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

Charles Plessy, Nicolas Bertin, Hazuki Takahashi, Roberto Simone, Md Salimullah, Timo Lassmann, Morana Vitezic, Jessica Severin, Signe Olivarius, Dejan Lazarevic, Nadine Hornig, Valerio Orlando, Ian Bell, Hui Gao, Jacqueline Dumais, Philipp Kapranov, Huaien Wang, Carrie A. Davis, Thomas R. Gingeras, Jun KawaiCarsten O. Daub, Yoshihide Hayashizaki, Stefano Gustincich*, Piero Carninci

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

119 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)528-534
Number of pages7
JournalNature Methods
Issue number7
StatePublished - Jul 1 2010

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology


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