Mechanically regulated transcriptional and DNA methylation programs in skeletal muscle stem cells

RhoA-mediated mechanical signaling is an important regulator of muscle stem cell (MuSC) quiescence and activation. To define how RhoA influences gene regulation in MuSCs, we performed RNA sequencing (RNA-seq) and enzymatic methyl sequencing (EM-seq) on freshly isolated MuSCs from control and SC-RhoAfl/+ mice. RNA-seq analysis revealed widespread transcriptional changes associated with RhoA depletion, including genes involved in cytoskeletal organization, cell adhesion, and stem cell activation. In addition, we identified extensive alternative splicing events, indicating that RhoA signaling influences transcript isoform diversity. EM-seq profiling uncovered global changes in DNA methylation, with differentially methylated regions enriched in gene bodies. Comparative analysis suggests links between DNA methylation, transcriptional output, and splicing regulation at loci associated with cell-matrix interactions and stem cell state transitions. Together, these datasets provide a resource to understand how mechanical signaling through RhoA coordinates transcriptional, epigenetic, and splicing programs in MuSCs.