Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach

Jiandong Ding,Uwe Ohler,Jihong Guan,Shuigeng Zhou,Danqing Li

doi:10.1186/1471-2164-13-s3-s3

Jiandong Ding, Uwe Ohler + Show 3 more

Open Access

https://doi.org/10.1186/1471-2164-13-s3-s3

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Journal: BMC Genomics	Publication Date: Jun 1, 2012
Citations: 74	License type: CC BY 2.0

Affiliation: Fudan University, Duke University, Tongji University

Abstract

BackgroundMiRNA are about 22nt long small noncoding RNAs that post transcriptionally regulate gene expression in animals, plants and protozoa. Confident identification of MiRNA-Target Interactions (MTI) is vital to understand their function. Currently, several integrated computational programs and databases are available for animal miRNAs, the mechanisms of which are significantly different from plant miRNAs.MethodsHere we present an integrated MTI prediction and analysis toolkit (imiRTP) for Arabidopsis thaliana. It features two important functions: (i) combination of several effective plant miRNA target prediction methods provides a sufficiently large MTI candidate set, and (ii) different filters allow for an efficient selection of potential targets. The modularity of imiRTP enables the prediction of high quality targets on genome-wide scale. Moreover, predicted MTIs can be presented in various ways, which allows for browsing through the putative target sites as well as conducting simple and advanced analyses.ResultsResults show that imiRTP could always find high quality candidates compared with single method by choosing appropriate filter and parameter. And we also reveal that a portion of plant miRNA could bind target genes out of coding region. Based on our results, imiRTP could facilitate the further study of Arabidopsis miRNAs in real use. All materials of imiRTP are freely available under a GNU license at (http://admis.fudan.edu.cn/projects/imiRTP.htm).

Highlights

MiRNA are about 22nt long small noncoding RNAs that post transcriptionally regulate gene expression in animals, plants and protozoa
MicroRNAs [1] are a class of 20-nt to 24-nt small non-coding RNA that has emerged as a key regulator of gene activity
Plant miRNAs generally show a nearperfect complementary target mRNA which immensely facilitates computational predictions [8]. Taking advantage of this property, several methods were developed to search for antisense hits to known miRNAs on Arabidopsis mRNAs [9,10]. While both animals and plants rely to a different extent on RNA complementarity to define their targets, some comparable features are employed in target prediction methods/tools for both animal and plant miRNAs

Summary

Introduction

MiRNA are about 22nt long small noncoding RNAs that post transcriptionally regulate gene expression in animals, plants and protozoa. The miRNA:miRNA* duplex is methylated and translocated to Unlike animals, plant miRNAs generally show a nearperfect complementary target mRNA which immensely facilitates computational predictions [8]. Taking advantage of this property, several methods were developed to search for antisense hits to known miRNAs on Arabidopsis mRNAs [9,10]. RNAhybrid [11] was first developed to identify miRNA-Target duplexes in D. melanogaster, D. pseudoobscura, and A. gambiae, and was more recently adapted to the specific requirements of plant miRNA target prediction, with outstanding results in Arabidopsis thaliana [12,13]

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