Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

Mark B. Gerstein; Zhi John Lu; Eric L. Van Nostrand; Chao Cheng; Bradley I. Arshinoff; Tao Liu; Kevin Y. Yip; Rebecca Robilotto; Andreas Rechtsteiner; Kohta Ikegami; Pedro Alves; Aurelien Chateigner; Marc Perry; Mitzi Morris; Raymond K. Auerbach; Xin Feng; Jing Leng; Anne Vielle; Wei Niu; Kahn Rhrissorrakrai; Ashish Agarwal; Roger P. Alexander; Galt Barber; Cathleen M. Brdlik; Jennifer Brennan; Jeremy Jean Brouillet; Adrian Carr; Ming-Sin Cheung; Hiram Clawson; Sergio Contrino; Luke O. Dannenberg; Abby F. Dernburg; Arshad Desai; Lindsay Dick; Andréa C. Dosé; Jiang Du; Thea Egelhofer; Sevinc Ercan; Ghia Euskirchen; Brent Ewing; Elise A. Feingold; Reto Gassmann; Peter J. Good; Phil Green; Francois Gullier; Michelle Gutwein; Mark S. Guyer; Lukas Habegger; Ting Han; Jorja G. Henikoff; Stefan R. Henz; Angie Hinrichs; Heather Holster; Tony Hyman; A. Leo Iniguez; Judith Janette; Morten Jensen; Masaomi Kato; W. James Kent; Ellen Kephart; Vishal Khivansara; Ekta Khurana; John K. Kim; Paulina Kolasinska-Zwierz; Eric C. Lai; Isabel Latorre; Amber Leahey; Suzanna Lewis; Paul Lloyd; Lucas Lochovsky; Rebecca F. Lowdon; Yaniv Lubling; Rachel Lyne; Michael MacCoss; Sebastian D. Mackowiak; Marco Mangone; Sheldon McKay; Desirea Mecenas; Gennifer Merrihew; David M. Miller; Andrew Muroyama; John I. Murray; Siew-Loon Ooi; Hoang Pham; Taryn Phippen; Elicia A. Preston; Nikolaus Rajewsky; Gunnar Rätsch; Heidi Rosenbaum; Joel Rozowsky; Kim Rutherford; Peter Ruzanov; Mihail Sarov; Rajkumar Sasidharan; Andrea Sboner; Paul Scheid; Eran Segal; Hyunjin Shin; Chong Shou; Frank J. Slack; Cindie Slightam; Richard Smith; William C. Spencer; E. O. Stinson; Scott Taing; Teruaki Takasaki; Dionne Vafeados; Ksenia Voronina; Guilin Wang; Nicole L. Washington; Christina M. Whittle; Beijing Wu; Koon-Kiu Yan; Georg Zeller; Zheng Zha; Mei Zhong; Xingliang Zhou; Julie Ahringer; Susan Strome; Kristin C. Gunsalus; Gos Micklem; X. Shirley Liu; Valerie Reinke; Stuart K. Kim; LaDeana W. Hillier; Steven Henikoff; Fabio Piano; Michael Snyder; Lincoln Stein; Jason D. Lieb; Robert H. Waterston; modENCODE Consortium

doi:10.1126/science.1196914

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Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

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Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

Mark B. Gerstein, Zhi John Lu, Eric L. Van Nostrand, Chao Cheng, Bradley I. Arshinoff, Tao Liu, Kevin Y. Yip, Rebecca Robilotto, Andreas Rechtsteiner, Kohta Ikegami, …

Science (American Association for the Advancement of Science), Vol.330(6012), pp.1775-1787

24/12/2010

DOI: https://doi.org/10.1126/science.1196914

PMCID: PMC3142569

PMID: 21177976

Abstract

From Genome to Regulatory Networks For biologists, having a genome in hand is only the beginning—much more investigation is still needed to characterize how the genome is used to help to produce a functional organism (see the Perspective by Blaxter ). In this vein, Gerstein et al. (p. 1775 ) summarize for the Caenorhabditis elegans genome, and The modENCODE Consortium (p. 1787 ) summarize for the Drosophila melanogaster genome, full transcriptome analyses over developmental stages, genome-wide identification of transcription factor binding sites, and high-resolution maps of chromatin organization. Both studies identified regions of the nematode and fly genomes that show highly occupied targets (or HOT) regions where DNA was bound by more than 15 of the transcription factors analyzed and the expression of related genes were characterized. Overall, the studies provide insights into the organization, structure, and function of the two genomes and provide basic information needed to guide and correlate both focused and genome-wide studies. Extensive analysis of the Caenorhabditis elegans genome reveals regions highly occupied by multiple transcription factors. We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans , a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor–binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of transcription factor–binding and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome arms and centers, with similarly prominent differences between autosomes and the X chromosome. Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome.

