Identification of some Echinophora platyloba miRNAs using computational methods and the effect of these miRNAs in the expression of TLN2 and ZNF521 genes in different human body organs

Abstract

MicroRNAs (miRNAs) are small (~22 nucleotides) non-coding endogenous RNA molecules that negatively regulate gene expression at the post-transcriptional level by degrading the target protein-coding mRNA genes or suppressing translation in plants, which consequently participate in a variety of biological and metabolic processes in both animals and plants. Detection of miRNAs is chiefly carried out by microarray, real-time-PCR, northern blot, and bioinformatics approaches. Bioinformatics or in silico-based approaches are the easiest and cheapest ways to identify desired miRNAs. In this study, several miRNAs in Echinophora platyloba were identified, and their potential roles were reported. E. platyloba, which belongs to the Umbelliferae family, is an endemic plant in Iran found in the Kermanshah, Hamedan, and Lorestan provinces; it has important medicinal uses such as cytotoxic activity in breast cancer, treatment of dysmenorrhea, central and peripheral analgesic effects, and hepatoprotective effects on acute acetaminophen-induced liver injuries. To this end, the RNA was extracted from E. platyloba leaf and sent to the Beijing genome institute for RNA sequencing. After quality control, low-quality data was filtered, and de novo assembly was performed. Detection of miRNAs was then performed by miRDeep (v37) and miRBase tools. Accordingly, we identified seven miRNAs from the leaf dataset, and their secondary structures were evaluated. Target genes of the detected miRNAs were identified through the psRNA target website.

Keywords

• echinophora platyloba
• microrna
• ngs
• rna-seq
• transcriptome