The effects of age, sex, weight and breed on canid methylomes

Unlike genomes, which are static throughout the lifespan of an organism, DNA methylomes are dynamic. To study these dynamics we developed quantitative models that measure the effect of multiple factors on DNA methylomes including, age, sex, weight and genetics. We conducted our study in canids, which prove to be an ideal species to assess epigenetic moderators due to their extreme variability in size and well-characterized genetic structure. We collected buccal swabs from 217 canids (207 domestic dogs and 10 gray wolves) and used targeted bisulfite sequencing to measure methylomes. We also measured genotypes at over one thousand single nucleotide polymorphisms (SNPs). We found that DNA methylomes are strongly associated with age, enabling the construction of epigenetic clocks. We also show that methylomes are strongly impacted by sex, weight and sterilization status, leading to accurate predators of these factors. Methylomes are also affected by genetics and we observe multiple associations between SNP loci and methylated CpGs. Finally, we show that several factors moderate the relationship between epigenetic ages and real ages, such as body weight, which increases epigenetic aging. In conclusion, we demonstrate that the plasticity of DNA methylomes is impacted by myriad genetic and physiological factors, and that DNA methylation biomarkers are accurate predictors of age, sex and sterilization status.