Impact of DNA methylation on 3D genome structure

Abstract The extreme complexity of epigenetic regulation in higher organisms makes the determination of the intrinsic effect of DNA methylation in chromatin structure and function challenging. We investigated the role of DNA methylation in a simpler model system, budding yeast (Saccharomyces cerevisiae), an organism in which methylation-related machinery is normally absent thus making it a perfect model system to study the intrinsic role of methylation in chromatin structure and function. With this aim, we expressed the murine DNA Methyl Transferases in S. cerevisiae and analyzed the correlation between DNA methylation, nucleosome positioning, gene expression and 3D genome organization. We showed that despite the lack of machinery for positioning and reading of methylation marks, the methylation pattern follows a conserved pattern, the level of DNA methylation being very low at the 5’ end of the gene, and then increasing gradually toward the 3’ end, mimicking mammalian behavior. DNA methylation and gene expression correlate as DNA methylation is lower at the TSS and higher at the TTS in highly expressed genes compared to lowly expressed ones, mimicking again mammalian behavior. We found that methylated DNA is unlikely to be wrapped around nucleosomes, but is concentrated in linkers and nucleosome free regions. DNA methylation increases chromatin condensation in the peri-centromeric region, decreases overall DNA flexibility and favors the heterochromatin state. Taken together, these results demonstrate that methylation intrinsically modulates chromatin structure and function even in the absence of cellular machinery evolved to recognize and process the methylation signal.