http://www.rssboard.org/rss-specification 720 https://escholarship.org/uc/ucr_som_crnab_oapolicydeposits/rss Recent eScholarship items from Open Access Policy Deposits Thu, 2 Jul 2026 10:51:14 +0000 https://escholarship.org/uc/item/8vx2b572 Neural crest (NC) cells are multipotent cells unique to vertebrates that arise early in development, at the edge of the neural plate, and subsequently undergo an epithelial to mesenchymal transition, migrate throughout the body, and differentiate into many different derivatives, contributing to the formation of many organs and systems. NC induction research from multiple modeling organisms has identified critical roles for a few signaling pathways, including Wnt, BMP, FGF, Notch/ Delta, Indian Hedgehog, and Endothelin signaling (Prasad et al., 2019). Given the limitations of human embryo studies, pluripotent stem cell models of human NC formation have provided a resourceful alternative (Lee et al., 2007). Intriguingly, while TGFβ inhibition had not been identified as a signaling requirement for NC formation in any in vivo model organism, several pluripotent stem cell (PSC) models of human NC induction rely on TGFβ inhibition (Chambers et al., 2009). To address this issue, we evaluate... https://escholarship.org/uc/item/8vx2b572 Sun, 7 Jun 2026 00:00:00 +0000 Gomez, Gustavo A Parmar, Bhaval Wong, Man Hernandez, Jacqueline C Guimarães-Andrade, Iris Paula Garcia-Castro, Martin I https://orcid.org/0000-0001-5128-0004 https://escholarship.org/uc/item/9fn6w55v Correction to: Nature Microbiologyhttps://doi.org/10.1038/s41564-025-02116-2, published online 26 September 2025. In the version of this article initially published, in the first paragraph of the “Survey on data reuse” section, a note on participant consent, confidentiality and institutional review was missing and has now been inserted in the HTML and PDF versions of the article. https://escholarship.org/uc/item/9fn6w55v Fri, 5 Jun 2026 00:00:00 +0000 Hug, Laura A Hatzenpichler, Roland Moraru, Cristina Soares, André R Meyer, Folker Heyder, Anke Probst, Alexander J https://escholarship.org/uc/item/8xg946qf Decoding the origins of cellular self-organization for engineered biology https://escholarship.org/uc/item/8xg946qf Thu, 4 Jun 2026 00:00:00 +0000 Chen, Qi https://orcid.org/0000-0001-6353-9589 Zernicka-Goetz, Magdalena https://orcid.org/0000-0002-7004-2471 https://escholarship.org/uc/item/5nk3p96w BackgroundEastern hellbenders (Cryptobranchus alleganiensis alleganiensis) have undergone substantial population declines throughout their range, leading them to become the focus of increased conservation efforts, including care in zoo and university settings. However, effective implementation of such conservation strategies often relies on a comprehensive understanding of host health, which can be directly influenced by the gut microbiome, yet characterization of gut microbiota often remains overlooked in ex situ conservation facilities. Additionally, effects on the gut microbiome associated with releasing zoo-reared animals into the wild are poorly understood. Therefore, these circumstances make hellbenders an ideal species to examine the relationship between zoo management strategies and gut microbial dynamics.Methods16S rRNA sequencing was used to investigate dissimilarities between the gut microbiome of hellbenders in zoo and wild settings and to evaluate the impact of implementing... https://escholarship.org/uc/item/5nk3p96w Mon, 25 May 2026 00:00:00 +0000 Cummins, Chloe Sutton, William McLeod, Taina Dallas, Jason W Ghotbi, Mitra Vargas-Gastélum, Lluvia Alexander, N Reed Rurik, Alexander J McGinnity, Dale Reinsch, Sherri Doro Sandonato, Pia Arbour, Jessica Freake, Michael Ashley, Anthony Ternes, William Culp, Elizabeth Spatafora, Joseph McPhail, Kerry Stajich, Jason E https://orcid.org/0000-0002-7591-0020 Hardman, Rebecca Walker, Donald M https://escholarship.org/uc/item/98g718zp We address the problem of comparing multiple genome-wide maps representing nucleosome positions or specific histone marks. These maps can originate from the comparative analysis of ChIP-Seq/MNase-Seq/FAIRE-Seq data for different cell types/tissues or multiple time points. The input to the problem is a set of maps, each of which is a list of genomics locations for nucleosomes or histone marks. The output is an alignment of nucleosomes/histone marks across time points (that we call trajectories), allowing small movements and gaps in some of the maps. We present a tool called ThIEF (TrackIng of Epigenetic Features) that can efficiently compute these trajectories. ThIEF comes into two "flavors": ThIEF:Iterative finds the trajectories progressively using bipartite matching, while ThIEF:LP solves a k-partite matching problem on a hyper graph using linear programming. ThIEF:LP is guaranteed to find the optimal solution, but it is slower than ThIEF:Iterative. We demonstrate the utility... https://escholarship.org/uc/item/98g718zp Thu, 21 May 2026 00:00:00 +0000 Polishko, Anton Hasan, Md Abid Pan, Weihua Bunnik, Evelien M Le Roch, Karine https://orcid.org/0000-0002-4862-9292 Lonardi, Stefano https://orcid.org/0000-0002-2696-7274 https://escholarship.org/uc/item/7kk4q071 Due to the current limitations of sequencing technologies, de novo genome assembly is typically carried out in two stages, namely contig (sequence) assembly and scaffolding. While scaffolding is computationally easier than sequence assembly, the scaffolding problem can be challenging due to the high repetitive content of eukaryotic genomes, possible mis-joins in assembled contigs and inaccuracies in the linkage information. Genome scaffolding tools either use paired-end/mate-pair/linked/Hi-C reads or genome-wide maps (optical, physical or genetic) as linkage information. Optical maps (in particular Bionano Genomics maps) have been extensively used in many recent large-scale genome assembly projects (e.g., goat, apple, barley, maize, quinoa, sea bass, among others). However, the most commonly used scaffolding tools have a serious limitation: they can only deal with one optical map at a time, forcing users to alternate or iterate over multiple maps. In this paper, we introduce a... https://escholarship.org/uc/item/7kk4q071 Thu, 21 May 2026 00:00:00 +0000 Pan, Weihua Jiang, Tao https://orcid.org/0000-0003-3833-4498 Lonardi, Stefano https://orcid.org/0000-0002-2696-7274 https://escholarship.org/uc/item/7k5638gx MOTIVATION: High-throughput conformation capture experiments, such as Hi-C provide genome-wide maps of chromatin interactions, enabling life scientists to investigate the role of the three-dimensional structure of genomes in gene regulation and other essential cellular functions. A fundamental problem in the analysis of Hi-C data is how to compare two contact maps derived from Hi-C experiments. Detecting similarities and differences between contact maps are critical in evaluating the reproducibility of replicate experiments and for identifying differential genomic regions with biological significance. Due to the complexity of chromatin conformations and the presence of technology-driven and sequence-specific biases, the comparative analysis of Hi-C data is analytically and computationally challenging. RESULTS: We present a novel method called Selfish for the comparative analysis of Hi-C data that takes advantage of the structural self-similarity in contact maps. We define a novel... https://escholarship.org/uc/item/7k5638gx Thu, 21 May 2026 00:00:00 +0000 Ardakany, Abbas Roayaei Ay, Ferhat https://orcid.org/0000-0002-0708-6914 Lonardi, Stefano https://orcid.org/0000-0002-2696-7274 https://escholarship.org/uc/item/52x9m11r Various techniques are available to profile DNA methylation, either genome‐wide or targeted at specific regions, such as CpG islands and gene promoters. In general, these techniques are divided into two categories: enrichment based and bisulfite conversion based methods. DNA methylation has been associated with gene expression, imprinting, transposon silencing, X‐chromosome inactivation, embryonic development, and cancer. Bisulfite‐conversion‐based methods involve the following three steps: chemical conversion of non‐methylated cytosines to uracils by treating DNA with sodium bisulfite; PCR amplification, and sequencing size‐selected DNA fragments. Sequencing errors, adapter contamination, end‐repair, and single‐nucleotide polymorphisms (SNPs) may affect erroneous methylation calls. Two common major performance measurements of an aligner for BS‐reads are mapping accuracy and methylation call accuracy. Both local alignment and alignment with indels are needed in order to map the... https://escholarship.org/uc/item/52x9m11r Thu, 21 May 2026 00:00:00 +0000 Harris, Elena Lonardi, Stefano https://orcid.org/0000-0002-2696-7274 https://escholarship.org/uc/item/3sf0x1ph Continuous improvements to high-throughput conformation capture (Hi-C) are revealing richer information about the spatial organization of the chromatin and its role in cellular functions. Several studies have confirmed the existence of structural features of the genome 3D organization that are stable across cell types and conserved across species, called topological associating domains (TADs). The detection of TADs has become a critical step in the analysis of Hi-C data, e.g., to identify enhancer-promoter associations. Here we present East, a novel TAD identification algorithm based on fast 2D convolution of Haar-like features, that is as accurate as the state-of-the-art method based on the directionality index, but 75-80× faster. East is available in the public domain at https://github.com/ucrbioinfo/EAST. https://escholarship.org/uc/item/3sf0x1ph Thu, 21 May 2026 00:00:00 +0000 Ardakany, Abbas Roayaei Lonardi, Stefano https://orcid.org/0000-0002-2696-7274 https://escholarship.org/uc/item/2cv9x5hn Complex repetitive regions (also known as segmental duplications) in eukaryotic genomes often contain essential functional and regulatory information. Despite remarkable algorithmic progress in genome assembly in the last twenty years, modern de novo assemblers still struggle to accurately reconstruct these highly repetitive regions. When sequenced reads will be long enough to span all repetitive regions, the problem will be solved trivially. However, even the third generation of sequencing technologies on the market cannot yet produce reads that are sufficiently long (and accurate) to span every repetitive region in large eukaryotic genomes. In this work, we introduce a novel algorithm called RAmbler to resolve complex repetitive regions based on high-quality long reads (i.e., PacBio HiFi). We first identify potentially repetitive regions by mapping the HiFi reads to the draft genome assembly. Regions with sequencing coverage much higher then the average indicate a collapsed... https://escholarship.org/uc/item/2cv9x5hn Thu, 21 May 2026 00:00:00 +0000 Chakravarty, Sakshar Logsdon, Glennis Lonardi, Stefano https://orcid.org/0000-0002-2696-7274 https://escholarship.org/uc/item/11p5f3sc The growing number of metagenomic studies in medicine and environmental sciences is creating new computational demands in the analysis of these very large datasets. We have recently proposed a time-efficient algorithm called Clark that can accurately classify metagenomic sequences against a set of reference genomes. The competitive advantage of Clark depends on the use of discriminative contiguousk-mers. In default mode, Clark’s speed is currently unmatched and its precision is comparable to the state-of-the-art, however, its sensitivity still does not match the level of the most sensitive (but slowest) metagenomic classifier. In this paper, we introduce an algorithmic improvement that allows Clark’s classification sensitivity to match the best metagenomic classifier, without a significant loss of speed or precision compared to the original version. Finally, on real metagenomes, Clark can assign with high accuracy a much higher proportion of short reads than its closest competitor.... https://escholarship.org/uc/item/11p5f3sc Thu, 21 May 2026 00:00:00 +0000 Ounit, Rachid Lonardi, Stefano https://orcid.org/0000-0002-2696-7274 https://escholarship.org/uc/item/0qj532xn Computational tools for studying the structure of protein complexes are essential for providing mechanistic insights into protein-protein interactions and therapeutic drug design. Here, we present SPICE (Structural Protein Interaction Complex Evaluator), a web-based platform that allows structural biologists to perform rapid, modular analyses of protein complexes directly from Protein Data Bank (PDB) structures. SPICE allows users to define and execute analysis workflows via an intuitive web interface, reducing analysis times from minutes to seconds. The platform offers a broad range of analytical capabilities, including (i) detection of hydrogen bonds, salt bridges, and disulfide bonds; (ii) protein-protein interface mapping; and (iii) computation of solvent accessibility, van der Waals energetics, and other key geometric descriptors. SPICE further provides interactive 3D visualization and supports comparative analyses across multiple complexes, enabling the study of mutational... https://escholarship.org/uc/item/0qj532xn Thu, 21 May 2026 00:00:00 +0000 Ashraf, Faisal Bin https://orcid.org/0000-0003-4006-5389 Lonardi, Stefano https://orcid.org/0000-0002-2696-7274 https://escholarship.org/uc/item/0gx8r0hn Cancer is a complex disease associated with abnormal DNA mutations. Not all tumors are cancerous and not all cancers are the same. Correct cancer type diagnosis can indicate the most effective drug therapy and increase survival rate. At the molecular level, it has been shown that cancer type classification can be carried out from the analysis of somatic point mutation. However, the high dimensionality and sparsity of genomic mutation data, coupled with its small sample size has been a hindrance in accurate classification of cancer. We address these problems by introducing a novel classification method called mClass that accounts for the sparsity of the data. mClass is a feature selection method that ranks genes based on their similarity across samples and employs their normalized mutual information to determine the set of genes that provide optimal classification accuracy. Experimental results on TCGA datasets show that mClass significantly improves testing accuracy compared to... https://escholarship.org/uc/item/0gx8r0hn Thu, 21 May 2026 00:00:00 +0000 Hasan, Md Abid Lonardi, Stefano https://orcid.org/0000-0002-2696-7274 https://escholarship.org/uc/item/1wh3c8n2 Science benefits from rapid open data sharing, but current guidelines for data reuse were established two decades ago, when databases were several million times smaller than they are today. These guidelines are largely unfamiliar to the scientific community, and, owing to the rapid increase in biological data generated in the past decade, they are also outdated. As a result, there is a lack of community standards suited to the current landscape and inconsistent implementation of data sharing policies across institutions. Here we discuss current sequence data sharing policies and their benefits and drawbacks, and present a roadmap to establish guidelines for equitable sequence data reuse, developed in consultation with a data consortium of 167 microbiome