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.
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| Wortham, Matthew; Guo, Changcun; Zhang, Monica et al. (2014) Chromatin accessibility mapping identifies mediators of basal transcription and retinoid-induced repression of OTX2 in medulloblastoma. PLoS One 9:e107156 |
| Yard?mc?, Galip Gürkan; Frank, Christopher L; Crawford, Gregory E et al. (2014) Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection. Nucleic Acids Res 42:11865-78 |
| Tsumagari, Koji; Baribault, Carl; Terragni, Jolyon et al. (2013) Early de novo DNA methylation and prolonged demethylation in the muscle lineage. Epigenetics 8:317-32 |
| Sheffield, Nathan C; Thurman, Robert E; Song, Lingyun et al. (2013) Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions. Genome Res 23:777-88 |
| Winter, Deborah R; Song, Lingyun; Mukherjee, Sayan et al. (2013) DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types. Genome Res 23:1118-29 |
| Flicek, Paul; Ahmed, Ikhlak; Amode, M Ridwan et al. (2013) Ensembl 2013. Nucleic Acids Res 41:D48-55 |
| Perez-Pinera, Pablo; Kocak, D Dewran; Vockley, Christopher M et al. (2013) RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat Methods 10:973-6 |
| Perez-Pinera, Pablo; Ousterout, David G; Brunger, Jonathan M et al. (2013) Synergistic and tunable human gene activation by combinations of synthetic transcription factors. Nat Methods 10:239-42 |
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