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Identification of functional elements and regulatory circuits by Drosophila modENCODE.

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 SC | 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
Science (New York, N.Y.) | Dec 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.

Pubmed ID: 21177974 RIS Download

Mesh terms: Animals | Binding Sites | Chromatin | Computational Biology | Drosophila Proteins | Drosophila melanogaster | Epigenesis, Genetic | Gene Expression Regulation | Gene Regulatory Networks | Genes, Insect | Genome, Insect | Genomics | Histones | Molecular Sequence Annotation | Nucleosomes | Promoter Regions, Genetic | RNA, Small Untranslated | Transcription Factors | Transcription, Genetic

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Associated grants

  • Agency: NHGRI NIH HHS, Id: U01HG004271
  • Agency: NHGRI NIH HHS, Id: U01 HG004271
  • Agency: Intramural NIH HHS, Id: ZIA DK015600-14
  • Agency: NHGRI NIH HHS, Id: R01 HG004037
  • Agency: NHGRI NIH HHS, Id: U01HG004261
  • Agency: NHGRI NIH HHS, Id: R01HG004037
  • Agency: NHGRI NIH HHS, Id: U01HG004279
  • Agency: NHGRI NIH HHS, Id: U41HG004269
  • Agency: NHGRI NIH HHS, Id: U01 HG004279
  • Agency: NHGRI NIH HHS, Id: U01HG004264
  • Agency: Howard Hughes Medical Institute, Id: R01 GM081871
  • Agency: NIGMS NIH HHS, Id: U01HG004274
  • Agency: NHGRI NIH HHS, Id: U01HG004258
  • Agency: NHGRI NIH HHS, Id: U01 HG004258
  • Agency: NHGRI NIH HHS, Id: RC2HG005639
  • Agency: NHGRI NIH HHS, Id:

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