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Title: Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project
Creators - without role: Mark B. Gerstein - Yale University
Zhi John Lu - Yale University
Eric L. Van Nostrand - Stanford Medicine
Chao Cheng - Yale University
Bradley I. Arshinoff - University of Toronto
Tao Liu - Dana-Farber Cancer Institute
Kevin Y. Yip - Yale University
Rebecca Robilotto - Yale University
Andreas Rechtsteiner - University of California, Santa Cruz
Kohta Ikegami - University of North Carolina at Chapel Hill
Pedro Alves - Yale University
Aurelien Chateigner - University of Cambridge
Marc Perry - Ontario Institute for Cancer Research
Mitzi Morris - Center for Genomics and Systems Biology, Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, NY 10003–6688, USA
Raymond K. Auerbach - Yale University
Xin Feng - Ontario Institute for Cancer Research, 101 College Street, Suite 800, Toronto, Ontario M5G 0A3, Canada., Department of Biomedical Engineering, State University of New York at Stonybrook, Stonybrook, NY 11794, USA
Jing Leng - Yale University
Anne Vielle - University of Cambridge
Wei Niu - University of New Haven
Kahn Rhrissorrakrai - Center for Genomics and Systems Biology, Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, NY 10003–6688, USA
Ashish Agarwal - Yale University
Roger P. Alexander - Yale University
Galt Barber - University of California, Santa Cruz
Cathleen M. Brdlik - Stanford Medicine
Jennifer Brennan - University of North Carolina at Chapel Hill
Jeremy Jean Brouillet - Stanford Medicine
Adrian Carr - University of Cambridge
Ming-Sin Cheung - University of Cambridge
Hiram Clawson - University of California, Santa Cruz
Sergio Contrino - University of Cambridge
Luke O. Dannenberg - Roche NimbleGen, 500 South Rosa Road, Madison, WI 53719, USA
Abby F. Dernburg - University of California, Berkeley
Arshad Desai - University of California, San Diego
Lindsay Dick - Rockefeller University
Andréa C. Dosé - University of California, Berkeley
Jiang Du - Yale University
Thea Egelhofer - University of California, Santa Cruz
Sevinc Ercan - University of North Carolina at Chapel Hill
Ghia Euskirchen - University of New Haven
Brent Ewing - University of Washington School of Medicine
Elise A. Feingold - National Human Genome Research Institute
Reto Gassmann - University of California, San Diego
Peter J. Good - National Human Genome Research Institute
Phil Green - University of Washington School of Medicine
Francois Gullier - University of Cambridge
Michelle Gutwein - Center for Genomics and Systems Biology, Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, NY 10003–6688, USA
Mark S. Guyer - National Human Genome Research Institute
Lukas Habegger - Yale University
Ting Han - Life Sciences Institute, Department of Human Genetics, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109–2216, USA
Jorja G. Henikoff - North Seattle College
Stefan R. Henz - Max Planck Institute for Developmental Biology
Angie Hinrichs - University of California, Santa Cruz
Heather Holster - Roche NimbleGen, 500 South Rosa Road, Madison, WI 53719, USA
Tony Hyman - Max Planck Institute of Molecular Cell Biology and Genetics
A. Leo Iniguez - Roche NimbleGen, 500 South Rosa Road, Madison, WI 53719, USA
Judith Janette - Yale University
Morten Jensen - University of North Carolina at Chapel Hill
Masaomi Kato - University of New Haven
W. James Kent - University of California, Santa Cruz
Ellen Kephart - Ontario Institute for Cancer Research
Vishal Khivansara - Life Sciences Institute, Department of Human Genetics, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109–2216, USA
Ekta Khurana - Yale University
John K. Kim - Life Sciences Institute, Department of Human Genetics, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109–2216, USA
