Efficient Genome-Wide Chromatin Profiling by CUT&RUN with Low Numbers of Muscle Stem Cells

Adult muscle stem cells (MuSCs), also called satellite cells, are situated under the basal lamina of myofibers in skeletal muscles. MuSCs are instrumental for postnatal muscle growth and regeneration of skeletal muscles. Under physiological conditions, the majority of MuSCs is actively maintained in a quiescent state but becomes rapidly activated during muscle regeneration, which is accompanied with massive changes in the epigenome. Moreover, aging, but also pathological conditions, such as in muscle dystrophy, results in profound changes of the epigenome, which can be monitored with different approaches. However, a better understanding of the role of chromatin dynamics in MuSCs and its function for skeletal muscle physiology and disease has been hampered by technical limitations, mostly due to the relatively low number of MuSCs but also due to the strongly condensed chromatin state of quiescent MuSCs. Traditional chromatin immunoprecipitation (ChIP) usually requires large amounts of cells and has several other shortcomings. Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is a simple alternative to ChIP for chromatin profiling, providing higher efficiency and better resolution at lower costs. CUT&RUN maps genome-wide chromatin features, including genome-wide localization of transcription factor binding in small numbers of freshly isolated MuSCs, facilitating analysis of different subpopulations of MuSCs. Here we describe an optimized protocol to profile global chromatin in freshly isolated MuSCs using CUT&RUN.