Structures of MeCP2 bound to nucleosomes reveal distinct mechanisms of Rett syndrome mutations
Year: 2026
Type: preprint
Abstract: Methyl-CpG binding protein 2 (MeCP2) is a chromatin-associated regulator essential for neuronal gene regulation, and pathogenic mutations in MeCP2 cause Rett syndrome (RTT). However, the mechanisms governing MeCP2 engagement on chromatin and the effects of RTT mutations on nucleosome interactions remain poorly understood. We determined cryo-EM structures of MeCP2 bound to mono-nucleosomes with or without linker DNA methylation. In the absence of linker DNA methylation, the methyl-CpG binding domain (MBD) engages nucleosomal DNA near superhelical location ±7, whereas a methylated linker CpG redirects MBD to the linker methylation site. Quantitative EMSA, MNase footprinting, and fluorescence polarization show that both MBD and AT-hook regions cooperate to stabilize nucleosome binding, and that six common RTT variants (R133C, T158M, R306C, R168X, R255X, R270X) fall into four mechanistic classes. Loss-of-function truncations progressively weaken binding, whereas missense variants show near-WT DNA affinity. Among the variants, R133C shows near wild-type affinity for naked DNA but loses methylation-directed nucleosome engagement. Our analysis of human neuronal transcriptomic and chromatin occupancy datasets showed that RTT variants R133C and R168X lose CpG-island specificity and redistribute in the genome through distinct biochemical routes. Together, this work establishes a framework linking variant-specific defects in nucleosome binding to chromatin-targeting failure and transcriptional dysregulation in RTT.
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: green
Awards: Bridges to the Baccalaureate Research Training Program at University of Colorado Boulder, Transposon-mediated rewiring of gene regulatory networks, Modernization/operational improvements to basic centrifugation infrastructure of the Shared Instruments Pool in the Department of Biochemistry University of Colorado Boulder, Pacific Northwest Center for Cryo-EM, Structure and Mechanism of Epigenetic Gene Silencing, Predoctoral Training Program in Biological Data Science (BDS)
OpenAlex ID: W7212319431