DNA Methylation Induces a More Compact and Rigid Nucleosome Structure

Abstract

Cytosine methylation in CpG dinucleotides is an important epigenetic modification in eukaryotes with roles in regulating a variety of genome transactions. There have been many studies of DNA methyltransferases and methyl-CpG binding proteins elucidating their roles in various genome activities. However, less is known about how methylated CpGs directly affect nucleosome structure. We implemented a single molecule FRET coupled with anisotropy that can simultaneously measure dynamic distance changes and flexibility of the two ends of a nucleosomal DNA. Using the method, we monitored effects of DNA methylation on the structure of mononucleosomes. In the absence of methylation, most nucleosomes displayed two low FRET states (FRET efficiency <0.5). When treated with a CpG methyltansferase, we observed a >40-fold increase in the number of nucleosomes that made excursions to a high FRET state (FRET efficiency >0.7). Moreover, based on the anisotropy measurements, a stronger association between the DNA ends and the histone octamer was observed from the nucleosomes in the high FRET state. The increased FRET and anisotropy after DNA methylation strongly suggest a more compact and rigid nucleosomal structure and provide a basic biophysical understanding of how DNA methylation may contribute to the formation of a repressive and transcriptionally inactive chromatin structure.