Fig. 3

Comparisons of differentially methylated CGIs between cell types, cattle breeds and cattle lineages. A Upset plot of differentially methylated CGIs (methylation difference ≥ 25%, q value ≥ 0.01) identified in labelled pairwise comparisons. The bars on the right hand side show the number of significantly differentially methylated CGIs in each comparison. The annotated bars along the top show the number of CGIs significantly differentially methylated across the comparisons indicated by black dots. Only sets of comparisons involving at least 6 significantly differentially methylated CGIs are shown. The box plot along the bottom shows the distribution of distances of the CGIs within each combination set to their nearest TSS of a protein-coding gene. The text along the left hand side denotes the groups compared in each pairwise comparison, where ‘.’ separates group 1 and group 2. B Heatmap of CGIs differentially methylated between Holstein Friesian and Nelore and/or between taurine (Holstein Friesian and N’Dama) and Nelore. CGIs were restricted to those within 2000 bp of a TSS and where the mean expression of the nearest gene was >10 TPM across all samples. The RNA-seq log2FC is the log2 fold change between the mean Holstein Friesian RNA-seq signal and the mean Nelore RNA-seq signal, where positive log2FC (red points) indicate higher expression in the Holstein Friesian cattle and negative log2FC (blue points) indicate higher expression in the Nelore cattle. Bcell = B cell, CD4 = CD4 T cell, CD8 = CD8 T cell, gdT = γδ T cell, NK = NK cell, mono = monocyte and gran = granulocyte