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 Candeias; Joseph 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; modENCODE Consortium

doi:10.1126/science.1198374

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Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

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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, …

Science (American Association for the Advancement of Science), Vol.330(6012), pp.1787-1797

24/12/2010

DOI: https://doi.org/10.1126/science.1198374

PMID: 21177974

Résumé

Multidisciplinary Sciences

Science & Technology

Science & Technology - Other Topics

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.

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Titre: Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE
Créateurs - sans rôle: Sushmita Roy - MIT, Comp Sci & Artificial Intelligence Lab, Cambridge, MA 02139 USA
Jason Ernst - MIT, Comp Sci & Artificial Intelligence Lab, Cambridge, MA 02139 USA
Peter V. Kharchenko - Harvard Univ, Sch Med, Ctr Biomed Informat, Boston, MA 02115 USA
Pouya Kheradpour - MIT, Comp Sci & Artificial Intelligence Lab, Cambridge, MA 02139 USA
Nicolas Negre - Univ Chicago, Inst Genom & Syst Biol, Dept Human Genet, Chicago, IL 60637 USA
Matthew L. Eaton - Duke Univ, Med Ctr, Dept Pharmacol & Canc Biol, Durham, NC 27710 USA
Jane M. Landolin - Lawrence Berkeley Natl Lab, Dept Genome Dynam, Berkeley, CA 94720 USA
Christopher A. Bristow - MIT, Comp Sci & Artificial Intelligence Lab, Cambridge, MA 02139 USA
Lijia Ma - University of Chicago
Michael F. Lin - MIT, Comp Sci & Artificial Intelligence Lab, Cambridge, MA 02139 USA
Stefan Washietl - MIT, Comp Sci & Artificial Intelligence Lab, Cambridge, MA 02139 USA
Bradley I. Arshinoff - Univ Toronto, Dept Mol Genet, Toronto, ON M5S 1A1, Canada
Ferhat Ay - MIT, Comp Sci & Artificial Intelligence Lab, Cambridge, MA 02139 USA
Patrick E. Meyer - MIT, Comp Sci & Artificial Intelligence Lab, Cambridge, MA 02139 USA
Nicolas Robine - Sloan Kettering Inst, New York, NY 10065 USA
Nicole L. Washington - LBNL, Genome Sci Div, Berkeley, CA 94720 USA
Luisa Di Stefano - MIT, Comp Sci & Artificial Intelligence Lab, Cambridge, MA 02139 USA
Eugene Berezikov - Royal Netherlands Acad Arts & Sci, Hubrecht Inst, Utrecht, Netherlands
Christopher D. Brown - Univ Chicago, Inst Genom & Syst Biol, Dept Human Genet, Chicago, IL 60637 USA
Rogerio Candeias - MIT, Comp Sci & Artificial Intelligence Lab, Cambridge, MA 02139 USA
Joseph W. Carlson - Lawrence Berkeley Natl Lab, Dept Genome Dynam, Berkeley, CA 94720 USA
Adrian Carr - Univ Cambridge, Dept Genet, Cambridge CB2 3EH, England
Irwin Jungreis - MIT, Comp Sci & Artificial Intelligence Lab, Cambridge, MA 02139 USA
Daniel Marbach - MIT, Comp Sci & Artificial Intelligence Lab, Cambridge, MA 02139 USA
Rachel Sealfon - MIT, Comp Sci & Artificial Intelligence Lab, Cambridge, MA 02139 USA
Michael Y. Tolstorukov - Harvard Univ, Sch Med, Ctr Biomed Informat, Boston, MA 02115 USA
Sebastian Will - MIT, Comp Sci & Artificial Intelligence Lab, Cambridge, MA 02139 USA
Artyom A. Alekseyenko - Harvard Univ, Brigham & Womens Hosp, Sch Med, Dept Med, Boston, MA 02115 USA
