Bioinformatics study of microRNAs effect on the expression of genes involved in the process of tissue repair and regeneration of zebrafish (Danio rerio)

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.