What is the effect of CpG content on the MeDIP reaction?
Studies by Weber et al. (Nat. Genet. 2005, 37(8):853-862) have shown that the more more methylated CpG dinucleotides within a given fragment, the more DNA that is immunoprecipitated. The increase immunoprecipitated material is due to the 5-methylcytidine antibody having more available epitopes (methylated CpG).