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Open Access Publications from the University of California

Scholarly Works (5 results)

  • Thesis
  • Peer Reviewed
UC Riverside Electronic Theses and Dissertations (2018)

The 3’ untranslated region (UTR) of mRNAs is extensively targeted by a myriad of RNA-binding proteins (RBPs) and microRNAs (miRNAs) for mRNA decay and translation control. HuR, a ubiquitously expressed RBP, shares many target mRNAs with miRNAs, and their combinatorial control of gene expression has been recently reported. However, the whole picture of this regulation paradigm across the transcriptome remains largely unclear. Here, we investigate the interactions between Ago2 (the core RBP in miRNA machinery) and HuR at the transcriptome-wide level. Using HITS-CLIP, we determined the binding locations and binding levels of HuR and Ago2 on mRNAs. To detect HuR-Ago2 interactions, we measured the CLIP signals of Ago2 while manipulating the protein level of HuR. Globally, occupancies of the most extreme changing Ago2 sites upon HuR knockdown were affected by the HuR’s presence on the same 3’UTRs, suggesting that HuR exerts influence on Ago2 binding to mRNAs. In addition, HuR and Ago2 sites largely overlap on 3’UTRs. To study HuR-miRNA interactions at individual sites, thirteen overlapping CLIP sites were selected, and their activities were tested by luciferase assays. Overall, we found three sites where HuR altered the miRNA repression effects, indicating their interaction at those sites. Additionally, we performed sequence analysis to determine the identities of three uncharacterized bands in HuR CLIP. Our results show that the composition of the sequences in these bands was different from the major band; instead, motif analysis implied that they might not be HuR bands, though higher depth sequencing data were required for confirmation. Taken together, we present an integrated approach to study the interactions between the miRNA machinery and HuR on a transcriptome-wide scale, and define the prevalence and versatility of their interactions on mRNA targets.

    Cover page: Transcriptome-Wide Identification and Validation of Interactions Between the miRNA Machinery and HuR on mRNA TargetsCreative Commons 'BY-NC-SA' version 4.0 license
    • Article
    • Peer Reviewed
    UC Riverside Previously Published Works (2018)
    Approximately 1500 RNA-binding proteins (RBPs) profoundly impact mammalian cellular function by controlling distinct sets of transcripts, often using sequence-specific binding to 3' untranslated regions (UTRs) to regulate mRNA stability and translation. Aside from their individual effects, higher-order combinatorial interactions between RBPs on specific mRNAs have been proposed to underpin the regulatory network. To assess the extent of such co-regulatory control, we took a global experimental approach followed by targeted validation to examine interactions between two well-characterized and highly conserved RBPs, Argonaute2 (AGO2) and Pumilio (PUM1 and PUM2). Transcriptome-wide changes in AGO2-mRNA binding upon PUM knockdown were quantified by CLIP-seq, and the presence of PUM binding on the same 3'UTR corresponded with cooperative and antagonistic effects on AGO2 occupancy. In addition, PUM binding sites that overlap with AGO2 showed differential, weakened binding profiles upon abrogation of AGO2 association, indicative of cooperative interactions. In luciferase reporter validation of candidate 3'UTR sites where AGO2 and PUM colocalized, three sites were identified to host antagonistic interactions, where PUM counteracts miRNA-guided repression. Interestingly, the binding sites for the two proteins are too far for potential antagonism due to steric hindrance, suggesting an alternate mechanism. Our data experimentally confirms the combinatorial regulatory model and indicates that the mostly repressive PUM proteins can change their behavior in a context-dependent manner. Overall, the approach underscores the importance of further elucidation of complex interactions between RBPs and their transcriptome-wide extent.
      Cover page: Antagonistic and cooperative AGO2-PUM interactions in regulating mRNAs
      • Article
      • Peer Reviewed
      UC Berkeley Previously Published Works (2022)
      The Betta fish displays a remarkable variety of phenotypes selected during domestication. However, the genetic basis underlying these traits remains largely unexplored. Here, we report a high-quality genome assembly and resequencing of 727 individuals representing diverse morphotypes of the Betta fish. We show that current breeds have a complex domestication history with extensive introgression with wild species. Using a genome-wide association study, we identify the genetic basis of multiple traits, including coloration patterns, the "Dumbo" phenotype with pectoral fin outgrowth, extraordinary enlargement of body size that we map to a major locus on chromosome 8, the sex determination locus that we map to dmrt1, and the long-fin phenotype that maps to the locus containing kcnj15. We also identify a polygenic signal related to aggression, involving multiple neural system-related genes such as esyt2, apbb2, and pank2. Our study provides a resource for developing the Betta fish as a genetic model for morphological and behavioral research in vertebrates.
        Cover page: The genetic architecture of phenotypic diversity in the Betta fish (<i>Betta splendens</i>).
        • Article
        • Peer Reviewed
        UCLA Previously Published Works (2024)
        Perovskite photovoltaics, typically based on a solution-processed perovskite layer with a film thickness of a few hundred nanometres, have emerged as a leading thin-film photovoltaic technology. Nevertheless, many critical issues pose challenges to its commercialization progress, including industrial compatibility, stability, scalability and reliability. A thicker perovskite film on a scale of micrometres could mitigate these issues. However, the efficiencies of thick-film perovskite cells lag behind those with nanometre film thickness. With the mechanism remaining elusive, the community has long been under the impression that the limiting factor lies in the short carrier lifetime as a result of defects. Here, by constructing a perovskite system with extraordinarily long carrier lifetime, we rule out the restrictions of carrier lifetime on the device performance. Through this, we unveil the critical role of the ignored lattice strain in thick films. Our results provide insights into the factors limiting the performance of thick-film perovskite devices.
          Cover page: Strain regulates the photovoltaic performance of thick-film perovskites.
          • Article
          • Peer Reviewed
          UC Davis Previously Published Works (2020)
          Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is one of the most destructive diseases that pose a great threat to wheat production. Wheat landraces represent a rich source of powdery mildew resistance. Here, we report the map-based cloning of powdery mildew resistance gene Pm24 from Chinese wheat landrace Hulutou. It encodes a tandem kinase protein (TKP) with putative kinase-pseudokinase domains, designated WHEAT TANDEM KINASE 3 (WTK3). The resistance function of Pm24 was validated by transgenic assay, independent mutants, and allelic association analyses. Haplotype analysis revealed that a rare 6-bp natural deletion of lysine-glycine codons, endemic to wheat landraces of Shaanxi Province, China, in the kinase I domain (Kin I) of WTK3 is critical for the resistance function. Transgenic assay of WTK3 chimeric variants revealed that only the specific two amino acid deletion, rather than any of the single or more amino acid deletions, in the Kin I of WTK3 is responsible for gaining the resistance function of WTK3 against the Bgt fungus.
            Cover page: A rare gain of function mutation in a wheat tandem kinase confers resistance to powdery mildew.
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