline the contents of Stem Cell Reports' first special issue, on chromatin and nuclear architecture in stem cells. It features both reviews and original research articles, covering emerging topics in nuclear architecture including 3D genome organization in stem cells and early development, membraneless organelles, epigenetics-related therapy, and more.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Stem Cell Research - Nonembryonic - Non-Human (rcdc)Human Genome (rcdc)Regenerative Medicine (rcdc)Stem Cell Research (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell - Human (rcdc)Stem Cell Research - Nonembryonic - Human (rcdc)Stem Cell Research - Induced Pluripotent Stem Cell (rcdc)5.2 Cellular and gene therapies (hrcs-rac)Animals (mesh)Cell Nucleus (mesh)Chromatin (mesh)Gene Expression Regulation (mesh)Humans (mesh)Stem Cells (mesh)Cell Nucleus (mesh)Chromatin (mesh)Stem Cells (mesh)Animals (mesh)Humans (mesh)Gene Expression Regulation (mesh)Animals (mesh)Cell Nucleus (mesh)Chromatin (mesh)Gene Expression Regulation (mesh)Humans (mesh)Stem Cells (mesh)0601 Biochemistry and Cell Biology (for)1103 Clinical Sciences (for)3101 Biochemistry and cell biology (for-2020)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/6b64n0mjhttps://escholarship.org/content/qt6b64n0mj/qt6b64n0mj.pdfinfo:doi/10.1016/j.stemcr.2020.11.012articleStem Cell Reports, vol 15, iss 61155 - 1157oai:escholarship.org:ark:/13030/qt9jx3h2zj2025-12-27T05:42:25Zqt9jx3h2zjIdentification and characterization of constrained non-exonic bases lacking predictive epigenomic and transcription factor binding annotationsGrujic, OliveraPhung, Tanya NKwon, Soo BinArneson, AdrianaLee, YujuLohmueller, Kirk EErnst, Jason2020-01-01Annotations of evolutionary sequence constraint based on multi-species genome alignments and genome-wide maps of epigenomic marks and transcription factor binding provide important complementary information for understanding the human genome and genetic variation. Here we developed the Constrained Non-Exonic Predictor (CNEP) to quantify the evidence of each base in the genome being in an evolutionarily constrained non-exonic element from an input of over 60,000 epigenomic and transcription factor binding features. We find that the CNEP score outperforms baseline and related existing scores at predicting evolutionarily constrained non-exonic bases from such data. However, a subset of them are still not well predicted by CNEP. We developed a complementary Conservation Signature Score by CNEP (CSS-CNEP) that is predictive of those bases. We further characterize the nature of constrained non-exonic bases with low CNEP scores using additional types of information. CNEP and CSS-CNEP are resources for analyzing constrained non-exonic bases in the genome.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)3105 Genetics (for-2020)Genetics (rcdc)Human Genome (rcdc)Animals (mesh)Base Sequence (mesh)EpigenesisGenetic (mesh)EvolutionMolecular (mesh)Exons (mesh)Gene Ontology (mesh)Genome (mesh)Humans (mesh)Introns (mesh)Invertebrates (mesh)Molecular Sequence Annotation (mesh)Protein Binding (mesh)Sequence Alignment (mesh)Sequence HomologyNucleic Acid (mesh)Transcription Factors (mesh)Vertebrates (mesh)Animals (mesh)Vertebrates (mesh)Humans (mesh)Invertebrates (mesh)Transcription Factors (mesh)Sequence Alignment (mesh)EvolutionMolecular (mesh)EpigenesisGenetic (mesh)Base Sequence (mesh)Protein Binding (mesh)Sequence HomologyNucleic Acid (mesh)Genome (mesh)Introns (mesh)Exons (mesh)Molecular Sequence Annotation (mesh)Gene Ontology (mesh)Animals (mesh)Base Sequence (mesh)EpigenesisGenetic (mesh)EvolutionMolecular (mesh)Exons (mesh)Gene Ontology (mesh)Genome (mesh)Humans (mesh)Introns (mesh)Invertebrates (mesh)Molecular Sequence Annotation (mesh)Protein Binding (mesh)Sequence Alignment (mesh)Sequence HomologyNucleic Acid (mesh)Transcription Factors (mesh)Vertebrates (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/9jx3h2zjhttps://escholarship.org/content/qt9jx3h2zj/qt9jx3h2zj.pdfinfo:doi/10.1038/s41467-020-19962-9articleNature Communications, vol 11, iss 16168oai:escholarship.org:ark:/13030/qt4dm1743s2025-12-27T02:24:14Zqt4dm1743sAn Allosteric Modulator of RNA Binding Targeting the N‑Terminal Domain of TDP-43 Yields Neuroprotective PropertiesMollasalehi, NiloufarFrancois-Moutal, LibertyScott, David DTello, Judith AWilliams, HaleyMahoney, BrendanCarlson, Jacob MDong, YueLi, XingliMiranda, Victor GGokhale, VijayWang, WeiBarmada, Sami JKhanna, May2020-11-20In this study, we targeted the N-terminal domain (NTD) of transactive response (TAR) DNA binding protein (TDP-43), which is implicated in several neurodegenerative diseases. In silico docking of 50K compounds to the NTD domain of TDP-43 identified a small molecule (nTRD22) that is bound to the N-terminal domain. Interestingly, nTRD22 caused allosteric modulation of the RNA binding domain (RRM) of TDP-43, resulting in decreased binding to RNA in vitro. Moreover, incubation of primary motor neurons with nTRD22 induced a reduction of TDP-43 protein levels, similar to TDP-43 RNA binding-deficient mutants and supporting a disruption of TDP-43 binding to RNA. Finally, nTRD22 mitigated motor impairment in a Drosophila model of amyotrophic lateral sclerosis. Our findings provide an exciting way of allosteric modulation of the RNA-binding region of TDP-43 through the N-terminal domain.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Rare Diseases (rcdc)ALS (rcdc)Neurosciences (rcdc)Neurodegenerative (rcdc)Genetics (rcdc)Brain Disorders (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Neurological (hrcs-hc)Generic health relevance (hrcs-hc)Allosteric Regulation (mesh)Amyotrophic Lateral Sclerosis (mesh)Animals (mesh)Binding Sites (mesh)DNA-Binding Proteins (mesh)Disease ModelsAnimal (mesh)Drosophila (mesh)Humans (mesh)Molecular Docking Simulation (mesh)Protein Domains (mesh)RNA (mesh)Small Molecule Libraries (mesh)Animals (mesh)Humans (mesh)Drosophila (mesh)Amyotrophic Lateral Sclerosis (mesh)Disease ModelsAnimal (mesh)DNA-Binding Proteins (mesh)RNA (mesh)Allosteric Regulation (mesh)Binding Sites (mesh)Small Molecule Libraries (mesh)Molecular Docking Simulation (mesh)Protein Domains (mesh)Allosteric Regulation (mesh)Amyotrophic Lateral Sclerosis (mesh)Animals (mesh)Binding Sites (mesh)DNA-Binding Proteins (mesh)Disease ModelsAnimal (mesh)Drosophila (mesh)Humans (mesh)Molecular Docking Simulation (mesh)Protein Domains (mesh)RNA (mesh)Small Molecule Libraries (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)Organic Chemistry (science-metrix)31 Biological sciences (for-2020)34 Chemical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4dm1743shttps://escholarship.org/content/qt4dm1743s/qt4dm1743s.pdfinfo:doi/10.1021/acschembio.0c00494articleACS Chemical Biology, vol 15, iss 112854 - 2859oai:escholarship.org:ark:/13030/qt9c80x7q62025-12-27T00:49:01Zqt9c80x7q6MicroED in natural product and small molecule researchDanelius, EmmaHalaby, Stevevan der Donk, Wilfred AGonen, Tamir2021-03-01Covering: 2013 to 2020The electron cryo-microscopy (cryo-EM) method Microcrystal Electron Diffraction (MicroED) allows the collection of high-resolution structural data from vanishingly small crystals that appear like amorphous powders or very fine needles. Since its debut in 2013, data collection and analysis schemes have been fine-tuned, and there are currently close to 100 structures determined by MicroED. Although originally developed to study proteins, MicroED is also very powerful for smaller systems, with some recent and very promising examples from the field of natural products. Herein, we review what has been achieved so far and provide examples of natural product structures, as well as demonstrate the expected future impact of MicroED to the field of natural product and small molecule research.3404 Medicinal and Biomolecular Chemistry (for-2020)34 Chemical Sciences (for-2020)Biotechnology (rcdc)Biological Products (mesh)Biomedical Research (mesh)Cryoelectron Microscopy (mesh)Crystallization (mesh)Drug Discovery (mesh)Ligands (mesh)MicroscopyElectronTransmission (mesh)ModelsMolecular (mesh)Proteins (mesh)Small Molecule Libraries (mesh)Proteins (mesh)Biological Products (mesh)Ligands (mesh)Cryoelectron Microscopy (mesh)MicroscopyElectronTransmission (mesh)Crystallization (mesh)ModelsMolecular (mesh)Biomedical Research (mesh)Small Molecule Libraries (mesh)Drug Discovery (mesh)Biological Products (mesh)Biomedical Research (mesh)Cryoelectron Microscopy (mesh)Crystallization (mesh)Drug Discovery (mesh)Ligands (mesh)MicroscopyElectronTransmission (mesh)ModelsMolecular (mesh)Proteins (mesh)Small Molecule Libraries (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Organic Chemistry (science-metrix)3404 Medicinal and biomolecular chemistry (for-2020)4208 Traditionalcomplementary and integrative medicine (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/9c80x7q6https://escholarship.org/content/qt9c80x7q6/qt9c80x7q6.pdfinfo:doi/10.1039/d0np00035carticleNatural Product Reports, vol 38, iss 3423 - 431oai:escholarship.org:ark:/13030/qt6118p4w42025-12-26T22:44:40Zqt6118p4w4Interlaboratory Study for Characterizing Monoclonal Antibodies by Top-Down and Middle-Down Mass SpectrometrySrzentić, KristinaFornelli, LucaTsybin, Yury OLoo, Joseph ASeckler, HenriqueAgar, Jeffrey NAnderson, Lissa CBai, Dina LBeck, AlainBrodbelt, Jennifer Svan der Burgt, Yuri EMChamot-Rooke, JuliaChatterjee, SnehaChen, YunqiuClarke, David JDanis, Paul ODiedrich, Jolene KD’Ippolito, Robert ADupré, MathieuGasilova, NataliaGe, YingGoo, Young AhGoodlett, David RGreer, SylvesterHaselmann, Kim FHe, LidongHendrickson, Christopher LHinkle, Joshua DHolt, Matthew VHughes, SamHunt, Donald FKelleher, Neil LKozhinov, Anton NLin, ZiqingMalosse, ChristianMarshall, Alan GMenin, LaureMillikin, Robert JNagornov, Konstantin ONicolardi, SimonePaša-Tolić, LjiljanaPengelley, StuartQuebbemann, Neil RResemann, AnjaSandoval, WendySarin, RichaSchmitt, Nicholas DShabanowitz, JeffreyShaw, Jared BShortreed, Michael RSmith, Lloyd MSobott, FrankSuckau, DetlevToby, TimothyWeisbrod, Chad RWildburger, Norelle CYates, John RYoon, Sung HwanYoung, Nicolas LZhou, Mowei2020-09-02The Consortium for Top-Down Proteomics (www.topdownproteomics.org) launched the present study to assess the current state of top-down mass spectrometry (TD MS) and middle-down mass spectrometry (MD MS) for characterizing monoclonal antibody (mAb) primary structures, including their modifications. To meet the needs of the rapidly growing therapeutic antibody market, it is important to develop analytical strategies to characterize the heterogeneity of a therapeutic product's primary structure accurately and reproducibly. The major objective of the present study is to determine whether current TD/MD MS technologies and protocols can add value to the more commonly employed bottom-up (BU) approaches with regard to confirming protein integrity, sequencing variable domains, avoiding artifacts, and revealing modifications and their locations. We also aim to gather information on the common TD/MD MS methods and practices in the field. A panel of three mAbs was selected and centrally provided to 20 laboratories worldwide for the analysis: Sigma mAb standard (SiLuLite), NIST mAb standard, and the therapeutic mAb Herceptin (trastuzumab). Various MS instrument platforms and ion dissociation techniques were employed. The present study confirms that TD/MD MS tools are available in laboratories worldwide and provide complementary information to the BU approach that can be crucial for comprehensive mAb characterization. The current limitations, as well as possible solutions to overcome them, are also outlined. A primary limitation revealed by the results of the present study is that the expert knowledge in both experiment and data analysis is indispensable to practice TD/MD MS.3401 Analytical Chemistry (for-2020)34 Chemical Sciences (for-2020)Biotechnology (rcdc)Animals (mesh)AntibodiesMonoclonal (mesh)Complementarity Determining Regions (mesh)Humans (mesh)Mass Spectrometry (mesh)Mice (mesh)Proteomics (mesh)Therapeutic proteinglycoformintact mass measurementtandem mass spectrometryMS/MSFourier transform mass spectrometryFTMSAnimals (mesh)Humans (mesh)Mice (mesh)Complementarity Determining Regions (mesh)AntibodiesMonoclonal (mesh)Proteomics (mesh)Mass Spectrometry (mesh)FTMSFourier transform mass spectrometryMS/MSTherapeutic proteinglycoformintact mass measurementtandem mass spectrometryAnimals (mesh)AntibodiesMonoclonal (mesh)Complementarity Determining Regions (mesh)Humans (mesh)Mass Spectrometry (mesh)Mice (mesh)Proteomics (mesh)0301 Analytical Chemistry (for)0304 Medicinal and Biomolecular Chemistry (for)0306 Physical Chemistry (incl. Structural) (for)Analytical Chemistry (science-metrix)3401 Analytical chemistry (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/6118p4w4https://escholarship.org/content/qt6118p4w4/qt6118p4w4.pdfinfo:doi/10.1021/jasms.0c00036articleJournal of The American Society for Mass Spectrometry, vol 31, iss 91783 - 1802oai:escholarship.org:ark:/13030/qt5rc3c6cc2025-12-26T22:10:04Zqt5rc3c6ccThe ASM Journals Committee Values the Contributions of Black MicrobiologistsSchloss, Patrick DJunior, MelissaAlvania, RebeccaArias, Cesar ABaumler, AndreasCasadevall, ArturoDetweiler, CorrellaDrake, HaroldGilbert, JackImperiale, Michael JLovett, SusanMaloy, StanleyMcAdam, Alexander JNewton, Irene LGSadowsky, Michael JSandri-Goldin, Rozanne MSilhavy, Thomas JTontonoz, PeterYoung, Jo-Anne HCameron, Craig ECann, IsaacFuller, A OvetaKozik, Ariangela J2020-08-063107 Microbiology (for-2020)31 Biological Sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/5rc3c6cchttps://escholarship.org/content/qt5rc3c6cc/qt5rc3c6cc.pdfinfo:doi/10.1128/mra.00833-20articleMicrobiology Resource Announcements, vol 9, iss 3210.1128/mra.00833 - 10.1128/mra.00820oai:escholarship.org:ark:/13030/qt4m62r9g42025-12-26T22:09:57Zqt4m62r9g4The ASM Journals Committee Values the Contributions of Black MicrobiologistsSchloss, Patrick DJunior, MelissaAlvania, RebeccaArias, Cesar ABaumler, AndreasCasadevall, ArturoDetweiler, CorrellaDrake, HaroldGilbert, JackImperiale, Michael JLovett, SusanMaloy, StanleyMcAdam, Alexander JNewton, Irene LGSadowsky, Michael JSandri-Goldin, Rozanne MSilhavy, Thomas JTontonoz, PeterYoung, Jo-Anne HCameron, Craig ECann, IsaacFuller, A OvetaKozik, Ariangela J2020-08-25application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4m62r9g4https://escholarship.org/content/qt4m62r9g4/qt4m62r9g4.pdfinfo:doi/10.1128/msystems.00678-20articlemSystems, vol 5, iss 410.1128/msystems.00678 - 10.1128/msystems.00620oai:escholarship.org:ark:/13030/qt1tn0v8m22025-12-26T21:54:51Zqt1tn0v8m2Aster Proteins Regulate the Accessible Cholesterol Pool in the Plasma MembraneFerrari, AlessandraHe, CuiwenKennelly, John PaulSandhu, JaspreetXiao, XuChi, XunJiang, HaiboYoung, Stephen GTontonoz, Peter2020-09-14Recent studies have demonstrated the existence of a discrete pool of cholesterol in the plasma membranes (PM) of mammalian cells-referred to as the accessible cholesterol pool-that can be detected by the binding of modified versions of bacterial cytolysins (e.g., anthrolysin O). When the amount of accessible cholesterol in the PM exceeds a threshold level, the excess cholesterol moves to the endoplasmic reticulum (ER), where it regulates the SREBP2 pathway and undergoes esterification. We reported previously that the Aster/Gramd1 family of sterol transporters mediates nonvesicular movement of cholesterol from the PM to the ER in multiple mammalian cell types. Here, we investigated the PM pool of accessible cholesterol in cholesterol-loaded fibroblasts with a knockdown of Aster-A and in mouse macrophages from Aster-B and Aster-A/B-deficient mice. Nanoscale secondary ion mass spectrometry (NanoSIMS) analyses revealed expansion of the accessible cholesterol pool in cells lacking Aster expression. The increased accessible cholesterol pool in the PM was accompanied by reduced cholesterol movement to the ER, evidenced by increased expression of SREBP2-regulated genes. Cosedimentation experiments with liposomes revealed that the Aster-B GRAM domain binds to membranes in a cholesterol concentration-dependent manner and that the binding is facilitated by the presence of phosphatidylserine. These studies revealed that the Aster-mediated nonvesicular cholesterol transport pathway controls levels of accessible cholesterol in the PM, as well as the activity of the SREBP pathway.