Paulina Kolasinska-Zwierz - University of Cambridge
Eric C. Lai - Sloan-Kettering Institute, 1275 York Avenue, Post Office Box 252, New York, NY 10065, USA
Isabel Latorre - University of Cambridge
Amber Leahey - University of Washington School of Medicine
Suzanna Lewis - Lawrence Berkeley National Laboratory
Paul Lloyd - Ontario Institute for Cancer Research
Lucas Lochovsky - Yale University
Rebecca F. Lowdon - National Human Genome Research Institute
Yaniv Lubling - Weizmann Institute of Science
Rachel Lyne - University of Cambridge
Michael MacCoss - University of Washington School of Medicine
Sebastian D. Mackowiak - Max
Marco Mangone - Center for Genomics and Systems Biology, Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, NY 10003–6688, USA
Sheldon McKay - Cold Spring Harbor Laboratory
Desirea Mecenas - Center for Genomics and Systems Biology, Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, NY 10003–6688, USA
Gennifer Merrihew - University of Washington School of Medicine
David M. Miller - Vanderbilt University
Andrew Muroyama - University of California, San Diego
John I. Murray - University of Washington School of Medicine
Siew-Loon Ooi - North Seattle College
Hoang Pham - University of California, Berkeley
Taryn Phippen - University of California, Santa Cruz
Elicia A. Preston - University of Washington School of Medicine
Nikolaus Rajewsky - Max
Gunnar Rätsch - Friedrich Miescher Laboratory
Heidi Rosenbaum - ROSA
Joel Rozowsky - Yale University
Kim Rutherford - University of Cambridge
Peter Ruzanov - Ontario Institute for Cancer Research
Mihail Sarov - Max Planck Institute of Molecular Cell Biology and Genetics
Rajkumar Sasidharan - Yale University
Andrea Sboner - Yale University
Paul Scheid - Center for Genomics and Systems Biology, Department of Biology, New York University, 1009 Silver Center, 100 Washington Square East, New York, NY 10003–6688, USA
Eran Segal - Weizmann Institute of Science
Hyunjin Shin - Dana-Farber Cancer Institute
Chong Shou - Yale University
Frank J. Slack - University of New Haven
Cindie Slightam - Stanford Medicine
Richard Smith - University of Cambridge
William C. Spencer - Vanderbilt University
E. O. Stinson - Lawrence Berkeley National Laboratory
Scott Taing - Dana-Farber Cancer Institute
Teruaki Takasaki - University of California, Santa Cruz
Dionne Vafeados - University of Washington School of Medicine
Ksenia Voronina - University of California, San Diego
Guilin Wang - Yale University
Nicole L. Washington - Lawrence Berkeley National Laboratory
Christina M. Whittle - University of North Carolina at Chapel Hill
Beijing Wu - Stanford Medicine
Koon-Kiu Yan - Yale University
Georg Zeller - Friedrich Miescher Laboratory
Zheng Zha - Ontario Institute for Cancer Research
Mei Zhong - University of New Haven
Xingliang Zhou - University of North Carolina at Chapel Hill
Julie Ahringer - University of Cambridge
Susan Strome - University of California, Santa Cruz
Kristin C. Gunsalus - New York University Abu Dhabi
Gos Micklem - University of Cambridge
X. Shirley Liu - Dana-Farber Cancer Institute
Valerie Reinke - Yale University
Stuart K. Kim - Stanford Medicine
LaDeana W. Hillier - University of Washington School of Medicine
Steven Henikoff - North Seattle College
Fabio Piano - New York University Abu Dhabi
Michael Snyder - Stanford Medicine
Lincoln Stein - University of Toronto
Jason D. Lieb - University of North Carolina at Chapel Hill
Robert H. Waterston - University of Washington School of Medicine
modENCODE Consortium
Publication Details: Science (American Association for the Advancement of Science), Vol.330(6012), pp.1775-1787
Identifiers: 9945466508331
Academic Unit: King Abdullah University of Science & Technology
Language: English
Resource Type: Journal article