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Published on: September 7, 2017
Differential DNA methylation landscape of miRNAs genes in mice liver fibrosis
Deming Li1, Wentong Yang1, Jiaojiao Pang1
1State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis (111 Project), College of Life Science, Henan Normal University, Xinxiang, Henan, China.
Background:
Patients with chronic liver disease were found nearly all to have liver fibrosis, which is characterized by excess accumulation of extracellular matrix (ECM) proteins. While ECM accumulation can prevent liver infection and injury, it can destroy normal liver function and architecture. miRNA's own regulation was involved in DNA methylation change. The purpose of this study is to detect DNA methylation landscape of miRNAs genes in mice liver fibrosis tissues.
Methods:
Male mice (10-12 weeks) were injected CCl4 from abdominal cavity to induced liver fibrosis. 850 K BeadChips were used to examine DNA methylation change in whole genome. The methylation change of 16 CpG dinucleotides located in promoter regions of 4 miRNA genes were detected by bisulfite sequencing polymerase chain reaction (BSP) to verify chip data accuracy, and these 4 miRNA genes' expressions were detected by RT-qPCR methods.
Results:
There are 769 differential methylation sites (DMS) in total between fibrotic liver tissue and normal mice liver tissue, which were related with 148 different miRNA genes. Chips array data were confirmed by bisulfite sequencing polymerase chain reaction (R = 0.953; P < 0.01). GO analysis of the target genes of 2 miRNA revealed that protein binding, cytoplasm and chromatin binding activity were commonly enriched; KEGG pathway enrichment analysis displayed that TGF-beta signaling pathway was commonly enriched.
Conclusion:
The DNA of 148 miRNA genes was found to have methylation change in liver fibrosis tissue. These discoveries in miRNA genes are beneficial to future miRNA function research in liver fibrosis.
Insights
Liver fibrosis in mice involves significant DNA methylation changes in 148 microRNA (miRNA) genes. These findings offer insights into miRNA gene regulation and potential therapeutic targets for liver fibrosis.
Area of Science:
- Epigenetics
- Molecular Biology
- Hepatology
Background:
- Chronic liver disease often leads to liver fibrosis, characterized by excessive extracellular matrix accumulation that disrupts liver function.
- MicroRNA (miRNA) regulation is implicated in DNA methylation changes within the liver.
- Understanding these epigenetic modifications is crucial for addressing liver fibrosis pathology.
Purpose of the Study:
- To investigate the DNA methylation landscape of miRNA genes in a mouse model of liver fibrosis.
- To identify specific miRNA genes affected by DNA methylation during fibrosis development.
Main Methods:
- Liver fibrosis was induced in male mice using carbon tetrachloride (CCl4) injection.
- Genome-wide DNA methylation was analyzed using 850K BeadChips.
- Bisulfite sequencing polymerase chain reaction (BSP) and RT-qPCR were employed to validate chip data and assess miRNA gene expression.
Main Results:
- A total of 769 differential methylation sites (DMS) were identified between fibrotic and normal liver tissues, associated with 148 unique miRNA genes.
- Chip array data were validated by BSP (R=0.953; P<0.01).
- Gene Ontology (GO) and KEGG pathway analyses indicated enrichment in protein binding, cytoplasm, chromatin binding, and the TGF-beta signaling pathway for target genes of two specific miRNAs.
Conclusions:
- Significant DNA methylation changes were observed in 148 miRNA genes within liver fibrosis tissues.
- These findings provide a foundation for future research into the functional roles of specific miRNAs in the pathogenesis of liver fibrosis.
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