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)3T3-L1 Cells (mesh)Animals (mesh)Bacterial Proteins (mesh)Cell Membrane (mesh)Cholesterol (mesh)Endoplasmic Reticulum (mesh)Fibroblasts (mesh)Liposomes (mesh)MacrophagesPeritoneal (mesh)Membrane Glycoproteins (mesh)Mice (mesh)MiceInbred C57BL (mesh)MiceKnockout (mesh)SpectrometryMassSecondary Ion (mesh)Sterol Regulatory Element Binding Protein 2 (mesh)3T3-L1 Cells (mesh)Cell Membrane (mesh)Endoplasmic Reticulum (mesh)Fibroblasts (mesh)MacrophagesPeritoneal (mesh)Animals (mesh)MiceInbred C57BL (mesh)MiceKnockout (mesh)Mice (mesh)Cholesterol (mesh)Bacterial Proteins (mesh)Membrane Glycoproteins (mesh)Liposomes (mesh)SpectrometryMassSecondary Ion (mesh)Sterol Regulatory Element Binding Protein 2 (mesh)3T3-L1 Cells (mesh)Animals (mesh)Bacterial Proteins (mesh)Cell Membrane (mesh)Cholesterol (mesh)Endoplasmic Reticulum (mesh)Fibroblasts (mesh)Liposomes (mesh)MacrophagesPeritoneal (mesh)Membrane Glycoproteins (mesh)Mice (mesh)MiceInbred C57BL (mesh)MiceKnockout (mesh)SpectrometryMassSecondary Ion (mesh)Sterol Regulatory Element Binding Protein 2 (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)42 Health sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1tn0v8m2https://escholarship.org/content/qt1tn0v8m2/qt1tn0v8m2.pdfinfo:doi/10.1128/mcb.00255-20articleMolecular and Cellular Biology, vol 40, iss 19e00255 - e00220oai:escholarship.org:ark:/13030/qt07v9b8k12025-12-26T20:07:04Zqt07v9b8k1Beyond protein structure determination with MicroEDNguyen, ChiGonen, Tamir2020-10-01Microcrystal electron diffraction (MicroED) was first coined and developed in 2013 at the Janelia Research Campus as a new modality in electron cryomicroscopy (cryoEM). Since then, MicroED has not only made important contributions in pushing the resolution limits of cryoEM protein structure characterization but also of peptides, small-organic and inorganic molecules, and natural-products that have resisted structure determination by other methods. This review showcases important recent developments in MicroED, highlighting the importance of the technique in fields of studies beyond protein structure determination where MicroED is beginning to have paradigm shifting roles.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Generic health relevance (hrcs-hc)Cryoelectron Microscopy (mesh)Electrons (mesh)Peptides (mesh)Proteins (mesh)Peptides (mesh)Proteins (mesh)Cryoelectron Microscopy (mesh)Electrons (mesh)Cryoelectron Microscopy (mesh)Electrons (mesh)Peptides (mesh)Proteins (mesh)0304 Medicinal and Biomolecular Chemistry (for)0601 Biochemistry and Cell Biology (for)Biophysics (science-metrix)3101 Biochemistry and cell biology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/07v9b8k1https://escholarship.org/content/qt07v9b8k1/qt07v9b8k1.pdfinfo:doi/10.1016/j.sbi.2020.05.018articleCurrent Opinion in Structural Biology, vol 6451 - 58oai:escholarship.org:ark:/13030/qt6wq8q8n12025-12-26T20:02:34Zqt6wq8q8n1Promoter and Terminator Optimization for DNA Methylation Targeting in ArabidopsisGardiner, JasonZhao, Jenny MChaffin, KendallJacobsen, Steven E2020-01-01DNA methylation is an important epigenetic mark involved in gene regulation and silencing of transposable elements. The presence or absence of DNA methylation at specific sites can influence nearby gene expression and cause phenotypic changes that remain stable over generations. Recently, development of new technologies has enabled the targeted addition or removal of DNA methylation at specific sites of the genome. Of these new technologies, the targeting of the catalytic domain of Nicotiana tabacum DOMAINS REARRANGED METHYLTRANSFERASE 2 (ntDRM2cd) offers a promising tool for the addition of DNA methylation as it can directly methylate DNA. However, the methylation targeting efficiency of constructs using ntDRM2cd thus far has been relatively low. Previous studies have shown that the use of different promoters or terminators can greatly improve genome-editing efficiencies. In this study, we systematically survey a variety of promoter and terminator combinations to identify optimal combinations to use when targeting the addition of DNA methylation in Arabidopsis thaliana.31 Biological Sciences (for-2020)3105 Genetics (for-2020)Human Genome (rcdc)Genetics (rcdc)Biotechnology (rcdc)epigeneticsDNA methylationtargetingzinc fingerArabidopsisplanttranscriptionpromoterterminatorRNA-directed DNA methylation (RdDM)silencingArabidopsisDNA methylationRNA-directed DNA methylation (RdDM)epigeneticsplantpromotersilencingtargetingterminatortranscriptionzinc finger3105 Genetics (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/6wq8q8n1https://escholarship.org/content/qt6wq8q8n1/qt6wq8q8n1.pdfinfo:doi/10.3390/epigenomes4020009articleEpigenomes, vol 4, iss 29oai:escholarship.org:ark:/13030/qt3cd793pr2025-12-26T19:47:19Zqt3cd793prNon-photopic and photopic visual cycles differentially regulate immediate, early, and late phases of cone photoreceptor-mediated visionWard, RebeccaKaylor, Joanna JCobice, Diego FPepe, Dionissia AMcGarrigle, Eoghan MBrockerhoff, Susan EHurley, James BTravis, Gabriel HKennedy, Breandán N2020-05-01Cone photoreceptors in the retina enable vision over a wide range of light intensities. However, the processes enabling cone vision in bright light (i.e. photopic vision) are not adequately understood. Chromophore regeneration of cone photopigments may require the retinal pigment epithelium (RPE) and/or retinal Müller glia. In the RPE, isomerization of all-trans-retinyl esters to 11-cis-retinol is mediated by the retinoid isomerohydrolase Rpe65. A putative alternative retinoid isomerase, dihydroceramide desaturase-1 (DES1), is expressed in RPE and Müller cells. The retinol-isomerase activities of Rpe65 and Des1 are inhibited by emixustat and fenretinide, respectively. Here, we tested the effects of these visual cycle inhibitors on immediate, early, and late phases of cone photopic vision. In zebrafish larvae raised under cyclic light conditions, fenretinide impaired late cone photopic vision, while the emixustat-treated zebrafish unexpectedly had normal vision. In contrast, emixustat-treated larvae raised under extensive dark-adaptation displayed significantly attenuated immediate photopic vision concomitant with significantly reduced 11-cis-retinaldehyde (11cRAL). Following 30 min of light, early photopic vision was recovered, despite 11cRAL levels remaining significantly reduced. Defects in immediate cone photopic vision were rescued in emixustat- or fenretinide-treated larvae following exogenous 9-cis-retinaldehyde supplementation. Genetic knockout of Des1 (degs1) or retinaldehyde-binding protein 1b (rlbp1b) did not eliminate photopic vision in zebrafish. Our findings define molecular and temporal requirements of the nonphotopic or photopic visual cycles for mediating vision in bright light.32 Biomedical and Clinical Sciences (for-2020)3212 Ophthalmology and Optometry (for-2020)Neurosciences (rcdc)Eye Disease and Disorders of Vision (rcdc)Eye (hrcs-hc)Animals (mesh)Carrier Proteins (mesh)Color Vision (mesh)Ependymoglial Cells (mesh)Fatty Acid Desaturases (mesh)Gene Deletion (mesh)Retinal Cone Photoreceptor Cells (mesh)Vitamin A (mesh)Zebrafish (mesh)cis-trans-Isomerases (mesh)vitamin Avisionzebrafishretinapharmacologychemical biologycone-based visual behaviorRpe65visual cyclezebrafishAnimals (mesh)Zebrafish (mesh)Vitamin A (mesh)cis-trans-Isomerases (mesh)Fatty Acid Desaturases (mesh)Carrier Proteins (mesh)Gene Deletion (mesh)Retinal Cone Photoreceptor Cells (mesh)Color Vision (mesh)Ependymoglial Cells (mesh)Rpe65chemical biologycone-based visual behaviorpharmacologyretinavisionvisual cyclevitamin AzebrafishAnimals (mesh)Carrier Proteins (mesh)Color Vision (mesh)Ependymoglial Cells (mesh)Fatty Acid Desaturases (mesh)Gene Deletion (mesh)Retinal Cone Photoreceptor Cells (mesh)Vitamin A (mesh)Zebrafish (mesh)cis-trans-Isomerases (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biochemistry & Molecular Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)publiceScholarship, University of Californiahttps://escholarship.org/uc/item/3cd793prinfo:doi/10.1074/jbc.ra119.011374articleJournal of Biological Chemistry, vol 295, iss 196482 - 6497oai:escholarship.org:ark:/13030/qt5147t46x2025-12-26T18:54:49Zqt5147t46xCrystal structure of a conformational antibody that binds tau oligomers and inhibits pathological seeding by extracts from donors with Alzheimer's diseaseAbskharon, RomanySeidler, Paul MSawaya, Michael RCascio, DuilioYang, Tianxiao PPhilipp, StephanWilliams, Christopher KazuNewell, Kathy LGhetti, BernardinoDeTure, Michael ADickson, Dennis WVinters, Harry VFelgner, Philip LNakajima, RieGlabe, Charles GEisenberg, David S2020-07-01Soluble oligomers of aggregated tau accompany the accumulation of insoluble amyloid fibrils, a histological hallmark of Alzheimer disease (AD) and two dozen related neurodegenerative diseases. Both oligomers and fibrils seed the spread of Tau pathology, and by virtue of their low molecular weight and relative solubility, oligomers may be particularly pernicious seeds. Here, we report the formation of in vitro tau oligomers formed by an ionic liquid (IL15). Using IL15-induced recombinant tau oligomers and a dot blot assay, we discovered a mAb (M204) that binds oligomeric tau, but not tau monomers or fibrils. M204 and an engineered single-chain variable fragment (scFv) inhibited seeding by IL15-induced tau oligomers and pathological extracts from donors with AD and chronic traumatic encephalopathy. This finding suggests that M204-scFv targets pathological structures that are formed by tau in neurodegenerative diseases. We found that M204-scFv itself partitions into oligomeric forms that inhibit seeding differently, and crystal structures of the M204-scFv monomer, dimer, and trimer revealed conformational differences that explain differences among these forms in binding and inhibition. The efficiency of M204-scFv antibodies to inhibit the seeding by brain tissue extracts from different donors with tauopathies varied among individuals, indicating the possible existence of distinct amyloid polymorphs. We propose that by binding to oligomers, which are hypothesized to be the earliest seeding-competent species, M204-scFv may have potential as an early-stage diagnostic for AD and tauopathies, and also could guide the development of promising therapeutic antibodies.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)Aging (rcdc)Dementia (rcdc)Brain Disorders (rcdc)Alzheimer's Disease (rcdc)Biotechnology (rcdc)Neurodegenerative (rcdc)Acquired Cognitive Impairment (rcdc)Neurosciences (rcdc)2.1 Biological and endogenous factors (hrcs-rac)5.1 Pharmaceuticals (hrcs-rac)Neurological (hrcs-hc)Alzheimer Disease (mesh)CrystallographyX-Ray (mesh)Humans (mesh)Protein Multimerization (mesh)Single-Chain Antibodies (mesh)tau Proteins (mesh)amyloidtauprioninhibitorfibrilprotein structureantibodyneurodegenerationtauopathyprotein aggregationneurodegenerative diseaseoligomerizationAlzheimer diseaseantibody engineeringprotein crystallizationinhibitortauHumans (mesh)Alzheimer Disease (mesh)tau Proteins (mesh)CrystallographyX-Ray (mesh)Protein Multimerization (mesh)Single-Chain Antibodies (mesh)Alzheimer diseaseamyloidantibodyantibody engineeringfibrilinhibitorneurodegenerationneurodegenerative diseaseoligomerizationprionprotein aggregationprotein crystallizationprotein structuretautauopathyAlzheimer Disease (mesh)CrystallographyX-Ray (mesh)Humans (mesh)Protein Multimerization (mesh)Single-Chain Antibodies (mesh)tau Proteins (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biochemistry & Molecular Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/5147t46xhttps://escholarship.org/content/qt5147t46x/qt5147t46x.pdfinfo:doi/10.1074/jbc.ra120.013638articleJournal of Biological Chemistry, vol 295, iss 3110662 - 10676oai:escholarship.org:ark:/13030/qt298935g52025-12-26T16:20:48Zqt298935g5Metabolic Regulation of Tissue Stem CellsShapira, Suzanne NChristofk, Heather R2020-07-01Adult tissue stem cells mediate organ homeostasis and regeneration and thus are continually making decisions about whether to remain quiescent, proliferate, or differentiate into mature cell types. These decisions often integrate external cues, such as energy balance and the nutritional status of the organism. Metabolic substrates and byproducts that regulate epigenetic and signaling pathways are now appreciated to have instructive rather than bystander roles in regulating cell fate decisions. In this review, we highlight recent literature focused on how metabolites and dietary manipulations can impact cell fate decisions, with a focus on the regulation of adult tissue stem cells.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Stem Cell Research (rcdc)Regenerative Medicine (rcdc)Stem Cell Research - Nonembryonic - Non-Human (rcdc)Nutrition (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Animals (mesh)Diet (mesh)EpigenesisGenetic (mesh)Homeostasis (mesh)Humans (mesh)Neoplasms (mesh)Organ Specificity (mesh)Stem Cells (mesh)Stem Cells (mesh)Animals (mesh)Humans (mesh)Neoplasms (mesh)Diet (mesh)Organ Specificity (mesh)EpigenesisGenetic (mesh)Homeostasis (mesh)adult stem cellsdietdifferentiationmetabolismmetabolomicsAnimals (mesh)Diet (mesh)EpigenesisGenetic (mesh)Homeostasis (mesh)Humans (mesh)Neoplasms (mesh)Organ Specificity (mesh)Stem Cells (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/298935g5https://escholarship.org/content/qt298935g5/qt298935g5.pdfinfo:doi/10.1016/j.tcb.2020.04.004articleTrends in Cell Biology, vol 30, iss 7566 - 576oai:escholarship.org:ark:/13030/qt2s59v7kg2025-12-26T14:36:55Zqt2s59v7kgHigh Mass Analysis with a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer: From Inorganic Salt Clusters to Antibody Conjugates and BeyondCampuzano, Iain DGNshanian, MichaelSpahr, ChristopherLantz, CarterNetirojjanakul, ChawitaLi, HuilinWongkongkathep, PiriyaWolff, Jeremy JLoo, Joseph A2020-05-06Analysis of proteins and complexes under native mass spectrometric (MS) and solution conditions was typically performed using time-of-flight (ToF) analyzers, due to their routine high m/z transmission and detection capabilities. However, over recent years, the ability of Orbitrap-based mass spectrometers to transmit and detect a range of high molecular weight species is well documented. Herein, we describe how a 15 Tesla Fourier transform ion cyclotron resonance mass spectrometer (15 T FT-ICR MS) is more than capable of analyzing a wide range of ions in the high m/z scale (>5000), in both positive and negative instrument polarities, ranging from the inorganic cesium iodide salt clusters; a humanized IgG1k monoclonal antibody (mAb; 148.2 kDa); an IgG1-mertansine drug conjugate (148.5 kDa, drug-to-antibody ratio; DAR 2.26); an IgG1-siRNA conjugate (159.1 kDa; ribonucleic acid to antibody ratio; RAR 1); the membrane protein aquaporin-Z (97.2 kDa) liberated from a C8E4 detergent micelle; the empty MSP1D1-nanodisc (142.5 kDa) and the tetradecameric chaperone protein complex GroEL (806.2 kDa; GroEL dimer at 1.6 MDa). We also investigate different regions of the FT-ICR MS that impact ion transmission and desolvation. Finally, we demonstrate how the transmission of these species and resultant spectra are highly consistent with those previously generated on both quadrupole-ToF (Q-ToF) and Orbitrap instrumentation. This report serves as an impactful example of how FT-ICR mass analyzers are competitive to Q-ToFs and Orbitraps for high mass detection at high m/z.3401 Analytical Chemistry (for-2020)34 Chemical Sciences (for-2020)3406 Physical Chemistry (for-2020)Immunization (rcdc)Bioengineering (rcdc)Biotechnology (rcdc)AntibodiesMonoclonal (mesh)Cesium (mesh)Chaperonin 60 (mesh)Cyclotrons (mesh)Fourier Analysis (mesh)Immunoconjugates (mesh)Immunoglobulin G (mesh)Immunoglobulin kappa-Chains (mesh)Iodides (mesh)Mass Spectrometry (mesh)Maytansine (mesh)Molecular Weight (mesh)RNASmall Interfering (mesh)Salts (mesh)Fourier transform ion cyclotron resonancenative-MSmonoclonal antibodiescesium iodidemembrane proteinsantibody drug conjugatessiRNAnanodiscsGroELIodides (mesh)Cesium (mesh)Salts (mesh)Maytansine (mesh)Immunoglobulin G (mesh)Chaperonin 60 (mesh)RNASmall Interfering (mesh)AntibodiesMonoclonal (mesh)Immunoconjugates (mesh)Molecular Weight (mesh)Fourier Analysis (mesh)Cyclotrons (mesh)Immunoglobulin kappa-Chains (mesh)Mass Spectrometry (mesh)Fourier transform ion cyclotron resonanceGroELantibody drug conjugatescesium iodidemembrane proteinsmonoclonal antibodiesnanodiscsnative-MSsiRNAAntibodiesMonoclonal (mesh)Cesium (mesh)Chaperonin 60 (mesh)Cyclotrons (mesh)Fourier Analysis (mesh)Immunoconjugates (mesh)Immunoglobulin G (mesh)Immunoglobulin kappa-Chains (mesh)Iodides (mesh)Mass Spectrometry (mesh)Maytansine (mesh)Molecular Weight (mesh)RNASmall Interfering (mesh)Salts (mesh)0301 Analytical Chemistry (for)0304 Medicinal and Biomolecular Chemistry (for)0306 Physical Chemistry (incl. Structural) (for)Analytical Chemistry (science-metrix)3401 Analytical chemistry (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2s59v7kghttps://escholarship.org/content/qt2s59v7kg/qt2s59v7kg.pdfinfo:doi/10.1021/jasms.0c00030articleJournal of The American Society for Mass Spectrometry, vol 31, iss 51155 - 1162oai:escholarship.org:ark:/13030/qt1pt403bx2025-12-26T14:25:51Zqt1pt403bxGlycolysis-Independent Glucose Metabolism Distinguishes TE from ICM Fate during Mammalian EmbryogenesisChi, FangtaoSharpley, Mark SNagaraj, RaghavendraRoy, Shubhendu SenBanerjee, Utpal2020-04-01The mouse embryo undergoes compaction at the 8-cell stage, and its transition to 16 cells generates polarity such that the outer apical cells are trophectoderm (TE) precursors and the inner cell mass (ICM) gives rise to the embryo. Here, we report that this first cell fate specification event is controlled by glucose. Glucose does not fuel mitochondrial ATP generation, and glycolysis is dispensable for blastocyst formation. Furthermore, glucose does not help synthesize amino acids, fatty acids, and nucleobases. Instead, glucose metabolized by the hexosamine biosynthetic pathway (HBP) allows nuclear localization of YAP1. In addition, glucose-dependent nucleotide synthesis by the pentose phosphate pathway (PPP), along with sphingolipid (S1P) signaling, activates mTOR and allows translation of Tfap2c. YAP1, TEAD4, and TFAP2C interact to form a complex that controls TE-specific gene transcription. Glucose signaling has no role in ICM specification, and this process of developmental metabolism specifically controls TE cell fate.