Age related disorder in DNA methylation patterns underlies epigenetic clock signals, but displays distinct responses to epigenetic rejuvenation events

Abstract Changes in DNA methylation with age are observed across the tree of life. The stereotypical nature of these changes can be modeled to produce epigenetic clocks capable of predicting biological age with unprecedented accuracy. Despite the predictive ability of epigenetic clocks, the underlying processes that produce clock signals are not resolved but are hypothesized to be rooted in stochastic processes leading to an erosion in the epigenetic landscape. Here, we test this hypothesis using a novel computational approach for measuring disorder in DNA methylation patterns across the epigenome. We find that loci comprising conventional epigenetic clocks are enriched in regions that both accumulate and lose disorder with age, suggesting a direct link between DNA methylation disorder and epigenetic clock(definition) signals. Across the murine lifespan, disorder accumulates in Polycomb Repressive Complex 2 target genes and decreases in CTCF and transcription factor binding sites, resulting in genomic hotspots of age-related epigenetic disorder. We further investigate the connections between age-related changes in disorder and epigenetic clock signals by comparing the influences of development, lifespan interventions, and cellular dedifferentiation using a series of newly developed epigenetic clocks based on regional disorder, average methylation states, and commonly used measures of entropy. We identify both common responses as well as critical differences between canonical epigenetic clocks and those based on regional disorder, demonstrating a fundamental decoupling of epigenetic aging processes. Collectively, this work identifies key linkages between epigenetic disorder and epigenetic clock signals, and simultaneously demonstrates the multifaceted nature of epigenetic aging in which stochastic processes occurring at non-random loci produce predictable outcomes.