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

[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...

Descripción completa

Detalles Bibliográficos
Autores: Santpere, Gabriel, López Valenzuela, María, Petit-Marty, Natalia, Navarro, Arcadi, Espinosa-Parrilla, Yolanda
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2016
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/150607
Acceso en línea:http://hdl.handle.net/10261/150607
Access Level:acceso abierto
Palabra clave:MicroRNAs
Acceleration rates
Primates
Divergence
microRNA cluster
Evolution
id ES_d1a2caf2bb607851243bb6d8680fe34e
oai_identifier_str oai:digital.csic.es:10261/150607
network_acronym_str ES
network_name_str España
repository_id_str
spelling Differences in molecular evolutionary rates among microRNAs in the human and chimpanzee genomesSantpere, GabrielLópez Valenzuela, MaríaPetit-Marty, NataliaNavarro, ArcadiEspinosa-Parrilla, YolandaMicroRNAsAcceleration ratesPrimatesDivergencemicroRNA clusterEvolution[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.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). This publication has been cofinanced by FEDER —European Regional Development Fund “A way to build Europe.” MLV is funded by a Beca per a la Formació de Personal Investigador (FI) fellowship from the Agència de Gestió d’Ajuts Universitaris i de Recerca, Generalitat de Catalunya.Peer reviewedBioMed CentralMinisterio de Ciencia e Innovación (España)Generalitat de CatalunyaEuropean CommissionConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]201720172016info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/150607reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/EC/FP7/236836info:eu-repo/grantAgreement/EC/FP7/612583http://dx.doi.org/10.1186/s12864-016-2863-3Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/1506072026-05-22T06:33:51Z
dc.title.none.fl_str_mv Differences in molecular evolutionary rates among microRNAs in the human and chimpanzee genomes
title Differences in molecular evolutionary rates among microRNAs in the human and chimpanzee genomes
spellingShingle Differences in molecular evolutionary rates among microRNAs in the human and chimpanzee genomes
Santpere, Gabriel
MicroRNAs
Acceleration rates
Primates
Divergence
microRNA cluster
Evolution
title_short Differences in molecular evolutionary rates among microRNAs in the human and chimpanzee genomes
title_full Differences in molecular evolutionary rates among microRNAs in the human and chimpanzee genomes
title_fullStr Differences in molecular evolutionary rates among microRNAs in the human and chimpanzee genomes
title_full_unstemmed Differences in molecular evolutionary rates among microRNAs in the human and chimpanzee genomes
title_sort Differences in molecular evolutionary rates among microRNAs in the human and chimpanzee genomes
dc.creator.none.fl_str_mv Santpere, Gabriel
López Valenzuela, María
Petit-Marty, Natalia
Navarro, Arcadi
Espinosa-Parrilla, Yolanda
author Santpere, Gabriel
author_facet Santpere, Gabriel
López Valenzuela, María
Petit-Marty, Natalia
Navarro, Arcadi
Espinosa-Parrilla, Yolanda
author_role author
author2 López Valenzuela, María
Petit-Marty, Natalia
Navarro, Arcadi
Espinosa-Parrilla, Yolanda
author2_role author
author
author
author
dc.contributor.none.fl_str_mv Ministerio de Ciencia e Innovación (España)
Generalitat de Catalunya
European Commission
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv MicroRNAs
Acceleration rates
Primates
Divergence
microRNA cluster
Evolution
topic MicroRNAs
Acceleration rates
Primates
Divergence
microRNA cluster
Evolution
description [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.
publishDate 2016
dc.date.none.fl_str_mv 2016
2017
2017
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/150607
url http://hdl.handle.net/10261/150607
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/EC/FP7/236836
info:eu-repo/grantAgreement/EC/FP7/612583
http://dx.doi.org/10.1186/s12864-016-2863-3
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1869420280499142656
score 15,812455

Similares en LA Referencia