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. (December 2010) Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project. Science, 330 (6012). pp. 1775-1787. ISSN 0036-8075
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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: | December 2010 |
| Date Deposited: | 07 Oct 2011 13:51 |
| Last Modified: | 02 Oct 2019 15:38 |
| PMCID: | PMC3142569 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/15420 |
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