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

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.

Pubmed ID: 21177976

Authors

  • 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

Journal

Science (New York, N.Y.)

Publication Data

December 24, 2010

Associated Grants

  • Agency: Wellcome Trust, Id: 054523
  • Agency: NIGMS NIH HHS, Id: R01 GM088565
  • Agency: NIGMS NIH HHS, Id: R01 GM088565-03
  • Agency: NIGMS NIH HHS, Id: R01GM088565
  • Agency: Howard Hughes Medical Institute, Id:
  • Agency: Wellcome Trust, Id:

Mesh Terms

  • Animals
  • Caenorhabditis elegans
  • Caenorhabditis elegans Proteins
  • Chromatin
  • Chromosomes
  • Computational Biology
  • Conserved Sequence
  • Evolution, Molecular
  • Gene Expression Profiling
  • Gene Expression Regulation
  • Gene Regulatory Networks
  • Genes, Helminth
  • Genome, Helminth
  • Genomics
  • Histones
  • Models, Genetic
  • Molecular Sequence Annotation
  • RNA, Helminth
  • RNA, Untranslated
  • Regulatory Sequences, Nucleic Acid
  • Transcription Factors