Authors

Sarah Petersen, Kenyon CollegeFollow
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 III
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 Takasak
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
modENCODE Consortium
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

Document Type

Article

Publication Date

7-24-2011

Abstract

We systematically generated large-scale data sets to improve genome annotation for the nematodeCaenorhabditis 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.

Comments

DOI: 10.1126/science.1196914

modENCODE Consortium is a group of NHGRI-funded investigators defining genomic elements in C. elegans and D. melanogaster

Journal

Science

Volume

330

Issue

6012

First Page

1775

Last Page

1787

Included in

Genomics Commons

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