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Genome-wide dynamics of alternative polyadenylation in rice

Alternative polyadenylation (APA), in which a transcript uses one of the poly(A) sites to define its 3′-end, is a common regulatory mechanism in eukaryotic gene expression. However, the potential of APA in determining crop agronomic traits remains elusive. This study systematically tallied poly(A) s...

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Autores principales: Fu, Haihui, Yang, Dewei, Su, Wenyue, Ma, Liuyin, Shen, Yingjia, Ji, Guoli, Ye, Xinfu, Wu, Xiaohui, Li, Qingshun Q.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5131826/
https://www.ncbi.nlm.nih.gov/pubmed/27733415
http://dx.doi.org/10.1101/gr.210757.116
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author Fu, Haihui
Yang, Dewei
Su, Wenyue
Ma, Liuyin
Shen, Yingjia
Ji, Guoli
Ye, Xinfu
Wu, Xiaohui
Li, Qingshun Q.
author_facet Fu, Haihui
Yang, Dewei
Su, Wenyue
Ma, Liuyin
Shen, Yingjia
Ji, Guoli
Ye, Xinfu
Wu, Xiaohui
Li, Qingshun Q.
author_sort Fu, Haihui
collection PubMed
description Alternative polyadenylation (APA), in which a transcript uses one of the poly(A) sites to define its 3′-end, is a common regulatory mechanism in eukaryotic gene expression. However, the potential of APA in determining crop agronomic traits remains elusive. This study systematically tallied poly(A) sites of 14 different rice tissues and developmental stages using the poly(A) tag sequencing (PAT-seq) approach. The results indicate significant involvement of APA in developmental and quantitative trait loci (QTL) gene expression. About 48% of all expressed genes use APA to generate transcriptomic and proteomic diversity. Some genes switch APA sites, allowing differentially expressed genes to use alternate 3′ UTRs. Interestingly, APA in mature pollen is distinct where differential expression levels of a set of poly(A) factors and different distributions of APA sites are found, indicating a unique mRNA 3′-end formation regulation during gametophyte development. Equally interesting, statistical analyses showed that QTL tends to use APA for regulation of gene expression of many agronomic traits, suggesting a potential important role of APA in rice production. These results provide thus far the most comprehensive and high-resolution resource for advanced analysis of APA in crops and shed light on how APA is associated with trait formation in eukaryotes.
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spelling pubmed-51318262017-06-01 Genome-wide dynamics of alternative polyadenylation in rice Fu, Haihui Yang, Dewei Su, Wenyue Ma, Liuyin Shen, Yingjia Ji, Guoli Ye, Xinfu Wu, Xiaohui Li, Qingshun Q. Genome Res Resource Alternative polyadenylation (APA), in which a transcript uses one of the poly(A) sites to define its 3′-end, is a common regulatory mechanism in eukaryotic gene expression. However, the potential of APA in determining crop agronomic traits remains elusive. This study systematically tallied poly(A) sites of 14 different rice tissues and developmental stages using the poly(A) tag sequencing (PAT-seq) approach. The results indicate significant involvement of APA in developmental and quantitative trait loci (QTL) gene expression. About 48% of all expressed genes use APA to generate transcriptomic and proteomic diversity. Some genes switch APA sites, allowing differentially expressed genes to use alternate 3′ UTRs. Interestingly, APA in mature pollen is distinct where differential expression levels of a set of poly(A) factors and different distributions of APA sites are found, indicating a unique mRNA 3′-end formation regulation during gametophyte development. Equally interesting, statistical analyses showed that QTL tends to use APA for regulation of gene expression of many agronomic traits, suggesting a potential important role of APA in rice production. These results provide thus far the most comprehensive and high-resolution resource for advanced analysis of APA in crops and shed light on how APA is associated with trait formation in eukaryotes. Cold Spring Harbor Laboratory Press 2016-12 /pmc/articles/PMC5131826/ /pubmed/27733415 http://dx.doi.org/10.1101/gr.210757.116 Text en © 2016 Fu et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
spellingShingle Resource
Fu, Haihui
Yang, Dewei
Su, Wenyue
Ma, Liuyin
Shen, Yingjia
Ji, Guoli
Ye, Xinfu
Wu, Xiaohui
Li, Qingshun Q.
Genome-wide dynamics of alternative polyadenylation in rice
title Genome-wide dynamics of alternative polyadenylation in rice
title_full Genome-wide dynamics of alternative polyadenylation in rice
title_fullStr Genome-wide dynamics of alternative polyadenylation in rice
title_full_unstemmed Genome-wide dynamics of alternative polyadenylation in rice
title_short Genome-wide dynamics of alternative polyadenylation in rice
title_sort genome-wide dynamics of alternative polyadenylation in rice
topic Resource
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5131826/
https://www.ncbi.nlm.nih.gov/pubmed/27733415
http://dx.doi.org/10.1101/gr.210757.116
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