title: 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.
authors: a Plant Biology Division; Samuel Roberts Noble Foundation ; Ardmore , OK USA.
authors: Firoz
authors: F
authors: Ahmed
authors: Muthappa
authors: M
authors: Senthil-Kumar
authors: Seonghee
authors: S
authors: Lee
authors: Xinbin
authors: X
authors: Dai
authors: Kirankumar S
authors: KS
authors: Mysore
authors: Patrick Xuechun
authors: PX
authors: Zhao
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic / Q000706:statistics & numerical data; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D035683:MicroRNAs / Q000235:genetics*; D008969:Molecular Sequence Data; D012322:RNA Precursors / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics*; D058727:RNA, Small Untranslated / Q000235:genetics*; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017423:Sequence Analysis, RNA / Q000379:methods / Q000706:statistics & numerical data; D017386:Sequence Homology, Amino Acid
chemical_list: D029681:Arabidopsis Proteins; D035683:MicroRNAs; D012322:RNA Precursors; D012333:RNA, Messenger; D018749:RNA, Plant; D058727:RNA, Small Untranslated
keywords: RNA-Seq; arabidopsis; bioinformatics; isomiRs; miRNA; miRNA target prediction
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