Carlo Artieri - NIDDK, Sect Dev Genom, Cellular & Dev Biol Lab, NIH, Bethesda, MD 20892 USA
Benjamin W. Booth - Lawrence Berkeley Natl Lab, Dept Genome Dynam, Berkeley, CA 94720 USA
Angela N. Brooks - Univ Calif Berkeley, Dept Mol & Cell Biol, Berkeley, CA 94720 USA
Qi Dai - Sloan Kettering Inst, New York, NY 10065 USA
Carrie A. Davis - Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA
Michael O. Duff - Univ Connecticut, Stem Cell Inst, Dept Genet & Dev Biol, Farmington, CT 06030 USA
Xin Feng - Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA
Andrey A. Gorchakov - Harvard Univ, Brigham & Womens Hosp, Sch Med, Dept Med, Boston, MA 02115 USA
Tingting Gu - Washington Univ, Dept Biol, St Louis, MO 63130 USA
Jorja G. Henikoff - Sloan Kettering Inst, New York, NY 10065 USA
Philipp Kapranov - Affymetrix, Santa Clara, CA 95051 USA
Renhua Li - NHGRI, Div Extramural Res, NIH, Bethesda, MD 20892 USA
Heather K. MacAlpine - Duke Univ, Med Ctr, Dept Pharmacol & Canc Biol, Durham, NC 27710 USA
John Malone - NIDDK, Sect Dev Genom, Cellular & Dev Biol Lab, NIH, Bethesda, MD 20892 USA
Aki Minoda - Lawrence Berkeley Natl Lab, Dept Genome Dynam, Berkeley, CA 94720 USA
Jared Nordman - Whitehead Inst, Cambridge, MA 02142 USA
Katsutomo Okamura - Sloan Kettering Inst, New York, NY 10065 USA
Marc Perry - Ontario Inst Canc Res, Toronto, ON M5G 0A3, Canada
Sara K. Powell - Duke Univ, Med Ctr, Dept Pharmacol & Canc Biol, Durham, NC 27710 USA
Nicole C. Riddle - Washington Univ, Dept Biol, St Louis, MO 63130 USA
Akiko Sakai - Harvard Univ, Sch Med, Dept Biol Chem & Mol Pharmacol, Boston, MA 02115 USA
Anastasia Samsonova - Harvard Univ, Sch Med, Dept Genet, Boston, MA 02115 USA
Jeremy E. Sandler - Lawrence Berkeley Natl Lab, Dept Genome Dynam, Berkeley, CA 94720 USA
Yuri B. Schwartz - Harvard Univ, Sch Med, Ctr Biomed Informat, Boston, MA 02115 USA
Noa Sher - Whitehead Inst, Cambridge, MA 02142 USA
Rebecca Spokony - University of Chicago
David Sturgill - NIDDK, Sect Dev Genom, Cellular & Dev Biol Lab, NIH, Bethesda, MD 20892 USA
Marijke van Baren - Washington Univ, Ctr Genome Sci, St Louis, MO 63108 USA
Kenneth H. Wan - Lawrence Berkeley Natl Lab, Dept Genome Dynam, Berkeley, CA 94720 USA
Li Yang - Univ Connecticut, Stem Cell Inst, Dept Genet & Dev Biol, Farmington, CT 06030 USA
Charles Yu - Lawrence Berkeley Natl Lab, Dept Genome Dynam, Berkeley, CA 94720 USA
Elise Feingold - NHGRI, Div Extramural Res, NIH, Bethesda, MD 20892 USA
Peter Good - NHGRI, Div Extramural Res, NIH, Bethesda, MD 20892 USA
Mark Guyer - NHGRI, Div Extramural Res, NIH, Bethesda, MD 20892 USA
Rebecca Lowdon - NHGRI, Div Extramural Res, NIH, Bethesda, MD 20892 USA
Kami Ahmad - Harvard Univ, Sch Med, Dept Biol Chem & Mol Pharmacol, Boston, MA 02115 USA
Justen Andrews - Indiana Univ, Dept Biol, Bloomington, IN 47405 USA
Bonnie Berger - MIT, Comp Sci & Artificial Intelligence Lab, Cambridge, MA 02139 USA
Steven E. Brenner - Univ Calif Berkeley, Dept Mol & Cell Biol, Berkeley, CA 94720 USA
Michael R. Brent - Washington Univ, Ctr Genome Sci, St Louis, MO 63108 USA
Lucy Cherbas - Indiana Univ, Dept Biol, Bloomington, IN 47405 USA
Sarah C. R. Elgin - Washington Univ, Dept Biol, St Louis, MO 63130 USA
Thomas R. Gingeras - Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA
