A comprehensive map of the ageing blood methylome

Abstract

During ageing, the human methylome exhibits both differential (i.e. change in mean) and variable (i.e. change in variance) shifts, along with a general rise in entropy. However, it remains unclear whether DNA methylation sites that increasingly diverge between people (i.e. variably methylated positions (VMPs)) are distinct from those undergoing changes in mean methylation levels (i.e. differentially methylated positions (DMPs)), which changes drive entropy, how they contribute to epigenetic age measured by epigenetic clocks, and whether cell type heterogeneity plays a role in these alterations. To address these questions, we conducted a comprehensive analysis using > 32,000 human blood methylomes from 56 datasets (age range = 6-101 years). Our findings revealed an unprecedented proportion of the blood methylome that is differentially methylated with age (48% DMPs; FDR< 0.005) and variably methylated with age (37% VMPs; FDR< 0.005), with many sites overlapping between the two groups (59% of DMPs are VMPs). We observed that bivalent and Polycomb regions become increasingly methylated and divergent between individuals, while quiescent regions lose methylation in a more homogeneous manner between individuals. Unexpectedly, both chronological and biological clocks, but not pace-of-aging clocks, show a strong enrichment for those CpGs that accrue both mean and variance changes during aging. Furthermore, we uncovered that it is the accumulation of DMPs shifting towards a methylation fraction of 50% that drive the increase in entropy, resulting in an overall smoothening of the epigenetic landscape. However, approximately a quarter of DMPs oppose this direction of change, exhibiting anti-entropic effects. While DMPs were mostly unaffected by changes in cell type composition, VMPs and entropy measurements showed moderate sensitivity to such alterations. This investigation represents the largest to date of genome-wide DNA methylation changes and ageing in a single tissue, offering valuable insights into primary molecular changes that hold meaning for chronological and biological ageing.