Long-term DNA methylation changes induced by age and elevated CO₂ in skeletal muscle

Skeletal muscle dysfunction and elevated CO₂ in the blood, or hypercapnia, are both associated with higher mortality in acute and chronic pulmonary diseases. Hypercapnia-, aging and autophagy dysfunction-induced skeletal muscle phenotypes are highly overlapping. While DNA methylation regulates aging-associated cellular processes, no comparative study of CO₂- and age-induced changes in skeletal muscle has ever been conducted. Moreover, while previously reported skeletal muscle DNA methylation analyses involve about 1% of the genomic areas susceptible to this epigenetic modification, hypercapnia- and age-induced DNA methylation changes have never been investigated at the whole genome level.

C57BL/6 mice previously exposed to normo- and hypercapnia were compared with room air-maintained aged animals of similar background. Muscles from these mice were processed for whole genome methylation sequencing (WGMS) and RNA sequencing. The overlap between hypercapnia- and age-induced DNA methylation and transcript expression levels were established. Skeletal muscle-specific autophagy genetic ablation and mass spectrometry analyses were conducted to investigate the potential mechanisms regulating hypercapnia-induced DNA methylation changes.

Hypercapnic mice demonstrate aberrant DNA methylation patterns in comparison to animals never exposed to elevated CO₂. These animals also elicit changes in myofiber type composition and protracted muscle mass deterioration even after returning to normocapnia. While aging leads to consistent DNA methylation changes over time, these epigenetic changes do not overlap with CO₂-induced differential methylation. Hypercapnia does not regulate the methylome via autophagy or substrate imbalance-related mechanisms.

Hypercapnia causes durable muscle wasting that persists even after regaining ambient air environment, which is associated with a perturbed methylome landscape. High CO₂-induced DNA methylation changes do not overlap with age-induced differentially methylation positions and are independent of substrate imbalances and autophagy regulation.