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Animals (mesh)Blastocyst (mesh)Cell Differentiation (mesh)EmbryoMammalian (mesh)Embryonic Development (mesh)Gene Expression RegulationDevelopmental (mesh)Glucose (mesh)Glycolysis (mesh)Homeodomain Proteins (mesh)Mice (mesh)Transcription Factors (mesh)Blastocyst (mesh)Animals (mesh)Mice (mesh)Glucose (mesh)Homeodomain Proteins (mesh)Transcription Factors (mesh)Cell Differentiation (mesh)Gene Expression RegulationDevelopmental (mesh)Glycolysis (mesh)Embryonic Development (mesh)EmbryoMammalian (mesh)S1P signalingTfap2cYAP1developmental metabolismglucosehexosamine biosynthetic pathwaymorula blastocystpentose phosphate pathwaypreimplantation embryotrophectodermAnimals (mesh)Blastocyst (mesh)Cell Differentiation (mesh)EmbryoMammalian (mesh)Embryonic Development (mesh)Gene Expression RegulationDevelopmental (mesh)Glucose (mesh)Glycolysis (mesh)Homeodomain Proteins (mesh)Mice (mesh)Transcription Factors (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1pt403bxhttps://escholarship.org/content/qt1pt403bx/qt1pt403bx.pdfinfo:doi/10.1016/j.devcel.2020.02.015articleDevelopmental Cell, vol 53, iss 19 - 26.e4oai:escholarship.org:ark:/13030/qt3js6q9k32025-12-26T14:10:56Zqt3js6q9k3Lipid Mediated Regulation of Adult Stem Cell BehaviorClémot, MarieDemarco, Rafael SênosJones, D Leanne2020-01-01Adult stem cells constitute an important reservoir of self-renewing progenitor cells and are crucial for maintaining tissue and organ homeostasis. The capacity of stem cells to self-renew or differentiate can be attributed to distinct metabolic states, and it is now becoming apparent that metabolism plays instructive roles in stem cell fate decisions. Lipids are an extremely vast class of biomolecules, with essential roles in energy homeostasis, membrane structure and signaling. Imbalances in lipid homeostasis can result in lipotoxicity, cell death and diseases, such as cardiovascular disease, insulin resistance and diabetes, autoimmune disorders and cancer. Therefore, understanding how lipid metabolism affects stem cell behavior offers promising perspectives for the development of novel approaches to control stem cell behavior either in vitro or in patients, by modulating lipid metabolic pathways pharmacologically or through diet. In this review, we will first address how recent progress in lipidomics has created new opportunities to uncover stem-cell specific lipidomes. In addition, genetic and/or pharmacological modulation of lipid metabolism have shown the involvement of specific pathways, such as fatty acid oxidation (FAO), in regulating adult stem cell behavior. We will describe and compare findings obtained in multiple stem cell models in order to provide an assessment on whether unique lipid metabolic pathways may commonly regulate stem cell behavior. We will then review characterized and potential molecular mechanisms through which lipids can affect stem cell-specific properties, including self-renewal, differentiation potential or interaction with the niche. Finally, we aim to summarize the current knowledge of how alterations in lipid homeostasis that occur as a consequence of changes in diet, aging or disease can impact stem cells and, consequently, tissue homeostasis and repair.3205 Medical Biochemistry and Metabolomics (for-2020)3101 Biochemistry and Cell Biology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)Stem Cell Research - Nonembryonic - Non-Human (rcdc)Regenerative Medicine (rcdc)Stem Cell Research (rcdc)Nutrition (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Generic health relevance (hrcs-hc)Metabolic and endocrine (hrcs-hc)lipidmetabolismfatty acidsstem cellsnichefatty acidslipidmetabolismnichestem cells31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/3js6q9k3https://escholarship.org/content/qt3js6q9k3/qt3js6q9k3.pdfinfo:doi/10.3389/fcell.2020.00115articleFrontiers in Cell and Developmental Biology, vol 8115oai:escholarship.org:ark:/13030/qt3dv402d52025-12-26T08:36:58Zqt3dv402d5Regulation of Cell Cycle Entry and Exit: A Single Cell PerspectiveColler, Hilary A2020-01-01The transition between proliferating and quiescent states must be carefully regulated to ensure that cells divide to create the cells an organism needs only at the appropriate time and place. Cyclin-dependent kinases (CDKs) are critical for both transitioning cells from one cell cycle state to the next, and for regulating whether cells are proliferating or quiescent. CDKs are regulated by association with cognate cyclins, activating and inhibitory phosphorylation events, and proteins that bind to them and inhibit their activity. The substrates of these kinases, including the retinoblastoma protein, enforce the changes in cell cycle status. Single cell analysis has clarified that competition among factors that activate and inhibit CDK activity leads to the cell's decision to enter the cell cycle, a decision the cell makes before S phase. Signaling pathways that control the activity of CDKs regulate the transition between quiescence and proliferation in stem cells, including stem cells that generate muscle and neurons. © 2020 American Physiological Society. Compr Physiol 10:317-344, 2020.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Stem Cell Research (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Animals (mesh)Cell Cycle (mesh)Cell Proliferation (mesh)Humans (mesh)Single-Cell Analysis (mesh)Stem Cells (mesh)Stem Cells (mesh)Animals (mesh)Humans (mesh)Cell Cycle (mesh)Cell Proliferation (mesh)Single-Cell Analysis (mesh)Animals (mesh)Cell Cycle (mesh)Cell Proliferation (mesh)Humans (mesh)Single-Cell Analysis (mesh)Stem Cells (mesh)3109 Zoology (for-2020)3208 Medical physiology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/3dv402d5https://escholarship.org/content/qt3dv402d5/qt3dv402d5.pdfinfo:doi/10.1002/cphy.c190014articleCOMPREHENSIVE PHYSIOLOGY, vol 10, iss 1317 - 344oai:escholarship.org:ark:/13030/qt7sn8s9h52025-12-26T08:07:46Zqt7sn8s9h5Splicing Busts a Move: Isoform Switching Regulates MigrationMitra, MithunLee, Ha NeulColler, Hilary A2020-01-01Cell migration is essential for normal development, neural patterning, pathogen eradication, and cancer metastasis. Pre-mRNA processing events such as alternative splicing and alternative polyadenylation result in greater transcript and protein diversity as well as function and activity. A critical role for alternative pre-mRNA processing in cell migration has emerged in axon outgrowth during neuronal development, immune cell migration, and cancer metastasis. These findings suggest that migratory signals result in expression changes of post-translational modifications of splicing or polyadenylation factors, leading to splicing events that generate promigratory isoforms. We summarize this recent progress and suggest emerging technologies that may facilitate a deeper understanding of the role of alternative splicing and polyadenylation in cell migration.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Cancer (rcdc)2.1 Biological and endogenous factors (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)Alternative Splicing (mesh)Animals (mesh)Cell Movement (mesh)Humans (mesh)ModelsBiological (mesh)Polyadenylation (mesh)Protein Isoforms (mesh)RNA ProcessingPost-Transcriptional (mesh)Animals (mesh)Humans (mesh)Protein Isoforms (mesh)Cell Movement (mesh)RNA ProcessingPost-Transcriptional (mesh)Polyadenylation (mesh)Alternative Splicing (mesh)ModelsBiological (mesh)axonscleavage and polyadenylationmetastasismigrationsplicingAlternative Splicing (mesh)Animals (mesh)Cell Movement (mesh)Humans (mesh)ModelsBiological (mesh)Polyadenylation (mesh)Protein Isoforms (mesh)RNA ProcessingPost-Transcriptional (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7sn8s9h5https://escholarship.org/content/qt7sn8s9h5/qt7sn8s9h5.pdfinfo:doi/10.1016/j.tcb.2019.10.007articleTrends in Cell Biology, vol 30, iss 174 - 85oai:escholarship.org:ark:/13030/qt4sm3q6202025-12-26T07:31:23Zqt4sm3q620Tailoring Tryptophan Synthase TrpB for Selective Quaternary Carbon Bond FormationDick, MarkusSarai, Nicholas SMartynowycz, Michael WGonen, TamirArnold, Frances H2019-12-18We previously engineered the β-subunit of tryptophan synthase (TrpB), which catalyzes the condensation of l-serine and indole to l-tryptophan, to synthesize a range of noncanonical amino acids from l-serine and indole derivatives or other nucleophiles. Here we employ directed evolution to engineer TrpB to accept 3-substituted oxindoles and form C-C bonds leading to new quaternary stereocenters. Initially, the variants that could use 3-substituted oxindoles preferentially formed N-C bonds on N1 of the substrate. Protecting N1 encouraged evolution toward C-alkylation, which persisted when protection was removed. Six generations of directed evolution resulted in TrpB Pfquat with a 400-fold improvement in activity for alkylation of 3-substituted oxindoles and the ability to selectively form a new, all-carbon quaternary stereocenter at the γ-position of the amino acid products. The enzyme can also alkylate and form all-carbon quaternary stereocenters on structurally similar lactones and ketones, where it exhibits excellent regioselectivity for the tertiary carbon. The configurations of the γ-stereocenters of two of the products were determined via microcrystal electron diffraction (MicroED), and we report the MicroED structure of a small molecule obtained using the Falcon III direct electron detector. Highly thermostable and expressed at >500 mg/L E. coli culture, TrpB Pfquat offers an efficient, sustainable, and selective platform for the construction of diverse noncanonical amino acids bearing all-carbon quaternary stereocenters.3405 Organic Chemistry (for-2020)34 Chemical Sciences (for-2020)Biotechnology (rcdc)Alkylation (mesh)Carbon (mesh)ModelsMolecular (mesh)Protein Conformation (mesh)Protein Engineering (mesh)Tryptophan Synthase (mesh)Carbon (mesh)Tryptophan Synthase (mesh)Protein Engineering (mesh)Protein Conformation (mesh)Alkylation (mesh)ModelsMolecular (mesh)Alkylation (mesh)Carbon (mesh)ModelsMolecular (mesh)Protein Conformation (mesh)Protein Engineering (mesh)Tryptophan Synthase (mesh)03 Chemical Sciences (for)General Chemistry (science-metrix)34 Chemical sciences (for-2020)40 Engineering (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4sm3q620https://escholarship.org/content/qt4sm3q620/qt4sm3q620.pdfinfo:doi/10.1021/jacs.9b09864articleJournal of the American Chemical Society, vol 141, iss 5019817 - 19822oai:escholarship.org:ark:/13030/qt0cm4r7hp2025-12-26T04:22:06Zqt0cm4r7hpStructure-based inhibitors halt prion-like seeding by Alzheimer’s disease–and tauopathy–derived brain tissue samplesSeidler, Paul MatthewBoyer, David RMurray, Kevin AYang, Tianxiao PBentzel, MeganSawaya, Michael RRosenberg, GregoryCascio, DuilioWilliams, Christopher KazuNewell, Kathy LGhetti, BernardinoDeTure, Michael ADickson, Dennis WVinters, Harry VEisenberg, David S2019-11-01In Alzheimer's disease (AD) and tauopathies, tau aggregation accompanies progressive neurodegeneration. Aggregated tau appears to spread between adjacent neurons and adjacent brain regions by prion-like seeding. Hence, inhibitors of this seeding offer a possible route to managing tauopathies. Here, we report the 1.0 Å resolution micro-electron diffraction structure of an aggregation-prone segment of tau with the sequence SVQIVY, present in the cores of patient-derived fibrils from AD and tauopathies. This structure illuminates how distinct interfaces of the parent segment, containing the sequence VQIVYK, foster the formation of distinct structures. Peptide-based fibril-capping inhibitors designed to target the two VQIVYK interfaces blocked proteopathic seeding by patient-derived fibrils. These VQIVYK inhibitors add to a panel of tau-capping inhibitors that targets specific polymorphs of recombinant and patient-derived tau fibrils. Inhibition of seeding initiated by brain tissue extracts differed among donors with different tauopathies, suggesting that particular fibril polymorphs of tau are associated with certain tauopathies. Donors with progressive supranuclear palsy exhibited more variation in inhibitor sensitivity, suggesting that fibrils from these donors were more polymorphic and potentially vary within individual donor brains. Our results suggest that a subset of inhibitors from our panel could be specific for particular disease-associated polymorphs, whereas inhibitors that blocked seeding by extracts from all of the tauopathies tested could be used to broadly inhibit seeding by multiple disease-specific tau polymorphs. Moreover, we show that tau-capping inhibitors can be transiently expressed in HEK293 tau biosensor cells, indicating that nucleic acid-based vectors can be used for inhibitor delivery.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)Alzheimer's Disease (rcdc)Alzheimer's Disease Related Dementias (ADRD) (rcdc)Neurodegenerative (rcdc)Brain Disorders (rcdc)Frontotemporal Dementia (FTD) (rcdc)Aging (rcdc)Acquired Cognitive Impairment (rcdc)Neurosciences (rcdc)Dementia (rcdc)5.1 Pharmaceuticals (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Neurological (hrcs-hc)Alzheimer Disease (mesh)Brain (mesh)HEK293 Cells (mesh)Humans (mesh)Neurons (mesh)Prions (mesh)Protein AggregationPathological (mesh)Tauopathies (mesh)tau Proteins (mesh)amyloidtau proteintauopathyprionfibrilcrystal structureinhibitorprotein aggregationseedingprotein structureneurodegenerationstructural biologyseedingzipper interfaceBrain (mesh)Neurons (mesh)Humans (mesh)Alzheimer Disease (mesh)Tauopathies (mesh)tau Proteins (mesh)Prions (mesh)HEK293 Cells (mesh)Protein AggregationPathological (mesh)amyloidcrystal structurefibrilinhibitorneurodegenerationprionprotein aggregationprotein structureseedingstructural biologytau proteintauopathyzipper interfaceAlzheimer Disease (mesh)Brain (mesh)HEK293 Cells (mesh)Humans (mesh)Neurons (mesh)Prions (mesh)Protein AggregationPathological (mesh)Tauopathies (mesh)tau Proteins (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biochemistry & Molecular Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/0cm4r7hphttps://escholarship.org/content/qt0cm4r7hp/qt0cm4r7hp.pdfinfo:doi/10.1074/jbc.ra119.009688articleJournal of Biological Chemistry, vol 294, iss 4416451 - 16464oai:escholarship.org:ark:/13030/qt8h14v30v2025-12-26T04:21:22Zqt8h14v30vThe paradox of metabolism in quiescent stem cellsColler, Hilary A2019-10-01The shift between a proliferating and a nonproliferating state is associated with significant changes in metabolic needs. Proliferating cells tend to have higher metabolic rates, and their metabolic profiles facilitate biosynthesis, as compared to those of nondividing cells of the same sort. Recent studies have elucidated specific molecules that control metabolic changes while cells shift between proliferation and quiescence. Embryonic stem cells, which are rapidly proliferating, tend to have metabolic patterns that are similar to those of nonstem cells in a proliferative state. Moreover, although adult stem cells tend to be quiescent, their metabolic profiles have been reported in multiple organs to more closely resemble those of proliferating than those of nondividing cells in some respects. The findings raise questions about whether there are metabolic profiles that are required for stemness, and whether these profiles relate to the metabolic properties that may be required for quiescence. Here, we review the literature on how metabolism changes upon commitment to proliferation and compare the proliferating and nonproliferating metabolic states of differentiated cells and embryonic and adult stem cells.