ChIPping away at gene regulation

被引:41
作者
Massie, Charles E. [1 ]
Mills, Ian G. [1 ]
机构
[1] CRUK Cambridge Res Inst, Uro Oncol Res Grp, Li Ka Shing Ctr, Cambridge CB2 ORE, England
基金
英国医学研究理事会;
关键词
chromatin immunoprecipitation; gene expression; transcription factor;
D O I
10.1038/embor.2008.44
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The coordinated regulation of gene expression in higher eukaryotes is complex and poorly understood. Recent technological advances have allowed the first insights into these networks on a genome-wide scale. These investigations have identified transcription factor target sites in the genome and successfully predicted cooperative interactions with other factors. However, a detailed understanding of the processes that coordinate gene expression remains elusive. Here, we highlight the advances that have been made using current methods, and the need for new technologies to address the gaps in our knowledge and to map these complex pathways further.
引用
收藏
页码:337 / 343
页数:7
相关论文
共 51 条
[1]   Structure and evolution of transcriptional regulatory networks [J].
Babu, MM ;
Luscombe, NM ;
Aravind, L ;
Gerstein, M ;
Teichmann, SA .
CURRENT OPINION IN STRUCTURAL BIOLOGY, 2004, 14 (03) :283-291
[2]   New androgen response elements in the murine Pem promoter mediate selective transactivation [J].
Barbulescu, K ;
Geserick, C ;
Schüttke, I ;
Schleuning, WD ;
Haendler, B .
MOLECULAR ENDOCRINOLOGY, 2001, 15 (10) :1803-1816
[3]   Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE) [J].
Bhinge, Akshay A. ;
Kim, Jonghwan ;
Euskirchen, Ghia M. ;
Snyder, Michael ;
Iyer, Vishwanath R. .
GENOME RESEARCH, 2007, 17 (06) :910-916
[4]   An initial blueprint for myogenic differentiation [J].
Blais, A ;
Tsikitis, M ;
Acosta-Alvear, D ;
Sharan, R ;
Kluger, Y ;
Dynlacht, BD .
GENES & DEVELOPMENT, 2005, 19 (05) :553-569
[5]   Cell- and gene-specific regulation of primary target genes by the androgen receptor [J].
Bolton, Eric C. ;
So, Alex Y. ;
Chaivorapol, Christina ;
Haqq, Christopher M. ;
Li, Hao ;
Yamamoto, Keith R. .
GENES & DEVELOPMENT, 2007, 21 (16) :2005-2017
[6]   Core transcriptional regulatory circuitry in human embryonic stem cells [J].
Boyer, LA ;
Lee, TI ;
Cole, MF ;
Johnstone, SE ;
Levine, SS ;
Zucker, JR ;
Guenther, MG ;
Kumar, RM ;
Murray, HL ;
Jenner, RG ;
Gifford, DK ;
Melton, DA ;
Jaenisch, R ;
Young, RA .
CELL, 2005, 122 (06) :947-956
[7]   Genome-wide analysis of estrogen receptor binding sites [J].
Carroll, Jason S. ;
Meyer, Clifford A. ;
Song, Jun ;
Li, Wei ;
Geistlinger, Timothy R. ;
Eeckhoute, Jerome ;
Brodsky, Alexander S. ;
Keeton, Erika Krasnickas ;
Fertuck, Kirsten C. ;
Hall, Giles F. ;
Wang, Qianben ;
Bekiranov, Stefan ;
Sementchenko, Victor ;
Fox, Edward A. ;
Silver, Pamela A. ;
Gingeras, Thomas R. ;
Liu, X. Shirley ;
Brown, Myles .
NATURE GENETICS, 2006, 38 (11) :1289-1297
[8]   Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1 [J].
Carroll, JS ;
Liu, XS ;
Brodsky, AS ;
Li, W ;
Meyer, CA ;
Szary, AJ ;
Eeckhoute, J ;
Shao, WL ;
Hestermann, EV ;
Geistlinger, TR ;
Fox, EA ;
Silver, PA ;
Brown, M .
CELL, 2005, 122 (01) :33-43
[9]   Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs [J].
Cawley, S ;
Bekiranov, S ;
Ng, HH ;
Kapranov, P ;
Sekinger, EA ;
Kampa, D ;
Piccolboni, A ;
Sementchenko, V ;
Cheng, J ;
Williams, AJ ;
Wheeler, R ;
Wong, B ;
Drenkow, J ;
Yamanaka, M ;
Patel, S ;
Brubaker, S ;
Tammana, H ;
Helt, G ;
Struhl, K ;
Gingeras, TR .
CELL, 2004, 116 (04) :499-509
[10]   Chop it, ChIP it, check it: the current status of chromatin immunoprecipitation [J].
Collas, Philippe ;
Dahl, John Arne .
FRONTIERS IN BIOSCIENCE-LANDMARK, 2008, 13 :929-943