An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

被引：571

作者：

Ravasi, Timothy ^{[1
,3
,4
,5
]}

Suzuki, Harukazu ^{[1
,2
,6
]}

Cannistraci, Carlo Vittorio ^{[1
,3
,4
,5
,7
,8
,9
]}

Katayama, Shintaro ^{[1
,2
,6
]}

Bajic, Vladimir B. ^{[1
,5
,10
]}

Tan, Kai ^{[1
,3
,4
]}

Akalin, Altuna ^{[1
,11
]}

Schmeier, Sebastian ^{[1
,10
]}

Kanamori-Katayama, Mutsumi ^{[1
,2
,6
]}

Bertin, Nicolas ^{[1
,2
,6
]}

Carninci, Piero ^{[1
,2
,6
]}

Daub, Carsten O. ^{[1
,2
,6
]}

Forrest, Alistair R. R. ^{[1
,2
,6
,12
]}

Gough, Julian ^{[1
,13
]}

Grimmond, Sean ^{[1
,14
]}

Han, Jung-Hoon ^{[1
,5
,15
]}

Hashimoto, Takehiro ^{[1
,2
,6
]}

Hide, Winston ^{[1
,10
,16
]}

Hofmann, Oliver ^{[1
,10
]}

Kawaji, Hideya ^{[1
,2
,6
]}

Kubosaki, Atsutaka ^{[1
,2
,6
]}

Lassmann, Timo ^{[1
,2
,6
]}

van Nimwegen, Erik ^{[1
,17
,18
]}

Ogawa, Chihiro ^{[1
,2
,6
]}

Teasdale, Rohan D. ^{[1
,14
]}

Tegner, Jesper ^{[1
,19
,20
]}

Lenhard, Boris ^{[1
,11
]}

Teichmann, Sarah A. ^{[1
,15
]}

Arakawa, Takahiro ^{[1
,2
,6
]}

Ninomiya, Noriko ^{[1
,2
,6
]}

Murakami, Kayoko ^{[1
,2
,6
]}

Tagami, Michihira ^{[1
,2
,6
]}

Fukuda, Shiro ^{[1
,2
,6
]}

Imamura, Kengo ^{[1
,2
,6
]}

Kai, Chikatoshi ^{[1
,2
,6
]}

Ishihara, Ryoko ^{[1
,2
,6
]}

Kitazume, Yayoi ^{[1
,2
,6
]}

Kawai, Jun ^{[1
,2
,6
]}

Hume, David A. ^{[1
,21
,22
]}

Ideker, Trey ^{[1
,3
,4
,23
]}

Hayashizaki, Yoshihide ^{[1
,2
,6
]}

机构：

[1] Univ Calif San Diego, FANTOM Consortium, La Jolla, CA 92093 USA

[2] Univ Calif San Diego, RIKEN Om Sci Ctr, La Jolla, CA 92093 USA

[3] Univ Calif San Diego, Dept Med, La Jolla, CA 92093 USA

[4] Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA

[5] King Abdullah Univ Sci & Technol, Computat Biosci Res Ctr, Div Chem & Life Sci & Engn, Red Sea Integrat Syst Biol Lab, Jeddah, Saudi Arabia

[6] RIKEN Yokohama Inst, RIKEN Om Sci Ctr, Tsurumi Ku, Kanagawa 2300045, Japan

[7] Politecn Torino, Dept Mech, I-10129 Turin, Italy

[8] Ist Sci San Raffaele, I-20132 Milan, Italy

[9] Politecn Torino, CMP Grp Microsoft Res, I-10129 Turin, Italy

[10] Univ Western Cape, S African Natl Bioinformat Inst, ZA-7535 Bellville, South Africa

[11] Bergen Ctr Computat Sci, N-5008 Bergen, Norway

[12] Griffith Univ, Eskitis Inst Cell & Mol Therapies, Griffith, Qld 4111, Australia

[13] Univ Bristol, Dept Comp Sci, Bristol BS8 1UB, Avon, England

[14] Univ Queensland, Inst Mol Biosci, Australian Res Council, Special Res Ctr Funct & Appl Genom, St Lucia, Qld 4072, Australia

[15] MRC Lab Mol Biol, Cambridge CB2 0QH, England

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

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

[18] Swiss Inst Bioinformat, CH-4056 Basel, Switzerland

[19] Karolinska Univ Hosp Solna, Karolinska Inst, Dept Med, Atherosclerosis Res Unit,Ctr Mol Med,Computat Med, SE-17176 Stockholm, Sweden

[20] Linkoping Univ, Dept Phys Chem & Biol, SE-58183 Linkoping, Sweden

[21] Univ Edinburgh, Roslin Inst, Roslin EH25 9PS, Midlothian, Scotland

[22] Univ Edinburgh, Royal Dick Sch Vet Studies, Roslin EH25 9PS, Midlothian, Scotland

