A key goal in characterizing the human genome is to acquire a complete catalog of chromatin regulatory elements and sequence determinants of chromatin state. In this application, we propose to undertake a large-scale project to map the genomewide locations of >35 histone modifications and related proteins in >20 human cell types by coupling chromatin IP with massive-throughput sequencing on the Solexa platform. Our preliminary data demonstrate that this approach is highly accurate and a major advance over existing technologies in terms of cell requirements, genome coverage, throughput and cost-effectiveness. A sequencing pipeline will be applied to generate more than 500 genomewide datasets of chromatin structure by sequencing >1000 samples. A computational pipeline will then convert the sequencing reads into high resolution, genomewide maps that can be visualized in genome browsers and used for downstream analysis. Comparative genomic analysis and motif-finding tools will be applied to classify genomic sites based on associated chromatin structures and to identify underlying sequence determinants. Cell and molecular biology methods will be used to validate inferred functions for a representative subset of discovered elements. Chromatin regulation is extensively implicated in many aspects of human development and disease. In particular, cancer cells may universally exhibit aberrant chromatin states. The proposed systematic identification and characterization of chromatin regulatory elements in the human genome will offer unprecedented insight into the structure and function of chromatin, and provide an invaluable resource for investigators in chromatin, genomics, cancer and many other fields of research. All data collected in the context of the proposed project will be made available pre-publication to the greater scientific community once reliability has been confirmed.
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