An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

Handle URI:
http://hdl.handle.net/10754/575669
Title:
An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man
Authors:
Ravasi, Timothy ( 0000-0002-9950-465X ) ; Suzuki, Harukazu; Cannistraci, Carlo; Katayama, Shintaro; Bajic, Vladimir B. ( 0000-0001-5435-4750 ) ; Tan, Kai; Akalin, Altuna; Schmeier, Sebastian; Kanamori-Katayama, Mutsumi; Bertin, Nicolas; Carninci, Piero; Daub, Carsten O.; Forrest, Alistair R.R.; Gough, Julian; Grimmond, Sean; Han, Jung-Hoon; Hashimoto, Takehiro; Hide, Winston; Hofmann, Oliver; Kamburov, Atanas; Kaur, Mandeep; Kawaji, Hideya; Kubosaki, Atsutaka; Lassmann, Timo; van Nimwegen, Erik; MacPherson, Cameron Ross; Ogawa, Chihiro; Radovanovic, Aleksandar; Schwartz, Ariel; Teasdale, Rohan D.; Tegnér, Jesper; Lenhard, Boris; Teichmann, Sarah A.; Arakawa, Takahiro; Ninomiya, Noriko; Murakami, Kayoko; Tagami, Michihira; Fukuda, Shiro; Imamura, Kengo; Kai, Chikatoshi; Ishihara, Ryoko; Kitazume, Yayoi; Kawai, Jun; Hume, David A.; Ideker, Trey; Hayashizaki, Yoshihide
Abstract:
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.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Bioscience Program; Computational Bioscience Research Center (CBRC); Bioscience Program; Integrative Systems Biology Lab; Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division; Applied Mathematics and Computational Science Program; Computational Bioscience Research Center (CBRC); Applied Mathematics and Computational Science Program
Publisher:
Elsevier BV
Journal:
Cell
Issue Date:
Mar-2010
DOI:
10.1016/j.cell.2010.01.044
Type:
Article
ISSN:
0092-8674
Sponsors:
The work for the RIKEN Omics Science Center was supported by grants from the Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT) through the Genome Network Project and for the RIKEN Omics Science Center (YH, Principal Investigator). Members of the FANTOM Consortium were supported by grant MH062261 from the US National Institute of Mental Health (TR, KT, TI), the King Abdullah University of Science and Technology (TR, VBB), the Max Planck Society for the Advancement of Science (AK), the SA National Bioinformatics Network (SS, AR, VBB, WAH), the Claude Leon Foundation (MK), a CJ Martin Fellowship from the Australian NHMRC (ARRF), and the Scuola Interpolitecnica di Dottorato (CVC). The authors gratefully acknowledge S. Choi for critical feedback on the manuscript.
Appears in Collections:
Articles; Red Sea Research Center (RSRC); Bioscience Program; Applied Mathematics and Computational Science Program; Computational Bioscience Research Center (CBRC); Biological and Environmental Sciences and Engineering (BESE) Division; Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorRavasi, Timothyen
dc.contributor.authorSuzuki, Harukazuen
dc.contributor.authorCannistraci, Carloen
dc.contributor.authorKatayama, Shintaroen
dc.contributor.authorBajic, Vladimir B.en
dc.contributor.authorTan, Kaien
dc.contributor.authorAkalin, Altunaen
dc.contributor.authorSchmeier, Sebastianen
dc.contributor.authorKanamori-Katayama, Mutsumien
dc.contributor.authorBertin, Nicolasen
dc.contributor.authorCarninci, Pieroen
dc.contributor.authorDaub, Carsten O.en
dc.contributor.authorForrest, Alistair R.R.en
dc.contributor.authorGough, Julianen
dc.contributor.authorGrimmond, Seanen
dc.contributor.authorHan, Jung-Hoonen
dc.contributor.authorHashimoto, Takehiroen
dc.contributor.authorHide, Winstonen
dc.contributor.authorHofmann, Oliveren
dc.contributor.authorKamburov, Atanasen
dc.contributor.authorKaur, Mandeepen
dc.contributor.authorKawaji, Hideyaen
dc.contributor.authorKubosaki, Atsutakaen
dc.contributor.authorLassmann, Timoen
dc.contributor.authorvan Nimwegen, Eriken
dc.contributor.authorMacPherson, Cameron Rossen
dc.contributor.authorOgawa, Chihiroen
dc.contributor.authorRadovanovic, Aleksandaren
dc.contributor.authorSchwartz, Arielen
dc.contributor.authorTeasdale, Rohan D.en
dc.contributor.authorTegnér, Jesperen
dc.contributor.authorLenhard, Borisen
dc.contributor.authorTeichmann, Sarah A.en
dc.contributor.authorArakawa, Takahiroen
dc.contributor.authorNinomiya, Norikoen
dc.contributor.authorMurakami, Kayokoen
dc.contributor.authorTagami, Michihiraen
dc.contributor.authorFukuda, Shiroen
dc.contributor.authorImamura, Kengoen
