Integrative analysis of the caenorhabditis elegans genome by the modENCODE project

Item Type:	Article
Title:	Integrative analysis of the caenorhabditis elegans genome by the modENCODE project
Creators Name:	Gerstein, M.B. and Lu, Z.J. and Van Nostrand, E.L. and Cheng, C. and Arshinoff, B.I. and Liu, T. and Yip, K.Y. and Robilotto, R. and Rechtsteiner, A. and Ikegami, K. and Alves, P. and Chateigner, A. and Perry, M. and Morris, M. and Auerbach, R.K. and Feng, X. and Leng, J. and Vielle, A. and Niu, W. and Rhrissorrakrai, K. and Agarwal, A. and Alexander, R.P. and Barber, G. and Brdlik, C.M. and Brennan, J. and Brouillet, J.J. and Carr, A. and Cheung, M.S. and Clawson, H. and Contrino, S. and Dannenberg, L.O. and Dernburg, A.F. and Desai, A. and Dick, L. and Dose, A.C. and Du, J. and Egelhofer, T. and Ercan, S. and Euskirchen, G. and Ewing, B. and Feingold, E.A. and Gassmann, R. and Good, P.J. and Green, P. and Gullier, F. and Gutwein, M. and Guyer, M.S. and Habegger, L. and Han, T. and Henikoff, J.G. and Henz, S.R. and Hinrichs, A. and Holster, H. and Hyman, T. and Iniguez, A.L. and Janette, J. and Jensen, M. and Kato, M. and Kent, W.J. and Kephart, E. and Khivansara, V. and Khurana, E. and Kim, J.K. and Kolasinska-Zwierz, P. and Lai, E.C. and Latorre, I. and Leahey, A. and Lewis, S. and Lloyd, P. and Lochovsky, L. and Lowdon, R.F. and Lubling, Y. and Lyne, R. and Maccoss, M. and Mackowiak, S.D. and Mangone, M. and McKay, S. and Mecenas, D. and Merrihew, G. and Miller, D.M. and Muroyama, A. and Murray, J.I. and Ooi, S.L. and Pham, H. and Phippen, T. and Preston, E.A. and Rajewsky, N. and Raetsch, G. and Rosenbaum, H. and Rozowsky, J. and Rutherford, K. and Ruzanov, P. and Sarov, M. and Sasidharan, R. and Sboner, A. and Scheid, P. and Segal, E. and Shin, H. and Shou, C. and Slack, F.J. and Slightam, C. and Smith, R. and Spencer, W.C. and Stinson, E.O. and Taing, S. and Takasaki, T. and Vafeados, D. and Voronina, K. and Wang, G. and Washington, N.L. and Whittle, C.M. and Wu, B. and Yan, K.K. and Zeller, G. and Zha, Z. and Zhong, M. and Zhou, X. and Ahringer, J. and Strome, S. and Gunsalus, K.C. and Micklem, G. and Liu, X.S. and Reinke, V. and Kim, S.K. and Hillier, L.W. and Henikoff, S. and Piano, F. and Snyder, M. and Stein, L. and Lieb, J.D. and Waterston, R.H.
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.
Keywords:	Caenorhabditis Elegans Proteins, Chromatin, Chromosomes, Computational Biology, Conserved Sequence, Gene Expression Profiling, Gene Expression Regulation, Gene Regulatory Networks, Genetic Models, Genomics, Helminth Genes, Helminth Genome, Helminth RNA, Histones, Molecular Evolution, Molecular Sequence Annotation, Nucleic Acid Regulatory Sequences, Transcription Factors, Untranslated RNA, Animals, Caenorhabditis Elegans
Source:	Science
ISSN:	0036-8075
Publisher:	American Association for the Advancement of Science
Volume:	330
Number:	6012
Page Range:	1775-1787
Date:	24 December 2010
Official Publication:	https://doi.org/10.1126/science.1196914
PubMed:	View item in PubMed

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