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Background  Many genome- and epigenome-wide association studies (GWAS and EWAS) and studies of promoter methylation of candidate genes for inflammatory bowel disease (IBD) have demonstrated significant associations between genetic and epigenetic changes and IBD. Independent GWA studies have identified genetic variants in the  BACH2 ,  IL6ST ,  LAMB1 ,  IKZF1 , and  MGAT3  loci to be associated with both IBD and immunoglobulin G (IgG) glycosylation.Methods  Using bisulfite pyrosequencing, we analyzed CpG methylation in promoter regions of these five genes from peripheral blood of several hundred IBD patients and healthy controls (HCs) from two independent cohorts, respectively.    Results  We found significant differences in the methylation levels in the  MGAT3  and  BACH2  genes between both Crohn’s disease and ulcerative colitis when compared to HC. The same pattern of methylation changes was identified for both genes in CD19 +  B cells isolated from the whole blood of a subset of the IBD patients. A correlation analysis was performed between the  MGAT3  and  BACH2  promoter methylation and individual IgG glycans, measured in the same individuals of the two large cohorts.  MGAT3  promoter methylation correlated significantly with galactosylation, sialylation, and bisecting GlcNAc on IgG of the same patients, suggesting that activity of the GnT-III enzyme, encoded by this gene, might be altered in IBD. The correlations between the  BACH2  promoter methylation and IgG glycans were less obvious, since  BACH2  is not a glycosyltransferase and therefore may affect IgG glycosylation only indirectly.    Conclusions  Our results suggest that epigenetic deregulation of key glycosylation genes might lead to an increase in pro-inflammatory properties of IgG in IBD through a decrease in galactosylation and sialylation and an increase of bisecting GlcNAc on digalactosylated glycan structures. Finally, we showed that CpG methylation in the promoter of the  MGAT3  gene is altered in CD3 +  T cells isolated from inflamed mucosa of patients with ulcerative colitis from a third smaller cohort, for which biopsies were available, suggesting a functional role of this glyco-gene in IBD pathogenesis.    Electronic supplementary material  The online version of this article (10.1186/s13148-018-0507-y) contains supplementary material, which is available to authorized users.

Promoter methylation of the MGAT3 and BACH2 genes correlates with the composition of the immunoglobulin G glycome in inflammatory bowel disease