Fig. 1

The epigenomes of wild-type and Ames dwarf mice diverge with age. a Global percentage methylation per liver sample, for 2-month-old wild-type (WTY), 22-month-old wild-type (WTO), 2-month-old Ames dwarf (DY) and 22-month-old Ames dwarf (DO) mice. All p > 0.05 (two tailed t-test on arcsine transformed proportions). b UCSC genome browser trace of percentage methylation over chromosome 1, showing pooled WTY (light blue), WTO (dark blue), DY (light red), DO (dark red) replicate tracks. c Principal component analysis of CpG percentage methylation, for WTY (light blue), WTO (dark blue), DY (light red) and DO (dark red) liver samples. Principal component (PC)1 proportion of variance = 12.38%, and PC2 proportion of variance = 7.64%. d The number of significantly differentially methylated CpGs (5% FDR, Fisher’s exact test) between four pooled WT and four pooled Ames dwarf replicates (gCpGs) in liver of 2-month-old (young) and 22-month-old (old) mice. Hyper- and hypomethylated gCpGs are higher and lower in Ames dwarf mice, respectively. e As d but showing significantly differentially methylated regions (gDMRs; 5% FDR, Fisher’s exact test, 500-bp windows). Regions of heterogeneity (chi-squared test <0.05) across the four replicates in each cohort were removed. DY-WTY versus DO-WTO hypermethylation, p < 0.05 (marked with an asterisk). See also Additional file 3: Table S1e. f The percentage methylation across all 2-month-old (left) and 22-month-old (right) gDMRs. Replicate samples (four mouse livers) are in rows and the gDMRs in columns. The intensity of the heatmap represents column scaled percentage methylation (Z-score), with values ranging from lower to higher methylation shown as blue to yellow. g Kernel smoothed line plots of selected gDMRs, ±5 kb. WTY, DY, WTO and DO replicates are represented by solid blue, solid red, dashed blue and dashed red lines, respectively. DMRs are highlighted in pink and CpGs in black