Profiling the immune epigenome across global cattle breeds
Item statusRestricted Access
Embargo end date08/12/2022
Cattle are economically important animals, providing a valuable food source for people around the world. There are two main subspecies of cattle, Bos taurus taurus (taurine) and Bos taurus indicus (indicine), which began to diverge from each other over 210,000 years ago. Today, there are hundreds of established breeds that each display unique phenotypes. Understanding the variation between cattle breeds that are adapted to different local environments is essential for breeding animals with improved climate and disease resistance. Nevertheless, bovine research is dominated by European taurine breeds. In addition, studies of cattle diversity have concentrated on genetic variation, with alternative mechanisms largely overlooked. Variation at the epigenetic level is of particular interest because of its role in the development and function of the immune system. However, the tools and reference resources to study this variation in cattle are almost entirely lacking. This research focussed on building and interrogating genome-wide maps of chromatin accessibility and DNA methylation for seven immune cell types across three genetically distinct cattle breeds. Holstein Friesian, N’Dama and Nelore cattle were selected to represent the European taurine, African taurine and indicine cattle lineages, respectively. Gene expression data for Holstein Friesian was also analysed. Chapter 2 involved the development, validation, and selection of methods to best study chromatin accessibility and DNA methylation in cattle. Based on its performance using bovine monocytes, a modified version of the original assay for transposase-accessible chromatin using sequencing (ATAC-seq) protocol was chosen to profile regions of open chromatin. Reduced representation bisulfite sequencing (RRBS) and whole genome bisulfite sequencing were compared at similar sequencing costs, with the former selected due to its better coverage of likely functional regions. Chapter 3 used RRBS to generate DNA methylation reference profiles for seven purified immune cell populations (monocytes, neutrophils, B cells, CD4 T cells, CD8 T cells, γδ T cells and NK cells) from the three cattle breeds. RNA-seq was also used to profile the transcriptome of corresponding purified cell types for Holstein Friesian cattle. These reference panels were demonstrated to be able to successfully estimate cell type abundances in mixed cell populations using a computational tool called CIBERSORTX. The cell type proportions estimated by CIBERSORTX, using gene expression data, were highly correlated to the known compositions of ten in silico cellular mixtures. Cell type proportions were also accurately imputed for six in vitro and nine lysed blood mixtures using RRBS data, often even when the reference panels and mixtures were derived from different breeds. Finally, chapter 4 examined the chromatin accessibility, DNA methylation and transcriptional maps generated for each cell type and breed. Extensive epigenetic divergence was found between the taurine and indicine cattle lineages across cell types, with most variation at regions distal to the transcription start site. Furthermore, distinct sub-categories of CpG islands based on their chromatin and methylation profiles were identified that discriminate between classes of distal and gene proximal islands linked to discrete transcriptional states. The data generated in this research provide a comprehensive resource to help exploit the diversity among cattle breeds and improve cattle productivity for farming communities in low and middle income countries.