Fig. 1

Investigation of chromatin landscapes in primary blood cells from three genetically diverse cattle breeds. A Overview of cell types collected from up to nine female Holstein Friesian, N’Dama and Nelore cattle (three of each breed) for RRBS, ATAC-seq and RNA-seq. The total numbers of RRBS, ATAC-seq and RNA-seq samples collected for each breed is shown at the bottom of the schematic. B PCA of cattle genotype data. Analysis was performed using 27,379,808 variants from 298 cattle. Filled points symbolise Holstein Friesian, N’Dama and Nelore cattle, of which the labelled points highlight the animals used in this study. C Percentage methylation, chromatin accessibility and gene expression of immune-related genes. Heatmaps showing the percentage methylation (left) and chromatin accessibility (middle) at promoters (defined as 1000 bp upstream and 500 bp downstream of TSSs) of immune-related genes and their corresponding expression (right). Bars on the right show the distance of the TSS of each transcript to the nearest CGI. Black bars in the methylation heatmap represent samples where fewer than 5 CpG sites covered by a minimum of 5 reads were found at a given promoter. SIRPA denotes SIRPα and gdT cell denotes γδ T cell. This figure also highlights that, consistent with previous reports, the number of CD4+CD8+ double positive T cells is likely small given the expression of CD4 and CD8 are largely specific to the respective cell types [34]