Dynamic reprogramming of chromatin accessibility during Drosophila embryo development

被引:133
作者
Thomas, Sean [1 ]
Li, Xiao-Yong [2 ,3 ]
Sabo, Peter J. [1 ]
Sandstrom, Richard [1 ]
Thurman, Robert E. [1 ]
Canfield, Theresa K. [1 ]
Giste, Erika [1 ]
Fisher, William [2 ,3 ]
Hammonds, Ann [2 ,3 ]
Celniker, Susan E. [2 ,3 ]
Biggin, Mark D. [2 ,3 ]
Stamatoyannopoulos, John A. [1 ]
机构
[1] Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA
[2] Univ Calif Berkeley, Lawrence Berkeley Lab, Genom Div, Berkeley, CA 94720 USA
[3] Univ Calif Berkeley, Lawrence Berkeley Lab, Div Life Sci, Berkeley, CA 94720 USA
来源
GENOME BIOLOGY | 2011年 / 12卷 / 05期
基金
美国国家卫生研究院;
关键词
TRANSCRIPTION FACTORS; HYPERSENSITIVE SITES; IN-VIVO; 5; ENDS; BINDING; GENES; ELEMENTS; GENOME; DNA; SEGMENTATION;
D O I
10.1186/gb-2011-12-5-r43
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Background: The development of complex organisms is believed to involve progressive restrictions in cellular fate. Understanding the scope and features of chromatin dynamics during embryogenesis, and identifying regulatory elements important for directing developmental processes remain key goals of developmental biology. Results: We used in vivo DNaseI sensitivity to map the locations of regulatory elements, and explore the changing chromatin landscape during the first 11 hours of Drosophila embryonic development. We identified thousands of conserved, developmentally dynamic, distal DNaseI hypersensitive sites associated with spatial and temporal expression patterning of linked genes and with large regions of chromatin plasticity. We observed a nearly uniform balance between developmentally up-and down-regulated DNaseI hypersensitive sites. Analysis of promoter chromatin architecture revealed a novel role for classical core promoter sequence elements in directing temporally regulated chromatin remodeling. Another unexpected feature of the chromatin landscape was the presence of localized accessibility over many protein-coding regions, subsets of which were developmentally regulated or associated with the transcription of genes with prominent maternal RNA contributions in the blastoderm. Conclusions: Our results provide a global view of the rich and dynamic chromatin landscape of early animal development, as well as novel insights into the organization of developmentally regulated chromatin features.
引用
收藏
页数:17
相关论文
共 64 条
[1]   The genome sequence of Drosophila melanogaster [J].
Adams, MD ;
Celniker, SE ;
Holt, RA ;
Evans, CA ;
Gocayne, JD ;
Amanatides, PG ;
Scherer, SE ;
Li, PW ;
Hoskins, RA ;
Galle, RF ;
George, RA ;
Lewis, SE ;
Richards, S ;
Ashburner, M ;
Henderson, SN ;
Sutton, GG ;
Wortman, JR ;
Yandell, MD ;
Zhang, Q ;
Chen, LX ;
Brandon, RC ;
Rogers, YHC ;
Blazej, RG ;
Champe, M ;
Pfeiffer, BD ;
Wan, KH ;
Doyle, C ;
Baxter, EG ;
Helt, G ;
Nelson, CR ;
Miklos, GLG ;
Abril, JF ;
Agbayani, A ;
An, HJ ;
Andrews-Pfannkoch, C ;
Baldwin, D ;
Ballew, RM ;
Basu, A ;
Baxendale, J ;
Bayraktaroglu, L ;
Beasley, EM ;
Beeson, KY ;
Benos, PV ;
Berman, BP ;
Bhandari, D ;
Bolshakov, S ;
Borkova, D ;
Botchan, MR ;
Bouck, J ;
Brokstein, P .
SCIENCE, 2000, 287 (5461) :2185-2195
[2]   The developmental expression dynamics of Drosophila melanogaster transcription factors [J].
Adryan, Boris ;
Teichmann, Sarah A. .
GENOME BIOLOGY, 2010, 11 (04)
[3]   CHANGING RATES OF DNA AND RNA-SYNTHESIS IN DROSOPHILA EMBRYOS [J].
ANDERSON, KV ;
LENGYEL, JA .
DEVELOPMENTAL BIOLOGY, 1981, 82 (01) :127-138
[4]   MEME SUITE: tools for motif discovery and searching [J].
Bailey, Timothy L. ;
Boden, Mikael ;
Buske, Fabian A. ;
Frith, Martin ;
Grant, Charles E. ;
Clementi, Luca ;
Ren, Jingyuan ;
Li, Wilfred W. ;
Noble, William S. .
NUCLEIC ACIDS RESEARCH, 2009, 37 :W202-W208
[5]   CONTROLLING THE FALSE DISCOVERY RATE - A PRACTICAL AND POWERFUL APPROACH TO MULTIPLE TESTING [J].
BENJAMINI, Y ;
HOCHBERG, Y .
JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY, 1995, 57 (01) :289-300
[6]   Computational identification of developmental enhancers:: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura -: art. no. R61 [J].
Berman, BP ;
Pfeiffer, BD ;
Laverty, TR ;
Salzberg, SL ;
Rubin, GM ;
Eisen, MB ;
Celniker, SE .
GENOME BIOLOGY, 2004, 5 (09)
[7]   Transcriptional regulation in Drosophila: The post-genome challenge [J].
Biggin M.D. ;
Tjian R. .
Functional & Integrative Genomics, 2001, 1 (4) :223-234
[8]   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
[9]   Nucleosome retention and the stochastic nature of promoter chromatin remodeling for transcription [J].
Boeger, Hinrich ;
Griesenbeck, Joachim ;
Kornberg, Roger D. .
CELL, 2008, 133 (04) :716-726
[10]   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