MeCP2 requires interactions with nucleosome linker DNA to read chromatin DNA methylation

Methyl-CpG-binding protein 2 (MeCP2) is a clinically important epigenetic reader that is essential for neuronal function, but how it binds methylated DNA within the protein-DNA complexes that comprise chromatin is unclear. Using designer nucleosomes, we observe that MeCP2 is able to engage methylated DNA at multiple sites on the nucleosome surface. Surprisingly, even methyl-cytosine placed in bent, histone-contacting, core nucleosomal DNA can be bound. However, we find that this ability requires interactions with inter-nucleosomal linker DNA. Nucleosome core DNA methylation reading involves regions of MeCP2 beyond its canonical methyl-CpG binding domain and we define a novel DNA-binding region in MeCP2 that is required for this function. We further demonstrate that histone H1 antagonises the MeCP2-nucleosome interactions by competing for linker DNA. Overall, our study reveals that MeCP2 gains access to methylated chromatinised DNA, independent of nucleosome structure, via essential nonspecific interactions with linker DNA.