Mapping regulatory information throughout the human genome is essential for both determining the function of the human genome and for understanding human development and disease. We propose to establish a high throughput production facility to identify the DNA binding sites for transcription factors and chromatin modifying proteins in human cells. Transcription factor targets, chromatin modifications and modifying enzymes will be mapped across the genome using chromatin immunoprecipitation experiments. This binding information will be validated and analyzed to ensure that it is of high quality and then compared to other genomic annotations. Our three aims are: 1) To establish a production facility for mapping targets of transcription factors. The pipeline will consist of five components: a) cell preparation, b) antibody validation and chromatin immunoprecipitation, c) DNA target analysis, d) target validation and e) sample tracking and databases. 2) To use the pipeline to map targets of 600 transcription factors, chromatin modifications and chromatin modifying enzymes in at least two major cell lines (HeLa S3 and HepG2), and targets of other factors in additional cell lines. 3) To maintain our results in a database and also make them accessible through public databases. We will interrelate our genomic annotations with those determined by other groups (particularly those from the ENCODE consortium), focusing on correlating patterns of transcription-factor binding and chromatin modifications with gene expression. We expect this project to contribute significant information to the identification of regulatory and functional elements in the human genome.
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