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PMID: 21177976 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

Science (New York, N.Y.) ·Vol. 330 ·No. 6012 ·2010-12-24 ·Pages 1775-87

Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X, modENCODE Consortium, Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH

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.

MeSH Terms
Animals Caenorhabditis elegans/genetics,growth & development,metabolism Caenorhabditis elegans Proteins/genetics,metabolism Chromatin/genetics,metabolism,ultrastructure Chromosomes/genetics,metabolism,ultrastructure Computational Biology/methods Conserved Sequence Evolution, Molecular Gene Expression Profiling Gene Expression Regulation Gene Regulatory Networks Genes, Helminth Genome, Helminth Genomics/methods Histones/metabolism Models, Genetic Molecular Sequence Annotation RNA, Helminth/genetics,metabolism RNA, Untranslated/genetics,metabolism Regulatory Sequences, Nucleic Acid Transcription Factors/genetics,metabolism
Chemicals
Caenorhabditis elegans Proteins Chromatin Histones RNA, Helminth RNA, Untranslated Transcription Factors
Authors & Affiliations
132 authors, click to expand affiliations / ORCID
Gerstein Mark B
Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA. modencode.worm.pi@gersteinlab.org
Lu Zhi John
Van Nostrand Eric L
Cheng Chao
Arshinoff Bradley I
Liu Tao
Yip Kevin Y
Robilotto Rebecca
Rechtsteiner Andreas
Ikegami Kohta
Alves Pedro
Chateigner Aurelien
Perry Marc
Morris Mitzi
Auerbach Raymond K
Feng Xin
Leng Jing
Vielle Anne
Niu Wei
Rhrissorrakrai Kahn
Agarwal Ashish
Alexander Roger P
Barber Galt
Brdlik Cathleen M
Brennan Jennifer
Brouillet Jeremy Jean
Carr Adrian
Cheung Ming-Sin
Clawson Hiram
Contrino Sergio
Dannenberg Luke O
Dernburg Abby F
Desai Arshad
Dick Lindsay
Dosé Andréa C
Du Jiang
Egelhofer Thea
Ercan Sevinc
Euskirchen Ghia
Ewing Brent
Feingold Elise A
Gassmann Reto
Good Peter J
Green Phil
Gullier Francois
Gutwein Michelle
Guyer Mark S
Habegger Lukas
Han Ting
Henikoff Jorja G
Henz Stefan R
Hinrichs Angie
Holster Heather
Hyman Tony
Iniguez A Leo
Janette Judith
Jensen Morten
Kato Masaomi
Kent W James
Kephart Ellen
Khivansara Vishal
Khurana Ekta
Kim John K
Kolasinska-Zwierz Paulina
Lai Eric C
Latorre Isabel
Leahey Amber
Lewis Suzanna
Lloyd Paul
Lochovsky Lucas
Lowdon Rebecca F
Lubling Yaniv
Lyne Rachel
MacCoss Michael
Mackowiak Sebastian D
Mangone Marco
McKay Sheldon
Mecenas Desirea
Merrihew Gennifer
Miller David M
Muroyama Andrew
Murray John I
Ooi Siew-Loon
Pham Hoang
Phippen Taryn
Preston Elicia A
Rajewsky Nikolaus
Rätsch Gunnar
Rosenbaum Heidi
Rozowsky Joel
Rutherford Kim
Ruzanov Peter
Sarov Mihail
Sasidharan Rajkumar
Sboner Andrea
Scheid Paul
Segal Eran
Shin Hyunjin
Shou Chong
Slack Frank J
Slightam Cindie
Smith Richard
Spencer William C
Stinson E O
Taing Scott
Takasaki Teruaki
Vafeados Dionne
Voronina Ksenia
Wang Guilin
Washington Nicole L
Whittle Christina M
Wu Beijing
Yan Koon-Kiu
Zeller Georg
Zha Zheng
Zhong Mei
Zhou Xingliang
modENCODE Consortium
Ahringer Julie
Strome Susan
Gunsalus Kristin C
Micklem Gos
Liu X Shirley
Reinke Valerie
Kim Stuart K
Hillier LaDeana W
Henikoff Steven
Piano Fabio
Snyder Michael
Stein Lincoln
Lieb Jason D
Waterston Robert H
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Article Info
Journal
Science (New York, N.Y.)
Abbr.
Science
ISSN
1095-9203
DOI
10.1126/science.1196914
Email
modencode.worm.pi@gersteinlab.org
Published
2010-12-24
Epub
2010-00-22
Pages
1775-87
Language
English
Region
United States
NLM ID
0404511
PMCID
PMC3142569
Subset
IM
Grants
NIGMS NIH HHS · R01 GM088565-03 · United States
Wellcome Trust · 054523 · United Kingdom
Howard Hughes Medical Institute · United States
NHGRI NIH HHS · U01 HG004270 · United States
NIGMS NIH HHS · R01 GM088565 · United States
NIGMS NIH HHS · R01GM088565 · United States
Corrections
ErratumIn
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CommentIn
PMID: 21177977
CommentIn
PMID: 21245826
CommentIn
PMID: 21473021
External Links
PubMed source DOI: 10.1126/science.1196914 PMC Full Text View journal details
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