Late-life exercise mitigates skeletal muscle epigenetic aging

Abstract

There are functional benefits to exercise in muscle, even when performed late in life, but the contributions of epigenetic factors to late-life exercise adaptation are poorly defined. Using reduced representation bisulfite sequencing (RRBS), ribosomal DNA (rDNA) and mitochondrial-specific examination of methylation, targeted high-resolution methylation analysis, and DNAge™ epigenetic aging clock analysis with a translatable model of voluntary murine endurance/resistance exercise training (progressive weighted wheel running, PoWeR), we provide evidence that exercise may mitigate epigenetic aging in skeletal muscle. Late-life PoWeR from 22-24 months of age modestly but significantly attenuates an age-associated shift toward promoter hypermethylation. The epigenetic age of muscle from old mice that PoWeR-trained for eight weeks was approximately eight weeks younger than 24-month-old sedentary counterparts, which represents ~8% of the expected murine lifespan. These data provide a molecular basis for exercise as a therapy to attenuate skeletal muscle aging.

Keywords: Rbm10; Timm8a1; Horvath clock; PoWeR; rDNA.

FIGURE 1

Promoter methylation changes in young, aged sedentary, and aged progressive weighted wheel running (PoWeR) muscles. (a) Percent methylation of promoter CpGs (≤ 1 kb from the transcription start site) in gastrocnemius muscle from aged sedentary versus young mice (all sites *FDR<0.05 aged sedentary versus young; aged PoWeR methylation for the same CpGs shown for reference). (b) Promoters of tricarboxylic acid (TCA) cycle genes hypermethylated with age relative to young mice (all CpG sites *FDR<0.05 aged sedentary versus young, aged PoWeR shown for reference; mean +/‐ SEM); inset shows the average methylation of these CpGs in the promoter. (c) Promoter regions of genes hypomethylated in muscle of aged sedentary mice relative to young mice (*FDR<0.05), but not hypomethylated in aged PoWeR mice relative to young mice. (d) Promoter regions of genes hypermethylated in muscle of aged sedentary mice relative to young mice (*FDR<0.05) but not hypermethylated in aged PoWeR mice relative to young mice. (e) Promoter region methylation of Rbm10 and Timm8a1; x‐axis represents the chromosomal position of individual CpG loci in the promoter region of the gene (*FDR<0.05 aged sedentary relative to young mice). N = 5 per group; line at median in (e). Repeated gene names = multiple CpG sites, see supplementary tables for CpG locations. A generalized linear model accounting for all groups was used to determine differential methylation, with a correction for multiple comparisons by controlling false discovery rate (FDR) using the Benjamini–Hochberg method (α = 0.05)

FIGURE 2

Ribosomal DNA (rDNA) methylation and DNAge™ analysis. (a) rDNA CpGs (listed by chromosomal position) hypomethylated in muscle from aged sedentary versus young animals (*FDR<0.05), but not hypomethylated in muscle from aged PoWeR versus young animals. (b) rDNA CpGs (listed by chromosomal position) hypermethylated in muscle from aged sedentary versus young animals (*FDR<0.05), but not hypermethylated in muscle from aged PoWeR versus young animals. (c) DNAge™ analysis of muscle from aged sedentary versus aged PoWeR muscle, analyzed using a directional t‐test. A generalized linear model accounting for all groups was used to determine differential methylation in (a) and (b), with a correction for multiple comparisons by controlling false discovery rate (FDR) using the Benjamini–Hochberg method (α = 0.05); histograms depict median with a line