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Regenerative Medicine (rcdc)Stem Cell Research (rcdc)Adult Stem Cells (mesh)Amino Acids (mesh)Animals (mesh)Cell Differentiation (mesh)Cell Division (mesh)Cell Lineage (mesh)Cell Proliferation (mesh)Embryonic Stem Cells (mesh)Fatty Acids (mesh)Fibroblasts (mesh)Glycolysis (mesh)Humans (mesh)Neurons (mesh)Nucleotides (mesh)Oxidative Phosphorylation (mesh)cell cycleepigeneticsfatty acid metabolismglutamine metabolismglycolysismetabolismnucleotide metabolismoxidative phosphorylationquiescencestem cellsNeurons (mesh)Fibroblasts (mesh)Animals (mesh)Humans (mesh)Nucleotides (mesh)Fatty Acids (mesh)Amino Acids (mesh)Cell Division (mesh)Cell Differentiation (mesh)Cell Proliferation (mesh)Oxidative Phosphorylation (mesh)Glycolysis (mesh)Cell Lineage (mesh)Embryonic Stem Cells (mesh)Adult Stem Cells (mesh)cell cycleepigeneticsfatty acid metabolismglutamine metabolismglycolysismetabolismnucleotide metabolismoxidative phosphorylationquiescencestem cellsAdult Stem Cells (mesh)Amino Acids (mesh)Animals (mesh)Cell Differentiation (mesh)Cell Division (mesh)Cell Lineage (mesh)Cell Proliferation (mesh)Embryonic Stem Cells (mesh)Fatty Acids (mesh)Fibroblasts (mesh)Glycolysis (mesh)Humans (mesh)Neurons (mesh)Nucleotides (mesh)Oxidative Phosphorylation (mesh)0304 Medicinal and Biomolecular Chemistry (for)0601 Biochemistry and Cell Biology (for)0603 Evolutionary Biology (for)Biochemistry & Molecular Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8h14v30vhttps://escholarship.org/content/qt8h14v30v/qt8h14v30v.pdfinfo:doi/10.1002/1873-3468.13608articleFEBS Letters, vol 593, iss 202817 - 2839oai:escholarship.org:ark:/13030/qt53s8m2f32025-12-26T04:17:30Zqt53s8m2f3MicroED with the Falcon III direct electron detectorHattne, JohanMartynowycz, Michael WPenczek, Pawel AGonen, Tamir2019-09-01Microcrystal electron diffraction (MicroED) combines crystallography and electron cryo-microscopy (cryo-EM) into a method that is applicable to high-resolution structure determination. In MicroED, nanosized crystals, which are often intractable using other techniques, are probed by high-energy electrons in a transmission electron microscope. Diffraction data are recorded by a camera in movie mode: the nanocrystal is continuously rotated in the beam, thus creating a sequence of frames that constitute a movie with respect to the rotation angle. Until now, diffraction-optimized cameras have mostly been used for MicroED. Here, the use of a direct electron detector that was designed for imaging is reported. It is demonstrated that data can be collected more rapidly using the Falcon III for MicroED and with markedly lower exposure than has previously been reported. The Falcon III was operated at 40 frames per second and complete data sets reaching atomic resolution were recorded in minutes. The resulting density maps to 2.1 Å resolution of the serine protease proteinase K showed no visible signs of radiation damage. It is thus demonstrated that dedicated diffraction-optimized detectors are not required for MicroED, as shown by the fact that the very same cameras that are used for imaging applications in electron microscopy, such as single-particle cryo-EM, can also be used effectively for diffraction measurements.51 Physical Sciences (for-2020)5104 Condensed Matter Physics (for-2020)Biotechnology (rcdc)Bioengineering (rcdc)microcrystal electron diffractionMicroEDFalcon IIIdirect electron detectorsFalcon IIIMicroEDdirect electron detectorsmicrocrystal electron diffraction0202 AtomicMolecularNuclearParticle and Plasma Physics (for)0204 Condensed Matter Physics (for)0306 Physical Chemistry (incl. Structural) (for)3406 Physical chemistry (for-2020)5104 Condensed matter physics (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/53s8m2f3https://escholarship.org/content/qt53s8m2f3/qt53s8m2f3.pdfinfo:doi/10.1107/s2052252519010583articleIUCrJ, vol 6, iss Pt 5921 - 926oai:escholarship.org:ark:/13030/qt6wb6944w2025-12-26T02:22:06Zqt6wb6944wArabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z depositionPotok, Magdalena EWang, YafeiXu, LinhaoZhong, ZhenhuiLiu, WanluFeng, SuhuaNaranbaatar, BilguudeiRayatpisheh, ShimaWang, ZonghuaWohlschlegel, James AAusin, IsraelJacobsen, Steven E2019-01-01Deposition of the histone variant H2A.Z by the SWI2/SNF2-Related 1 chromatin remodeling complex (SWR1-C) is important for gene regulation in eukaryotes, but the composition of the Arabidopsis SWR1-C has not been thoroughly characterized. Here, we aim to identify interacting partners of a conserved Arabidopsis SWR1 subunit ACTIN-RELATED PROTEIN 6 (ARP6). We isolate nine predicted components and identify additional interactors implicated in histone acetylation and chromatin biology. One of the interacting partners, methyl-CpG-binding domain 9 (MBD9), also strongly interacts with the Imitation SWItch (ISWI) chromatin remodeling complex. MBD9 is required for deposition of H2A.Z at a distinct subset of ARP6-dependent loci. MBD9 is preferentially bound to nucleosome-depleted regions at the 5’ ends of genes containing high levels of activating histone marks. These data suggest that MBD9 is a SWR1-C interacting protein required for H2A.Z deposition at a subset of actively transcribing genes.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Arabidopsis (mesh)Arabidopsis Proteins (mesh)Chromatin Assembly and Disassembly (mesh)Gene Expression RegulationPlant (mesh)Histone Acetyltransferases (mesh)Histones (mesh)Microfilament Proteins (mesh)Protein Binding (mesh)Arabidopsis (mesh)Microfilament Proteins (mesh)Histones (mesh)Arabidopsis Proteins (mesh)Chromatin Assembly and Disassembly (mesh)Gene Expression RegulationPlant (mesh)Protein Binding (mesh)Histone Acetyltransferases (mesh)Arabidopsis (mesh)Arabidopsis Proteins (mesh)Chromatin Assembly and Disassembly (mesh)Gene Expression RegulationPlant (mesh)Histone Acetyltransferases (mesh)Histones (mesh)Microfilament Proteins (mesh)Protein Binding (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/6wb6944whttps://escholarship.org/content/qt6wb6944w/qt6wb6944w.pdfinfo:doi/10.1038/s41467-019-11291-warticleNature Communications, vol 10, iss 13352oai:escholarship.org:ark:/13030/qt5vg8s8062025-12-26T01:43:19Zqt5vg8s806Systematic discovery of conservation states for single-nucleotide annotation of the human genomeArneson, AdrianaErnst, Jason2019-07-02Comparative genomics sequence data is an important source of information for interpreting genomes. Genome-wide annotations based on this data have largely focused on univariate scores or binary elements of evolutionary constraint. Here we present a complementary whole genome annotation approach, ConsHMM, which applies a multivariate hidden Markov model to learn de novo ‘conservation states’ based on the combinatorial and spatial patterns of which species align to and match a reference genome in a multiple species DNA sequence alignment. We applied ConsHMM to a 100-way vertebrate sequence alignment to annotate the human genome at single nucleotide resolution into 100 conservation states. These states have distinct enrichments for other genomic information including gene annotations, chromatin states, repeat families, and bases prioritized by various variant prioritization scores. Constrained elements have distinct heritability partitioning enrichments depending on their conservation state assignment. ConsHMM conservation states are a resource for analyzing genomes and genetic variants.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)3105 Genetics (for-2020)Human Genome (rcdc)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Chromatin (mesh)Cluster Analysis (mesh)Computational Biology (mesh)Epigenomics (mesh)GenomeHuman (mesh)Genome-Wide Association Study (mesh)Genomics (mesh)Humans (mesh)Markov Chains (mesh)Molecular Sequence Annotation (mesh)Multivariate Analysis (mesh)Nucleotides (mesh)Phenotype (mesh)PolymorphismSingle Nucleotide (mesh)Reproducibility of Results (mesh)Chromatin (mesh)Humans (mesh)Nucleotides (mesh)Multivariate Analysis (mesh)Cluster Analysis (mesh)Markov Chains (mesh)Reproducibility of Results (mesh)Computational Biology (mesh)Genomics (mesh)Phenotype (mesh)PolymorphismSingle Nucleotide (mesh)GenomeHuman (mesh)Genome-Wide Association Study (mesh)Epigenomics (mesh)Molecular Sequence Annotation (mesh)Comparative genomicsEvolutionary geneticsGenome informaticsChromatin (mesh)Cluster Analysis (mesh)Computational Biology (mesh)Epigenomics (mesh)GenomeHuman (mesh)Genome-Wide Association Study (mesh)Genomics (mesh)Humans (mesh)Markov Chains (mesh)Molecular Sequence Annotation (mesh)Multivariate Analysis (mesh)Nucleotides (mesh)Phenotype (mesh)PolymorphismSingle Nucleotide (mesh)Reproducibility of Results (mesh)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/5vg8s806https://escholarship.org/content/qt5vg8s806/qt5vg8s806.pdfinfo:doi/10.1038/s42003-019-0488-1articleCommunications Biology, vol 2, iss 1248oai:escholarship.org:ark:/13030/qt4dj3x34m2025-12-26T00:49:15Zqt4dj3x34mFast genetic mapping of complex traits in C. elegans using millions of individuals in bulkBurga, AlejandroBen-David, EyalLemus Vergara, TzitzikiBoocock, JamesKruglyak, Leonid2019-01-01Genetic studies of complex traits in animals have been hindered by the need to generate, maintain, and phenotype large panels of recombinant lines. We developed a new method, C. elegans eXtreme Quantitative Trait Locus (ceX-QTL) mapping, that overcomes this obstacle via bulk selection on millions of unique recombinant individuals. We use ceX-QTL to map a drug resistance locus with high resolution. We also map differences in gene expression in live worms and discovered that mutations in the co-chaperone sti-1 upregulate the transcription of HSP-90. Lastly, we use ceX-QTL to map loci that influence fitness genome-wide confirming previously reported causal variants and uncovering new fitness loci. ceX-QTL is fast, powerful and cost-effective, and will accelerate the study of complex traits in animals.31 Biological Sciences (for-2020)3105 Genetics (for-2020)Human Genome (rcdc)Genetics (rcdc)Biotechnology (rcdc)2.1 Biological and endogenous factors (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Animals (mesh)Caenorhabditis elegans (mesh)Chromosome Mapping (mesh)Drug Resistance (mesh)Female (mesh)Gene Expression Regulation (mesh)Genetic Fitness (mesh)Male (mesh)Quantitative Trait Loci (mesh)Quantitative TraitHeritable (mesh)Time Factors (mesh)Animals (mesh)Caenorhabditis elegans (mesh)Chromosome Mapping (mesh)Gene Expression Regulation (mesh)Drug Resistance (mesh)Quantitative TraitHeritable (mesh)Quantitative Trait Loci (mesh)Time Factors (mesh)Female (mesh)Male (mesh)Genetic Fitness (mesh)Animals (mesh)Caenorhabditis elegans (mesh)Chromosome Mapping (mesh)Drug Resistance (mesh)Female (mesh)Gene Expression Regulation (mesh)Genetic Fitness (mesh)Male (mesh)Quantitative Trait Loci (mesh)Quantitative TraitHeritable (mesh)Time Factors (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/4dj3x34mhttps://escholarship.org/content/qt4dj3x34m/qt4dj3x34m.pdfinfo:doi/10.1038/s41467-019-10636-9articleNature Communications, vol 10, iss 12680oai:escholarship.org:ark:/13030/qt9qv7n5g52025-12-25T23:45:57Zqt9qv7n5g5IL-3 and Oncogenic Abl Regulate the Myeloblast Transcriptome by Altering mRNA StabilityErnst, JasonGhanem, LouisBar-Joseph, ZivMcNamara, MichaelBrown, JasonSteinman, Richard ABlagosklonny, Mikhail V2009-01-01The growth factor interleukin-3 (IL-3) promotes the survival and growth of multipotent hematopoietic progenitors and stimulates myelopoiesis. It has also been reported to oppose terminal granulopoiesis and to support leukemic cell growth through autocrine or paracrine mechanisms. The degree to which IL-3 acts at the posttranscriptional level is largely unknown. We have conducted global mRNA decay profiling and bioinformatic analyses in 32Dcl3 myeloblasts indicating that IL-3 caused immediate early stabilization of hundreds of transcripts in pathways relevant to myeloblast function. Stabilized transcripts were enriched for AU-Response elements (AREs), and an ARE-containing domain from the interleukin-6 (IL-6) 3'-UTR rendered a heterologous gene responsive to IL-3-mediated transcript stabilization. Many IL-3-stabilized transcripts had been associated with leukemic transformation. Deregulated Abl kinase shared with IL-3 the ability to delay turnover of transcripts involved in proliferation or differentiation blockade, relying, in part, on signaling through the Mek/Erk pathway. These findings support a model of IL-3 action through mRNA stability control and suggest that aberrant stabilization of an mRNA network linked to IL-3 contributes to leukemic cell growth.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Stem Cell Research - Nonembryonic - Non-Human (rcdc)Genetics (rcdc)Cancer (rcdc)Stem Cell Research (rcdc)Rare Diseases (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Amino Acid Motifs (mesh)Animals (mesh)Computational Biology (mesh)Extracellular Signal-Regulated MAP Kinases (mesh)Gene Expression RegulationNeoplastic (mesh)Granulocyte Precursor Cells (mesh)Humans (mesh)Interleukin-3 (mesh)MAP Kinase Kinase 1 (mesh)Mice (mesh)Oligonucleotide Array Sequence Analysis (mesh)Proto-Oncogene Proteins c-abl (mesh)RNA ProcessingPost-Transcriptional (mesh)RNA Stability (mesh)Response Elements (mesh)Granulocyte Precursor Cells (mesh)Animals (mesh)Humans (mesh)Mice (mesh)MAP Kinase Kinase 1 (mesh)Extracellular Signal-Regulated MAP Kinases (mesh)Proto-Oncogene Proteins c-abl (mesh)Interleukin-3 (mesh)Oligonucleotide Array Sequence Analysis (mesh)Computational Biology (mesh)Gene Expression RegulationNeoplastic (mesh)RNA ProcessingPost-Transcriptional (mesh)Amino Acid Motifs (mesh)Response Elements (mesh)RNA Stability (mesh)Amino Acid Motifs (mesh)Animals (mesh)Computational Biology (mesh)Extracellular Signal-Regulated MAP Kinases (mesh)Gene Expression RegulationNeoplastic (mesh)Granulocyte Precursor Cells (mesh)Humans (mesh)Interleukin-3 (mesh)MAP Kinase Kinase 1 (mesh)Mice (mesh)Oligonucleotide Array Sequence Analysis (mesh)Proto-Oncogene Proteins c-abl (mesh)RNA ProcessingPost-Transcriptional (mesh)RNA Stability (mesh)Response Elements (mesh)General Science & Technology (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/9qv7n5g5https://escholarship.org/content/qt9qv7n5g5/qt9qv7n5g5.pdfinfo:doi/10.1371/journal.pone.0007469articlePLOS ONE, vol 4, iss 10e7469oai:escholarship.org:ark:/13030/qt21t068rg2025-12-25T23:45:53Zqt21t068rgLarge Scale Comparison of Innate Responses to Viral and Bacterial Pathogens in Mouse and MacaqueZinman, GuyBrower-Sinning, RachelEmeche, Chineye HErnst, JasonHuang, Grace Tzu-WeiMahony, ShaunMyers, Amy JO'Dee, Dawn MFlynn, JoAnne LNau, Gerard JRoss, Ted MSalter, Russell DBenos, Panayiotis VJoseph, Ziv BarMorel, Penelope ASchönbach, Christian2011-01-01Viral and bacterial infections of the lower respiratory tract are major causes of morbidity and mortality worldwide. Alveolar macrophages line the alveolar spaces and are the first cells of the immune system to respond to invading pathogens. To determine the similarities and differences between the responses of mice and macaques to invading pathogens we profiled alveolar macrophages from these species following infection with two viral (PR8 and Fuj/02 influenza A) and two bacterial (Mycobacterium tuberculosis and Francisella tularensis Schu S4) pathogens. Cells were collected at 6 time points following each infection and expression profiles were compared across and between species. Our analyses identified a core set of genes, activated in both species and across all pathogens that were predominantly part of the interferon response pathway. In addition, we identified similarities across species in the way innate immune cells respond to lethal versus non-lethal pathogens. On the other hand we also found several species and pathogen specific response patterns. These results provide new insights into mechanisms by which the innate immune system responds to, and interacts with, invading pathogens.3207 Medical Microbiology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)3204 Immunology (for-2020)Influenza (rcdc)Infectious Diseases (rcdc)Emerging Infectious Diseases (rcdc)Pneumonia & Influenza (rcdc)Biodefense (rcdc)Rare Diseases (rcdc)2.2 Factors relating to the physical environment (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Inflammatory and immune system (hrcs-hc)Infection (hrcs-hc)3 Good Health and Well Being (sdg)Animals (mesh)Bacteria (mesh)Francisella tularensis (mesh)Gene Expression Profiling (mesh)Gene Expression Regulation (mesh)Host-Pathogen Interactions (mesh)ImmunityInnate (mesh)Influenza A virus (mesh)Interferon Regulatory Factor-7 (mesh)Macaca (mesh)MacrophagesAlveolar (mesh)Mice (mesh)Mycobacterium tuberculosis (mesh)Oligonucleotide Array Sequence Analysis (mesh)Orthomyxoviridae Infections (mesh)Signal Transduction (mesh)Species Specificity (mesh)Tuberculosis (mesh)Tularemia (mesh)Up-Regulation (mesh)Viruses (mesh)MacrophagesAlveolar (mesh)Animals (mesh)Macaca (mesh)Mice (mesh)Bacteria (mesh)Francisella tularensis (mesh)Mycobacterium tuberculosis (mesh)Viruses (mesh)Influenza A virus (mesh)Tularemia (mesh)Tuberculosis (mesh)Orthomyxoviridae Infections (mesh)Oligonucleotide Array Sequence Analysis (mesh)Gene Expression Profiling (mesh)Signal Transduction (mesh)Species Specificity (mesh)Gene Expression Regulation (mesh)Up-Regulation (mesh)Interferon Regulatory Factor-7 (mesh)Host-Pathogen Interactions (mesh)ImmunityInnate (mesh)Animals (mesh)Bacteria (mesh)Francisella tularensis (mesh)Gene Expression Profiling (mesh)Gene Expression Regulation (mesh)Host-Pathogen Interactions (mesh)ImmunityInnate (mesh)Influenza A virus (mesh)Interferon Regulatory Factor-7 (mesh)Macaca (mesh)MacrophagesAlveolar (mesh)Mice (mesh)Mycobacterium tuberculosis (mesh)Oligonucleotide Array Sequence Analysis (mesh)Orthomyxoviridae Infections (mesh)Signal Transduction (mesh)Species Specificity (mesh)Tuberculosis (mesh)Tularemia (mesh)Up-Regulation (mesh)Viruses (mesh)General Science & Technology (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/21t068rghttps://escholarship.org/content/qt21t068rg/qt21t068rg.pdfinfo:doi/10.1371/journal.pone.0022401articlePLOS ONE, vol 6, iss 7e22401oai:escholarship.org:ark:/13030/qt47r1n67b2025-12-25T23:45:50Zqt47r1n67bMapping and analysis of chromatin state dynamics in nine human cell typesErnst, JasonKheradpour, PouyaMikkelsen, Tarjei SShoresh, NoamWard, Lucas DEpstein, Charles BZhang, XiaolanWang, LiIssner, RobbynCoyne, MichaelKu, ManchingDurham, TimothyKellis, ManolisBernstein, Bradley E2011-05-01Chromatin profiling has emerged as a powerful means of genome annotation and detection of regulatory activity. The approach is especially well suited to the characterization of non-coding portions of the genome, which critically contribute to cellular phenotypes yet remain largely uncharted. Here we map nine chromatin marks across nine cell types to systematically characterize regulatory elements, their cell-type specificities and their functional interactions. Focusing on cell-type-specific patterns of promoters and enhancers, we define multicell activity profiles for chromatin state, gene expression, regulatory motif enrichment and regulator expression. We use correlations between these profiles to link enhancers to putative target genes, and predict the cell-type-specific activators and repressors that modulate them. The resulting annotations and regulatory predictions have implications for the interpretation of genome-wide association studies. Top-scoring disease single nucleotide polymorphisms are frequently positioned within enhancer elements specifically active in relevant cell types, and in some cases affect a motif instance for a predicted regulator, thus suggesting a mechanism for the association. Our study presents a general framework for deciphering cis-regulatory connections and their roles in disease.