Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage

Toshiyuki Shiraki, Shinji Kondo, Shintaro Katayama, Kazunori Waki, Takeya Kasukawa, Hideya Kawaji, Rimantas Kodzius, Akira Watahiki, Mari Nakamura, Takahiro Arakawa, Shiro Fukuda, Daisuke Sasaki, Anna Podhajska, Matthias Harbers, Jun Kawai, Piero Carninci*, Yoshihide Hayashizaki

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

483 Scopus citations

Abstract

We introduce cap analysis gene expression (CAGE), which is based on preparation and sequencing of concatamers of DNA tags deriving from the initial 20 nucleotides from 5′ end mRNAs. CAGE allows high-throughout gene expression analysis and the profiling of transcriptional start points (TSP), including promoter usage analysis. By analyzing four libraries (brain, cortex, hippocampus, and cerebellum), we redefined more accurately the TSPs of 11-27% of the analyzed transcriptional units that were hit. The frequency of CAGE tags correlates well with results from other analyses, such as serial analysis of gene expression, and furthermore maps the TSPs more accurately, including in tissue-specific cases. The high-throughput nature of this technology paves the way for understanding gene networks via correlation of promoter usage and gene transcriptional factor expression.

Original languageEnglish (US)
Pages (from-to)15776-15781
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume100
Issue number26
DOIs
StatePublished - Dec 23 2003

Keywords

  • Cap-trapping
  • Full-length cDNA
  • Sequencing
  • Transcriptome

ASJC Scopus subject areas

  • General

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