(a) Global differential methylation histograms per age group comparison. A cutoff of 5% methylation difference was used. (b) Proportion of hypermethylated and hypomethylated regions (DMR) compared to distance from the closest transcription start site (TSS). (c) Venn diagram for the number of DMR within 20 k bp distance of the nearest TSS based on age group comparisons. A cutoff of false discovery rate (FDR) <0.05, >5% CpG mean change, and at least 3 CpG differential DMR site per block was used. Hypermethylated and hypomethylated changes are indicated by the noted colors. (d) Summary of gene set enrichment analysis for DMRs in proximity of TSSs (<20 k bp). Analysis was performed for three age groups: young (3–8 months), middle-aged (13–17 months), and old (22–27 months). Combined score was calculated as −log10(FDR) × fold enrichment. YM - young vs. middle-aged; MO - middle-aged vs. old; YO - young vs. old. The list of hypomethylated DMRs for the MO comparison had statistically significant enrichments. For a full enrichment analysis see Table S4. (e) Individual methylation levels of regions near the Runx1 and Dnmt3a genes. Left panel - Runx1; middle panel - methylation map in the Runx1 TSS; right panel - Dnmt3a. (f) Global differential methylation histograms of mouse (Sziráki et al., 2018) and human (Hannum et al., 2013). A cutoff of 5% methylation difference was used. (g) Heatmap depicting concordance of DMRs near orthologous gene sites between rat (left), mouse (center), and human (right) datasets. Only genes identified as differentially methylated in old rats are shown, the rightmost panel depicts the coverage for each dataset, where missing data is black.