scientists. We propose the use of a Data Reuse Information (DRI) tag for public sequence data, which will be associated with at least one Open Researcher and Contributor ID (ORCID) account. The machine-readable DRI tag indicates... https://escholarship.org/uc/item/1wh3c8n2 Mon, 27 Apr 2026 00:00:00 +0000 Hug, Laura A Hatzenpichler, Roland Moraru, Cristina Soares, André R Meyer, Folker Heyder, Anke Probst, Alexander J https://escholarship.org/uc/item/71p7w8n8 Gene expression patterns are determined to a large extent by transcription factor (TF) binding to noncoding regulatory regions in the genome. However, gene expression cannot yet be systematically predicted from genome sequences, in part because nonfunctional matches to the sequence patterns (motifs) recognized by TFs occur frequently throughout the genome. Large-scale functional genomics data for many TFs has enabled characterization of regulatory networks in experimentally accessible cells such as budding yeast. Beyond yeast, fungi are important industrial organisms and pathogens, but large-scale functional data is only sporadically available. Uncharacterized regulatory networks control key pathways and gene expression programs associated with fungal phenotypes. Here, we explore a sequence-only approach to inferring regulatory networks by leveraging the 100s of genomes now available for many clades of fungi. We use gene orthology as the learning signal to infer interpretable,... https://escholarship.org/uc/item/71p7w8n8 Thu, 23 Apr 2026 00:00:00 +0000 Moses, Alan M Stajich, Jason E https://orcid.org/0000-0002-7591-0020 Gasch, Audrey P Knowles, David A https://escholarship.org/uc/item/3rg68828 Basidiomycetous yeasts are taxonomically and ecologically diverse. While the phyllosphere of plants in China has been the subject of extensive research on yeast biodiversity, many unique and remote habitats remain significantly underexplored for their yeast species. The objective of this study was to investigate the hidden taxonomic novelty of basidiomycetous yeasts in these distinctive niches to comprehensively refine the current phylogenetic understanding. During intensive investigations, 164 yeast strains were identified from various samples collected from the phyllosphere and tidal flats in China. These isolates underwent detailed multi-gene phylogenetic analyses combined with phenotypic characterization for taxonomic placement. The analyses revealed a remarkable level of hidden diversity. These 164 isolates represent one new order (Sterigmoblongales), two new families (Sterigmoblongaceae and Turchettiaceae), five new genera (Nakasea, Sterigmoblongus, Buzzinia, Gracilitas,... https://escholarship.org/uc/item/3rg68828 Thu, 23 Apr 2026 00:00:00 +0000 Sun, JQ Du, ZN Zhu, HY Luo, JZ Zheng, AK Boekhout, T Groenewald, M Hui, FL Li, AH Stajich, JE https://orcid.org/0000-0002-7591-0020 Zang, W Bai, FY Liu, XZ https://escholarship.org/uc/item/38w905dc ABSTRACT Background Eastern hellbenders ( Cryptobranchus alleganiensis alleganiensis ) have undergone substantial population declines throughout their range, leading them to become the focus of increased conservation efforts, including care in zoo and university settings. However, effective implementation of such conservation strategies often relies on a comprehensive understanding of host health, which can be directly influenced by the gut microbiome, yet characterization of gut microbiota often remains overlooked in ex situ conservation facilities. Additionally, effects on the gut microbiome associated with releasing zoo-reared animals into the wild are poorly understood. Therefore, these circumstances make hellbenders an ideal species to examine the relationship between zoo management strategies and gut microbial dynamics. Methods 16S rRNA sequencing was used to investigate dissimilarities between the gut microbiome of hellbenders in zoo and wild settings and to evaluate... https://escholarship.org/uc/item/38w905dc Thu, 23 Apr 2026 00:00:00 +0000 Cummins, Chloe Sutton, William McLeod, Taina Dallas, Jason W Ghotbi, Mitra Vargas-Gastélum, Lluvia Alexander, N Reed Rurik, Alexander J McGinnity, Dale Reinsch, Sherri Doro Sandonato, Pia Arbour, Jessica Freake, Michael Ashley, Anthony Ternes, William Culp, Elizabeth Spatafora, Joseph McPhail, Kerry Stajich, Jason E https://orcid.org/0000-0002-7591-0020 Hardman, Rebecca Walker, Donald M https://escholarship.org/uc/item/2q20z718 Phyling is a fast, scalable, and user-friendly tool supporting phylogenomic reconstruction of species phylogenies directly from protein-encoded genomic data. It identifies orthologous genes by searching protein sequences against a curated set of hidden Markov model profiles, consisting of single-copy orthologs derived from the BUSCO database. To optimize the speed of the final inference, Phyling includes a module to filter aligned orthologs based on their phylogenetic informativeness. Finally, Phyling provides a companion wrapper for automated species tree construction using either consensus or concatenation strategies. Phyling efficiently resolves large phylogenies by optimizing memory usage and data processing. Its checkpoint system enables users to incrementally add or remove samples without repeating the entire search process. For analyses involving closely related taxa, Phyling supports the use of nucleotide coding sequences, which may capture phylogenetic signals missed... https://escholarship.org/uc/item/2q20z718 Thu, 23 Apr 2026 00:00:00 +0000 Tsai, Cheng-Hung Stajich, Jason E https://orcid.org/0000-0002-7591-0020 https://escholarship.org/uc/item/1v48j0gb Black fungi are among the most stress-resistant organisms known, yet the genetic and ecological foundations of their extraordinary resilience remain poorly understood. This study explores the adaptation strategies of the melanised fungus Elasticomyces elasticus by integrating genomic and ecological data. To uncover the mechanisms of adaptation, we combined whole-genome sequencing, functional annotation, environmental metadata, and large-scale soil metabarcoding analyses. Phylogenomic approaches were employed to delineate evolutionary lineages and assess ploidy levels. The results revealed that the global distribution of Elasticomyces phylotypes is primarily influenced by temperature, UV radiation, and soil organic carbon, suggesting that different phylotypes have evolved heterogeneous strategies for stress resistance. Comparative genomic analyses identified a set of 'sentinel pathways,' notably glutathione metabolism and nucleotide biosynthesis, which were enriched in strains... https://escholarship.org/uc/item/1v48j0gb Thu, 23 Apr 2026 00:00:00 +0000 Coleine, Claudia Biagioli, Federico Sáez‐Sandino, Tadeo Gostincar, Cene Turco, Silvia Muggia, Lucia Donati, Claudio Cestaro, Alessandro Kurbessoian, Tania Egidi, Eleonora Stajich, Jason E https://orcid.org/0000-0002-7591-0020 Tedersoo, Leho Delgado‐Baquerizo, Manuel https://escholarship.org/uc/item/5nq8r43t When sequencing a new genome, it is common practice to expect that 30-50× sequencing depth will be sufficient for a complete and highly contiguous assembly. With the rapid decrease in the cost of sequencing DNA, on small genomes it is not uncommon to have excessive sequencing data, sometimes exceeding 1000× sequencing depth (which we call ultra-deep). Because ultra-deep sequencing data significantly degrades the quality of the final assembly (for reasons not entirely clear to us), one faces the problem of how to select a subsample of the data for optimal assembly. The optimal read selection problem for genome assembly is largely unexplored. Here we first show that this problem is related to the minimum tiling path (MTP) problem which is known to be NP-hard. Then, we propose a heuristic (called AWinK) based on single-copy k-mer to select a subset of ultra-deep sequencing reads that maximizes the genomic coverage. Our experiments on both synthetic and real ultra-deep sequencing... https://escholarship.org/uc/item/5nq8r43t Thu, 12 Mar 2026 00:00:00 +0000 Chakravarty, Sakshar Lonardi, Stefano https://orcid.org/0000-0002-2696-7274 https://escholarship.org/uc/item/352106jb Persistent plant viruses are widespread in natural ecosystems. However, little is known about why persistent infection with these viruses may cause little or no harm to their host. Here, we discovered a new polerovirus that persistently infected wild rice plants by deep sequencing and assembly of virus-derived small-interfering RNAs (siRNAs). The new virus was named Rice tiller inhibition virus 2 (RTIV2) based on the symptoms developed in cultivated rice varieties following Agrobacterium-mediated inoculation with an infectious RTIV2 clone. We showed that RTIV2 infection induced antiviral RNA interference (RNAi) in both the wild and cultivated rice plants as well as Nicotiana benthamiana. It is known that virulent virus infection in plants depends on effective suppression of antiviral RNAi by viral suppressors of RNAi (VSRs). Notably, the P0 protein of RTIV2 exhibited weak VSR activity and carries alanine substitutions of two amino acids broadly conserved among diverse poleroviruses.... https://escholarship.org/uc/item/352106jb Thu, 12 Mar 2026 00:00:00 +0000 Zhu, Li‐Juan Zhu, Yu Zou, Chengwu Su, Lan‐Yi Zhang, Chong‐Tao Wang, Chi Bai, Ya‐Ni Chen, Baoshan Li, Rongbai Wu, Qingfa Ding, Shou‐Wei https://orcid.org/0000-0002-4697-8413 Wu, Jian‐Guo Han, Yan‐Hong https://escholarship.org/uc/item/2hn3z2rg The prediction of DNA methylation from the primary DNA sequence allows one to impute the methylation status of cytosines with insufficient sequencing coverage. Various deep learning models have been proposed in the literature, including transformer-based models and convolutional neural networks. In this study, we investigate the performance of long-range state-space models based on the Hyena architecture on the task of DNA methylation prediction on six plant species. First, we train the HyenaDNA framework to obtain a genome-wide foundation model for each species. Then, we fine-tune these foundation models using the sequence data surrounding the methylated or unmethylated cytosines. Extensive experimental results show that our model predicts DNA methylation with higher accuracy than state-of-the-art methods in the literature. https://escholarship.org/uc/item/2hn3z2rg Thu, 12 Mar 2026 00:00:00 +0000 Feng, Hao Chakravarty, Sakshar Lonardi, Stefano https://orcid.org/0000-0002-2696-7274 https://escholarship.org/uc/item/1sj3d7f5 A zoonotic <i>Babesia</i> species previously referred to as <i>Babesia sp</i>. <i>MO1</i> is formally described and named here as <i>Babesia hegotelforum sp. nov</i>. This taxon is distinct from <i>Babesia divergens</i> based on genome-wide sequence divergence, phylogenetic placement, host associations, and clinical presentation. The parasite infects erythrocytes of humans, and eastern cottontail rabbits (<i>Sylvilagus floridanus</i>), and is transmitted by <i>Ixodes dentatus</i>. The holotype consists of a Giemsa-stained thin blood smear and cryopreserved infected erythrocytes from the cloned isolate BML-<i>Bh</i>-B12 at ≤10 passages in continuous in vitro culture. Paratype material includes five additional clones (BML-<i>Bh</i>-H1, BML-<i>Bh</i>-F12, BML-<i>Bh</i>-H6, BML-<i>Bh</i>-A3, and BML-<i>Bh</i>-F1) derived from BEI Resources strain NR-50441, along with the original mixed isolate NR-50441. This species description meets the requirements of the International Code of Zoological... https://escholarship.org/uc/item/1sj3d7f5 Thu, 12 Mar 2026 00:00:00 +0000 Singh, Pallavi https://orcid.org/0000-0003-2318-5960 Estrada, Karel https://orcid.org/0000-0002-7671-6959 Gonzalez, Luis Miguel https://orcid.org/0000-0002-9107-2450 Grande, Ricardo Sánchez-Prieto, Sergio https://orcid.org/0000-0001-9903-6203 Cornillot, Emmanuel https://orcid.org/0000-0002-1202-1162 Harb, Omar https://orcid.org/0000-0003-4446-6200 Sanchez-Flores, Alejandro https://orcid.org/0000-0003-0476-3139 Montero, Estrella https://orcid.org/0000-0002-3852-960X Le Roch, Karine G https://orcid.org/0000-0002-4862-9292 Lonardi, Stefano https://orcid.org/0000-0002-2696-7274 Mamoun, Choukri Ben https://orcid.org/0000-0001-5028-1400 https://escholarship.org/uc/item/0h47j4v6 The small interfering RNA (siRNA) pathway directs broad-spectrum antiviral defense through RNA silencing so that virulent infection requires efficient suppression of the defense mechanism. Here, we show that strigolactone (SL) hormone signaling promotes antiviral silencing in rice plants by transcriptional activation of RNA-dependent RNA polymerase 1 (RDR1) and RDR6. We demonstrate that protein P3 of the rice grassy stunt virus (RGSV) blocks SL signaling by directly sequestering the receptor DWARF14 from DWARF3. Structural and functional analyses of the P3-DWARF14 complex reveal that the aspartic acid at position 102 (D102) of DWARF14 is essential for the P3 interaction but not for SL perception. Notably, a single D102N substitution of DWARF14, introduced into two rice cultivars by cytosine base editing (CBE) confers resistance against RGSV by blocking viral suppression of SL signaling-dependent antiviral silencing. Our findings establish a transgene-free strategy for engineering... https://escholarship.org/uc/item/0h47j4v6 Thu, 12 Mar 2026 00:00:00 +0000 Yang, Guoyi Wu, Ming Zhang, Shuai Huang, Yucen Liu, Yixiao Yu, Xiyuan Hu, Jiayang Mi, Le Gan, Peng Wu, Yuansheng Zou, Jing Zhang, Baogang Hu, Qun Hu, Jie Yao, Ruifeng Zhong, Bojian Huang, Xianbo Xie, Huiting Ji, Yinghua Li, Yi Zhang, Jie Yan, Liming Ding, Shou-wei https://orcid.org/0000-0002-4697-8413 Zhao, Shanshan Wu, Jianguo https://escholarship.org/uc/item/0606n5np Nucleotide salvage is crucial for maintaining DNA replication when de novo nucleotide synthesis is limited, but this metabolic flexibility poses potential threats to genome stability. Salvage kinases phosphorylate nucleosides broadly, allowing for oxidized and alkylated 2-deoxynucleosides as well as posttranscriptionally modified ribonucleosides to enter the 2-deoxynucleoside triphosphate (dNTP) pool. The ensuing contamination of the dNTP pool and the subsequent incorporation of modified nucleotides into genomic DNA promote mutagenesis, induce replication stress, elicit double-strand breaks, and disrupt epigenetic signaling. Although only a small subset of modified nucleosides have been assessed for salvage and genomic incorporation, the scope of salvageable substrates is probably much wider, with significant implications in mutational burden, chromatin instability, and epigenetic regulation. This overlooked aspect of genome instability is especially relevant in biological contexts... https://escholarship.org/uc/item/0606n5np Tue, 17 Feb 2026 00:00:00 +0000 Wang, Pengcheng Wang, Chen Wang, Yinsheng https://escholarship.org/uc/item/2j2859sf Abstract Fungi play pivotal roles in terrestrial ecosystems as decomposers, pathogens, and endophytes, yet their significance in marine environments is often understudied. Seagrasses, as globally distributed marine flowering plants, have critical ecological functions, but knowledge about their associated fungal communities remains relatively limited. Previous amplicon surveys of the fungal community associated with the seagrass, Zostera marina have revealed an abundance of potentially novel chytrids. In this study, we employed deep