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Conservation of alternative polyadenylation patterns in mammalian genes

BACKGROUND: Alternative polyadenylation is a widespread mechanism contributing to transcript diversity in eukaryotes. Over half of mammalian genes are alternatively polyadenylated. Our understanding of poly(A) site evolution is limited by the lack of a reliable identification of conserved, equivalen...

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Autores principales: Ara, Takeshi, Lopez, Fabrice, Ritchie, William, Benech, Philippe, Gautheret, Daniel
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1550727/
https://www.ncbi.nlm.nih.gov/pubmed/16872498
http://dx.doi.org/10.1186/1471-2164-7-189
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author Ara, Takeshi
Lopez, Fabrice
Ritchie, William
Benech, Philippe
Gautheret, Daniel
author_facet Ara, Takeshi
Lopez, Fabrice
Ritchie, William
Benech, Philippe
Gautheret, Daniel
author_sort Ara, Takeshi
collection PubMed
description BACKGROUND: Alternative polyadenylation is a widespread mechanism contributing to transcript diversity in eukaryotes. Over half of mammalian genes are alternatively polyadenylated. Our understanding of poly(A) site evolution is limited by the lack of a reliable identification of conserved, equivalent poly(A) sites among species. We introduce here a working definition of conserved poly(A) sites as sites that are both (i) properly aligned in human and mouse orthologous 3' untranslated regions (UTRs) and (ii) supported by EST or cDNA data in both species. RESULTS: We identified about 4800 such conserved poly(A) sites covering one third of the orthologous gene set studied. Characteristics of conserved poly(A) sites such as processing efficiency and tissue-specificity were analyzed. Conserved sites show a higher processing efficiency but no difference in tissular distribution when compared to non-conserved sites. In general, alternative poly(A) sites are species-specific and involve minor, non-conserved sites that are unlikely to play essential roles. However, there are about 500 genes with conserved tandem poly(A) sites. A significant fraction of these conserved tandems display a conserved arrangement of major/minor sites in their 3' UTR, suggesting that these alternative 3' ends may be under selection. CONCLUSION: This analysis allows us to identify potential functional alternative poly(A) sites and provides clues on the selective mechanisms at play in the appearance of multiple poly(A) sites and their maintenance in the 3' UTRs of genes.
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spelling pubmed-15507272006-08-24 Conservation of alternative polyadenylation patterns in mammalian genes Ara, Takeshi Lopez, Fabrice Ritchie, William Benech, Philippe Gautheret, Daniel BMC Genomics Research Article BACKGROUND: Alternative polyadenylation is a widespread mechanism contributing to transcript diversity in eukaryotes. Over half of mammalian genes are alternatively polyadenylated. Our understanding of poly(A) site evolution is limited by the lack of a reliable identification of conserved, equivalent poly(A) sites among species. We introduce here a working definition of conserved poly(A) sites as sites that are both (i) properly aligned in human and mouse orthologous 3' untranslated regions (UTRs) and (ii) supported by EST or cDNA data in both species. RESULTS: We identified about 4800 such conserved poly(A) sites covering one third of the orthologous gene set studied. Characteristics of conserved poly(A) sites such as processing efficiency and tissue-specificity were analyzed. Conserved sites show a higher processing efficiency but no difference in tissular distribution when compared to non-conserved sites. In general, alternative poly(A) sites are species-specific and involve minor, non-conserved sites that are unlikely to play essential roles. However, there are about 500 genes with conserved tandem poly(A) sites. A significant fraction of these conserved tandems display a conserved arrangement of major/minor sites in their 3' UTR, suggesting that these alternative 3' ends may be under selection. CONCLUSION: This analysis allows us to identify potential functional alternative poly(A) sites and provides clues on the selective mechanisms at play in the appearance of multiple poly(A) sites and their maintenance in the 3' UTRs of genes. BioMed Central 2006-07-26 /pmc/articles/PMC1550727/ /pubmed/16872498 http://dx.doi.org/10.1186/1471-2164-7-189 Text en Copyright © 2006 Ara et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Ara, Takeshi
Lopez, Fabrice
Ritchie, William
Benech, Philippe
Gautheret, Daniel
Conservation of alternative polyadenylation patterns in mammalian genes
title Conservation of alternative polyadenylation patterns in mammalian genes
title_full Conservation of alternative polyadenylation patterns in mammalian genes
title_fullStr Conservation of alternative polyadenylation patterns in mammalian genes
title_full_unstemmed Conservation of alternative polyadenylation patterns in mammalian genes
title_short Conservation of alternative polyadenylation patterns in mammalian genes
title_sort conservation of alternative polyadenylation patterns in mammalian genes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1550727/
https://www.ncbi.nlm.nih.gov/pubmed/16872498
http://dx.doi.org/10.1186/1471-2164-7-189
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