Dynamic GATA4 enhancers shape the chromatin landscape central to heart development and disease

被引:124
作者
He, Aibin [1 ,2 ]
Gu, Fei [1 ]
Hu, Yong [1 ]
Ma, Qing [1 ]
Ye, Lillian Yi [1 ]
Akiyama, Jennifer A. [3 ]
Visel, Axel [3 ,4 ,5 ]
Pennacchio, Len A. [3 ,4 ]
Pu, William T. [1 ,6 ]
机构
[1] Boston Childrens Hosp, Dept Cardiol, Boston, MA 02115 USA
[2] Peking Univ, Peking Tsinghua Ctr Life Sci, Inst Mol Med, Beijing 100871, Peoples R China
[3] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Genom Div, Berkeley, CA 94720 USA
[4] US Dept Energy Joint Genome Inst, Walnut Creek, CA 94598 USA
[5] Univ Calif, Sch Nat Sci, Merced, CA 95343 USA
[6] Harvard Univ, Harvard Stem Cell Inst, Cambridge, MA 02138 USA
关键词
TRANSCRIPTION FACTORS; TRI-METHYLATION; EXPRESSION; MORPHOGENESIS; HYPERTROPHY; REQUIREMENT; PROMOTERS; REGULATOR; INTERACT;
D O I
10.1038/ncomms5907
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
How stage-specific enhancer dynamics modulate gene expression patterns essential for organ development, homeostasis and disease is not well understood. Here, we addressed this question by mapping chromatin occupancy of GATA4-a master cardiac transcription factor-in heart development and disease. We find that GATA4 binds and participates in establishing active chromatin regions by stimulating H3K27ac deposition, which facilitates GATA4-driven gene expression. GATA4 chromatin occupancy changes markedly between fetal and adult heart, with a limited binding sites overlap. Cardiac stress restored GATA4 occupancy to a subset of fetal sites, but many stress-associated GATA4 binding sites localized to loci not occupied by GATA4 during normal heart development. Collectively, our data show that dynamic, context-specific transcription factors occupancy underlies stage-specific events in development, homeostasis and disease.
引用
收藏
页数:14
相关论文
共 52 条
  • [1] Differential expression analysis for sequence count data
    Anders, Simon
    Huber, Wolfgang
    [J]. GENOME BIOLOGY, 2010, 11 (10):
  • [2] MEME SUITE: tools for motif discovery and searching
    Bailey, Timothy L.
    Boden, Mikael
    Buske, Fabian A.
    Frith, Martin
    Grant, Charles E.
    Clementi, Luca
    Ren, Jingyuan
    Li, Wilfred W.
    Noble, William S.
    [J]. NUCLEIC ACIDS RESEARCH, 2009, 37 : W202 - W208
  • [3] DREME: motif discovery in transcription factor ChIP-seq data
    Bailey, Timothy L.
    [J]. BIOINFORMATICS, 2011, 27 (12) : 1653 - 1659
  • [4] High-resolution profiling of histone methylations in the human genome
    Barski, Artern
    Cuddapah, Suresh
    Cui, Kairong
    Roh, Tae-Young
    Schones, Dustin E.
    Wang, Zhibin
    Wei, Gang
    Chepelev, Iouri
    Zhao, Keji
    [J]. CELL, 2007, 129 (04) : 823 - 837
  • [5] Gata4 is required for maintenance of postnatal cardiac function and protection from pressure overload-induced heart failure
    Bisping, Egbert
    Ikeda, Sadakatsu
    Kong, Sek Won
    Tarnavski, Oleg
    Bodyak, Natalya
    McMullen, Julie R.
    Rajagopal, Satish
    Son, Jennifer K.
    Ma, Qing
    Springer, Zhangli
    Kang, Peter M.
    Izumo, Seigo
    Pu, William T.
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2006, 103 (39) : 14471 - 14476
  • [6] ChIP-Seq identification of weakly conserved heart enhancers
    Blow, Matthew J.
    McCulley, David J.
    Li, Zirong
    Zhang, Tao
    Akiyama, Jennifer A.
    Holt, Amy
    Plajzer-Frick, Ingrid
    Shoukry, Malak
    Wright, Crystal
    Chen, Feng
    Afzal, Veena
    Bristow, James
    Ren, Bing
    Black, Brian L.
    Rubin, Edward M.
    Visel, Axel
    Pennacchio, Len A.
    [J]. NATURE GENETICS, 2010, 42 (09) : 806 - U107
  • [7] NFATc3 and NFATc4 are required for cardiac development and mitochondrial function
    Bushdid, PB
    Osinska, H
    Waclaw, RR
    Molkentin, JD
    Yutzey, KE
    [J]. CIRCULATION RESEARCH, 2003, 92 (12) : 1305 - 1313
  • [8] Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4
    Cirillo, LA
    Lin, FR
    Cuesta, I
    Friedman, D
    Jarnik, M
    Zaret, KS
    [J]. MOLECULAR CELL, 2002, 9 (02) : 279 - 289
  • [9] Histone H3K27ac separates active from poised enhancers and predicts developmental state
    Creyghton, Menno P.
    Cheng, Albert W.
    Welstead, G. Grant
    Kooistra, Tristan
    Carey, Bryce W.
    Steine, Eveline J.
    Hanna, Jacob
    Lodato, Michael A.
    Frampton, Garrett M.
    Sharp, Phillip A.
    Boyer, Laurie A.
    Young, Richard A.
    Jaenisch, Rudolf
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2010, 107 (50) : 21931 - 21936
  • [10] The transcription factors GATA4 and dHAND physically interact to synergistically activate cardiac gene expression through a p300-dependent mechanism
    Dai, YS
    Cserjesi, P
    Markham, BE
    Molkentin, JD
    [J]. JOURNAL OF BIOLOGICAL CHEMISTRY, 2002, 277 (27) : 24390 - 24398