Skeletal muscle makes up about 40% of body mass, and its aging raises the risk of weakness, falls, and death. Previous work on transcriptomic and epigenomic changes in muscle either analyzed whole tissue, losing differences between cell types, or used small samples. This study stands somewhat apart: nearby in the archive are studies on collagen molecular mechanics, tumor genealogy, and cell aging, but direct neighbors on muscle epigenome are almost absent. This is the first large-scale check of age-related chromatin changes in individual muscle fiber types that also accounts for sex.
Frozen vastus lateralis biopsies from 287 donors (123 women, 164 men) aged 20–79 were used. Nuclei were isolated and sequenced for RNA and open chromatin (snRNA-seq and snATAC-seq). Clustering revealed 13 cell types. For each fiber type (1, 2a, 2x), the link between gene expression and chromatin accessibility with age was tested using linear mixed models adjusted for sex, body mass index, batch, and other factors. Additionally, a pseudobulk approach with DESeq2 was compared.
With age, the proportion of nuclei from fast glycolytic type 2x fibers dropped significantly, while the share of neurons and neuromuscular junction nuclei rose. In the fiber transcriptome, hundreds of genes were linked to age: 216 in type 1, 384 in type 2a, 344 in type 2x. The direction of changes matched between sexes at 72–81% and between fiber types at 86–96%. In the epigenome, more regions closed than opened (68–72% of age-associated regions closed). The closing regions were enriched for active enhancers and depleted of active transcription start sites. Motifs for transcription factors NR3C1 (glucocorticoid receptor), NR3C2, and NR3C4 (androgen receptor) were most enriched in the closing chromatin of male type 2a fibers, whereas in women, motifs of the NFI family were more common. Motifs for CEBPB and ATF4 were enriched in opening regions of type 2 fibers.
This work stands out from its archive neighbors in scale and subject: it is the first study of the aging epigenome at the level of individual muscle fiber nuclei with such a sample. Unlike studies on collagen or cell aging, it shows that aging changes the accessibility of regulatory elements, not the transcribed regions themselves. This shifts the focus from genes to their switches.
The field could move toward testing cause-and-effect links: whether closing of regions with hormone receptor motifs truly reduces muscle sensitivity to signals. Experiments activating these receptors in aging models are possible. Expanding the donor age range to include younger and older people is also promising.
The results will affect gerontology, sports medicine, and endocrinology, as they point to a potential role for hormonal regulation in age-related muscle loss.
The next step is functional validation of the role of NR3C1 and other factors in muscle cells, for example through knockdown or activation in culture. It is also important to compare epigenomic changes across different muscles to see how universal the findings are.
The work connects to an unsolved problem in muscle biology: why fast type 2 fibers are preferentially lost with aging and what role denervation plays. It provides an epigenomic layer of data that was missing for testing hypotheses about reduced sensitivity to anabolic signals.
The chromatin regions that close with age are most often far from genes (more than 5 thousand base pairs from the transcription start site), meaning aging hits the 'control panels,' not the genes themselves.
Not published on arXiv. Here are its page, the PDF and the formalization: you can check it yourself, not only read our account.