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Identification of functional elements and regulatory circuits by Drosophila modENCODE.

Publication ,  Journal Article
modENCODE Consortium, ; Roy, S; Ernst, J; Kharchenko, PV; Kheradpour, P; Negre, N; Eaton, ML; Landolin, JM; Bristow, CA; Ma, L; Lin, MF; Ay, F ...
Published in: Science
December 24, 2010

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.

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Published In

Science

DOI

EISSN

1095-9203

Publication Date

December 24, 2010

Volume

330

Issue

6012

Start / End Page

1787 / 1797

Location

United States

Related Subject Headings

  • Transcription, Genetic
  • Transcription Factors
  • RNA, Small Untranslated
  • Promoter Regions, Genetic
  • Nucleosomes
  • Molecular Sequence Annotation
  • Histones
  • Genomics
  • Genome, Insect
  • Genes, Insect
 

Citation

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modENCODE Consortium, ., Roy, S., Ernst, J., Kharchenko, P. V., Kheradpour, P., Negre, N., … Kellis, M. (2010). Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science, 330(6012), 1787–1797. https://doi.org/10.1126/science.1198374
Consortium, Manolis modENCODE, Sushmita Roy, Jason Ernst, Peter V. Kharchenko, Pouya Kheradpour, Nicolas Negre, Matthew L. Eaton, et al. “Identification of functional elements and regulatory circuits by Drosophila modENCODE.Science 330, no. 6012 (December 24, 2010): 1787–97. https://doi.org/10.1126/science.1198374.
modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 2010 Dec 24;330(6012):1787–97.
modENCODE Consortium, Manolis, et al. “Identification of functional elements and regulatory circuits by Drosophila modENCODE.Science, vol. 330, no. 6012, Dec. 2010, pp. 1787–97. Pubmed, doi:10.1126/science.1198374.
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. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 2010 Dec 24;330(6012):1787–1797.
Journal cover image

Published In

Science

DOI

EISSN

1095-9203

Publication Date

December 24, 2010

Volume

330

Issue

6012

Start / End Page

1787 / 1797

Location

United States

Related Subject Headings

  • Transcription, Genetic
  • Transcription Factors
  • RNA, Small Untranslated
  • Promoter Regions, Genetic
  • Nucleosomes
  • Molecular Sequence Annotation
  • Histones
  • Genomics
  • Genome, Insect
  • Genes, Insect