Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation

Nat Struct Mol Biol. 2012 Aug;19(8):845-52. doi: 10.1038/nsmb.2345. Epub 2012 Jul 22.


It has recently been shown that RNA 3'-end formation plays a more widespread role in controlling gene expression than previously thought. To examine the impact of regulated 3'-end formation genome-wide, we applied direct RNA sequencing to A. thaliana. Here we show the authentic transcriptome in unprecedented detail and describe the effects of 3'-end formation on genome organization. We reveal extreme heterogeneity in RNA 3' ends, discover previously unrecognized noncoding RNAs and propose widespread reannotation of the genome. We explain the origin of most poly(A)(+) antisense RNAs and identify cis elements that control 3'-end formation in different registers. These findings are essential to understanding what the genome actually encodes, how it is organized and how regulated 3'-end formation affects these processes.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics*
  • Arabidopsis / metabolism*
  • Base Sequence
  • Chromosome Mapping
  • Gene Expression Regulation, Plant
  • Genes, Plant
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Oligodeoxyribonucleotides / metabolism
  • Polyadenylation
  • RNA 3' End Processing
  • RNA, Antisense / genetics
  • RNA, Antisense / metabolism
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • RNA, Plant / chemistry
  • RNA, Plant / genetics*
  • RNA, Plant / metabolism*
  • RNA, Small Nucleolar / genetics
  • RNA, Small Nucleolar / metabolism
  • RNA, Untranslated / chemistry
  • RNA, Untranslated / genetics
  • RNA, Untranslated / metabolism
  • Sequence Analysis, RNA


  • Oligodeoxyribonucleotides
  • RNA, Antisense
  • RNA, Messenger
  • RNA, Plant
  • RNA, Small Nucleolar
  • RNA, Untranslated
  • oligo (dT)