Identification of functional elements and regulatory circuits by Drosophila modENCODE.

Published

Journal Article

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.

Full Text

Duke Authors

Cited Authors

  • modENCODE Consortium, ; Roy, S; Ernst, J; Kharchenko, PV; Kheradpour, P; Negre, N; Eaton, ML; Landolin, JM; Bristow, CA; Ma, L; Lin, MF; Washietl, S; Arshinoff, BI; Ay, F; Meyer, PE; Robine, N; Washington, NL; Di Stefano, L; Berezikov, E; Brown, CD; Candeias, R; Carlson, JW; Carr, A; Jungreis, I; Marbach, D; Sealfon, R; Tolstorukov, MY; Will, S; Alekseyenko, AA; Artieri, C; Booth, BW; Brooks, AN; Dai, Q; Davis, CA; Duff, MO; Feng, X; Gorchakov, AA; Gu, T; Henikoff, JG; Kapranov, P; Li, R; MacAlpine, HK; Malone, J; Minoda, A; Nordman, J; Okamura, K; Perry, M; Powell, SK; Riddle, NC; Sakai, A; Samsonova, A; Sandler, JE; Schwartz, YB; Sher, N; Spokony, R; Sturgill, D; van Baren, M; Wan, KH; Yang, L; Yu, C; Feingold, E; Good, P; Guyer, M; Lowdon, R; Ahmad, K; Andrews, J; Berger, B; Brenner, SE; Brent, MR; Cherbas, L; Elgin, SCR; Gingeras, TR; Grossman, R; Hoskins, RA; Kaufman, TC; Kent, W; Kuroda, MI; Orr-Weaver, T; Perrimon, N; Pirrotta, V; Posakony, JW; Ren, B; Russell, S; Cherbas, P; Graveley, BR; Lewis, S; Micklem, G; Oliver, B; Park, PJ; Celniker, SE; Henikoff, S; Karpen, GH; Lai, EC; MacAlpine, DM; Stein, LD; White, KP; Kellis, M

Published Date

  • December 22, 2010

Published In

Volume / Issue

  • 330 / 6012

Start / End Page

  • 1787 - 1797

PubMed ID

  • 21177974

Pubmed Central ID

  • 21177974

Electronic International Standard Serial Number (EISSN)

  • 1095-9203

International Standard Serial Number (ISSN)

  • 0036-8075

Digital Object Identifier (DOI)

  • 10.1126/science.1198374

Language

  • eng