ACL injury reprograms quadriceps myonuclear epigenetic and transcriptional signatures in mice

ACL injury is a debilitating sport-related injury that induces prolonged deficits in muscle size and strength. Using a time-course of in vivo fluorescent metabolic labeling of nascent RNA in an ACL injury mouse model, we identified upregulated myonuclear transcriptional output early following the injury. To define altered myonuclear transcription, we bred HSA rtTA/rtTA :TetO-H2B-GFP mice to allow for stable in vivo fluorescent labeling and sorting of resident (non-satellite cell-derived) myonuclei 3-days post ACL transection surgery. We performed myonucleus-specific RNA sequencing (RNAseq) and reduced representation bisulfite sequencing (RRBS) to capture altered myonuclear transcriptional and epigenetic signatures following ACL injury. Integration of these datasets revealed transcriptional reprogramming of quadriceps myonuclei following ACL injury toward upregulation of fibrosis related genes and downregulation of metabolism related genes. When integrating bulk tissue RRBS with bulk tissue RNAseq, we demonstrate a similar, but more robust pattern of transcriptional reprogramming, suggesting the altered epigenetic landscape following ACL injury extends beyond myonuclei. Our results support a model of epigenetically-encoded muscle maladaptation following orthopedic injury, with implications for understanding a “muscle memory” of persistent dysfunction.