Muscle progenitor specification and myogenic differentiation are associated with changes in chromatin topology.

Using Hi-C, promoter-capture Hi-C (pCHi-C), and other genome-wide approaches in inducible Pax7-expressing skeletal muscle progenitors that inducibly express a master transcription factor, Pax7, we systematically characterized at high-resolution the spatio-temporal re-organization of compartments and promoter-anchored interactions as a consequence of myogenic commitment and differentiation. We identified key promoter-enhancer interaction motifs, namely, cliques and networks, and interactions that were dependent on Pax7 binding. Remarkably, we found that the majority of super-enhancers were bound by Pax7 and a cadre of associated factors that maintained an epigenetic memory of active enhancers in the absence of Pax7. Lastly, we identified a previously uncharacterized Pax7-bound enhancer hub that simultaneously regulates the essential myosin heavy chain cluster during skeletal muscle cell differentiation. Our studies lay the groundwork for understanding the three-dimensional conformation of chromatin in muscle stem cells. Overall design: Examination of chromatin structure re-organizaion during myogenic differentiation in the inducible Pax7-expressing (iPax7) skeletal muscle progenitors. (1) in situ Hi-C in both undifferentiated progenitor (doxycyline treated, +Dox) and differentiated (-Dox) iPax7 cells; (2) promoter capture Hi-C (pCHi-C) in both undifferentiated progenitor (+Dox) and differentiated (-Dox) iPax7 cells; (3) ChIP-seq of CTCF and Smc3 in both undifferentiated progenitor (+Dox) and differentiated (-Dox) iPax7 cells; (4) ATAC-seq of iPax7 ESC (-Dox), wild-type (WT) and Myod1 knock-out primary myoblasts.