Secondary structure impacts patterns of selection in human IncRNAs
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- dc.contributor.author Pegueroles Queralt, Maria Cintaca
- dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-ca
- dc.date.accessioned 2016-11-22T16:33:36Z
- dc.date.available 2016-11-22T16:33:36Z
- dc.date.issued 2016ca
- dc.description.abstract Background: Metazoans transcribe many long non-coding RNAs (lncRNAs) that are poorly conserved and whose function remains unknown. This has raised the questions of what fraction of the predicted lncRNAs is actually functional, and whether selection can effectively constrain lncRNAs in species with small effective population sizes such as human populations. Results: Here we evaluate signatures of selection in human lncRNAs using inter-specific data and intra-specific comparisons from five major populations, as well as by assessing relationships between sequence variation and predictions of secondary structure. In all analyses we included a reference of functionally characterized lncRNAs. Altogether, our results show compelling evidence of recent purifying selection acting on both characterized and predicted lncRNAs. We found that RNA secondary structure constrains sequence variation in lncRNAs, so that polymorphisms are depleted in paired regions with low accessibility and tend to be neutral with respect to structural stability. Conclusions: Important implications of our results are that secondary structure plays a role in the functionality of lncRNAs, and that the set of predicted lncRNAs contains a large fraction of functional ones that may play key roles that remain to be discovered.
- dc.description.sponsorship Toni Gabaldon's (TG’s) group acknowledges support from the Spanish Ministry of Economy and Competitiveness grants “Centro de Excelencia Severo Ochoa 2013-2017” SEV-2012-0208 and BFU2015-67107, cofounded by the European Regional Development Fund (ERDF); from the European Union and ERC Seventh Framework Programme (FP7/2007-2013) under grant agreements FP7-PEOPLE-2013-ITN-606786 and ERC-2012-StG-310325; and a grant from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement number H2020-MSCA-ITN-2014-642095.
- dc.format.mimetype application/pdfca
- dc.identifier.citation Pegueroles C, Gabaldón T. Secondary structure impacts patterns of selection in human IncRNAs. BMC Biology. 2016;14:60. DOI: 10.1186/s12915-016-0283-0ca
- dc.identifier.doi http://dx.doi.org/10.1186/s12915-016-0283-0
- dc.identifier.issn 1741-7007ca
- dc.identifier.uri http://hdl.handle.net/10230/27572
- dc.language.iso engca
- dc.publisher BioMed Centralca
- dc.relation.ispartof BMC Biology. 2016;14:60
- dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/SEV2012-0208
- dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2015-67107
- dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/606786
- dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/642095
- dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/310325
- dc.rights © 2016 Pegueroles and Gabaldon. Open Access. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.ca
- dc.rights.accessRights info:eu-repo/semantics/openAccessca
- dc.rights.uri http://creativecommons.org/licenses/by/4.0/
- dc.subject.keyword lncRNA
- dc.subject.keyword Purifying selection
- dc.subject.keyword Divergence
- dc.subject.keyword Polymorphism
- dc.subject.keyword Secondary structure
- dc.title Secondary structure impacts patterns of selection in human IncRNAsca
- dc.type info:eu-repo/semantics/articleca
- dc.type.version info:eu-repo/semantics/publishedVersionca