Fig. 5.

Highly methylated promoters are not bound by MeCP2. (Center) The 1,524 promoters with the highest levels of MeCP2 binding identified in Fig. 4 were compared with the 4,062 most highly methylated promoters, revealing an overlap of only 91 genes. Therefore, only 2.2% of highly methylated promoters were bound by MeCP2, and only 6.0% of MeCP2-bound promoters were highly methylated. (Left and Right) Two replicate MeDIP assays were performed on genomic DNA from SH-SY5Y cells (Right) differentiated identically to those used for MeCP2 promoter ChIP–chip (Left) and expression profiling (see Materials and Methods). The median top 5,000 log2 promoter signals were selected from each experiment, and, after the removal of duplicate promoters, the overlap produced 4,062 genes in common.