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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 \u00b17, 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.<\/jats:p>","DOI":"10.64898\/2026.09.08.750195","type":"posted-content","created":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T15:55:21Z","timestamp":1789142121000},"source":"Crossref","is-referenced-by-count":0,"title":["Structures of MeCP2 bound to nucleosomes reveal distinct mechanisms of Rett syndrome mutations"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8344-6531","authenticated-orcid":false,"given":"Liqi","family":"Yao","sequence":"first","affiliation":[{"name":"Department of Biochemistry, University of Colorado Boulder, Boulder, CO, 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