Investigation into the miRNA/5' isomiRNAs function and drought-mediated miRNA processing in rice

MicroRNAs lie at the core of biological regulatory networks in plants. The recent discovery of isomiRs that are length variants of the annotated mature miRNAs has further unveiled the complexity of miRNome. Delineation of their functional relevance is critical to understand the complete functional spectrum of the miRNome. To apprehend the role of 5′ isomiRs in rice, we performed a comprehensive analysis of the annotated miRNA pool using 8 deep-sequencing datasets from flag leaf and spikelet tissues from two cultivars of rice viz. N22 and PB1 grown under control and drought conditions. The products of the 5′ start site variability termed as “5 ' isomiRs” were found to be widespread in all the datasets. It was possible to identify several 5′ isomiRs that were highly distinct and abundant and supported by more than 90% of the tags that map in the region. Majority of miRNA/5′ isomiR pair share similar tissue and drought-mediated expression dynamics. Analysis of the degradome data identified targets for several of these 5′ isomiRs, thereby confirming their biological activity. Since the isomiRs are length variants at the 5′ end, the target sites were found to be accordingly shifted as compared to the target site of the annotated miRNA. Further we also observed that drought affects the processing accuracy of several miRNAs across all tissues of both the cultivars leading to differential accumulation of 5′ isomiR/miRNA pair.