Skip to main content
Journal cover image

A cis-regulatory map of the Drosophila genome.

Publication ,  Journal Article
Nègre, N; Brown, CD; Ma, L; Bristow, CA; Miller, SW; Wagner, U; Kheradpour, P; Eaton, ML; Loriaux, P; Sealfon, R; Li, Z; Ishii, H; Chen, J ...
Published in: Nature
March 24, 2011

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.

Duke Scholars

Altmetric Attention Stats
Dimensions Citation Stats

Published In

Nature

DOI

EISSN

1476-4687

Publication Date

March 24, 2011

Volume

471

Issue

7339

Start / End Page

527 / 531

Location

England

Related Subject Headings

  • Transcription Factors
  • Silencer Elements, Transcriptional
  • Reproducibility of Results
  • Regulatory Sequences, Nucleic Acid
  • Promoter Regions, Genetic
  • Molecular Sequence Annotation
  • Insulator Elements
  • Histone Deacetylases
  • Genome, Insect
  • General Science & Technology
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Nègre, N., Brown, C. D., Ma, L., Bristow, C. A., Miller, S. W., Wagner, U., … White, K. P. (2011). A cis-regulatory map of the Drosophila genome. Nature, 471(7339), 527–531. https://doi.org/10.1038/nature09990
Nègre, Nicolas, Christopher D. Brown, Lijia Ma, Christopher Aaron Bristow, Steven W. Miller, Ulrich Wagner, Pouya Kheradpour, et al. “A cis-regulatory map of the Drosophila genome.Nature 471, no. 7339 (March 24, 2011): 527–31. https://doi.org/10.1038/nature09990.
Nègre N, Brown CD, Ma L, Bristow CA, Miller SW, Wagner U, et al. A cis-regulatory map of the Drosophila genome. Nature. 2011 Mar 24;471(7339):527–31.
Nègre, Nicolas, et al. “A cis-regulatory map of the Drosophila genome.Nature, vol. 471, no. 7339, Mar. 2011, pp. 527–31. Pubmed, doi:10.1038/nature09990.
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. A cis-regulatory map of the Drosophila genome. Nature. 2011 Mar 24;471(7339):527–531.
Journal cover image

Published In

Nature

DOI

EISSN

1476-4687

Publication Date

March 24, 2011

Volume

471

Issue

7339

Start / End Page

527 / 531

Location

England

Related Subject Headings

  • Transcription Factors
  • Silencer Elements, Transcriptional
  • Reproducibility of Results
  • Regulatory Sequences, Nucleic Acid
  • Promoter Regions, Genetic
  • Molecular Sequence Annotation
  • Insulator Elements
  • Histone Deacetylases
  • Genome, Insect
  • General Science & Technology