Studying bacterial transcriptomes using RNA-seq

Curr Opin Microbiol. 2010 Oct;13(5):619-24. doi: 10.1016/j.mib.2010.09.009. Epub 2010 Sep 29.


Genome-wide studies of bacterial gene expression are shifting from microarray technology to second generation sequencing platforms. RNA-seq has a number of advantages over hybridization-based techniques, such as annotation-independent detection of transcription, improved sensitivity and increased dynamic range. Early studies have uncovered a wealth of novel coding sequences and non-coding RNA, and are revealing a transcriptional landscape that increasingly mirrors that of eukaryotes. Already basic RNA-seq protocols have been improved and adapted to looking at particular aspects of RNA biology, often with an emphasis on non-coding RNAs, and further refinements to current techniques will improve our understanding of gene expression, and genome content, in the future.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Gene Expression Profiling*
  • Genes, Bacterial
  • Oligonucleotide Array Sequence Analysis
  • RNA, Bacterial / analysis*
  • RNA, Bacterial / genetics
  • Sequence Analysis, RNA / methods*


  • RNA, Bacterial