metagenomic sequencing to extract metagenome-assembled genomes (MAGs) from these chytrids and other microbial eukaryotes associated with Z. marina leaves. Our efforts resulted in the recovery of five eukaryotic MAGs, including a single fungal MAG in the order Loubulomycetales (65% BUSCO completeness), three MAGs representing diatoms in the family Bacillariaceae (93%, 70% and 31% BUSCO completeness) and a single MAG representing a haptophyte algae in... https://escholarship.org/uc/item/2j2859sf Wed, 24 Dec 2025 00:00:00 +0000 Ettinger, Cassandra L Eisen, Jonathan A https://orcid.org/0000-0002-0159-2197 Stajich, Jason E https://orcid.org/0000-0002-7591-0020 https://escholarship.org/uc/item/9rx4r1cb Transfer RNA-derived small RNAs (tsRNAs) have emerged as crucial players in diverse biological processes. Yet, their involvement in lipid metabolism and cardiovascular disease remains elusive. Using an advanced PANDORA-seq method, we identify tsRNA-Glu-CTC as the most abundant tsRNA in mouse liver. Intriguingly, tsRNA-Glu-CTC is cholesterol responsive. Overexpression of tsRNA-Glu-CTC elicits hypercholesterolemia and hepatic steatosis, whereas its knockdown protects against diet-induced hypercholesterolemia and atherosclerosis in mice. Mechanistically, tsRNA-Glu-CTC regulates key hepatic lipogenic genes including Srebp2, a master regulator of lipid metabolism. tsRNA-Glu-CTC interacts with SREBP2 to regulate its own transcription through an E-box motif. We further identify site-specific RNA modifications of endogenous tsRNA-Glu-CTC by a mass spectrometry-based MLC-seq and demonstrate the modified tsRNA-Glu-CTC as a more potent regulator of cholesterol homeostasis compared to its... https://escholarship.org/uc/item/9rx4r1cb Mon, 22 Dec 2025 00:00:00 +0000 Li, Xiuchun Hernandez, Rebecca https://orcid.org/0000-0002-8031-2949 Zhang, Xudong Tang, Sijie Yuan, Xiaohong Wu, Jing Pham, Kathy Rawal, Hukam C Heinrich, Erica C Zhang, Shenglong Chen, Qi https://orcid.org/0000-0001-6353-9589 Zhou, Tong Zhou, Changcheng https://escholarship.org/uc/item/86x0713x Abstract Scalable identification of antigen-specific antibodies from whole immune repertoire V(D)J sequences is a central challenge in biomedical engineering. We show that protein language models (PLMs) fine-tuned on antibody heavy-chain sequences can directly predict antigen specificity from unselected immune repertoires. We assessed our model, Antigen Specificity Predictor (ASPred), against SARS-CoV-2, influenza, and HIV-AIDS antigens, observing comparable predictive performance. In the whole immune repertoire V(D)J sequences of mice immunized with the SARS-CoV-2 spike protein’s receptor-binding domain (RBD), ASPred identified antibody sequences specific to RBD. Several candidate sequences were validated, including one as a heavy chain-only nanobody with 20.7 nM dissociation constant. Molecular dynamics simulations supported the predicted interactions at coarse-grained and atomic levels. Benchmarking against Barcode-Enabled Antigen Mapping (BEAM) of B cell receptor sequence... https://escholarship.org/uc/item/86x0713x Thu, 4 Dec 2025 00:00:00 +0000 Paco, Karen Mendivil, Mariana Paco Zhang, Zihao Zebardast, Sanaz Davila, Christian Mooney, Ryan M Olatoyinbo, Peace Yang, Tristan Bassi, Sebastian Gonzalez, Virginia Chen, Eva Bin Ashraf, Faisal Roman, Isabel Condori Felix, Jonathan R Alam, Rashid M Lay, Jordan A Johal, Malkiat S Le Roch, Karine G Tolstorukov, Ilya Hernandez, Jeniffer B da Silva, Fernando L Barroso Lonardi, Stefano https://orcid.org/0000-0002-2696-7274 Sazinsky, Matthew H Ray, Animesh https://escholarship.org/uc/item/6qg0w6sw MOTIVATION: Single-cell Hi-C (scHi-C) technologies have significantly advanced our understanding of the 3D genome organization. However, scHi-C data are often sparse and noisy, leading to substantial computational challenges in downstream analyses. RESULTS: In this study, we introduce SHICEDO, a novel deep-learning model specifically designed to enhance scHi-C contact matrices by imputing missing or sparsely captured chromatin contacts through a generative adversarial framework. SHICEDO leverages the unique structural characteristics of scHi-C matrices to derive customized features that enable effective data enhancement. Additionally, the model incorporates a channel-wise attention mechanism to mitigate the over-smoothing issue commonly associated with scHi-C enhancement methods. Through simulations and real-data applications, we demonstrate that SHICEDO outperforms the state-of-the-art methods, achieving superior quantitative and qualitative results. Moreover, SHICEDO enhances... https://escholarship.org/uc/item/6qg0w6sw Thu, 4 Dec 2025 00:00:00 +0000 Huang, Jingong Ma, Rui Strobel, Michael Hu, Yangyang Ye, Tiantian Jiang, Tao https://orcid.org/0000-0003-3833-4498 Ma, Wenxiu https://orcid.org/0000-0003-4097-1621 https://escholarship.org/uc/item/6mr6m8m5 Alternative splicing plays a crucial role in protein diversity and gene expression regulation in higher eukaryotes, and mutations causing dysregulated splicing underlie a range of genetic diseases. Computational prediction of alternative splicing from genomic sequences not only provides insight into gene-regulatory mechanisms but also helps identify disease-causing mutations and drug targets. However, the current methods for the quantitative prediction of splice site usage still have limited accuracy. Here, we present DeltaSplice, a deep neural network model optimized to learn the impact of mutations on quantitative changes in alternative splicing from the comparative analysis of homologous genes. The model architecture enables DeltaSplice to perform "reference-informed prediction" by incorporating the known splice site usage of a reference gene sequence to improve its prediction on splicing-altering mutations. We benchmarked DeltaSplice and several other state-of-the-art methods... https://escholarship.org/uc/item/6mr6m8m5 Thu, 4 Dec 2025 00:00:00 +0000 Xu, Chencheng Bao, Suying Wang, Ye Li, Wenxing Chen, Hao Shen, Yufeng Jiang, Tao https://orcid.org/0000-0003-3833-4498 Zhang, Chaolin https://escholarship.org/uc/item/6k59b1wr Alternative splicing plays a crucial role in protein diversity and gene expression regulation in higher eukaryotes and mutations causing dysregulated splicing underlie a range of genetic diseases. Computational prediction of alternative splicing from genomic sequences not only provides insight into gene-regulatory mechanisms but also helps identify disease-causing mutations and drug targets. However, the current methods for the quantitative prediction of splice site usage still have limited accuracy. Here, we present DeltaSplice, a deep neural network model optimized to learn the impact of mutations on quantitative changes in alternative splicing from the comparative analysis of homologous genes. The model architecture enables DeltaSplice to perform "reference-informed prediction" by incorporating the known splice site usage of a reference gene sequence to improve its prediction on splicing-altering mutations. We benchmarked DeltaSplice and several other state-of-the-art methods... https://escholarship.org/uc/item/6k59b1wr Thu, 4 Dec 2025 00:00:00 +0000 Xu, Chencheng Bao, Suying Chen, Hao Jiang, Tao https://orcid.org/0000-0003-3833-4498 Zhang, Chaolin https://escholarship.org/uc/item/6qc7389s Infections caused by the emerging pathogenic yeast <i>Clavispora (Candida) lusitaniae</i> can be difficult to manage due to multi-drug resistance. Resistance to the frontline antifungal fluconazole (FLZ) in <i>Candida</i> spp. is commonly acquired through gain-of-function (GOF) mutations in the gene encoding the transcription factor Mrr1. These activated Mrr1 variants enhance FLZ efflux via upregulation of the multi-drug transporter gene <i>MDR1</i>. Recently, it was reported that, unlike in the well-studied <i>Candida albicans</i> species, <i>C. lusitaniae</i> and <i>Candida parapsilosis</i> with activated Mrr1 also have high expression of <i>CDR1</i>, which encodes another multi-drug transporter with overlapping but distinct transported substrate profiles and Cdr1-dependent FLZ resistance. To better understand the mechanisms of Mrr1 regulation of <i>MDR1</i> and <i>CDR1</i>, and other co-regulated genes, we performed Cleavage Under Targets and Release Using Nuclease (CUT&amp;RUN)... https://escholarship.org/uc/item/6qc7389s Fri, 21 Nov 2025 00:00:00 +0000 Rajesh-Khanna, Dhanabala-Subhiksha Páez, Carolina G Piña He, Susu Dolan, Elora G Mirpuri, Kiran S Stajich, Jason E https://orcid.org/0000-0002-7591-0020 Hogan, Deborah A https://escholarship.org/uc/item/5rm3n5ww Specialized metabolites of the herptile gut fungus, Basidiobolus https://escholarship.org/uc/item/5rm3n5ww Fri, 21 Nov 2025 00:00:00 +0000 Neuhaus, George F Trautman, Ian A Tehan, Richard M Vargas-Gastélum, Lluvia Romer, Alexander S Alexander, N Reed Ghotbi, Marjan Moe, Kylie C Shadmani, Leila Tabima, Javier F Stajich, Jason E https://orcid.org/0000-0002-7591-0020 Walker, Donald M Spatafora, Joseph W L.McPhail, Kerry https://escholarship.org/uc/item/59x051c3 BackgroundGenetic and epigenetic perturbation of cis-regulatory sequences can shift patterns of gene expression and result in novel phenotypes. Phased genome assemblies now enable the local dissection of linkages between cis-regulatory sequences, including their epigenetic state, and allele-specific gene expression to further characterize gene regulation and resulting phenotypes in heterozygous genomes.ResultsWe assembled a locally phased genome for a mandarin hybrid named ‘Fairchild’ to explore the molecular signatures of allele-specific gene expression. With local genome phasing, genes with allele-specific expression were paired with haplotype-specific chromatin states, including levels of chromatin accessibility, histone modifications, and DNA methylation. We found that 30% of variation in allele-specific expression could be attributed to haplotype associated factors, with allelic levels of chromatin accessibility and three histone modifications in gene bodies having the most... https://escholarship.org/uc/item/59x051c3 Fri, 21 Nov 2025 00:00:00 +0000 Diaz, Isaac A Ostovar, Talieh Chen, Jinfeng de Dios, Emmanuel Avila Piscatella, Ryan Perez-Alfaro, Ruth S Zayed, Omar Saddoris, Sarah Schmitz, Robert J Wessler, Susan R https://orcid.org/0000-0001-6823-5541 Stajich, Jason E https://orcid.org/0000-0002-7591-0020 Seymour, Danelle K https://escholarship.org/uc/item/22n7x5bt Radical cure of <i>Plasmodium vivax</i> malaria must include elimination of quiescent 'hypnozoite' forms in the liver; however, the only FDA-approved treatments are contraindicated in many vulnerable populations. To identify new drugs and drug targets for hypnozoites, we screened the Repurposing, Focused Rescue, and Accelerated Medchem (ReFRAME) library and a collection of epigenetic inhibitors against <i>P. vivax</i> liver stages. From both libraries, we identified inhibitors targeting epigenetics pathways as selectively active against <i>P. vivax</i> and <i>P. cynomolgi</i> hypnozoites. These include DNA methyltransferase inhibitors as well as several inhibitors targeting histone post-translational modifications. Immunofluorescence staining of <i>Plasmodium</i> liver forms showed strong nuclear 5-methylcystosine signal, indicating liver stage parasite DNA is methylated. Using bisulfite sequencing, we mapped genomic DNA methylation in sporozoites, revealing DNA methylation signals... https://escholarship.org/uc/item/22n7x5bt Thu, 23 Oct 2025 00:00:00 +0000 Maher, Steven P Bakowski, Malina A Vantaux, Amélie Flannery, Erika L Andolina, Chiara Gupta, Mohit Antonova-Koch, Yevgeniya Argomaniz, Magdalena Cabrera-Mora, Monica Campo, Brice Chao, Alexander T Chatterjee, Arnab K Cheng, Wayne T Chuenchob, Vorada Cooper, Caitlin A Cottier, Karissa Galinski, Mary R Harupa-Chung, Anke Ji, Hana Joseph, Sean B Lenz, Todd Lonardi, Stefano https://orcid.org/0000-0002-2696-7274 Matheson, Jessica Mikolajczak, Sebastian A Moeller, Timothy Orban, Agnes Padín-Irizarry, Vivian Pan, Kastin Péneau, Julie Prudhomme, Jacques Roesch, Camille Ruberto, Anthony Sabnis, Saniya S Saney, Celia L Sattabongkot, Jetsumon Sereshki, Saleh Suriyakan, Sangrawee Ubalee, Ratawan Wang, Yinsheng Wasisakun, Praphan Yin, Jiekai Popovici, Jean McNamara, Case W Joyner, Chester Nosten, François H Witkowski, Benoît Le Roch, Karine G Kyle, Dennis E https://escholarship.org/uc/item/9871v4ms This exploratory study surveyed seven contaminated brownfields and Superfund sites in Southern California to identify locally adapted species tolerant of mixed organic and metal contamination under arid and semi-arid conditions. Five novel native plants, including Brickellia californica, Baccharis salicifolia, Baccharis sarothroides, Eriogonum fasciculatum, and Heterotheca grandiflora were identified as hyperaccumulators of copper (Cu), alongside a non-native species from the Asteraceae family, Helminthotheca echioides. Additional metal-accumulating plants (including native plants) for lead (Pb), chromium (Cr), arsenic (As), and nickel (Ni) were identified, and warrant further evaluation for their phytoremediation potential. Dominant microbial communities included fungal taxa from the Ascomycota and bacterial taxa from the Proteobacteria, with bioremediation candidates detected across sites. Redundancy and principal component analyses revealed that site variability, water-extractable... https://escholarship.org/uc/item/9871v4ms Wed, 24 Sep 2025 00:00:00 +0000 Stevenson, Danielle Maltz, Mia R Kurbessoian, Tania Shapiro, Nicholas https://orcid.org/0000-0002-4348-5525 Freund, Linton Aronson, Emma L Stajich, Jason E https://orcid.org/0000-0002-7591-0020 Ying, Samantha C https://escholarship.org/uc/item/0gw6p30w Cell movement and division are complex behaviors driven by a dynamic internal cytoskeleton. The molecular components and principles of cytoskeletal assembly are well studied, but less is known about cytoskeletal remodeling events, including how centrioles transition from ciliary base to centrosome. Here, we address this using the chytrid <i>Rhizoclosmatium globosum,</i> a zoosporic fungus that has centrioles and cilia, lost in most fungal lineages. Chytrids undergo reorganization of their microtubule cytoskeleton as they grow from zoospore to multinucleated coenocyte. We use evolutionary comparison, RNA-sequencing, and expansion microscopy to understand this reorganization and further develop this organism as a model for evolutionary cell biology. We find that when motile zoospores transition to sessile sporangia, cilia are retracted into the cytoplasm and degraded, while centrioles detach from the ciliary axoneme yet persist. During the mitotic cycles, short centrioles are associated... https://escholarship.org/uc/item/0gw6p30w Thu, 11 Sep 2025 00:00:00 +0000 Long, Alexandra F Vasudevan, Krishnakumar Swafford, Andrew JM Venard, Claire M Stajich, Jason E https://orcid.org/0000-0002-7591-0020 Fritz-Laylin, Lillian K Feldman, Jessica L Stearns, Tim https://escholarship.org/uc/item/9zm954ng Designing CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)&nbsp;single&nbsp;guide RNA (sgRNA) libraries targeting entire kingdoms of life will significantly advance genetic research in diverse and underexplored taxa. Current sgRNA design tools are often species-specific and fail to scale to large, phylogenetically