An atlas of combinatorial transcriptional regulation in mouse and man

Ravasi, Timothy, Suzuki, Harukazu, Cannistraci, Carlo Vittorio, Katayama, Shintaro, Bajic, Vladimir B., Tan, Kai, Akalin, Altuna, Schmeier, Sebastian, Kanamori-Katayama, Mutsumi, Carninci, Piero, Bertin, Nicholas, Daub, Cartsten 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., Tegner, 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 and Hayashizaki, Yoshihide (2010) An atlas of combinatorial transcriptional regulation in mouse and man. Cell, 140 5: 744-752. doi:10.1016/j.cell.2010.01.044


Author Ravasi, Timothy
Suzuki, Harukazu
Cannistraci, Carlo Vittorio
Katayama, Shintaro
Bajic, Vladimir B.
Tan, Kai
Akalin, Altuna
Schmeier, Sebastian
Kanamori-Katayama, Mutsumi
Carninci, Piero
Bertin, Nicholas
Daub, Cartsten 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.
Tegner, 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
Title An atlas of combinatorial transcriptional regulation in mouse and man
Journal name Cell   Check publisher's open access policy
ISSN 0092-8674
1097-4172
Publication date 2010-03-05
Sub-type Article (original research)
DOI 10.1016/j.cell.2010.01.044
Open Access Status Not Open Access
Volume 140
Issue 5
Start page 744
End page 752
Total pages 9
Place of publication Cambridge, MA, United
Publisher Cell Press
Language eng
Subject C1
0601 Biochemistry and Cell Biology
Abstract MicroRNAs (miRNAs) are short non-coding RNAs with key roles in cellular regulation. As part of the fifth edition of the Functional Annotation of Mammalian Genome (FANTOM5) project, we created an integrated expression atlas of miRNAs and their promoters by deep-sequencing 492 short RNA (sRNA) libraries, with matching Cap Analysis Gene Expression (CAGE) data, from 396 human and 47 mouse RNA samples. Promoters were identified for 1,357 human and 804 mouse miRNAs and showed strong sequence conservation between species. We also found that primary and mature miRNA expression levels were correlated, allowing us to use the primary miRNA measurements as a proxy for mature miRNA levels in a total of 1,829 human and 1,029 mouse CAGE libraries. We thus provide a broad atlas of miRNA expression and promoters in primary mammalian cells, establishing a foundation for detailed analysis of miRNA expression patterns and transcriptional control regions.
Formatted 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.
©2010 Elsevier Inc.

Keyword Embryonic stem-cells
Protein interactions
Gene-expression
Networks
DNA
Binding
Family
Yeast
Lipopolysaccharide
Differentiation
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2011 Collection
Institute for Molecular Bioscience - Publications
 
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Created: Sun, 21 Mar 2010, 10:09:15 EST