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dc.contributor.authorShen, En-Zhi
dc.contributor.authorChen, Hao
dc.contributor.authorOzturk, Ahmet R.
dc.contributor.authorTu, Shikui
dc.contributor.authorShirayama, Masaki
dc.contributor.authorTang, Wen
dc.contributor.authorDing, Yue-He
dc.contributor.authorDai, Siyuan
dc.contributor.authorWeng, Zhiping
dc.contributor.authorMello, Craig C.
dc.date2022-08-11T08:07:59.000
dc.date.accessioned2022-08-23T15:37:59Z
dc.date.available2022-08-23T15:37:59Z
dc.date.issued2018-02-22
dc.date.submitted2018-06-11
dc.identifier.citationShen 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.
dc.identifier.issn0092-8674 (Linking)
dc.identifier.doi10.1016/j.cell.2018.02.002
dc.identifier.pmid29456082
dc.identifier.urihttp://hdl.handle.net/20.500.14038/25839
dc.description.abstractpiRNAs (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.
dc.language.isoen_US
dc.relation.urlhttps://doi.org/10.1016/j.cell.2018.02.002
dc.subjectBiochemistry, Biophysics, and Structural Biology
dc.subjectBioinformatics
dc.subjectComputational Biology
dc.titleIdentification of piRNA Binding Sites Reveals the Argonaute Regulatory Landscape of the C. elegans Germline
dc.typeJournal Article
dc.source.journaltitleCell
dc.source.volume172
dc.source.issue5
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/bioinformatics_pubs/130
dc.identifier.contextkey12289641
html.description.abstract<p>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.</p>
dc.identifier.submissionpathbioinformatics_pubs/130
dc.contributor.departmentProgram in Bioinformatics and Integrative Biology
dc.contributor.departmentRNA Therapeutics Institute
dc.source.pages937-951.e18
dc.contributor.studentSiyuan Dai
dc.description.thesisprogramInterdisciplinary


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