diverse datasets, limiting their applicability to comparative genomics, evolutionary studies, and biotechnology. Here, we introduce ALLEGRO, a combinatorial optimization algorithm designed to compose minimal, yet highly effective sgRNA libraries targeting thousands of species at the same time. Leveraging integer linear programming, ALLEGRO identified compact sgRNA sets simultaneously targeting multiple genes of interest for over 2000 species across the fungal kingdom. We experimentally validated sgRNAs designed by ALLEGRO in Kluyveromyces marxianus, Komagataella phaffii, Yarrowia lipolytica, and Saccharomyces cerevisiae, confirming successful genome... https://escholarship.org/uc/item/9zm954ng Thu, 28 Aug 2025 00:00:00 +0000 Mohseni, Amirsadra Nia, Reyhane Ghorbani Tafrishi, Aida López, Mario León Liu, Xin-Zhan Stajich, Jason E https://orcid.org/0000-0002-7591-0020 Lonardi, Stefano https://orcid.org/0000-0002-2696-7274 Wheeldon, Ian https://orcid.org/0000-0002-3492-7539 https://escholarship.org/uc/item/8013r74d The fungus <i>Aspergillus melleus</i> is an important biosynthesis host for varied commercial applications. Gene annotation of a previously published genome produced 12,841 protein-coding genes and identified 102 biosynthetic gene clusters. https://escholarship.org/uc/item/8013r74d Thu, 28 Aug 2025 00:00:00 +0000 Stajich, Jason E https://orcid.org/0000-0002-7591-0020 Garvey, Sean M Gil-Serna, Jéssica https://escholarship.org/uc/item/29f233sj The host microbiome is integral to metabolism, immune function, and pathogen resistance. Yet, reliance on relative abundance in microbiome studies introduces compositional biases that obscure ecological interpretation, while the absence of robust tools for absolute abundance quantification has limited biological discovery. Here, we apply absolute abundance profiling to uncover host-specific microbial patterns across herpetofauna orders that are masked in relative abundance data. Relative- and absolute abundance-derived bacterial and fungal microbiomes exhibit divergent profiles shaped by compositional bias and multifactorial effects. Absolute abundance identified key genera, Lactococcus, Parabacteroides, and Cetobacterium in salamanders, and Basidiobolus and Mortierella in lizards, turtles, snakes, and tortoises, that consistently emerged as core taxa, revealing host-associated patterns previously obscured by compositional constraints. In closely related Desmognathus species,... https://escholarship.org/uc/item/29f233sj Thu, 28 Aug 2025 00:00:00 +0000 Ghotbi, Mitra Stajich, Jason E https://orcid.org/0000-0002-7591-0020 Dallas, Jason W Rurik, Alexander J Cummins, Chloe Vargas-Gastélum, Lluvia Ghotbi, Marjan Spatafora, Joseph W Kelly, Kian Alexander, Nicholas Reed Moe, Kylie C Syring, Kimberly C Shadmani, Leila Perez-Marron, Julissa Walker, Donald M https://escholarship.org/uc/item/0np4q6kp Fungal secondary metabolites (SMs) are complex organic compounds comprising a variety of biological activities that are essential in medicine. These natural products can be found in various environments, with studies demonstrating the importance of studying marine-sourced fungi due to the increased potency of the compounds they produce. In this study, we sourced a <i>Penicillium rubens</i> YAP001 strain isolated from <i>Exaiptasia diaphana</i> and explored an avenue for the upregulation of its SMs by combining the one-strain-many-compounds (OSMAC) strategy with genetic manipulation of negative global regulator of secondary metabolism, <i>mcrA</i>. Here, we generated a <i>mcrA</i>Δ strain of marine <i>P. rubens</i> (YAP001), which led to the detection of sorbicillinoids, which is significant due to the prior discovery that these compounds illicit cytotoxic effects that have the potential as an anticancer agent. Specifically, we found that sorbicillin was not only upregulated but... https://escholarship.org/uc/item/0np4q6kp Thu, 28 Aug 2025 00:00:00 +0000 Shyong, Jennifer Huynh, Quoc-Dung Tran Dziedzic, Stella Aguirre, Emily Rabot, Chris Yuan, Bo Herrero-MacKenzie, Hugo Edward Stajich, Jason E https://orcid.org/0000-0002-7591-0020 Lee, Ching-Kuo Kenkel, Carly D Wang, Clay CC https://escholarship.org/uc/item/0n5635cx Predicting antibody-antigen interactions is a critical step in developing new therapeutics to defend against viral infections. However, measuring the extent of these interactions <i>in vitro</i> is costly and time-consuming. With the increased availability of experimental data, predictive methods using machine learning, particularly large language models (LLMs), have emerged as a powerful alternative to wet lab experiments. Here we focus on antibodies targeting SARS-CoV-2 variants, given the abundance of data on this highly contagious virus and the impact of COVID-19 on human life. The objective of this work is to predict the binding and the neutralizing properties of SARS-CoV-2 antibodies. While there are many studies on predicting binding, to the best of our knowledge, we are the first to address the problem of predicting the neutralizing properties of SARS-CoV-2 antibodies. Here we propose a new classifier that combines LLMs with structural information. Extensive experimental... https://escholarship.org/uc/item/0n5635cx Thu, 28 Aug 2025 00:00:00 +0000 Bin Ashraf, Faisal Madrigal, Vinz Angelo Lonardi, Stefano https://orcid.org/0000-0002-2696-7274 https://escholarship.org/uc/item/9mq2t4vd Phyling is a fast, scalable, and user-friendly tool supporting phylogenomic reconstruction of species phylogenies directly from protein-encoded genomic data. It identifies orthologous genes by searching a sample's protein sequences against a Hidden Markov Models marker set, containing single-copy orthologs, retrieved from the BUSCO database. In the final step, users can choose between consensus and concatenation strategies to construct the species tree from the aligned orthologs. Phyling efficiently resolves large phylogenies by optimizing memory usage and data processing. Its checkpoint system enables users to incrementally add or remove samples without repeating the entire search process. For analyses involving closely related taxa, Phyling supports the use of nucleotide coding sequences, which may capture phylogenetic signals missed by protein sequences. The benchmark results show that Phyling substantially runs faster than OrthoFinder, a Reciprocal Best Hit based method, while... https://escholarship.org/uc/item/9mq2t4vd Thu, 14 Aug 2025 00:00:00 +0000 Tsai, Cheng-Hung Stajich, Jason E https://orcid.org/0000-0002-7591-0020 https://escholarship.org/uc/item/87g2x4ph Fungal infections are difficult to prevent and treat in large part due to strain heterogeneity, which confounds diagnostic predictability. Yet, the genetic mechanisms driving strain-to-strain variation remain poorly understood. Here, we determined the extent to which <i>Starships</i>-giant transposons capable of mobilizing numerous fungal genes-generate genetic and phenotypic variability in the opportunistic human pathogen <i>Aspergillus fumigatus</i>. We analyzed 519 diverse strains, including 11 newly sequenced with long-read technology and multiple isolates of the same reference strain, to reveal 20 distinct <i>Starships</i> that are generating genomic heterogeneity over timescales relevant for experimental reproducibility. <i>Starship</i>-mobilized genes encode diverse functions, including known biofilm-related virulence factors and biosynthetic gene clusters, and many are differentially expressed during infection and antifungal exposure in a strain-specific manner. These... https://escholarship.org/uc/item/87g2x4ph Thu, 14 Aug 2025 00:00:00 +0000 Gluck-Thaler, Emile Forsythe, Adrian Puerner, Charles Gutierrez-Perez, Cecilia Stajich, Jason E https://orcid.org/0000-0002-7591-0020 Croll, Daniel Cramer, Robert A Vogan, Aaron A https://escholarship.org/uc/item/4xv1q5b2 The Fifth International Symposium on Fungal Stress (ISFUS) brought together in Brazil many of the leaders in the field of fungal stress responses, from fourteen countries, for four days of outstanding science ranging from basic research to studies with agricultural, medical, industrial, and environmental significance. In addition to the excellent oral and poster presentations, the Symposium organisers ensured that all participants had ample opportunity to engage, socialise, and network to exchange ideas and share research. The conference was enhanced by the world-class venue near Iguazu Falls, probably the greatest natural phenomenon in South America. https://escholarship.org/uc/item/4xv1q5b2 Thu, 14 Aug 2025 00:00:00 +0000 Alder-Rangel, Alene Rangel, Amanda EA Casadevall, Arturo Gusa, Asiya Xue, Chaoyang Boone, Charles M Hittinger, Chris Todd Masuda, Claudio A Olivares-Yañez, Consuelo Bell-Pedersen, Deborah Washington, Erica J Braus, Gerhard Janbon, Guilhem Pócsi, István Stajich, Jason E https://orcid.org/0000-0002-7591-0020 Dunlap, Jay C Bennett, Joan W Heitman, Joseph Lu, Ling Landi, Lucia Shinohara, Mari L Del Poeta, Maurizio Acheampong, Mavis A Maltz, Mia R Lorenz, Michael C Nowrousian, Minou Glass, N Louise Broderick, Nichole A Pedrini, Nicolás Osherov, Nir Billmyre, R Blake Sarrocco, Sabrina LeibundGut-Landmann, Salomé Vicente, Vânia Aparecida Lin, Xiaorong Zhao, Xin-Qing Bahn, Yong-Sun Lewis, Zachary A Rangel, Drauzio EN https://escholarship.org/uc/item/4032v498 The cyanosphere contains heterotrophic microorganisms living within the exopolysaccharide sheath of cyanobacteria and serves as an interface between the cyanobacteria and their surrounding ecosystem. The symbiosis between the cyanobacterial host and its cyanosphere microbes spans the mutualistic-antagonistic spectrum. Understanding these relationships will predict the success of terrestrial cyanobacteria and the ecosystem services they provide including primary production in often oligotrophic environments. However, our understanding of the microbial diversity within the cyanosphere is limited. In this study, we used metagenomic sequencing to construct 528 metagenome-assembled genomes (MAGs) from the cyanosphere microbes associated with 50 unialgal terrestrial Cyanobacteria cultures, spanning 12 orders. We found that the composition of cyanosphere microbial communities was unique between Cyanobacteria hosts and was largely influenced by environmental (habitat, precipitation, and... https://escholarship.org/uc/item/4032v498 Thu, 14 Aug 2025 00:00:00 +0000 Pietrasiak, Nicole Palmer, Brianne Couradeau, Estelle Stajich, Jason https://orcid.org/0000-0002-7591-0020 https://escholarship.org/uc/item/3jb343fd The fungus <i>Conoideocrella luteorostrata</i> is a recently discovered pathogen of invasive elongate hemlock scale insects (EHS; <i>Fiorinia externa</i>) in Christmas tree farms in the eastern U.S. Here, we report a scaffold-level genome and assembly along with an initial survey of biosynthetic gene clusters for strain ARSEF 14590 from EHS. https://escholarship.org/uc/item/3jb343fd Thu, 14 Aug 2025 00:00:00 +0000 Lovett, Brian Stajich, Jason E https://orcid.org/0000-0002-7591-0020 Barrett, Hana Kasson, Lindsay R Panaccione, Daniel G Reiter, Cecilia A Fuss, Jessica L Biddle, Gregory Kasson, Matt T https://escholarship.org/uc/item/2nv0796d A draft genome sequence was assembled and annotated for an uncultured archaeon reconstructed from shotgun metagenomes obtained from Antarctic endoliths. The assembled genome is 1.99 megabases and encodes 2,405 predicted protein-coding genes. This genome sequence provides insights into the microbial diversity and functional potential of extremophiles inhabiting Antarctic rock environments. https://escholarship.org/uc/item/2nv0796d Thu, 14 Aug 2025 00:00:00 +0000 Coleine, Claudia Micheletti, Diego Pindo, Massimo Larger, Simone Stefani, Erika Biagioli, Federico Stajich, Jason E https://orcid.org/0000-0002-7591-0020 Donati, Claudio https://escholarship.org/uc/item/0f26j0r6 Did you know that fungi, like mushrooms and molds, are super important for our planet? Fungi can form critical relationships with other organisms. For example, many plants rely on fungi to help them grow and thrive. However, fungi are not always friendly and sometimes they can hurt plants by causing disease. Did you also know that there are fungi in the ocean? While you might not be able to see these fungi when you go to the beach (because they can only be seen with a microscope), they are found everywhere in the ocean. Marine fungi are pretty cool, but we do not know a lot about them yet or what roles they play in the ocean. Scientists are starting to learn more about how marine fungi help the ocean and keep our planet healthy. This article will explore the amazing world of marine fungi! https://escholarship.org/uc/item/0f26j0r6 Thu, 14 Aug 2025 00:00:00 +0000 Arroyo, Jennifer Stajich, Jason E https://orcid.org/0000-0002-7591-0020 Ettinger, Cassie L https://escholarship.org/uc/item/9fs9w67h The increase in the incidence of obesity has coincided with changes in lifestyle, diet, and environment. Comorbidities associated with obesity include cardiovascular disease, diabetes, musculoskeletal disorders, stroke, and thromboembolism, affecting public health. The effect of increased weight has recently become even more obvious, since obesity has been significantly associated with increased severity and higher mortality among COVID-19 patients. The need to decrease rates of obesity prompted a surge in the use of glucagon-like peptide-1 agonist medications. Twin studies, however, determined that increased weight has a large genetic component, estimating the heritability of obesity to be 45% to 70%. Surprisingly, obesity due to known single gene mutation comprises only 5% to 10% of individuals, who mostly exhibit early-onset severe obesity. Genome-wide linkage studies and association studies identified more than 250 genes associated with obesity, but each of these has a relatively... https://escholarship.org/uc/item/9fs9w67h Mon, 4 Aug 2025 00:00:00 +0000 Ruggiero-Ruff, Rebecca E Coss, Djurdjica https://orcid.org/0000-0003-0692-1612 https://escholarship.org/uc/item/2nd2352b The highly repetitive content of eukaryotic genomes, including long tandem repeats, segmental duplications, and centromeres, makes haplotype-resolved genome assembly hard. Repeat sequences introduce gaps or mis-joins in the assemblies. We introduce TRFill, a novel algorithm that can close the gaps in a draft chromosome-level assembly using exclusively PacBio HiFi and Hi-C data. Experimental results on human centromeres and tomato subtelomeres show that TRFill can improve the completeness and correctness of about two-thirds of the tandem repeats. We also show that the improved completeness of subtelomeric tandem repeats in the tomato pangenome enables a population-level analysis of these complex repeats. https://escholarship.org/uc/item/2nd2352b Thu, 31 Jul 2025 00:00:00 +0000 Wen, Huaming Yang, Jinbao Zhao, Xianjia Wang, Xingbin Lei, Jiawei Li, Yanchun Du, Wenjie Li, Dongxi Xu, Yun Lonardi, Stefano https://orcid.org/0000-0002-2696-7274 Pan, Weihua https://escholarship.org/uc/item/6dr135jj The phytochrome B (phyB) photoreceptor and EARLY FLOWERING 3 (ELF3) are two major plant thermosensors that monitor high temperatures primarily at night. However, high temperatures naturally occur during the daytime; the mechanism of daytime thermosensing and whether these thermosensors