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Differences in molecular evolutionary rates among microRNAs in the human and chimpanzee genomes

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dc.contributor.author Santpere Baró, Gabriel, 1981-
dc.contributor.author López Valenzuela, María, 1982-
dc.contributor.author Petit-Marty, Natalia
dc.contributor.author Navarro i Cuartiellas, Arcadi, 1969-
dc.contributor.author Espinosa Parrilla, Yolanda, 1971-
dc.date.accessioned 2016-11-21T16:09:48Z
dc.date.available 2016-11-21T16:09:48Z
dc.date.issued 2016
dc.identifier.citation Santpere G, Lopez-Valenzuela M, Petit-Marty N, Navarro A, Espinosa-Parrilla Y. Differences in molecular evolutionary rates among microRNAs in the human and chimpanzee genomes. BMC Genomics. 2016; 17:528. DOI: 10.1186/s12864-016-2863-3
dc.identifier.issn 1471-2164
dc.identifier.uri http://hdl.handle.net/10230/27555
dc.description.abstract Background: The rise of the primate lineage is accompanied by an outstanding emergence of microRNAs, small non-coding RNAs with a prominent role in gene regulation. In spite of their biological importance little is known about the way in which natural selection has influenced microRNAs in the human lineage. To study the recent evolutionary history of human microRNAs and to analyze the signatures of natural selection in genomic regions harbouring microRNAs we have investigated the nucleotide substitution rates of 1,872 human microRNAs in the human and chimpanzee lineages. Results: We produced a depurated set of microRNA alignments of human, chimpanzee and orang-utan orthologs combining BLAT and liftOver and selected 1,214 microRNA precursors presenting optimal secondary structures. We classified microRNAs in categories depending on their genomic organization, duplication status and conservation along evolution. We compared substitution rates of the aligned microRNAs between human and chimpanzee using Tajima’s Relative Rate Test taking orang-utan as out-group and found several microRNAs with particularly high substitution rates in either the human or chimpanzee branches. We fitted different models of natural selection on these orthologous microRNA alignments and compared them using a likelihood ratio test that uses ancestral repeats and microRNA flanking regions as neutral sequences. We found that although a large fraction of human microRNAs is highly conserved among the three species studied, significant differences in rates of molecular evolution exist among microRNA categories. Particularly, primate-specific microRNAs, which are enriched in isolated and single copy microRNAs, more than doubled substitution rates of those belonging to older, non primate-specific microRNA families. Conclusions: Our results corroborate the remarkable conservation of microRNAs, a proxy of their functional relevance, and indicate that a subset of human microRNAs undergo nucleotide substitutions at higher rates, which may be suggestive of the action of positive selection.
dc.description.sponsorship This work was supported by the Ministerio de Ciencia e Innovación, España (BFU2012-38236, BFU2010-18477, BFU2009-06974, and CGL2009-09013), Direcció General de Recerca de la Generalitat de Catalunya” (2009SGR-1101, 2014SGR-866 and SGR2014-1311) and European Union Seventh Framework Programme (PIOF-GA-2009-236836 and PIRSES-GA-2013-612583).
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher BioMed Central
dc.relation.ispartof BMC Genomics. 2016;17:528
dc.rights © 2016 The Author(s). 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.
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.title Differences in molecular evolutionary rates among microRNAs in the human and chimpanzee genomes
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1186/s12864-016-2863-3
dc.subject.keyword MicroRNAs
dc.subject.keyword Acceleration rates
dc.subject.keyword Primates
dc.subject.keyword Divergence
dc.subject.keyword MicroRNA cluster
dc.subject.keyword Evolution
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BFU2012-38236
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BFU2010-18477
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/236836
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/612583
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

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