While the role of genetic events of DNA mutations in gene expression changes is well established, increasing evidence suggests that epigenetic changes of DNA methylation and histone modifications play important role in the regulation of gene expression. DNA methylation is the most frequent epigenetic alteration observed in mammalian genomes, and it frequently mediates transcriptional repression. Various methods are available for detection of DNA methylation changes. Methylation Sensitive-Random Amplified Polymorphic DNA-Polymerase Chain Reaction (MS-RAPD-PCR) is a restriction enzyme digestion and PCR-based method for analysis of DNA methylation changes. This method is cost-effective, requires simple and basic instrumentation, and therefore can easily be performed in any laboratory with basic setup with a regular DNA thermal cycler and DNA gel electrophoresis system. Other advantages of this method over other methods for DNA methylation analysis are that it requires very less DNA amount and can screen DNA methylation changes globally at genome wide level with high sensitivity. This method has been successfully used to detect DNA methylation changes associated with various human diseases including cancer. This chapter describes the detailed experimental protocol for MS-RAPD-PCR.
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