Identification of functional elements and regulatory circuits by Drosophila modENCODE

Sushmita Roy, Jason Ernst, Peter V. Kharchenko, Pouya Kheradpour, Nicolas Negre, Matthew L. Eaton, Jane M. Landolin, Christopher A. Bristow, Lijia Ma, Michael F. Lin, Stefan Washietl, Bradley I. Arshinoff, Ferhat Ay, Patrick E. Meyer, Nicolas Robine, Nicole L. Washington, Luisa Di Stefano, Eugene Berezikov, Christopher D. Brown, Rogerio CandeiasJoseph W. Carlson, Adrian Carr, Irwin Jungreis, Daniel Marbach, Rachel Sealfon, Michael Y. Tolstorukov, Sebastian Will, Artyom A. Alekseyenko, Carlo Artieri, Benjamin W. Booth, Angela N. Brooks, Qi Dai, Carrie A. Davis, Michael O. Duff, Xin Feng, Andrey A. Gorchakov, Tingting Gu, Jorja G. Henikoff, Philipp Kapranov, Renhua Li, Heather K. MacAlpine, John Malone, Aki Minoda, Jared Nordman, Katsutomo Okamura, Marc Perry, Sara K. Powell, Nicole C. Riddle, Akiko Sakai, Anastasia Samsonova, Jeremy E. Sandler, Yuri B. Schwartz, Noa Sher, Rebecca Spokony, David Sturgill, Marijke van Baren, Kenneth H. Wan, Li Yang, Charles Yu, Elise Feingold, Peter Good, Mark Guyer, Rebecca Lowdon, Kami Ahmad, Justen Andrews, Bonnie Berger, Steven E. Brenner, Michael R. Brent, Lucy Cherbas, Sarah C R Elgin, Thomas R. Gingeras, Robert Grossman, Roger A. Hoskins, Thomas C. Kaufman, William Kent, Mitzi I. Kuroda, Terry Orr-Weaver, Norbert Perrimon, Vincenzo Pirrotta, James W. Posakony, Bing Ren, Steven Russell, Peter Cherbas, Brenton R. Graveley, Suzanna Lewis, Gos Micklem, Brian Oliver, Peter J. Park, Susan E. Celniker, Steven Henikoff, Gary H. Karpen, Eric C. Lai, David M. MacAlpine, Lincoln D. Stein, Kevin P. White, Manolis Kellis, Benjamin Booth, Anastasia A. Samsonova, Marijke van Baren, Thomas R. Gingeras, Roger A. Hoskins, Charles L G Comstock, Alex Dobin, Jorg Drenkow, Kasper Daniel Hansen, Jacqueline Dumais, Delphine Fagegaltier, Srinka Ghosh, Kasper D. Hansen, Sonali Jha, Laura Langton, Wei Lin, David Miller, Aaron E. Tenney, Huaien Wang, Aarron T. Willingham, Chris Zaleski, Dayu Zhang, David Acevedo, Eric P. Bishop, Sarah E. Gadel, Youngsook L. Jung, Cameron D. Kennedy, Ok Kyung Lee, Daniela Linder-Basso, Sarah E. Marchetti, Gregory Shanower, Nicolas Nègre, Robert L. Grossman, Richard Auburn, Hugo J. Bellen, Jia Chen, Marc H. Domanus, David Hanley, Elizabeth Heinz, Zirong Li, Folker Meyer, Steven W. Miller, Carolyn A. Morrison, Douglas A. Scheftner, Lionel Senderowicz, Parantu K. Shah, Sarah Suchy, Feng Tian, Koen J T Venken, Robert White, Jared Wilkening, Jennifer Zieba, Jared T. Nordman, Terry L. Orr-Weaver, Leyna C. DeNapoli, Queying Ding, Thomas Eng, Helena Kashevsky, Sharon Li, Joseph A. Prinz, Qi Dai, Gregory J. Hannon, Martin Hirst, Marco Marra, Michelle Rooks, Yongjun Zhao, Terri D. Bryson, Marc D. Perry, William J. Kent, Suzanna E. Lewis, Galt Barber, Aurelien Chateigner, Hiram Clawson, Sergio Contrino, Francois Guillier, Angie S. Hinrichs, Ellen T. Kephart, Paul Lloyd, Rachel Lyne, Sheldon McKay, Richard A. Moore, Chris Mungall, Kim M. Rutherford, Peter Ruzanov, Richard Smith, E. O. Stinson, Zheng Zha, Carlo G. Artieri, John H. Malone, Lichun Jiang, Nicolas Mattiuzzo, Elise A. Feingold, Peter J. Good, Mark S. Guyer, Rebecca F. Lowdon

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)1787-1797
Number of pages11
JournalScience
Volume330
Issue number6012
DOIs
StatePublished - Dec 24 2010
Externally publishedYes

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ASJC Scopus subject areas

  • General

Cite this

Roy, S., Ernst, J., Kharchenko, P. V., Kheradpour, P., Negre, N., Eaton, M. L., Landolin, J. M., Bristow, C. A., Ma, L., Lin, M. F., Washietl, S., Arshinoff, B. I., Ay, F., Meyer, P. E., Robine, N., Washington, N. L., Di Stefano, L., Berezikov, E., Brown, C. D., ... Lowdon, R. F. (2010). Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science, 330(6012), 1787-1797. https://doi.org/10.1126/science.1198374