Fig. 2

SNVs heterogeneously accumulate across brain regions in Polg^D181A mice and cause mtDNA position-specific mutational patterns. a Dot plot illustrating the age-dependent increase in the load of SNVs in Polg^D181A mice across the investigated brain regions (as indicated by the colour legend) normalised to the mean of WT samples at 10 weeks. Grey diamonds indicate the mean of WT-derived brain region samples for reference (same as in Fig. 1f). Red diamonds indicate the mean of Polg^D181A-derived brain region samples and the 95% confidence interval is shown. Three-way ANOVA (age, region, and animal) of Polg^D181A-derived samples showed that age significantly contributed to SNV levels (p values of post hoc Tukey’s test are shown). Three-way ANOVA showed a significant contribution of all variables (age, genotype, region). p values of post hoc Tukey’s test comparing WT and Polg^D181A at each age are shown. For region contribution, we found a significant contribution of COR, NAc, and PVT to SNV levels in Polg^D181A mice using a linear model for main effects. b SNVs were counted in 10-bp non-overlapping bins for WT (grey) and Polg^D181A (red) mice at 10, 50, and 80 weeks, and the number of regions with SNV in each bin calculated. Note that in the case that one region has more than one SNV in a bin, it is only counted as one instance of an SNV. The overlap was visualised for non-overlapping bins (“1”), bins shared across two or three regions (“2–3”), and bins shared across four to six regions (“4–6”). c SNVs were counted in 10-bp non-overlapping bins for WT (grey) and Polg^D181A (red) mice at 50 weeks, and the number of individual animals with SNVs in each bin calculated. Note that in the case that one animal has more than one SNV in a bin, it is only counted as one instance of an SNV. The overlap was visualised for non-overlapping bins (“1”), bins shared across two or three animals (“2–3”), and bins shared by four or more animals (“≥ 4”). d Cumulative percentage of SNVs detected in each examined brain region (thin lines) for both WT (grey) and Polg^D181A (red) at 10, 50, and 80 weeks old. Bold lines indicate the smooth conditional mean for each genotype. e The relative average SNV allele frequency for each region for WT (grey) and Polg^D181A (red) mice at 10, 50, and 80 weeks as indicated shown as boxplots. p values of two-sided t tests are shown. f SNVs across brain regions were pooled for each genotype at each age and divided into 100-bp bins across the mtDNA reference and the allele fraction for SNVs in each bin summed and normalised (i.e. highest peak set to 1). Grey areas indicate mtDNA regions where peaks are found across all variables (α), peaks that are ageing-dependent (β), and ageing-induced Polg^D181A-dependent peaks (γ)