[23] Univ Calif San Diego, Inst Genom Med, La Jolla, CA 92093 USA

来源：

CELL | 2010年 / 140卷 / 05期

基金：

英国生物技术与生命科学研究理事会; 澳大利亚国家健康与医学研究理事会;

关键词：

EMBRYONIC STEM-CELLS; PROTEIN INTERACTIONS; GENE-EXPRESSION; NETWORKS; DNA; BINDING; FAMILY; YEAST; LIPOPOLYSACCHARIDE; DIFFERENTIATION;

D O I：

10.1016/j.cell.2010.01.044

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Combinatorial interactions among transcription factors are critical to directing tissue-specific gene expression. To build a global atlas of these combinations, we have screened for physical interactions among the majority of human and mouse DNA-binding transcription factors (TFs). The complete networks contain 762 human and 877 mouse interactions. Analysis of the networks reveals that highly connected TFs are broadly expressed across tissues, and that roughly half of the measured interactions are conserved between mouse and human. The data highlight the importance of TF combinations for determining cell fate, and they lead to the identification of a SMAD3/FLI1 complex expressed during development of immunity. The availability of large TF combinatorial networks in both human and mouse will provide many opportunities to study gene regulation, tissue differentiation, and mammalian evolution.

引用

页码：744 / 752

页数：9

共 41 条

[1] A role for AP-1 in apoptosis: the case for and against [J].

Ameyar, M ;

Wisniewska, M ;

Weitzman, JB .

BIOCHIMIE, 2003, 85 (08) :747-752

[2] EWS-FLI1 suppresses NOTCH-activated p53 in Ewing's sarcoma [J].

Ban, Jozef ;

Bennani-Baiti, Idriss M. ;

Kauer, Max ;

Schaefer, Karl-Ludwig ;

Poremba, Christopher ;

Jug, Gunhild ;

Schwentner, Raphaela ;

Smrzka, Oskar ;

Muehlbacher, Karin ;

Aryee, Dave N. T. ;

Kovar, Heinrich .

CANCER RESEARCH, 2008, 68 (17) :7100-7109

[3] Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences [J].

Berger, Michael F. ;

Badis, Gwenael ;

Gehrke, Andrew R. ;

Talukder, Shaheynoor ;

Philippakis, Anthony A. ;

Pena-Castillo, Lourdes ;

Alleyne, Trevis M. ;

Mnaimneh, Sanie ;

Botvinnik, Olga B. ;

Chan, Esther T. ;

Khalid, Faiqua ;

Zhang, Wen ;

Newburger, Daniel ;

Jaeger, Savina A. ;

Morris, Quaid D. ;

Bulyk, Martha L. ;

Hughes, Timothy R. .

CELL, 2008, 133 (07) :1266-1276

[4] Tcf3 is an integral component of the core regulatory circuitry of embryonic stem cells [J].

Cole, Megan F. ;

Johnstone, Sarah E. ;

Newman, Jamie J. ;

Kagey, Michael H. ;

Young, Richard A. .

GENES & DEVELOPMENT, 2008, 22 (06) :746-755

[5] A genomic regulatory network for development [J].

Davidson, EH ;

Rast, JP ;

Oliveri, P ;

Ransick, A ;

Calestani, C ;

Yuh, CH ;

Minokawa, T ;

Amore, G ;

Hinman, V ;

Arenas-Mena, C ;

Otim, O ;

Brown, CT ;

Livi, CB ;

Lee, PY ;

Revilla, R ;

Rust, AG ;

Pan, ZJ ;

Schilstra, MJ ;

Clarke, PJC ;

Arnone, MI ;

Rowen, L ;

Cameron, RA ;

McClay, DR ;

Hood, L ;

Bolouri, H .

SCIENCE, 2002, 295 (5560) :1669-1678

[6] Role of homeobox genes in the patterning, specification, and differentiation of ectodermal appendages in mammals [J].

Duverger, Olivier ;

Morasso, Maria I. .

JOURNAL OF CELLULAR PHYSIOLOGY, 2008, 216 (02) :337-346

[7] Nuclear architecture and gene regulation [J].

Fedorova, Elena ;

Zink, Daniele .

BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH, 2008, 1783 (11) :2174-2184

[8] Design of protein-interaction specificity gives selective bZIP-binding peptides [J].

Grigoryan, Gevorg ;

Reinke, Aaron W. ;

Keating, Amy E. .

NATURE, 2009, 458 (7240) :859-U2

[9] Stem cells, pluripotency and nuclear reprogramming [J].

Jaenisch, R. .

JOURNAL OF THROMBOSIS AND HAEMOSTASIS, 2009, 7 :21-23

[10] Hubs with Network Motifs Organize Modularity Dynamically in the Protein-Protein Interaction Network of Yeast [J].

Jin, Guangxu ;

Zhang, Shihua ;

Zhang, Xiang-Sun ;

Chen, Luonan .

PLOS ONE, 2007, 2 (11)

← 1 2 3 4 5 →