The goal of this proposal is to obtain a coordinated and comprehensive picture of the transcribed regions and factors that regulate or affect transcriptional activity in the genomic regions selected as part of the ENCODE project. This proposal builds on our experience in genomic analysis using chromosome 22 tiling arrays. We will first prepare and test several types of genomic DNA arrays that tile the unique sequences of the ENCODE regions. We will then identify transcription coding segments in these regions using several RNA sources. In conjunction with the coding region identification, we will map the binding sites for at least 150 sequence-specific or general transcription factors, chromatin modifying or remodeling factors, and transcription related histone modifications using chromatin immunoprecipiation and probing of the arrays (ChiP chip). In parallel, we will explore the status of DNA methylation through this region. Our results will be made publicly accessible in a comprehensive web database and we will interrelate our genomic annotations with those determined by other groups. We expect these pilot studies of the ENCODE region to be scaleable to the analysis of the entire human genome.
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