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dc.contributor.authorKelley, David Ren_US
dc.contributor.authorHendrickson, David Gen_US
dc.contributor.authorTenen, Danielleen_US
dc.contributor.authorRinn, John Len_US
dc.date.accessioned2015-01-05T18:25:59Z
dc.date.issued2014en_US
dc.identifier.citationKelley, David R, David G Hendrickson, Danielle Tenen, and John L Rinn. 2014. “Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions.” Genome Biology 15 (12): 537. doi:10.1186/s13059-014-0537-5. http://dx.doi.org/10.1186/s13059-014-0537-5.en
dc.identifier.issn1465-6906en
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:13581018
dc.description.abstractBackground: Transposable elements (TEs) have significantly influenced the evolution of transcriptional regulatory networks in the human genome. Post-transcriptional regulation of human genes by TE-derived sequences has been observed in specific contexts, but has yet to be systematically and comprehensively investigated. Here, we study a collection of 75 CLIP-Seq experiments mapping the RNA binding sites for a diverse set of 51 human proteins to explore the role of TEs in post-transcriptional regulation of human mRNAs and lncRNAs via RNA-protein interactions. Results: We detect widespread interactions between RNA binding proteins (RBPs) and many families of TE-derived sequence in the CLIP-Seq data. Further, alignment coverage peaks on specific positions of the TE consensus sequences, illuminating a diversity of TE-specific RBP binding motifs. Evidence of binding and conservation of these motifs in the nonrepetitive transcriptome suggests that TEs have generally appropriated existing sequence preferences of the RBPs. Depletion assays for numerous RBPs show that TE-derived binding sites affect transcript abundance and splicing similarly to nonrepetitive sites. However, in a few cases the effect of RBP binding depends on the specific TE family bound; for example, the ubiquitously expressed RBP HuR confers transcript stability unless bound to an Alu element. Conclusions: Our meta-analysis suggests a widespread role for TEs in shaping RNA-protein regulatory networks in the human genome. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0537-5) contains supplementary material, which is available to authorized users.en
dc.language.isoen_USen
dc.publisherBioMed Centralen
dc.relation.isversionofdoi:10.1186/s13059-014-0537-5en
dc.relation.hasversionhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC4272801/pdf/en
dash.licenseLAAen_US
dc.titleTransposable elements modulate human RNA abundance and splicing via specific RNA-protein interactionsen
dc.typeJournal Articleen_US
dc.description.versionVersion of Recorden
dc.relation.journalGenome Biologyen
dash.depositing.authorKelley, David Ren_US
dc.date.available2015-01-05T18:25:59Z
dc.identifier.doi10.1186/s13059-014-0537-5*
dash.contributor.affiliatedTenen, Danielle
dash.contributor.affiliatedHendrickson, David Gillis
dash.contributor.affiliatedKelley, David Roy
dash.contributor.affiliatedRinn, John


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