Variation in Transcription Factor Binding Among Humans

被引：418

作者：

Kasowski, Maya ^{[2
]}

Grubert, Fabian ^{[2
,3
]}

Heffelfinger, Christopher ^{[2
]}

Hariharan, Manoj ^{[2
,3
]}

Asabere, Akwasi ^{[2
]}

Waszak, Sebastian M. ^{[1
,4
]}

Habegger, Lukas ^{[5
]}

Rozowsky, Joel ^{[6
]}

Shi, Minyi ^{[2
,3
]}

Urban, Alexander E. ^{[2
,7
]}

Hong, Mi-Young ^{[2
]}

Karczewski, Konrad J. ^{[3
]}

Huber, Wolfgang ^{[1
]}

Weissman, Sherman M. ^{[7
]}

Gerstein, Mark B. ^{[5
,6
,8
]}

Korbel, Jan O. ^{[1
,9
]}

Snyder, Michael ^{[2
,3
]}

机构：

[1] European Mol Biol Lab, Genome Biol Res Unit, Heidelberg, Germany

[2] Yale Univ, Dept Mol Cellular & Dev Biol, New Haven, CT 06520 USA

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

[4] Weihenstephan Triesdorf Univ Appl Sci, Dept Biotechnol & Bioinformat, D-85350 Freising Weihenstephan, Germany

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

[6] Yale Univ, Dept Mol Biophys & Biochem, New Haven, CT 06520 USA

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

[8] Yale Univ, Dept Comp Sci, New Haven, CT 06520 USA

[9] European Mol Biol Lab European Bioinformat Inst, Hinxton CB10 1SD, England

来源：

SCIENCE | 2010年 / 328卷 / 5975期

关键词：

STRUCTURAL VARIATION;

D O I：

10.1126/science.1183621

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：

Differences in gene expression may play a major role in speciation and phenotypic diversity. We examined genome-wide differences in transcription factor (TF) binding in several humans and a single chimpanzee by using chromatin immunoprecipitation followed by sequencing. The binding sites of RNA polymerase II (PolII) and a key regulator of immune responses, nuclear factor kappa B (p65), were mapped in 10 lymphoblastoid cell lines, and 25 and 7.5% of the respective binding regions were found to differ between individuals. Binding differences were frequently associated with single-nucleotide polymorphisms and genomic structural variants, and these differences were often correlated with differences in gene expression, suggesting functional consequences of binding variation. Furthermore, comparing PolII binding between humans and chimpanzee suggests extensive divergence in TF binding. Our results indicate that many differences in individuals and species occur at the level of TF binding, and they provide insight into the genetic events responsible for these differences.

引用

页码：232 / 235

页数：4

共 16 条

[1] Divergence of transcription factor binding sites across related yeast species [J].

Borneman, Anthony R. ;

Gianoulis, Tara A. ;

Zhang, Zhengdong D. ;

Yu, Haiyuan ;

Rozowsky, Joel ;

Seringhaus, Michael R. ;

Wang, Lu Yong ;

Gerstein, Mark ;

Snyder, Michael .

SCIENCE, 2007, 317 (5839) :815-819

[2] Human brain evolution [J].

Creely, Hilliary ;

Khaitovich, Philipp .

FUNCTIONAL GENOMICS AND PROTEOMICS IN THE CLINICAL NEUROSCIENCES, 2006, 158 :295-309

[3] The B subunit of the CAAT-binding factor NFY binds the central segment of the co-activator p300 [J].

Faniello, MC ;

Bevilacqua, MA ;

Condorelli, G ;

de Crombrugghe, B ;

Maity, SN ;

Avvedimento, VE ;

Cimino, F ;

Costanzo, F .

JOURNAL OF BIOLOGICAL CHEMISTRY, 1999, 274 (12) :7623-7626

[4] A second generation human haplotype map of over 3.1 million SNPs [J].

Frazer, Kelly A. ;

Ballinger, Dennis G. ;

Cox, David R. ;

Hinds, David A. ;

Stuve, Laura L. ;

Gibbs, Richard A. ;

Belmont, John W. ;

Boudreau, Andrew ;

Hardenbol, Paul ;

Leal, Suzanne M. ;

Pasternak, Shiran ;

Wheeler, David A. ;

Willis, Thomas D. ;

Yu, Fuli ;

Yang, Huanming ;

Zeng, Changqing ;

Gao, Yang ;

Hu, Haoran ;

Hu, Weitao ;

Li, Chaohua ;

Lin, Wei ;

Liu, Siqi ;

Pan, Hao ;

Tang, Xiaoli ;

Wang, Jian ;

Wang, Wei ;

Yu, Jun ;

Zhang, Bo ;

Zhang, Qingrun ;

Zhao, Hongbin ;

Zhao, Hui ;

Zhou, Jun ;

Gabriel, Stacey B. ;

Barry, Rachel ;

Blumenstiel, Brendan ;

Camargo, Amy ;

Defelice, Matthew ;

Faggart, Maura ;

Goyette, Mary ;

Gupta, Supriya ;

Moore, Jamie ;

Nguyen, Huy ;

Onofrio, Robert C. ;

Parkin, Melissa ;

Roy, Jessica ;

Stahl, Erich ;

Winchester, Ellen ;

Ziaugra, Liuda ;

Altshuler, David ;

Shen, Yan .

