Identifying and Characterizing Regulatory Sequences in the Human Genome with Chromatin Accessibility Assays

被引:24
作者
Sheffield, Nathan C. [1 ]
Furey, Terrence S. [2 ,3 ]
机构
[1] Duke Univ, Program Computat Biol & Bioinformat, Inst Genome Sci & Policy, Durham, NC 27708 USA
[2] Univ N Carolina, Lineberger Comprehens Canc Ctr, Carolina Ctr Genome Sci, Dept Genet, Chapel Hill, NC 27599 USA
[3] Univ N Carolina, Lineberger Comprehens Canc Ctr, Carolina Ctr Genome Sci, Dept Biol, Chapel Hill, NC 27599 USA
来源
GENES | 2012年 / 3卷 / 04期
基金
美国国家科学基金会;
关键词
open chromatin; DNaseI; transcriptional regulation; ENCODE; GENE-EXPRESSION; DNA; ELEMENTS; REGIONS; ENHANCER; CTCF; ORGANIZATION; ASSOCIATIONS; PREDICTION; MAP;
D O I
10.3390/genes3040651
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
After finishing a human genome reference sequence in 2002, the genomics community has turned to the task of interpreting it. A primary focus is to identify and characterize not only protein-coding genes, but all functional elements in the genome. The effort includes both individual investigators and large-scale projects like the Encyclopedia of DNA Elements (ENCODE) project. As part of the ENCODE project, several groups have identified millions of regulatory elements in hundreds of human cell-types using DNase-seq and FAIRE-seq experiments that detect regions of nucleosome-free open chromatin. ChIP-seq experiments have also been used to discover transcription factor binding sites and map histone modifications. Nearly all identified elements are found in non-coding DNA, hypothesizing a function for previously unannotated sequence. In this review, we provide an overview of the ENCODE effort to define regulatory elements, summarize the main results, and discuss implications of the millions of regulatory elements distributed throughout the genome.
引用
收藏
页码:651 / 670
页数:20
相关论文
共 76 条
[1]   Annotating non-coding regions of the genome [J].
Alexander, Roger P. ;
Fang, Gang ;
Rozowsky, Joel ;
Snyder, Michael ;
Gerstein, Mark B. .
NATURE REVIEWS GENETICS, 2010, 11 (08) :559-571
[2]   Chromosomal Dynamics at the Shh Locus: Limb Bud-Specific Differential Regulation of Competence and Active Transcription [J].
Amano, Takanori ;
Sagai, Tomoko ;
Tanabe, Hideyuki ;
Mizushina, Yoichi ;
Nakazawa, Hiromi ;
Shiroishi, Toshihiko .
DEVELOPMENTAL CELL, 2009, 16 (01) :47-57
[3]   Mapping accessible chromatin regions using Sono-Seq [J].
Auerbach, Raymond K. ;
Euskirchen, Ghia ;
Rozowsky, Joel ;
Lamarre-Vincent, Nathan ;
Moqtaderi, Zarmik ;
Lefrancois, Philippe ;
Struhl, Kevin ;
Gerstein, Mark ;
Snyder, Michael .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (35) :14926-14931
[4]   Predicting gene expression from sequence [J].
Beer, MA ;
Tavazoie, S .
CELL, 2004, 117 (02) :185-198
[5]   Transcription Factor AP1 Potentiates Chromatin Accessibility and Glucocorticoid Receptor Binding [J].
Biddie, Simon C. ;
John, Sam ;
Sabo, Pete J. ;
Thurman, Robert E. ;
Johnson, Thomas A. ;
Schiltz, R. Louis ;
Miranda, Tina B. ;
Sung, Myong-Hee ;
Trump, Saskia ;
Lightman, Stafford L. ;
Vinson, Charles ;
Stamatoyannopoulos, John A. ;
Hager, Gordon L. .
MOLECULAR CELL, 2011, 43 (01) :145-155
[6]   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
[7]   Allele-specific and heritable chromatin signatures in humans [J].
Birney, Ewan ;
Lieb, Jason D. ;
Furey, Terrence S. ;
Crawford, Gregory E. ;
Iyer, Vishwanath R. .
HUMAN MOLECULAR GENETICS, 2010, 19 :R204-R209
[8]   High-resolution mapping and characterization of open chromatin across the genome [J].
Boyle, Alan P. ;
Davis, Sean ;
Shulha, Hennady P. ;
Meltzer, Paul ;
Margulies, Elliott H. ;
Weng, Zhiping ;
Furey, Terrence S. ;
Crawford, Gregory E. .
CELL, 2008, 132 (02) :311-322
[9]   High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells [J].
Boyle, Alan P. ;
Song, Lingyun ;
Lee, Bum-Kyu ;
London, Darin ;
Keefe, Damian ;
Birney, Ewan ;
Iyer, Vishwanath R. ;
Crawford, Gregory E. ;
Furey, Terrence S. .
GENOME RESEARCH, 2011, 21 (03) :456-464
[10]   Functional and Mechanistic Diversity of Distal Transcription Enhancers [J].
Bulger, Michael ;
Groudine, Mark .
CELL, 2011, 144 (03) :327-339