Assessment of DNA methylation in porcine immune cells reveals novel regulatory elements associated with cell-specific gene expression and immune capacity traits

Background Genetics studies in the porcine immune system have enhanced selection practices for disease resistance phenotypes and increased the efficacy of porcine models in biomedical research; however limited functional annotation of the porcine immunome has hindered progress on both fronts. Among epigenetic mechanisms that regulate gene expression, DNA methylation is the most ubiquitous modification made to the DNA molecule and influences transcription factor binding as well as gene and phenotype expression. Human and mouse DNA methylation studies have improved mapping of regulatory elements in these species, but comparable studies in the pig have been limited in scope. Results We performed whole-genome bisulfite sequencing to assess DNA methylation patterns in nine pig immune cell populations: CD21(+) and CD21(-) B cells, four T cell fractions (CD4(+), CD8(+), CD8(+)CD4(+), and SWC6 gamma delta(+)), natural killer and myeloid cells, and neutrophils. We identified 54,391 cell differentially methylated regions (cDMRs), and clustering by cDMR methylation rate grouped samples by cell lineage. 32,737 cDMRs were classified as cell lowly methylated regions (cLMRs) in at least one cell type, and cLMRs were broadly enriched in genes and regions of intermediate CpG density. We observed strong correlations between differential methylation and expression across immune cell populations, with cell-specific low methylation disproportionately impacting genes exhibiting enriched gene expression in the same cell type. Motif analysis of cLMRs revealed cell type-specific enrichment of transcription factor binding motifs, indicating that cell-specific methylation patterns may influence accessibility by trans-acting factors. Lastly, cDMRs were enriched for immune capacity GWAS SNPs, and many such overlaps occurred within genes known to influence immune cell development and function (CD8B, NDRG1). Conclusion Our DNA methylation data improve functional annotation of the porcine genome through characterization of epigenomic regulatory patterns that contribute to immune cell identity and function, and increase the potential for identifying mechanistic links between genotype and phenotype.

Automated summary

In this study, whole-genome bisulfite sequencing was performed to assess DNA methylation patterns in pig immune cell populations. The study identified differentially methylated regions (DMRs) and observed correlations between differential methylation and gene expression across immune cell populations. Cell-specific low methylation was found to disproportionately impact genes exhibiting enriched expression in the same cell type. The study also revealed cell type-specific enrichment of transcription factor binding motifs in lowly methylated regions. Furthermore, DMRs were enriched for immune capacity GWAS SNPs, suggesting their importance in immune cell development and function. These findings improve the functional annotation of the porcine genome and enhance the understanding of the links between genotype and phenotype.