DNA methylation and chromatin accessibility predict age in the domestic dog

• Published in: Aging cell Vol. 23; no. 4; p. e14079
• Main Authors: Jin, Kelly, McCoy, Brianah M, Goldman, Elisabeth A, Usova, Viktoria, Tkachev, Victor, Chitsazan, Alex D, Kakebeen, Anneke, Jeffery, Unity, Creevy, Kate E, Wills, Andrea, Snyder-Mackler, Noah, Promislow, Daniel E L
• Format: Journal Article
• Language: English
• Published: England John Wiley and Sons Inc 01.04.2024
• Subjects: DNA methylation; dogs; ATAC‐seq; aging; epigenetic clock
• ISSN: 1474-9718; 1474-9726; 1474-9726
• DOI: 10.1111/acel.14079

Across mammals, the epigenome is highly predictive of chronological age. These "epigenetic clocks," most of which have been built using DNA methylation (DNAm) profiles, have gained traction as biomarkers of aging and organismal health. While the ability of DNAm to predict chronological age has been repeatedly demonstrated, the ability of other epigenetic features to predict age remains unclear. Here, we use two types of epigenetic information-DNAm, and chromatin accessibility as measured by ATAC-seq-to develop age predictors in peripheral blood mononuclear cells sampled from a population of domesticated dogs. We measured DNAm and ATAC-seq profiles for 71 dogs, building separate predictive clocks from each, as well as the combined dataset. We also use fluorescence-assisted cell sorting to quantify major lymphoid populations for each sample. We found that chromatin accessibility can accurately predict chronological age (R  = 26%), though less accurately than the DNAm clock (R  = 33%), and the clock built from the combined datasets was comparable to both (R  = 29%). We also observed various populations of CD62L+ T cells significantly correlated with dog age. Finally, we found that all three clocks selected features that were in or near at least two protein-coding genes: BAIAP2 and SCARF2, both previously implicated in processes related to cognitive or neurological impairment. Taken together, these results highlight the potential of chromatin accessibility as a complementary epigenetic resource for modeling and investigating biologic age.