can also operate under intense sunlight remain ambiguous. Here, we show that phyB plays a substantial role in daytime thermosensing in Arabidopsis, and its thermosensing function becomes negligible only when the red light intensity reaches 50 μmol m−2 s−1. Leveraging this restrictive condition for phyB thermosensing, we reveal that triggering daytime thermomorphogenesis requires two additional thermosensory pathways. High temperatures induce starch breakdown in chloroplasts and the production of sucrose, which stabilizes the central thermal regulator PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) by antagonizing phyB-dependent PIF4 degradation. In parallel, high temperatures release the inhibition of PIF4... https://escholarship.org/uc/item/6dr135jj Thu, 19 Jun 2025 00:00:00 +0000 Fan, De https://orcid.org/0009-0001-9154-8949 Hu, Wei https://orcid.org/0000-0001-9602-1428 Xu, Nan Seto, Ethan R Lagarias, John Clark https://orcid.org/0000-0002-2093-0403 Chen, Xuemei https://orcid.org/0000-0002-5209-1157 Chen, Meng https://orcid.org/0000-0003-0351-5897 https://escholarship.org/uc/item/7w9981gk The Global Panzootic Lineage (GPL) of Batrachochytrium dendrobatidis (Bd) has been described as a main driver of amphibian extinctions. Pathogen studies have benefited from three Bd-GPL strain genomes, but identifying the genetic and molecular features that distinguish the B. dendrobatidis lineages requires additional high-quality genomes from diverse lineages. We sequenced and assembled genomes with Oxford Nanopore Technologies to produce assemblies of three Bd-BRAZIL isolates and one nonpathogen outgroup species Polyrhizophydium stewartii. The Bd-BRAZIL assembly sizes ranged between 22.0 and 26.1 Mb with 8,495 to 8,620 predicted protein-coding genes. We sought to categorize the pangenome of the species by identifying homologous genes across the sampled genomes as either being core and present in all strains, or accessory and shared among strains in a lineage, an analysis that has not yet been conducted on B. dendrobatidis and its lineages. We identified a core genome consisting... https://escholarship.org/uc/item/7w9981gk Thu, 5 Jun 2025 00:00:00 +0000 Yacoub, Mark N Stajich, Jason E https://orcid.org/0000-0002-7591-0020 https://escholarship.org/uc/item/4dd6s394 The genus Aspergillus is diverse, including species of industrial importance, human pathogens, plant pests, and model organisms. Aspergillus includes species from sections Usti and Cavernicolus, which until recently were joined in section Usti, but have now been proposed to be non-monophyletic and were split by section Nidulantes, Aenei and Raperi. To learn more about these sections, we have sequenced the genomes of 13 Aspergillus species from section Cavernicolus (A. cavernicola, A. californicus, and A. egyptiacus), section Usti (A. carlsbadensis, A. germanicus, A. granulosus, A. heterothallicus, A. insuetus, A. keveii, A. lucknowensis, A. pseudodeflectus and A. pseudoustus), and section Nidulantes (A. quadrilineatus, previously A. tetrazonus). We compared these genomes with 16 additional species from Aspergillus to explore their genetic diversity, based on their genome content, repeat-induced point mutations (RIPs), transposable elements, carbohydrate-active enzyme (CAZyme)... https://escholarship.org/uc/item/4dd6s394 Thu, 22 May 2025 00:00:00 +0000 Nybo, JL Vesth, TC Theobald, S Frisvad, JC Larsen, TO Kjaerboelling, I Rothschild-Mancinelli, K Lyhne, EK Barry, K https://orcid.org/0000-0002-8999-6785 Clum, A Yoshinaga, Y https://orcid.org/0000-0002-4978-9394 Ledsgaard, L Daum, C https://orcid.org/0000-0003-3895-5892 Lipzen, A https://orcid.org/0000-0003-2293-9329 Kuo, A Riley, R https://orcid.org/0000-0003-0224-0975 Mondo, S https://orcid.org/0000-0001-5797-0647 Labutti, K https://orcid.org/0000-0002-5838-1972 Haridas, S Pangalinan, J Salamov, AA Simmons, BA https://orcid.org/0000-0002-1332-1810 Magnuson, JK Chen, J Drula, E Henrissat, B Wiebenga, A Lubbers, RJM Müller, A dos Santos Gomes, AC Mäkelä, MR Stajich, JE https://orcid.org/0000-0002-7591-0020 Grigoriev, IV Mortensen, UH de Vries, RP Baker, SE Andersen, MR https://escholarship.org/uc/item/5kt560ff Genetic linkage maps are an essential tool in population genetics and plant breeding research, yet user-friendly online tools for constructing and visualizing them remain scarce. MSTmap Online addresses this gap by providing a modern, accessible platform for generating high-quality genetic linkage maps from genotypic data. The web server quickly computes linkage groups using the MSTmap algorithm and generates detailed output files, including publication-ready PDF visualizations of linkage groups. The server supports bookmarking and asynchronous processing, allowing users to revisit their results at a later time. A companion Python library for MSTmap Online enables seamless integration into custom analysis pipelines. MSTmap Online is free and open to all users with no login requirement at https://mstmap.org. The companion Python library is available at https://pypi.org/project/mstmap/. https://escholarship.org/uc/item/5kt560ff Thu, 8 May 2025 00:00:00 +0000 Mohseni, Amirsadra Lonardi, Stefano https://orcid.org/0000-0002-2696-7274 https://escholarship.org/uc/item/5676g8fj The genus <i>Aspergillus</i> is diverse, including species of industrial importance, human pathogens, plant pests, and model organisms. <i>Aspergillus</i> includes species from sections <i>Usti</i> and <i>Cavernicolus</i>, which until recently were joined in section <i>Usti</i>, but have now been proposed to be non-monophyletic and were split by section <i>Nidulantes, Aenei</i> and <i>Raperi</i>. To learn more about these sections, we have sequenced the genomes of 13 <i>Aspergillus</i> species from section <i>Cavernicolus</i> (<i>A. cavernicola, A. californicus</i>, and <i>A. egyptiacus</i>), section <i>Usti</i> (<i>A. carlsbadensis, A. germanicus, A. granulosus, A. heterothallicus, A. insuetus, A. keveii, A. lucknowensis, A. pseudodeflectus</i> and <i>A. pseudoustus</i>), and section <i>Nidulantes</i> (<i>A. quadrilineatus</i>, previously <i>A. tetrazonus</i>). We compared these genomes with 16 additional species from <i>Aspergillus</i> to explore their genetic diversity, based... https://escholarship.org/uc/item/5676g8fj Thu, 8 May 2025 00:00:00 +0000 Nybo, JL Vesth, TC Theobald, S Frisvad, JC Larsen, TO Kjaerboelling, I Rothschild-Mancinelli, K Lyhne, EK Barry, K https://orcid.org/0000-0002-8999-6785 Clum, A Yoshinaga, Y Ledsgaard, L Daum, C Lipzen, A https://orcid.org/0000-0003-2293-9329 Kuo, A https://orcid.org/0000-0003-3514-3530 Riley, R Mondo, S LaButti, K https://orcid.org/0000-0002-5838-1972 Haridas, S Pangalinan, J Salamov, AA Simmons, BA https://orcid.org/0000-0002-1918-3463 Magnuson, JK Chen, J Drula, E Henrissat, B Wiebenga, A Lubbers, RJM Müller, A dos Santos Gomes, AC Mäkelä, MR Stajich, JE https://orcid.org/0000-0002-7591-0020 Grigoriev, IV https://orcid.org/0000-0002-3136-8903 Mortensen, UH de Vries, RP Baker, SE Andersen, MR https://escholarship.org/uc/item/70f247vt Ribonucleases (RNases) are ubiquitous enzymes that process or degrade RNA, essential for cellular functions and immune responses. The EndoU-like superfamily includes endoribonucleases conserved across bacteria, eukaryotes, and certain viruses, with an ancient evolutionary link to the ribonuclease A-like superfamily. Both bacterial EndoU and animal RNase A share a similar fold and function independently of cofactors. In contrast, the eukaryotic EndoU catalytic domain requires divalent metal ions for catalysis, possibly due to an N-terminal extension near the catalytic core. In this study, we use biophysical and computational techniques along with in vitro assays to investigate the calcium-dependent activation of human EndoU. We determine the crystal structure of EndoU bound to calcium and find that calcium binding remote from the catalytic triad triggers water-mediated intramolecular signaling and structural changes, activating the enzyme through allostery. Calcium binding involves... https://escholarship.org/uc/item/70f247vt Mon, 14 Apr 2025 00:00:00 +0000 Malard, Florian Dias, Kristen Baudy, Margaux Thore, Stéphane Vialet, Brune Barthélémy, Philippe Fribourg, Sébastien Karginov, Fedor V Campagne, Sébastien https://escholarship.org/uc/item/5p66p8pw The advent of 5' single-cell RNA sequencing (scRNA-seq) technologies offers unique opportunities to identify and analyze transcription start sites (TSSs) at a single-cell resolution. These technologies have the potential to uncover the complexities of transcription initiation and alternative TSS usage across different cell types and conditions. Despite the emergence of computational methods designed to analyze 5' RNA sequencing data, current methods often lack comparative evaluations in single-cell contexts and are predominantly tailored for paired-end data, neglecting the potential of single-end data. This study introduces scTSS, a computational pipeline developed to bridge this gap by accommodating both paired-end and single-end 5' scRNA-seq data. scTSS enables joint analysis of multiple single-cell samples, starting with TSS cluster prediction and quantification, followed by differential TSS usage analysis. It employs a Binomial generalized linear mixed model to accurately... https://escholarship.org/uc/item/5p66p8pw Mon, 14 Apr 2025 00:00:00 +0000 Fu, Shiwei Li, Wei Vivian https://orcid.org/0000-0002-2087-2709 https://escholarship.org/uc/item/40t039sd Alkyl phosphotriester (alkyl-PTE) lesions in DNA are shown to be poorly repaired; however, little is known about how these lesions impact DNA replication in human cells. Here, we investigated how the <i>S</i>_P and <i>R</i>_P diastereomers of four alkyl-PTE lesions (alkyl = Me, Et, <i>n</i>Pr, or <i>n</i>Bu) at the TT site perturb DNA replication in HEK293T cells. We found that these lesions moderately impede DNA replication and that their replicative bypass is accurate. Moreover, CRISPR-Cas9-mediated depletion of Pol η or Pol ζ resulted in significantly attenuated bypass efficiencies for both diastereomers of <i>n</i>Pr- and <i>n</i>Bu-PTE adducts, and the <i>S</i>_P diastereomer of Et-PTE. Diminished bypass efficiencies were also detected for the <i>R</i>_p diastereomer of <i>n</i>Pr- and <i>n</i>Bu-PTE lesions upon ablation of Pol κ. Together, our study uncovered the impact of the alkyl-PTE lesions on DNA replication in human cells and... https://escholarship.org/uc/item/40t039sd Tue, 1 Apr 2025 00:00:00 +0000 Wu, Jun Wu, Jiabin Clabaugh, Garrit Wang, Yinsheng https://escholarship.org/uc/item/1rr587dw Graph theory, a branch of mathematics that focuses on the study of graphs (networks of nodes and edges), provides a robust framework for analysing the structural and functional properties of biomolecules. By leveraging molecular dynamics (MD) simulations, atoms or groups of atoms can be represented as nodes, while their dynamic interactions are depicted as edges. This network-based approach facilitates the characterization of properties such as connectivity, centrality, and modularity, which are essential for understanding the behaviour of molecular systems. This review details the application and development of graph theory-based models in studying biomolecular systems. We introduce key concepts in graph theory and demonstrate their practical applications, illustrating how innovative graph theory approaches can be employed to design biomolecular systems with enhanced functionality. Specifically, we explore the integration of graph theoretical methods with MD simulations to gain... https://escholarship.org/uc/item/1rr587dw Tue, 1 Apr 2025 00:00:00 +0000 Patel, Amun C Sinha, Souvik Palermo, Giulia https://orcid.org/0000-0003-1404-8737 https://escholarship.org/uc/item/3f44p87z Repetitive regions in eukaryotic genomes often contain important functional or regulatory elements. Despite significant algorithmic and technological advancements in genome sequencing and assembly over the past three decades, modern de novo assemblers still struggle to accurately reconstruct highly repetitive regions. In this work, we introduce RAmbler (Repeat Assembler), a reference-guided assembler specialized for the assembly of complex repetitive regions exclusively from Pacific Biosciences (PacBio) HiFi reads. RAmbler (1) identifies repetitive regions by detecting unusually high coverage regions after mapping HiFi reads to the draft genome assembly, (2) finds single-copy <i>k</i>-mers from the HiFi reads, (i.e., <i>k</i>-mers that are expected to occur only once in the genome), (3) uses the relative location of single-copy <i>k</i>-mers to barcode each HiFi read, (4) clusters HiFi reads based on their shared barcodes, (5) generates contigs by assembling the reads in each... https://escholarship.org/uc/item/3f44p87z Thu, 27 Mar 2025 00:00:00 +0000 Chakravarty, Sakshar Logsdon, Glennis Lonardi, Stefano https://orcid.org/0000-0002-2696-7274 https://escholarship.org/uc/item/2hd4w7c4 DNA methylation is an epigenetic marker that directly or indirectly regulates several critical cellular processes. While cytosines in mammalian genomes generally maintain stable methylation patterns over time, other cytosines that belong to specific regulatory regions, such as promoters and enhancers, can exhibit dynamic changes. These changes in methylation are driven by a complex cellular machinery, in which the enzymes DNMT3 and TET play key roles. The objective of this study is to design a machine learning model capable of accurately predicting which cytosines have a fluctuating methylation level [hereafter called differentially methylated cytosines (DMCs)] from the surrounding DNA sequence. Here, we introduce L-MAP, a transformer-based large language model that is trained on DNMT3-knockout and TET-knockout data in human and mouse embryonic stem cells. Our extensive experimental results demonstrate the high accuracy of L-MAP in predicting DMCs. Our experiments also explore... https://escholarship.org/uc/item/2hd4w7c4 Thu, 27 Mar 2025 00:00:00 +0000 Sereshki, Saleh Lonardi, Stefano https://orcid.org/0000-0002-2696-7274 https://escholarship.org/uc/item/2wr0z6pv xCas9 is an evolved variant of the CRISPR-Cas9 genome editing system, engineered to improve specificity and reduce undesired off-target effects. How xCas9 expands the DNA targeting capability of Cas9 by recognising a series of alternative protospacer adjacent motif (PAM) sequences while ignoring others is unknown. Here, we elucidate the molecular mechanism underlying xCas9's expanded PAM recognition and provide critical insights for expanding DNA targeting. We demonstrate that while wild-type Cas9 enforces stringent guanine selection through the rigidity of its interacting arginine dyad, xCas9 introduces flexibility in R1335, enabling selective recognition of specific PAM sequences. This increased flexibility confers a pronounced entropic preference, which also improves recognition of the canonical TGG PAM. Furthermore, xCas9 enhances DNA binding to alternative PAM sequences during the early evolution cycles, while favouring binding to the canonical PAM in the final evolution... https://escholarship.org/uc/item/2wr0z6pv Mon, 3 Mar 2025 00:00:00 +0000 Hossain, Kazi A Nierzwicki, Lukasz Orozco, Modesto Czub, Jacek Palermo, Giulia https://orcid.org/0000-0003-1404-8737 