Quantifying the natural inter-individual variation in DNA methylation patterns is important for identifying its contribution to phenotypic variation, but also for understanding how the environment affects variability, and for incorporation into statistical analyses. The inter-individual variation in DNA methylation patterns in female cattle and the effect that a prenatal stressor has on such variability have yet to be quantified. Thus, the objective of this study was to utilize methylation data from mature Brahman females to quantify the inter-individual variation in DNA methylation. Pregnant Brahman cows were transported for 2 h durations at days 60 ± 5; 80 ± 5; 100 ± 5; 120 ± 5; and 140 ± 5 of gestation. A non-transport group was maintained as a control. Leukocytes, amygdala, and anterior pituitary glands were harvested from eight cows born from the non-transport group (Control) and six from the transport group (PNS) at 5 years of age. The DNA harvested from the anterior pituitary contained the greatest variability in DNA methylation of cytosine-phosphate-guanine (mCpG) sites from both the PNS and Control groups, and the amygdala had the least. Numerous variable mCpG sites were associated with retrotransposable elements and highly repetitive regions of the genome. Some of the genomic features that had high variation in DNA methylation are involved in immune responses, signaling, responses to stimuli, and metabolic processes. The small overlap of highly variable CpG sites and features between tissues and leukocytes supports the role of variable DNA methylation in regulating tissue-specific gene expression. Many of the CpG sites that exhibited high variability in DNA methylation were common between the PNS and Control groups within a tissue, but there was little overlap in genomic features with high variability. The interaction between the prenatal environment and the genome could be responsible for the differences in location of the variable DNA methylation.

Background/Objectives: Alteration in gene expression caused by stress may serve as a potential mechanism behind a range of differences previously observed in progeny exposed to prenatal stress. The objective of this study was to examine the impact of prenatal transportation stress on differential exon usage in expressed genes of stress-axis tissues of control and prenatally stressed Brahman cattle at five years of age. Methods: Pregnant Brahman cows were transported for 2 h sessions at 20-day intervals from the 60th to the 140th day of gestation, while pregnant herdmates served as controls. Blood samples were collected from six prenatally stressed (PNS) and eight control (control) females obtained when they were 5 years of age. Tissue samples were harvested from the adrenal medulla, adrenal cortex, anterior pituitary and hypothalamic paraventricular nucleus of the PNS and control cows at 5 years of age. Differential exon usage was analyzed by the DEXSeq tool to identify genes that were not previously identified by RNA sequencing analyses. Results: Differential exon usage (FDR ≤ 0.05) was detected in three exons (two genes) in the adrenal medulla, six exons (five genes) in the adrenal cortex, 13 exons (12 genes) in the anterior pituitary, and 37 exons (33 genes) in the hypothalamic paraventricular nucleus. Conclusions: The correspondence of prenatal stress to changes in exon usage across multiple tissues and genes could indicate investigative opportunities in postnatally affected physiological processes, including myelination, brain development, stress responses and metabolism.