Transcriptome analysis following an acute loading-induced skeletal muscle growth stimulus in mice yields tools for discerning global and MYC regulatory networks

We investigated global, actively transcribed, stable, and myonucleus-specific transcriptomes following an acute hypertrophic stimulus in mouse plantaris. With these datasets we define global and Myc-specific dynamics at the onset of rapid loading-induced muscle fiber growth. Experiment 1 defines the global transcriptome using RNA-sequencing (RNA-seq) during 72 hours of plantaris muscle mechanical overload in the mouse. Experiments 2 and 3 used the tissue from Experiment 1 to provide information on the contribution of active transcription versus mRNA stability to global gene expression with overload (i.e. transcriptional dynamics). Experiment 4 details the myonucleus-specific transcriptome during overload to identify muscle-fiber enriched genes, which is further informed by Experiments 2 and 3. Myonuclei only comprise ~30% of all nuclei after short-term mechanical overload, so defining the transcriptome specifically in myonuclei is critical to understanding muscle fiber adaptation. The transcriptional regulation and localization of Myc and its impact on muscle gene expression was explored using data from Experiments 1-4. Experiment 5 utilized a doxycycline-inducible muscle fiber-specific in vivo Myc pulse in the plantaris to understand what genes Myc controls within muscle fibers, and how this relates to myonuclear gene expression during overload (Experiment 4).