Methylation SNaPshot: a method for the quantification of site-specific DNA methylation levels.

As the role for epigenetic signals in genome regulation becomes increasingly understood, the ability to accurately measure levels of DNA methylation at individual cytosines throughout the genome is becoming increasingly important. In contrast to traditional methods for the quantification of cytosine methylation, such as cloning and sequencing of PCR fragments amplified from sodium bisulfite-modified DNA, recent developments have created a fast and effective alternative called methylation-sensitive single nucleotide primer extension (Ms-SNuPE). The following protocol outlines the steps necessary to design and perform Ms-SNuPE experiments using the SNaPshot chemistry and associated capillary electrophoresis platforms available through Applied Biosystems.