Whole-genome analysis of DNA methylation in alcohol dependence

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DESCRIPTION (provided by applicant): Alcoholism is a chronic relapsing disorder characterized by compulsive use of alcohol and impairment in an individual's social and occupational functioning. Mounting evidence suggests that epigenetic mechanisms may contribute to the neuroadaptation that are involved in alcohol dependence and tolerance. However, a more thorough investigation of epigenetic alterations induced by alcohol dependence and withdrawal is needed to understand the role of epigenetic mechanisms in alcohol's long-lasting actions. As part of our ongoing effort to identify genes involved in alcohol-induced adaptations, we have observed coordinated changes in DNA methylation and gene expression in models of alcohol exposure both with one-gene-at-a-time and high-throughput approaches. These preliminary results suggest that changes in DNA methylation are likely to be a key mechanism of alcohol's effects and motivate the proposed genome-wide survey of patterns of methylation in alcohol dependence and withdrawal. The introduction of new strategies and tools such as high-density DNA arrays designed to investigate chromatin regulation on a genome-wide scale now makes it possible to systematically analyze epigenetic alterations. While DNA methylation is not the only epigenetic modification, it is the only covalent modification of DNA in higher eukaryotes and a large body of evidence has established its role in neurological and peripheral organ disease. Since Affymetrix does not produce and is not planning to produce tiling arrays for the rat genome, in the present application we will be limited to mice. This proposal is aimed at profiling changes in DNA methylation on a global basis in a mouse model of alcohol dependence, withdrawal and dependence-induced drinking. To this aim, we will use the recently released generation of Affymetrix GeneChip(r) microarrays denominated 'tiling' because their probes are designed to cover either the entire promoter region of all known and putative genes in the genome with a single microarray or the entire genome in an unbiased way with a set of microarrays. We will use methylcytosine-immunoprecipitation (mCIP) as the primary means to detect differential DNA methylation. It is expected that a systematic elucidation of the role of altered DNA methylation in alcohol-induced gene expression changes will foster the identification of new pathogenic hypotheses and therapeutic targets for the prevention and treatment of alcohol abuse.