Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

作者：Sushmita Mimi Roy, Jason Ernst, Peter V. Kharchenko, Pouya Kheradpour, Nicolas Nègre, Matthew L. Eaton, Jane M. Landolin, Christopher Aaron Bristow, Lijia Ma, Michael F. Lin, Stefan Washietl, Bradley I. Arshinoff, Ferhat Ay, Patrick E. Meyer, Nicolas Robine, Nicole L. Washington, Luisa Di Stefano, Eugène Berezikov, Christopher D. Brown, Rogerio Candeias, Joseph W. Carlson, Adrian R. Carr, Irwin Jungreis, Daniel Marbach, Rachel S. G. Sealfon, Michael Yevgeniy Tolstorukov, Sebastian Will, Artyom A. Alekseyenko, Carlo G. Artieri, Benjamin W. Booth, Angela Norie Brooks, Qi Dai, Carrie Davis, Michael O. Duff, Xin Feng, Andrey A. Gorchakov, Tingting Gu, Jorja G. Henikoff, Philipp Kapranov, Renhua Li, Heather K. MacAlpine, John H. Malone, Aki Minoda, Jared T. Nordman, Katsutomo Okamura, Marc D. Perry, Sara Powell, Nicole C. Riddle, A. Sakai, Anastasia A. Samsonova, Jeremy E. Sandler, Yuri B. Schwartz, Noa Sher, Rebecca F. Spokony, David M. Sturgill, Marijke van Baren, Kenneth H. Wan, Li Yang, Charles Yu, Elise A. Feingold, Peter J. Good, Mark S. Guyer, Rebecca F. Lowdon, Kami Ahmad, Justen Andrews, Bonnie Berger, Steven E. Brenner, Michael Richard Brent, Lucy Cherbas, Sarah C. R. Elgin, T Gingeras, Robert L. Grossman, Roger A. Hoskins, Thomas C. Kaufman, W. James Kent, Mitzi I. Kuroda, Terry L. Orr‐Weaver, Norbert Perrimon, Vincenzo Pirrotta, James W. Posakony, Bing Ren, Steven R. H. Russell, Peter T. Cherbas, Brenton R. Graveley, Suzanna Lewis, Gos Micklem, Brian Oliver, Peter J. Park, S Celniker, Steven Henikoff, Gary H. Karpen, Eric C. Lai, David M. MacAlpine, Lincoln Stein, Kevin P. White, Manolis Kellis, Daniel Estrada Acevedo, Richard P. Auburn, Galt P Barber, Hugo Jozef Bellen, Eric P. Bishop, Terri D. Bryson, Aurélien Chateigner, Jia Chen, Hiram Clawson, Charles L.G. Comstock, Sergio Contrino, Leyna DeNapoli, Queying Ding, Alexander Yu. Dobin, Marc H. Domanus, Jörg Drenkow, Sandrine Dudoit, Jackie Dumais, Thomas Eng, Delphine Fagegaltier, Sarah Gadel, Srinka Ghosh, Francois Guillier, David A. Hanley, Gregory James Hannon, Kasper D. Hansen, Elizabeth Heinz, Angie S. Hinrichs, Martin Hirst, Sonali Jha, Lichun Jiang, Youngsook Lucy Jung, Helena Kashevsky, Cameron Kennedy, Ellen Towle Kephart, Laura Langton, Ok-Kyung Lee, Sharon Li, Zirong Li, Wei Lin, Daniela Linder-Basso, Paul Lloyd, Rachel Lyne, Sarah E. Marchetti, Marco A. Marra, Nicolas R. Mattiuzzo, Sheldon McKay, Folker Meyer, David M. Miller, Steven W. Miller, Richard A. Moore, Carolyn A. Morrison, Joseph A. Prinz, Michelle G. Rooks, Richard A. Moore, Kim Rutherford, Peter Ruzanov, Douglas A. Scheftner, Lionel Senderowicz, Parantu K. Shah, Gregory Shanower, Richard Nigel Smith, Eo Stinson, Sarah Suchy, Aaron E. Tenney, Feng Tian, Koen J. T. Venken, Huaien Wang, Robert A. White, Jared Wilkening, Aarron T. Willingham, Chris Zaleski, Zheng Zha, Dayu Zhang, Yongjun Zhao, Jennifer T. Zieba · 发表于：Science · 年份：2010 · DOI：10.1126/science.1198374 · 被引用次数：1314 · 研究领域：Neurobiology and Insect Physiology Research、Insect Resistance and Genetics、Genetics, Aging, and Longevity in Model Organisms

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.