Genome-wide DNA methylation dynamics in carbon tetrachloride-induced mice liver fibrosis

Objective(s): Many persistent harmful stimuli can result in chronic liver diseases, which lead to about ۲ million deaths per year in the whole world. Liver fibrosis was found to exist in all kinds of chronic liver diseases. Many studies suggested that DNA methylation was associated with the pathogenesis of liver fibrosis. This study aimed to quantitatively detect DNA methylation changes in the whole genome in fibrotic liver tissues of mice.Materials and Methods: Liver fibrosis was induced by intraperitoneal injection of carbon tetrachloride (CCl۴) for ۴ weeks. A genome-wide methylome analysis was performed using ۸۵۰K BeadChips assays. The methylation status of ۲۷ CpG dinucleotides located in ۳ genes was detected by pyrosequencing to confirm chip data accuracy, and mRNA expressions of these ۳ genes were examined by RT-qPCR methods.Results: A total of ۱۳۰,۰۶۸ differentially methylated sites (DMS, ۵۸,۴۷۴ hypermethylated, and ۷۱,۵۹۴ hypomethylated) between fibrotic liver tissues and control mice liver tissues were identified by the ۸۵۰k BeadChips array. Consistency between pyrosequencing data and ۸۵۰k BeadChips array data was observed (R=۰.۹۲۸; P<۰.۰۱). Apoptosis, positive regulation of transcription of Notch receptor target, and negative regulation of p۳۸MAPK signal cascade activities were significantly enriched in the Gene Ontology (GO) analyses. Cholesterol metabolism, bile secretion, and more biosynthesis and metabolism pathways were enriched in KEGG pathway analyses. Ten key genes were identified by the Cytoscape plugin cytoHubba. Conclusion: ۷۸۵۰ genes were found to have methylation change in fibrotic liver tissues of mice, which facilitates future research for clinical application.

Keywords:

CCl۴ , DNA , Fibrosis , Liver , Methylation