Profiling the epigenomic landscape of late embryonic and adult mouse hind limb muscles

Skeletal muscles are essential for movement, supporting a wide range of locomotor behaviors. Muscle tissue is composed of multiple cell types including "fast" and "slow" myofibers, whose contractile properties are largely influenced by selective expression of myosin heavy chain (MyHC) isoforms. While 'super-enhancers' regulating MyHC gene clusters have been identified, the cis-regulatory elements (CREs) controlling non-MyHC genes important to myofiber physiology remain less defined. Here, we profile the regulatory landscape of two pairs of mouse hind limb muscles differing in MyHC expression at a late embryonic (E18.5) and adult time point to identify candidate CREs that may regulate genes important to myofiber type. Gene expression and chromatin accessibility analyses revealed that epigenetic differences at E18.5 largely reflect limb patterning, whereas adult differences reflect myofiber differentiation. We identified thousands of differentially accessible regions that may regulate genes important for muscle development, muscle biology, and myofiber identity. Among these, twelve conserved, muscle-specific CREs associated with myofiber type were tested for regulatory activity. Nine enhanced and three reduced gene activity in vitro, although their phenotypic effects remain unknown. By profiling multiple muscles across two time points, our study extends current understanding of conserved, muscle-specific CREs that regulate gene expression during myogenesis.