Methylation Analysis by DNA Immunoprecipitation (MeDIP)
Alteration in epigenetic regulation of gene expression is a common event in human cancer and developmental disease. CpG island hypermethylation and consequent gene silencing is observed for many genes involved in a diverse range of functions and pathways that become deregulated in the disease state. Comparative profiling of the methylome is therefore useful in disease gene discovery. The ability to identify epigenetic alterations on a global scale is imperative to understanding the patterns of gene silencing that parallel disease progression. Methylated DNA immunoprecipitation (MeDIP) is a technique that isolates methylated DNA fragments by immunoprecipitating with 5′-methylcytosine-specific antibodies. The enriched methylated DNA can then be analyzed in a locus-specific manner using PCR assay or in a genome-wide fashion by comparative genomic hybridization against a sample without MeDIP enrichment. This article describes the detailed protocol for MeDIP and hybridization of MeDIP DNA to a whole-genome tiling path BAC array.
Key wordsEpigenetics DNA methylation hypermethylation hypomethylation CpG islands methylated DNA immunoprecipitation epigenetic methods and technologies array-based methylation analysis MeDIP aCGH
The authors wish to thank Bradley Coe, Chad Malloff, and Spencer Watson for useful discussion and assistance with this manuscript. This work was supported by funds from the Canadian Institutes for Health Research, Canadian Breast Cancer Research Alliance, Genome Canada/British Columbia, and National Institute of Dental and Craniofacial Research (NIDCR) grant R01 DE15965.
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