Cell-to-cell variability and gain of methylation at polycomb CpG islands as a hallmark of aging

Masika, H.; Ruppo, S.; Clark, S. J.; Bonder, M. J.; von Meyenn, F.; Hecht, M.; Orlanski, S.; Katsman, E.; Vardi, O.; Zlotogorski, A.; Elgavish, S.; Dor, Y.; Reik, W.; Kaplan, T.; Cedar, H.

doi:10.64898/2026.03.09.710505

bioRxiv · 10.64898/2026.03.09.710505

Cell-to-cell variability and gain of methylation at polycomb CpG islands as a hallmark of aging

Masika, H.·Ruppo, S.·Clark, S. J.·Bonder, M. J.·von Meyenn, F.·Hecht, M.·Orlanski, S.·Katsman, E.·Vardi, O.·Zlotogorski, A.·Elgavish, S.·Dor, Y.·Reik, W.·Kaplan, T.·Cedar, H.

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Abstract

Aging is a complex multifactorial process that affects cellular function and tissue homeostasis over time. Despite extensive research, the molecular mechanisms driving cellular aging remain poorly understood1,2. Many studies have focused on changes in DNA methylation as an indicator of aging3. In particular, the degree of methylation at polycomb CpG islands has been shown to be predictive of phenotypic changes associated with aging4,5. Since many age-related pathological processes, are thought to be of single-cell origin (e.g. cancer), we questioned whether polycomb DNA methylation also occurs preferentially in a subset of cells within the overall population. Using single-cell whole-genome methylation data from multiple ages and tissues, we identify Average Polycomb CpG Methylation as a hallmark of cellular aging. This revealed that aging occurs at varying rates within specific cells, with faster proliferating cells showing accelerated levels. Gene expression analysis in "young" and "old" single cells identified changes in immune response, translation regulation, tumorigenesis, neurodegeneration and other cellular processes associated with aging. These results challenge traditional models of homogeneous cellular aging and suggest that aging itself is a highly individualized process at the single-cell level that may be driven by programmed changes in polycomb CpG island DNA methylation.

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Masika, H., Ruppo, S., Clark, S. J., Bonder, M. J., von Meyenn, F., Hecht, M., Orlanski, S., Katsman, E., Vardi, O., Zlotogorski, A., Elgavish, S., Dor, Y., Reik, W., Kaplan, T., Cedar, H.. 2026-03-11. Cell-to-cell variability and gain of methylation at polycomb CpG islands as a hallmark of aging. https://doi.org/10.64898/2026.03.09.710505

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