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)3105 Genetics (for-2020)Human Genome (rcdc)Genetics (rcdc)2.1 Biological and endogenous factors (hrcs-rac)1.1 Normal biological development and functioning (hrcs-rac)Binding Sites (mesh)Cell Line (mesh)Cell LineTumor (mesh)Cell Physiological Phenomena (mesh)CellsCultured (mesh)Chromatin (mesh)Chromosome Mapping (mesh)Gene Expression Regulation (mesh)GenomeHuman (mesh)Hep G2 Cells (mesh)Humans (mesh)Promoter RegionsGenetic (mesh)Reproducibility of Results (mesh)Transcription Factors (mesh)CellsCultured (mesh)Cell Line (mesh)Cell LineTumor (mesh)Chromatin (mesh)Humans (mesh)Transcription Factors (mesh)Reproducibility of Results (mesh)Chromosome Mapping (mesh)Gene Expression Regulation (mesh)Binding Sites (mesh)GenomeHuman (mesh)Cell Physiological Phenomena (mesh)Promoter RegionsGenetic (mesh)Hep G2 Cells (mesh)Binding Sites (mesh)Cell Line (mesh)Cell LineTumor (mesh)Cell Physiological Phenomena (mesh)CellsCultured (mesh)Chromatin (mesh)Chromosome Mapping (mesh)Gene Expression Regulation (mesh)GenomeHuman (mesh)Hep G2 Cells (mesh)Humans (mesh)Promoter RegionsGenetic (mesh)Reproducibility of Results (mesh)Transcription Factors (mesh)General Science & Technology (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/47r1n67bhttps://escholarship.org/content/qt47r1n67b/qt47r1n67b.pdfinfo:doi/10.1038/nature09906articleNature, vol 473, iss 734543 - 49oai:escholarship.org:ark:/13030/qt45g6b6vh2025-12-25T23:45:46Zqt45g6b6vhReconstructing dynamic regulatory mapsErnst, JasonVainas, OdedHarbison, Christopher TSimon, ItamarBar‐Joseph, Ziv2007-01-01Even simple organisms have the ability to respond to internal and external stimuli. This response is carried out by a dynamic network of protein–DNA interactions that allows the specific regulation of genes needed for the response. We have developed a novel computational method that uses an input–output hidden Markov model to model these regulatory networks while taking into account their dynamic nature. Our method works by identifying bifurcation points, places in the time series where the expression of a subset of genes diverges from the rest of the genes. These points are annotated with the transcription factors regulating these transitions resulting in a unified temporal map. Applying our method to study yeast response to stress, we derive dynamic models that are able to recover many of the known aspects of these responses. Predictions made by our method have been experimentally validated leading to new roles for Ino4 and Gcn4 in controlling yeast response to stress. The temporal cascade of factors reveals common pathways and highlights differences between master and secondary factors in the utilization of network motifs and in condition‐specific regulation.3101 Biochemistry and Cell Biology (for-2020)3102 Bioinformatics and Computational Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Algorithms (mesh)Amino Acids (mesh)Basic-Leucine Zipper Transcription Factors (mesh)Cluster Analysis (mesh)Computational Biology (mesh)Computer Simulation (mesh)DNA-Binding Proteins (mesh)DatabasesGenetic (mesh)Gene Expression Profiling (mesh)Gene Expression RegulationFungal (mesh)Gene Regulatory Networks (mesh)Markov Chains (mesh)ModelsGenetic (mesh)Normal Distribution (mesh)Oligonucleotide Array Sequence Analysis (mesh)Reproducibility of Results (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)Time Factors (mesh)Trans-Activators (mesh)Transcription Factors (mesh)dynamicshidden Markov modelsregulatory networksSaccharomyces cerevisiae (mesh)Amino Acids (mesh)DNA-Binding Proteins (mesh)Trans-Activators (mesh)Saccharomyces cerevisiae Proteins (mesh)Transcription Factors (mesh)Oligonucleotide Array Sequence Analysis (mesh)Cluster Analysis (mesh)Markov Chains (mesh)Normal Distribution (mesh)Reproducibility of Results (mesh)Gene Expression Profiling (mesh)Computational Biology (mesh)Gene Expression RegulationFungal (mesh)Algorithms (mesh)ModelsGenetic (mesh)Time Factors (mesh)Computer Simulation (mesh)DatabasesGenetic (mesh)Basic-Leucine Zipper Transcription Factors (mesh)Gene Regulatory Networks (mesh)Algorithms (mesh)Amino Acids (mesh)Basic-Leucine Zipper Transcription Factors (mesh)Cluster Analysis (mesh)Computational Biology (mesh)Computer Simulation (mesh)DNA-Binding Proteins (mesh)DatabasesGenetic (mesh)Gene Expression Profiling (mesh)Gene Expression RegulationFungal (mesh)Gene Regulatory Networks (mesh)Markov Chains (mesh)ModelsGenetic (mesh)Normal Distribution (mesh)Oligonucleotide Array Sequence Analysis (mesh)Reproducibility of Results (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)Time Factors (mesh)Trans-Activators (mesh)Transcription Factors (mesh)0601 Biochemistry and Cell Biology (for)0699 Other Biological Sciences (for)Bioinformatics (science-metrix)3101 Biochemistry and cell biology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/45g6b6vhhttps://escholarship.org/content/qt45g6b6vh/qt45g6b6vh.pdfinfo:doi/10.1038/msb4100115articleMolecular Systems Biology, vol 3, iss 1msb4100115 - 74oai:escholarship.org:ark:/13030/qt2ht9t8pf2025-12-25T23:45:39Zqt2ht9t8pfAlzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other lociDe Jager, Philip LSrivastava, GyanLunnon, KatieBurgess, JeremySchalkwyk, Leonard CYu, LeiEaton, Matthew LKeenan, Brendan TErnst, JasonMcCabe, CristinTang, AnnaRaj, TowfiqueReplogle, JosephBrodeur, WendyGabriel, StaceyChai, High SYounkin, CurtisYounkin, Steven GZou, FanggengSzyf, MosheEpstein, Charles BSchneider, Julie ABernstein, Bradley EMeissner, AlexErtekin-Taner, NiluferChibnik, Lori BKellis, ManolisMill, JonathanBennett, David A2014-09-01Aging can lead to cognitive decline associated with neural pathology and Alzheimer's disease (AD). Here the authors scan the methylation status of CpGs across the entire genome of brain samples from aged subjects in an epigenome-wide association study (EWAS). Several loci, including ANK1, were associated with AD pathology, gene expression and AD genetic risk networks.5202 Biological Psychology (for-2020)52 Psychology (for-2020)Acquired Cognitive Impairment (rcdc)Genetics (rcdc)Prevention (rcdc)Dementia (rcdc)Neurosciences (rcdc)Human Genome (rcdc)Neurodegenerative (rcdc)Aging (rcdc)Brain Disorders (rcdc)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)Alzheimer's Disease (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Neurological (hrcs-hc)Adaptor ProteinsSignal Transducing (mesh)Aged (mesh)Aged80 and over (mesh)Alzheimer Disease (mesh)Amyloidosis (mesh)Ankyrins (mesh)Brain (mesh)Carrier Proteins (mesh)CpG Islands (mesh)DNA Methylation (mesh)Female (mesh)Genetic Predisposition to Disease (mesh)Genome-Wide Association Study (mesh)Humans (mesh)Intracellular Signaling Peptides and Proteins (mesh)Male (mesh)Middle Aged (mesh)Nuclear Proteins (mesh)Protein Interaction Maps (mesh)Tumor Suppressor Proteins (mesh)Brain (mesh)Humans (mesh)Alzheimer Disease (mesh)Amyloidosis (mesh)Genetic Predisposition to Disease (mesh)Intracellular Signaling Peptides and Proteins (mesh)Adaptor ProteinsSignal Transducing (mesh)Ankyrins (mesh)Carrier Proteins (mesh)Tumor Suppressor Proteins (mesh)Nuclear Proteins (mesh)DNA Methylation (mesh)CpG Islands (mesh)Aged (mesh)Aged80 and over (mesh)Middle Aged (mesh)Female (mesh)Male (mesh)Genome-Wide Association Study (mesh)Protein Interaction Maps (mesh)Adaptor ProteinsSignal Transducing (mesh)Aged (mesh)Aged80 and over (mesh)Alzheimer Disease (mesh)Amyloidosis (mesh)Ankyrins (mesh)Brain (mesh)Carrier Proteins (mesh)CpG Islands (mesh)DNA Methylation (mesh)Female (mesh)Genetic Predisposition to Disease (mesh)Genome-Wide Association Study (mesh)Humans (mesh)Intracellular Signaling Peptides and Proteins (mesh)Male (mesh)Middle Aged (mesh)Nuclear Proteins (mesh)Protein Interaction Maps (mesh)Tumor Suppressor Proteins (mesh)1109 Neurosciences (for)1701 Psychology (for)1702 Cognitive Sciences (for)Neurology & Neurosurgery (science-metrix)3209 Neurosciences (for-2020)5202 Biological psychology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/2ht9t8pfhttps://escholarship.org/content/qt2ht9t8pf/qt2ht9t8pf.pdfinfo:doi/10.1038/nn.3786articleNature Neuroscience, vol 17, iss 91156 - 1163oai:escholarship.org:ark:/13030/qt2145n5362025-12-25T23:45:36Zqt2145n536A Semi-Supervised Method for Predicting Transcription Factor–Gene Interactions in Escherichia coliErnst, JasonBeg, Qasim KKay, Krin ABalázsi, GáborOltvai, Zoltán NBar-Joseph, ZivStormo, Gary2008-01-01While Escherichia coli has one of the most comprehensive datasets of experimentally verified transcriptional regulatory interactions of any organism, it is still far from complete. This presents a problem when trying to combine gene expression and regulatory interactions to model transcriptional regulatory networks. Using the available regulatory interactions to predict new interactions may lead to better coverage and more accurate models. Here, we develop SEREND (SEmi-supervised REgulatory Network Discoverer), a semi-supervised learning method that uses a curated database of verified transcriptional factor-gene interactions, DNA sequence binding motifs, and a compendium of gene expression data in order to make thousands of new predictions about transcription factor-gene interactions, including whether the transcription factor activates or represses the gene. Using genome-wide binding datasets for several transcription factors, we demonstrate that our semi-supervised classification strategy improves the prediction of targets for a given transcription factor. To further demonstrate the utility of our inferred interactions, we generated a new microarray gene expression dataset for the aerobic to anaerobic shift response in E. coli. We used our inferred interactions with the verified interactions to reconstruct a dynamic regulatory network for this response. The network reconstructed when using our inferred interactions was better able to correctly identify known regulators and suggested additional activators and repressors as having important roles during the aerobic-anaerobic shift interface.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)Human Genome (rcdc)Genetics (rcdc)Artificial Intelligence (mesh)Base Sequence (mesh)Escherichia coli (mesh)Escherichia coli Proteins (mesh)Gene Expression Profiling (mesh)Gene Expression RegulationBacterial (mesh)Molecular Sequence Data (mesh)Pattern RecognitionAutomated (mesh)Protein Interaction Mapping (mesh)Sequence AnalysisDNA (mesh)Transcription Factors (mesh)Escherichia coli (mesh)Escherichia coli Proteins (mesh)Transcription Factors (mesh)Gene Expression Profiling (mesh)Sequence AnalysisDNA (mesh)Protein Interaction Mapping (mesh)Gene Expression RegulationBacterial (mesh)Base Sequence (mesh)Artificial Intelligence (mesh)Molecular Sequence Data (mesh)Pattern RecognitionAutomated (mesh)Artificial Intelligence (mesh)Base Sequence (mesh)Escherichia coli (mesh)Escherichia coli Proteins (mesh)Gene Expression Profiling (mesh)Gene Expression RegulationBacterial (mesh)Molecular Sequence Data (mesh)Pattern RecognitionAutomated (mesh)Protein Interaction Mapping (mesh)Sequence AnalysisDNA (mesh)Transcription Factors (mesh)01 Mathematical Sciences (for)06 Biological Sciences (for)08 Information and Computing Sciences (for)Bioinformatics (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/2145n536https://escholarship.org/content/qt2145n536/qt2145n536.pdfinfo:doi/10.1371/journal.pcbi.1000044articlePLOS Computational Biology, vol 4, iss 3e1000044oai:escholarship.org:ark:/13030/qt1984850q2025-12-25T23:45:33Zqt1984850qSTEM: a tool for the analysis of short time series gene expression dataErnst, JasonBar-Joseph, Ziv2006-12-01BackgroundTime series microarray experiments are widely used to study dynamical biological processes. Due to the cost of microarray experiments, and also in some cases the limited availability of biological material, about 80% of microarray time series experiments are short (3–8 time points). Previously short time series gene expression data has been mainly analyzed using more general gene expression analysis tools not designed for the unique challenges and opportunities inherent in short time series gene expression data.ResultsWe introduce the Short Time-series Expression Miner (STEM) the first software program specifically designed for the analysis of short time series microarray gene expression data. STEM implements unique methods to cluster, compare, and visualize such data. STEM also supports efficient and statistically rigorous biological interpretations of short time series data through its integration with the Gene Ontology.ConclusionThe unique algorithms STEM implements to cluster and compare short time series gene expression data combined with its visualization capabilities and integration with the Gene Ontology should make STEM useful in the analysis of data from a significant portion of all microarray studies. STEM is available for download for free to academic and non-profit users at http://www.cs.cmu.edu/~jernst/stem.31 Biological Sciences (for-2020)3102 Bioinformatics and Computational Biology (for-2020)Biotechnology (rcdc)Networking and Information Technology R&D (NITRD) (rcdc)Genetics (rcdc)Stem Cell Research (rcdc)1.5 Resources and infrastructure (underpinning) (hrcs-rac)Cluster Analysis (mesh)Computer Simulation (mesh)Gene Expression Profiling (mesh)Gene Expression Regulation (mesh)ModelsBiological (mesh)Oligonucleotide Array Sequence Analysis (mesh)Pattern RecognitionAutomated (mesh)Signal Transduction (mesh)Software (mesh)Time Factors (mesh)Transcription Factors (mesh)Transcription Factors (mesh)Oligonucleotide Array Sequence Analysis (mesh)Cluster Analysis (mesh)Gene Expression Profiling (mesh)Signal Transduction (mesh)Gene Expression Regulation (mesh)ModelsBiological (mesh)Time Factors (mesh)Computer Simulation (mesh)Software (mesh)Pattern RecognitionAutomated (mesh)Cluster Analysis (mesh)Computer Simulation (mesh)Gene Expression Profiling (mesh)Gene Expression Regulation (mesh)ModelsBiological (mesh)Oligonucleotide Array Sequence Analysis (mesh)Pattern RecognitionAutomated (mesh)Signal Transduction (mesh)Software (mesh)Time Factors (mesh)Transcription Factors (mesh)01 Mathematical Sciences (for)06 Biological Sciences (for)08 Information and Computing Sciences (for)Bioinformatics (science-metrix)31 Biological sciences (for-2020)46 Information and computing sciences (for-2020)49 Mathematical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/1984850qhttps://escholarship.org/content/qt1984850q/qt1984850q.pdfinfo:doi/10.1186/1471-2105-7-191articleBMC Bioinformatics, vol 7, iss 1191oai:escholarship.org:ark:/13030/qt20q5x2wd2025-12-25T23:45:29Zqt20q5x2wdChromatin-state discovery and genome annotation with ChromHMMErnst, JasonKellis, Manolis2017-12-01This protocol describes how to use ChromHMM, a robust open-source software package that enables the learning of chromatin states, annotates their occurrences across the genome, and facilitates their biological interpretation.31 Biological Sciences (for-2020)3105 Genetics (for-2020)Genetics (rcdc)Networking and Information Technology R&D (NITRD) (rcdc)Human Genome (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Animals (mesh)Biomedical Research (mesh)Chromatin (mesh)Chromatin Assembly and Disassembly (mesh)DNAIntergenic (mesh)EpigenesisGenetic (mesh)Epigenomics (mesh)Genomics (mesh)Humans (mesh)Markov Chains (mesh)ModelsGenetic (mesh)Molecular