Fig. 4
DNA methylation changes in the mouse liver in response to dietary restriction (DR). a Number of significantly (p < 0.05) differentially methylated regions (DMRs) (DNA methylation difference > ±10%) between ad libitum-fed (AL) and DR at young and old age. b Density scatter plot indicating the magnitude of DNA methylation changes between diets with respect to the methylation level of old AL animals. Lines indicate median of methylation levels for hypo- and hypermethylated DMRs. Average DNA methylation levels were significantly different between hypo- and hypermethylated Old-DR DMRs. *** p < 0.001, Wilcoxon-rank-sum test. c, d Enrichment analysis of hyper- (c) and hypomethylated (d) Old-DR DMRs over genomic elements. e, f Scatterplot of expression differences versus methylation differences of Old-DR DMRs in young (e) and old (f) animals. Dashed lines indicate DNA methylation cutoff of > ±10%. There was no significant correlation between DNA methylation and gene expression in young animals (Fisher’s test p = 1). In contrast, DNA methylation and gene expression were significantly negatively correlated in old animals (Fisher’s test p <0.001, Pearson correlation −0.387 for all genes; p <0.001, Pearson correlation −0.556 for differentially expressed genes). Number of differentially methylated genes in each quadrant is indicated in blue and red, for all genes and differentially expressed genes, respectively. g Gene ontology and reactome enrichment of genes with a negative correlation of gene expression and methylation. Lengths of bars represent negative log-transformed, adjusted p values using Fisher’s exact enrichment test. Cells indicate log2-fold changes (log2FC) between AL and DR per gene. CGI CpG island