Ageing affects DNA methylation drift and transcriptional cell-to-cell variability in mouse muscle stem cells

Irene Hernando-Herraez,Marc Jan Bonder,Wolf Reik,Pierre-Henri Commere,Simon Andrews,Shahragim Tajbakhsh,Brendan Evano,Stephen Clark,Thomas Stubbs

doi:10.1038/s41467-019-12293-4

Abstract

Age-related tissue alterations have been associated with a decline in stem cell number and function. Although increased cell-to-cell variability in transcription or epigenetic marks has been proposed to be a major hallmark of ageing, little is known about the molecular diversity of stem cells during ageing. Here we present a single cell multi-omics study of mouse muscle stem cells, combining single-cell transcriptome and DNA methylome profiling. Aged cells show a global increase of uncoordinated transcriptional heterogeneity biased towards genes regulating cell-niche interactions. We find context-dependent alterations of DNA methylation in aged stem cells. Importantly, promoters with increased methylation heterogeneity are associated with increased transcriptional heterogeneity of the genes they drive. These results indicate that epigenetic drift, by accumulation of stochastic DNA methylation changes in promoters, is associated with the degradation of coherent transcriptional networks during stem cell ageing. Furthermore, our observations also shed light on the mechanisms underlying the DNA methylation clock.

Highlights

Age-related tissue alterations have been associated with a decline in stem cell number and function
Notwithstanding the close associations with age, age-related methylation changes are poorly correlated with transcriptional variation, presumably because the changes are generally small and may not occur homogeneously in all cells[2], a phenomenon known as epigenetic drift
While several reports indicate a loss of clonal diversity during early life stages[9,10,11], little is known about how cell-to-cell variability at the molecular level is involved in stem cell ageing

Summary

Results

Transcriptomic profiling of young and old muscle stem cells. Muscle stem cells with high expression of Pax[7] were shown to be in a deep quiescent, or dormant, state[15,16]. To investigate the molecular effects of ageing in a defined population that is less poised to enter the cell cycle, we isolated single muscle stem cells by fluorescence-activated cell sorting (FACS) from young (1.5 months) and old (26 months) Tg:Pax7-nGFP mice[17] and selected those with high levels of GFP, to which we applied scM&T-seq (Fig. 1a). This approach allows us to study variability while minimising key confounder factors such as differences in cell cycle or differentiation states between ages. To further investigate the increased expression variability with age, we sequenced by scRNA-seq the total population of Pax[7] positive cells in four individuals (two young, two old) and a

Old 2 c

Discussion

Methods