A cis-regulatory map of the Drosophila genome

Nicolas Nègre, Christopher D. Brown, Lijia Ma, Christopher Aaron Bristow, Steven W. Miller, Ulrich Wagner, Pouya Kheradpour, Matthew L. Eaton, Paul Loriaux, Rachel Sealfon, Zirong Li, Haruhiko Ishii, Rebecca F. Spokony, Jia Chen, Lindsay Hwang, Chao Cheng, Richard P. Auburn, Melissa B. Davis, Marc Domanus, Parantu K. Shah, Carolyn A. Morrison, Jennifer Zieba, Sarah Suchy, Lionel Senderowicz, Alec Victorsen, Nicholas A. Bild, A. Jason Grundstad, David Hanley, David M. MacAlpine, Mattias Mannervik, Koen Venken, Hugo Bellen, Robert White, Mark Gerstein, Steven Russell, Robert L. Grossman, Bing Ren, James W. Posakony, Manolis Kellis and Kevin P. White ()
Additional contact information
Nicolas Nègre: Institute for Genomics and Systems Biology, The University of Chicago
Christopher D. Brown: Institute for Genomics and Systems Biology, The University of Chicago
Lijia Ma: Institute for Genomics and Systems Biology, The University of Chicago
Christopher Aaron Bristow: Massachusetts Institute of Technology, Computer Science and Artificial Intelligence Laboratory, Broad Institute of MIT and Harvard
Steven W. Miller: University of California San Diego
Ulrich Wagner: Ludwig Institute for Cancer Research, 9500 Gilman Drive
Pouya Kheradpour: Massachusetts Institute of Technology, Computer Science and Artificial Intelligence Laboratory, Broad Institute of MIT and Harvard
Matthew L. Eaton: Duke University Medical Center
Paul Loriaux: Signaling Systems Laboratory, University of California, San Diego, 9500 Gilman Drive
Rachel Sealfon: Massachusetts Institute of Technology, Computer Science and Artificial Intelligence Laboratory, Broad Institute of MIT and Harvard
Zirong Li: Ludwig Institute for Cancer Research, 9500 Gilman Drive
Haruhiko Ishii: University of California San Diego
Rebecca F. Spokony: Institute for Genomics and Systems Biology, The University of Chicago
Jia Chen: National Center for Data Mining, University of Illinois at Chicago
Lindsay Hwang: Ludwig Institute for Cancer Research, 9500 Gilman Drive
Chao Cheng: Program in Computational Biology & Bioinformatics, Yale University
Richard P. Auburn: University of Cambridge
Melissa B. Davis: Institute for Genomics and Systems Biology, The University of Chicago
Marc Domanus: Institute for Genomics and Systems Biology, The University of Chicago
Parantu K. Shah: Dana-Farber Cancer Institute, Harvard School of Public Health
Carolyn A. Morrison: Institute for Genomics and Systems Biology, The University of Chicago
Jennifer Zieba: Institute for Genomics and Systems Biology, The University of Chicago
Sarah Suchy: Institute for Genomics and Systems Biology, The University of Chicago
Lionel Senderowicz: Institute for Genomics and Systems Biology, The University of Chicago
Alec Victorsen: Institute for Genomics and Systems Biology, The University of Chicago
Nicholas A. Bild: Institute for Genomics and Systems Biology, The University of Chicago
A. Jason Grundstad: Institute for Genomics and Systems Biology, The University of Chicago
David Hanley: National Center for Data Mining, University of Illinois at Chicago
David M. MacAlpine: Duke University Medical Center
Mattias Mannervik: Wenner-Gren Institute, Arrhenius Laboratories E3, Stockholm University
Koen Venken: BCM
Hugo Bellen: BCM
Robert White: Development and Neuroscience, University of Cambridge
Mark Gerstein: Program in Computational Biology & Bioinformatics, Yale University
Steven Russell: University of Cambridge
Robert L. Grossman: Institute for Genomics and Systems Biology, The University of Chicago
Bing Ren: Ludwig Institute for Cancer Research, 9500 Gilman Drive
James W. Posakony: University of California San Diego
Manolis Kellis: Massachusetts Institute of Technology, Computer Science and Artificial Intelligence Laboratory, Broad Institute of MIT and Harvard
Kevin P. White: Institute for Genomics and Systems Biology, The University of Chicago

Nature, 2011, vol. 471, issue 7339, 527-531

Abstract: Elements of gene function Three papers in this issue of Nature report on the modENCODE initiative, which aims to characterize functional DNA elements in the fruitfly Drosophila melanogaster and the roundworm Caenorhabditis elegans. Kharchenko et al. present a genome-wide chromatin landscape of the fruitfly, based on 18 histone modifications. They describe nine prevalent chromatin states. Integrating these analyses with other data types reveals individual characteristics of different genomic elements. Graveley et al. have used RNA-Seq, tiling microarrays and cDNA sequencing to explore the transcriptome in 30 distinct developmental stages of the fruitfly. Among the results are scores of new genes, coding and non-coding transcripts, as well as splicing and editing events. Finally, Nègre et al. have produced a map of the regulatory part of the fruitfly genome, defining a vast array of putative regulatory elements, such as enhancers, promoters, insulators and silencers.

Date: 2011
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DOI: 10.1038/nature09990

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