Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

Author manuscript; available in PMC 2011 October 13.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.National Science Foundation (U.S.) (Computing Research Association for the CIFellows Project Grant 0937060)National Science Foundation (U.S.) (Computing Research Association for the CIFellows Project Award 0905968)National Institutes of Health (U.S.). Ruth L. Kirschstein National Research Service Award (Postdoctoral Fellowship)Leukemia & Lymphoma Society of America (Fellowship)National Institutes of Health (U.S.) (Grant R01HG004037)National Science Foundation (U.S.) (CAREER Award 0644282)Alfred P. Sloan FoundationNational Institutes of Health (U.S.). National Human Genome Research Institute (modENCODE Project Grant RC2HG005639)American Society for Engineering Education. National Defense Science and Engineering Graduate Fellowshi