Identification of mirtrons in rice using MirtronPred: A tool for predicting plant mirtrons

Studies from flies and insects have reported the existence of a special class of miRNA, called mirtrons that are produced from spliced-out introns in a DROSHA-independent manner. The spliced-out lariat is debranched and refolded into a stem–loop structure resembling the pre-miRNA, which can then be processed by DICER into mature ~ 21 nt species. The mirtrons have not been reported from plants. In this study, we present MirtronPred, a web based server to predict mirtrons from intronic sequences. We have used the server to predict 70 mirtrons in rice introns that were put through a stringent selection filter to shortlist 16 best sequences. The prediction accuracy was subsequently validated by northern analysis and RT-PCR of a predicted Os-mirtron-109. The target sequences for this mirtron were also found in the rice degradome database. The possible role of the mirtron in rice regulon is discussed. The MirtronPred web server is available at http://bioinfo.icgeb.res.in/mirtronPred.

► Development of MirtronPred, a web based server to predict mirtons from introns.
► The server predicted 70 mirtrons from which 16 sequences were stringently filtered.
► A predicted mirtron, Os-mirton-109 was cloned and validated experimentally.
► The predicted mirtrons identified in the small RNA NGS (Illumina) database of rice.
► Identified the putative targets for the mirtronic miRNA in rice degradome database.