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    Identification of piRNA Binding Sites Reveals the Argonaute Regulatory Landscape of the C. elegans Germline

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    Authors
    Shen, En-Zhi
    Chen, Hao
    Ozturk, Ahmet R.
    Tu, Shikui
    Shirayama, Masaki
    Tang, Wen
    Ding, Yue-He
    Dai, Siyuan
    Weng, Zhiping
    Mello, Craig C.
    Student Authors
    Siyuan Dai
    Academic Program
    Interdisciplinary
    UMass Chan Affiliations
    Program in Bioinformatics and Integrative Biology
    RNA Therapeutics Institute
    Document Type
    Journal Article
    Publication Date
    2018-02-22
    Keywords
    Biochemistry, Biophysics, and Structural Biology
    Bioinformatics
    Computational Biology
    
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    Link to Full Text
    https://doi.org/10.1016/j.cell.2018.02.002
    Abstract
    piRNAs (Piwi-interacting small RNAs) engage Piwi Argonautes to silence transposons and promote fertility in animal germlines. Genetic and computational studies have suggested that C. elegans piRNAs tolerate mismatched pairing and in principle could target every transcript. Here we employ in vivo cross-linking to identify transcriptome-wide interactions between piRNAs and target RNAs. We show that piRNAs engage all germline mRNAs and that piRNA binding follows microRNA-like pairing rules. Targeting correlates better with binding energy than with piRNA abundance, suggesting that piRNA concentration does not limit targeting. In mRNAs silenced by piRNAs, secondary small RNAs accumulate at the center and ends of piRNA binding sites. In germline-expressed mRNAs, however, targeting by the CSR-1 Argonaute correlates with reduced piRNA binding density and suppression of piRNA-associated secondary small RNAs. Our findings reveal physiologically important and nuanced regulation of individual piRNA targets and provide evidence for a comprehensive post-transcriptional regulatory step in germline gene expression.
    Source
    Shen EZ, Chen H, Ozturk AR, Tu S, Shirayama M, Tang W, Ding YH, Dai SY, Weng Z, Mello CC. Identification of piRNA Binding Sites Reveals the Argonaute Regulatory Landscape of the C. elegans Germline. Cell. 2018 Feb 22;172(5):937-951.e18. doi: 10.1016/j.cell.2018.02.002. Epub 2018 Feb 15. PMID: 29456082; PMCID: PMC5905434.
    DOI
    10.1016/j.cell.2018.02.002
    Permanent Link to this Item
    http://hdl.handle.net/20.500.14038/25839
    PubMed ID
    29456082
    ae974a485f413a2113503eed53cd6c53
    10.1016/j.cell.2018.02.002
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    Program in Bioinformatics and Integrative Biology Publications

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