Fig. 4

Fertility-related DMCs target different genome features according to their methylation status in subfertile bulls. A The background CpGs10 and DMCs were annotated as described in the Methods. The percentage of each genome element in three functional genome features (genes, repetitive elements and CpG islands) is indicated on the different pie charts. DMCs were split into hypo- and hypermethylated DMCs according to their methylation status in subfertile bulls compared to fertile bulls. TSS: transcription start site, TTS: transcription termination site, UTR: untranslated region, upstream region: up to − 10 kb from the TSS, downstream region: up to + 10 kb from the TTS. B DNA methylation percentages (y-axis) were obtained for 60 individual CpGs10 included in the consensus sequence of the LINE L1 element (x-axis) after the alignment of RRBS sequences on a Repbase artificial genome. Each dot represents one sample, with fertile and subfertile bulls shown in red and blue, respectively. Red and blue lines indicate the trend over the 60 CpGs in fertile and subfertile bulls, respectively, and were obtained using the geom_smooth function of the ggplot2 R library. The 95% confidence interval is shown in light grey. The L1 element was slightly but consistently less methylated in subfertile bulls than in fertile bulls at all CpG positions