A rat epigenetic clock recapitulates phenotypic aging and co-localizes with heterochromatin

Elife. 2020 Nov 12;9:e59201. doi: 10.7554/eLife.59201.

Abstract

Robust biomarkers of aging have been developed from DNA methylation in humans and more recently, in mice. This study aimed to generate a novel epigenetic clock in rats-a model with unique physical, physiological, and biochemical advantages-by incorporating behavioral data, unsupervised machine learning, and network analysis to identify epigenetic signals that not only track with age, but also relates to phenotypic aging. Reduced representation bisulfite sequencing (RRBS) data was used to train an epigenetic age (DNAmAge) measure in Fischer 344 CDF (F344) rats. This measure correlated with age at (r = 0.93) in an independent sample, and related to physical functioning (p=5.9e-3), after adjusting for age and cell counts. DNAmAge was also found to correlate with age in male C57BL/6 mice (r = 0.79), and was decreased in response to caloric restriction. Our signatures driven by CpGs in intergenic regions that showed substantial overlap with H3K9me3, H3K27me3, and E2F1 transcriptional factor binding.

Keywords: DNA methylation; biological age; caloric restriction; computational biology; epigenetic clock; genetics; genomics; mouse; rat; systems biology.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Aging / genetics
  • Aging / metabolism*
  • Aging / physiology
  • Animals
  • Biological Clocks / genetics
  • Biological Clocks / physiology*
  • Biomarkers
  • DNA Methylation / genetics
  • DNA Methylation / physiology
  • Epigenesis, Genetic / physiology*
  • Heterochromatin / metabolism*
  • Male
  • Mice, Inbred C57BL
  • Phenotype
  • Rats
  • Rats, Inbred F344
  • Unsupervised Machine Learning

Substances

  • Biomarkers
  • Heterochromatin

Associated data

  • GEO/GSE161141
  • GEO/GSE80672