Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

• Published in: Science (American Association for the Advancement of Science) Vol. 330; no. 6012; pp. 1787 - 1797
• Main Authors: 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 E, 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
• Format: Journal Article Web Resource
• Language: English
• Published: Washington, DC American Association for the Advancement of Science 24.12.2010; The American Association for the Advancement of Science
• Subjects: Animals; Binding Sites; Biochemistry, biophysics & molecular biology; Biochimie, biophysique & biologie moléculaire; Biological and medical sciences; Cellular; Chromatin; Chromatin - genetics; Chromatin - metabolism; Chromatin/genetics/metabolism; Classical genetics, quantitative genetics, hybrids; Coding; Computational Biology - methods; data collection; Datasets; Deoxyribonucleic acid; Developmental Programs; Developmental stages; DNA; Drosophila; Drosophila melanogaster - genetics; Drosophila melanogaster - growth & development; Drosophila melanogaster - metabolism; Drosophila melanogaster/genetics/growth & development/metabolism; Drosophila Proteins - genetics; Drosophila Proteins - metabolism; Drosophila Proteins/genetics/metabolism; Epigenesis, Genetic; Fundamental and applied biological sciences. Psychology; gene expression; Gene Expression Regulation; Gene Regulatory Networks; Genes; Genes, Insect; Genetics of eukaryotes. Biological and molecular evolution; Genome, Insect; Genomes; Genomics; Genomics - methods; Histones; Histones - metabolism; Invertebrata; Life sciences; Mathematical models; MicroRNA; Molecular Sequence Annotation; Networks; Nucleosomes; Nucleosomes - genetics; Nucleosomes - metabolism; Nucleosomes/genetics/metabolism; prediction; Promoter Regions, Genetic; Proteins; Replication; Ribonucleic acids; RNA; RNA, Small Untranslated - genetics; RNA, Small Untranslated - metabolism; RNA, Small Untranslated/genetics/metabolism; Sciences du vivant; transcription (genetics); transcription factors; Transcription Factors - metabolism; Transcription, Genetic; translation (genetics); Chromatin; Insecta; Drosophila; Genomics; Information; Drosophilidae; Coding; Arthropoda; Genetics; Replication; Regulatory sequence; Invertebrata; Diptera
• ISSN: 0036-8075; 1095-9203; 1095-9203
• DOI: 10.1126/science.1198374

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.