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

Toshiyuki Shiraki; Shinji Kondo; Shintaro Katayama; Kazunori Waki; Takeya Kasukawa; Hideya Kawaji; Rimantas Kodzius; Akira Watahiki; Mari Nakamura; Takahiro Arakawa; Shiro Fukuda; Daisuke Sasaki; Anna Podhajska; Matthias Harbers; Jun Kawai; Piero Carninci; Yoshihide Hayashizaki

doi:10.1073/pnas.2136655100

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

Toshiyuki Shiraki, Shinji Kondo, Shintaro Katayama, Kazunori Waki, Takeya Kasukawa, Hideya Kawaji, Rimantas Kodzius, Akira Watahiki, Mari Nakamura, Takahiro Arakawa, Shiro Fukuda, Daisuke Sasaki, Anna Podhajska, Matthias Harbers, Jun Kawai, Piero Carninci^*, Yoshihide Hayashizaki

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

587 Scopus citations

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.

Original language	English (US)
Pages (from-to)	15776-15781
Number of pages	6
Journal	PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume	100
Issue number	26
DOIs	https://doi.org/10.1073/pnas.2136655100
State	Published - Dec 23 2003
Externally published	Yes

Keywords

Cap-trapping
Full-length cDNA
Sequencing
Transcriptome

ASJC Scopus subject areas

General

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10.1073/pnas.2136655100

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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. (2003). Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 100(26), 15776-15781. https://doi.org/10.1073/pnas.2136655100

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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.",

keywords = "Cap-trapping, Full-length cDNA, Sequencing, Transcriptome",

author = "Toshiyuki Shiraki and Shinji Kondo and Shintaro Katayama and Kazunori Waki and Takeya Kasukawa and Hideya Kawaji and Rimantas Kodzius and Akira Watahiki and Mari Nakamura and Takahiro Arakawa and Shiro Fukuda and Daisuke Sasaki and Anna Podhajska and Matthias Harbers and Jun Kawai and Piero Carninci and Yoshihide Hayashizaki",

year = "2003",

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day = "23",

doi = "10.1073/pnas.2136655100",

language = "English (US)",

volume = "100",

pages = "15776--15781",

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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 2003, 'Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 100, no. 26, pp. 15776-15781. https://doi.org/10.1073/pnas.2136655100

Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. / Shiraki, Toshiyuki; Kondo, Shinji; Katayama, Shintaro et al.
In: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol. 100, No. 26, 23.12.2003, p. 15776-15781.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage

AU - Shiraki, Toshiyuki

AU - Kondo, Shinji

AU - Katayama, Shintaro

AU - Waki, Kazunori

AU - Kasukawa, Takeya

AU - Kawaji, Hideya

AU - Kodzius, Rimantas

AU - Watahiki, Akira

AU - Nakamura, Mari

AU - Arakawa, Takahiro

AU - Fukuda, Shiro

AU - Sasaki, Daisuke

AU - Podhajska, Anna

AU - Harbers, Matthias

AU - Kawai, Jun

AU - Carninci, Piero

AU - Hayashizaki, Yoshihide

PY - 2003/12/23

Y1 - 2003/12/23

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AB - 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.

KW - Cap-trapping

KW - Full-length cDNA

KW - Sequencing

KW - Transcriptome

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DO - 10.1073/pnas.2136655100

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C2 - 14663149

AN - SCOPUS:9144233601

SN - 0027-8424

VL - 100

SP - 15776

EP - 15781

JO - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

JF - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

IS - 26

ER -

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

Abstract

Keywords

ASJC Scopus subject areas

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