DNA Methylation Landscape Reflects the Spatial Organization of Chromatin in Different Cells

The relation between DNA methylation and chromatin structure is still largely unknown. By analyzing a large set of sequencing data, we observed a long-range power law correlation of DNA methylation with cell-class-specific scaling exponents in the range of thousands to millions of base pairs. We showed such cell-class-specific scaling exponents are caused by different patchiness of DNA methylation in different cells. By modeling the chromatin structure using Hi-C data and mapping the methylation level onto the modeled structure, we demonstrated the patchiness of DNA methylation is related to chromatin structure. The scaling exponents of the power law correlation is thus a display of the spatial organization of chromatin. Besides, the local correlation of DNA methylation is associated with nucleosome positioning and different between partially-methylated-domain and non-partially-methylated-domain, suggesting their different chromatin structures at several nucleosomes level. Our study provides a novel view of the spatial organization of chromatin structure from a perspective of DNA methylation, in which both long-range and local correlations of DNA methylation along the genome reflect the spatial organization of chromatin.