Comparative analysis of regulatory information and circuits across distant species

被引：138

作者：

Boyle, Alan P. ^{[1
]}

Araya, Carlos L. ^{[1
]}

Brdlik, Cathleen ^{[1
]}

Cayting, Philip ^{[1
]}

Cheng, Chao ^{[2
]}

Cheng, Yong ^{[1
]}

Gardner, Kathryn ^{[3
]}

Hillier, LaDeana W. ^{[4
]}

Janette, Judith ^{[3
]}

Jiang, Lixia ^{[1
]}

Kasper, Dionna ^{[3
]}

Kawli, Trupti ^{[1
]}

Kheradpour, Pouya ^{[6
]}

Kundaje, Anshul ^{[5
,6
]}

Li, Jingyi Jessica ^{[7
,8
]}

Ma, Lijia ^{[4
]}

Niu, Wei ^{[3
]}

Rehm, E. Jay ^{[9
]}

Rozowsky, Joel ^{[2
]}

Slattery, Matthew ^{[9
]}

Spokony, Rebecca ^{[9
]}

Terrell, Robert ^{[4
]}

Vafeados, Dionne ^{[4
]}

Wang, Daifeng ^{[2
]}

Weisdepp, Peter

Wu, Yi-Chieh ^{[6
]}

Xie, Dan ^{[1
]}

Yan, Koon-Kiu ^{[2
]}

Feingold, Elise A. ^{[10
]}

Good, Peter J. ^{[10
]}

Pazin, Michael J. ^{[10
]}

Huang, Haiyan ^{[7
]}

Bickel, Peter J. ^{[7
]}

Brenner, Steven E. ^{[11
,12
]}

Reinke, Valerie ^{[3
]}

Waterston, Robert H. ^{[4
]}

Gerstein, Mark ^{[2
]}

White, Kevin P. ^{[9
]}

Kellis, Manolis ^{[6
]}

Snyder, Michael ^{[1
]}

机构：

[1] Stanford Univ, Sch Med, Dept Genet, Stanford, CA 94305 USA

[2] Yale Univ, Program Computat Biol & Bioinformat, New Haven, CT 06520 USA

[3] Yale Univ, Sch Med, Dept Genet, New Haven, CT 06520 USA

[4] Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA

[5] Stanford Univ, Dept Comp Sci, Stanford, CA 94305 USA

[6] MIT, Comp Sci & Artificial Intelligence Lab, Cambridge, MA 02139 USA

[7] Univ Calif Berkeley, Dept Stat, Berkeley, CA 94720 USA

[8] Univ Calif Los Angeles, Dept Stat, Los Angeles, CA 90095 USA

[9] Univ Chicago, Inst Genom & Syst Biol, Chicago, IL 60637 USA

[10] NHGRI, NIH, Bethesda, MD 20892 USA

[11] Univ Calif Berkeley, Dept Mol & Cell Biol, Berkeley, CA 94720 USA

[12] Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA

来源：

NATURE | 2014年 / 512卷 / 7515期

基金：

美国国家科学基金会;

关键词：

TRANSCRIPTION FACTOR-BINDING; CHIP-SEQ; HISTONE DEACETYLASE; CHROMATIN-IMMUNOPRECIPITATION; DROSOPHILA-MELANOGASTER; FACTOR COLOCALIZATION; MOTIF DISCOVERY; HIGH-THROUGHPUT; HUMAN-CELLS; RNA-SEQ;

D O I：

10.1038/nature13668

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Despite the large evolutionary distances between metazoan species, they can show remarkable commonalities in their biology, and this has helped to establish fly and worm as model organisms for human biology(1,2). Although studies of individual elements and factors have explored similarities in gene regulation, a large-scale comparative analysis of basic principles of transcriptional regulatory features is lacking. Here we map the genome-wide binding locations of 165 human, 93 worm and 52 fly transcription regulatory factors, generating a total of 1,019 data sets from diverse cell types, developmental stages, or conditions in the three species, of which 498 (48.9%) are presented here for the first time. We find that structural properties of regulatory networks are remarkably conserved and that orthologous regulatory factor families recognize similar binding motifs in vivo and show some similar co-associations. Our results suggest that gene-regulatory properties previously observed for individual factors are general principles of metazoan regulation that are remarkably well-preserved despite extensive functional divergence of individual network connections. The comparative maps of regulatory circuitry provided here will drive an improved understanding of the regulatory underpinnings of model organism biology and how these relate to human biology, development and disease.

引用

页码：453 / +

页数：16

共 54 条

[51] Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors [J].

Yip, Kevin Y. ;

Cheng, Chao ;

Bhardwaj, Nitin ;

Brown, James B. ;

Leng, Jing ;

Kundaje, Anshul ;

Rozowsky, Joel ;

Birney, Ewan ;

Bickel, Peter ;

Snyder, Michael ;

Gerstein, Mark .

GENOME BIOLOGY, 2012, 13 (09)

[52] Model-based Analysis of ChIP-Seq (MACS) [J].

Zhang, Yong ;

Liu, Tao ;

Meyer, Clifford A. ;

Eeckhoute, Jerome ;

Johnson, David S. ;

Bernstein, Bradley E. ;

Nussbaum, Chad ;

Myers, Richard M. ;

Brown, Myles ;

Li, Wei ;

Liu, X. Shirley .

GENOME BIOLOGY, 2008, 9 (09)

[53] Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response [J].

Zhong, Mei ;

Niu, Wei ;

Lu, Zhi John ;

Sarov, Mihail ;

Murray, John I. ;

Janette, Judith ;

Raha, Debasish ;

Sheaffer, Karyn L. ;

Lam, Hugo Y. K. ;

Preston, Elicia ;

Slightham, Cindie ;

Hillier, LaDeana W. ;

Brock, Trisha ;

Agarwal, Ashish ;

Auerbach, Raymond ;

Hyman, Anthony A. ;

Gerstein, Mark ;

Mango, Susan E. ;

Kim, Stuart K. ;

Waterston, Robert H. ;

Reinke, Valerie ;

Snyder, Michael .

PLOS GENETICS, 2010, 6 (02)

[54] ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data [J].

Zhu, Lihua J. ;

Gazin, Claude ;

Lawson, Nathan D. ;

Pages, Herve ;

Lin, Simon M. ;

Lapointe, David S. ;

Green, Michael R. .

BMC BIOINFORMATICS, 2010, 11

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