Epigenetic Clocks for Mice Based on Age-Associated Regions That are Conserved Between Mouse Strains and Human

Aging of mice can be tracked by DNA methylation changes at specific sites in the genome. In this study, we used the recently released Infinium Mouse Methylation BeadChip to compare such epigenetic modifications in C57BL/6 (B6) and DBA/2J (DBA) mice. We observed marked differences in age-associated DNA methylation in these commonly used inbred mouse strains, indicating that epigenetic clocks for one strain cannot be simply applied to other strains without further verification. In B6 mice age-associated hypomethylation prevailed with focused hypermethylation at CpG islands, whereas in DBA mice CpG islands revealed rather hypomethylation upon aging. Interestingly, the CpGs with highest age-correlation were still overlapping in B6 and DBA mice and included the genes Hsf4, Prima1, Aspa, and Wnt3a. Notably, Hsf4 and Prima1 were also top candidates in previous studies based on whole genome deep sequencing approaches. Furthermore, Hsf4, Aspa, and Wnt3a revealed highly significant age-associated DNA methylation in the homologous regions in human. Subsequently, we used pyrosequencing of the four relevant regions to establish a targeted epigenetic clock that provided very high correlation with chronological age in independent cohorts of B6 (R-2 = 0.98) and DBA (R-2 = 0.91). Taken together, the methylome differs extensively between B6 and DBA mice, while prominent age-associated changes are conserved among these strains and even in humans. Our new targeted epigenetic clock with 4 CpGs provides a versatile tool for other researchers analyzing aging in mice.

Automated summary

The aging of mice can be tracked by changes in DNA methylation at specific sites in the genome. This study compared the epigenetic modifications in C57BL/6 (B6) and DBA/2J (DBA) mice using the Infinium Mouse Methylation BeadChip. It was found that there were significant differences in age-associated DNA methylation between these two commonly used inbred mouse strains, suggesting that epigenetic clocks are not interchangeable without further verification. Certain CpG islands showed hypomethylation in aging B6 mice, while hypomethylation was observed in CpG islands in aging DBA mice. Interestingly, some CpGs showed high age-correlation in both strains and were related to genes Hsf4, Prima1, Aspa, and Wnt3a. These genes also exhibited significant age-associated DNA methylation in homologous regions in humans. A targeted epigenetic clock using pyrosequencing of these four regions was established and showed high correlation with chronological age in independent cohorts of B6 (R-2 = 0.98) and DBA (R-2 = 0.91) mice.