Methylation status analysis of non CpG sites. - (Mar/26/2014 )
I want to know how we can check the non CpG methylation status of a gene. Can MSP be used for this purpose?
Yes. It will pick up any methylated cytosine.
it is tricky to use MSP to check non-cpg C methylation since there is not many place you can put your primers in without including a non-cpg C.
You can use primers that are degenerate (have a Y instead of a C or T, and an R instead of a G or A).
If a software for designing MSP or BSP primers shows: "lack of CpG islands in the promoter" of studied gene, how can be determined methylation of such gene ?