RESUMEN

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.

Asunto(s)

Caenorhabditis elegans/genética , Cromosomas , Perfilación de la Expresión Génica , Regulación de la Expresión Génica , Genoma de los Helmintos , Anotación de Secuencia Molecular , Animales , Caenorhabditis elegans/crecimiento & desarrollo , Caenorhabditis elegans/metabolismo , Proteínas de Caenorhabditis elegans/genética , Proteínas de Caenorhabditis elegans/metabolismo , Cromatina/genética , Cromatina/metabolismo , Cromatina/ultraestructura , Cromosomas/genética , Cromosomas/metabolismo , Cromosomas/ultraestructura , Biología Computacional/métodos , Secuencia Conservada , Evolución Molecular , Redes Reguladoras de Genes , Genes de Helminto , Genómica/métodos , Histonas/metabolismo , Modelos Genéticos , ARN de Helminto/genética , ARN de Helminto/metabolismo , ARN no Traducido/genética , ARN no Traducido/metabolismo , Secuencias Reguladoras de Ácidos Nucleicos , Factores de Transcripción/genética , Factores de Transcripción/metabolismo