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Evolution of MicroRNAs and the Diversification of Species
MicroRNAs (miRNAs) are ancient, short noncoding RNA molecules that regulate the transcriptome through post-transcriptional mechanisms. miRNA riboregulation is involved in a diverse range of biological processes, and misregulation is implicated in disease. It is generally thought that miRNAs function...
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Formato: | Texto |
Lenguaje: | English |
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Oxford University Press
2010
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3017390/ https://www.ncbi.nlm.nih.gov/pubmed/21169229 http://dx.doi.org/10.1093/gbe/evq085 |
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author | Loh, Yong-Hwee E. Yi, Soojin V. Streelman, J.Todd |
author_facet | Loh, Yong-Hwee E. Yi, Soojin V. Streelman, J.Todd |
author_sort | Loh, Yong-Hwee E. |
collection | PubMed |
description | MicroRNAs (miRNAs) are ancient, short noncoding RNA molecules that regulate the transcriptome through post-transcriptional mechanisms. miRNA riboregulation is involved in a diverse range of biological processes, and misregulation is implicated in disease. It is generally thought that miRNAs function to canalize cellular outputs, for instance as “fail-safe” repressors of gene misexpression. Genomic surveys in humans have revealed reduced genetic polymorphism and the signature of negative selection for both miRNAs themselves and the target sequences to which they are predicted to bind. We investigated the evolution of miRNAs and their binding sites across cichlid fishes from Lake Malawi (East Africa), where hundreds of diverse species have evolved in the last million years. Using low-coverage genome sequence data, we identified 100 cichlid miRNA genes with mature regions that are highly conserved in other animal species. We computationally predicted target sites on the 3′-untranslated regions (3′-UTRs) of cichlid genes to which miRNAs may bind and found that these sites possessed elevated single nucleotide polymorphism (SNP) densities. Furthermore, polymorphic sites in predicted miRNA targets showed higher minor allele frequencies on average and greater genetic differentiation between Malawi lineages when compared with a neutral expectation and nontarget 3′-UTR SNPs. Our data suggest that divergent selection on miRNA riboregulation may have contributed to the diversification of cichlid species and may similarly play a role in rapid phenotypic evolution of other natural systems. |
format | Text |
id | pubmed-3017390 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-30173902011-01-07 Evolution of MicroRNAs and the Diversification of Species Loh, Yong-Hwee E. Yi, Soojin V. Streelman, J.Todd Genome Biol Evol Research Articles MicroRNAs (miRNAs) are ancient, short noncoding RNA molecules that regulate the transcriptome through post-transcriptional mechanisms. miRNA riboregulation is involved in a diverse range of biological processes, and misregulation is implicated in disease. It is generally thought that miRNAs function to canalize cellular outputs, for instance as “fail-safe” repressors of gene misexpression. Genomic surveys in humans have revealed reduced genetic polymorphism and the signature of negative selection for both miRNAs themselves and the target sequences to which they are predicted to bind. We investigated the evolution of miRNAs and their binding sites across cichlid fishes from Lake Malawi (East Africa), where hundreds of diverse species have evolved in the last million years. Using low-coverage genome sequence data, we identified 100 cichlid miRNA genes with mature regions that are highly conserved in other animal species. We computationally predicted target sites on the 3′-untranslated regions (3′-UTRs) of cichlid genes to which miRNAs may bind and found that these sites possessed elevated single nucleotide polymorphism (SNP) densities. Furthermore, polymorphic sites in predicted miRNA targets showed higher minor allele frequencies on average and greater genetic differentiation between Malawi lineages when compared with a neutral expectation and nontarget 3′-UTR SNPs. Our data suggest that divergent selection on miRNA riboregulation may have contributed to the diversification of cichlid species and may similarly play a role in rapid phenotypic evolution of other natural systems. Oxford University Press 2010-12-15 /pmc/articles/PMC3017390/ /pubmed/21169229 http://dx.doi.org/10.1093/gbe/evq085 Text en © The Author(s) 2011. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Articles Loh, Yong-Hwee E. Yi, Soojin V. Streelman, J.Todd Evolution of MicroRNAs and the Diversification of Species |
title | Evolution of MicroRNAs and the Diversification of Species |
title_full | Evolution of MicroRNAs and the Diversification of Species |
title_fullStr | Evolution of MicroRNAs and the Diversification of Species |
title_full_unstemmed | Evolution of MicroRNAs and the Diversification of Species |
title_short | Evolution of MicroRNAs and the Diversification of Species |
title_sort | evolution of micrornas and the diversification of species |
topic | Research Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3017390/ https://www.ncbi.nlm.nih.gov/pubmed/21169229 http://dx.doi.org/10.1093/gbe/evq085 |
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