The overall aim of this research proposal is to localize and analyze a comprehensive catalogue of transcriptional regulatory elements affecting a broad spectrum of inflammatory response genes, with the goal of identifying genetic determinants of inter-individual variability in inflammatory response. The strategy employed will commence with precise localization of all DNasel hypersensitive sites (HSs) within 100kb of 200 inflammatory response genes for which substantial genetic variation data exist. A novel, tested high-throughput methodology developed by the investigators - Quantitative Chromatin Profiling (QCP) - will be applied to chart the cz's-regulatory landscapes of these gene loci (Specific Aim 1). This approach is capable of creating high-resolution maps of DNasel sensitivity across genomic distances and of sequence-specific localization of DNase HSs. Targeted re-sequencing of 1000 identified HS elements will be undertaken in 96 unrelated individuals to produce a comprehensive catalogue of genetic variation within candidate regulatory regions (Specific Aim 2). The size of the survey sample will permit identification of substantially all (99.99%) alleles of >5% frequency and >87% of 1% frequency alleles. To ensure timely dissemination of both polymorphism and HS data to the scientific community, a robust dedicated web-based project resource will be implemented (Specific Aim 3). It is expected that the results of this study will provide a rich supply of novel information concerning the genetics of gene regulation, and will provide a springboard for subsequent population-based studies surrounding a gene set of major clinical importance.
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