NATURE, 2007, 449 (7164) :851-U3

[5] Mapping and sequencing of structural variation from eight human genomes (Reprinted from Nature, vol 453, pg 56-64, 2008) [J].

Kidd, Jeffrey M. ;

Cooper, Gregory M. ;

Donahue, William F. ;

Hayden, Hillary S. ;

Sampas, Nick ;

Graves, Tina ;

Hansen, Nancy ;

Teague, Brian ;

Alkan, Can ;

Antonacci, Francesca ;

Haugen, Eric ;

Zerr, Troy ;

Yamada, N. Alice ;

Tsang, Peter ;

Newman, Tera L. ;

Tuzun, Eray ;

Cheng, Ze ;

Ebling, Heather M. ;

Tusneem, Nadeem ;

David, Robert ;

Gillett, Will ;

Phelps, Karen A. ;

Weaver, Molly ;

Saranga, David ;

Brand, Adrianne ;

Tao, Wei ;

Gustafson, Erik ;

McKernan, Kevin ;

Chen, Lin ;

Malig, Maika ;

Smith, Joshua D. ;

Korn, Joshua M. ;

McCarroll, Steven A. ;

Altshuler, David A. ;

Peiffer, Daniel A. ;

Dorschner, Michael ;

Stamatoyannopoulos, John ;

Schwartz, David ;

Nickerson, Deborah A. ;

Mullikin, James C. ;

Wilson, Richard K. ;

Bruhn, Laurakay ;

Olson, Maynard V. ;

Kaul, Rajinder ;

Smith, Douglas R. ;

Eichler, Evan E. .

NATURE GENETICS, 2009, :S22-S30

[6]

Korbel JO, 2007, SCIENCE, V318, P420, DOI 10.1126/science.1149504

[7] Acetylation of Stat1 modulates NF-κB activity [J].

Krämer, OH ;

Baus, D ;

Knauer, SK ;

Stein, S ;

Jäger, E ;

Stauber, RH ;

Grez, M ;

Pfitzner, E ;

Heinzel, T .

GENES & DEVELOPMENT, 2006, 20 (04) :473-485

[8] The diploid genome sequence of an individual human [J].

Levy, Samuel ;

Sutton, Granger ;

Ng, Pauline C. ;

Feuk, Lars ;

Halpern, Aaron L. ;

Walenz, Brian P. ;

Axelrod, Nelson ;

Huang, Jiaqi ;

Kirkness, Ewen F. ;

Denisov, Gennady ;

Lin, Yuan ;

MacDonald, Jeffrey R. ;

Pang, Andy Wing Chun ;

Shago, Mary ;

Stockwell, Timothy B. ;

Tsiamouri, Alexia ;

Bafna, Vineet ;

Bansal, Vikas ;

Kravitz, Saul A. ;

Busam, Dana A. ;

Beeson, Karen Y. ;

Mclntosh, Tina C. ;

Remington, Karin A. ;

Abril, Josep F. ;

Gill, John ;

Borman, Jon ;

Rogers, Yu-Hui ;

Frazier, Marvin E. ;

Scherer, Stephen W. ;

Strausberg, Robert L. ;

Venter, J. Craig .

PLOS BIOLOGY, 2007, 5 (10) :2113-2144

[9] Integrated detection and population-genetic analysis of SNPs and copy number variation [J].

McCarroll, Steven A. ;

Kuruvilla, Finny G. ;

Korn, Joshua M. ;

Cawley, Simon ;

Nemesh, James ;

Wysoker, Alec ;

Shapero, Michael H. ;

de Bakker, Paul I. W. ;

Maller, Julian B. ;

Kirby, Andrew ;

Elliott, Amanda L. ;

Parkin, Melissa ;

Hubbell, Earl ;

Webster, Teresa ;

Mei, Rui ;

Veitch, James ;

Collins, Patrick J. ;

Handsaker, Robert ;

Lincoln, Steve ;

Nizzari, Marcia ;

Blume, John ;

Jones, Keith W. ;

Rava, Rich ;

Daly, Mark J. ;

Gabriel, Stacey B. ;

Altshuler, David .

NATURE GENETICS, 2008, 40 (10) :1166-1174

[10] Genetics of global gene expression [J].

Rockman, Matthew V. ;

Kruglyak, Leonid .

NATURE REVIEWS GENETICS, 2006, 7 (11) :862-872

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