Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

Nat Methods. 2010 Jul;7(7):528-34. doi: 10.1038/nmeth.1470. Epub 2010 Jun 13.


Large-scale sequencing projects have revealed an unexpected complexity in the origins, structures and functions of mammalian transcripts. Many loci are known to produce overlapping coding and noncoding RNAs with capped 5' ends that vary in size. Methods to identify the 5' ends of transcripts will facilitate the discovery of new promoters and 5' ends derived from secondary capping events. Such methods often require high input amounts of RNA not obtainable from highly refined samples such as tissue microdissections and subcellular fractions. Therefore, we developed nano-cap analysis of gene expression (nanoCAGE), a method that captures the 5' ends of transcripts from as little as 10 ng of total RNA, and CAGEscan, a mate-pair adaptation of nanoCAGE that captures the transcript 5' ends linked to a downstream region. Both of these methods allow further annotation-agnostic studies of the complex human transcriptome.

Publication types

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

MeSH terms

  • Gene Expression Profiling*
  • Gene Expression Regulation / physiology*
  • Genome, Human
  • Humans
  • Nanotechnology / methods*
  • Promoter Regions, Genetic / physiology*
  • RNA / genetics
  • RNA / metabolism*


  • RNA