Comprehensive analysis of small RNA-seq data reveals that combination of miRNA with its isomiRs increase the accuracy of target prediction in Arabidopsis thaliana

Abstract

Along with the canonical miRNA, distinct miRNA-like sequences called sibling miRNAs (sib-miRs) are generated from the same pre-miRNA. Among them, isomeric sequences featuring slight variations at the terminals, relative to the canonical miRNA, constitute a pool of isomeric sibling miRNAs (isomiRs). Despite the high prevalence of isomiRs in eukaryotes, their features and relevance remain elusive. In this study, we performed a comprehensive analysis of mature precursor miRNA (pre-miRNA) sequences from Arabidopsis to understand their features and regulatory targets. The influence of isomiR terminal heterogeneity in target binding was examined comprehensively. Our comprehensive analyses suggested a novel computational strategy that utilizes miRNA and its isomiRs to enhance the accuracy of their regulatory target prediction in Arabidopsis. A few targets are shared by several members of isomiRs; however, this phenomenon was not typical. Gene Ontology (GO) enrichment analysis showed that commonly targeted mRNAs were enriched for certain GO terms. Moreover, comparison of these commonly targeted genes with validated targets from published data demonstrated that the validated targets are bound by most isomiRs and not only the canonical miRNA. Furthermore, the biological role of isomiRs in target cleavage was supported by degradome data. Incorporating this finding, we predicted potential target genes of several miRNAs and confirmed them by experimental assays. This study proposes a novel strategy to improve the accuracy of predicting miRNA targets through combined use of miRNA with its isomiRs.

A Role for the F-Box Protein HAWAIIAN SKIRT in Plant microRNA Function

“…S8; Supplemental Table S5). Among those 217 broadly HWS-dependent genes, three were part of our silencing gene list, and even found amid the overlapping DE genes in hws-5; MIM156: the miRNAbiogenesis-related GLY-RICH RNA-BINDING PROTEIN7 (GRP7, At2G21660, also detected in mass spectroscopy), and the two miRNA-targets COPPER/ZINC SUPEROXIDE DISMUTASE 1 (CSD1, AT1G08830) and OLIGOPEPTIDE TRANSPORTER1 (OPT1, AT5G55930; van Nocker and Vierstra, 1993; Sunkar et al, 2006;Ahmed et al, 2014;Köster et al, 2014). Two of those, GRP7 and CSD1, are absent in the comparison of MIM156 to Col-0.…”

Biogenesis and biological implications of isomiRs in mammals- a review

“…The analysis of degradome data available in this experiment indicates the biological role of isomiRs in target cleavage. Further, the comparison of novel predicted and validated target genes with commonly targeted mRNA genes from Gene Ontology (GO) demonstrated that the validated targets are bound to isomiRs along with canonical miRNA [35]. IsomiRs have also been identified in human lymphoblastoid cell lines whose expression was population specific as well as gender-dependent.…”

isomiRs: Increasing Evidences of isomiRs Complexity in Plant Stress Functional Biology

“…On the basis of accumulated knowledge about isomiRs, as well as their abundance and involvement in target cleavage (Ahmed et al, 2014 ), several algorithms either as web-based or standalone tool have been developed, using read mapping approaches to delineate the repertoire of isomiRs abundance and expression (Table 1 ). Previously, we developed the first web-based tool, isomiRex (bioinfo1.uni-plovdiv.bg/isomiRex/), which provides the high-throughput classification and differential expression of isomiRs and supports a broad range of organisms including plants (Sablok et al, 2013 ).…”

“…revealed an abundance of tissue-specific isomiRs (392 isomiRs—miRNA and miRNA * -related—corresponding to 26 putative miRNA coding loci), which supports the hypothesis that the origin of isomiRs is not just a random functional event in plant post-transcriptional machinery (Colaiacovo et al, 2012 ). Realizing the potential of isomiRs and their ability to cleave targets (Ahmed et al, 2014 ), several studies started exploring their functional role in plants. In Phaseolus vulgaris , as many as 57 functional isomiRs spanning across 25 families have been identified in nodule development and phasiRNAs generation (Formey et al, 2015 ).…”