Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project Journal Article
| Authors: | Gerstein, M. B.; Lu, Z. J.; Van Nostrand, E. L.; Cheng, C.; Arshinoff, B. I.; Liu, T.; Yip, K. Y.; Robilotto, R.; Rechtsteiner, A.; Ikegami, K.; Alves, P.; Chateigner, A.; Perry, M.; Morris, M.; Auerbach, R. K.; Feng, X.; Leng, J.; Vielle, A.; Niu, W.; Rhrissorrakrai, K.; Agarwal, A.; Alexander, R. P.; Barber, G.; Brdlik, C. M.; Brennan, J.; Brouillet, J. J.; Carr, A.; Cheung, M. S.; Clawson, H.; Contrino, S.; Dannenberg, L. O.; Dernburg, A. F.; Desai, A.; Dick, L.; Dosé, A. C.; Du, J.; Egelhofer, T.; Ercan, S.; Euskirchen, G.; Ewing, B.; Feingold, E. A.; Gassmann, R.; Good, P. J.; Green, P.; Gullier, F.; Gutwein, M.; Guyer, M. S.; Habegger, L.; Han, T.; Henikoff, J. G.; Henz, S. R.; Hinrichs, A.; Holster, H.; Hyman, T.; Iniguez, A. L.; Janette, J.; Jensen, M.; Kato, M.; Kent, W. J.; Kephart, E.; Khivansara, V.; Khurana, E.; Kim, J. K.; Kolasinska-Zwierz, P.; Lai, E. C.; Latorre, I.; Leahey, A.; Lewis, S.; Lloyd, P.; Lochovsky, L.; Lowdon, R. F.; Lubling, Y.; Lyne, R.; MacCoss, M.; Mackowiak, S. D.; Mangone, M.; McKay, S.; Mecenas, D.; Merrihew, G.; Miller, D. M. 3rd; Muroyama, A.; Murray, J. I.; Ooi, S. L.; Pham, H.; Phippen, T.; Preston, E. A.; Rajewsky, N.; Ratsch, G.; Rosenbaum, H.; Rozowsky, J.; Rutherford, K.; Ruzanov, P.; Sarov, M.; Sasidharan, R.; Sboner, A.; Scheid, P.; Segal, E.; Shin, H.; Shou, C.; Slack, F. J. |
| Article Title: | Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project |
| 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: | nonhuman; genetic analysis; animals; gene expression; gene expression profiling; computational biology; protein; transcription factor; transcription factors; evolution, molecular; gene expression regulation; conserved sequence; chromatin; alternative rna splicing; genomics; x chromosome; binding site; genome; models, genetic; caenorhabditis elegans; untranslated rna; genome, helminth; rna, helminth; rna, untranslated; transcriptome; histones; genetic conservation; chromosomes; nematode; regulatory sequences, nucleic acid; gene regulatory networks; chemical binding; data set; hierarchical system; chromosome arm; histone modification; protozoal genetics; pseudogene; caenorhabditis elegans proteins; genes, helminth; molecular sequence annotation |
| Journal Title: | Science |
| Volume: | 330 |
| Issue: | 6012 |
| ISSN: | 0036-8075 |
| Publisher: | American Association for the Advancement of Science |
| Date Published: | 2010-12-24 |
| Start Page: | 1775 |
| End Page: | 1787 |
| Language: | English |
| DOI: | 10.1126/science.1196914 |
| PUBMED: | 21177976 |
| PROVIDER: | scopus |
| PMCID: | PMC3142569 |
| DOI/URL: | |
| Notes: | --- - "Cited By (since 1996): 21" - "Export Date: 20 April 2011" - "CODEN: SCIEA" - "Source: Scopus" |
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