The purpose of this study was to evaluate genome-wide DNA methylation changes in intestinal mucosa tissue of adult patients with
Crohn's disease comprehensively. DNA methylation chip was used to analyze abnormal methylation sites among penetrating and non-penetrating intestinal mucosa tissue of
Crohn's disease and normal intestinal mucosa tissue of healthy controls. Methylation abnormalities of different locus were verified by pyrosequencing and quantitative polymerase chain reaction. Differential DNA methylation sites were participated in the positive regulation of apoptosis and the positive regulation of
IL-8 production and were enriched in signaling pathways related to
inflammatory bowel disease and
extracellular matrix receptor interaction signaling pathways. Correlation analysis showed that the methylation abnormalities of
HLA-DRB1 (r = - 0.62, P < 0.001), MUC1 (r = - 0.45, P = 0.01), YPEL5 (r = - 0.55, P = 0.001) and CBLB (r = - 0.62, P < 0.001) were significantly negatively correlated with their relative expression levels. The degree of methylation abnormality of MUC1 was negatively correlated with the disease activity score of
Crohn's disease (r = - 0.50, P = 0.01). Apoptosis,
interleukin-8 production and abnormal extracellular matrix might be involved in the mechanism of penetrating intestinal mucosal lesions in
Crohn's disease. The degree of abnormal methylation of MUC1 was negatively correlated with the disease activity of
Crohn's disease.