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Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3′-end of genes

mRNA polyadenylation is an essential step for the maturation of almost all eukaryotic mRNAs, and is tightly coupled with termination of transcription in defining the 3′-end of genes. Large numbers of human and mouse genes harbor alternative polyadenylation sites [poly(A) sites] that lead to mRNA var...

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Autores principales: Lee, Ju Youn, Ji, Zhe, Tian, Bin
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2553571/
https://www.ncbi.nlm.nih.gov/pubmed/18757892
http://dx.doi.org/10.1093/nar/gkn540
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author Lee, Ju Youn
Ji, Zhe
Tian, Bin
author_facet Lee, Ju Youn
Ji, Zhe
Tian, Bin
author_sort Lee, Ju Youn
collection PubMed
description mRNA polyadenylation is an essential step for the maturation of almost all eukaryotic mRNAs, and is tightly coupled with termination of transcription in defining the 3′-end of genes. Large numbers of human and mouse genes harbor alternative polyadenylation sites [poly(A) sites] that lead to mRNA variants containing different 3′-untranslated regions (UTRs) and/or encoding distinct protein sequences. Here, we examined the conservation and divergence of different types of alternative poly(A) sites across human, mouse, rat and chicken. We found that the 3′-most poly(A) sites tend to be more conserved than upstream ones, whereas poly(A) sites located upstream of the 3′-most exon, also termed intronic poly(A) sites, tend to be much less conserved. Genes with longer evolutionary history are more likely to have alternative polyadenylation, suggesting gain of poly(A) sites through evolution. We also found that nonconserved poly(A) sites are associated with transposable elements (TEs) to a much greater extent than conserved ones, albeit less frequently utilized. Different classes of TEs have different characteristics in their association with poly(A) sites via exaptation of TE sequences into polyadenylation elements. Our results establish a conservation pattern for alternative poly(A) sites in several vertebrate species, and indicate that the 3′-end of genes can be dynamically modified by TEs through evolution.
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spelling pubmed-25535712009-01-22 Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3′-end of genes Lee, Ju Youn Ji, Zhe Tian, Bin Nucleic Acids Res Molecular Biology mRNA polyadenylation is an essential step for the maturation of almost all eukaryotic mRNAs, and is tightly coupled with termination of transcription in defining the 3′-end of genes. Large numbers of human and mouse genes harbor alternative polyadenylation sites [poly(A) sites] that lead to mRNA variants containing different 3′-untranslated regions (UTRs) and/or encoding distinct protein sequences. Here, we examined the conservation and divergence of different types of alternative poly(A) sites across human, mouse, rat and chicken. We found that the 3′-most poly(A) sites tend to be more conserved than upstream ones, whereas poly(A) sites located upstream of the 3′-most exon, also termed intronic poly(A) sites, tend to be much less conserved. Genes with longer evolutionary history are more likely to have alternative polyadenylation, suggesting gain of poly(A) sites through evolution. We also found that nonconserved poly(A) sites are associated with transposable elements (TEs) to a much greater extent than conserved ones, albeit less frequently utilized. Different classes of TEs have different characteristics in their association with poly(A) sites via exaptation of TE sequences into polyadenylation elements. Our results establish a conservation pattern for alternative poly(A) sites in several vertebrate species, and indicate that the 3′-end of genes can be dynamically modified by TEs through evolution. Oxford University Press 2008-10 2008-08-30 /pmc/articles/PMC2553571/ /pubmed/18757892 http://dx.doi.org/10.1093/nar/gkn540 Text en © 2008 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Molecular Biology
Lee, Ju Youn
Ji, Zhe
Tian, Bin
Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3′-end of genes
title Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3′-end of genes
title_full Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3′-end of genes
title_fullStr Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3′-end of genes
title_full_unstemmed Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3′-end of genes
title_short Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3′-end of genes
title_sort phylogenetic analysis of mrna polyadenylation sites reveals a role of transposable elements in evolution of the 3′-end of genes
topic Molecular Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2553571/
https://www.ncbi.nlm.nih.gov/pubmed/18757892
http://dx.doi.org/10.1093/nar/gkn540
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AT tianbin phylogeneticanalysisofmrnapolyadenylationsitesrevealsaroleoftransposableelementsinevolutionofthe3endofgenes