Chromatin structure profiling of mouse muscle stem cells by ATAC-seq

Regulation of chromatin accessibility is critical for cell fate decisions. Chromatin architecture responds to extrinsic environments rapidly. The traditional adult stem cell isolation approach requires tissue dissociation, and adult stem cells respond to the stimulation and adapt a different chromatin conformation. Here, we characterized the DNA regulatory landscape and transcriptomic profile of muscle stem cell quiescence exit and self-renewal by time-course profiling of the in situ fixed SCs upon injury-induced activation and during aging. Detailed analysis of the chromatin accessibility profiles leads to the identification of enhancer elements for SC quiescence. Constant activation of the enhancer elements promotes stemness and prevents SCs from differentiation, whereas loss of them causes cell-cycle arrest and essentially leads to defects in SC activation. Interestingly, we also showed that aged SCs display a more open chromatin environment than young SCs. Our compre hensive characterization of the chromatin accessibility and transcriptomic landscapes during SC quiescence exit and self-renewal broadens our understanding of this process and identifies functional distal regulatory elements for SC function. Overall design: By comparing ATAC-seq from satellite cells (SCs) activated for different time points, we showed the trajectory of chromatin accessibility changes during SCs quiescence exit, activation and regeneration. Our data showed that QSCs have a relatively closed chromatin environment. Upon activation, scs have a dramatic increase in chromatin accessibility and re-establish the closed chromatin environment during regeneration. Examination of chromatin accessibility using ATAC-seq in quiescent SCs, activated and regenerating SCs across different injury time course.