Methyl-binding domain. Methylated CpG recognition is often mediated by MBD-containing
proteins. MBD proteins can recruit HDACs and histone methyltransferases to sites of CpG meth-
ylation, leading to local chromatin rearrangement. These relatively small domains that consist of a twisted beta sheet and alpha helix scan DNA’s major grove and detect CpG sites through a pair
of Arg residues that chelate the complimentary guanine rings (20). The crystal structure shown in
Figure 2 is that of methyl CpG–binding protein 2 (MeCP2) that binds dimethyl CpG sites 50-fold
more tightly than unmethylated sites and in which inactivating mutations cause the neurodevel-
opmental disorder Rett syndrome (21). The mC groups are detected via interactions with Tyr123
and Arg133, residues conserved in the MBD family of proteins with the exception of MBD3, which
does not recognize CpG methylation and in which the equivalent Tyr residue is mutated. Perhaps
not surprisingly, the stabilization of Arg133 by Glu137 is important for MeCP2’s function, and
although the equivalent glutamic acid is present in MBD1, which also binds dimethyl CpG sites
strongly, it is mutated in MBD2–4, which have weaker affinities. Mutations of Glu137 in MeCP2
cause mental retardation, X-linked, syndromic 13 rather than Rett syndrome (22). Interestingly,
oxidation of one mC to hmC reduces the affinity of MeCP2, MBD1, and MBD2 for the CpG site,
whereas dihydroxymethylation erases all selectivity over unmethylated CpGs.