Differential dynamics specify MeCP2 function at methylated DNA and nucleosomes (Chua et al., NSMB 2024)
Working model for MeCP2 functioning at chromatin. MeCP2 rapidly scans unmethylated bare DNA regions and becomes trapped upon encountering methyl-DNA sites, where it performs methylation-dependent activities such as recruiting transcriptional co-repressors. In contrast, MeCP2 stably engages with nucleosomes and protects them from mechanical perturbation. This interaction also facilitates the recruitment of binding partners to nucleosome sites. Finally, nucleosomes capture the majority of MeCP2 molecules in the nucleus, leaving only a fraction of free proteins to bind bare DNA. This provides a plausible explanation for why even a modest change in the MeCP2 level can drastically alter its regulatory function. Therefore, MeCP2 plays both direct and indirect roles in chromatin organization and gene regulation dependent on its differential dynamics at various regions of the genome.
Methyl-CpG-binding protein 2 (MeCP2) is an essential chromatin-binding protein whose mutations cause Rett syndrome (RTT), a leading cause of monogenic intellectual disabilities in females. Targeted therapeutic intervention against RTT is still lacking, in large part due to insufficient understanding of the heterogenous molecular behavior of MeCP2. Here we use smCFFM to directly visualize the dynamics and distribution of MeCP2 on DNA and chromatin. We discover that MeCP2 exhibits distinct diffusion kinetics when bound to unmethylated and CpG methylated bare DNA and exploits these differences to fulfill methylation-specific activities such as the recruitment of co-repressors. We show that on chromatinized DNA, nucleosomes titrate MeCP2 away from bare DNA, modulating its genomic distribution. MeCP2 is also found to stabilize nucleosomes from mechanical perturbation. Moreover, we show that RTT mutations differentially alter the biophysical properties of MeCP2-chromatin interaction, explaining their heterogeneous clinical phenotypes in disease. Our work reveals the molecular mechanisms underlying MeCP2’s DNA methylation- and nucleosome-dependent functions as well as dosage sensitivity, demonstrating its multifaceted regulation of chromatin structure and gene expression.