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CAGE-TSSchip: promoter-based expression profiling using the 5'-leading label of capped transcripts

Shintaro Katayama1, Mutsumi Kanamori-Katayama1, Kazumi Yamaguchi12, Piero Carninci13 and Yoshihide Hayashizaki13*

Author Affiliations

1 Laboratory for Genome Exploration Research Group, Genomic Sciences Center, RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan

2 Bioinformatics Solutions Division, Nittetsu Hitachi Systems Engineering, Inc., Akashi-cho, Chuo-ku, Tokyo 104-6591, Japan

3 Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Main Campus, Hirosawa, Wako 351-0198, Japan

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Genome Biology 2007, 8:R42  doi:10.1186/gb-2007-8-3-r42

Published: 26 March 2007

Abstract

Cap analysis gene expression (CAGE) technology has revealed numerous transcription start sites (TSSs) in mammals and has suggested complex promoter-based patterns of regulation. We developed the CAGE-TSSchip to detect promoter-based transcriptional activity. The CAGE-TSSchip is a customized oligonucleotide array that targets known TSSs identified by CAGE. A new labeling method, labeling capped transcripts from the 5'-end, had to be developed. The CAGE-TSSchip is accurate and sensitive, and represents the activity of each TSS.