Integrative Analysis of the <i>Caenorhabditis elegans</i> Genome by the modENCODE Project
Mark Gerstein(Yale University), Zhi John Lu(Yale University), Eric L. Van Nostrand(Stanford Medicine), Chao Cheng(Yale University), Bradley I. Arshinoff(Ontario Institute for Cancer Research), Tao Liu(Harvard University), Kevin Y. Yip(Yale University), R. Robilotto(Yale University), Andreas Rechtsteiner(University of California, Santa Cruz), Kohta Ikegami(University of North Carolina at Chapel Hill), Pedro Alves(Yale University), Aurélien Chateigner(University of Cambridge), Marc D. Perry(Ontario Institute for Cancer Research), Mitzi Morris(New York Genome Center), Raymond K. Auerbach(Yale University), Xin Feng(Ontario Institute for Cancer Research), Jing Leng(Yale University), Anne Vielle(University of Cambridge), Wei Niu(Yale University), Kahn Rhrissorrakrai(New York Genome Center), Ashish Agarwal(Yale University), Roger P. Alexander(Yale University), Galt P Barber(University of California, Santa Cruz), Cathleen Brdlik(Stanford Medicine), Jennifer Brennan(University of North Carolina at Chapel Hill), Jeremy Brouillet(Stanford Medicine), Adrian R. 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(La Roche College), Abby F. Dernburg(Lawrence Berkeley National Laboratory), Arshad Desai(University of California San Diego), Lindsay L. Dick(Rockefeller University), Andrea C. Dosé(Lawrence Berkeley National Laboratory), Jiang Du(Yale University), Thea A. Egelhofer(University of California, Santa Cruz), Sevinç Ercan(University of North Carolina at Chapel Hill), Ghia Euskirchen(Yale University), Brent Ewing(Seattle Pacific University), 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(Seattle Pacific University), F. Gullier(University of Cambridge), Michelle Gutwein(New York Genome Center), Mark S. Guyer(National Human Genome Research Institute), Lukas Habegger(Yale University), Ting Han(Washtenaw Community College), Jorja G. Henikoff(North Seattle College), Stefan R. Henz(Max Planck Institute for Developmental Biology), Angie S. Hinrichs(University of California, Santa Cruz), H. Holster(La Roche College), Tony Hyman(Max Planck Institute of Molecular Cell Biology and Genetics), Al Iniguez(La Roche College), J. Janette(Yale University), Morten B. Jensen(University of North Carolina at Chapel Hill), Masaomi Kato(Yale University), W. James Kent(University of California, Santa Cruz), Ellen Kephart(Ontario Institute for Cancer Research), Vishal Khivansara(Washtenaw Community College), Ekta Khurana(Yale University), John K. Kim(Washtenaw Community College), Paulina Kolasinska-Zwierz(University of Cambridge), Eric C. Lai(Kettering University), Isabel Latorre(University of Cambridge), A. Leahey(Seattle Pacific University), 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 J. MacCoss(Seattle Pacific University), Sebastian D. Mackowiak(Max Delbrück Center), Marco Mangone(New York Genome Center), Sheldon McKay(Cold Spring Harbor Laboratory), Desirea Mecenas(New York Genome Center), Gennifer E. Merrihew(Seattle Pacific University), David M. Miller(Vanderbilt University), Andrew Muroyama(University of California San Diego), John I. Murray(Seattle Pacific University), Siew-Loon Ooi(North Seattle College), Vu Pham(Lawrence Berkeley National Laboratory), T. Phippen(University of California, Santa Cruz), Elicia Preston(Seattle Pacific University), Nikolaus Rajewsky(Max Delbrück Center), Gunnar Rätsch(Max Planck Society), Heidi Rosenbaum(La Roche College), 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(New York Genome Center), Eran Segal(Weizmann Institute of Science), Hyunjin Shin(Harvard University), Chong Shou(Yale University), Frank J. Slack(Yale University), C. Slightam(Stanford University), Richard Smith(University of Cambridge), William C. Spencer(Vanderbilt University), Eo Stinson(Lawrence Berkeley National Laboratory), S. Taing(Dana-Farber Cancer Institute), Teruaki Takasaki(University of California, Santa Cruz), Dionne Vafeados(Seattle Pacific University), K. Voronina(University of California San Diego), Guilin Wang(Yale University), Nicole Washington(Lawrence Berkeley National Laboratory), Christina M. Whittle(University of North Carolina at Chapel Hill), Beijing Wu(Stanford University), Koon-Kiu Yan(Yale University), Georg Zeller(Max Planck Society), Zheng Zha(Ontario Institute for Cancer Research), Mei Zhong(Yale University), 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), Xuyuan Liu(Harvard University), V Reinke(Yale University), Stuart K. Kim(Stanford Medicine), LaDeana Hillier(Seattle Pacific University), Steven Henikoff(North Seattle College), Fabio Piano(New York University Abu Dhabi), M Snyder(Yale University), Lincoln Stein(Ontario Institute for Cancer Research), Jason D. Lieb(University of North Carolina at Chapel Hill), R Waterston(Seattle Pacific University)
Cited by 1,036
Abstract
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.