Local CpG density affects the trajectory and variance of age-associated DNA methylation changes

Abstract

Background DNA methylation is an epigenetic mark associated with the repression of gene promoters. Its pattern in the genome is disrupted with age and these changes can be used to statistically predict age with epigenetic clocks. Altered rates of aging inferred from these clocks are observed in human disease. However, the molecular mechanisms underpinning age-associated DNA methylation changes remain unknown. Local DNA sequence can program steady-state DNA methylation levels, but how it influences age-associated methylation changes is unknown. Results We analyze longitudinal human DNA methylation trajectories at 345,895 CpGs from 600 individuals aged between 67 and 80 to understand the factors responsible for age-associated epigenetic changes at individual CpGs. We show that changes in methylation with age occur at 182,760 loci largely independently of variation in cell type proportions. These changes are especially apparent at 8322 low CpG density loci. Using SNP data from the same individuals, we demonstrate that methylation trajectories are affected by local sequence polymorphisms at 1487 low CpG density loci. More generally, we find that low CpG density regions are particularly prone to change and do so variably between individuals in people aged over 65. This differs from the behavior of these regions in younger individuals where they predominantly lose methylation. Conclusions Our results, which we reproduce in two independent groups of individuals, demonstrate that local DNA sequence influences age-associated DNA methylation changes in humans in vivo. We suggest that this occurs because interactions between CpGs reinforce maintenance of methylation patterns in CpG dense regions.

The inactive X chromosome accumulates widespread epigenetic variability with age

“…aVMCs were common in females and rare in males and highly consistent across replication cohorts including in samples of purified monocytes. This suggests that the occurrence of X-linked aVMCs may be cell-intrinsic phenomenon in line with previous reports for autosomal aVMCs [9,12,47]. More commonly studied aDMCs, however, were rare in females and common in males, showed a poor replication rate, in particular in purified monocytes indicating that X-linked aDMCs were frequently driven by changes in blood cell composition with age.…”

“…Table 2 and Fig. 1f), which may be partly explained by earlier observations that aVMCs are less dependent on cell type composition of blood [9,12,47]. In total, 987 females aVMCs (located in 72 DMRs) and 37 males aVMCs replicated in both external data sets (Table 2, Additional File1: Figure S4, Additional File2: Table S4 and Table S5).…”

Probabilistic inference of epigenetic age acceleration from cellular dynamics

“…Further, the genomic locus that correlated strongest with age in Generation Scotland and other studies 6 “cg16867657” ( ELOVL2 ), shows a dynamic range in methylation that is inconsistent with cell-type composition changes at old age. Although these remarks are not conclusive, the hypothesis that changes in cell-type composition cannot account for the observed trends in methylation changes at clock CpG sites has already been convincingly argued in previous studies 28 .…”

Simultaneous mapping of epigenetic inter-haplotype, inter-cell and inter-individual variation via the discovery of jointly regulated CpGs in pooled sequencing data

“…To what extent CpG-poor regions contribute to the functional regulation landscape is hard to say. For instance, these regions are typically of later replication timing and of poorer DNA methylation maintenance (Zhou et al 2018; Petryk et al 2021; Higham et al 2022); thus, relying on such regions for proper genomic regulation may be less robust. On the contrary, the emergence of non-jointly regulated CpGs at intermediately methylated regions at CpG-rich regions is harder to envision.…”