63 DNA methylome wide profile associates differentially methylated loci and regions with cow’s ileal lymph node response to Mycobacterium avium subsp. paratuberculosis

Abstract

Abstract Johne’s Disease (JD), caused by Mycobacterium avim spp paratuberculosis (MAP), is a chronic and incurable disease of ruminants with devastating consequences to the dairy industry. MAP can alter the expression of genes and biological processes during the progression of JD. While some studies have examined the role of gene expression regulators like microRNA in the pathogenesis of JD, no study has explored the role of DNA methylation. This study therefore examined the effect of MAP on DNA methylation profile in the ileum lymph node (ILLN) of cows with subclinical MAP infection. DNA from ILLN tissues from five cows positive for MAP (MAP positive) and five negative cows (MAP negative) were extracted and subjected to whole genome bisulfite sequencing and bioinformatics analysis. A total of 6,394 differentially methylated cytosines (DMCs) and 3,946 differentially methylated regions (DMRs) (FDR < 0.05) were identified between MAP positive and negative cows. DMRs were annotated to 2,488 genes, including the promoters of 238 genes. Some genes with hypermethylated promoters like GRB10, EIF4E, SLC30A3, SOX30 or hypomethylated promoters like SLC11A1, HOXA4, SLC18A1 have been associated with JD or mycobacterial infections in cattle and/or humans. Functional annotation of DMR genes indicated enrichment in pathways previously associated with JD or human diseases with similar pathological conditions as JD, such as T/B cell receptor signaling pathway, Th17 cell differentiation, Cell adhesion molecules, Leukocyte transendothelial migration, HIF-1 signaling pathway and Chagas disease. Furthermore, enriched gene ontology terms like negative regulation of immune system process, negative regulation of cytokine secretion/production and negative regulation of inflammatory response suggest that MAP prevented or reduced the host immune response. Our data demonstrate that DNA methylation changes contribute to regulation of host immune responses to MAP infection and may be one of the mechanisms that MAP uses to subvert host immune responses for its long-term survival.