A promoter-level mammalian expression atlas

FANTOM Consortium; RIKEN PMI CLST DGT

doi:10.1038/nature13182

A promoter-level mammalian expression atlas

FANTOM Consortium, RIKEN PMI CLST DGT

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

Abstract

Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. We find that few genes are truly ‘housekeeping’, whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles. TSSs specific to different cell types evolve at different rates, whereas promoters of broadly expressed genes are the most conserved. Promoter-based expression analysis reveals key transcription factors defining cell states and links them to binding-site motifs. The functions of identified novel transcripts can be predicted by coexpression and sample ontology enrichment analyses. The functional annotation of the mammalian genome 5 (FANTOM5) project provides comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes with wide applications in biomedical research.

Original language	English
Pages (from-to)	462-470
Number of pages	9
Journal	Nature
Volume	507
Issue number	7493
Early online date	26 Mar 2014
DOIs	https://doi.org/10.1038/nature13182
Publication status	Published - 27 Mar 2014

Keywords / Materials (for Non-textual outputs)

Animals
Atlases as Topic
Cell Line
Cells, Cultured
Cluster Analysis
Conserved Sequence
Gene Expression Regulation
Gene Regulatory Networks
Genes, Essential
Genome
Humans
Mice
Molecular Sequence Annotation
Open Reading Frames
Organ Specificity
Promoter Regions, Genetic
RNA, Messenger
Transcription Factors
Transcription Initiation Site
Transcription, Genetic
Transcriptome

Access to Document

10.1038/nature13182

Innate immunity and endemic diseases in livestock species
Collie, D. (Principal Investigator), Beard, P. (Co-investigator), Bishop, S. (Co-investigator), Bronsvoort, M. (Co-investigator), Burt, D. (Co-investigator), Fitzgerald, R. (Co-investigator), Freeman, T. (Co-investigator), Gally, D. (Co-investigator), Gill, A. (Co-investigator), Glass, E. (Co-investigator), Hocking, P. (Co-investigator), Hope, J. (Co-investigator), Hume, D. (Co-investigator), Kaiser, P. (Co-investigator), Mabbott, N. (Co-investigator), McLachlan, G. (Co-investigator), Morrison, L. (Co-investigator), Stevens, J. (Co-investigator), Stevens, M. (Co-investigator) & Watson, M. (Co-investigator)
BBSRC
1/04/12 → 31/03/17
Project: Research
ISP1: Analysis and prediction in complex animal systems
Tenesa, A. (Principal Investigator), Archibald, A. (Co-investigator), Beard, P. (Co-investigator), Bishop, S. (Co-investigator), Bronsvoort, M. (Co-investigator), Burt, D. (Co-investigator), Freeman, T. (Co-investigator), Haley, C. (Co-investigator), Hocking, P. (Co-investigator), Houston, R. (Co-investigator), Hume, D. (Co-investigator), Joshi, A. (Co-investigator), Law, A. (Co-investigator), Michoel, T. (Co-investigator), Summers, K. (Co-investigator), Vernimmen, D. (Co-investigator), Watson, M. (Co-investigator), Wiener, P. (Co-investigator), Wilson, A. (Co-investigator), Woolliams, J. (Co-investigator), Ait-Ali, T. (Researcher), Barnett, M. (Researcher), Carlisle, A. (Researcher), Finlayson, H. (Researcher), Haga, I. (Researcher), Karavolos, M. (Researcher), Matika, O. (Researcher), Paterson, T. (Researcher), Paton, B. (Researcher), Pong-Wong, R. (Researcher), Robert, C. (Researcher) & Robertson, G. (Researcher)
BBSRC
1/04/12 → 31/03/17
Project: Research
A complete transcriptional map of the human body: systems Biology in toto (Japanese Partnering Grant)
Hume, D. (Principal Investigator), Freeman, T. (Co-investigator) & Summers, K. (Co-investigator)
BBSRC
1/10/11 → 30/09/14
Project: Research

Kenneth Baillie
- Deanery of Clinical Sciences - Personal Chair of Experimental Medicine
- Centre for Inflammation Research
Person: Academic: Research Active
James Prendergast
- James.Prendergastroslin.ed.acuk
- Royal (Dick) School of Veterinary Studies - Personal Chair of Bioinformatics
Person: Academic: Research Active
Colin Semple
- colin.sempleed.acuk
- MRC Human Genetics Unit
Person: Academic: Research Active

Cite this

@article{df46f31d21db454ba0d3fca42155f17d,

title = "A promoter-level mammalian expression atlas",

abstract = "Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. We find that few genes are truly {\textquoteleft}housekeeping{\textquoteright}, whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles. TSSs specific to different cell types evolve at different rates, whereas promoters of broadly expressed genes are the most conserved. Promoter-based expression analysis reveals key transcription factors defining cell states and links them to binding-site motifs. The functions of identified novel transcripts can be predicted by coexpression and sample ontology enrichment analyses. The functional annotation of the mammalian genome 5 (FANTOM5) project provides comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes with wide applications in biomedical research.",

keywords = "Animals, Atlases as Topic, Cell Line, Cells, Cultured, Cluster Analysis, Conserved Sequence, Gene Expression Regulation, Gene Regulatory Networks, Genes, Essential, Genome, Humans, Mice, Molecular Sequence Annotation, Open Reading Frames, Organ Specificity, Promoter Regions, Genetic, RNA, Messenger, Transcription Factors, Transcription Initiation Site, Transcription, Genetic, Transcriptome",

