Identification of Functional Elements and Regulatory Circuits by <i>Drosophila</i> modENCODE
Sushmita Roy(Broad Institute), Jason Ernst(Broad Institute), Peter V. Kharchenko(Harvard University), Pouya Kheradpour(Broad Institute), Nicolas Nègre(University of Chicago), Matthew L. Eaton(Duke Medical Center), Jane M. Landolin(Lawrence Berkeley National Laboratory), Christopher A. Bristow(Broad Institute), Lijia Ma(University of Chicago), Michael F. Lin(Broad Institute), Stefan Washietl(Massachusetts Institute of Technology), Bradley I. Arshinoff(Ontario Institute for Cancer Research), Ferhat Ay(University of Florida), Patrick Meyer(Université Libre de Bruxelles), Nicolas Robine(Kettering University), Nicole Washington(Cyclotron (Netherlands)), Luisa Di Stefano(Harvard University), Eugène Berezikov(Royal Netherlands Academy of Arts and Sciences), Christopher D. Brown(University of Chicago), Rogerio Candeias(Massachusetts Institute of Technology), Joseph W. Carlson(Lawrence Berkeley National Laboratory), Adrian R. Carr(University of Cambridge), Irwin Jungreis(Broad Institute), Daniel Marbach(Broad Institute), Rachel Sealfon(Broad Institute), Michael Tolstorukov(Harvard University), Sebastian Will(Massachusetts Institute of Technology), Artyom A. Alekseyenko(Brigham and Women's Hospital), Carlo G. Artieri(National Institute of Diabetes and Digestive and Kidney Diseases), Benjamin W. Booth(Lawrence Berkeley National Laboratory), Angela N. Brooks(University of California, Berkeley), Qi Dai(Kettering University), Carrie Davis(Cold Spring Harbor Laboratory), Michael O. Duff(University of Connecticut), Xin Feng(Ontario Institute for Cancer Research), Andrey A. Gorchakov(Brigham and Women's Hospital), Tingting Gu(Washington University in St. Louis), Jorja G. Henikoff(Kettering University), Philipp Kapranov, Renhua Li(National Human Genome Research Institute), Heather K. MacAlpine(Duke Medical Center), John H. Malone(National Institute of Diabetes and Digestive and Kidney Diseases), Aki Minoda(Lawrence Berkeley National Laboratory), Jared T. Nordman(Whitehead Institute for Biomedical Research), Katsutomo Okamura(Kettering University), Marc D. Perry(Ontario Institute for Cancer Research), Sara Powell(Duke Medical Center), Nicole C. Riddle(Washington University in St. Louis), A. Sakai(Harvard University), Anastasia Samsonova(Massachusetts Mental Health Center), Jeremy E. Sandler(Lawrence Berkeley National Laboratory), Yuri B. Schwartz(Harvard University), Noa Sher(Whitehead Institute for Biomedical Research), Rebecca Spokony(University of Chicago), David Sturgill(National Institute of Diabetes and Digestive and Kidney Diseases), Marijke van Baren(Washington University in St. Louis), Kenneth H. Wan(Lawrence Berkeley National Laboratory), Li Yang(University of Connecticut), Charles Yu(Lawrence Berkeley National Laboratory), Elise A. Feingold(National Human Genome Research Institute), Peter J. Good(National Human Genome Research Institute), Mark S. Guyer(National Human Genome Research Institute), Rebecca F. Lowdon(National Human Genome Research Institute), Kami Ahmad(Harvard University), Justen Andrews(Indiana University Bloomington), Bonnie Berger(Broad Institute), Steven E. Brenner(University of California, Berkeley), Michael R. Brent(Washington University in St. Louis), Lucy Cherbas(Indiana University Bloomington), Sarah C. R. Elgin(Washington University in St. Louis), T Gingeras(Cold Spring Harbor Laboratory), Robert L. Grossman(University of Chicago), Roger A. Hoskins(Lawrence Berkeley National Laboratory), Thomas C. Kaufman(Indiana University Bloomington), W. James Kent(Howard Hughes Medical Institute), Mitzi I. Kuroda(Brigham and Women's Hospital), Terry L. Orr‐Weaver(Whitehead Institute for Biomedical Research), Norbert Perrimon(Massachusetts Mental Health Center), Vincenzo Pirrotta(Rutgers, The State University of New Jersey), James W. Posakony(University of California San Diego), Bing Ren(University of California San Diego), Steven Russell(University of Cambridge), Peter Cherbas(Indiana University Bloomington), Brenton R. Graveley(University of Connecticut), Suzanna Lewis(Cyclotron (Netherlands)), Gos Micklem(University of Cambridge), Brian Oliver(National Institute of Diabetes and Digestive and Kidney Diseases), Peter J. Park(Harvard University), S Celniker(Lawrence Berkeley National Laboratory), Steven Henikoff(North Seattle College), Gary H. Karpen(Lawrence Berkeley National Laboratory), Eric C. Lai(Kettering University), David M. MacAlpine(Duke Medical Center), Lincoln Stein(Ontario Institute for Cancer Research), Kevin P. White(University of Chicago), Manolis Kellis(Broad Institute), Daniel Estrada Acevedo(Duke University), Richard P. Auburn, Galt P Barber, Hugo J. Bellen, Eric Bishop, Terri D. Bryson, Aurélien Chateigner, Jia Chen(Harvard University Press), Hiram Clawson, Charles L.G. Comstock, Sergio Contrino, Leyna DeNapoli, Queying Ding, Alexander Dobin, Marc Domanus, Jörg Drenkow, Sandrine Dudoit, Jackie Dumais, Thomas Eng(Ontario Institute for Cancer Research), Delphine Fagegaltier, Sarah Gadel(Berkeley College), Srinka Ghosh, Francois Guillier, David A. Hanley(Duke University), Gregory J. Hannon, Kasper D. Hansen, Elizabeth Heinz, Angie S. Hinrichs, Martin Hirst, Sonali Jha, Lichun Jiang, Youngsook L. Jung(Broad Institute), Helena Kashevsky, Cameron Kennedy, Ellen Kephart, Laura Langton, Ok-Kyung Lee, Sharon Li(Broad Institute), Zirong Li(Broad Institute), Wei Lin(Ontario Institute for Cancer Research), Daniela Linder-Basso, Paul Lloyd, Rachel Lyne(Broad Institute), Sarah E. Marchetti(Berkeley College), Marco A. Marra, Nicolas R. Mattiuzzo(Memorial Sloan Kettering Cancer Center), Sheldon McKay, Folker Meyer(University of Liège), David M. Miller(Duke University), Steven W. Miller, Richard A. Moore, Carolyn A. Morrison, Joseph A. Prinz(Lawrence Berkeley National Laboratory), Michelle Rooks(University of California, Berkeley), Richard A. Moore, Kim Rutherford, Peter Ruzanov(Harvard University Press), Douglas A. Scheftner, Lionel Senderowicz, Parantu K. Shah, Gregory Shanower, Richard Smith, Eo Stinson, Sarah Suchy(Washington University in St. Louis), Aaron Tenney, Feng Tian(Massachusetts Institute of Technology), Koen J. T. Venken, Huaien Wang, Robert A. White(University of Chicago), Jared Wilkening(Massachusetts Institute of Technology), Aarron Willingham, Chris Zaleski(University of Chicago), Zheng Zha, Dayu Zhang, Yongjun Zhao, Jennifer Zieba
Cited by 1,303Open Access
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.
Related Papers
No related papers found
Powered by citation graph analysis