Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

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., Dose, A. C., Du, J. A., 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. J., Mecenas, D., Merrihew, G., Miller, D. M., 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. J., Shou, C., Slack, F. J., Stein, L. D. (2010) Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project. Science, 330 (6012). pp. 1775-1787. ISSN 0036-8075

URL: https://www.ncbi.nlm.nih.gov/pubmed/21177976
DOI: 10.1126/science.1196914

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.

Item Type: Paper
Uncontrolled Keywords: C. ELEGANS NUCLEOSOME ORGANIZATION TRANSCRIPTION FACTORS RNA-SEQ REVEALS EXPRESSION EMBRYOS NETWORK DNA CHROMATIN
Subjects: organism description > animal > C elegans
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > miRNA
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > miRNA

bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > ncRNA
CSHL Authors:
Communities: CSHL labs > Stein lab
Dolan DNA Learning Center
Depositing User: CSHL Librarian
Date Deposited: 07 Oct 2011 13:51
Last Modified: 02 Mar 2018 19:39
PMCID: PMC3142569
Related URLs:
URI: http://repository.cshl.edu/id/eprint/15420

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