dc.contributor.authorKai, Chikatoshien
dc.contributor.authorIshihara, Ryokoen
dc.contributor.authorKitazume, Yayoien
dc.contributor.authorKawai, Junen
dc.contributor.authorHume, David A.en
dc.contributor.authorIdeker, Treyen
dc.contributor.authorHayashizaki, Yoshihideen
dc.date.accessioned2015-08-24T08:35:28Zen
dc.date.available2015-08-24T08:35:28Zen
dc.date.issued2010-03en
dc.identifier.issn0092-8674en
dc.identifier.doi10.1016/j.cell.2010.01.044en
dc.identifier.urihttp://hdl.handle.net/10754/575669en
dc.description.abstractCombinatorial 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.en
dc.description.sponsorshipThe work for the RIKEN Omics Science Center was supported by grants from the Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT) through the Genome Network Project and for the RIKEN Omics Science Center (YH, Principal Investigator). Members of the FANTOM Consortium were supported by grant MH062261 from the US National Institute of Mental Health (TR, KT, TI), the King Abdullah University of Science and Technology (TR, VBB), the Max Planck Society for the Advancement of Science (AK), the SA National Bioinformatics Network (SS, AR, VBB, WAH), the Claude Leon Foundation (MK), a CJ Martin Fellowship from the Australian NHMRC (ARRF), and the Scuola Interpolitecnica di Dottorato (CVC). The authors gratefully acknowledge S. Choi for critical feedback on the manuscript.en
dc.publisherElsevier BVen
dc.titleAn Atlas of Combinatorial Transcriptional Regulation in Mouse and Manen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentBioscience Programen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.contributor.departmentBioscience Programen
dc.contributor.departmentIntegrative Systems Biology Laben
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Divisionen
dc.contributor.departmentApplied Mathematics and Computational Science Programen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.contributor.departmentApplied Mathematics and Computational Science Programen
dc.identifier.journalCellen
dc.contributor.institutionUniv Calif San Diego, FANTOM Consortium, La Jolla, CA 92093 USAen
dc.contributor.institutionUniv Calif San Diego, RIKEN Om Sci Ctr, La Jolla, CA 92093 USAen
dc.contributor.institutionUniv Calif San Diego, Dept Med, La Jolla, CA 92093 USAen
dc.contributor.institutionUniv Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USAen
dc.contributor.institutionRIKEN Yokohama Inst, RIKEN Om Sci Ctr, Tsurumi Ku, Kanagawa 2300045, Japanen
dc.contributor.institutionPolitecn Torino, Dept Mech, I-10129 Turin, Italyen
dc.contributor.institutionIst Sci San Raffaele, I-20132 Milan, Italyen
dc.contributor.institutionPolitecn Torino, CMP Grp Microsoft Res, I-10129 Turin, Italyen
dc.contributor.institutionUniv Western Cape, S African Natl Bioinformat Inst, ZA-7535 Bellville, South Africaen
dc.contributor.institutionBergen Ctr Computat Sci, N-5008 Bergen, Norwayen
dc.contributor.institutionGriffith Univ, Eskitis Inst Cell & Mol Therapies, Griffith, Qld 4111, Australiaen
dc.contributor.institutionUniv Bristol, Dept Comp Sci, Bristol BS8 1UB, Avon, Englanden
dc.contributor.institutionUniv Queensland, Inst Mol Biosci, Australian Res Council, Special Res Ctr Funct & Appl Genom, St Lucia, Qld 4072, Australiaen
dc.contributor.institutionMRC Lab Mol Biol, Cambridge CB2 0QH, Englanden
dc.contributor.institutionHarvard Univ, Sch Publ Hlth, Dept Biostat, Boston, MA 02115 USAen
dc.contributor.institutionUniv Basel, Biozentrum, CH-4056 Basel, Switzerlanden
dc.contributor.institutionSwiss Inst Bioinformat, CH-4056 Basel, Switzerlanden
dc.contributor.institutionKarolinska Univ Hosp Solna, Karolinska Inst, Dept Med, Atherosclerosis Res Unit,Ctr Mol Med,Computat Med, SE-17176 Stockholm, Swedenen
dc.contributor.institutionLinkoping Univ, Dept Phys Chem & Biol, SE-58183 Linkoping, Swedenen
dc.contributor.institutionUniv Edinburgh, Roslin Inst, Roslin EH25 9PS, Midlothian, Scotlanden
dc.contributor.institutionUniv Edinburgh, Royal Dick Sch Vet Studies, Roslin EH25 9PS, Midlothian, Scotlanden
dc.contributor.institutionUniv Calif San Diego, Inst Genom Med, La Jolla, CA 92093 USAen
kaust.authorRavasi, Timothyen
kaust.authorBajic, Vladimir B.en
kaust.authorCannistraci, Carloen
kaust.authorHan, Jung-Hoonen
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