Integrative Analysis of the <i>Caenorhabditis elegans</i> Genome by the modENCODE Project
- Mark Gerstein
- Zhi John Lu
- Eric L. Van Nostrand
- Chao Cheng
- Bradley I. Arshinoff
- TLTao Liu
- Kevin Y. Yip
- R. Robilotto
- Andreas Rechtsteiner
- Kohta Ikegami
- Pedro Alves
- Aurélien Chateigner
- Marc D. Perry
- Mitzi Morris
- Raymond K. Auerbach
- Xin Feng
- Jing Leng
- Anne Vielle
- Wei Niu
- Kahn Rhrissorrakrai
- Ashish Agarwal
- Roger P. Alexander
- Galt P Barber
- Cathleen Brdlik
- Jennifer Brennan
- Jeremy Brouillet
- Adrian R. Carr
- Ming-Sin Cheung
- Hiram Clawson
- Sergio Contrino
- Luke O. Dannenberg
- Abby F. Dernburg
- Arshad Desai
- Lindsay L. Dick
- Andrea C. Dosé
- Jiang Du
- Thea A. Egelhofer
- Sevinç Ercan
- Ghia Euskirchen
- Brent Ewing
- Elise A. Feingold
- Reto Gassmann
- Peter J. Good
- Phil Green
- F. Gullier
- Michelle Gutwein
- Mark S. Guyer
- Lukas Habegger
- Ting Han
- Jorja G. Henikoff
- Stefan R. Henz
- Angie S. Hinrichs
- H. Holster
- Tony Hyman
- Al Iniguez
- J. Janette
- Morten B. Jensen
- Masaomi Kato
- W. James Kent
- Ellen Kephart
- Vishal Khivansara
- Ekta Khurana
- John K. Kim
- Paulina Kolasinska-Zwierz
- Eric C. Lai
- Isabel Latorre
- A. Leahey
- Suzanna Lewis
- Paul Lloyd
- Lucas Lochovsky
- Rebecca F. Lowdon
- Yaniv Lubling
- Rachel Lyne
- Michael J. MacCoss
- Sebastian D. Mackowiak
- Marco Mangone
- Sheldon McKay
- Desirea Mecenas
- Gennifer E. Merrihew
- David M. Miller
- Andrew Muroyama
- John I. Murray
- Siew-Loon Ooi
- Vu Pham
- T. Phippen
- Elicia 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
- TLTao Liu
Science · 2010 · American Association for the Advancement of Science
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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.