Identification of functional elements and regulatory circuits by Drosophila modENCODE Journal Article

   

Authors:	Roy, S.; Ernst, J.; Kharchenko, P. V.; Kheradpour, P.; Negre, N.; Eaton, M. L.; Landolin, J. M.; Bristow, C. A.; Ma, L.; Lin, M. F.; Washietl, S.; Arshinoff, B. I.; Ay, F.; Meyer, P. E.; Robine, N.; Washington, N. L.; Di Stefano, L.; Berezikov, E.; Brown, C. D.; Candeias, R.; Carlson, J. W.; Carr, A.; Jungreis, I.; Marbach, D.; Sealfon, R.; Tolstorukov, M. Y.; Will, S.; Alekseyenko, A. A.; Artieri, C.; Booth, B. W.; Brooks, A. N.; Dai, Q.; Davis, C. A.; Duff, M. O.; Feng, X.; Gorchakov, A. A.; Gu, T.; Henikoff, J. G.; Kapranov, P.; Li, R.; MacAlpine, H. K.; Malone, J.; Minoda, A.; Nordman, J.; Okamura, K.; Perry, M.; Powell, S. K.; Riddle, N. C.; Sakai, A.; Samsonova, A.; Sandler, J. E.; Schwartz, Y. B.; Sher, N.; Spokony, R.; Sturgill, D.; Van Baren, M.; Wan, K. H.; Yang, L.; Yu, C.; Feingold, E.; Good, P.; Guyer, M.; Lowdon, R.; Ahmad, K.; Andrews, J.; Berger, B.; Brenner, S. E.; Brent, M. R.; Cherbas, L.; Elgin, S. C. R.; Gingeras, T. R.; Grossman, R.; Hoskins, R. A.; Kaufman, T. C.; Kent, W.; Kuroda, M. I.; Orr-Weaver, T.; Perrimon, N.; Pirrotta, V.; Posakony, J. W.; Ren, B.; Russell, S.; Cherbas, P.; Graveley, B. R.; Lewis, S.; Micklem, G.; Oliver, B.; Park, P. J.; Celniker, S. E.; Henikoff, S.; Karpen, G. H.; Lai, E. C.; MacAlpine, D. M.; Stein, L. D.; White, K. P.; Kellis, M.
Article Title:	Identification of functional elements and regulatory circuits by Drosophila modENCODE
Abstract:	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.
Keywords:	nonhuman; genetic analysis; animals; gene expression; computational biology; cell line; protein; transcription factor; drosophila; gene function; genetic transcription; transcription, genetic; proteomics; transcription factors; gene expression regulation; chromatin; epigenesis, genetic; promoter regions, genetic; genomics; genome; binding sites; fly; drosophila melanogaster; untranslated rna; chromosome protein; drosophila proteins; histones; genome, insect; nucleosome; nucleosomes; gene regulatory networks; genes, insect; histone modification; molecular sequence annotation; rna replication; rna, small untranslated
Journal Title:	Science
Volume:	330
Issue:	6012
ISSN:	0036-8075
Publisher:	American Association for the Advancement of Science
Date Published:	2010-12-24
Start Page:	1787
End Page:	1797
Language:	English
DOI:	10.1126/science.1198374
PUBMED:	21177974
PROVIDER:	scopus
PMCID:	PMC3192495
DOI/URL:	http://www.scopus.com/inward/record.url?eid=2-s2.0-78650331647&partnerID=40&md5=50d3ec78715fa6af71dc2f8ecb934f92
Notes:	--- - "Cited By (since 1996): 21" - "Export Date: 20 April 2011" - "CODEN: SCIEA" - "Source: Scopus"

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