https://escholarship.org/uc/item/2nv9q0hw Pseudouridine (Ψ) is the most abundant RNA modification in nature; however, not much is known about the biological functions of this modified nucleoside. Employing an unbiased quantitative proteomics method, we identified multiple candidate reader proteins of Ψ in RNA, including a cytoskeletal protein profilin-1 (PFN1). We demonstrated that PFN1 binds directly and selectively to Ψ-containing RNA. Additionally, we discovered approximately 4000 binding sites of PFN1 in human cells, including a known dyskerin (DKC1)-installed Ψ site in <i>TPI1</i> mRNA, which encodes triosephosphate isomerase. Moreover, we showed that PFN1 and DKC1 are crucial for regulating the stability and translation efficiency of <i>TPI1</i> mRNA through modulating PFN1-Ψ interaction. Together, we identified PFN1 as a reader protein of Ψ in RNA and illustrated a potential role of PFN1-Ψ interaction in post-transcriptional regulation. These findings provide new insights into the functions of Ψ in RNA biology... https://escholarship.org/uc/item/2nv9q0hw Sat, 1 Mar 2025 00:00:00 +0000 Wei, Songbo Dai, Xiaoxia Yuan, Jun https://orcid.org/0000-0002-6240-7151 He, Shiyang Shah, Kriti Guo, Shiyuan Duan, Zheng Murn, Jernej Wang, Yinsheng https://escholarship.org/uc/item/62t1b57z Programmed-cell death is an antimicrobial defense mechanism that promotes clearance of intracellular pathogens. Toxoplasma counteracts host immune defenses by secreting effector proteins into host cells; however, how the parasite evades lytic cell death and the effectors involved remain poorly characterized. We identified ROP55, a rhoptry protein that promotes parasite survival by preventing lytic cell death in absence of IFN-γ stimulation. RNA-Seq analysis revealed that ROP55 acts as a repressor of host pro-inflammatory responses. In THP-1 monocytes ΔROP55 infection increased NF-κB p65 nuclear translocation, IL-1β production, and GSDMD cleavage compared to wild type or complemented parasites. ΔROP55 infection also induced RIPK3-dependent necroptosis in human and mouse primary macrophages. Moreover, ΔROP55 parasites were significantly impaired in virulence in female mice and prevented NF-κB activation and parasite clearance in mBMDM. These findings place ROP55 as a major virulence... https://escholarship.org/uc/item/62t1b57z Thu, 27 Feb 2025 00:00:00 +0000 Grilo Ruivo, Margarida T Shin, Ji-hun Lenz, Todd Matsuno, Stephanie Y Yanes, Katherine Olivia Graindorge, Arnault Hamie, Maguy Berry-Sterkers, Laurence Gissot, Mathieu El Hajj, Hiba Le Roch, Karine G https://orcid.org/0000-0002-4862-9292 Lodoen, Melissa B https://orcid.org/0000-0002-3366-6840 Lebrun, Maryse Penarete-Vargas, Diana Marcela https://escholarship.org/uc/item/06q7w44r Abstract Colletotrichum spp. have a complicated history of association with land plants. Perhaps most well-known as plant pathogens for the devastating effect they can have on agricultural crops, some Colletotrichum spp. have been reported as beneficial plant endophytes. However, there have been only a handful of reports of Colletotrichum spp. isolated from aquatic plant hosts and their ecological role in the marine ecosystem is underexplored. To address this, we present the draft genome and annotation of Colletotrichum sp. CLE4, previously isolated from rhizome tissue from the seagrass Zostera marina . This genome (48.03 Mbp in length) is highly complete (BUSCO ascomycota: 98.8%) and encodes 12,015 genes, of which 5.7% are carbohydrate-active enzymes (CAZymes) and 12.6% are predicted secreted proteins. Phylogenetic placement puts Colletotrichum sp. CLE4 within the C. acutatum complex, closely related to C. godetiae . We found a 8.69% smaller genome size, 21.90% smaller gene... https://escholarship.org/uc/item/06q7w44r Mon, 10 Feb 2025 00:00:00 +0000 Ettinger, Cassandra L Eisen, Jonathan A https://orcid.org/0000-0002-0159-2197 Stajich, Jason E https://orcid.org/0000-0002-7591-0020 https://escholarship.org/uc/item/8kg3d133 The exploration of our solar system for microbial extraterrestrial life is the primary goal of several space agencies. Mars has attracted substantial attention owing to its Earth-like geological history and potential niches for microbial life. This study evaluated the suitability of the polyextremophilic fungal strain <i>Rhinocladiella similis</i> LaBioMMi 1217 as a model eukaryote for astrobiology. Comprehensive genomic analysis, including taxonomic and functional characterization, revealed several <i>R. similis</i> genes conferring resistance to Martian-like stressors, such as osmotic pressure and ultraviolet radiation. When cultured in a synthetic Martian regolith (MGS-1), <i>R. similis</i> exhibited altered morphology and produced unique metabolites, including oxylipins, indolic acid derivatives, and siderophores, which might be potential biosignatures. Notably, oxylipins were detected using laser desorption ionization mass spectrometry, a technique slated for its use in the... https://escholarship.org/uc/item/8kg3d133 Thu, 6 Feb 2025 00:00:00 +0000 dos Santos, Alef Schultz, Júnia Dal’Rio, Isabella Molodon, Fluvio Trapp, Marilia Almeida Tenório, Bernardo Guerra Stajich, Jason E https://orcid.org/0000-0002-7591-0020 de Melo Teixeira, Marcus Pilau, Eduardo Jorge Rosado, Alexandre Soares Rodrigues-Filho, Edson https://escholarship.org/uc/item/52920703 Multicellular organisms control environmental interactions through specialized barriers in specific cell types. A conserved barrier in plant roots is the endodermal Casparian strip (CS), a ring-like structure made of polymerized lignin that seals the endodermal apoplastic space. Most angiosperms have another root cell type, the exodermis, that is reported to form a barrier. Our understanding of exodermal developmental and molecular regulation and function is limited as this cell type is absent from Arabidopsis thaliana. We demonstrate that in tomato (Solanum lycopersicum), the exodermis does not form a CS. Instead, it forms a polar lignin cap (PLC) with equivalent barrier function to the endodermal CS but distinct genetic control. Repression of the exodermal PLC in inner cortical layers is conferred by the SlSCZ and SlEXO1 transcription factors, and these two factors genetically interact to control its polar deposition. Several target genes that act downstream of SlSCZ and SlEXO1... https://escholarship.org/uc/item/52920703 Wed, 5 Feb 2025 00:00:00 +0000 Manzano, Concepcion Morimoto, Kevin W Shaar-Moshe, Lidor Mason, G Alex Cantó-Pastor, Alex Gouran, Mona De Bellis, Damien Ursache, Robertas Kajala, Kaisa Sinha, Neelima https://orcid.org/0000-0002-1494-7065 Bailey-Serres, Julia https://orcid.org/0000-0002-8568-7125 Geldner, Niko del Pozo, J Carlos Brady, Siobhan M https://orcid.org/0000-0001-9424-8055 https://escholarship.org/uc/item/0z5275h1 Conventionally, the size, shape, and biomechanics of cartilages are determined by their voluminous extracellular matrix. By contrast, we found that multiple murine cartilages consist of lipid-filled cells called lipochondrocytes. Despite resembling adipocytes, lipochondrocytes were molecularly distinct and produced lipids exclusively through de novo lipogenesis. Consequently, lipochondrocytes grew uniform lipid droplets that resisted systemic lipid surges and did not enlarge upon obesity. Lipochondrocytes also lacked lipid mobilization factors, which enabled exceptional vacuole stability and protected cartilage from shrinking upon starvation. Lipid droplets modulated lipocartilage biomechanics by decreasing the tissue's stiffness, strength, and resilience. Lipochondrocytes were found in multiple mammals, including humans, but not in nonmammalian tetrapods. Thus, analogous to bubble wrap, superstable lipid vacuoles confer skeletal tissue with cartilage-like properties without "packing... https://escholarship.org/uc/item/0z5275h1 Wed, 29 Jan 2025 00:00:00 +0000 Ramos, Raul Pham, Kim T Prince, Richard C Leiser-Miller, Leith B Prasad, Maneeshi S Wang, Xiaojie https://orcid.org/0000-0003-4817-5830 Nordberg, Rachel C https://orcid.org/0000-0001-6047-6009 Bielajew, Benjamin J Hu, Jerry C Yamaga, Kosuke Oh, Ji Won Peng, Tao Datta, Rupsa Astrowskaja, Aksana Almet, Axel A Burns, John T Liu, Yuchen Guerrero-Juarez, Christian Fernando Tran, Bryant Q Chu, Yi-Lin Nguyen, Anh M Hsi, Tsai-Ching Lim, Norman T-L Schoeniger, Sandra Liu, Ruiqi Pai, Yun-Ling Vadivel, Chella K Ingleby, Sandy McKechnie, Andrew E van Breukelen, Frank Hoehn, Kyle L Rasweiler, John J Kohara, Michinori Loughry, William J Weldy, Scott H Cosper, Raymond Yang, Chao-Chun Lin, Sung-Jan Cooper, Kimberly L Santana, Sharlene E Bradley, Jeffrey E Kiebish, Michael A Digman, Michelle https://orcid.org/0000-0003-4611-7100 James, David E Merrill, Amy E Nie, Qing https://orcid.org/0000-0002-8804-3368 Schilling, Thomas F https://orcid.org/0000-0003-1798-8695 Astrowski, Aliaksandr A Potma, Eric O https://orcid.org/0000-0003-3916-6131 García-Castro, Martín I Athanasiou, Kyriacos A https://orcid.org/0000-0001-5387-8405 Behringer, Richard R Plikus, Maksim V https://escholarship.org/uc/item/0f82g52x The fungal genus <i>Neonectria</i> contains many phytopathogenic species currently impacting forests and fruit trees worldwide. Despite their importance, a majority of <i>Neonectria</i> spp. lack sufficient genomic resources to resolve suspected cryptic species. Here, we report draft genomes and assemblies for <i>Neonectria magnoliae</i> NRRL 64651 and <i>Neonectria punicea</i> NRRL 64653. https://escholarship.org/uc/item/0f82g52x Tue, 28 Jan 2025 00:00:00 +0000 Petronek, Hannah M Kasson, Matt T Metheny, Amy M Stauder, Cameron M Lovett, Brian Lynch, Shannon C Garnas, Jeff R Kasson, Lindsay R Stajich, Jason E https://orcid.org/0000-0002-7591-0020 https://escholarship.org/uc/item/70326624 Obesity is associated with hypogonadism in males, characterized by low testosterone and sperm number. Previous studies determined that these stem from dysregulation of hypothalamic circuitry that regulates reproduction, by unknown mechanisms. Herein, we used mice fed chronic high-fat diet, which mimics human obesity, to determine mechanisms of impairment at the level of the hypothalamus, in particular gonadotropin-releasing hormone (GnRH) neurons that regulate luteinizing hormone (LH), which then regulates testosterone. Consistent with obese humans, we demonstrated lower LH, and lower pulse frequency of LH secretion, but unchanged pituitary responsiveness to GnRH. LH pulse frequency is regulated by pulsatile GnRH secretion, which is controlled by kisspeptin. Peripheral and central kisspeptin injections, and DREADD-mediated activation of kisspeptin neurons, demonstrated that kisspeptin neurons were suppressed in obese mice. Thus, we investigated regulators of kisspeptin secretion.... https://escholarship.org/uc/item/70326624 Wed, 22 Jan 2025 00:00:00 +0000 Villa, Pedro A Ruggiero-Ruff, Rebecca E Jamieson, Bradley B Campbell, Rebecca E Coss, Djurdjica https://orcid.org/0000-0003-0692-1612 https://escholarship.org/uc/item/9hz3651g Intestinal microbiota confers susceptibility to diet-induced obesity, yet many probiotic species that synthesize tryptophan (trp) actually attenuate this effect, although the underlying mechanisms are unclear. We monocolonized germ-free mice with a widely consumed probiotic&nbsp;Lacticaseibacillus rhamnosus GG (LGG) under trp-free or -sufficient dietary conditions. We obtained untargeted metabolomics from the mouse feces and serum using liquid chromatography-mass spectrometry and obtained intestinal transcriptomic profiles via bulk-RNA sequencing. When comparing LGG-monocolonized mice with germ-free mice, we found a synergy between LGG and dietary trp in markedly promoting the transcriptome of fatty acid metabolism and β-oxidation. Upregulation was specific and was not observed in transcriptomes of trp-fed conventional mice and mice monocolonized with Ruminococcus gnavus. Metabolomics showed that fecal and serum metabolites were also modified by LGG-host-trp interaction. We developed... https://escholarship.org/uc/item/9hz3651g Tue, 21 Jan 2025 00:00:00 +0000 Suntornsaratoon, Panan Ferraris, Ronaldo P Ambat, Jayanth Antonio, Jayson M Flores, Juan Jones, Abigail Su, Xiaoyang Gao, Nan Li, Wei Vivian https://orcid.org/0000-0002-2087-2709 https://escholarship.org/uc/item/8jm007mj Legionella pneumophila utilizes the Dot/Icm type IVB secretion system to deliver hundreds of effector proteins inside eukaryotic cells to ensure intracellular replication. Our understanding of the molecular functions of the largest pathogenic arsenal known to the bacterial world remains incomplete. By leveraging advancements in 3D protein structure prediction, we provide a comprehensive structural analysis of 368 L. pneumophila effectors, representing a global atlas of predicted functional domains summarized in a database (https://pathogens3d.org/legionella-pneumophila). Our analysis identified 157 types of diverse functional domains in 287 effectors, including 159 effectors with no prior functional annotations. Furthermore, we identified 35 cryptic domains in 30 effector models that have no similarity with experimentally structurally characterized proteins, thus, hinting at novel functionalities. Using this analysis, we demonstrate the activity of thirteen functional domains,... https://escholarship.org/uc/item/8jm007mj Mon, 20 Jan 2025 00:00:00 +0000 Patel, Deepak T Stogios, Peter J Jaroszewski, Lukasz Urbanus, Malene L Sedova, Mayya Semper, Cameron Le, Cathy Takkouche, Abraham Ichii, Keita Innabi, Julie Patel, Dhruvin H Ensminger, Alexander W Godzik, Adam Savchenko, Alexei https://escholarship.org/uc/item/4bj2f8d7 BackgroundX chromosome inactivation (XCI) is a female-specific process in which one X chromosome is silenced to balance X-linked gene expression between the sexes. XCI is initiated in early development by upregulation of the lncRNA Xist on the future inactive X (Xi). A subset of X-linked genes escape silencing and thus have higher expression in females, suggesting female-specific functions. One of these genes is the highly conserved gene Kdm6a, which encodes a histone demethylase that removes methyl groups at H3K27 to facilitate gene expression. KDM6A mutations have been implicated in congenital disorders such as Kabuki Syndrome, as well as in sex differences in development and cancer.MethodsKdm6a was knocked out (KO) using CRISPR/Cas9 gene editing in hybrid female mouse embryonic stem (ES) cells derived either from a 129 × Mus castaneus (cast) cross or a BL6 x cast cross. In one of the lines a transcriptional stop signal inserted in Tsix results in completely skewed X silencing... https://escholarship.org/uc/item/4bj2f8d7 Mon, 13 Jan 2025 00:00:00 +0000 Lin, Josephine Zhang, Jinli Ma, Li Fang, He Ma, Rui Groneck, Camille Filippova, Galina N Deng, Xinxian Kinoshita, Chizuru Young, Jessica E Ma, Wenxiu Disteche, Christine M Berletch, Joel B https://escholarship.org/uc/item/0xk362p4 The human malaria parasites, including Plasmodium falciparum, persist as a major cause of global morbidity and mortality. The recent stalling of progress toward malaria elimination substantiates a need for novel interventions. Controlled gene expression is central to the parasite's numerous life cycle transformations and adaptation. With few specific transcription factors (TFs) identified, crucial roles for chromatin states and epigenetics in parasite