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

Abstract

Methyl-CpG-binding protein 2 (MeCP2) is an epigenetic reader essential for neuronal function, but how it binds DNA methylation within chromatin is unclear. Using designer nucleosomes we observe that MeCP2 preferentially engages DNA methylation positioned at multiple sites around the nucleosome. Surprisingly, MeCP2 can bind methylated DNA in bent, histone-contacting core nucleosomal DNA. However, this activity requires additional DNA linker interactions, using MeCP2 regions beyond its canonical methyl binding domain. We mapped a novel DNA-binding region in MeCP2 required for this function. Furthermore, histone H1 antagonises the MeCP2-nucleosome interaction by competing for linker DNA. Overall, this reveals that MeCP2 combines nonspecific but essential interactions with linker DNA to aid specific binding to nucleosomal methylated DNA, independent of nucleosome structure. Our findings reveal a novel contribution to full MeCP2 function, and mechanistic insight into how this clinically important protein interacts with chromatin.