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

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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
 
Creator Ahmed, Firoz
Senthil-Kumar, Muthappa
Lee, Seonghee
Dai, Xinbin
Mysore, Kirankumar S
Zhao, Patrick Xuechun
 
Subject arabidopsis
bioinformatics
isomiRs
miRNA
miRNA target prediction
RNA-Seq
 
Description Accepted date: 29 Oct 2014
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.
Project funding support: National Science Foundation (Grant
No. ABI-0960897); Oklahoma Center for the Advancement of
Science and Technology (OCAST Project No. PSB11–004);
Samuel Roberts Noble Foundation.
 
Date 2015-11-26T09:47:46Z
2015-11-26T09:47:46Z
2014
 
Type Article
 
Identifier RNA Biol., 11(11): 1414-1429
1547-6286
http://172.16.0.77:8080/jspui/handle/123456789/391
http://www.tandfonline.com/doi/full/10.1080/15476286.2014.996474
10.1080/15476286.2014.996474
 
Language en_US
 
Publisher Taylor & Francis Group