transcription have become evident. Although many chromatin-modifying enzymes are known, less is known about which factors mediate their impacts on transcriptional variation. Like those of higher eukaryotes, long noncoding RNAs (lncRNAs) have recently been shown to have integral roles in parasite gene regulation. This review aims to summarize recent developments and key findings on the role of lncRNAs in P. falciparum. https://escholarship.org/uc/item/0xk362p4 Wed, 8 Jan 2025 00:00:00 +0000 Thompson, Trevor A Chahine, Zeinab Le Roch, Karine G https://escholarship.org/uc/item/8mx3c60v CRISPR-based DNA adenine base editors (ABEs) hold remarkable promises to address human genetic diseases caused by point mutations. ABEs were developed by combining CRISPR-Cas9 with a transfer RNA (tRNA) adenosine deaminase enzyme and through directed evolution, conferring the ability to deaminate DNA. However, the molecular mechanisms driving the efficient DNA deamination in the evolved ABEs remain unresolved. Here, extensive molecular simulations and biochemical experiments reveal the biophysical basis behind the astonishing base editing efficiency of ABE8e, the most efficient ABE to date. We demonstrate that the ABE8e's DNA deaminase domain, TadA8e, forms remarkably stable dimers compared to its tRNA-deaminating progenitor and that the strength of TadA dimerization is crucial for DNA deamination. The TadA8e dimer forms robust interactions involving its R98 and R129 residues, the RuvC domain of Cas9 and the DNA. These locking interactions are exclusive to ABE8e, distinguishing... https://escholarship.org/uc/item/8mx3c60v Mon, 6 Jan 2025 00:00:00 +0000 Arantes, Pablo R https://orcid.org/0000-0003-1946-2750 Chen, Xiaoyu Sinha, Souvik Saha, Aakash Patel, Amun C Sample, Matthew Nierzwicki, Łukasz Lapinaite, Audrone https://orcid.org/0000-0002-9427-9342 Palermo, Giulia https://orcid.org/0000-0003-1404-8737 https://escholarship.org/uc/item/91c4x7jv Chemical modification of RNAs is important for posttranscriptional gene regulation. The METTL3-METTL14 complex generates most <i>N</i>⁶-methyladenosine (m⁶A) modifications in messenger RNAs (mRNAs), and dysregulated methyltransferase expression has been linked to cancers. Here we show that a changed sequence context for m⁶A can promote oncogenesis. A gain-of-function missense mutation from patients with cancer, METTL14^R298P, increases malignant cell growth in culture and transgenic mice without increasing global m⁶A levels in mRNAs. The mutant methyltransferase preferentially modifies noncanonical sites containing a GGAU motif, in vitro and in vivo. The m⁶A in GGAU context is detected by the YTH family of readers similarly to the canonical sites but is demethylated less efficiently by an eraser, ALKBH5. Combining the biochemical and structural data, we provide a model for how the cognate RNA sequences are selected... https://escholarship.org/uc/item/91c4x7jv Sat, 4 Jan 2025 00:00:00 +0000 Zhang, Chi Scott, Robyn L Tunes, Luiza Hsieh, Meng-Hsiung Wang, Ping Kumar, Ashwani Khadgi, Brijesh B Yang, Yen-Yu Lacy, Katelyn A Doxtader Herrell, Emily Zhang, Xunzhi Evers, Bret Wang, Yinsheng Xing, Chao Zhu, Hao Nam, Yunsun https://escholarship.org/uc/item/785050nr A hallmark of tightly regulated high-fidelity enzymes is that they become activated only after encountering cognate substrates, often by an induced-fit mechanism rather than conformational selection. Upon analysis of molecular dynamics trajectories, we recently discovered that the Cas9 HNH domain exists in three conformations: 1) Y836 (which is two residues away from the catalytic D839 and H840 residues) is hydrogen bonded to the D829 backbone amide, 2) Y836 is hydrogen bonded to the backbone amide of D861 (which is one residue away from the third catalytic residue N863), and 3) Y836 is not hydrogen bonded to either residue. Each of the three conformers differs from the active state of HNH. The conversion between the inactive and active states involves a local unfolding-refolding process that displaces the Cα and side chain of the catalytic N863 residue by ∼5&nbsp;Å and ∼10&nbsp;Å, respectively. In this study, we report the two largest principal components of coordinate variance... https://escholarship.org/uc/item/785050nr Thu, 2 Jan 2025 00:00:00 +0000 Wang, Jimin Maschietto, Federica Qiu, Tianyin Arantes, Pablo R Skeens, Erin Palermo, Giulia https://orcid.org/0000-0003-1404-8737 Lisi, George P Batista, Victor S https://escholarship.org/uc/item/5c82w1sh DNA from organelles called mitochondria is not inherited from the father. But mitochondrial RNAs that sense paternal diet and mitochondrial quality are delivered from sperm to egg, affecting offspring metabolism. https://escholarship.org/uc/item/5c82w1sh Mon, 16 Dec 2024 00:00:00 +0000 Cai, Chen Chen, Qi https://orcid.org/0000-0001-6353-9589 https://escholarship.org/uc/item/3tv4530n Single-cell Hi-C (scHi-C) techniques have significantly advanced our understanding of the 3D genome organization, providing crucial insights into the spatial genome architecture within individual nuclei. Numerous computational and statistical methods have been developed to analyze scHi-C data, with embedding methods playing a key role. Embedding reduces the dimensionality of complex scHi-C contact maps, making it easier to extract biologically meaningful patterns. These methods not only enhance cell clustering based on chromatin structures but also facilitate visualization and other downstream analyses. Most scHi-C embedding methods incorporate strategies such as normalization and imputation to address the inherent sparsity of scHi-C data, thereby further improving data quality and interpretability. In this review, we systematically examine the existing methods designed for scHi-C embedding, outlining their methodologies and discussing their capabilities in handling normalization... https://escholarship.org/uc/item/3tv4530n Sat, 14 Dec 2024 00:00:00 +0000 Ma, Rui Huang, Jingong Jiang, Tao https://orcid.org/0000-0003-3833-4498 Ma, Wenxiu https://escholarship.org/uc/item/5ng2q27p Photosynthesis requires chloroplasts, in which most proteins are nucleus-encoded and produced via cytoplasmic translation. The translation initiation factor eIF5B gates the transition from initiation (I) to elongation (E), and the Kozak motif is associated with translation efficiency, but their relationship is previously unknown. Here, with ribosome profiling, we determined the genome-wide I-E transition efficiencies. We discovered that the most prevalent Kozak motif is associated with high I-E transition efficiency in Arabidopsis, rice, and wheat, thus implicating the potential of the Kozak motif in facilitating the I-E transition. Indeed, the effects of Kozak motifs in promoting translation depend on HOT3/eIF5B1 in Arabidopsis. HOT3 preferentially promotes the translation of photosynthesis-associated nuclear genes in a Kozak motif-dependent manner, which explains the chloroplast defects and reduced photosynthesis activity of hot3 mutants. Our study linked the Kozak motif to... https://escholarship.org/uc/item/5ng2q27p Mon, 2 Dec 2024 00:00:00 +0000 Hang, Runlai Li, Hao Liu, Wenjing Wang, Runyu Hu, Hao Chen, Meng https://orcid.org/0000-0003-0351-5897 You, Chenjiang Chen, Xuemei https://orcid.org/0000-0002-5209-1157 https://escholarship.org/uc/item/00g0z278 tRNA function is based on unique structures that enable mRNA decoding using anticodon trinucleotides. These structures interact with specific aminoacyl-tRNA synthetases and ribosomes using 3D shape and sequence signatures. Beyond translation, tRNAs serve as versatile signaling molecules interacting with other RNAs and proteins. Through evolutionary processes, tRNA fragmentation emerges as not merely random degradation but an act of recreation, generating specific shorter molecules called tRNA-derived small RNAs (tsRNAs). These tsRNAs exploit their linear sequences and newly arranged 3D structures for unexpected biological functions, epitomizing the tRNA "renovatio" (from Latin, meaning renewal, renovation, and rebirth). Emerging methods to uncover full tRNA/tsRNA sequences and modifications, combined with techniques to study RNA structures and to integrate AI-powered predictions, will enable comprehensive investigations of tRNA fragmentation products and new interaction potentials... https://escholarship.org/uc/item/00g0z278 Thu, 28 Nov 2024 00:00:00 +0000 Kuhle, Bernhard Chen, Qi https://orcid.org/0000-0001-6353-9589 Schimmel, Paul https://escholarship.org/uc/item/71h4q4bq Humans are exposed to DNA alkylating agents through endogenous metabolism, environmental exposure and cancer chemotherapy. The resulting alkylated DNA adducts may elicit genome instability by perturbing DNA replication and transcription. R-loops regulate various cellular processes, including transcription, DNA repair, and telomere maintenance. However, unscheduled R-loops are also recognized as potential sources of DNA damage and genome instability. In this study, by employing fluorescence microscopy and R-loop sequencing approaches, we uncovered, for the first time, that minor-groove N2-alkyl-dG lesions elicit elevated R-loop accumulation in chromatin and in plasmid DNA in cells. We also demonstrated that the N2-alkyl-dG-induced R-loops impede transcription elongation and compromise genome integrity. Moreover, genetic depletion of DDX23, a R-loop helicase, renders cells more sensitive toward benzo[a]pyrene diolepoxide, a carcinogen that induces mainly the minor-groove N2-dG adduct.... https://escholarship.org/uc/item/71h4q4bq Mon, 25 Nov 2024 00:00:00 +0000 Wang, Yinan Tang, Feng Zhao, Ting Yuan, Jun https://orcid.org/0000-0002-6240-7151 Kellum, Andrew H Wang, Yinsheng https://escholarship.org/uc/item/2461750g DNA methylation is one of the major epigenetic mechanisms crucial for gene regulation and genome stability. De novo DNA methyltransferase DNMT3C is required for silencing evolutionarily young transposons during mice spermatogenesis. Mutation of DNMT3C led to a sterility phenotype that cannot be rescued by its homologs DNMT3A and DNMT3B. However, the structural basis of DNMT3C-mediated DNA methylation remains unknown. Here, we report the structure and mechanism of DNMT3C-mediated DNA methylation. The DNMT3C methyltransferase domain recognizes CpG-containing DNA in a manner similar to that of DNMT3A and DNMT3B, in line with their high sequence similarity. However, two evolutionary covariation sites, C543 and E590, diversify the substrate interaction among DNMT3C, DNMT3A, and DNMT3B, resulting in distinct DNA methylation activity and specificity between DNMT3C, DNMT3A, and DNMT3B in&nbsp;vitro. In addition, our combined structural and biochemical analysis reveals that the disease-causing... https://escholarship.org/uc/item/2461750g Mon, 25 Nov 2024 00:00:00 +0000 Khudaverdyan, Nelli Lu, Jiuwei https://orcid.org/0000-0002-6478-4081 Chen, Xinyi Herle, Genevieve Song, Jikui https://orcid.org/0000-0002-4958-1032 https://escholarship.org/uc/item/9413k6md DNA methylation is an important epigenetic mechanism essential for transposon silencing and genome integrity. Across evolution, the substrates of DNA methylation have diversified between kingdoms. In plants, chromomethylase3 (CMT3) and CMT2 mediate CHG and CHH methylation, respectively. However, how these two methyltransferases diverge on substrate specificities during evolution remains unknown. Here, we reveal that CMT2 originates from a duplication of an evolutionarily ancient CMT3 in flowering plants. Lacking a key arginine residue recognizing CHG in CMT2 impairs its CHG methylation activity in most flowering plants. An engineered V1200R mutation empowers CMT2 to restore CHG and CHH methylations in <i>Arabidopsis cmt2cmt3</i> mutant, testifying a loss-of-function effect for CMT2 during evolution. CMT2 has evolved a long and unstructured amino terminus critical for protein stability, especially under heat stress, and is plastic to tolerate various natural mutations. Together,... https://escholarship.org/uc/item/9413k6md Fri, 22 Nov 2024 00:00:00 +0000 Jiang, Jianjun Gwee, Jia Fang, Jian https://orcid.org/0000-0002-8652-1768 Leichter, Sarah M Sanders, Dean Ji, Xinrui Song, Jikui https://orcid.org/0000-0002-4958-1032 Zhong, Xuehua https://escholarship.org/uc/item/4n64r36r CRISPR-Cas systems have transformed the field of synthetic biology by providing a versatile method for genome editing. The efficiency of CRISPR systems is largely dependent on the sequence of the constituent sgRNA, necessitating the development of computational methods for designing active sgRNAs. While deep learning-based models have shown promise in predicting sgRNA activity, the accuracy of prediction is primarily governed by the data set used in model training. Here, we trained a convolutional neural network (CNN) model and a large language model (LLM) on balanced and imbalanced data sets generated from CRISPR-Cas12a screening data for the yeast <i>Yarrowia lipolytica</i> and evaluated their ability to predict high- and low-activity sgRNAs. We further tested whether prediction performance can be improved by training on imbalanced data sets augmented with synthetic sgRNAs. Lastly, we demonstrated that adding synthetic sgRNAs to inherently imbalanced CRISPR-Cas9 data sets from... https://escholarship.org/uc/item/4n64r36r Thu, 21 Nov 2024 00:00:00 +0000 Trivedi, Varun Mohseni, Amirsadra Lonardi, Stefano https://orcid.org/0000-0002-2696-7274 Wheeldon, Ian https://orcid.org/0000-0002-3492-7539 https://escholarship.org/uc/item/1bb6h6w3 BACKGROUND &amp; AIMS: Lacticaseibacillus rhamnosus GG (LGG) is the world's most consumed probiotic but its mechanism of action on intestinal permeability and differentiation along with its interactions with an essential source of signaling metabolites, dietary tryptophan (trp), are unclear. METHODS: Untargeted metabolomic and transcriptomic analyses were performed in LGG monocolonized germ-free mice fed trp-free or -sufficient diets. LGG-derived metabolites were profiled in&nbsp;vitro under anaerobic and aerobic conditions. Multiomic correlations using a newly developed algorithm discovered novel metabolites tightly linked to tight junction and cell differentiation genes whose abundances were regulated by LGG and dietary trp. Barrier-modulation by these metabolites were functionally tested in Caco2 cells, mouse enteroids, and dextran sulfate sodium experimental colitis. The contribution of these metabolites to barrier protection is delineated at specific tight junction proteins... https://escholarship.org/uc/item/1bb6h6w3 Mon, 18 Nov 2024 00:00:00 +0000 Suntornsaratoon, Panan Antonio, Jayson M Flores, Juan Upadhyay, Ravij Veltri, John Bandyopadhyay, Sheila Dadala, Rhema Kim, Michael Liu, Yue Balasubramanian, Iyshwarya Turner, Jerrold R Su, Xiaoyang Li, Wei Vivian https://orcid.org/0000-0002-2087-2709 Gao, Nan Ferraris, Ronaldo P https://escholarship.org/uc/item/0fz1787r On the basis of a streamlined route to the pyrroloiminoquinone (PIQ) core, we made 16 natural products spread across four classes of biosynthetically related alkaloid natural products, and multiple structural analogs, all in ≤8 steps longest linear sequence (LLS). The strategy features a Larock indole synthesis as the key operation in a five-step synthesis of a key methoxy-PIQ intermediate. Critically, this compound was readily diverged via selective