Crescentic glomerulonephritis (CRGN) is a significant cause of renal failure in humans and often has an autoimmune aetiology. The Wistar-Kyoto (WKY) rat has a marked susceptibility to CRGN, whilst the Lewis (Lew) rat is resistant, making this a useful model system to study molecular mechanisms underlying the disease. Previous work has demonstrated the importance of macrophages in CRGN and defined some of the genetic determinants underlying CRGN susceptibility. Given emerging data linking epigenetic modifications to both macrophage activation and autoimmune diseases, I hypothesized that variation in DNA methylation in macrophages could contribute to susceptibility to glomerulonephritis in the WKY rat.

This thesis investigated this hypothesis using both experimental and bioinformatic approaches. Experimental methods including locus-specific sequencing of differentially expressed genes and unbiased whole genome sequencing allowed investigation of variability in DNA methylation between the two rat strains. Further analyses of methylation in the pathogenesis of CRGN was achieved by both in vivo experiments in WKY rats and in vitro work on cultured macrophages using an inhibitor of DNA methylation. Bioinformatic analysis of sequencing and transcriptional data allowed examination of the affect of DNA methylation on gene expression in rat macrophages, and histone and transcription factor binding site data were used to explore the interaction of methylation and distant gene regulatory sequences.

Whole genome shotgun bisulfite sequencing revealed that WKY bone marrow-derived macrophages were generally less methylated than Lew, and more than 13,000 CpG dinucleotides were robustly differentially methylated between the two strains. Multiplexed PCR sequencing was used to verify whole genome methylation signatures. At the genome-wide level, the relationship between methylation and expression was complex but my analyses suggested that differentially methylated CpGs might be enriched at distant gene regulatory elements.

These data offer evidence of an association between DNA methylation and susceptibility to CRGN and therefore impart a basis for understanding the distinct genes, pathways and gene regulatory elements that could underlie this association.