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

Shintaro Katayama^*¹ , Mutsumi Kanamori-Katayama^*¹ , Kazumi Yamaguchi¹^,2 , Piero Carninci¹^,3 and Yoshihide Hayashizaki¹^,3

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

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

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

author email corresponding author email* Contributed equally

Genome Biology 2007, 8:R42doi:10.1186/gb-2007-8-3-r42


Published:	26 March 2007

Subject areas: Bioinformatics, Genome studies

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.