In silico identification of rice and human miRNAs sequences within tRFs of Oryza sativa and expression analysis of rice tRFs with their corresponding miRNAs

Abstract

Both tRFs (tRNA-derived fragments) and miRNAs (microRNAs) are the nearly same size and can be generated from tRNAs. Hence, it is essential to elucidate these contemporary sequences in the context of miRNA/tRF generation and sequencing data analysis. In India, rice is a staple food and drought, and infections of rice fields pose significant challenges to achieve maximum productions. Understanding the roles of tRFs and miRNAs in such harsh conditions will give insights into managing crop productivity. Hence, we analyzed the miRNA sequences within tRFs of Oryza sativa. About 2554 tRF sequences were analyzed for miRNA sequences in miRBAse. Our data suggested that tRFs PT19254 and PT449163 harbor miR-1871 and miR-1440a/b. The tRFs were subjected to mRNA target analysis. Also, we analyzed the expression of three miRNAs with their corresponding tRFs and found that miR-1871, miR-1440b/a, PT403117, PT449163 and PT19254 showed higher expression in leaf than shoot or root. Furthermore, miRNAs derived from plants can target genes in plant-consuming organisms, and these are designated as cross-kingdom miRNAs. We analyzed for human miRNA sequences within tRFs (n = 168) from O.sativa and found 20 human miRNA sequences within tRFs. Of these, miR-4778-3p, miR-43c-3p, miR-1260a, miR-127-5p and miR-1183 are implicated in cancer. To summarize, our results give insights in choosing tRF/miRNAs for analysis in the context of cancer therapeutics or rice crop management.