Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE
Author(s)Kheradpour, Pouya; Bristow, Christopher A.; Mag Washietl, Stefan; Ay, Ferhat; Jungreis, Irwin; Marbach, Daniel; Sealfon, Rachel Sima; Will, Sebastian; Berger, Bonnie; Kellis, Manolis; Roy, Sushmita; Ernst, Jason; Lin, Michael F.; Meyer, Patrick E.; Di Stefano, Luisa; Candeias, Rogerio; Nordman, Jared T.; Orr-Weaver, Terry L.; ... Show more Show less
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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 manuscript; available in PMC 2011 October 13.
DepartmentMassachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory; Massachusetts Institute of Technology. Department of Biology; Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science; Massachusetts Institute of Technology. Department of Mathematics
American Association for the Advancement of Science (AAAS)
Roy, S., J. Ernst, P. V. Kharchenko, P. Kheradpour, N. Negre, M. L. Eaton, J. M. Landolin, et al. “Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE.” Science 330, no. 6012 (December 23, 2010): 1787-1797.
Author's final manuscript