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

Xiaohui Wu, Man Liu, Bruce Downie, Chun Liang, Guoli Ji, Qingshun Q. Li, Arthur G. Hunt

Research output: Contribution to journalArticlepeer-review

222 Scopus citations

Abstract

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.

Original languageEnglish
Pages (from-to)12533-12538
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume108
Issue number30
DOIs
StatePublished - Jul 26 2011

Keywords

  • Alternative processing
  • Antisense transcription
  • Nonstop mRNAs

ASJC Scopus subject areas

  • General

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