The prediction and expression of miR-203a-p and miR-29b against DNMT3B as well as TNFAIP3 in melanoma

The development of melanoma could be derived by microRNA (miRNA)-mediated epigenetic regulation of tumor suppressor genes and oncogenes. miRNAs target some genes such as DNA methyltransferase 3-beta (DNMT3B) and consequently, DNMT3B could induce the expression of various genes like TNFAIP3. Therefore, the present study predicted the miRNAs targeting DNMT3B, and also evaluated the expression of TNFAIP3 in the melanoma cell lines. Analysis of gene suppression pathways and prediction of the targets of miRNAs including 3′UTR mRNA of DNMT3B gene was performed through various popular algorithms including miRanda, miRDB, miRWalk, RNAhybrid, PICTAR4, PICTAR5, PITA, RNA22, and Targetscan. Total RNA was extracted from the A375 cell line as melanoma cell and melanocyte cell line as a normal cell line. The expression of miRNAs, DNAMT3B, and TNFAIP3 was measured using Real-time PCR. More than twenty miRNAs gained the highest scores by targeting the DNMT3B which among them hsa-miR-203a-p and hsa-miR-29b* were selected. A reduction in miRNAs and TNFAIP3 expression was observed according to the Real-time PCR (p-value 0.0323 and fold change 0.656). Also, the expression of DNMT3B increased significantly compared to the control group (p-value 0.0015 and fold change 3.482). The current study exhibited a decrease in the expression of TNFAIP3, miR-203a-pa-p, and miR-29b along with an increase in the expression of DNMT3B. These findings provided a helpful view of a new epigenetic-based approach for the early diagnosis of melanoma. •Melanoma could be regulated by epigenetic changes.•miRNAs induce epigenetic changes by targeting specific genes.•miR-203a-3p and miR-29a* demonstrated the highest score to target the DNMT3B gene.•The expression of miR-203a-3p, miR-29a* and TNFAIP3 was reduced while DNMT3B elevated.