microRNAs have attracted interest because of their regulatory effects on gene expression. Experimental detection of potential targets of miRNAs is a laborious task. Considering the expensive techniques of detection, computational approaches for miRNA target prediction can be used as the first step in miRNA research. A large number of tools and algorithms have been developed during the last two decades, led to problems such as confusion in selecting an appropriate tool and false positive or negative results. Therefore, one of the most frequent problems and critical issues of miRNA research is finding a reliable miRNA target prediction tool. In this study, we have proposed a research direction and introduced user-friendly and current databases and tools with the highest accuracy. To verify whether our proposed research direction is practical, we have provided a case example of predicting a miRNA which can target negative regulators of osteogenesis and experimentally evaluated the accuracy of the prediction results by Real-Time PCR and Luciferase assay. The results of RT-qPCR and Luciferase assay indicated a significant decline in expression of Dickkopf-related protein 1 (DKK1) and tumor necrosis factor ligand superfamily member 11 (TNFSF11) as the key negative regulators of osteogenesis upon overexpression of miR-4699-3p. The results emphasize the validity and importance of accurate in silico investigation as the first step in experimental studies. This is the first report detailing the prediction and validation of miR-4699-3p target genes. We suggest hsa-miR-4699 for further investigation as an osteogenic miRNA for therapeutics purposes.
Keywords: DKK1; TNFSF11; miRNA; regulators of osteogenesis.
© 2018 Wiley Periodicals, Inc.