A robust and practical myogenic cell system to explore cellular and genomic features of muscle differentiation [ChIP-Seq]
The ability to recapitulate muscle differentiation in vitro has proven invaluable to investigate mechanisms of myogenesis, muscle cell function and muscle diseases. However, obtaining myoblasts from patients with neuromuscular diseases poses ethical and procedural challenges which limit investigations of molecular mechanisms of muscle pathophysiology. Alternative myogenic models have been developed, such as the derivation of myogenic cells from skin fibroblasts through activation of an endogenous myogenic program triggered by exogenous expression of murine Myod. In the context of this ChIP-seq dataset, we compared the transcriptome and lamina-associated domains (LADs) as genome organizers in myo-converted human fibroblasts and in isogenic myotubes differentiated from myoblasts. We show that myogenic induction of fibroblasts elicits genome-wide transcriptomic changes indicative of myogenic commitment and differentiation. Yet, myotubes are further along myogenic commitment than myo-converted fibroblasts under the conditions tested. LADs with typical LAD properties (low gene density, containing mostly repressed genes, and H3K9me3-rich) are shared between the two cell types, but each cell type also displays nearly 700 unique LADs. Strikingly, myotube-specific LADs are smaller, more gene-rich and less heterochromatic than shared LADs or LADs unique to myo-converted fibroblasts. Thus, myo-converted fibroblasts and myotubes retain some cell type specificity of genome organization at this level. Although these myogenic cell types are not identical, our results favor a view of myo-converted fibroblasts as a robust and practical model to investigate cellular and genomic properties of cells from patients with muscle pathologies. Overall design: We investigated lamin A/C (LaA)-associated domains (LADs) and H3K9me3 profiles in two myogenic cell types. We differentiated immortalized myoblasts into  myotubes  for 5 days in 3 indpendent differentiation replicates, and mapped LADs in the differentiated myotubes in each replicate by ChIP-seq of lamin A/C . We also elicited a myogenic conversion of immortalized fibroblasts for 5 days (here, 'Myoconv') in 3 independent replicates (Rep 1-3), and mapped lamin A/C ('LaA') LADs in the myo-converted fibroblasts. We also mapped the histone modification H3K9me3  in day-5 myo-converted fibroblasts and day-5 myotubes by ChIP-seq of H3K9me3 in one replicate of each.