WGA shows a bias against CpG-rich promoters. (A) The histogram represents the distribution of observed versus expected CpG frequencies for all gene promoters analyzed. Six promoter populations were defined based on their CpG contents (vertical lines). (B-C) Box plots showing the MeDIP signals per promoter from metMeDIP (B) or metMeDIPWGA (C) assays according to the promoter populations defined in (A). (D) Examples of methylation profiles for promoters with low, intermediate and high CpG contents. The presence of a CpG island in the gene promoter shown in example #3 is indicated.