A DNA methylation-based clock for age estimates in the wood mouse (Apodemus sylvaticus)

Abstract

Although short-lived, easily manipulated wild systems could be useful for studying ageing, developing epigenetic clocks for them is challenging because their chronological age is often unknown. Here, we present a multi-tissue epigenetic clock for the wood mouse (Apodemus sylvaticus) that was developed in a laboratory colony and then applied to wild individuals. We used the mammalian methylation array to profile CpG sites across highly conserved stretches of DNA in blood, ear, spleen, and liver of colony-reared mice. We trained an elastic net model with Leave-One-Out-Cross Validation (LOOCV), which identified 77 key age-related CpG sites as being highly predictive of chronological age (r = 0.99; MAE = 3.29 days). Upon validation in an independent dataset, the LOOCV clock predicted age with an MAE of 54.68 days. Epigenome-wide association study and Genomic Regions Enrichment of Annotations Tool analysis of age-related CpGs primarily revealed hypermethylation of promoter regions linked to development and transcription factor activity, particularly via changes in methylation of PRC2 targets sites. Critically, our epigenetic clock was able to predict broad age categories in wild mice and increased over chronological time in 75% of individuals. This and similar clock developments in other short-lived wild systems, that can be bred in captivity, will enhance our ability to conduct experimental manipulations of ageing in ecology and evolution.