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

被引：502

作者：

Shiraki, T

Kondo, S

Katayama, S

Waki, K

Kasukawa, T

Kawaji, H

Kodzius, R

Watahiki, A

Nakamura, M

Arakawa, T

Fukuda, S

Sasaki, D

Podhajska, A

Harbers, M

Kawai, J

Carninci, P

Hayashizaki, Y

机构：

[1] RIKEN, Genomic Sci Ctr, Lab Genome Explorat Res Grp, Yokohama Inst,Tsurumi Ku, Yokohama, Kanagawa 2300045, Japan

[2] RIKEN, Genome Sci Lab, Wako, Saitama, Japan

[3] Univ Gdansk, Dept Biotechnol, Intercollegiate Fac Biotechnol, PL-80822 Gdansk, Poland

[4] Med Univ Gdansk, PL-80822 Gdansk, Poland

[5] Yokohama City Univ, Grad Sch Integrated Sci, Div Genomic Informat Resources Sci Biol Supramol, Tsurumi Ku, Yokohama, Kanagawa 2300045, Japan

[6] NTT Software Corp, Network Serv Solut Business Grp, Naka Ku, Yokohama, Kanagawa 2318551, Japan

[7] Danform Inc, Ami, Ibaraki 3000332, Japan

来源：

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA | 2003年 / 100卷 / 26期

关键词：

full-length cDNA; transcriptome; sequencing; cap-trapping;

D O I：

10.1073/pnas.2136655100

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页码：15776 / 15781

页数：6

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