Binding of the Rett syndrome protein, MeCP2, to methylated and unmethylated DNA and chromatin

Abstract

Methylated CpG Binding Protein 2 (MeCP2) is a nuclear protein named for its ability to selectively recognize methylated DNA. Much attention has been focused on understanding MeCP2 structure and function in the context of its role in Rett syndrome, a severe neurodevelopmental disorder that afflicts one in 10,000-15,000 girls. Early studies suggested a connection between DNA methylation, MeCP2, and establishment of a repressive chromatin structure at specific gene promoters. However, it is now recognized that MeCP2 can both activate and repress specific genes depending on the context. Likewise, in the cell, MeCP2 is bound to unmethylated DNA and chromatin in addition to methylated DNA. Thus, to understand the molecular basis of MeCP2 functionality, it is necessary to unravel the complex interrelationships between MeCP2 binding to unmethylated and methylated regions of the genome. MeCP2 is unusual and interesting in that it is an intrinsically disordered protein, that is, much of its primary sequence fails to fold into secondary structure and yet is functional. The unique structure of MeCP2 is the subject of the first section of this article. We then discuss recent investigations of the in vitro binding of MeCP2 to unmethylated and methylated DNA, and the potential ramifications of this work for in vivo function. We close by focusing on mechanistic studies indicating that the binding of MeCP2 to chromatin results in compaction into local (secondary) and global (tertiary) higher order structures. MeCP2 also competes with histone H1 for nucleosomal binding sites. The recent finding that MeCP2 is found at near stoichiometric levels with nucleosomes in neuronal cells underscores the multiple modes of engagement of MeCP2 with the genome, which include the cooperative tracking of methylation density.

Figure 1

Domain organization and properties of human MeCP2. Shown are the six MeCP2 domains defined based on trypsin digestion (10). Listed at the bottom are the residue numbers at the domain junctions. Red bars along the bottom are regions predicted by PONDR-VLXT to be disordered, while green bars are regions of predicted order (14). Blue bars along the top are sites of predicted MoRFs (15). The domains with yellow stars above them bind unmethylated DNA with high affinity in vitro (14). The orange star above the MBD highlights that this domain binds methylated DNA with high affinity and unmethylated DNA with lower affinity (14, 16).