A cis-regulatory map of the Drosophila genome

Nicolas Négre, 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. ShahCarolyn 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, Kevin P. White

Research output: Contribution to journalArticle

331 Scopus citations

Abstract

Systematic annotation of gene regulatory elements is a major challenge in genome science. Direct mapping of chromatin modification marks and transcriptional factor binding sites genome-wide has successfully identified specific subtypes of regulatory elements. In Drosophila several pioneering studies have provided genome-wide identification of Polycomb response elements, chromatin states, transcription factor binding sites, RNA polymerase II regulation and insulator elements; however, comprehensive annotation of the regulatory genome remains a significant challenge. Here we describe results from the modENCODE cis-regulatory annotation project. We produced a map of the Drosophila melanogaster regulatory genome on the basis of more than 300 chromatin immunoprecipitation data sets for eight chromatin features, five histone deacetylases and thirty-eight site-specific transcription factors at different stages of development. Using these data we inferred more than 20,000 candidate regulatory elements and validated a subset of predictions for promoters, enhancers and insulators in vivo. We identified also nearly 2,000 genomic regions of dense transcription factor binding associated with chromatin activity and accessibility. We discovered hundreds of new transcription factor co-binding relationships and defined a transcription factor network with over 800 potential regulatory relationships.

Original languageEnglish (US)
Pages (from-to)527-531
Number of pages5
JournalNature
Volume471
Issue number7339
DOIs
StatePublished - Mar 24 2011

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    Négre, N., Brown, C. D., Ma, L., Bristow, C. A., Miller, S. W., Wagner, U., Kheradpour, P., Eaton, M. L., Loriaux, P., Sealfon, R., Li, Z., Ishii, H., Spokony, R. F., Chen, J., Hwang, L., Cheng, C., Auburn, R. P., Davis, M. B., Domanus, M., ... White, K. P. (2011). A cis-regulatory map of the Drosophila genome. Nature, 471(7339), 527-531. https://doi.org/10.1038/nature09990