A promoter-level mammalian expression atlas

被引：1412

作者：

Forrest, Alistair R. R. ^{[1
,2
]}

Kawaji, Hideya ^{[1
,2
,3
]}

Rehli, Michael ^{[4
,5
]}

Baillie, J. Kenneth ^{[6
,7
]}

de Hoon, Michiel J. L. ^{[1
,2
]}

Haberle, Vanja ^{[8
,9
]}

Lassmann, Timo ^{[1
,2
]}

Kulakovskiy, Ivan V. ^{[10
,11
]}

Lizio, Marina ^{[1
,2
]}

Itoh, Masayoshi ^{[1
,2
,3
]}

Andersson, Robin ^{[12
,13
]}

Mungall, Christopher J. ^{[14
]}

Meehan, Terrence F. ^{[15
]}

Schmeier, Sebastian ^{[16
,17
]}

Bertin, Nicolas ^{[1
,2
]}

Jorgensen, Mette ^{[12
,13
]}

Dimont, Emmanuel ^{[18
]}

Arner, Erik ^{[1
,2
]}

Schmidl, Christian ^{[4
]}

Schaefer, Ulf ^{[16
]}

Medvedeva, Yulia A. ^{[11
,16
]}

Plessy, Charles ^{[1
,2
]}

Vitezic, Morana ^{[1
,19
]}

Severin, Jessica ^{[1
,2
]}

Semple, Colin A. ^{[20
]}

Ishizu, Yuri ^{[1
,2
]}

Young, Robert S. ^{[20
]}

Francescatto, Margherita ^{[21
,22
]}

Alam, Intikhab ^{[16
]}

Albanese, Davide ^{[23
]}

Altschuler, Gabriel M. ^{[18
]}

Arakawa, Takahiro ^{[1
,2
]}

Archer, John A. C. ^{[16
]}

Arner, Peter ^{[24
]}

Babina, Magda ^{[25
]}

Rennie, Sarah ^{[20
]}

Balwierz, Piotr J. ^{[26
]}

Beckhouse, Anthony G. ^{[27
,28
]}

Pradhan-Bhatt, Swati ^{[29
]}

Blake, Judith A. ^{[30
]}

Blumenthal, Antje ^{[28
,31
]}

Bodega, Beatrice ^{[32
]}

Bonetti, Alessandro ^{[1
,2
]}

Briggs, James ^{[27
]}

Brombacher, Frank ^{[33
,34
]}

Burroughs, A. Maxwell ^{[1
]}

Califano, Andrea ^{[35
,36
,37
,38
]}

Cannistraci, Carlo V. ^{[39
,40
]}

Carbajo, Daniel ^{[41
]}

Chen, Yun ^{[12
,13
]}

机构：

[1] RIKEN, OSC, Tsurumi Ku, Yokohama, Kanagawa 2300045, Japan

[2] RIKEN, CLST, DGT, Tsurumi Ku, Yokohama, Kanagawa 2300045, Japan

[3] RIKEN, Prevent Med & Diag Innovat Program PMI, Wako, Saitama 3510198, Japan

[4] Univ Hosp Regensburg, Dept Internal Med 3, D-93042 Regensburg, Germany

[5] Regensburg Ctr Intervent Immunol RCI, D-93042 Regensburg, Germany

[6] Univ Edinburgh, Roslin Inst, Edinburgh EH25 9RG, Midlothian, Scotland

[7] Univ Edinburgh, Royal Dick Sch Vet Studies, Edinburgh EH25 9RG, Midlothian, Scotland

[8] Univ Bergen, Dept Biol, NO-5006 Bergen, Norway

[9] Univ London Imperial Coll Sci Technol & Med, Fac Med, Inst Clin Sci, MRC Clin Sci Ctr, London W12 0NN, England

[10] Russian Acad Sci, VA Engelhardt Mol Biol Inst, Moscow 119991, Russia

[11] Russian Acad Sci, Vavilov Inst Gen Genet, Moscow 119991, Russia

[12] Univ Copenhagen, Bioinformat Ctr, Dept Biol, DK-2200 Copenhagen, Denmark

[13] Univ Copenhagen, BRIC, DK-2200 Copenhagen, Denmark

[14] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Genom Div, Berkeley, CA 94720 USA

[15] European Bioinformat Inst, European Mol Biol Lab, Cambridge CB10 1SD, England

