Several microRNAs (miRNAs) are involved in the differentiation of neurons and neurogenesis in vertebrates’ brain. However, there is scant knowledge of miRNAs and their Target genes in fish. Microarray is recognized as a standard method for a general study of genes that are under miRNAs’ control, although the high cost of this method has limited its application. With advances in bioinformatics algorithms and computer simulation, mRNA Targets for miRNAs can be predicted. Therefore, this study tries to determine genes and the relevant miRNAs by investigating the bioinformatics of genes and miRNAs involved in regulating active genes in differentiating neurons and neurogenesis in the brain of zebrafish with the help of Target Scan and DIANA tools. The results of bioinformatics investigations indicate that expression of neurod6b, neurod2, neurod4, olfm1a and olfm1b, gle1, sox11a and sox11b, c adm1b, notch2 and notch1b genes is more likely to be influenced by dremiRNAs during neurogenesis. In conclusion, the product of these genes can be used as a new appropriate candidate in experimental studies for understanding neurogenesis in the brain of zebrafish.

Regeneration is an endogenous process that culminates in restoring tissue and organ function completely. While the regeneration capacity in mammals is limited to specific tissues, lower vertebrates such as zebrafish can regenerate entire organs and most adult tissues. MicroRNAs are small non-coding molecules that regulate various biological processes (such as repair, differentiation, apoptosis, etc.) by controlling the expression of Target genes. An important challenge in the study of microRNAs is to identify and predict the genes that are Targeted by these small molecules. In recent years, various methods such as microarray, northern blot, and qRT-PCR have been introduced to identify the Target genes of microRNAs, but the high cost has limited the use of these methods. With the advancement of computational methods and bioinformatics algorithms, Target genes of microRNAs can be identified and predicted at a lower cost. In this study, an attempt was made to identify the genes and microRNAs involved in the repair and regeneration processes of zebrafish (Danio rerio) tissues using the software of Target Scan and DIANA databases with a bioinformatics approach. This research showed that the expression of Stat3, Dot1l, Pax6b, Smarca5, Mmp9, Cx43, Tnfb, Sox2, Ascl1a, and Hspd1 genes is most likely to be regulated in the process of repair and regeneration of zebrafish tissues under the influence of different microRNAs. Therefore, the mentioned genes can be suitable candidates for the laboratory investigation of genes involved in the tissue repair and regeneration process of the desired species.

Objective(s): An earlier meta-analysis on gene expression data derived from four microarray, two cDNA library, and one SAGE experiment had identified RGS5 as one of only ten non-housekeeping genes that were reported to be expressed in human trabecular meshwork (TM) cells by all studies. RGS5 encodes regulator of G-protein signaling-5. The TM tissue is the route of aqueous fluid outflow, and is relevant to the pathology of glaucoma. MicroRNAs constitute the most recently identified components of the cellular machinery for gene regulation in eukaryotic cells. Given our long standing interest in glaucoma, we aimed to identify miRNAs that may Target RGS5.Materials and Methods: Eight miRNAs were selected for study using bioinformatics tools and available data on miRNAs expressed in the eye. Their effects were assessed using the dual luciferase assay. 3’-UTR segments of RGS5 mRNA were cloned downstream of a luciferase coding gene in psiCHECK2 vectors, and these were co-transfected with each of the miRNAs into HEK293 cells.Results: The outcomes evidenced that one or more of the segments are in fact Targeted by miR-7, miR-9, miR-96, miR-23a, miR-23b, miR-204, and miR-211. Down regulations by the miRNAs were statistically significant. The effect of miR-204 is considered particularly important as this miRNA is well known to regulate eye development and to affect multiple ocular functions.Conclusion: Our results justify further studies on regulation of RGS5 expression and RGS5 downstream functions by these miRNAs.