Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

Charles Plessy; Nicolas Bertin; Hazuki Takahashi; Roberto Simone; Md Salimullah; Timo Lassmann; Morana Vitezic; Jessica Severin; Signe Olivarius; Dejan Lazarevic; Nadine Hornig; Valerio Orlando; Ian Bell; Hui Gao; Jacqueline Dumais; Philipp Kapranov; Huaien Wang; Carrie A. Davis; Thomas R. Gingeras; Jun Kawai; Carsten O. Daub; Yoshihide Hayashizaki; Stefano Gustincich; Piero Carninci

doi:10.1038/nmeth.1470

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

Charles Plessy, Nicolas Bertin, Hazuki Takahashi, Roberto Simone, Md Salimullah, Timo Lassmann, Morana Vitezic, Jessica Severin, Signe Olivarius, Dejan Lazarevic, Nadine Hornig, Valerio Orlando, Ian Bell, Hui Gao, Jacqueline Dumais, Philipp Kapranov, Huaien Wang, Carrie A. Davis, Thomas R. Gingeras, Jun KawaiCarsten O. Daub, Yoshihide Hayashizaki, Stefano Gustincich^*, Piero Carninci

^*Corresponding author for this work

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

130 Scopus citations

Abstract

Large-scale sequencing projects have revealed an unexpected complexity in the origins, structures and functions of mammalian transcripts. Many loci are known to produce overlapping coding and noncoding RNAs with capped 5′ ends that vary in size. Methods to identify the 5′ ends of transcripts will facilitate the discovery of new promoters and 5′ ends derived from secondary capping events. Such methods often require high input amounts of RNA not obtainable from highly refined samples such as tissue microdissections and subcellular fractions. Therefore, we developed nano-cap analysis of gene expression (nanoCAGE), a method that captures the 5′ ends of transcripts from as little as 10 ng of total RNA, and CAGEscan, a mate-pair adaptation of nanoCAGE that captures the transcript 5′ ends linked to a downstream region. Both of these methods allow further annotation-agnostic studies of the complex human transcriptome.

Original language	English (US)
Pages (from-to)	528-534
Number of pages	7
Journal	Nature Methods
Volume	7
Issue number	7
DOIs	https://doi.org/10.1038/nmeth.1470
State	Published - Jul 2010
Externally published	Yes

Bibliographical note

Funding Information:
This work was funded by a grant of the 6th Framework of the European Union commission to the Neuro Functional Genomics consortium, by a grant of the 7th Framework to P.C. and S.G. (Dopaminet), a Grant-in-Aids for Scientific Research (A) 20241047 for P.C. and a Research Grant for RIKEN Omics Science Center from the Japanese Ministry of Education, Culture, Sports, Science and Technology to Y.H. This project was also partially supported by the U.S. National Human Genome Research Institute grant U54 HG004557. C.P. was supported by the Japanese Society for the Promotion of Science long-term fellowship P05880. S.G. was funded by a career developmental award from The Giovanni Armenise-Harvard Foundation. We thank A. Forrest for critical discussions, M. Josserand for experimental assistance and RIKEN Genome Network Analysis Service for data production.

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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Plessy, C., Bertin, N., Takahashi, H., Simone, R., Salimullah, M., Lassmann, T., Vitezic, M., Severin, J., Olivarius, S., Lazarevic, D., Hornig, N., Orlando, V., Bell, I., Gao, H., Dumais, J., Kapranov, P., Wang, H., Davis, C. A., Gingeras, T. R., ... Carninci, P. (2010). Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nature Methods, 7(7), 528-534. https://doi.org/10.1038/nmeth.1470

@article{0e333f34d62f4ce3b4a4ded03b8d2d32,

title = "Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan",

abstract = "Large-scale sequencing projects have revealed an unexpected complexity in the origins, structures and functions of mammalian transcripts. Many loci are known to produce overlapping coding and noncoding RNAs with capped 5′ ends that vary in size. Methods to identify the 5′ ends of transcripts will facilitate the discovery of new promoters and 5′ ends derived from secondary capping events. Such methods often require high input amounts of RNA not obtainable from highly refined samples such as tissue microdissections and subcellular fractions. Therefore, we developed nano-cap analysis of gene expression (nanoCAGE), a method that captures the 5′ ends of transcripts from as little as 10 ng of total RNA, and CAGEscan, a mate-pair adaptation of nanoCAGE that captures the transcript 5′ ends linked to a downstream region. Both of these methods allow further annotation-agnostic studies of the complex human transcriptome.",

