Histone modifications in activated and freshly isolated mouse muscle stem cells by ChIP-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: We report the application of ChIPmentation on examination of H3K27ac histone marks in freshly isolated satellite cells (FISC) and activated satellite cells isolated after 2.5 days post-injury (ASC). We observed increase of H3K27ac marks around transcription start sites (TSS) and distinct peak patterns in distal intergenic regions during satellite cell activation. Examination of H3K27ac marks in FISC and ASC.

染色质可及性（chromatin accessibility）的调控对于细胞命运决定至关重要。染色质结构可快速响应外界环境变化。传统成体干细胞分离方法需进行组织解离，此过程会使成体干细胞受到刺激并改变其染色质构象。本研究通过对损伤诱导激活过程中及衰老阶段的原位固定卫星细胞（satellite cells, SCs）进行时序谱分析，解析了肌肉干细胞退出静息状态与自我更新过程中的DNA调控图谱与转录组特征。通过对染色质可及性图谱的细致分析，本研究鉴定出了调控卫星细胞静息状态的增强子元件。持续激活这些增强子元件可维持干细胞干性并抑制卫星细胞分化，而增强子元件的缺失则会导致细胞周期阻滞，最终造成卫星细胞激活缺陷。有趣的是，本研究还发现衰老卫星细胞的染色质开放程度高于年轻卫星细胞。本研究对卫星细胞退出静息状态与自我更新过程中的染色质可及性及转录组图谱进行了全面解析，加深了我们对该过程的理解，并鉴定出了调控卫星细胞功能的功能性远端调控元件。

实验设计概述：本研究应用ChIPmentation技术检测新鲜分离卫星细胞（freshly isolated satellite cells, FISC）与损伤后2.5天分离的激活卫星细胞（activated satellite cells, ASC）中的组蛋白H3K27ac修饰标记。研究观察到，在卫星细胞激活过程中，转录起始位点（transcription start sites, TSS）附近的H3K27ac修饰标记水平升高，且远端基因间区呈现出独特的峰型分布。本研究同时对FISC与ASC中的H3K27ac修饰标记进行了检测。