Protocol

Microarray Analysis of the Physical Genome

Volume 556 of the series Methods in Molecular Biology™ pp 141-153

Date:

Methylation Analysis by DNA Immunoprecipitation (MeDIP)

  • Emily A. VucicAffiliated withBritish Columbia Cancer Research Centre
  • , Ian M. WilsonAffiliated withBritish Columbia Cancer Research Centre
  • , Jennifer M. CampbellAffiliated withBritish Columbia Cancer Research Centre
  • , Wan L. LamAffiliated withBritish Columbia Cancer Research Centre

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Abstract

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 words

Epigenetics DNA methylation hypermethylation hypomethylation CpG islands methylated DNA immunoprecipitation epigenetic methods and technologies array-based methylation analysis MeDIP aCGH