Discovering Numerical Differences between Animal and Plant microRNAs.

Rongsheng Zhu,Zhanguo Zhang,Yang Li,Dawei Xin,Zhenbang Hu,Qingshan Chen,Zhaoming Qi

doi:10.1371/journal.pone.0165152

Abstract

Previous studies have confirmed that there are many differences between animal and plant microRNAs (miRNAs), and that numerical features based on sequence and structure can be used to predict the function of individual miRNAs. However, there is little research regarding numerical differences between animal and plant miRNAs, and whether a single numerical feature or combination of features could be used to distinguish animal and plant miRNAs or not. Therefore, in current study we aimed to discover numerical features that could be used to accomplish this. We performed a large-scale analysis of 132 miRNA numerical features, and identified 17 highly significant distinguishing features. However, none of the features independently could clearly differentiate animal and plant miRNAs. By further analysis, we found a four-feature subset that included helix number, stack number, length of pre-miRNA, and minimum free energy, and developed a logistic classifier that could distinguish animal and plant miRNAs effectively. The precision of the classifier was greater than 80%. Using this tool, we confirmed that there were universal differences between animal and plant miRNAs, and that a single feature was unable to adequately distinguish the difference. This feature set and classifier represent a valuable tool for identifying differences between animal and plant miRNAs at a molecular level.

Highlights

IntroductionPlant and animal microRNAs (miRNAs) play crucial roles in developmental timing[1,2,3,4,5,6,7,8,9,10], cellular differentiation[11, 12], proliferation[13,14,15,16,17,18,19,20], apoptosis[21,22,23,24,25,26], cell identity and fate[1], and response to environmental stress[11, 12, 27], and appear to predominantly exert their influence by controlling their target genes
We found several numerical features, which include helix number, stack number, length of pre-miRNA, minimum free energy (MFE) and so on that could be used to differentiate between plant and animal miRNA genes
There were significant differences between animal and plant miRNAs based on each of the 17 numerical features, none of them could be used in isolation to reliably assess miRNAs

Summary

Introduction

Plant and animal microRNAs (miRNAs) play crucial roles in developmental timing[1,2,3,4,5,6,7,8,9,10], cellular differentiation[11, 12], proliferation[13,14,15,16,17,18,19,20], apoptosis[21,22,23,24,25,26], cell identity and fate[1], and response to environmental stress[11, 12, 27], and appear to predominantly exert their influence by controlling their target genes. There are many obvious similarities between plant and animal miRNAs [28,29,30,31]. Their mature lengths always range from 19 to 24 nucleotides, they regulate gene expression through interactions with target mRNAs, and these targets are often involved in regulating key developmental events. The first step of animal miRNA biogenesis involves DROSHA nuclease, but this role is carried out by DCL1 in plants.

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Conclusion