An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

Timothy Ravasi; Harukazu Suzuki; Carlo Cannistraci; Shintaro Katayama; Vladimir 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; Hideya Kawaji; Atsutaka Kubosaki; Timo Lassmann; Erik van Nimwegen; Chihiro Ogawa; Rohan D. Teasdale; Jesper Tegner; 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 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, Hideya KawajiAtsutaka Kubosaki, Timo Lassmann, Erik van Nimwegen, Chihiro Ogawa, Rohan D. Teasdale, Jesper Tegner, 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

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

586 Scopus citations

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

Keywords

DNA

ASJC Scopus subject areas

General Biochemistry, Genetics and Molecular Biology

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10.1016/j.cell.2010.01.044

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Ravasi, T., Suzuki, H., Cannistraci, C., Katayama, S., Bajic, V., 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

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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.",

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author = "Timothy Ravasi and Harukazu Suzuki and Carlo Cannistraci and Shintaro Katayama and Vladimir Bajic 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 Han, {Jung Hoon} and Takehiro Hashimoto and Winston Hide and Oliver Hofmann and Hideya Kawaji and Atsutaka Kubosaki and Timo Lassmann and {van Nimwegen}, Erik and Chihiro Ogawa and Teasdale, {Rohan D.} and Jesper Tegner 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",

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Ravasi, T, Suzuki, H, Cannistraci, C, Katayama, S, Bajic, V, Tan, K, Akalin, A, Schmeier, S, Kanamori-Katayama, M, Bertin, N, Carninci, P, Daub, CO, Forrest, ARR, Gough, J, Grimmond, S, Han, JH, Hashimoto, T, Hide, W, Hofmann, O, Kawaji, H, Kubosaki, A, Lassmann, T, van Nimwegen, E, Ogawa, C, Teasdale, RD, Tegner, 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

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AU - Ravasi, Timothy

AU - Suzuki, Harukazu

AU - Cannistraci, Carlo

AU - Katayama, Shintaro

AU - Bajic, Vladimir

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 - Kawaji, Hideya

AU - Kubosaki, Atsutaka

AU - Lassmann, Timo

AU - van Nimwegen, Erik

AU - Ogawa, Chihiro

AU - Teasdale, Rohan D.

AU - Tegner, 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

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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.

KW - DNA

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DO - 10.1016/j.cell.2010.01.044

M3 - Article

C2 - 20211142

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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Keywords

ASJC Scopus subject areas

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