CHIP on Chip array - (Nov/02/2005 )
One more question about this methylation ChIP on chip using anti 5-methylcytosine.
There are multiple CG sites on one piece of DNA (a few hundred base pair long after sherring or digestion), How I could tell the difference if there are only one CG site methylated in the control and more than one CG sites methylated in the treated sample since both of them are going to be pulled down by the antibody?
simple answer is you won't get single nucleotide resolution!
the problem you have raised is valid and can not be resolved by a anti-5mC column. This assay will tell you regions of hypo/hyper methylation and from there you would then use bisulfite sequencing to "soom in" and look at particular regions of possible interest.