A promoter-level mammalian expression atlas

Alistair R R Forrest; Hideya Kawaji; Michael Rehli; J Kenneth Baillie; Michiel J L de Hoon; Vanja Haberle; Timo Lassman; Ivan V Kulakovskiy; Marina Lizio; Masayoshi Itoh; Robin Andersson; Christopher J Mungall; Terrence F Meehan; Sebastian Schmeier; Nicolas Bertin; Mette Jørgensen; Emmanuel Dimont; Erik Arner; Christian Schmidl; Ulf Schaefer; Yulia A Medvedeva; Charles Plessy; Morana Vitezic; Jessica Severin; Colin A Semple; Yuri Ishizu; Robert S Young; Margherita Francescatto; Intikhab Alam; Davide Albanese; Gabriel M Altschuler; Takahiro Arakawa; John A C Archer; Peter Arner; Magda Babina; Sarah Rennie; Piotr J Balwierz; Anthony G Beckhouse; Swati Pradhan-Bhatt; Judith A Blake; Antje Blumenthal; Beatrice Bodega; Alessandro Bonetti; James Briggs; Frank Brombacher; A Maxwell Burroughs; Andrea Califano; Carlo V Cannistraci; Hans C Clevers; Christine L Mummery

doi:10.1038/nature13182

A promoter-level mammalian expression atlas

Alistair R R Forrest, Hideya Kawaji, Michael Rehli, J Kenneth Baillie, Michiel J L de Hoon, Vanja Haberle, Timo Lassman, Ivan V Kulakovskiy, Marina Lizio, Masayoshi Itoh, Robin Andersson, Christopher J Mungall, Terrence F Meehan, Sebastian Schmeier, Nicolas Bertin, Mette Jørgensen, Emmanuel Dimont, Erik Arner, Christian Schmidl, Ulf SchaeferYulia A Medvedeva, Charles Plessy, Morana Vitezic, Jessica Severin, Colin A Semple, Yuri Ishizu, Robert S Young, Margherita Francescatto, Intikhab Alam, Davide Albanese, Gabriel M Altschuler, Takahiro Arakawa, John A C Archer, Peter Arner, Magda Babina, Sarah Rennie, Piotr J Balwierz, Anthony G Beckhouse, Swati Pradhan-Bhatt, Judith A Blake, Antje Blumenthal, Beatrice Bodega, Alessandro Bonetti, James Briggs, Frank Brombacher, A Maxwell Burroughs, Andrea Califano, Carlo V Cannistraci, Hans C Clevers, Christine L Mummery,

Hubrecht Institute

Onderzoeksoutput: Bijdrage aan wetenschappelijk tijdschrift/periodieke uitgave › Artikel › Wetenschappelijk › peer review

1410 Citaten (Scopus)

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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.

Originele taal-2	Engels
Pagina's (van-tot)	462-70
Aantal pagina's	9
Tijdschrift	Nature
Volume	507
Nummer van het tijdschrift	7493
DOI's	https://doi.org/10.1038/nature13182
Status	Gepubliceerd - 27 mrt. 2014

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10.1038/nature13182

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Forrest, A. R. R., Kawaji, H., Rehli, M., Baillie, J. K., de Hoon, M. J. L., Haberle, V., Lassman, T., Kulakovskiy, I. V., Lizio, M., Itoh, M., Andersson, R., Mungall, C. J., Meehan, T. F., Schmeier, S., Bertin, N., Jørgensen, M., Dimont, E., Arner, E., Schmidl, C. (2014). A promoter-level mammalian expression atlas. Nature, 507(7493), 462-70. https://doi.org/10.1038/nature13182

@article{018953d49a564871877a3f82a9491c29,

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 '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.",

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 = "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 Lassman 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 J{\o}rgensen 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 Beatrice Bodega and Alessandro Bonetti and James Briggs and Frank Brombacher and Burroughs, {A Maxwell} and Andrea Califano and Cannistraci, {Carlo V} and Clevers, {Hans C} and Mummery, {Christine L}",

year = "2014",

month = mar,

day = "27",

doi = "10.1038/nature13182",

language = "English",

volume = "507",

pages = "462--70",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Publishing Group",

number = "7493",

}

Forrest, ARR, Kawaji, H, Rehli, M, Baillie, JK, de Hoon, MJL, Haberle, V, Lassman, T, Kulakovskiy, IV, Lizio, M, Itoh, M, Andersson, R, Mungall, CJ, Meehan, TF, Schmeier, S, Bertin, N, Jørgensen, M, Dimont, E, Arner, E, Schmidl, C, Schaefer, U, Medvedeva, YA, Plessy, C, Vitezic, M, Severin, J, Semple, CA, Ishizu, Y, Young, RS, Francescatto, M, Alam, I, Albanese, D, Altschuler, GM, Arakawa, T, Archer, JAC, Arner, P, Babina, M, Rennie, S, Balwierz, PJ, Beckhouse, AG, Pradhan-Bhatt, S, Blake, JA, Blumenthal, A, Bodega, B, Bonetti, A, Briggs, J, Brombacher, F, Burroughs, AM, Califano, A, Cannistraci, CV, Clevers, HC, Mummery, CL 2014, 'A promoter-level mammalian expression atlas', Nature, vol. 507, nr. 7493, blz. 462-70. https://doi.org/10.1038/nature13182

TY - JOUR

T1 - A promoter-level mammalian expression atlas

AU - Forrest, Alistair R R

AU - Kawaji, Hideya

AU - Rehli, Michael

AU - Baillie, J Kenneth

AU - de Hoon, Michiel J L

AU - Haberle, Vanja

AU - Lassman, Timo

AU - Kulakovskiy, Ivan V

AU - Lizio, Marina

AU - Itoh, Masayoshi

AU - Andersson, Robin

AU - Mungall, Christopher J

AU - Meehan, Terrence F

AU - Schmeier, Sebastian

AU - Bertin, Nicolas

AU - Jørgensen, Mette

AU - Dimont, Emmanuel

AU - Arner, Erik

AU - Schmidl, Christian

AU - Schaefer, Ulf

AU - Medvedeva, Yulia A

AU - Plessy, Charles

AU - Vitezic, Morana

AU - Severin, Jessica

AU - Semple, Colin A

AU - Ishizu, Yuri

AU - Young, Robert S

AU - Francescatto, Margherita

AU - Alam, Intikhab

AU - Albanese, Davide

AU - Altschuler, Gabriel M

AU - Arakawa, Takahiro

AU - Archer, John A C

AU - Arner, Peter

AU - Babina, Magda

AU - Rennie, Sarah

AU - Balwierz, Piotr J

AU - Beckhouse, Anthony G

AU - Pradhan-Bhatt, Swati

AU - Blake, Judith A

AU - Blumenthal, Antje

AU - Bodega, Beatrice

AU - Bonetti, Alessandro

AU - Briggs, James

AU - Brombacher, Frank

AU - Burroughs, A Maxwell

AU - Califano, Andrea

AU - Cannistraci, Carlo V

AU - Clevers, Hans C

AU - Mummery, Christine L

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

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