Sequence Annotation (mesh)Software (mesh)Software Design (mesh)Chromatin (mesh)Animals (mesh)Humans (mesh)DNAIntergenic (mesh)Markov Chains (mesh)Genomics (mesh)Chromatin Assembly and Disassembly (mesh)EpigenesisGenetic (mesh)ModelsGenetic (mesh)Biomedical Research (mesh)Software (mesh)Software Design (mesh)Epigenomics (mesh)Molecular Sequence Annotation (mesh)Animals (mesh)Biomedical Research (mesh)Chromatin (mesh)Chromatin Assembly and Disassembly (mesh)DNAIntergenic (mesh)EpigenesisGenetic (mesh)Epigenomics (mesh)Genomics (mesh)Humans (mesh)Markov Chains (mesh)ModelsGenetic (mesh)Molecular Sequence Annotation (mesh)Software (mesh)Software Design (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Bioinformatics (science-metrix)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/20q5x2wdhttps://escholarship.org/content/qt20q5x2wd/qt20q5x2wd.pdfinfo:doi/10.1038/nprot.2017.124articleNature Protocols, vol 12, iss 122478 - 2492oai:escholarship.org:ark:/13030/qt9k63h9xv2025-12-25T23:45:26Zqt9k63h9xvInvestigating enhancer evolution with massively parallel reporter assaysKwon, Soo BinErnst, Jason2018-12-01A recent study in Genome Biology has characterized the evolution of candidate hominoid-specific liver enhancers by using massively parallel reporter assays (MPRAs).46 Information and Computing Sciences (for-2020)31 Biological Sciences (for-2020)3105 Genetics (for-2020)Liver Disease (rcdc)Digestive Diseases (rcdc)Human Genome (rcdc)Genetics (rcdc)Animals (mesh)Base Sequence (mesh)CpG Islands (mesh)Deamination (mesh)Enhancer ElementsGenetic (mesh)EvolutionMolecular (mesh)GenesReporter (mesh)High-Throughput Nucleotide Sequencing (mesh)Humans (mesh)Liver (mesh)Phylogeny (mesh)Primates (mesh)Liver (mesh)Animals (mesh)Primates (mesh)Humans (mesh)EvolutionMolecular (mesh)Phylogeny (mesh)Base Sequence (mesh)CpG Islands (mesh)Deamination (mesh)GenesReporter (mesh)Enhancer ElementsGenetic (mesh)High-Throughput Nucleotide Sequencing (mesh)Animals (mesh)Base Sequence (mesh)CpG Islands (mesh)Deamination (mesh)Enhancer ElementsGenetic (mesh)EvolutionMolecular (mesh)GenesReporter (mesh)High-Throughput Nucleotide Sequencing (mesh)Humans (mesh)Liver (mesh)Phylogeny (mesh)Primates (mesh)05 Environmental Sciences (for)06 Biological Sciences (for)08 Information and Computing Sciences (for)Bioinformatics (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/9k63h9xvhttps://escholarship.org/content/qt9k63h9xv/qt9k63h9xv.pdfinfo:doi/10.1186/s13059-018-1502-5articleGenome Biology, vol 19, iss 1114oai:escholarship.org:ark:/13030/qt8hc6p3h12025-12-25T23:45:23Zqt8hc6p3h1ChromTime: modeling spatio-temporal dynamics of chromatin marksFiziev, PetkoErnst, Jason2018-12-01To model spatial changes of chromatin mark peaks over time we develop and apply ChromTime, a computational method that predicts peaks to be either expanding, contracting, or holding steady between time points. Predicted expanding and contracting peaks can mark regulatory regions associated with transcription factor binding and gene expression changes. Spatial dynamics of peaks provide information about gene expression changes beyond localized signal density changes. ChromTime detects asymmetric expansions and contractions, which for some marks associate with the direction of transcription. ChromTime facilitates the analysis of time course chromatin data in a range of biological systems.3101 Biochemistry and Cell Biology (for-2020)3102 Bioinformatics and Computational Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)Generic health relevance (hrcs-hc)Chromatin (mesh)DatabasesGenetic (mesh)Deoxyribonuclease I (mesh)Gene Expression Regulation (mesh)Histones (mesh)Methylation (mesh)ModelsGenetic (mesh)Protein Binding (mesh)Reproducibility of Results (mesh)Software (mesh)Time Factors (mesh)Transcription Factors (mesh)TranscriptionGenetic (mesh)EpigenomicsTime courseSpatial dynamicsHistone modificationsChromatin marksChromatin (mesh)Deoxyribonuclease I (mesh)Histones (mesh)Transcription Factors (mesh)Reproducibility of Results (mesh)TranscriptionGenetic (mesh)Gene Expression Regulation (mesh)Protein Binding (mesh)Methylation (mesh)ModelsGenetic (mesh)Time Factors (mesh)Software (mesh)DatabasesGenetic (mesh)Chromatin marksEpigenomicsHistone modificationsSpatial dynamicsTime courseChromatin (mesh)DatabasesGenetic (mesh)Deoxyribonuclease I (mesh)Gene Expression Regulation (mesh)Histones (mesh)Methylation (mesh)ModelsGenetic (mesh)Protein Binding (mesh)Reproducibility of Results (mesh)Software (mesh)Time Factors (mesh)Transcription Factors (mesh)TranscriptionGenetic (mesh)05 Environmental Sciences (for)06 Biological Sciences (for)08 Information and Computing Sciences (for)Bioinformatics (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/8hc6p3h1https://escholarship.org/content/qt8hc6p3h1/qt8hc6p3h1.pdfinfo:doi/10.1186/s13059-018-1485-2articleGenome Biology, vol 19, iss 1109oai:escholarship.org:ark:/13030/qt7sh5x5722025-12-25T23:22:03Zqt7sh5x572NMR experiments redefine the hemoglobin binding properties of bacterial NEAr‐iron Transporter domainsMacdonald, RamsayMahoney, Brendan JEllis‐Guardiola, KenMaresso, AnthonyClubb, Robert T2019-08-01Iron is a versatile metal cofactor that is used in a wide range of essential cellular processes. During infections, many bacterial pathogens acquire iron from human hemoglobin (Hb), which contains the majority of the body's total iron content in the form of heme (iron protoporphyrin IX). Clinically important Gram-positive bacterial pathogens scavenge heme using an array of secreted and cell-wall-associated receptors that contain NEAr-iron Transporter (NEAT) domains. Experimentally defining the Hb binding properties of NEAT domains has been challenging, limiting our understanding of their function in heme uptake. Here we show that solution-state NMR spectroscopy is a powerful tool to define the Hb binding properties of NEAT domains. The utility of this method is demonstrated using the NEAT domains from Bacillus anthracis and Listeria monocytogenes. Our results are compatible with the existence of at least two types of NEAT domains that are capable of interacting with either Hb or heme. These binding properties can be predicted from their primary sequences, with Hb- and heme-binding NEAT domains being distinguished by the presence of (F/Y)YH(Y/F) and S/YXXXY motifs, respectively. The results of this work should enable the functions of a wide range of NEAT domain containing proteins in pathogenic bacteria to be reliably predicted.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Hematology (rcdc)Infectious Diseases (rcdc)Emerging Infectious Diseases (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Amino Acid Sequence (mesh)Bacillus anthracis (mesh)Bacterial Proteins (mesh)Heme (mesh)Hemoglobins (mesh)Listeria monocytogenes (mesh)Nuclear Magnetic ResonanceBiomolecular (mesh)Protein Binding (mesh)Protein StructureTertiary (mesh)Sequence Alignment (mesh)NEAT domainhemoglobinNMR spectroscopyhemebacteriapathogenNEAT domainhemoglobinNMR spectroscopyhemebacteriapathogenBacillus anthracis (mesh)Listeria monocytogenes (mesh)Heme (mesh)Bacterial Proteins (mesh)Hemoglobins (mesh)Nuclear Magnetic ResonanceBiomolecular (mesh)Sequence Alignment (mesh)Amino Acid Sequence (mesh)Protein StructureTertiary (mesh)Protein Binding (mesh)NEAT domainNMR spectroscopybacteriahemehemoglobinpathogenAmino Acid Sequence (mesh)Bacillus anthracis (mesh)Bacterial Proteins (mesh)Heme (mesh)Hemoglobins (mesh)Listeria monocytogenes (mesh)Nuclear Magnetic ResonanceBiomolecular (mesh)Protein Binding (mesh)Protein StructureTertiary (mesh)Sequence Alignment (mesh)0601 Biochemistry and Cell Biology (for)0802 Computation Theory and Mathematics (for)0899 Other Information and Computing Sciences (for)Biophysics (science-metrix)3101 Biochemistry and cell biology (for-2020)3404 Medicinal and biomolecular chemistry (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/7sh5x572https://escholarship.org/content/qt7sh5x572/qt7sh5x572.pdfinfo:doi/10.1002/pro.3662articleProtein Science, vol 28, iss 81513 - 1523oai:escholarship.org:ark:/13030/qt8566m21n2025-12-25T23:16:19Zqt8566m21nMulti-level Modulation of Light Signaling by GIGANTEA Regulates Both the Output and Pace of the Circadian ClockNohales, Maria ALiu, WanluDuffy, TomasNozue, KazunariSawa, MarikoPruneda-Paz, Jose LMaloof, Julin NJacobsen, Steven EKay, Steve A2019-06-01Integration of environmental signals with endogenous biological processes is essential for organisms to thrive in their natural environment. Being entrained by periodic environmental changes, the circadian clock incorporates external information to coordinate physiological processes, phasing them to the optimal time of the day and year. Here, we present a pivotal role for the clock component GIGANTEA (GI) as a genome-wide regulator of transcriptional networks mediating growth and adaptive processes in plants. We provide mechanistic details on how GI integrates endogenous timing with light signaling pathways through the global modulation of PHYTOCHROME-INTERACTING FACTORs (PIFs). Gating of the activity of these transcriptional regulators by GI directly affects a wide array of output rhythms, including photoperiodic growth. Furthermore, we uncover a role for PIFs in mediating light input to the circadian oscillator and show how their regulation by GI is required to set the pace of the clock in response to light-dark cycles.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Sleep Research (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Arabidopsis (mesh)Arabidopsis Proteins (mesh)Basic Helix-Loop-Helix Transcription Factors (mesh)Circadian Rhythm (mesh)Gene Expression RegulationPlant (mesh)Photoperiod (mesh)Plant Proteins (mesh)Signal Transduction (mesh)Nicotiana (mesh)Arabidopsis (mesh)Plant Proteins (mesh)Arabidopsis Proteins (mesh)Signal Transduction (mesh)Gene Expression RegulationPlant (mesh)Circadian Rhythm (mesh)Photoperiod (mesh)Basic Helix-Loop-Helix Transcription Factors (mesh)Nicotiana (mesh)ArabidopsisGIGANTEAcircadian clockclock synchronizationlight inputlight signalingoutputtranscriptional networksArabidopsis (mesh)Arabidopsis Proteins (mesh)Basic Helix-Loop-Helix Transcription Factors (mesh)Circadian Rhythm (mesh)Gene Expression RegulationPlant (mesh)Photoperiod (mesh)Plant Proteins (mesh)Signal Transduction (mesh)Nicotiana (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8566m21nhttps://escholarship.org/content/qt8566m21n/qt8566m21n.pdfinfo:doi/10.1016/j.devcel.2019.04.030articleDevelopmental Cell, vol 49, iss 6840 - 851.e8oai:escholarship.org:ark:/13030/qt4702t3g52025-12-25T23:01:46Zqt4702t3g5Light-Driven Regeneration of Cone Visual Pigments through a Mechanism Involving RGR Opsin in Müller Glial CellsMorshedian, AlaKaylor, Joanna JNg, Sze YinTsan, AvianFrederiksen, RikardXu, TongzhouYuan, LilySampath, Alapakkam PRadu, Roxana AFain, Gordon LTravis, Gabriel H2019-06-01While rods in the mammalian retina regenerate rhodopsin through a well-characterized pathway in cells of the retinal pigment epithelium (RPE), cone visual pigments are thought to regenerate in part through an additional pathway in Müller cells of the neural retina. The proteins comprising this intrinsic retinal visual cycle are unknown. Here, we show that RGR opsin and retinol dehydrogenase-10 (Rdh10) convert all-trans-retinol to 11-cis-retinol during exposure to visible light. Isolated retinas from Rgr+/+ and Rgr-/- mice were exposed to continuous light, and cone photoresponses were recorded. Cones in Rgr-/- retinas lost sensitivity at a faster rate than cones in Rgr+/+ retinas. A similar effect was seen in Rgr+/+ retinas following treatment with the glial cell toxin, α-aminoadipic acid. These results show that RGR opsin is a critical component of the Müller cell visual cycle and that regeneration of cone visual pigment can be driven by light.32 Biomedical and Clinical Sciences (for-2020)3212 Ophthalmology and Optometry (for-2020)Eye Disease and Disorders of Vision (rcdc)Neurosciences (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Eye (hrcs-hc)2-Aminoadipic Acid (mesh)Alcohol Oxidoreductases (mesh)Animals (mesh)Ependymoglial Cells (mesh)Excitatory Amino Acid Antagonists (mesh)Eye Proteins (mesh)Light (mesh)Mice (mesh)MiceKnockout (mesh)ReceptorsG-Protein-Coupled (mesh)Retinal Cone Photoreceptor Cells (mesh)Retinal Pigments (mesh)Vitamin A (mesh)Animals (mesh)MiceKnockout (mesh)Mice (mesh)2-Aminoadipic Acid (mesh)Vitamin A (mesh)Alcohol Oxidoreductases (mesh)Retinal Pigments (mesh)Eye Proteins (mesh)ReceptorsG-Protein-Coupled (mesh)Excitatory Amino Acid Antagonists (mesh)Light (mesh)Retinal Cone Photoreceptor Cells (mesh)Ependymoglial Cells (mesh)2-Aminoadipic Acid (mesh)Alcohol Oxidoreductases (mesh)Animals (mesh)Ependymoglial Cells (mesh)Excitatory Amino Acid Antagonists (mesh)Eye Proteins (mesh)Light (mesh)Mice (mesh)MiceKnockout (mesh)ReceptorsG-Protein-Coupled (mesh)Retinal Cone Photoreceptor Cells (mesh)Retinal Pigments (mesh)Vitamin A (mesh)1109 Neurosciences (for)1701 Psychology (for)1702 Cognitive Sciences (for)Neurology & Neurosurgery (science-metrix)3209 Neurosciences (for-2020)5202 Biological psychology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/4702t3g5https://escholarship.org/content/qt4702t3g5/qt4702t3g5.pdfinfo:doi/10.1016/j.neuron.2019.04.004articleNeuron, vol 102, iss 61172 - 1183.e5oai:escholarship.org:ark:/13030/qt6s6468rs2025-12-25T22:39:23Zqt6s6468rsStructure and mechanism of TagA, a novel membrane-associated glycosyltransferase that produces wall teichoic acids in pathogenic bacteriaKattke, Michele DGosschalk, Jason EMartinez, Orlando EKumar, GarimaGale, Robert TCascio, DuilioSawaya, Michael RPhilips, MartinBrown, Eric DClubb, Robert TZhang, Gongyi2019-01-01Staphylococcus aureus and other bacterial pathogens affix wall teichoic acids (WTAs) to their surface. These highly abundant anionic glycopolymers have critical functions in bacterial physiology and their susceptibility to β-lactam antibiotics. The membrane-associated TagA glycosyltransferase (GT) catalyzes the first-committed step in WTA biosynthesis and is a founding member of the WecB/TagA/CpsF GT family, more than 6,000 enzymes that synthesize a range of extracellular polysaccharides through a poorly understood mechanism. Crystal structures of TagA from T. italicus in its apo- and UDP-bound states reveal a novel GT fold, and coupled with biochemical and cellular data define the mechanism of catalysis. We propose that enzyme activity is regulated by interactions with the bilayer, which trigger a structural change that facilitates proper active site formation and recognition of the enzyme's lipid-linked substrate. These findings inform upon the molecular basis of WecB/TagA/CpsF activity and could guide the development of new anti-microbial drugs.3107 Microbiology (for-2020)3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Antimicrobial Resistance (rcdc)Biodefense (rcdc)Emerging Infectious Diseases (rcdc)Infectious Diseases (rcdc)2.2 Factors relating to the physical environment (hrcs-rac)Infection (hrcs-hc)Bacterial Proteins (mesh)Catalytic Domain (mesh)Cell Wall (mesh)CrystallographyX-Ray (mesh)Lipoproteins (mesh)ModelsMolecular (mesh)Protein Multimerization (mesh)Protein StructureTertiary (mesh)Staphylococcus aureus (mesh)Teichoic Acids (mesh)Cell Wall (mesh)Staphylococcus aureus (mesh)Teichoic Acids (mesh)Lipoproteins (mesh)Bacterial Proteins (mesh)CrystallographyX-Ray (mesh)Catalytic Domain (mesh)Protein StructureTertiary (mesh)ModelsMolecular (mesh)Protein Multimerization (mesh)Bacterial Proteins (mesh)Catalytic Domain (mesh)Cell Wall (mesh)CrystallographyX-Ray (mesh)Lipoproteins (mesh)ModelsMolecular (mesh)Protein Multimerization (mesh)Protein StructureTertiary (mesh)Staphylococcus aureus (mesh)Teichoic Acids (mesh)0605 Microbiology (for)1107 Immunology (for)1108 Medical Microbiology (for)Virology (science-metrix)3107 Microbiology (for-2020)3204 Immunology (for-2020)3207 Medical microbiology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/6s6468rshttps://escholarship.org/content/qt6s6468rs/qt6s6468rs.pdfinfo:doi/10.1371/journal.ppat.1007723articlePLOS Pathogens, vol 15, iss 4e1007723oai:escholarship.org:ark:/13030/qt1554z2w42025-12-25T22:08:21Zqt1554z2w4Corrigendum: Neospora Caninum Activates p38 MAPK as an Evasion Mechanism against Innate ImmunityMota, Caroline MOliveira, Ana CMDavoli-Ferreira, MarcelaSilva, Murilo VSantiago, Fernanda MNadipuram, Santhosh MVashisht, Ajay AWohlschlegel, James ABradley, Peter JSilva, João SMineo, José RMineo, Tiago WP2019-01-01[This corrects the article DOI: 10.3389/fmicb.2016.01456.].3107 Microbiology (for-2020)3207 Medical Microbiology (for-2020)32 Biomedical and Clinical Sciences (for-2020)31 Biological Sciences (for-2020)N. caninumimmune responsep38/MAPkevasionIL-12IL-12N. caninumevasionimmune responsep38/MAPk0502 Environmental Science and Management (for)0503 Soil Sciences (for)0605 Microbiology (for)3107 Microbiology (for-2020)3207 Medical microbiology (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/1554z2w4https://escholarship.org/content/qt1554z2w4/qt1554z2w4.pdfinfo:doi/10.3389/fmicb.2019.00548articleFrontiers in Microbiology, vol 10548oai:escholarship.org:ark:/13030/qt1md8v8rk2025-12-25T21:20:19Zqt1md8v8rkSyntrophus