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

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).

[1]  Ana Kozomara,et al.  miRBase: integrating microRNA annotation and deep-sequencing data , 2010, Nucleic Acids Res..

[2]  Tongbin Li,et al.  miRecords: an integrated resource for microRNA–target interactions , 2008, Nucleic Acids Res..

[3]  Chi-Ying F. Huang,et al.  miRTarBase: a database curates experimentally validated microRNA–target interactions , 2010, Nucleic Acids Res..

[4]  Hanah Margalit,et al.  RepTar: a database of predicted cellular targets of host and viral miRNAs , 2010, Nucleic Acids Res..

[5]  Baohong Zhang,et al.  Bioinformatics Applications Note Data and Text Mining Target-align: a Tool for Plant Microrna Target Identification , 2022 .

[6]  Martin Reczko,et al.  The database of experimentally supported targets: a functional update of TarBase , 2008, Nucleic Acids Res..

[7]  Scott B. Dewell,et al.  Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP , 2010, Cell.

[8]  Sun Mi Park,et al.  MicroRNAs: key players in the immune system, differentiation, tumorigenesis and cell death , 2008, Oncogene.

[9]  Shuigeng Zhou,et al.  MiRenSVM: towards better prediction of microRNA precursors using an ensemble SVM classifier with multi-loop features , 2010, BMC Bioinformatics.

[10]  Terry Gaasterland,et al.  Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets , 2004, Genome Biology.

[11]  Marc Rehmsmeier,et al.  Comprehensive prediction of novel microRNA targets in Arabidopsis thaliana , 2009, Nucleic acids research.

[12]  Dang D. Long,et al.  Potent effect of target structure on microRNA function , 2007, Nature Structural &Molecular Biology.

[13]  Xiaowei Wang,et al.  Sequence analysis Prediction of both conserved and nonconserved microRNA targets in animals , 2007 .

[14]  A. T. Freitas,et al.  Current tools for the identification of miRNA genes and their targets , 2009, Nucleic acids research.

[15]  R. Giegerich,et al.  Fast and effective prediction of microRNA/target duplexes. , 2004, RNA.

[16]  Kenji Suzuki,et al.  A detailed investigation of accessibilities around target sites of siRNAs and miRNAs , 2011, Bioinform..

[17]  V. Ambros,et al.  The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 , 1993, Cell.

[18]  James C. Carrington,et al.  Specificity of ARGONAUTE7-miR390 Interaction and Dual Functionality in TAS3 Trans-Acting siRNA Formation , 2008, Cell.

[19]  Ming Chen,et al.  RNA editing of nuclear transcripts in Arabidopsis thaliana , 2010, BMC Genomics.

[20]  D. Bartel,et al.  Endogenous siRNA and miRNA Targets Identified by Sequencing of the Arabidopsis Degradome , 2008, Current Biology.

[21]  Ivo L. Hofacker,et al.  Vienna RNA secondary structure server , 2003, Nucleic Acids Res..

[22]  Javier F. Palatnik,et al.  Specific effects of microRNAs on the plant transcriptome. , 2005, Developmental cell.

[23]  Shuigeng Zhou,et al.  miRFam: an effective automatic miRNA classification method based on n-grams and a multiclass SVM , 2011, BMC Bioinformatics.

[24]  David P. Bartel,et al.  A Two-Hit Trigger for siRNA Biogenesis in Plants , 2006, Cell.

[25]  Hui Zhou,et al.  starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data , 2010, Nucleic Acids Res..

[26]  O. Voinnet.  Origin, Biogenesis, and Activity of Plant MicroRNAs , 2009, Cell.

[27]  Yi-Hsuan Chen,et al.  miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes , 2007, Nucleic Acids Res..

[28]  Detlef Weigel,et al.  Highly Specific Gene Silencing by Artificial MicroRNAs in Arabidopsis[W][OA] , 2006, The Plant Cell Online.

