A cis-regulatory map of the Drosophila genome.

Journal Article (Journal Article)

Systematic annotation of gene regulatory elements is a major challenge in genome science. Direct mapping of chromatin modification marks and transcriptional factor binding sites genome-wide has successfully identified specific subtypes of regulatory elements. In Drosophila several pioneering studies have provided genome-wide identification of Polycomb response elements, chromatin states, transcription factor binding sites, RNA polymerase II regulation and insulator elements; however, comprehensive annotation of the regulatory genome remains a significant challenge. Here we describe results from the modENCODE cis-regulatory annotation project. We produced a map of the Drosophila melanogaster regulatory genome on the basis of more than 300 chromatin immunoprecipitation data sets for eight chromatin features, five histone deacetylases and thirty-eight site-specific transcription factors at different stages of development. Using these data we inferred more than 20,000 candidate regulatory elements and validated a subset of predictions for promoters, enhancers and insulators in vivo. We identified also nearly 2,000 genomic regions of dense transcription factor binding associated with chromatin activity and accessibility. We discovered hundreds of new transcription factor co-binding relationships and defined a transcription factor network with over 800 potential regulatory relationships.

Full Text

Duke Authors

Cited Authors

  • Nègre, N; Brown, CD; Ma, L; Bristow, CA; Miller, SW; Wagner, U; Kheradpour, P; Eaton, ML; Loriaux, P; Sealfon, R; Li, Z; Ishii, H; Spokony, RF; Chen, J; Hwang, L; Cheng, C; Auburn, RP; Davis, MB; Domanus, M; Shah, PK; Morrison, CA; Zieba, J; Suchy, S; Senderowicz, L; Victorsen, A; Bild, NA; Grundstad, AJ; Hanley, D; MacAlpine, DM; Mannervik, M; Venken, K; Bellen, H; White, R; Gerstein, M; Russell, S; Grossman, RL; Ren, B; Posakony, JW; Kellis, M; White, KP

Published Date

  • March 24, 2011

Published In

Volume / Issue

  • 471 / 7339

Start / End Page

  • 527 - 531

PubMed ID

  • 21430782

Pubmed Central ID

  • PMC3179250

Electronic International Standard Serial Number (EISSN)

  • 1476-4687

Digital Object Identifier (DOI)

  • 10.1038/nature09990


  • eng

Conference Location

  • England