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

Abstract

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.

Human mirtrons can express functional microRNAs simultaneously from both arms in a flanking exon-independent manner

“…29,30 Our results underline the importance of experimental validation of predicted mirtrons, especially in mammalian systems. In summary, we have confirmed that mir-877 and mir-1226 are typical mirtrons while mir-1233 might represent a different maturation pathway.…”

Most microRNAs in the single-cell alga Chlamydomonas reinhardtii are produced by Dicer-like 3-mediated cleavage of introns and untranslated regions of coding RNAs

“…This is a frequent feature of animal miRNAs whereas higher plant miRNAs are, with only few exceptions, from noncoding RNA precursors. It is estimated in animals that ∼40% of the entire miRNA population are from introns ) whereas, in plants, there are only three experimentally validated id-miRNAs (one and two in Arabidopsis thaliana and Oryza sativa, respectively) (Rajagopalan et al 2006;Zhu et al 2008;Joshi et al 2012). In one of these examples the Arabidopsis DCL1 strongly represses DCL1 mRNA abundance by cleavage of an miRNA precursor in intron 14 (Xie et al 2003;Rajagopalan et al 2006).…”

Active 5′ splice sites regulate the biogenesis efficiency of Arabidopsis microRNAs derived from intron-containing genes

“…Another specific class of miRNAs produced from introns are mirtrons, of which the maturation in animals does not require the nuclear step of miRNA biogenesis; instead, their precursors are products of spliceosome activity. In plants, 5 and 18 mirtron-like intervening sequences have been identified thus far in A. thaliana and Oryza sativa , respectively, using bioinformatics tools (42,43). However, the mechanism of their maturation comprising the involvement of the spliceosome and the microprocessor has still yet to be uncovered.…”