title: Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage.
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.
authors.affiliation: Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, Yokohama Institute 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Toshiyuki
authors.initials: T
authors.lastname: Shiraki
authors.forename: Shinji
authors.initials: S
authors.lastname: Kondo
authors.forename: Shintaro
authors.initials: S
authors.lastname: Katayama
authors.forename: Kazunori
authors.initials: K
authors.lastname: Waki
authors.forename: Takeya
authors.initials: T
authors.lastname: Kasukawa
authors.forename: Hideya
authors.initials: H
authors.lastname: Kawaji
authors.forename: Rimantas
authors.initials: R
authors.lastname: Kodzius
authors.forename: Akira
authors.initials: A
authors.lastname: Watahiki
authors.forename: Mari
authors.initials: M
authors.lastname: Nakamura
authors.forename: Takahiro
authors.initials: T
authors.lastname: Arakawa
authors.forename: Shiro
authors.initials: S
authors.lastname: Fukuda
authors.forename: Daisuke
authors.initials: D
authors.lastname: Sasaki
authors.forename: Anna
authors.initials: A
authors.lastname: Podhajska
authors.forename: Matthias
authors.initials: M
authors.lastname: Harbers
authors.forename: Jun
authors.initials: J
authors.lastname: Kawai
authors.forename: Piero
authors.initials: P
authors.lastname: Carninci
authors.forename: Yoshihide
authors.initials: Y
authors.lastname: Hayashizaki
mesh_terms: D000818:Animals; D001483:Base Sequence; D001923:Brain Chemistry; D043423:Carboxypeptidase H / Q000235:genetics; D004247:DNA / Q000737:chemistry / Q000235:genetics; D005786:Gene Expression Regulation; D005821:Genetic Techniques; D051379:Mice; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D011401:Promoter Regions, Genetic / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D015203:Reproducibility of Results; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D012333:RNA, Messenger; D004247:DNA; D043423:Carboxypeptidase H