The evolutionary dynamics of microRNAs in domestic mammals

Abstract MiRNAs are crucial regulators of gene expression found across both the plant and animal kingdoms. While the number of annotated miRNAs deposited in miRBase has greatly increased in recent years, few studies provided comparative analyses across sets of related species, or investigated the ro...

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Autores principales:	Luca Penso-Dolfin, Simon Moxon, Wilfried Haerty, Federica Di Palma
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Orthogroups miRNA Loci miRNA Turnover Target Repertoire miRBase Medicine R Science Q
Acceso en línea:	https://doaj.org/article/9a29e576b50547178d9e37d8af156ccc
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spelling	oai:doaj.org-article:9a29e576b50547178d9e37d8af156ccc2021-12-02T15:07:57ZThe evolutionary dynamics of microRNAs in domestic mammals10.1038/s41598-018-34243-82045-2322https://doaj.org/article/9a29e576b50547178d9e37d8af156ccc2018-11-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-34243-8https://doaj.org/toc/2045-2322Abstract MiRNAs are crucial regulators of gene expression found across both the plant and animal kingdoms. While the number of annotated miRNAs deposited in miRBase has greatly increased in recent years, few studies provided comparative analyses across sets of related species, or investigated the role of miRNAs in the evolution of gene regulation. We generated small RNA libraries across 5 mammalian species (cow, dog, horse, pig and rabbit) from 4 different tissues (brain, heart, kidney and testis). We identified 1676 miRBase and 413 novel miRNAs by manually curating the set of computational predictions obtained from miRCat and miRDeep2. Our dataset spanning five species has enabled us to investigate the molecular mechanisms and selective pressures driving the evolution of miRNAs in mammals. We highlight the important contributions of intronic sequences (366 orthogroups), duplication events (135 orthogroups) and repetitive elements (37 orthogroups) in the emergence of new miRNA loci. We use this framework to estimate the patterns of gains and losses across the phylogeny, and observe high levels of miRNA turnover. Additionally, the identification of lineage-specific losses enables the characterisation of the selective constraints acting on the associated target sites. Compared to the miRBase subset, novel miRNAs tend to be more tissue specific. 20 percent of novel orthogroups are restricted to the brain, and their target repertoires appear to be enriched for neuron activity and differentiation processes. These findings may reflect an important role for young miRNAs in the evolution of brain expression plasticity. Many seed sequences appear to be specific to either the cow or the dog. Analyses on the associated targets highlight the presence of several genes under artificial positive selection, suggesting an involvement of these miRNAs in the domestication process. Altogether, we provide an overview on the evolutionary mechanisms responsible for miRNA turnover in 5 domestic species, and their possible contribution to the evolution of gene regulation.Luca Penso-DolfinSimon MoxonWilfried HaertyFederica Di PalmaNature PortfolioarticleOrthogroupsmiRNA LocimiRNA TurnoverTarget RepertoiremiRBaseMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-13 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Orthogroups miRNA Loci miRNA Turnover Target Repertoire miRBase Medicine R Science Q
spellingShingle	Orthogroups miRNA Loci miRNA Turnover Target Repertoire miRBase Medicine R Science Q Luca Penso-Dolfin Simon Moxon Wilfried Haerty Federica Di Palma The evolutionary dynamics of microRNAs in domestic mammals
description	Abstract MiRNAs are crucial regulators of gene expression found across both the plant and animal kingdoms. While the number of annotated miRNAs deposited in miRBase has greatly increased in recent years, few studies provided comparative analyses across sets of related species, or investigated the role of miRNAs in the evolution of gene regulation. We generated small RNA libraries across 5 mammalian species (cow, dog, horse, pig and rabbit) from 4 different tissues (brain, heart, kidney and testis). We identified 1676 miRBase and 413 novel miRNAs by manually curating the set of computational predictions obtained from miRCat and miRDeep2. Our dataset spanning five species has enabled us to investigate the molecular mechanisms and selective pressures driving the evolution of miRNAs in mammals. We highlight the important contributions of intronic sequences (366 orthogroups), duplication events (135 orthogroups) and repetitive elements (37 orthogroups) in the emergence of new miRNA loci. We use this framework to estimate the patterns of gains and losses across the phylogeny, and observe high levels of miRNA turnover. Additionally, the identification of lineage-specific losses enables the characterisation of the selective constraints acting on the associated target sites. Compared to the miRBase subset, novel miRNAs tend to be more tissue specific. 20 percent of novel orthogroups are restricted to the brain, and their target repertoires appear to be enriched for neuron activity and differentiation processes. These findings may reflect an important role for young miRNAs in the evolution of brain expression plasticity. Many seed sequences appear to be specific to either the cow or the dog. Analyses on the associated targets highlight the presence of several genes under artificial positive selection, suggesting an involvement of these miRNAs in the domestication process. Altogether, we provide an overview on the evolutionary mechanisms responsible for miRNA turnover in 5 domestic species, and their possible contribution to the evolution of gene regulation.
format	article
author	Luca Penso-Dolfin Simon Moxon Wilfried Haerty Federica Di Palma
author_facet	Luca Penso-Dolfin Simon Moxon Wilfried Haerty Federica Di Palma
author_sort	Luca Penso-Dolfin
title	The evolutionary dynamics of microRNAs in domestic mammals
title_short	The evolutionary dynamics of microRNAs in domestic mammals
title_full	The evolutionary dynamics of microRNAs in domestic mammals
title_fullStr	The evolutionary dynamics of microRNAs in domestic mammals
title_full_unstemmed	The evolutionary dynamics of microRNAs in domestic mammals
title_sort	evolutionary dynamics of micrornas in domestic mammals
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/9a29e576b50547178d9e37d8af156ccc
work_keys_str_mv	AT lucapensodolfin theevolutionarydynamicsofmicrornasindomesticmammals AT simonmoxon theevolutionarydynamicsofmicrornasindomesticmammals AT wilfriedhaerty theevolutionarydynamicsofmicrornasindomesticmammals AT federicadipalma theevolutionarydynamicsofmicrornasindomesticmammals AT lucapensodolfin evolutionarydynamicsofmicrornasindomesticmammals AT simonmoxon evolutionarydynamicsofmicrornasindomesticmammals AT wilfriedhaerty evolutionarydynamicsofmicrornasindomesticmammals AT federicadipalma evolutionarydynamicsofmicrornasindomesticmammals
_version_	1718388334005321728

The evolutionary dynamics of microRNAs in domestic mammals

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