Differential genome‐wide DNA methylation patterns in young and old mice on calorie restricted or ad libitum diets

Abstract

Calorie restriction (CR) increases longevity and healthspan. We investigated how DNA methylation patterns change with aging and CR to gain insight into epigenetic mechanisms underlying healthspan extension. 14 week old C57BL6 mice were randomized to NIH31 Ad libitum diet (AL) or NIH31/NIA fortified CR diet to age 6 months (young) or 20 months (old). CR was initiated at 10% and increased to 40% over 2 weeks. DNA methylation was investigated in liver by the methylated DNA immunoprecipitationchip method on arrays covering all RefSeq genes and CpG islands. Data was normalized with the charm package in Bioconductor. Modified t‐tests and mean group differences were calculated per probe. We defined a differentially methylated probe (DMP) as p≤0.01 and mean difference ≥0.5. The age*diet interaction was investigated by a 2‐way ANOVA with DMP defined as the interaction p≤0.01. We identified 2918 DMPs in old vs young CR, 2256 in AL vs CR old, 1449 in young vs old AL, 943 in AL vs CR young and 1423 in the interaction. Unsupervised hierarchical clustering of interaction DMPs demonstrated that old CR and young AL cluster together and distinctly from the old AL and young CR. 1kb regions will be investigated, with differential methylation defined as ≥1‐DMPs and Wilcox Rank Sum FDR<0.1. This data supports that aging and CR modify DNA methylation independently and through an interaction. Supported by HNRCA Pilot grant.