[16] KAUST, Computat Biosci Res Ctr, Thuwal 239556900, Saudi Arabia

[17] Massey Univ, North Shore Mail Ctr, Inst Nat & Math Sci, Auckland 0745, New Zealand

[18] Harvard Univ, Sch Publ Hlth, Dept Biostat, Boston, MA 02115 USA

[19] Karolinska Inst, Dept Cell & Mol Biol, SE-17177 Stockholm, Sweden

[20] Univ Edinburgh, Western Gen Hosp, MRC Human Genet Unit, MRC IGMM, Edinburgh EH4 2XU, Midlothian, Scotland

[21] Vrije Univ Amsterdam, Dept Clin Genet, Med Ctr Amsterdam, NL-1081 BT Amsterdam, Netherlands

[22] Univ Porto, Grad Program Areas Basic & Appl Biol, Abel Salazar Biomed Sci Inst, P-4050313 Oporto, Portugal

[23] Fdn Bruno Kessler, I-38123 Trento, Italy

[24] Karolinska Inst, Dept Med, Karolinska Univ Hosp, SE-14186 Huddinge, Sweden

[25] Univ Med Berlin, Dept Dermatol & Allergy, D-10117 Berlin, Germany

[26] Univ Basel, Biozentrum, CH-4056 Basel, Switzerland

[27] Univ Queensland, AIBN, St Lucia, Qld 4072, Australia

[28] Univ Queensland, Australian Infect Dis Res Ctr AID, St Lucia, Qld 4072, Australia

[29] Univ Delaware, Dept Biol Sci, Newark, DE 19713 USA

[30] Jackson Lab, Bar Harbor, ME 04609 USA

[31] Univ Queensland, Diamantina Inst, St Lucia, Qld 4072, Australia

[32] IRCCS Fdn Santa Lucia, I-00143 Rome, Italy

[33] Int Ctr Genet Engn & Biotechnol ICGEB Cape Town C, ZA-7925 Cape Town, South Africa

[34] Univ Cape Town, Div Immunol, Inst Infect Dis & Mol Med IDM, ZA-7925 Cape Town, South Africa

[35] Columbia Univ, Med Ctr, Dept Syst Biol, New York, NY 10032 USA

[36] Columbia Univ, Med Ctr, Dept Biochem & Mol Biophys, New York, NY 10032 USA

[37] Columbia Univ, Med Ctr, Dept Biomed Informat, New York, NY 10032 USA

[38] Columbia Univ, Med Ctr, Herbert Irving Comprehens Canc Ctr, Inst Canc Genet, New York, NY 10032 USA

[39] KAUST, Biol & Environm Sci & Engn Div, Thuwal 239556900, Saudi Arabia

[40] KAUST, Appl Math & Computat Sci Program, Thuwal 239556900, Saudi Arabia

[41] Albert Einstein Coll Med, Dept Syst & Computat Biol, Bronx, NY 10461 USA

[42] LNCIB, I-34149 Trieste, Italy

[43] Hubrecht Inst, NL-3584 CT Utrecht, Netherlands

[44] Royal Netherlands Acad Arts & Sci, NL-1000 GC Amsterdam, Netherlands

[45] Univ Med Ctr Utrecht, NL-3508 GA Utrecht, Netherlands

[46] Cold Spring Harbor Lab, Cold Spring Harbor, NY 11797 USA

[47] ETH, Inst Pharmaceut Sci, CH-8093 Zurich, Switzerland

[48] SUNY Buffalo, Dept Neurol, Sch Med & Biomed Sci, New York State Ctr Excellence Bioinformat & Life, Buffalo, NY 14203 USA

[49] Natl Ctr Global Hlth & Med, Res Ctr Hepatitis & Immunol Res Inst, Ichikawa, Chiba 2728516, Japan

[50] Norwegian Univ Sci & Technol NTNU, Dept Canc Res & Mol Med, NO-7491 Trondheim, Norway

来源：

NATURE | 2014年 / 507卷 / 7493期

基金：

英国惠康基金; 英国生物技术与生命科学研究理事会;

关键词：

TRANSCRIPTION FACTOR; GENE-EXPRESSION; HOMEOBOX GENE; MICE LACKING; DIFFERENTIATION; MOUSE; CLASSIFICATION; SIGNATURES; MUTATIONS; DEAFNESS;

D O I：

10.1038/nature13182

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：

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 revealskey 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.

引用

页码：462 / +

页数：22

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