RNA sequencing: advances, challenges and opportunities

Nat Rev Genet. 2011 Feb;12(2):87-98. doi: 10.1038/nrg2934. Epub 2010 Dec 30.


In the few years since its initial application, massively parallel cDNA sequencing, or RNA-seq, has allowed many advances in the characterization and quantification of transcriptomes. Recently, several developments in RNA-seq methods have provided an even more complete characterization of RNA transcripts. These developments include improvements in transcription start site mapping, strand-specific measurements, gene fusion detection, small RNA characterization and detection of alternative splicing events. Ongoing developments promise further advances in the application of RNA-seq, particularly direct RNA sequencing and approaches that allow RNA quantification from very small amounts of cellular materials.

Publication types

  • Research Support, N.I.H., Extramural
  • Review

MeSH terms

  • Alternative Splicing
  • Animals
  • Humans
  • RNA / analysis*
  • RNA / genetics
  • Sequence Analysis, RNA
  • Transcription, Genetic


  • RNA