Comprehensive Identification of Active Functional Elements in Human Chromatin

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DESCRIPTION (provided by applicant): The goal of this proposal is to identify at high resolution all active gene regulatory elements in the human genome among cell types representative of most human tissues. We will accomplish this goal by identifying regions of open chromatin with two independent and complementary methods: DNasel hypersensitivity and Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE), combined with single-nucleosome mapping and chromatin immunoprecipitation (ChIP) for selected regulatory factors. The immediate benefit of success will be a high-quality public atlas of the human DNA regulatory elements that are likely to be active in each cell type. Identification of open chromatin regions has been one of the most accurate and robust methods to identify functional promoters, enhancers, silencers, insulators, and locus control regions in mammalian cells. A principal advantage of an open chromatin approach is that all potential sites in the genome are simultaneously assayed in an unbiased manner. DNasel hypersensitivity and FAIRE interrogate chromatin by entirely different underlying mechanisms, and therefore represent independent, cross-validating assessments of chromatin state. In addition, we will perform single-nucleosome mapping in selected cell types as an independent direct biochemical verification of open chromatin regions. For a selected subset of cell-types, we will further annotate open chromatin regions with respect to their biological activity by determining the binding location of proteins that mark transcription start sites, transcriptional units, insulators, or have broad regulatory function. The Aims of this proposal are 1) to identify all regions of open chromatin in 40 cell types by DNasel and FAIRE analyses, and 2) determine the biological function of open chromatin regions by ChIP and nucleosome mapping. To accomplish these Aims, we have assembled a team of five researchers who are leaders in their respective fields and who have contributed significantly to the ENCODE pilot project. Furthermore, we have developed a streamlined pipeline, which has been used to generate high quality whole-genome data from a number of cell types.