The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs
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- dc.contributor.author Johnson, Roryca
- dc.contributor.author Guigó Serra, Rodericca
- dc.date.accessioned 2015-06-18T09:59:48Z
- dc.date.available 2015-06-18T09:59:48Z
- dc.date.issued 2014ca
- dc.description.abstract Our genome contains tens of thousands of long noncoding RNAs (lncRNAs), many of which are likely to have genetic regulatory functions. It has been proposed that lncRNA are organized into combinations of discrete functional domains, but the nature of these and their identification remain elusive. One class of sequence elements that is enriched in lncRNA is represented by transposable elements (TEs), repetitive mobile genetic sequences that have contributed widely to genome evolution through a process termed exaptation. Here, we link these two concepts by proposing that exonic TEs act as RNA domains that are essential for lncRNA function. We term such elements Repeat Insertion Domains of LncRNAs (RIDLs). A growing number of RIDLs have been experimentally defined, where TE-derived fragments of lncRNA act as RNA-, DNA-, and protein-binding domains. We propose that these reflect a more general phenomenon of exaptation during lncRNA evolution, where inserted TE sequences are repurposed as recognition sites for both protein and nucleic acids. We discuss a series of genomic screens that may be used in the future to systematically discover RIDLs. The RIDL hypothesis has the potential to explain how functional evolution can keep pace with the rapid gene evolution observed in lncRNA. More practically, TE maps may in the future be used to predict lncRNA function.en
- dc.description.sponsorship R.J. is supported by a Ramón y Cajal fellowship RYC-2011-08851 from MICINNen
- dc.format.mimetype application/pdfca
- dc.identifier.citation Johnson R, Guigó R. The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs. RNA. 2014;20:959-76. DOI: 10.1261/rna.044560.114ca
- dc.identifier.doi http://dx.doi.org/10.1261/rna.044560.114
- dc.identifier.issn 1355-8382ca
- dc.identifier.uri http://hdl.handle.net/10230/23862
- dc.language.iso engca
- dc.publisher Cold Spring Harbor Laboratory Press (CSHL Press)ca
- dc.relation.ispartof RNA. 2014;20:959-76
- dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/RYC2011-08851
- dc.rights © 2014 Johnson and Guigó; Published by Cold Spring Harbor Laboratory Press for the RNA Society. This article, published in RNA, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.en
- dc.rights.accessRights info:eu-repo/semantics/openAccessca
- dc.rights.uri http://creativecommons.org/licenses/by/4.0/
- dc.subject.keyword Long noncoding RNAen
- dc.subject.keyword lncRNAen
- dc.subject.keyword Transposable elementen
- dc.subject.keyword Transposon repeat elementen
- dc.subject.keyword Genomeen
- dc.subject.keyword Evolutionen
- dc.subject.keyword Functional domainen
- dc.subject.other RNAca
- dc.subject.other Proteïnes -- Metabolismeca
- dc.subject.other Gens Mapatgeca
- dc.title The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAsen
- dc.type info:eu-repo/semantics/articleca
- dc.type.version info:eu-repo/semantics/publishedVersionca