Pervasive transcription: illuminating the dark matter of bacterial transcriptomes

Nat Rev Microbiol. 2014 Sep;12(9):647-53. doi: 10.1038/nrmicro3316. Epub 2014 Jul 28.


The conventional view of transcription posits that mRNAs are generated from the coding DNA strand and are delineated by gene boundaries; however, recent reports have mapped transcription start sites to unexpected locations in bacterial genomes, including the non-coding strand. The resultant RNAs were previously dismissed as artefacts, but models that describe such events as 'pervasive transcription' are now gaining support. In this Opinion article, we discuss our current understanding of pervasive transcription, its genetic origin and its regulation. On the basis of existing observations, we propose that RNAs that result from pervasive transcription are more than 'transcriptional noise' and have important functions in gene regulation and genome evolution.

Publication types

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

MeSH terms

  • Bacteria / genetics*
  • Bacterial Proteins / genetics
  • Evolution, Molecular
  • Gene Expression Regulation, Bacterial*
  • Genome, Bacterial / genetics*
  • RNA Stability
  • RNA, Antisense / genetics*
  • RNA, Bacterial / genetics
  • RNA, Messenger / genetics
  • RNA, Untranslated / genetics
  • Transcription Initiation Site
  • Transcription, Genetic*
  • Transcriptome*


  • Bacterial Proteins
  • RNA, Antisense
  • RNA, Bacterial
  • RNA, Messenger
  • RNA, Untranslated