author = "Charles Plessy and Nicolas Bertin and Hazuki Takahashi and Roberto Simone and Md Salimullah and Timo Lassmann and Morana Vitezic and Jessica Severin and Signe Olivarius and Dejan Lazarevic and Nadine Hornig and Valerio Orlando and Ian Bell and Hui Gao and Jacqueline Dumais and Philipp Kapranov and Huaien Wang and Davis, {Carrie A.} and Gingeras, {Thomas R.} and Jun Kawai and Daub, {Carsten O.} and Yoshihide Hayashizaki and Stefano Gustincich and Piero Carninci",

note = "Funding Information: This work was funded by a grant of the 6th Framework of the European Union commission to the Neuro Functional Genomics consortium, by a grant of the 7th Framework to P.C. and S.G. (Dopaminet), a Grant-in-Aids for Scientific Research (A) 20241047 for P.C. and a Research Grant for RIKEN Omics Science Center from the Japanese Ministry of Education, Culture, Sports, Science and Technology to Y.H. This project was also partially supported by the U.S. National Human Genome Research Institute grant U54 HG004557. C.P. was supported by the Japanese Society for the Promotion of Science long-term fellowship P05880. S.G. was funded by a career developmental award from The Giovanni Armenise-Harvard Foundation. We thank A. Forrest for critical discussions, M. Josserand for experimental assistance and RIKEN Genome Network Analysis Service for data production.",

year = "2010",

month = jul,

doi = "10.1038/nmeth.1470",

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pages = "528--534",

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Plessy, C, Bertin, N, Takahashi, H, Simone, R, Salimullah, M, Lassmann, T, Vitezic, M, Severin, J, Olivarius, S, Lazarevic, D, Hornig, N, Orlando, V, Bell, I, Gao, H, Dumais, J, Kapranov, P, Wang, H, Davis, CA, Gingeras, TR, Kawai, J, Daub, CO, Hayashizaki, Y, Gustincich, S & Carninci, P 2010, 'Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan', Nature Methods, vol. 7, no. 7, pp. 528-534. https://doi.org/10.1038/nmeth.1470

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T1 - Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

AU - Plessy, Charles

AU - Bertin, Nicolas

AU - Takahashi, Hazuki

AU - Simone, Roberto

AU - Salimullah, Md

AU - Lassmann, Timo

AU - Vitezic, Morana

AU - Severin, Jessica

AU - Olivarius, Signe

AU - Lazarevic, Dejan

AU - Hornig, Nadine

AU - Orlando, Valerio

AU - Bell, Ian

AU - Gao, Hui

AU - Dumais, Jacqueline

AU - Kapranov, Philipp

AU - Wang, Huaien

AU - Davis, Carrie A.

AU - Gingeras, Thomas R.

AU - Kawai, Jun

AU - Daub, Carsten O.

AU - Hayashizaki, Yoshihide

AU - Gustincich, Stefano

AU - Carninci, Piero

N1 - Funding Information: This work was funded by a grant of the 6th Framework of the European Union commission to the Neuro Functional Genomics consortium, by a grant of the 7th Framework to P.C. and S.G. (Dopaminet), a Grant-in-Aids for Scientific Research (A) 20241047 for P.C. and a Research Grant for RIKEN Omics Science Center from the Japanese Ministry of Education, Culture, Sports, Science and Technology to Y.H. This project was also partially supported by the U.S. National Human Genome Research Institute grant U54 HG004557. C.P. was supported by the Japanese Society for the Promotion of Science long-term fellowship P05880. S.G. was funded by a career developmental award from The Giovanni Armenise-Harvard Foundation. We thank A. Forrest for critical discussions, M. Josserand for experimental assistance and RIKEN Genome Network Analysis Service for data production.

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AB - Large-scale sequencing projects have revealed an unexpected complexity in the origins, structures and functions of mammalian transcripts. Many loci are known to produce overlapping coding and noncoding RNAs with capped 5′ ends that vary in size. Methods to identify the 5′ ends of transcripts will facilitate the discovery of new promoters and 5′ ends derived from secondary capping events. Such methods often require high input amounts of RNA not obtainable from highly refined samples such as tissue microdissections and subcellular fractions. Therefore, we developed nano-cap analysis of gene expression (nanoCAGE), a method that captures the 5′ ends of transcripts from as little as 10 ng of total RNA, and CAGEscan, a mate-pair adaptation of nanoCAGE that captures the transcript 5′ ends linked to a downstream region. Both of these methods allow further annotation-agnostic studies of the complex human transcriptome.

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DO - 10.1038/nmeth.1470

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JO - Nature Methods

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Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

Abstract

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ASJC Scopus subject areas

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