Journal
SCIENCE
Volume 330, Issue 6012, Pages 1775-1787Publisher
AMER ASSOC ADVANCEMENT SCIENCE
DOI: 10.1126/science.1196914
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Funding
- NHGRI of the NIH [R01GM088565]
- Muscular Dystrophy Association
- Pew Charitable Trusts
- Helmholtz-Alliance on Systems Biology (Max Delbruck Centrum Systems Biology Network)
- Wellcome Trust
- William H. Gates III Endowed Chair of Biomedical Sciences
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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.
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