[29]  Uwe Ohler,et al.  Assessing the Utility of Thermodynamic Features for microRNA Target Prediction under Relaxed Seed and No Conservation Requirements , 2011, PloS one.

[30]  Patrick Xuechun Zhao,et al.  psRNATarget: a plant small RNA target analysis server , 2011, Nucleic Acids Res..

[31]  S. Luo,et al.  Global identification of microRNA–target RNA pairs by parallel analysis of RNA ends , 2008, Nature Biotechnology.

[32]  Webb Miller,et al.  CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets , 2009, Bioinform..

[33]  Michal Linial,et al.  MiRror: a combinatorial analysis web tool for ensembles of microRNAs and their targets , 2010, Bioinform..

[34]  Sanghyuk Lee,et al.  miRGator v2.0 : an integrated system for functional investigation of microRNAs , 2010, Nucleic Acids Res..

[35]  J. Carrington,et al.  miRNA Target Prediction in Plants. , 2010, Methods in molecular biology.

[36]  D. Bartel.  MicroRNAs: Target Recognition and Regulatory Functions , 2009, Cell.

[37]  O. Voinnet,et al.  Biochemical Evidence for Translational Repression by Arabidopsis MicroRNAs[W] , 2009, The Plant Cell Online.

[38]  Yuanji Zhang,et al.  miRU: an automated plant miRNA target prediction server , 2005, Nucleic Acids Res..

[39]  J. Steitz,et al.  Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5′ UTR as in the 3′ UTR , 2007, Proceedings of the National Academy of Sciences.

[40]  Peter F. Stadler,et al.  Fast accessibility-based prediction of RNA-RNA interactions , 2011, Bioinform..

[41]  Rebecca L Poole.  The TAIR database. , 2007, Methods in molecular biology.

[42]  M. Axtell,et al.  Evolution of plant microRNAs and their targets. , 2008, Trends in plant science.

[43]  Vincent Moulton,et al.  A toolkit for analysing large-scale plant small RNA datasets , 2008, Bioinform..

[44]  R. Russell,et al.  Animal MicroRNAs Confer Robustness to Gene Expression and Have a Significant Impact on 3′UTR Evolution , 2005, Cell.

[45]  B. Reinhart,et al.  Prediction of Plant MicroRNA Targets , 2002, Cell.

[46]  N. Rajewsky,et al.  Widespread changes in protein synthesis induced by microRNAs , 2008, Nature.

[47]  Florian Buettner,et al.  The sufficient minimal set of miRNA seed types , 2011, Bioinform..

[48]  Timos K. Sellis,et al.  miRGen 2.0: a database of microRNA genomic information and regulation , 2009, Nucleic Acids Res..

[49]  Olivier Voinnet,et al.  Revisiting the principles of microRNA target recognition and mode of action , 2009, Nature Reviews Molecular Cell Biology.

[50]  Yadong Wang,et al.  miR2Disease: a manually curated database for microRNA deregulation in human disease , 2008, Nucleic Acids Res..

[51]  Yves Van de Peer,et al.  TAPIR, a web server for the prediction of plant microRNA targets, including target mimics , 2010, Bioinform..

[52]  Michael Kertesz,et al.  The role of site accessibility in microRNA target recognition , 2007, Nature Genetics.

[53]  Adam M. Gustafson,et al.  microRNA-Directed Phasing during Trans-Acting siRNA Biogenesis in Plants , 2005, Cell.

[54]  Kyle Kai-How Farh,et al.  Expanding the microRNA targeting code: functional sites with centered pairing. , 2010, Molecular cell.

[55]  Anton J. Enright,et al.  Human MicroRNA Targets , 2004, PLoS biology.

[56]  Patrick Xuechun Zhao,et al.  Computational analysis of miRNA targets in plants: current status and challenges , 2011, Briefings Bioinform..

[57]  Jason S. Cumbie,et al.  High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes , 2007, PloS one.

[58]  M. Zavolan,et al.  A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins , 2011, Nature Methods.