Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif

被引:29
作者
Cheng, Yong [1 ,2 ]
King, David C. [1 ,3 ]
Dore, Louis C. [4 ]
Zhang, Xinmin [5 ]
Zhou, Yuepin [1 ,2 ]
Zhang, Ying [1 ,6 ]
Dorman, Christine [1 ,2 ]
Abebe, Demesew [1 ,2 ]
Kumar, Swathi A. [1 ,6 ]
Chiaromonte, Francesca [1 ,7 ]
Miller, Webb [1 ,8 ,9 ]
Green, Roland D. [5 ]
Weiss, Mitchell J. [4 ]
Hardison, Ross C. [1 ,2 ]
机构
[1] Penn State Univ, Huck Inst Life Sci, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA
[2] Penn State Univ, Dept Biochem & Mol Biol, University Pk, PA 16802 USA
[3] Penn State Univ, Intercoll Grad Degree Program Integrat Biosci, University Pk, PA 16802 USA
[4] Childrens Hosp Philadelphia, Dept Pediat, Philadelphia, PA 19104 USA
[5] NimbleGen Syst Inc, Madison, WI 53719 USA
[6] Penn State Univ, Intercoll Grad Degree Program Genet, University Pk, PA 16802 USA
[7] Penn State Univ, Dept Stat, University Pk, PA 16802 USA
[8] Penn State Univ, Dept Comp Sci & Engn, University Pk, PA 16802 USA
[9] Penn State Univ, Dept Biol, University Pk, PA 16802 USA
关键词
D O I
10.1101/gr.083089.108
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
Tissue development and function are exquisitely dependent on proper regulation of gene expression, but it remains controversial whether the genomic signals controlling this process are subject to strong selective constraint. While some studies show that highly constrained noncoding regions act to enhance transcription, other studies show that DNA segments with biochemical signatures of regulatory regions, such as occupancy by a transcription factor, are seemingly unconstrained across mammalian evolution. To test the possible correlation of selective constraint with enhancer activity, we used chromatin immunoprecipitation as an approach unbiased by either evolutionary constraint or prior knowledge of regulatory activity to identify DNA segments within a 66-Mb region of mouse chromosome 7 that are occupied by the erythroid transcription factor GATA1. DNA segments bound by GATA1 were identified by hybridization to high-density tiling arrays, validated by quantitative PCR, and tested for gene regulatory activity in erythroid cells. Whereas almost all of the occupied segments contain canonical WGATAR binding site motifs for GATA1, in only 45% of the cases is the motif deeply preserved (found at the orthologous position in placental mammals or more distant species). However, GATA1-bound segments with high enhancer activity tend to be the ones with an evolutionarily preserved WGATAR motif, and this relationship was confirmed by a loss-of-function assay. Thus, GATA1 binding sites that regulate gene expression during erythroid maturation are under strong selective constraint, while nonconstrained binding may have only a limited or indirect role in regulation.
引用
收藏
页码:1896 / 1905
页数:10
相关论文
共 64 条
[1]   DETECTING CONSERVED REGULATORY ELEMENTS WITH THE MODEL GENOME OF THE JAPANESE PUFFER FISH, FUGU RUBRIPES [J].
APARICIO, S ;
MORRISON, A ;
GOULD, A ;
GILTHORPE, J ;
CHAUDHURI, C ;
RIGBY, P ;
KRUMLAUF, R ;
BRENNER, S .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1995, 92 (05) :1684-1688
[2]   EXPRESSION OF A BETA-GLOBIN GENE IS ENHANCED BY REMOTE SV40 DNA-SEQUENCES [J].
BANERJI, J ;
RUSCONI, S ;
SCHAFFNER, W .
CELL, 1981, 27 (02) :299-308
[3]   Comparative genomic analysis reveals a distant liver enhancer upstream of the COUP-TFII gene [J].
Baroukh, N ;
Ahituv, N ;
Chang, J ;
Shoukry, M ;
Afzal, V ;
Rubin, EM ;
Pennacchio, LA .
MAMMALIAN GENOME, 2005, 16 (02) :91-95
[4]   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
[5]   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
[6]   Aligning multiple genomic sequences with the threaded blockset aligner [J].
Blanchette, M ;
Kent, WJ ;
Riemer, C ;
Elnitski, L ;
Smit, AFA ;
Roskin, KM ;
Baertsch, R ;
Rosenbloom, K ;
Clawson, H ;
Green, ED ;
Haussler, D ;
Miller, W .
GENOME RESEARCH, 2004, 14 (04) :708-715
[7]  
BLOBEL GA, 2001, DISORDERS HEMOGLOBIN, P72
[8]   AN ENHANCER ELEMENT LIES 3' TO THE HUMAN A-GAMMA-GLOBIN GENE [J].
BODINE, DM ;
LEY, TJ .
EMBO JOURNAL, 1987, 6 (10) :2997-3004
[9]   Functional architecture and evolution of transcriptional elements that drive gene coexpression [J].
Brown, Christopher D. ;
Johnson, David S. ;
Sidow, Arend .
SCIENCE, 2007, 317 (5844) :1557-1560
[10]   A complex chromatin landscape revealed by patterns of nuclease sensitivity and histone modification within the mouse β-globin locus [J].
Bulger, M ;
Schübeler, D ;
Bender, MA ;
Hamilton, J ;
Farrell, CM ;
Hardison, RC ;
Groudine, M .
MOLECULAR AND CELLULAR BIOLOGY, 2003, 23 (15) :5234-5244