Protocol

Molecular Endocrinology

Volume 590 of the series Methods in Molecular Biology pp 165-176

Date:

Methylated DNA Immunoprecipitation and Microarray-Based Analysis: Detection of DNA Methylation in Breast Cancer Cell Lines

  • Yu-I WengAffiliated withHuman Cancer Genetics Program, The Ohio State University Comprehensive Cancer Center
  • , Tim H.-M. HuangAffiliated withHuman Cancer Genetics Program, The Ohio State University Comprehensive Cancer Center
  • , Pearlly S. YanAffiliated withHuman Cancer Genetics Program, The Ohio State University Comprehensive Cancer Center

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Abstract

The methylated DNA immunoprecipitation microarray (MeDIP-chip) is a genome-wide, high-resolution approach to detect DNA methylation in whole genome or CpG (cytosine base followed by a guanine base) islands. The method utilizes anti-methylcytosine antibody to immunoprecipitate DNA that contains highly methylated CpG sites. Enriched methylated DNA can be interrogated using DNA microarrays or by massive parallel sequencing techniques. This combined approach allows researchers to rapidly identify methylated regions in a genome-wide manner, and compare DNA methylation patterns between two samples with diversely different DNA methylation status. MeDIP-chip has been applied successfully for analyses of methylated DNA in the different targets including animal and plant tissues (1, 2). Here we present a MeDIP-chip protocol that is routinely used in our laboratory, illustrated with specific examples from MeDIP-chip analysis of breast cancer cell lines. Potential technical pitfalls and solutions are also provided to serve as workflow guidelines.

Key words

DNA methylation epigenetics MeDIP-chip microarray cancer