DNA Methylation variability among individuals is related to CpGs cluster density and evolutionary signatures

In recent years, epigenetics has gained a central role in the understanding of the process of natural selection. It is now clear how environmental impacts on the methylome could promote methylation variability with direct effects on disease etiology as well as phenotypic and genotypic variations in evolutionary processes. To identify possible factors influencing inter-individual methylation variability, we studied methylation values standard deviation of 166 healthy individuals searching for possible associations with genomic features and evolutionary signatures.

We analyzed methylation variability values in relation to CpG cluster density and we found a strong association between them (p-value < 2.2 × 10^- 16). Furthermore, we found that genes related to CpGs with high methylation variability values were enriched for immunological pathways; instead, those associated with low ones were enriched for pathways related to basic cellular functions. Finally, we found an association between methylation variability values and signals of both ancient (p-value < 2.2 × 10^- 16) and recent selective pressure (p-value < 1 × 10^- 4).

Our results indicate the presence of an intricate interplay between genetics, epigenetic code and evolutionary constraints in humans.