MeCP2 is a microsatellite binding protein that protects CA repeats from nucleosome invasion

The Rett syndrome protein MeCP2 was described as a methyl-CpG-binding protein, but its exact function remains unknown. Here we show that MeCP2 is a microsatellite binding protein that specifically recognizes hydroxymethylated CA repeats. Depletion of MeCP2 alters chromatin organization of CA repeats and lamina-associated domains and results in nucleosome accumulation on CA repeats and genome-wide transcriptional dysregulation. The structure of MeCP2 in complex with a hydroxymethylated CA repeat reveals a characteristic DNA shape, with significantly modified geometry at the 5-hydroxymethylcytosine, which is recognized specifically by Arg133, a key residue whose mutation causes Rett syndrome. Our work identifies MeCP2 as a microsatellite DNA binding protein that targets the 5hmC-modified CA-rich strand and maintains genome regions nucleosome-free, suggesting a role for MeCP2 dysfunction in Rett syndrome. Overall design: In this work we have carried out an in-depth study on the role of MeCP2 in mouse embryonic fibroblasts. The use of cell lines WT and KO for MeCP2 combined with biochemical, genomic and structural approaches, has allowed to demonstrate that MeCP2 is a (CA)n microsatellite DNA binding protein. We show that within the MBD family, MeCP2 is the only protein that specifically recognizes and binds to CA repeats, with much stronger affinity as compared to mCG and mCA. While MeCP2 can bind in vitro to modified and non-modified CA repeats, it exhibits impressive selectivity towards hydromethylated CA repeats, which are modified by the enzyme DNMT3A. The modified cytosine, only when located within a CA repeat, serves as a nucleation point for both MeCP2 accumulation and spreading around the repeat, which correlates in turn with nucleosome exclusion. In addition, loss of MeCP2 results in widespread increase in nucleosome density within lamina-associated domains (LADs) and transcriptional dysregulation of CA repeat–enriched genes located outside LADs.