An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

Timothy Ravasi; Harukazu Suzuki; Carlo Cannistraci; Shintaro Katayama; Vladimir B. Bajic; Kai Tan; Altuna Akalin; Sebastian Schmeier; Mutsumi Kanamori-Katayama; Nicolas Bertin; Piero Carninci; Carsten O. Daub; Alistair R.R. Forrest; Julian Gough; Sean Grimmond; Jung-Hoon Han; Takehiro Hashimoto; Winston Hide; Oliver Hofmann; Atanas Kamburov; Mandeep Kaur; Hideya Kawaji; Atsutaka Kubosaki; Timo Lassmann; Erik van Nimwegen; Cameron Ross MacPherson; Chihiro Ogawa; Aleksandar Radovanovic; Ariel Schwartz; Rohan D. Teasdale; Jesper Tegnér; Boris Lenhard; Sarah A. Teichmann; Takahiro Arakawa; Noriko Ninomiya; Kayoko Murakami; Michihira Tagami; Shiro Fukuda; Kengo Imamura; Chikatoshi Kai; Ryoko Ishihara; Yayoi Kitazume; Jun Kawai; David A. Hume; Trey Ideker; Yoshihide Hayashizaki

doi:10.1016/j.cell.2010.01.044

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

Timothy Ravasi, Harukazu Suzuki, Carlo Cannistraci, Shintaro Katayama, Vladimir B. Bajic, Kai Tan, Altuna Akalin, Sebastian Schmeier, Mutsumi Kanamori-Katayama, Nicolas Bertin, Piero Carninci, Carsten O. Daub, Alistair R.R. Forrest, Julian Gough, Sean Grimmond, Jung-Hoon Han, Takehiro Hashimoto, Winston Hide, Oliver Hofmann, Atanas KamburovMandeep Kaur, Hideya Kawaji, Atsutaka Kubosaki, Timo Lassmann, Erik van Nimwegen, Cameron Ross MacPherson, Chihiro Ogawa, Aleksandar Radovanovic, Ariel Schwartz, Rohan D. Teasdale, Jesper Tegnér, Boris Lenhard, Sarah A. Teichmann, Takahiro Arakawa, Noriko Ninomiya, Kayoko Murakami, Michihira Tagami, Shiro Fukuda, Kengo Imamura, Chikatoshi Kai, Ryoko Ishihara, Yayoi Kitazume, Jun Kawai, David A. Hume, Trey Ideker, Yoshihide Hayashizaki

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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.

Original language	English (US)
Pages (from-to)	744-752
Number of pages	9
Journal	Cell
Volume	140
Issue number	5
DOIs	https://doi.org/10.1016/j.cell.2010.01.044
State	Published - Mar 5 2010

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: 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.

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10.1016/j.cell.2010.01.044

https://repository.kaust.edu.sa/bitstream/10754/575669/1/nihms177825.pdf

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Ravasi, T., Suzuki, H., Cannistraci, C., Katayama, S., Bajic, V. B., Tan, K., Akalin, A., Schmeier, S., Kanamori-Katayama, M., Bertin, N., Carninci, P., Daub, C. O., Forrest, A. R. R., Gough, J., Grimmond, S., Han, J.-H., Hashimoto, T., Hide, W., Hofmann, O., ... Hayashizaki, Y. (2010). An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man. Cell, 140(5), 744-752. https://doi.org/10.1016/j.cell.2010.01.044

@article{061c89da62124c92937d4dd0a75ece80,

title = "An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man",

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.",

author = "Timothy Ravasi and Harukazu Suzuki and Carlo Cannistraci and Shintaro Katayama and Bajic, {Vladimir B.} and Kai Tan and Altuna Akalin and Sebastian Schmeier and Mutsumi Kanamori-Katayama and Nicolas Bertin and Piero Carninci and Daub, {Carsten O.} and Forrest, {Alistair R.R.} and Julian Gough and Sean Grimmond and Jung-Hoon Han and Takehiro Hashimoto and Winston Hide and Oliver Hofmann and Atanas Kamburov and Mandeep Kaur and Hideya Kawaji and Atsutaka Kubosaki and Timo Lassmann and {van Nimwegen}, Erik and MacPherson, {Cameron Ross} and Chihiro Ogawa and Aleksandar Radovanovic and Ariel Schwartz and Teasdale, {Rohan D.} and Jesper Tegn{\'e}r and Boris Lenhard and Teichmann, {Sarah A.} and Takahiro Arakawa and Noriko Ninomiya and Kayoko Murakami and Michihira Tagami and Shiro Fukuda and Kengo Imamura and Chikatoshi Kai and Ryoko Ishihara and Yayoi Kitazume and Jun Kawai and Hume, {David A.} and Trey Ideker and Yoshihide Hayashizaki",

