Assessing methylation levels - not CpG specific but across CpG island (Nov/11/2004 )
Does anyone have a suggestion for a way to assess quantitatively the methylation levels across a certain genomic region (e.g. a given CpG island)? I am not interested in specific CpG sites, but want to know the amount of methylation in a given genomic region. I am guessing that amplifying the region using PCR and then digesting with methylation-specific enzymes may work....but can this give a quantitative reading?
I don't know any current methods that can work that way, but I am certain you can not PCR your DNA and then detect methylation because after PCR, all 5m cytosines will become cytosine. I am currently developing a method which can meaure regional methylation levels. It works in a way similar to ChIP. You first sonicate your DNA into small pieces, and then precipitate it with a 5-methyl-cytosine antibody. After washing, amplify precipitated DNA by genomic PCR. The intensity of the PCR band will tell you the methylation level.
Sorry, I meant to say bisulfite treat before the PCR and then digest. But your proposed method sounds interesting - do you have any references or a published protocol we could look at?
The method I mentioned is under development and has not been published yet.