In diploid cells, genes are presumed to be expressed from both alleles to maintain gene dosage for normal development. However, a small number of genes reach haplosufficiency even with only one functional allele per cell. Most of these genes are regulated through genomic imprinting and X chromosome inactivation (XCI). DNA methylation is an essential epigenetic regulation for developmental programming in embryogenesis and play crucial roles in genomic imprinting and XCI. This dissertation presents 1) effects of maternal diets on genome imprinting in fetal sheep (Chapter Two), 2) dosage compensation of the X chromosomes in bovine germline, embryos and somatic tissues (Chapter Three), 3) Whole genome DNA methylation in bovine in vivo preimplantation development (Chapter Four). In chapter two, we report the first throughput study of genomic imprinting in sheep and report the identification of 13 new imprinted genes as well as demonstrating that maternal diets affect expression of imprinted genes in fetuses. Our results determine maternal diets influence imprinted gene expression while the parental-of-origin expression pattern was not affected, further suggesting that gene expression levels and imprinted patterns may be regulated through different epigenetic mechanisms. In chapter three, we reported the up-regulation of X chromosome in bovine germline, embryos and somatic tissues, supporting a balanced expression between a single active X and autosome pairs. However, deviating from Ohno’s theory, dosage compensation to rescue X haploinsufficiency appears to be an incomplete process for expressed genes but a complete process for “dosage-sensitive” genes. In chapter four, we adopted the scWGBS-seq method to comprehensive profile 5-MeC in single-cytosine resolution in bovine sperm, immature oocyte, in vivo/vitro mature single oocyte, and in vivo developed 2-, 4-, 8-, 16-cell single embryos. We observed global demethylation during bovine embryo cleavage up to 8-cell stage and de novo methylation at 16-cell stage. Our results refined the current knowledge on bovine embryo DNA methylation dynamics and provide valuable resources for future studies
