Methylation status analysis of non CpG sites. - (Mar/26/2014 )

Hi.

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).

Hi

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 ?

Robert on Tue May 13 13:34:31 2014 said:

Hi

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 ?

Hi Robert, 

I encountered the same problem as you and I'm stuck at this stage. Have you found any solution regarding to this? Or is it I'm putting the wrong sequence for promoter of my target gene? Thanks 

You need to understand what the software is doing, and not blindly rely on software that you don't understand.