The decline in muscle function with ageing presents a significant biomedical challenge, contributing to frailty and loss of independence. Epigenetic modifications, particularly DNA methylation (DNAm), play a crucial role in these age-related muscle dysfunctions. Transcription factors (TFs) are key regulators of gene expression and are essential for maintaining muscle homeostasis. As ageing progresses, changes in both DNAm patterns and TF expression lead to alterations in mitochondrial function, metabolism, and muscle structure. Understanding how DNAm influences TF regulation in skeletal muscle during ageing is critical for developing targeted interventions to preserve muscle health.
In this study, we utilised both open-access and in-house DNAm datasets to identify differentially methylated positions (DMPs) associated with ageing and exercise in human skeletal muscle. Bioinformatic analysis revealed significant hypo- and hyper-methylation patterns, which were further explored using UniBind to identify enriched TF binding sites. Approximately 200 TFs were identified as being enriched within the differentially methylated regions, with FOXA1 and FOXA2 emerging as key TFs linked to hypermethylation changes.
Functional assays in muscle cells, incorporating knock-in/knockout techniques and CUT&RUN, were employed to identify downstream gene targets regulated by FOXA1 and FOXA2. Our findings suggest that these TFs play a significant role in modulating the epigenetic landscape of muscle tissue, and their activity is influenced by both ageing and exercise training.
Our findings highlight the critical role of FOXA1 and FOXA2 in regulating the epigenetic landscape of skeletal muscle during ageing and exercise. By modulating DNAm patterns and TF activity, exercise training can influence the expression of these key transcription factors, potentially counteracting age-related changes in muscle structure and function. These insights lay the groundwork for developing therapeutic strategies targeting FOXA1 and FOXA2 to preserve muscle health, extend health span, and improve functional outcomes in ageing populations.