aciditrophicus uses the same enzymes in a reversible manner to degrade and synthesize aromatic and alicyclic acidsJames, Kimberly LKung, Johannes WCrable, Bryan RMouttaki, HousnaSieber, Jessica RNguyen, Hong HYang, YananXie, YongmingErde, JonathanWofford, Neil QKarr, Elizabeth ALoo, Joseph ALoo, Rachel R OgorzalekGunsalus, Robert PMcInerney, Michael J2019-05-01Syntrophy is essential for the efficient conversion of organic carbon to methane in natural and constructed environments, but little is known about the enzymes involved in syntrophic carbon and electron flow. Syntrophus aciditrophicus strain SB syntrophically degrades benzoate and cyclohexane-1-carboxylate and catalyses the novel synthesis of benzoate and cyclohexane-1-carboxylate from crotonate. We used proteomic, biochemical and metabolomic approaches to determine what enzymes are used for fatty, aromatic and alicyclic acid degradation versus for benzoate and cyclohexane-1-carboxylate synthesis. Enzymes involved in the metabolism of cyclohex-1,5-diene carboxyl-CoA to acetyl-CoA were in high abundance in S. aciditrophicus cells grown in pure culture on crotonate and in coculture with Methanospirillum hungatei on crotonate, benzoate or cyclohexane-1-carboxylate. Incorporation of 13 C-atoms from 1-[13 C]-acetate into crotonate, benzoate and cyclohexane-1-carboxylate during growth on these different substrates showed that the pathways are reversible. A protein conduit for syntrophic reverse electron transfer from acyl-CoA intermediates to formate was detected. Ligases and membrane-bound pyrophosphatases make pyrophosphate needed for the synthesis of ATP by an acetyl-CoA synthetase. Syntrophus aciditrophicus, thus, uses a core set of enzymes that operates close to thermodynamic equilibrium to conserve energy in a novel and highly efficient manner.31 Biological Sciences (for-2020)3106 Industrial Biotechnology (for-2020)Acetates (mesh)Acetyl Coenzyme A (mesh)Acids (mesh)Acyl Coenzyme A (mesh)Bacterial Proteins (mesh)Benzoates (mesh)Cyclohexanecarboxylic Acids (mesh)Deltaproteobacteria (mesh)Electron Transport (mesh)Methane (mesh)Methanospirillum (mesh)Proteomics (mesh)Deltaproteobacteria (mesh)Methanospirillum (mesh)Acids (mesh)Acetates (mesh)Benzoates (mesh)Cyclohexanecarboxylic Acids (mesh)Methane (mesh)Acyl Coenzyme A (mesh)Acetyl Coenzyme A (mesh)Bacterial Proteins (mesh)Proteomics (mesh)Electron Transport (mesh)Acetates (mesh)Acetyl Coenzyme A (mesh)Acids (mesh)Acyl Coenzyme A (mesh)Bacterial Proteins (mesh)Benzoates (mesh)Cyclohexanecarboxylic Acids (mesh)Deltaproteobacteria (mesh)Electron Transport (mesh)Methane (mesh)Methanospirillum (mesh)Proteomics (mesh)0603 Evolutionary Biology (for)0605 Microbiology (for)Microbiology (science-metrix)3103 Ecology (for-2020)3107 Microbiology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1md8v8rkhttps://escholarship.org/content/qt1md8v8rk/qt1md8v8rk.pdfinfo:doi/10.1111/1462-2920.14601articleEnvironmental Microbiology, vol 21, iss 51833 - 1846oai:escholarship.org:ark:/13030/qt2j83d4cx2025-12-25T21:05:37Zqt2j83d4cxHomochiral and racemic MicroED structures of a peptide repeat from the ice-nucleation protein InaZZee, Chih-TeGlynn, CalinaGallagher-Jones, MarcusMiao, JenniferSantiago, Carlos GCascio, DuilioGonen, TamirSawaya, Michael RRodriguez, Jose A2019-03-01The ice-nucleation protein InaZ from Pseudomonas syringae contains a large number of degenerate repeats that span more than a quarter of its sequence and include the segment GSTSTA. Ab initio structures of this repeat segment, resolved to 1.1 Å by microfocus X-ray crystallography and to 0.9 Å by the cryo-EM method MicroED, were determined from both racemic and homochiral crystals. The benefits of racemic protein crystals for structure determination by MicroED were evaluated and it was confirmed that the phase restriction introduced by crystal centrosymmetry increases the number of successful trials during the ab initio phasing of the electron diffraction data. Both homochiral and racemic GSTSTA form amyloid-like protofibrils with labile, corrugated antiparallel β-sheets that mate face to back. The racemic GSTSTA protofibril represents a new class of amyloid assembly in which all-left-handed sheets mate with their all-right-handed counterparts. This determination of racemic amyloid assemblies by MicroED reveals complex amyloid architectures and illustrates the racemic advantage in macromolecular crystallography, now with submicrometre-sized crystals.3402 Inorganic Chemistry (for-2020)34 Chemical Sciences (for-2020)Generic health relevance (hrcs-hc)amyloidracemicelectron diffractionice nucleationintermolecular interactionsco-crystalselectron crystallographystructural biologyamyloidco-crystalselectron crystallographyelectron diffractionice nucleationintermolecular interactionsracemicstructural biology0202 AtomicMolecularNuclearParticle and Plasma Physics (for)0204 Condensed Matter Physics (for)0306 Physical Chemistry (incl. Structural) (for)3406 Physical chemistry (for-2020)5104 Condensed matter physics (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/2j83d4cxhttps://escholarship.org/content/qt2j83d4cx/qt2j83d4cx.pdfinfo:doi/10.1107/s2052252518017621articleIUCrJ, vol 6, iss 2197 - 205oai:escholarship.org:ark:/13030/qt7112p00r2025-12-25T21:00:06Zqt7112p00rClathrin Adaptor Complex-interacting Protein Irc6 Functions through the Conserved C-Terminal DomainZhou, HuajunCostaguta, GiancarloPayne, Gregory S2019-01-01Clathrin coats drive transport vesicle formation from the plasma membrane and in pathways between the trans-Golgi network (TGN) and endosomes. Clathrin adaptors play central roles orchestrating assembly of clathrin coats. The yeast clathrin adaptor-interacting protein Irc6 is an orthologue of human p34, which is mutated in the inherited skin disorder punctate palmoplantar keratoderma type I. Irc6 and p34 bind to clathrin adaptor complexes AP-1 and AP-2 and are members of a conserved family characterized by a two-domain architecture. Irc6 is required for AP-1-dependent transport between the TGN and endosomes in yeast. Here we present evidence that the C-terminal two amino acids of Irc6 are required for AP-1 binding and transport function. Additionally, like the C-terminal domain, the N-terminal domain when overexpressed partially restores AP-1-mediated transport in cells lacking full-length Irc6. These findings support a functional role for Irc6 binding to AP-1. Negative genetic interactions with irc6∆ are enriched for genes related to membrane traffic and nuclear processes, consistent with diverse cellular roles for Irc6.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Generic health relevance (hrcs-hc)Adaptor ProteinsVesicular Transport (mesh)Amino Acid Sequence (mesh)Cell Membrane (mesh)Clathrin (mesh)Endosomes (mesh)Golgi Apparatus (mesh)Mutation (mesh)Protein Binding (mesh)Protein Domains (mesh)Protein Transport (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)Sequence HomologyAmino Acid (mesh)trans-Golgi Network (mesh)Cell Membrane (mesh)Endosomes (mesh)Golgi Apparatus (mesh)trans-Golgi Network (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)Adaptor ProteinsVesicular Transport (mesh)Clathrin (mesh)Amino Acid Sequence (mesh)Protein Binding (mesh)Sequence HomologyAmino Acid (mesh)Protein Transport (mesh)Mutation (mesh)Protein Domains (mesh)Adaptor ProteinsVesicular Transport (mesh)Amino Acid Sequence (mesh)Cell Membrane (mesh)Clathrin (mesh)Endosomes (mesh)Golgi Apparatus (mesh)Mutation (mesh)Protein Binding (mesh)Protein Domains (mesh)Protein Transport (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)Sequence HomologyAmino Acid (mesh)trans-Golgi Network (mesh)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/7112p00rhttps://escholarship.org/content/qt7112p00r/qt7112p00r.pdfinfo:doi/10.1038/s41598-019-40852-8articleScientific Reports, vol 9, iss 14436oai:escholarship.org:ark:/13030/qt17c349jc2025-12-25T19:48:17Zqt17c349jcSexually Dimorphic Control of Parenting Behavior by the Medial AmygdalaChen, Patrick BHu, Rongfeng KWu, Ye EmilyPan, LinHuang, ShanMicevych, Paul EHong, Weizhe2019-02-01Social behaviors, including behaviors directed toward young offspring, exhibit striking sex differences. Understanding how these sexually dimorphic behaviors are regulated at the level of circuits and transcriptomes will provide insights into neural mechanisms of sex-specific behaviors. Here, we uncover a sexually dimorphic role of the medial amygdala (MeA) in governing parental and infanticidal behaviors. Contrary to traditional views, activation of GABAergic neurons in the MeA promotes parental behavior in females, while activation of this population in males differentially promotes parental versus infanticidal behavior in an activity-level-dependent manner. Through single-cell transcriptomic analysis, we found that molecular sex differences in the MeA are specifically represented in GABAergic neurons. Collectively, these results establish crucial roles for the MeA as a key node in the neural circuitry underlying pup-directed behaviors and provide important insight into the connection between sex differences across transcriptomes, cells, and circuits in regulating sexually dimorphic behavior.32 Biomedical and Clinical Sciences (for-2020)3209 Neurosciences (for-2020)Neurosciences (rcdc)Behavioral and Social Science (rcdc)Basic Behavioral and Social Science (rcdc)Women's Health (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Amygdala (mesh)Animals (mesh)BehaviorAnimal (mesh)Corticomedial Nuclear Complex (mesh)Female (mesh)Male (mesh)Mice (mesh)MiceInbred C57BL (mesh)Neurons (mesh)Parenting (mesh)Sex Characteristics (mesh)Sex Factors (mesh)Sexual BehaviorAnimal (mesh)Social Behavior (mesh)Amygdala (mesh)Neurons (mesh)Animals (mesh)MiceInbred C57BL (mesh)Mice (mesh)BehaviorAnimal (mesh)Social Behavior (mesh)Parenting (mesh)Sex Factors (mesh)Sex Characteristics (mesh)Female (mesh)Male (mesh)Sexual BehaviorAnimal (mesh)Corticomedial Nuclear Complex (mesh)GABAergic neuronsgroominginfanticidemedical amygdalaoptogeneticsparenting behaviorsequencingsexual dimorphismsingle cellsocial behaviorAmygdala (mesh)Animals (mesh)BehaviorAnimal (mesh)Corticomedial Nuclear Complex (mesh)Female (mesh)Male (mesh)Mice (mesh)MiceInbred C57BL (mesh)Neurons (mesh)Parenting (mesh)Sex Characteristics (mesh)Sex Factors (mesh)Sexual BehaviorAnimal (mesh)Social Behavior (mesh)06 Biological Sciences (for)11 Medical and Health Sciences (for)Developmental Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/17c349jchttps://escholarship.org/content/qt17c349jc/qt17c349jc.pdfinfo:doi/10.1016/j.cell.2019.01.024articleCell, vol 176, iss 51206 - 1221.e18oai:escholarship.org:ark:/13030/qt90k1x0nf2025-12-25T18:28:44Zqt90k1x0nfProteomics identification of radiation-induced changes of membrane proteins in the rat model of arteriovenous malformation in pursuit of targets for brain AVM molecular therapySimonian, MargaretShirasaki, DynaLee, Vivienne SBervini, DavidGrace, MichaelLoo, Rachel R OgorzalekLoo, Joseph AMolloy, Mark PStoodley, Marcus A2018-12-01BackgroundRapid identification of novel targets and advancement of a vascular targeting strategy requires a comprehensive assessment of AVM endothelial membrane protein changes in response to irradiation. The aim of this study is to provide additional potential target protein molecules for evaluation in animal trials to promote intravascular thrombosis in AVM vessels post radiosurgery.MethodsWe employed in vivo biotinylation methodology that we developed, to label membrane proteins in the rat model of AVM post radiosurgery. Mass spectrometry expression (MSE) analysis was used to identify and quantify surface protein expression between irradiated and non irradiated rats, which mimics a radiosurgical treatment approach.ResultsOur proteomics data revealed differentially expressed membrane proteins between irradiated and non irradiated rats, e.g. profilin-1, ESM-1, ion channel proteins, annexin A2 and lumican.ConclusionThis work provides additional potential target protein molecules for evaluation in animal trials to promote intravascular thrombosis in AVM vessels post radiosurgery.3205 Medical Biochemistry and Metabolomics (for-2020)32 Biomedical and Clinical Sciences (for-2020)Biotechnology (rcdc)AVM animal modelIn vivo biotinylationMembrane proteinsRadiosurgeryBiochemistry & Molecular Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)3202 Clinical sciences (for-2020)3205 Medical biochemistry and metabolomics (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/90k1x0nfhttps://escholarship.org/content/qt90k1x0nf/qt90k1x0nf.pdfinfo:doi/10.1186/s12014-018-9217-xarticleClinical Proteomics, vol 15, iss 143oai:escholarship.org:ark:/13030/qt22h745hj2025-12-25T14:13:11Zqt22h745hjExpression of ABCA4 in the retinal pigment epithelium and its implications for Stargardt macular degenerationLenis, Tamara LHu, JaneNg, Sze YinJiang, ZhichunSarfare, ShantaLloyd, Marcia BEsposito, Nicholas JSamuel, WilliamJaworski, CynthiaBok, DeanFinnemann, Silvia CRadeke, Monte JRedmond, T MichaelTravis, Gabriel HRadu, Roxana A2018-11-20Recessive Stargardt disease (STGD1) is an inherited blinding disorder caused by mutations in the Abca4 gene. ABCA4 is a flippase in photoreceptor outer segments (OS) that translocates retinaldehyde conjugated to phosphatidylethanolamine across OS disc membranes. Loss of ABCA4 in Abca4-/- mice and STGD1 patients causes buildup of lipofuscin in the retinal pigment epithelium (RPE) and degeneration of photoreceptors, leading to blindness. No effective treatment currently exists for STGD1. Here we show by several approaches that ABCA4 is additionally expressed in RPE cells. (i) By in situ hybridization analysis and by RNA-sequencing analysis, we show the Abca4 mRNA is expressed in human and mouse RPE cells. (ii) By quantitative immunoblotting, we show that the level of ABCA4 protein in homogenates of wild-type mouse RPE is about 1% of the level in neural retina homogenates. (iii) ABCA4 immunofluorescence is present in RPE cells of wild-type and Mertk-/- but not Abca4-/- mouse retina sections, where it colocalizes with endolysosomal proteins. To elucidate the role of ABCA4 in RPE cells, we generated a line of genetically modified mice that express ABCA4 in RPE cells but not in photoreceptors. Mice from this line on the Abca4-/- background showed partial rescue of photoreceptor degeneration and decreased lipofuscin accumulation compared with nontransgenic Abca4-/- mice. We propose that ABCA4 functions to recycle retinaldehyde released during proteolysis of rhodopsin in RPE endolysosomes following daily phagocytosis of distal photoreceptor OS. ABCA4 deficiency in the RPE may play a role in the pathogenesis of STGD1.32 Biomedical and Clinical Sciences (for-2020)3212 Ophthalmology and Optometry (for-2020)Genetics (rcdc)Eye Disease and Disorders of Vision (rcdc)Rare Diseases (rcdc)Neurosciences (rcdc)Neurodegenerative (rcdc)Macular Degeneration (rcdc)2.1 Biological and endogenous factors (hrcs-rac)Eye (hrcs-hc)ATP-Binding Cassette Transporters (mesh)Animals (mesh)CellsCultured (mesh)Disease ModelsAnimal (mesh)Lipofuscin (mesh)Lysosomes (mesh)Macular Degeneration (mesh)Mice (mesh)MiceInbred BALB C (mesh)MiceKnockout (mesh)Phagocytosis (mesh)Photoreceptor Cells (mesh)Retina (mesh)Retinal Degeneration (mesh)Retinal Pigment Epithelium (mesh)Retinaldehyde (mesh)Rhodopsin (mesh)Stargardt Disease (mesh)c-Mer Tyrosine Kinase (mesh)Stargardt diseaseretinal pigment epitheliumbisretinoidlipofuscinABCA4Retina (mesh)CellsCultured (mesh)Lysosomes (mesh)Animals (mesh)MiceInbred BALB C (mesh)MiceKnockout (mesh)Mice (mesh)Retinal Degeneration (mesh)Macular Degeneration (mesh)Disease ModelsAnimal (mesh)Retinaldehyde (mesh)Lipofuscin (mesh)Rhodopsin (mesh)ATP-Binding Cassette Transporters (mesh)Phagocytosis (mesh)Photoreceptor Cells (mesh)Retinal Pigment Epithelium (mesh)c-Mer Tyrosine Kinase (mesh)Stargardt Disease (mesh)ABCA4Stargardt diseasebisretinoidlipofuscinretinal pigment epitheliumATP-Binding Cassette Transporters (mesh)Animals (mesh)CellsCultured (mesh)Disease ModelsAnimal (mesh)Lipofuscin (mesh)Lysosomes (mesh)Macular Degeneration (mesh)Mice (mesh)MiceInbred BALB C (mesh)MiceKnockout (mesh)Phagocytosis (mesh)Photoreceptor Cells (mesh)Retina (mesh)Retinal Degeneration (mesh)Retinal Pigment Epithelium (mesh)Retinaldehyde (mesh)Rhodopsin (mesh)Stargardt Disease (mesh)c-Mer Tyrosine Kinase (mesh)application/pdfCC-BY-NC-NDeScholarship, University of Californiahttps://escholarship.org/uc/item/22h745hjhttps://escholarship.org/content/qt22h745hj/qt22h745hj.pdfinfo:doi/10.1073/pnas.1802519115articleProceedings of the National Academy of Sciences of the United States of America, vol 115, iss 47e11120 - e11127oai:escholarship.org:ark:/13030/qt9cf335ck2025-12-25T14:07:43Zqt9cf335ckThe Yeast DNA Damage Checkpoint Kinase Rad53 Targets the Exoribonuclease, Xrn1Lao, Jessica PUlrich, Katie MJohnson, Jeffrey RNewton, Billy WVashisht, Ajay AWohlschlegel, James AKrogan, Nevan JToczyski, David P2018-12-01The highly conserved DNA damage response (DDR) pathway monitors the genomic integrity of the cell and protects against genotoxic stresses. The apical kinases, Mec1 and Tel1 (ATR and ATM in human, respectively), initiate the DNA damage signaling cascade through the effector kinases, Rad53 and Chk1, to regulate a variety of cellular processes including cell cycle progression, DNA damage repair, chromatin remodeling, and transcription. The DDR also regulates other cellular pathways, but direct substrates and mechanisms are still lacking. Using a mass spectrometry-based phosphoproteomic screen in Saccharomyces cerevisiae, we identified novel targets of Rad53, many of which are proteins that are involved in RNA metabolism. Of the 33 novel substrates identified, we verified that 12 are directly phosphorylated by Rad53 in vitro: Xrn1, Gcd11, Rps7b, Ded1, Cho2, Pus1, Hst1, Srv2, Set3, Snu23, Alb1, and Scp160. We further characterized Xrn1, a highly conserved 5' exoribonuclease that functions in RNA degradation and the most enriched in our phosphoproteomics screen. Phosphorylation of Xrn1 by Rad53 does not appear to affect Xrn1's intrinsic nuclease activity in vitro, but may affect its activity or specificity in vivo.