Insights from genomic profiling of transcription factors

被引：378

作者：

Farnham, Peggy J. ^{[1
,2
]}

机构：

[1] Univ Calif Davis, Dept Pharmacol, Davis, CA 95616 USA

[2] Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA

来源：

NATURE REVIEWS GENETICS | 2009年 / 10卷 / 09期

关键词：

FACTOR-BINDING SITES; CHIP-SEQ DATA; PROTEIN-DNA INTERACTIONS; CHROMATIN IMMUNOPRECIPITATION; GENE-EXPRESSION; WIDE IDENTIFICATION; HUMAN-CELLS; EPIGENETIC CHARACTERIZATION; PROMOTER STRUCTURE; HISTONE H3K4ME3;

D O I：

10.1038/nrg2636

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

A crucial question in the field of gene regulation is whether the location at which a transcription factor binds influences its effectiveness or the mechanism by which it regulates transcription. Comprehensive transcription factor binding maps are needed to address these issues, and genome-wide mapping is now possible thanks to the technological advances of ChIP-chip and ChIP-seq. This Review discusses how recent genomic profiling of transcription factors gives insight into how binding specificity is achieved and what features of chromatin influence the ability of transcription factors to interact with the genome. It also suggests future experiments that may further our understanding of the causes and consequences of transcription factor-genome interactions.

引用

页码：605 / 616

页数：12

共 82 条

[1] Genome-scale ChIP-chip analysis using 10,000 human cells [J].

Acevedo, Luis G. ;

Iniguez, A. Leonardo ;

Holster, Heather L. ;

Zhang, Xinmin ;

Green, Roland ;

Farnham, Peggy J. .

BIOTECHNIQUES, 2007, 43 (06) :791-797

[2] The chromatin structure of the dual c-myc promoter P1/P2 is regulated by separate elements [J].

Albert, T ;

Wells, J ;

Funk, JO ;

Pullner, A ;

Raschke, EE ;

Stelzer, G ;

Meisterernst, I ;

Farnham, PJ ;

Eick, D .

JOURNAL OF BIOLOGICAL CHEMISTRY, 2001, 276 (23) :20482-20490

[3] Epigenetic characterization of hematopoietic stem cell differentiation using miniChIP and bisulfite sequencing analysis [J].

Attema, Joanne L. ;

Papathanasiou, Peter ;

Forsberg, E. Camilla ;

Xu, Jian ;

Smale, Stephen T. ;

Weissman, Irving L. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (30) :12371-12376

[4] Diversity and Complexity in DNA Recognition by Transcription Factors [J].

Badis, Gwenael ;

Berger, Michael F. ;

Philippakis, Anthony A. ;

Talukder, Shaheynoor ;

Gehrke, Andrew R. ;

Jaeger, Savina A. ;

Chan, Esther T. ;

Metzler, Genita ;

Vedenko, Anastasia ;

Chen, Xiaoyu ;

Kuznetsov, Hanna ;

Wang, Chi-Fong ;

Coburn, David ;

Newburger, Daniel E. ;

Morris, Quaid ;

Hughes, Timothy R. ;

Bulyk, Martha L. .

SCIENCE, 2009, 324 (5935) :1720-1723

[5] Specialized transcription factories [J].

Bartlett, O ;

Blagojevic, J ;

Carter, D ;

Eskiw, C ;

Fromaget, M ;

Job, C ;

Shamsher, M ;

Trindade, IF ;

Xu, M ;

Cook, PR .

TRANSCRIPTION, 2006, 73 :67-75

[6] Interrogating genomes with combinatorial artificial transcription factor libraries: Asking zinc finger questions [J].

Beltran, Adriana ;

Liu, Yanzheng ;

Parikh, Shaunak ;

Temple, Brenda ;

Blancafort, Pilar .

ASSAY AND DRUG DEVELOPMENT TECHNOLOGIES, 2006, 4 (03) :317-331

[7] Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome [J].

Bieda, M ;

Xu, XQ ;

Singer, MA ;

Green, R ;

Farnham, PJ .

GENOME RESEARCH, 2006, 16 (05) :595-605

[8] Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project [J].

Birney, Ewan ;

Stamatoyannopoulos, John A. ;

Dutta, Anindya ;

Guigo, Roderic ;

Gingeras, Thomas R. ;

Margulies, Elliott H. ;

Weng, Zhiping ;

Snyder, Michael ;

Dermitzakis, Emmanouil T. ;

Stamatoyannopoulos, John A. ;

Thurman, Robert E. ;

Kuehn, Michael S. ;

Taylor, Christopher M. ;

Neph, Shane ;

Koch, Christoph M. ;

Asthana, Saurabh ;

Malhotra, Ankit ;

Adzhubei, Ivan ;

Greenbaum, Jason A. ;

Andrews, Robert M. ;

Flicek, Paul ;

Boyle, Patrick J. ;

Cao, Hua ;

Carter, Nigel P. ;

Clelland, Gayle K. ;

Davis, Sean ;

Day, Nathan ;

Dhami, Pawandeep ;

Dillon, Shane C. ;

Dorschner, Michael O. ;

Fiegler, Heike ;

Giresi, Paul G. ;

Goldy, Jeff ;

Hawrylycz, Michael ;

Haydock, Andrew ;

Humbert, Richard ;

James, Keith D. ;

Johnson, Brett E. ;

Johnson, Ericka M. ;

Frum, Tristan T. ;

Rosenzweig, Elizabeth R. ;

Karnani, Neerja ;

Lee, Kirsten ;

Lefebvre, Gregory C. ;

Navas, Patrick A. ;

Neri, Fidencio ;

Parker, Stephen C. J. ;

Sabo, Peter J. ;

Sandstrom, Richard ;

Shafer, Anthony .

NATURE, 2007, 447 (7146) :799-816

[9] DNA sequence-specific polyamides alleviate transcription inhibition associated with long GAA•TTC repeats in Friedreich's ataxia [J].

Burnett, Ryan ;

Melander, Christian ;

Puckett, James W. ;

Son, Leslie S. ;

Wells, Robert D. ;

Dervan, Peter B. ;

Gottesfeld, Joel M. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2006, 103 (31) :11497-11502

[10] Critical parameters for genome editing using zinc finger nucleases [J].

Camenisch, Todd D. ;

Brilliant, Murray H. ;

Segal, David J. .

MINI-REVIEWS IN MEDICINAL CHEMISTRY, 2008, 8 (07) :669-676

← 1 2 3 4 5 6 7 8 9 →