Exploration of the Effect on Genome-Wide DNA Methylation by miR-143 Knock-Out in Mice Liver

• Published in: International journal of molecular sciences Vol. 22; no. 23; p. 13075
• Main Authors: Chen, Xingping, Luo, Junyi, Liu, Jie, Chen, Ting, Sun, Jiajie, Zhang, Yongliang, Xi, Qianyun
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 03.12.2021; MDPI
• Subjects: Animals; Apoptosis; Binding sites; Bioinformatics; Biomarkers; Cell growth; Computer science; CpG Islands; CRISPR; DNA Methylation; Epigenesis, Genetic; Epigenetics; Epigenomics; GC Rich Sequence; Gene expression; Genome; Genomes; High-Throughput Nucleotide Sequencing; Interdisciplinary subjects; Kinases; Liver - metabolism; Liver cancer; Liver diseases; Male; Mammals; Metabolism; Mice; Mice, Knockout; MicroRNAs; MicroRNAs - genetics; MicroRNAs - metabolism; Physiology; Promoter Regions, Genetic; Proteins; Quality control; Sulfites; Transgenic animals; Whole Genome Sequencing; DNA methylation; liver diseases; Whole-Genome Bisulfite Sequencing; miR-143
• DOI: 10.3390/ijms222313075
• ISSN: 1422-0067; 1661-6596

MiR-143 play an important role in hepatocellular carcinoma and liver fibrosis via inhibiting hepatoma cell proliferation. DNA methyltransferase 3 alpha (DNMT3a), as a target of miR-143, regulates the development of primary organic solid tumors through DNA methylation mechanisms. However, the effect of miR-143 on DNA methylation profiles in liver is unclear. In this study, we used Whole-Genome Bisulfite Sequencing (WGBS) to detect the differentially methylated regions (DMRs), and investigated DMR-related genes and their enriched pathways by miR-143. We found that methylated cytosines increased 0.19% in the miR-143 knock-out (KO) liver fed with high-fat diet (HFD), compared with the wild type (WT). Furthermore, compared with the WT group, the CG methylation patterns of the KO group showed lower CG methylation levels in CG islands (CGIs), promoters and hypermethylation in CGI shores, 5′UTRs, exons, introns, 3′UTRs, and repeat regions. A total of 984 DMRs were identified between the WT and KO groups consisting of 559 hypermethylation and 425 hypomethylation DMRs. Furthermore, DMR-related genes were enriched in metabolism pathways such as carbon metabolism (serine hydroxymethyltransferase 2 (Shmt2), acyl-Coenzyme A dehydrogenase medium chain (Acadm)), arginine and proline metabolism (spermine synthase (Sms), proline dehydrogenase (Prodh2)) and purine metabolism (phosphoribosyl pyrophosphate synthetase 2 (Prps2)). In summary, we are the first to report the change in whole-genome methylation levels by miR-143-null through WGBS in mice liver, and provide an experimental basis for clinical diagnosis and treatment in liver diseases, indicating that miR-143 may be a potential therapeutic target and biomarker for liver damage-associated diseases and hepatocellular carcinoma.