Fig. 5: Analysis of sperm CpG methylation changes in F1 and F2 offspring.

a Violin plots showing the distribution of CpG methylation levels measured by whole genome bisulfite sequencing (WGBS-seq) of sperm of F1 CTR (n = 6), F1 HFD (n = 6), F2 CTR (n = 7) and F2 HFD (n = 7) offspring. Methylated cytosines were counted for each rolling 50 CpG window genome-wide and are expressed as percentage of total cytosines per window. b (left) Comparisons of the percentage of sperm CpG methylation of differentially methylated regions (DMRs) found in F1 offspring. (right) Comparisons of the percentage of CpG methylation of DMRs found in F2 offspring. The size of the dot represents the size of the DMR and the blue color scale indicates the p-value of the DMR. c Genomic percentage of F1 and F2 DMRs in Promoters (light blue), CpG-islands (CGI) (dark gray), Super enhancers (dark turquoise), Introns (middle blue), Exons (light gray) and Transposons (dark blue). d Example DMR in the Epx gene. The size of the bar and the color indicates the methylation level, with high methylation level being red and low methylation level blue. e Heatmap of CpG methylation of significant DMRs in F1 which have a similar methylation patterns in F2. (left) hypomethylated DMRs in HFD, (right) hypermethylated DMRs in HFD. DMRs are clustered into 3 clusters unsupervised by k means clustering. The column mean % of methylation is shown as a graph above each heatmap. Heatmaps were generated using the iheatmap R library