Transcriptional regulatory elements in the human genome

被引:585
作者
Maston, Glenn A. [1 ]
Evans, Sara K.
Green, Michael R.
机构
[1] Univ Massachusetts, Sch Med, Howard Hughes Med Inst, Program Gene Funct & Express, Worcester, MA 01605 USA
[2] Univ Massachusetts, Sch Med, Howard Hughes Med Inst, Program Mol Med, Worcester, MA 01605 USA
关键词
bioinformatics; functional genomics; transcription factors;
D O I
10.1146/annurev.genom.7.080505.115623
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
The faithful execution of biological processes requires a precise and carefully orchestrated set of steps that depend on the proper spatial and temporal expression of genes. Here we review the various classes of transcriptional regulatory elements (core promoters, proximal promoters, distal enhancers, silencers, insulators/boundary elements, and locus control regions) and the molecular machinery (general transcription factors, activators, and coactivators) that interacts with the regulatory elements to mediate precisely controlled patterns of gene expression. The biological importance of transcriptional regulation is highlighted by examples of how alterations in these transcriptional components can lead to disease. Finally, we discuss the methods currently used to identify transcriptional regulatory elements, and the ability of these methods to be scaled up for the purpose of annotating the entire human genome.
引用
收藏
页码:29 / 59
页数:31
相关论文
共 199 条
[1]   Hierarchical interactions control CD4 gene expression during thymocyte development [J].
Adlam, M ;
Siu, G .
IMMUNITY, 2003, 18 (02) :173-184
[2]   A haplotype map of the human genome [J].
Altshuler, D ;
Brooks, LD ;
Chakravarti, A ;
Collins, FS ;
Daly, MJ ;
Donnelly, P ;
Gibbs, RA ;
Belmont, JW ;
Boudreau, A ;
Leal, SM ;
Hardenbol, P ;
Pasternak, S ;
Wheeler, DA ;
Willis, TD ;
Yu, FL ;
Yang, HM ;
Zeng, CQ ;
Gao, Y ;
Hu, HR ;
Hu, WT ;
Li, CH ;
Lin, W ;
Liu, SQ ;
Pan, H ;
Tang, XL ;
Wang, J ;
Wang, W ;
Yu, J ;
Zhang, B ;
Zhang, QR ;
Zhao, HB ;
Zhao, H ;
Zhou, J ;
Gabriel, SB ;
Barry, R ;
Blumenstiel, B ;
Camargo, A ;
Defelice, M ;
Faggart, M ;
Goyette, M ;
Gupta, S ;
Moore, J ;
Nguyen, H ;
Onofrio, RC ;
Parkin, M ;
Roy, J ;
Stahl, E ;
Winchester, E ;
Ziaugra, L ;
Shen, Y .
NATURE, 2005, 437 (7063) :1299-1320
[3]   Polyalanine expansion and frameshift mutations of the paired-like homeobox gene PHOX2B in congenital central hypoventilation syndrome [J].
Amiel, J ;
Laudier, B ;
Attié-Bitach, T ;
Trang, H ;
de Pontual, L ;
Gener, B ;
Trochet, D ;
Etchevers, H ;
Ray, P ;
Simonneau, M ;
Vekemans, M ;
Munnich, A ;
Gaultier, C ;
Lyonnet, S .
NATURE GENETICS, 2003, 33 (04) :459-461
[4]   Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2 [J].
Amir, RE ;
Van den Veyver, IB ;
Wan, M ;
Tran, CQ ;
Francke, U ;
Zoghbi, HY .
NATURE GENETICS, 1999, 23 (02) :185-188
[5]   BETA-THALASSEMIA IN AMERICAN BLACKS - NOVEL MUTATIONS IN THE TATA BOX AND AN ACCEPTOR SPLICE SITE [J].
ANTONARAKIS, SE ;
IRKIN, SH ;
CHENG, TC ;
SCOTT, AF ;
SEXTON, JP ;
TRUSKO, SP ;
CHARACHE, S ;
KAZAZIAN, HH .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES, 1984, 81 (04) :1154-1158
[6]   FUNCTIONAL-ANALYSIS OF THE HUMAN ADENOSINE-DEAMINASE GENE THYMIC REGULATORY REGION AND ITS ABILITY TO GENERATE POSITION-INDEPENDENT TRANSGENE EXPRESSION [J].
ARONOW, BJ ;
SILBIGER, RN ;
DUSING, MR ;
STOCK, JL ;
YAGER, KL ;
POTTER, SS ;
HUTTON, JJ ;
WIGINTON, DA .
MOLECULAR AND CELLULAR BIOLOGY, 1992, 12 (09) :4170-4185
[7]   Gene annotation: Prediction and testing [J].
Ashurst, JL ;
Collins, JE .
ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS, 2003, 4 :69-88
[8]   ENHANCERS - MECHANISMS OF ACTION AND CELL SPECIFICITY [J].
ATCHISON, ML .
ANNUAL REVIEW OF CELL BIOLOGY, 1988, 4 :127-153
[9]  
Bailey T L, 1995, Proc Int Conf Intell Syst Mol Biol, V3, P21
[10]   Promoter prediction analysis on the whole human genome [J].
Bajic, VB ;
Tan, SL ;
Suzuki, Y ;
Sugano, S .
NATURE BIOTECHNOLOGY, 2004, 22 (11) :1467-1473