note = "KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: 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.",

year = "2010",

month = mar,

day = "5",

doi = "10.1016/j.cell.2010.01.044",

language = "English (US)",

volume = "140",

pages = "744--752",

journal = "Cell",

issn = "0092-8674",

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Ravasi, T, Suzuki, H, Cannistraci, C, Katayama, S, Bajic, VB, Tan, K, Akalin, A, Schmeier, S, Kanamori-Katayama, M, Bertin, N, Carninci, P, Daub, CO, Forrest, ARR, Gough, J, Grimmond, S, Han, J-H, Hashimoto, T, Hide, W, Hofmann, O, Kamburov, A, Kaur, M, Kawaji, H, Kubosaki, A, Lassmann, T, van Nimwegen, E, MacPherson, CR, Ogawa, C, Radovanovic, A, Schwartz, A, Teasdale, RD, Tegnér, J, Lenhard, B, Teichmann, SA, Arakawa, T, Ninomiya, N, Murakami, K, Tagami, M, Fukuda, S, Imamura, K, Kai, C, Ishihara, R, Kitazume, Y, Kawai, J, Hume, DA, Ideker, T & Hayashizaki, Y 2010, 'An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man', Cell, vol. 140, no. 5, pp. 744-752. https://doi.org/10.1016/j.cell.2010.01.044

TY - JOUR

T1 - An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

AU - Ravasi, Timothy

AU - Suzuki, Harukazu

AU - Cannistraci, Carlo

AU - Katayama, Shintaro

AU - Bajic, Vladimir B.

AU - Tan, Kai

AU - Akalin, Altuna

AU - Schmeier, Sebastian

AU - Kanamori-Katayama, Mutsumi

AU - Bertin, Nicolas

AU - Carninci, Piero

AU - Daub, Carsten O.

AU - Forrest, Alistair R.R.

AU - Gough, Julian

AU - Grimmond, Sean

AU - Han, Jung-Hoon

AU - Hashimoto, Takehiro

AU - Hide, Winston

AU - Hofmann, Oliver

AU - Kamburov, Atanas

AU - Kaur, Mandeep

AU - Kawaji, Hideya

AU - Kubosaki, Atsutaka

AU - Lassmann, Timo

AU - van Nimwegen, Erik

AU - MacPherson, Cameron Ross

AU - Ogawa, Chihiro

AU - Radovanovic, Aleksandar

AU - Schwartz, Ariel

AU - Teasdale, Rohan D.

AU - Tegnér, Jesper

AU - Lenhard, Boris

AU - Teichmann, Sarah A.

AU - Arakawa, Takahiro

AU - Ninomiya, Noriko

AU - Murakami, Kayoko

AU - Tagami, Michihira

AU - Fukuda, Shiro

AU - Imamura, Kengo

AU - Kai, Chikatoshi

AU - Ishihara, Ryoko

AU - Kitazume, Yayoi

AU - Kawai, Jun

AU - Hume, David A.

AU - Ideker, Trey

AU - Hayashizaki, Yoshihide

N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: 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.

PY - 2010/3/5

Y1 - 2010/3/5

N2 - 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.

AB - 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.

UR - http://hdl.handle.net/10754/575669

UR - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2836267

UR - http://www.scopus.com/inward/record.url?scp=77649299348&partnerID=8YFLogxK

U2 - 10.1016/j.cell.2010.01.044

DO - 10.1016/j.cell.2010.01.044

M3 - Article

SN - 0092-8674

VL - 140

SP - 744

EP - 752

JO - Cell

JF - Cell

IS - 5

ER -

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

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