Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

  • Consortium T
  • Roy S
  • Ernst J
 et al. 
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Abstract

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.

Author-supplied keywords

  • Animals
  • Binding Sites
  • Chromatin
  • Chromatin: genetics
  • Chromatin: metabolism
  • Computational Biology
  • Computational Biology: methods
  • Drosophila Proteins
  • Drosophila Proteins: genetics
  • Drosophila Proteins: metabolism
  • Drosophila melanogaster
  • Drosophila melanogaster: genetics
  • Drosophila melanogaster: growth & development
  • Drosophila melanogaster: metabolism
  • Epigenesis, Genetic
  • Gene Expression Regulation
  • Gene Regulatory Networks
  • Genes, Insect
  • Genome, Insect
  • Genomics
  • Genomics: methods
  • Histones
  • Histones: metabolism
  • Molecular Sequence Annotation
  • Nucleosomes
  • Nucleosomes: genetics
  • Nucleosomes: metabolism
  • Promoter Regions, Genetic
  • RNA, Small Untranslated
  • RNA, Small Untranslated: genetics
  • RNA, Small Untranslated: metabolism
  • Transcription Factors
  • Transcription Factors: metabolism
  • Transcription, Genetic

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Authors

  • The Consortium

  • Sushmita Roy

  • Jason Ernst

  • Peter V Kharchenko

  • Pouya Kheradpour

  • Nicolas Negre

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