author = "{FANTOM Consortium} and {RIKEN PMI CLST DGT} and Forrest, {Alistair R. R.} and Hideya Kawaji and Michael Rehli and Baillie, {J. Kenneth} and {de Hoon}, {Michiel J. L.} and Vanja Haberle and Timo Lassmann and Kulakovskiy, {Ivan V.} and Marina Lizio and Masayoshi Itoh and Robin Andersson and Mungall, {Christopher J.} and Meehan, {Terrence F.} and Sebastian Schmeier and Nicolas Bertin and Mette Jorgensen and Emmanuel Dimont and Erik Arner and Christian Schmidl and Ulf Schaefer and Medvedeva, {Yulia A.} and Charles Plessy and Morana Vitezic and Jessica Severin and Semple, {Colin A.} and Yuri Ishizu and Young, {Robert S.} and Margherita Francescatto and Intikhab Alam and Davide Albanese and Altschuler, {Gabriel M.} and Takahiro Arakawa and Archer, {John A. C.} and Peter Arner and Magda Babina and Sarah Rennie and Balwierz, {Piotr J.} and Beckhouse, {Anthony G.} and Swati Pradhan-Bhatt and Blake, {Judith A.} and Antje Blumenthal and Fisher, {Malcolm E.} and Ha, {Thomas J.} and Anagha Joshi and Alison Meynert and Prendergast, {James G. D.} and Summers, {Kim M.} and Freeman, {Tom C.} and Taylor, {Martin S.} and Hume, {David A.}",

year = "2014",

month = mar,

day = "27",

doi = "10.1038/nature13182",

language = "English",

volume = "507",

pages = "462--470",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Research",

number = "7493",

}

TY - JOUR

T1 - A promoter-level mammalian expression atlas

AU - FANTOM Consortium

AU - RIKEN PMI CLST DGT

A2 - Forrest, Alistair R. R.

A2 - Kawaji, Hideya

A2 - Rehli, Michael

A2 - Baillie, J. Kenneth

A2 - de Hoon, Michiel J. L.

A2 - Haberle, Vanja

A2 - Lassmann, Timo

A2 - Kulakovskiy, Ivan V.

A2 - Lizio, Marina

A2 - Itoh, Masayoshi

A2 - Andersson, Robin

A2 - Mungall, Christopher J.

A2 - Meehan, Terrence F.

A2 - Schmeier, Sebastian

A2 - Bertin, Nicolas

A2 - Jorgensen, Mette

A2 - Dimont, Emmanuel

A2 - Arner, Erik

A2 - Schmidl, Christian

A2 - Schaefer, Ulf

A2 - Medvedeva, Yulia A.

A2 - Plessy, Charles

A2 - Vitezic, Morana

A2 - Severin, Jessica

A2 - Semple, Colin A.

A2 - Ishizu, Yuri

A2 - Young, Robert S.

A2 - Francescatto, Margherita

A2 - Alam, Intikhab

A2 - Albanese, Davide

A2 - Altschuler, Gabriel M.

A2 - Arakawa, Takahiro

A2 - Archer, John A. C.

A2 - Arner, Peter

A2 - Babina, Magda

A2 - Rennie, Sarah

A2 - Balwierz, Piotr J.

A2 - Beckhouse, Anthony G.

A2 - Pradhan-Bhatt, Swati

A2 - Blake, Judith A.

A2 - Blumenthal, Antje

A2 - Fisher, Malcolm E.

A2 - Ha, Thomas J.

A2 - Joshi, Anagha

A2 - Meynert, Alison

A2 - Prendergast, James G. D.

A2 - Summers, Kim M.

A2 - Freeman, Tom C.

A2 - Taylor, Martin S.

A2 - Hume, David A.

PY - 2014/3/27

Y1 - 2014/3/27

N2 - Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. We find that few genes are truly ‘housekeeping’, whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles. TSSs specific to different cell types evolve at different rates, whereas promoters of broadly expressed genes are the most conserved. Promoter-based expression analysis reveals key transcription factors defining cell states and links them to binding-site motifs. The functions of identified novel transcripts can be predicted by coexpression and sample ontology enrichment analyses. The functional annotation of the mammalian genome 5 (FANTOM5) project provides comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes with wide applications in biomedical research.

AB - Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. We find that few genes are truly ‘housekeeping’, whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles. TSSs specific to different cell types evolve at different rates, whereas promoters of broadly expressed genes are the most conserved. Promoter-based expression analysis reveals key transcription factors defining cell states and links them to binding-site motifs. The functions of identified novel transcripts can be predicted by coexpression and sample ontology enrichment analyses. The functional annotation of the mammalian genome 5 (FANTOM5) project provides comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes with wide applications in biomedical research.

KW - Animals

KW - Atlases as Topic

KW - Cell Line

KW - Cells, Cultured

KW - Cluster Analysis

KW - Conserved Sequence

KW - Gene Expression Regulation

KW - Gene Regulatory Networks

KW - Genes, Essential

KW - Genome

KW - Humans

KW - Mice

KW - Molecular Sequence Annotation

KW - Open Reading Frames

KW - Organ Specificity

KW - Promoter Regions, Genetic

KW - RNA, Messenger

KW - Transcription Factors

KW - Transcription Initiation Site

KW - Transcription, Genetic

KW - Transcriptome

U2 - 10.1038/nature13182

DO - 10.1038/nature13182

M3 - Article

C2 - 24670764

SN - 0028-0836

VL - 507

SP - 462

EP - 470

JO - Nature

JF - Nature

IS - 7493

ER -

A promoter-level mammalian expression atlas

Abstract

Keywords / Materials (for Non-textual outputs)

Access to Document

Fingerprint

Projects

Innate immunity and endemic diseases in livestock species

ISP1: Analysis and prediction in complex animal systems

A complete transcriptional map of the human body: systems Biology in toto (Japanese Partnering Grant)

Profiles

Kenneth Baillie

James Prendergast

Colin Semple

Cite this