Hi Sharif, if it's a relatively small region you could just use traditional bisulfite sequencing (Identify a SNP, bisulfite treat your DNA, PCR a product containing the SNP and region thought to be differentially methylated between alleles, clone PCR product into Ecoli vectors and send for Sanger sequencing). This would allow you to identify the different alleles and their methylation status. Alternatively if you have access to a pyrosequencer you can use that to identify allele specific methylation. Hope this helps. 

Hi Hollie,

Thanks for the great answer.

Since we are pressed for time, some people suggested me to digest DNA of different samples with methylation-sensitive restriction enzymes followed by qPCR of the regions of interest, so that I can quantify the differences. Please let me know what you think about this comment.

Sharif

Hi Sharif, I've never tried this personally so I couldn't really comment. I know my lab has previously used methylation sensitive restriction digests, but I tend to see the bisulfite Sanger sequencing method in more recent papers for confirmation. Probably we're in different fields though and preferences for techniques will be different. Good luck anyway. Hollie 

Thank you Hollie.