Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage.
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.
Shiraki
Toshiyuki
T
Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, Yokohama Institute 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
Kondo
Shinji
S
Katayama
Shintaro
S
Waki
Kazunori
K
Kasukawa
Takeya
T
Kawaji
Hideya
H
Kodzius
Rimantas
R
Watahiki
Akira
A
Nakamura
Mari
M
Arakawa
Takahiro
T
Fukuda
Shiro
S
Sasaki
Daisuke
D
Podhajska
Anna
A
Harbers
Matthias
M
Kawai
Jun
J
Carninci
Piero
P
Hayashizaki
Yoshihide
Y
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*
D012333:RNA, Messenger; D004247:DNA; D043423:Carboxypeptidase H