methylation of either (or both) of the imine-like or pyrrole nitrogens, which then permitted further divergence by either <i>O-</i>demethylation to <i>o-</i>quinone natural products or displacement of the methoxy group with a range of amine nucleophiles. Based on a single, early report of their potential utility against the malaria parasite, we assayed these compounds against several strains of <i>Plasmodium falciparum</i>, as well as two species of the related protozoan parasite <i>Babesia</i>. In combination with evaluations of... https://escholarship.org/uc/item/0fz1787r Fri, 8 Nov 2024 00:00:00 +0000 Barnes, Griffin L Magann, Nicholas L Perrotta, Daniele Hörmann, Fabian M Fernandez, Sebastian Vydyam, Pratap Choi, Jae-Yeon Prudhomme, Jacques Neal, Armund Le Roch, Karine G https://orcid.org/0000-0002-4862-9292 Mamoun, Choukri Ben Vanderwal, Christopher D https://orcid.org/0000-0001-7218-4521 https://escholarship.org/uc/item/8qd430n4 Impaired inhibitory synapse development is suggested to drive neuronal hyperactivity in autism spectrum disorders (ASD) and epilepsy. We propose a novel mechanism by which astrocytes control the development of parvalbumin (PV)-specific inhibitory synapses in the hippocampus, implicating ephrin-B/EphB signaling. Here, we utilize genetic approaches to assess functional and structural connectivity between PV and pyramidal cells (PCs) through whole-cell patch-clamp electrophysiology, optogenetics, immunohistochemical analysis, and behaviors in male and female mice. While inhibitory synapse development is adversely affected by PV-specific expression of EphB2, a strong candidate ASD risk gene, astrocytic ephrin-B1 facilitates PV→PC connectivity through a mechanism involving EphB signaling in PV boutons. In contrast, the loss of astrocytic ephrin-B1 reduces PV→PC connectivity and inhibition, resulting in increased seizure susceptibility and an ASD-like phenotype. Our findings underscore... https://escholarship.org/uc/item/8qd430n4 Thu, 7 Nov 2024 00:00:00 +0000 Sutley-Koury, Samantha N Taitano-Johnson, Christopher Kulinich, Anna O Farooq, Nadia Wagner, Victoria A Robles, Marissa Hickmott, Peter W Santhakumar, Vijayalakshmi https://orcid.org/0000-0001-6278-4187 Mimche, Patrice N Ethell, Iryna M https://orcid.org/0000-0002-1324-6611 https://escholarship.org/uc/item/7sx65717 BACKGROUND: Fragile X syndrome (FXS) is a leading genetic cause of autism and intellectual disability with cortical hyperexcitability and sensory hypersensitivity attributed to loss and hypofunction of inhibitory parvalbumin-expressing (PV) cells. Our studies provide novel insights into the role of excitatory neurons in abnormal development of PV cells during a postnatal period of inhibitory circuit refinement. METHODS: To achieve Fragile X mental retardation gene (Fmr1) deletion and re-expression in excitatory neurons during the postnatal day (P)14-P21 period, we generated Cre^CaMKIIa/Fmr1^Flox/y (cOFF) and Cre^CaMKIIa/Fmr1^FloxNeo/y (cON) mice, respectively. Cortical phenotypes were evaluated in adult mice using biochemical, cellular, clinically relevant electroencephalogram (EEG) and behavioral tests. RESULTS: We found that similar to global Fmr1 KO mice, the density of PV-expressing cells, their activation, and sound-evoked gamma synchronization... https://escholarship.org/uc/item/7sx65717 Thu, 7 Nov 2024 00:00:00 +0000 Rais, Maham Lovelace, Jonathan W Shuai, Xinghao S Woodard, Walker Bishay, Steven Estrada, Leo Sharma, Ashwin R Nguy, Austin Kulinich, Anna Pirbhoy, Patricia S Palacios, Arnold R Nelson, David L Razak, Khaleel A Ethell, Iryna M https://orcid.org/0000-0002-1324-6611 https://escholarship.org/uc/item/2k90c0dv The function of astrocytes intertwines with the extracellular matrix, whose neuron and glial cell-derived components shape neuronal plasticity. Astrocyte abnormalities have been reported in the brain of the mouse model for fragile X syndrome (FXS), the most common cause of inherited intellectual disability, and a monogenic cause of autism spectrum disorder. We compared human FXS and control astrocytes generated from human induced pluripotent stem cells and we found increased expression of urokinase plasminogen activator (uPA), which modulates degradation of extracellular matrix. Several pathways associated with uPA and its receptor function were activated in FXS astrocytes. Levels of uPA were also increased in conditioned medium collected from FXS hiPSC-derived astrocyte cultures and correlated inversely with intracellular Ca²⁺ responses to activation of L-type voltage-gated calcium channels in human astrocytes. Increased uPA augmented neuronal phosphorylation of TrkB... https://escholarship.org/uc/item/2k90c0dv Thu, 7 Nov 2024 00:00:00 +0000 Peteri, Ulla‐Kaisa Pitkonen, Juho de Toma, Ilario Nieminen, Otso Utami, Kagistia Hana Strandin, Tomas M Corcoran, Padraic Roybon, Laurent Vaheri, Antti Ethell, Iryna https://orcid.org/0000-0002-1324-6611 Casarotto, Plinio Pouladi, Mahmoud A Castrén, Maija L https://escholarship.org/uc/item/2b07n7r8 Editorial: Neural markers of sensory processing in development https://escholarship.org/uc/item/2b07n7r8 Thu, 7 Nov 2024 00:00:00 +0000 Ethridge, Lauren E Auerbach, Benjamin D Contractor, Anis Ethell, Iryna M https://orcid.org/0000-0002-1324-6611 McCullagh, Elizabeth A Pedapati, Ernest V https://escholarship.org/uc/item/1hv069b2 Astrocytes have been implicated in oligodendrocyte development and myelination, however, the mechanisms by which astrocytes regulate oligodendrocytes remain unclear. Our findings suggest a new mechanism that regulates astrocyte-mediated oligodendrocyte development through ephrin-B1 signaling in astrocytes. Using a mouse model, we examined the role of astrocytic ephrin-B1 signaling in oligodendrocyte development by deleting ephrin-B1 specifically in astrocytes during the postnatal days (P)14-P28 period and used mRNA analysis, immunohistochemistry, and mouse behaviors to study its effects on oligodendrocytes and myelination. We found that deletion of astrocytic ephrin-B1 downregulated many genes associated with oligodendrocyte development, myelination, and lipid metabolism in the hippocampus and the corpus callosum. Additionally, we observed a reduced number of oligodendrocytes and impaired myelination in the corpus callosum of astrocyte-specific ephrin-B1 KO mice. Finally, our... https://escholarship.org/uc/item/1hv069b2 Thu, 7 Nov 2024 00:00:00 +0000 Sutley-Koury, Samantha N Anderson, Alyssa Taitano-Johnson, Christopher Ajayi, Moyinoluwa Kulinich, Anna O Contreras, Kimberly Regalado, Jasmin Tiwari-Woodruff, Seema K Ethell, Iryna M https://orcid.org/0000-0002-1324-6611 https://escholarship.org/uc/item/77b394c3 Profilin 1 (PFN1) is a cytoskeleton protein that modulates actin dynamics through binding to monomeric actin and polyproline-containing proteins. Mutations in PFN1 have been linked to the pathogenesis of familial amyotrophic lateral sclerosis (ALS). Here, we employed an unbiased proximity labeling strategy in combination with proteomic analysis for proteome-wide profiling of proteins that differentially interact with mutant and wild-type (WT) PFN1 proteins in human cells. We uncovered 11 mRNA splicing proteins that are preferentially enriched in the proximity proteomes of the two ALS-linked PFN1 variants, C71G and M114T, over that of wild-type PFN1. We validated the preferential interactions of the ALS-linked PFN1 variants with two mRNA splicing factors, hnRNPC and U2AF2, by immunoprecipitation, followed with immunoblotting. We also found that the two ALS-linked PFN1 variants promoted the exonization of <i>Alu</i> elements in the mRNAs of <i>MTO1</i>, <i>TCFL5</i>, <i>WRN</i>... https://escholarship.org/uc/item/77b394c3 Tue, 5 Nov 2024 00:00:00 +0000 Wei, Songbo https://orcid.org/0000-0001-9311-1823 Yang, YenYu Wang, Yinsheng https://escholarship.org/uc/item/70r4k41m Chronic infection of hepatitis B virus (HBV) is the major cause of hepatocellular carcinoma (HCC). Notably, 90% of HBV-positive HCC cases exhibit detectable HBV integrations, hinting at the potential early entanglement of these viral integrations in tumorigenesis and their subsequent oncogenic implications. Nevertheless, the precise chronology of integration events during HCC tumorigenesis, alongside their sequential structural patterns, has remained elusive thus far. In this study, we applied whole-genome sequencing to multiple biopsies extracted from six HBV-positive HCC cases. Through this approach, we identified point mutations and viral integrations, offering a blueprint for the intricate tumor phylogeny of these samples. The emergent narrative paints a rich tapestry of diverse evolutionary trajectories characterizing the analyzed tumors. We uncovered oncogenic integration events in some samples that appear to happen before and during the initiation stage of tumor development... https://escholarship.org/uc/item/70r4k41m Tue, 5 Nov 2024 00:00:00 +0000 Ren, Haozhen Chen, Xun Wang, Jinglin Chen, Ying Hafiz, Alex Xiao, Qian Fu, Shiwei Madireddy, Advaitha Li, Wei Vivian https://orcid.org/0000-0002-2087-2709 Shi, Xiaolei Cao, Jian https://escholarship.org/uc/item/08x970sr Despite the extensive use of next-generation sequencing (NGS) of RNA, simultaneous direct sequencing and quantitative mapping of multiple RNA nucleotide modifications remains challenging. Mass spectrometry (MS)-based sequencing can directly sequence all RNA modifications without being limited to specific ones, but it requires a perfect MS ladder that few tRNAs can provide. Here, we describe an MS ladder complementation sequencing approach (MLC-Seq) that circumvents the perfect ladder requirement, allowing de novo MS sequencing of full-length heterogeneous cellular tRNAs with multiple nucleotide modifications at single-nucleotide precision. Unlike NGS-based methods, which lose RNA modification information, MLC-Seq preserves RNA sequence diversity and modification information, revealing new detailed stoichiometric tRNA modification profiles and their changes upon treatment with the dealkylating enzyme AlkB. It can also be combined with reference sequences to provide quantitative... https://escholarship.org/uc/item/08x970sr Tue, 5 Nov 2024 00:00:00 +0000 Yuan, Xiaohong Su, Yue Johnson, Benjamin Kirchner, Michele Zhang, Xudong Xu, Sihang Jiang, Sophia Wu, Jing Shi, Shundi Russo, James J Chen, Qi https://orcid.org/0000-0001-6353-9589 Zhang, Shenglong https://escholarship.org/uc/item/109081xw Understanding the mechanisms of the cellular aging processes is crucial for attempting to extend organismal lifespan and for studying age-related degenerative diseases. Yeast cells divide through budding, providing a classical biological model for studying cellular aging. With their powerful genetics, relatively short cell cycle, and well-established signaling pathways also found in animals, yeast cells offer valuable insights into the aging process. Recent experiments suggested the existence of two aging modes in yeast characterized by nucleolar and mitochondrial declines, respectively. By analyzing experimental data, this study shows that cells evolving into those two aging modes behave differently when they are young. While buds grow linearly in both modes, cells that consistently generate spherical buds throughout their lifespan demonstrate greater efficacy in controlling bud size and growth rate at young ages. A three-dimensional multiscale chemical-mechanical model was developed... https://escholarship.org/uc/item/109081xw Wed, 30 Oct 2024 00:00:00 +0000 Tsai, Kevin Zhou, Zhen Yang, Jiadong Xu, Zhiliang Xu, Shixin Zandi, Roya Hao, Nan Chen, Weitao https://orcid.org/0000-0003-3362-5982 Alber, Mark https://orcid.org/0000-0002-7153-1138 https://escholarship.org/uc/item/2mv5x06t Male sterility enables hybrid crop breeding to increase yields and has been extensively studied. But thermo-sensitive female sterility, which is an ideal property that may enable full mechanization in hybrid rice breeding, has rarely been investigated due to the absence of such germplasm. Here we identify the spontaneous thermo-sensitive female sterility 1 (tfs1) mutation that confers complete sterility under regular/high temperature and partial fertility under low temperature as a point mutation in ARGONAUTE7 (AGO7). AGO7 associates with miR390 to form an RNA-Induced Silencing Complex (RISC), which triggers the biogenesis of small interfering RNAs (siRNAs) from TRANS-ACTING3 (TAS3) loci by recruiting SUPPRESSOR OF GENE SILENCING (SGS3) and RNA-DEPENDENT RNA POLYMERASE6 (RDR6) to TAS3 transcripts. These siRNAs are known as tasiR-ARFs as they act in trans to repress auxin response factor genes. The mutant TFS1 (mTFS1) protein is compromised in its ability to load the miR390/miR390*... https://escholarship.org/uc/item/2mv5x06t Mon, 21 Oct 2024 00:00:00 +0000 Li, Haoxuan You, Chenjiang Yoshikawa, Manabu Yang, Xiaoyu Gu, Haiyong Li, Chuanguo Cui, Jie Chen, Xuemei https://orcid.org/0000-0002-5209-1157 Ye, Nenghui Zhang, Jianhua Wang, Guanqun https://escholarship.org/uc/item/1jg273cg MicroRNAs (miRNAs) are short endogenous non-coding RNAs that regulate gene expression at the post-transcriptional level in a broad range of eukaryotic species. In animals, it is estimated that more than 60% of mammalian genes are targets of miRNAs, with miRNAs regulating cellular processes such as differentiation and proliferation. In plants, miRNAs regulate gene expression and play essential roles in diverse biological processes, including growth, development, and stress responses. Arabidopsis mutants with defective miRNA biogenesis are embryo lethal, and abnormal expression of miRNAs can cause severe developmental phenotypes. It is therefore crucial that the homeostasis of miRNAs is tightly regulated. In this review, we summarize the key mechanisms of plant miRNA biogenesis and stabilization. We provide an update on nuclear proteins with functions in miRNA biogenesis and proteins linking miRNA biogenesis to environmental triggers. https://escholarship.org/uc/item/1jg273cg Mon, 21 Oct 2024 00:00:00 +0000 Xu, Ye Chen, Xuemei https://orcid.org/0000-0002-5209-1157 https://escholarship.org/uc/item/0tk8j8v9 Ribosome biogenesis is essential for protein synthesis in gene expression. Yeast eIF5B has been shown biochemically to facilitate 18S ribosomal RNA (rRNA) 3' end maturation during late-stage 40S ribosomal subunit assembly and gate the transition from translation initiation to elongation. But the genome-wide effects of eIF5B have not been studied at the single-nucleotide resolution in any organism, and 18S rRNA 3' end maturation is poorly understood in plants. <i>Arabidopsis</i> HOT3/eIF5B1 was found to promote development and heat stress acclimation by translational regulation, but its molecular function remained unknown. Here, we show that HOT3 is a late-stage ribosome biogenesis factor that facilitates 18S rRNA 3' end processing and is a translation initiation factor that globally impacts the transition from initiation to elongation. By developing and implementing 18S-ENDseq, we revealed previously unknown events in 18S rRNA 3' end maturation or metabolism. We quantitatively... https://escholarship.org/uc/item/0tk8j8v9 Mon, 21 Oct 2024 00:00:00 +0000 Hang, Runlai Xu, Ye Wang, Xufeng Hu, Hao Flynn, Nora https://orcid.org/0000-0003-1177-1794 You, Chenjiang Chen, Xuemei https://orcid.org/0000-0002-5209-1157