Investigation into the miRNA/5' isomiRNAs function and drought-mediated miRNA processing in rice
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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.
KeywordsmiRNA 5′ isomiR Drought N22 miRNA-processing Rice
S.B. performed all the analysis related to miRNA processing and isomiR target identification, written and compiled the manuscript. S.V.J and R.J. developed the in silico pipeline. R.D.M analyzed the degradome data of rice for annotated miRs. S.R. was involved in the design, supervision, interpretation, and writing of the manuscript.
The present work was funded by the Department of Biotechnology (DBT), Government of India (Grant no. BT/PR10071/AGR/36/31/2007 and BT/PR628/AGR/36/674/2011) and the “Scheme to strengthen R&D Doctoral Research program” of Univ. of Delhi, Delhi, India. S.B. sincerely thanks the University of Delhi for the UTA fellowship for doctoral research. R.D.M. acknowledges University Grant Commission.
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