Article (Scientific journals)
Identification of functional elements and regulatory circuits by Drosophila modENCODE.
Roy, Sushmita; Ernst, Jason; Kharchenko, Peter V. et al.
2010In Science, 330 (6012), p. 1787-97
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Keywords :
Animals; Binding Sites; Chromatin/genetics/metabolism; Computational Biology/methods; Drosophila Proteins/genetics/metabolism; Drosophila melanogaster/genetics/growth & development/metabolism; Epigenesis, Genetic; Gene Expression Regulation; Gene Regulatory Networks; Genes, Insect; Genome, Insect; Genomics/methods; Histones/metabolism; Molecular Sequence Annotation; Nucleosomes/genetics/metabolism; Promoter Regions, Genetic; RNA, Small Untranslated/genetics/metabolism; Transcription Factors/metabolism; Transcription, Genetic
Abstract :
[en] To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Roy, Sushmita
Ernst, Jason
Kharchenko, Peter V.
Kheradpour, Pouya
Negre, Nicolas
Eaton, Matthew L.
Landolin, Jane M.
Bristow, Christopher A.
Ma, Lijia
Lin, Michael F.
Washietl, Stefan
Arshinoff, Bradley I.
Ay, Ferhat
Meyer, Patrick ;  Université de Liège - ULiège > Département des sciences de la vie > Biologie des systèmes et bioinformatique
Robine, Nicolas
Washington, Nicole L.
Di Stefano, Luisa
Berezikov, Eugene
Brown, Christopher D.
Candeias, Rogerio
Carlson, Joseph W.
Carr, Adrian
Jungreis, Irwin
Marbach, Daniel
Sealfon, Rachel
Tolstorukov, Michael Y.
Will, Sebastian
Alekseyenko, Artyom A.
Artieri, Carlo
Booth, Benjamin W.
Brooks, Angela N.
Dai, Qi
Davis, Carrie A.
Duff, Michael O.
Feng, Xin
Gorchakov, Andrey A.
Gu, Tingting
Henikoff, Jorja G.
Kapranov, Philipp
Li, Renhua
MacAlpine, Heather K.
Malone, John
Minoda, Aki
Nordman, Jared
Okamura, Katsutomo
Perry, Marc
Powell, Sara K.
Riddle, Nicole C.
Sakai, Akiko
Samsonova, Anastasia
Sandler, Jeremy E.
Schwartz, Yuri B.
Sher, Noa
Spokony, Rebecca
Sturgill, David
van Baren, Marijke
Wan, Kenneth H.
Yang, Li
Yu, Charles
Feingold, Elise
Good, Peter
Guyer, Mark
Lowdon, Rebecca
Ahmad, Kami
Andrews, Justen
Berger, Bonnie
Brenner, Steven E.
Brent, Michael R.
Cherbas, Lucy
Elgin, Sarah C. R.
Gingeras, Thomas R.
Grossman, Robert
Hoskins, Roger A.
Kaufman, Thomas C.
Kent, William
Kuroda, Mitzi I.
Orr-Weaver, Terry
Perrimon, Norbert
Pirrotta, Vincenzo
Posakony, James W.
Ren, Bing
Russell, Steven
Cherbas, Peter
Graveley, Brenton R.
Lewis, Suzanna
Micklem, Gos
Oliver, Brian
Park, Peter J.
Celniker, Susan E.
Henikoff, Steven
Karpen, Gary H.
Lai, Eric C.
MacAlpine, David M.
Stein, Lincoln D.
White, Kevin P.
Kellis, Manolis
More authors (86 more) Less
Language :
English
Title :
Identification of functional elements and regulatory circuits by Drosophila modENCODE.
Publication date :
2010
Journal title :
Science
ISSN :
0036-8075
eISSN :
1095-9203
Publisher :
American Association for the Advancement of Science, Washington, United States - District of Columbia
Volume :
330
Issue :
6012
Pages :
1787-97
Peer reviewed :
Peer Reviewed verified by ORBi
Available on ORBi :
since 05 March 2014

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