Abstract
DNA methylation (DNAm) patterns are tissue specific and aid in tissue specific gene expression changes. The use of DNAm patterns from peripheral blood leukocytes (PBL) as a surrogate for patterns in other tissues is common, especially in longitudinal studies when sampling of tissues is not plausible. Thus, the objective of this study was to investigate the suitability of using DNAm patterns of PBL as a surrogate for the DNAm patterns in neuroendocrine tissues responsible for stress responses and energy metabolism. Samples from the paraventricular region of the hypothalamus, anterior pituitary gland, adrenal cortex, and the adrenal medulla were harvested from 5-yr-old Brahman cows (n = 8) and DNA was extracted from each sample. Methylation was assessed using reduced representation sodium bisulfite sequencing and differentially methylated regions (DMR) between the PBL DNA and tissue DNA were identified using EdgeR from Bioconductor, R. Analysis revealed over 15,000 DMRs located within promoter regions of genes in each tissue, with the majority of the sites having increased methylation in the PBL (Table 1). To further evaluate the use of PBL DNA as a surrogate, Pearson correlation values were calculated for genes (n = 20) pertinent to each respective tissue using the mean methylation of the specific gene in the PBL and in the tissue (Table 2). Three correlations were significant (P ≤ 0.05), two of which were negative. The sizable differences indicate that DNA methylation patterns from PBL do not compare well to patterns from hypothalamic, pituitary, adrenal cortex, and adrenal medulla tissues from 5-yr-old Brahman cows. This is especially the case for the majority of the specific genes examined in this study. Whether DNAm in the surrogate PBL will shift in a direction similar to that of specific tissues of Brahman cows exposed to stressful stimuli during developmental periods remains to be determined.
Adaptation of the targeted capture Methyl-Seq platform for the mouse genome identifies novel tissue-specific DNA methylation patterns of genes involved in neurodevelopment
