Whole genome bisulfite sequencing of young and old satellite cells

The function of skeletal muscle stem cells (MuSC) declines during aging, contributing to the advent of age-related myopathies. However, whether this decline is the result of accumulating cellular damage, altered heterogeneity in stem cell populations or due to the effect of the changing niche environment remains largely unknown. By scRNA-Seq, we show that the age-related reduction in the MuSC pool is not stochastic, with different subpopulations being distinctly affected in aging. Using an in vivo allogeneic stem cell transplantation model, we show that exposure of MuSCs from old mice to a youthful niche environment significantly restores the gene expression of genes that are altered in aging. We show that age-related changes in the MuSC transcriptome are mainly driven by alterations in chromatin and transcription but are not due to posttranscriptional mechanisms affecting RNA stability. Furthermore, our data indicates that the portion of the genome that is activated in aging is significantly more responsive to restoration by niche factors compared to the repressed counterpart. Taken together, our data reveals that the niche environment plays a decisive role in controlling the transcriptional activity of MuSCs. Overall design: Satellite cells were isolated from 3 young and 3 aged male C57Bl/6J mice by Fluorescence-Activated Cell Sorting (FACS). The sorted cells were cultured into myoblasts and expanded in vitro to passage 5. Genomic DNA was extracted using phenol-chloroform extraction. Genomic DNA underwent bisulfite treatment and library preparation before sequencing.