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)Cell Cycle Proteins (mesh)Checkpoint Kinase 2 (mesh)DNA Damage (mesh)DNA Repair (mesh)Exoribonucleases (mesh)Phosphorylation (mesh)RNA Stability (mesh)RNAFungal (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)Substrate Specificity (mesh)DNA Damage ResponsecheckpointXrn1Rad53phosphoproteomicsSaccharomyces cerevisiae (mesh)DNA Damage (mesh)Exoribonucleases (mesh)Cell Cycle Proteins (mesh)Saccharomyces cerevisiae Proteins (mesh)RNAFungal (mesh)DNA Repair (mesh)RNA Stability (mesh)Substrate Specificity (mesh)Phosphorylation (mesh)Checkpoint Kinase 2 (mesh)DNA Damage ResponseRad53Xrn1checkpointphosphoproteomicsCell Cycle Proteins (mesh)Checkpoint Kinase 2 (mesh)DNA Damage (mesh)DNA Repair (mesh)Exoribonucleases (mesh)Phosphorylation (mesh)RNA Stability (mesh)RNAFungal (mesh)Saccharomyces cerevisiae (mesh)Saccharomyces cerevisiae Proteins (mesh)Substrate Specificity (mesh)0604 Genetics (for)3101 Biochemistry and cell biology (for-2020)3105 Genetics (for-2020)4905 Statistics (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/9cf335ckhttps://escholarship.org/content/qt9cf335ck/qt9cf335ck.pdfinfo:doi/10.1534/g3.118.200767articleG3: Genes, Genomes, Genetics, vol 8, iss 123931 - 3944oai:escholarship.org:ark:/13030/qt1gx5v0692025-12-25T13:57:16Zqt1gx5v069Rapid LC–MS Method for Accurate Molecular Weight Determination of Membrane and Hydrophobic ProteinsLippens, Jennifer LEgea, Pascal FSpahr, ChrisVaish, AmitKeener, James EMarty, Michael TLoo, Joseph ACampuzano, Iain DG2018-11-20Therapeutic target characterization involves many components, including accurate molecular weight (MW) determination. Knowledge of the accurate MW allows one to detect the presence of post-translational modifications, proteolytic cleavages, and importantly, if the correct construct has been generated and purified. Denaturing liquid chromatography-mass spectrometry (LC-MS) can be an attractive method for obtaining this information. However, membrane protein LC-MS methodology has remained relatively under-explored and under-incorporated in comparison to methods for soluble proteins. Here, systematic investigation of multiple gradients and column chemistries has led to the development of a 5 min denaturing LC-MS method for acquiring membrane protein accurate MW measurements. Conditions were interrogated with membrane proteins, such as GPCRs and ion channels, as well as bispecific antibody constructs of variable sizes with the aim to provide the community with rapid LC-MS methods necessary to obtain chromatographic and accurate MW measurements in a medium- to high-throughput manner. The 5 min method detailed has successfully produced MW measurements for hydrophobic proteins with a wide MW range (17.5 to 105.3 kDa) and provided evidence that some constructs indeed contain unexpected modifications or sequence clipping. This rapid LC-MS method is also capable of baseline separating formylated and nonformylated aquaporinZ membrane protein.3401 Analytical Chemistry (for-2020)34 Chemical Sciences (for-2020)Biotechnology (rcdc)Generic health relevance (hrcs-hc)ChromatographyLiquid (mesh)Hydrophobic and Hydrophilic Interactions (mesh)Mass Spectrometry (mesh)Membrane Proteins (mesh)Molecular Weight (mesh)Membrane Proteins (mesh)ChromatographyLiquid (mesh)Molecular Weight (mesh)Mass Spectrometry (mesh)Hydrophobic and Hydrophilic Interactions (mesh)ChromatographyLiquid (mesh)Hydrophobic and Hydrophilic Interactions (mesh)Mass Spectrometry (mesh)Membrane Proteins (mesh)Molecular Weight (mesh)0301 Analytical Chemistry (for)0399 Other Chemical Sciences (for)Analytical Chemistry (science-metrix)3205 Medical biochemistry and metabolomics (for-2020)3401 Analytical chemistry (for-2020)4004 Chemical engineering (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/1gx5v069https://escholarship.org/content/qt1gx5v069/qt1gx5v069.pdfinfo:doi/10.1021/acs.analchem.8b03843articleAnalytical Chemistry, vol 90, iss 2213616 - 13623oai:escholarship.org:ark:/13030/qt56w7c9gf2025-12-25T13:52:34Zqt56w7c9gfIdentification of two principal amyloid-driving segments in variable domains of Ig light chains in systemic light-chain amyloidosisBrumshtein, BorisEsswein, Shannon RSawaya, Michael RRosenberg, GregoryLy, Alan TLandau, MeytalEisenberg, David S2018-12-01Systemic light-chain amyloidosis (AL) is a human disease caused by overexpression of monoclonal immunoglobulin light chains that form pathogenic amyloid fibrils. These amyloid fibrils deposit in tissues and cause organ failure. Proteins form amyloid fibrils when they partly or fully unfold and expose segments capable of stacking into β-sheets that pair and thereby form a tight, dehydrated interface. These structures, termed steric zippers, constitute the spines of amyloid fibrils. Here, using a combination of computational (with ZipperDB and Boston University ALBase), mutational, biochemical, and protein structural analyses, we identified segments within the variable domains of Ig light chains that drive the assembly of amyloid fibrils in AL. We demonstrate that there are at least two such segments and that each one can drive amyloid fibril assembly independently of the other. Our analysis revealed that peptides derived from these segments form steric zippers featuring a typical dry interface with high-surface complementarity and occupy the same spatial location of the Greek-key immunoglobulin fold in both λ and κ variable domains. Of note, some predicted steric-zipper segments did not form amyloid fibrils or assembled into fibrils only when removed from the whole protein. We conclude that steric-zipper propensity must be experimentally validated and that the two segments identified here may represent therapeutic targets. In addition to elucidating the molecular pathogenesis of AL, these findings also provide an experimental approach for identifying segments that drive fibril formation in other amyloid diseases.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Rare Diseases (rcdc)Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) (rcdc)Neurosciences (rcdc)Neurodegenerative (rcdc)Brain Disorders (rcdc)Aging (rcdc)Alzheimer's Disease (rcdc)Acquired Cognitive Impairment (rcdc)Dementia (rcdc)Amino Acid Sequence (mesh)Amyloid (mesh)Immunoglobulin Light Chains (mesh)Immunoglobulin Light-chain Amyloidosis (mesh)ModelsMolecular (mesh)Molecular Targeted Therapy (mesh)Peptide Fragments (mesh)Protein Domains (mesh)amyloidantibodycrystallographyelectron microscopy (EM)protein aggregationlight chain (LC)light-chain amyloidosis (AL)steric zipperthioflavin T (ThT)variable domain (VL)Amyloid (mesh)Peptide Fragments (mesh)Amino Acid Sequence (mesh)ModelsMolecular (mesh)Immunoglobulin Light Chains (mesh)Molecular Targeted Therapy (mesh)Protein Domains (mesh)Immunoglobulin Light-chain Amyloidosis (mesh)amyloidantibodycrystallographyelectron microscopy (EM)light chain (LC)light-chain amyloidosis (AL)protein aggregationsteric zipperthioflavin T (ThT)variable domain (VL)Amino Acid Sequence (mesh)Amyloid (mesh)Immunoglobulin Light Chains (mesh)Immunoglobulin Light-chain Amyloidosis (mesh)ModelsMolecular (mesh)Molecular Targeted Therapy (mesh)Peptide Fragments (mesh)Protein Domains (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biochemistry & Molecular Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/56w7c9gfhttps://escholarship.org/content/qt56w7c9gf/qt56w7c9gf.pdfinfo:doi/10.1074/jbc.ra118.004142articleJournal of Biological Chemistry, vol 293, iss 5119659 - 19671oai:escholarship.org:ark:/13030/qt8f58q90j2025-12-25T13:34:35Zqt8f58q90jThe impact and prospect of natural product discovery in agricultureYan, YanLiu, QikunJacobsen, Steven ETang, Yi2018-11-01Graphical AbstractNatural products from plants and microorganisms are potent bioactive molecules that have been used in medicine, agriculture and cosmetics. Genomics and synthetic biology offer new tools to further explore their diversity for applications as fungicides or herbicides.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Biotechnology (rcdc)Agriculture (mesh)Biological Products (mesh)Drug ResistanceMicrobial (mesh)FungicidesIndustrial (mesh)GenomeMicrobial (mesh)GenomePlant (mesh)Metabolic Engineering (mesh)MicroorganismsGenetically-Modified (mesh)Multigene Family (mesh)Pesticides (mesh)Plants (mesh)Secondary Metabolism (mesh)Plants (mesh)Biological Products (mesh)Pesticides (mesh)FungicidesIndustrial (mesh)Drug ResistanceMicrobial (mesh)GenomePlant (mesh)Multigene Family (mesh)Agriculture (mesh)Metabolic Engineering (mesh)Secondary Metabolism (mesh)GenomeMicrobial (mesh)MicroorganismsGenetically-Modified (mesh)Agriculture (mesh)Biological Products (mesh)Drug ResistanceMicrobial (mesh)FungicidesIndustrial (mesh)GenomeMicrobial (mesh)GenomePlant (mesh)Metabolic Engineering (mesh)MicroorganismsGenetically-Modified (mesh)Multigene Family (mesh)Pesticides (mesh)Plants (mesh)Secondary Metabolism (mesh)0601 Biochemistry and Cell Biology (for)Developmental Biology (science-metrix)3101 Biochemistry and cell biology (for-2020)application/pdfpubliceScholarship, University of Californiahttps://escholarship.org/uc/item/8f58q90jhttps://escholarship.org/content/qt8f58q90j/qt8f58q90j.pdfinfo:doi/10.15252/embr.201846824articleEMBO Reports, vol 19, iss 11embr201846824oai:escholarship.org:ark:/13030/qt6xn194cv2025-12-25T12:48:32Zqt6xn194cvThe Streptococcus pyogenes Shr protein captures human hemoglobin using two structurally unique binding domainsMacdonald, RamsayCascio, DuilioCollazo, Michael JPhillips, MartinClubb, Robert T2018-11-01In order to proliferate and mount an infection, many bacterial pathogens need to acquire iron from their host. The most abundant iron source in the body is the oxygen transporter hemoglobin (Hb). Streptococcus pyogenes, a potentially lethal human pathogen, uses the Shr protein to capture Hb on the cell surface. Shr is an important virulence factor, yet the mechanism by which it captures Hb and acquires its heme is not well-understood. Here, we show using NMR and biochemical methods that Shr binds Hb using two related modules that were previously defined as domains of unknown function (DUF1533). These hemoglobin-interacting domains (HIDs), called HID1 and HID2, are autonomously folded and independently bind Hb. The 1.5 Å resolution crystal structure of HID2 revealed that it is a structurally unique Hb-binding domain. Mutagenesis studies revealed a conserved tyrosine in both HIDs that is essential for Hb binding. Our biochemical studies indicate that HID2 binds Hb with higher affinity than HID1 and that the Hb tetramer is engaged by two Shr receptors. NMR studies reveal the presence of a third autonomously folded domain between HID2 and a heme-binding NEAT1 domain, suggesting that this linker domain may position NEAT1 near Hb for heme capture.3101 Biochemistry and Cell Biology (for-2020)31 Biological Sciences (for-2020)Infectious Diseases (rcdc)Hematology (rcdc)Emerging Infectious Diseases (rcdc)2.1 Biological and endogenous factors (hrcs-rac)2.2 Factors relating to the physical environment (hrcs-rac)Bacterial Proteins (mesh)Heme (mesh)Hemoglobins (mesh)Host-Pathogen Interactions (mesh)Humans (mesh)Protein Binding (mesh)Protein Domains (mesh)Streptococcal Infections (mesh)Streptococcus pyogenes (mesh)Streptococcus pyogenes (Spyogenes)hemoglobinX-ray crystallographynuclear magnetic resonance (NMR)isothermal titration calorimetry (ITC)receptorbacterial pathogenDUF1533ShrHumans (mesh)Streptococcus pyogenes (mesh)Streptococcal Infections (mesh)Heme (mesh)Bacterial Proteins (mesh)Hemoglobins (mesh)Protein Binding (mesh)Host-Pathogen Interactions (mesh)Protein Domains (mesh)DUF1533ShrStreptococcus pyogenes (S. pyogenes)X-ray crystallographybacterial pathogenhemoglobinisothermal titration calorimetry (ITC)nuclear magnetic resonance (NMR)receptorBacterial Proteins (mesh)Heme (mesh)Hemoglobins (mesh)Host-Pathogen Interactions (mesh)Humans (mesh)Protein Binding (mesh)Protein Domains (mesh)Streptococcal Infections (mesh)Streptococcus pyogenes (mesh)03 Chemical Sciences (for)06 Biological Sciences (for)11 Medical and Health Sciences (for)Biochemistry & Molecular Biology (science-metrix)31 Biological sciences (for-2020)32 Biomedical and clinical sciences (for-2020)34 Chemical sciences (for-2020)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/6xn194cvhttps://escholarship.org/content/qt6xn194cv/qt6xn194cv.pdfinfo:doi/10.1074/jbc.ra118.005261articleJournal of Biological Chemistry, vol 293, iss 4718365 - 18377oai:escholarship.org:ark:/13030/qt1hw4h4992025-12-25T11:59:10Zqt1hw4h499Evidence of reduced recombination rate in human regulatory domainsLiu, YapingSarkar, AbhishekKheradpour, PouyaErnst, JasonKellis, Manolis2017-12-01BackgroundRecombination rate is non-uniformly distributed across the human genome. The variation of recombination rate at both fine and large scales cannot be fully explained by DNA sequences alone. Epigenetic factors, particularly DNA methylation, have recently been proposed to influence the variation in recombination rate.ResultsWe study the relationship between recombination rate and gene regulatory domains, defined by a gene and its linked control elements. We define these links using expression quantitative trait loci (eQTLs), methylation quantitative trait loci (meQTLs), chromatin conformation from publicly available datasets (Hi-C and ChIA-PET), and correlated activity links that we infer across cell types. Each link type shows a “recombination rate valley” of significantly reduced recombination rate compared to matched control regions. This recombination rate valley is most pronounced for gene regulatory domains of early embryonic development genes, housekeeping genes, and constitutive regulatory elements, which are known to show increased evolutionary constraint across species. Recombination rate valleys show increased DNA methylation, reduced doublestranded break initiation, and increased repair efficiency, specifically in the lineage leading to the germ line. Moreover, by using only the overlap of functional links and DNA methylation in germ cells, we are able to predict the recombination rate with high accuracy.ConclusionsOur results suggest the existence of a recombination rate valley at regulatory domains and provide a potential molecular mechanism to interpret the interplay between genetic and epigenetic variations.31 Biological Sciences (for-2020)3105 Genetics (for-2020)Biotechnology (rcdc)Human Genome (rcdc)Genetics (rcdc)1.1 Normal biological development and functioning (hrcs-rac)2.1 Biological and endogenous factors (hrcs-rac)Animals (mesh)ChromosomesHuman (mesh)DNA BreaksDouble-Stranded (mesh)DNA Methylation (mesh)Embryonic Development (mesh)Gene Expression (mesh)GenesEssential (mesh)Humans (mesh)Mice (mesh)Quantitative Trait Loci (mesh)RecombinationGenetic (mesh)Regulatory SequencesNucleic Acid (mesh)Recombination rateRegulatory domainDNA methylationChromosomesHuman (mesh)Animals (mesh)Humans (mesh)Mice (mesh)DNA Methylation (mesh)Gene Expression (mesh)RecombinationGenetic (mesh)Regulatory SequencesNucleic Acid (mesh)Embryonic Development (mesh)GenesEssential (mesh)Quantitative Trait Loci (mesh)DNA BreaksDouble-Stranded (mesh)DNA methylationRecombination rateRegulatory domainAnimals (mesh)ChromosomesHuman (mesh)DNA BreaksDouble-Stranded (mesh)DNA Methylation (mesh)Embryonic Development (mesh)Gene Expression (mesh)GenesEssential (mesh)Humans (mesh)Mice (mesh)Quantitative Trait Loci (mesh)RecombinationGenetic (mesh)Regulatory SequencesNucleic Acid (mesh)05 Environmental Sciences (for)06 Biological Sciences (for)08 Information and Computing Sciences (for)Bioinformatics (science-metrix)application/pdfCC-BYeScholarship, University of Californiahttps://escholarship.org/uc/item/1hw4h499https://escholarship.org/content/qt1hw4h499/qt1hw4h499.pdfinfo:doi/10.1186/s13059-017-1308-xarticleGenome Biology, vol 18, iss 1193oai_dc:uclabiolchem:500:1432:eyJmaXJzdCI6NTAwLCJiZWZvcmUiOiIyMDI2LTA5LTIxVDEwOjU1OjE0KzAwOjAwIiwiYWZ0ZXIiOiIyMDExLTAzLTE4VDE0OjMyOjQyKzAwOjAwIiwiaW5jbHVkZSI6WyJQVUJMSVNIRUQiLCJFTUJBUkdPRUQiXSwib3JkZXIiOiJVUERBVEVEX0RFU0MiLCJsYXN0SUQiOiJxdDFodzRoNDk5IiwibGFzdERhdGUiOiIyMDI1LTEyLTI1VDExOjU5OjEwKzAwOjAwIn0