Robert Grossman - University of Chicago
Roger A. Hoskins - Lawrence Berkeley Natl Lab, Dept Genome Dynam, Berkeley, CA 94720 USA
Thomas C. Kaufman - Indiana Univ, Dept Biol, Bloomington, IN 47405 USA
William Kent - Univ Calif Santa Cruz, Sch Engn, Ctr Biomol Sci & Engn, Santa Cruz, CA 95064 USA
Mitzi I. Kuroda - Harvard Univ, Brigham & Womens Hosp, Sch Med, Dept Med, Boston, MA 02115 USA
Terry Orr-Weaver - Whitehead Inst, Cambridge, MA 02142 USA
Norbert Perrimon - Harvard Univ, Sch Med, Dept Genet, Boston, MA 02115 USA
Vincenzo Pirrotta - Rutgers State Univ, Dept Mol Biol & Biochem, Piscataway, NJ 08854 USA
James W. Posakony - Univ Calif San Diego, Sect Cell & Dev Biol, Div Biol Sci, La Jolla, CA 92093 USA
Bing Ren - Univ Calif San Diego, Sect Cell & Dev Biol, Div Biol Sci, La Jolla, CA 92093 USA
Steven Russell - Univ Cambridge, Dept Genet, Cambridge CB2 3EH, England
Peter Cherbas - Indiana Univ, Dept Biol, Bloomington, IN 47405 USA
Brenton R. Graveley - Univ Connecticut, Stem Cell Inst, Dept Genet & Dev Biol, Farmington, CT 06030 USA
Suzanna Lewis - LBNL, Genome Sci Div, Berkeley, CA 94720 USA
Gos Micklem - Univ Cambridge, Dept Genet, Cambridge CB2 3EH, England
Brian Oliver - NIDDK, Sect Dev Genom, Cellular & Dev Biol Lab, NIH, Bethesda, MD 20892 USA
Peter J. Park - Harvard University
Susan E. Celniker - Lawrence Berkeley Natl Lab, Dept Genome Dynam, Berkeley, CA 94720 USA
Steven Henikoff - Fred Hutchinson Canc Res Ctr, Div Basic Sci, Seattle, WA 98109 USA
Gary H. Karpen - Lawrence Berkeley Natl Lab, Dept Genome Dynam, Berkeley, CA 94720 USA
Eric C. Lai - Sloan Kettering Inst, New York, NY 10065 USA
David M. MacAlpine - Duke Univ, Med Ctr, Dept Pharmacol & Canc Biol, Durham, NC 27710 USA
Lincoln D. Stein - Ontario Inst Canc Res, Toronto, ON M5G 0A3, Canada
Kevin P. White - University of Chicago
Manolis Kellis - MIT, Comp Sci & Artificial Intelligence Lab, Cambridge, MA 02139 USA
modENCODE Consortium
Détails de publication: Science (American Association for the Advancement of Science), Vol.330(6012), pp.1787-1797
Éditeur: Amer Assoc Advancement Science
Nombre de pages: 11
Note de subvention: WI 3628/1-1 / German Research Foundation; German Research Foundation (DFG) HHMI; Howard Hughes Medical Institute ZIADK015600 / National Institute of Diabetes and Digestive and Kidney Diseases; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Diabetes & Digestive & Kidney Diseases (NIDDK) Natural Sciences and Engineering Research Council of Canada (NSERC) Swiss National Science Foundation; Swiss National Science Foundation (SNSF) DE-AC02-05CH11231 / LBNL R01HG004037 / NIH; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA 0905968 / Direct For Biological Sciences; Div Of Biological Infrastructure; National Science Foundation (NSF); NSF - Directorate for Biological Sciences (BIO) NIDDK genomics core laboratory RC2HG005639; U01HG004271; U01HG004258; U01HG004264; U01HG004279; U01HG004261; U01HG004274; U41HG004269 / National Human Genome Research Institute; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Human Genome Research Institute (NHGRI)
Identifiants: 99136567409311
Unité académique: Diversité, Génomes et Interactions Microorganismes-Insectes - DGIMI
Langue: English
Type de ressource: Journal article