Genome-wide DNA methylation and transcriptome analyses reveal genes involved in immune responses of pig peripheral blood mononuclear cells to poly I:C

Abstract

DNA methylation changes play essential roles in regulating the activities of genes involved in immune responses. Understanding of variable DNA methylation linked to immune responses may contribute to identifying biologically promising epigenetic markers for pathogenesis of diseases. Here, we generated genome-wide DNA methylation and transcriptomic profiles of six pairs of polyinosinic-polycytidylic acid-treated pig peripheral blood mononuclear cell (PBMC) samples and corresponding controls using methylated DNA immunoprecipitation sequencing and RNA sequencing. Comparative methylome analyses identified 5,827 differentially methylated regions and 615 genes showing differential expression between the two groups. Integrative analyses revealed inverse associations between DNA methylation around transcriptional start site and gene expression levels. Furthermore, 70 differentially methylated and expressed genes were identified such as TNFRSF9, IDO1 and EBI3. Functional annotation revealed the enriched categories including positive regulation of immune system process and regulation of leukocyte activation. These findings demonstrated DNA methylation changes occurring in immune responses of PBMCs to poly I:C stimulation and a subset of genes potentially regulated by DNA methylation in the immune responses. The PBMC DNA methylome provides an epigenetic overview of this physiological system in response to viral infection, and we expect it to constitute a valuable resource for future epigenetic epidemiology studies in pigs.

Contrasting effects of acute and chronic stress on the transcriptome, epigenome, and immune response of Atlantic salmon

“…Evidence suggests that the relationship between DNA methylation and gene expression varies widely across the genome, and occurs on a gene-specific basis [48,49]. Here we found evidence of a significant, transcriptomewide negative correlation between DNA methylation level in putative promoters and gene expression, which is consistent with previous reports in mammals and fish [50][51][52]. In contrast, there was no linear relationship between gene-body methylation and gene expression; however there was some evidence of a more complex, heterogeneous, relationship.…”

Exogenous adrenocorticotropic hormone affects genome‐wide DNA methylation and transcriptome of corpus luteum in sows

“…DNA methylation is an epigenetic mechanism that regulates gene expression in response to environmental stimuli (39,41). Although the genome-wide DNA methylation patterns of many tissues have been reported (42)(43)(44), the methylation maps in CL remain largely undetermined. In this study, we systematically investigated the global methylation patterns of CLs in sows.…”

A Systems Approach to Study Immuno- and Neuro-Modulatory Properties of Antiviral Agents

“…The current approach can also utilize genomics and epigenomics [ 51 , 52 ]. Both techniques were used successfully to link certain viral diseases with genetic variants and epigenetic markers in resting and stimulated monocytes and dendritic cells [ 29 , 53 , 54 , 55 , 56 , 57 ]. Tying these techniques with transcriptomics, proteomics and metabolomics could allow identification of biomarkers for side effect susceptibility and provide a better understanding of how genetic and epigenetic variations contribute to the efficacy of treatment of viral infections.…”