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Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation.

Alternative polyadenylation (APA) has been shown to play an important role in gene expression regulation in animals and plants. However, the extent of sense and antisense APA at the genome level is not known. We developed a deep-sequencing protocol that queries the junctions of 3'UTR and poly(A) tai... Full description

Journal Title: Proceedings of the National Academy of Sciences of the United States of America July 26, 2011, Vol.108(30), pp.12533-12538
Main Author: Wu, Xiaohui
Other Authors: Liu, Man , Downie, Bruce , Liang, Chun , Ji, Guoli , Li, Qingshun Q , Hunt, Arthur G
Format: Electronic Article Electronic Article
Language: English
Subjects:
ID: E-ISSN: 1091-6490 ; DOI: 10.1073/pnas.1019732108
Link: http://search.proquest.com/docview/879678970/?pq-origsite=primo
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title: Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation.
format: Article
creator:
  • Wu, Xiaohui
  • Liu, Man
  • Downie, Bruce
  • Liang, Chun
  • Ji, Guoli
  • Li, Qingshun Q
  • Hunt, Arthur G
subjects:
  • 3' Untranslated Regions–Genetics
  • Alternative Splicing–Metabolism
  • Arabidopsis–Genetics
  • Binding Sites–Genetics
  • DNA, Plant–Metabolism
  • Gene Expression Profiling–Genetics
  • Genes, Plant–Metabolism
  • Genome-Wide Association Study–Genetics
  • Introns–Metabolism
  • Polyadenylation–Genetics
  • Promoter Regions, Genetic–Metabolism
  • RNA, Antisense–Metabolism
  • RNA, Messenger–Metabolism
  • RNA, Plant–Metabolism
  • 3' Untranslated Regions
  • DNA, Plant
  • RNA, Antisense
  • RNA, Messenger
  • RNA, Plant
ispartof: Proceedings of the National Academy of Sciences of the United States of America, July 26, 2011, Vol.108(30), pp.12533-12538
description: Alternative polyadenylation (APA) has been shown to play an important role in gene expression regulation in animals and plants. However, the extent of sense and antisense APA at the genome level is not known. We developed a deep-sequencing protocol that queries the junctions of 3'UTR and poly(A) tails and confidently maps the poly(A) tags to the annotated genome. The results of this mapping show that 70% of Arabidopsis genes use more than one poly(A) site, excluding microheterogeneity. Analysis of the poly(A) tags reveal extensive APA in introns and coding sequences, results of which can significantly alter transcript sequences and their encoding proteins. Although the interplay of intron splicing and polyadenylation potentially defines poly(A) site uses in introns, the polyadenylation signals leading to the use of CDS protein-coding region poly(A) sites are distinct from the rest of the genome. Interestingly, a large number of poly(A) sites correspond to putative antisense transcripts that overlap with the promoter of the associated sense transcript, a mode previously demonstrated to regulate sense gene expression. Our results suggest that APA plays a far greater role in gene expression in plants than previously expected. alternative processing | antisense transcription | nonstop mRNAs doi:10.1073/pnas.1019732108
language: eng
source:
identifier: E-ISSN: 1091-6490 ; DOI: 10.1073/pnas.1019732108
fulltext: fulltext
issn:
  • 10916490
  • 1091-6490
url: Link


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titleGenome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation.
creatorWu, Xiaohui ; Liu, Man ; Downie, Bruce ; Liang, Chun ; Ji, Guoli ; Li, Qingshun Q ; Hunt, Arthur G
contributorWu, Xiaohui (correspondence author) ; Wu, Xiaohui (record owner)
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identifierE-ISSN: 1091-6490 ; DOI: 10.1073/pnas.1019732108
subject3' Untranslated Regions–Genetics ; Alternative Splicing–Metabolism ; Arabidopsis–Genetics ; Binding Sites–Genetics ; DNA, Plant–Metabolism ; Gene Expression Profiling–Genetics ; Genes, Plant–Metabolism ; Genome-Wide Association Study–Genetics ; Introns–Metabolism ; Polyadenylation–Genetics ; Promoter Regions, Genetic–Metabolism ; RNA, Antisense–Metabolism ; RNA, Messenger–Metabolism ; RNA, Plant–Metabolism ; 3' Untranslated Regions ; DNA, Plant ; RNA, Antisense ; RNA, Messenger ; RNA, Plant
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descriptionAlternative polyadenylation (APA) has been shown to play an important role in gene expression regulation in animals and plants. However, the extent of sense and antisense APA at the genome level is not known. We developed a deep-sequencing protocol that queries the junctions of 3'UTR and poly(A) tails and confidently maps the poly(A) tags to the annotated genome. The results of this mapping show that 70% of Arabidopsis genes use more than one poly(A) site, excluding microheterogeneity. Analysis of the poly(A) tags reveal extensive APA in introns and coding sequences, results of which can significantly alter transcript sequences and their encoding proteins. Although the interplay of intron splicing and polyadenylation potentially defines poly(A) site uses in introns, the polyadenylation signals leading to the use of CDS protein-coding region poly(A) sites are distinct from the rest of the genome. Interestingly, a large number of poly(A) sites correspond to putative antisense transcripts that overlap with the promoter of the associated sense transcript, a mode previously demonstrated to regulate sense gene expression. Our results suggest that APA plays a far greater role in gene expression in plants than previously expected. alternative processing | antisense transcription | nonstop mRNAs doi:10.1073/pnas.1019732108
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titleGenome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation.
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03' Untranslated Regions–Genetics
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titleGenome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation.
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03' Untranslated Regions–Genetics
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