One Decade of Development and Evolution of MicroRNA Target Prediction Algorithms

Nearly two decades have passed since the publication of the first study reporting the discovery of microRNAs (miRNAs). The key role of miRNAs in post-transcriptional gene regulation led to the performance of an increasing number of studies focusing on origins, mechanisms of action and functionality of miRNAs. In order to associate each miRNA to a specific functionality it is essential to unveil the rules that govern miRNA action. Despite the fact that there has been significant improvement exposing structural characteristics of the miRNA–mRNA interaction, the entire physical mechanism is not yet fully understood. In this respect, the development of computational algorithms for miRNA target prediction becomes increasingly important. This manuscript summarizes the research done on miRNA target prediction. It describes the experimental data currently available and used in the field and presents three lines of computational approaches for target prediction. Finally, the authors put forward a number of considerations regarding current challenges and future directions.

[1]  V. Ambros,et al.  An Extensive Class of Small RNAs in Caenorhabditis elegans , 2001, Science.

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

[3]  Nectarios Koziris,et al.  Accurate microRNA target prediction correlates with protein repression levels , 2009, BMC Bioinformatics.

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

[5]  Yong Zhao,et al.  Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis , 2005, Nature.

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

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

[8]  T. Tuschl,et al.  Identification of Novel Genes Coding for Small Expressed RNAs , 2001, Science.

[9]  R. Knight,et al.  Regions and Fewer MicroRNA Target Sites Proliferating Cells Express mRNAs with Shortened 3 ' Untranslated , 2012 .

[10]  Doron Betel,et al.  Corrigendum: Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs , 2009 .

[11]  A. Hatzigeorgiou,et al.  A combined computational-experimental approach predicts human microRNA targets. , 2004, Genes & development.

[12]  M. Kiebler,et al.  Faculty Opinions recommendation of Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. , 2009 .

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

[14]  Mihaela Zavolan,et al.  Inference of miRNA targets using evolutionary conservation and pathway analysis , 2007, BMC Bioinformatics.

[15]  Louise C. Showe,et al.  Naïve Bayes for microRNA target predictions - machine learning for microRNA targets , 2007, Bioinform..

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

[17]  C. Burge,et al.  Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets , 2005, Cell.

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

[19]  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..

[20]  Mihaela Zavolan,et al.  Reproductive toxicology. Trichloroethylene. , 1997, BMC Bioinformatics.

[21]  Achuthsankar S. Nair,et al.  MTar: a computational microRNA target prediction architecture for human transcriptome , 2010, BMC Bioinformatics.

[22]  L. Lim,et al.  MicroRNA targeting specificity in mammals: determinants beyond seed pairing. , 2007, Molecular cell.

[23]  Quan Liu,et al.  Strategies to identify microRNA targets: new advances. , 2010, New biotechnology.

[24]  C. Burge,et al.  Most mammalian mRNAs are conserved targets of microRNAs. , 2008, Genome research.

[25]  Hanah Margalit,et al.  Clustering and conservation patterns of human microRNAs , 2005, Nucleic acids research.

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

[27]  Martin L. Miller,et al.  Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs , 2009, Nature Biotechnology.

[28]  J. Lieberman,et al.  Desperately seeking microRNA targets , 2010, Nature Structural &Molecular Biology.

[29]  W. Krzyzosiak,et al.  Practical Aspects of microRNA Target Prediction , 2011, Current molecular medicine.

[30]  D. Bartel.  MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.

[31]  Chunxiang Zhang,et al.  MicroRNA Expression Signature and Antisense-Mediated Depletion Reveal an Essential Role of MicroRNA in Vascular Neointimal Lesion Formation , 2007, Circulation research.

[32]  F. Slack,et al.  A 'pivotal' new rule for microRNA-mRNA interactions , 2012, Nature Structural &Molecular Biology.

[33]  Nectarios Koziris,et al.  TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support , 2011, Nucleic Acids Res..

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

[35]  Dmitrij Frishman,et al.  TargetSpy: a supervised machine learning approach for microRNA target prediction , 2010, BMC Bioinformatics.

[36]  Adam K. L. Wong,et al.  miRNA_Targets: a database for miRNA target predictions in coding and non-coding regions of mRNAs. , 2012, Genomics.

[37]  Gerben Duns,et al.  A high throughput experimental approach to identify miRNA targets in human cells , 2009, Nucleic acids research.

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

[39]  Nicholas T. Ingolia,et al.  Mammalian microRNAs predominantly act to decrease target mRNA levels , 2010, Nature.

[40]  Peter F. Stadler,et al.  Thermodynamics of RNA-RNA Binding , 2006, German Conference on Bioinformatics.

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

[42]  H. Mewes,et al.  A Novel Putative miRNA Target Enhancer Signal , 2009, PloS one.

[43]  D. Bartel,et al.  Weak Seed-Pairing Stability and High Target-Site Abundance Decrease the Proficiency of lsy-6 and Other miRNAs , 2011, Nature Structural &Molecular Biology.

[44]  Byoung-Tak Zhang,et al.  miTarget: microRNA target gene prediction using a support vector machine , 2006, BMC Bioinformatics.

[45]  Anders Krogh,et al.  Signatures of RNA binding proteins globally coupled to effective microRNA target sites. , 2010, Genome research.

[46]  D. Bartel,et al.  The impact of microRNAs on protein output , 2008, Nature.

[47]  Martin Reczko,et al.  Lost in translation: an assessment and perspective for computational microRNA target identification , 2009, Bioinform..

[48]  Boqin Qiang,et al.  Improving the prediction of human microRNA target genes by using ensemble algorithm , 2007, FEBS letters.

[49]  Jan Krüger,et al.  RNAhybrid: microRNA target prediction easy, fast and flexible , 2006, Nucleic Acids Res..

[50]  Anjali J. Koppal,et al.  Supplementary data: Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites , 2010 .

[51]  Oliver Hobert,et al.  Molecular architecture of a miRNA-regulated 3' UTR. , 2008, RNA.

[52]  Semih Ekimler,et al.  Computational Methods for MicroRNA Target Prediction , 2014, Genes.

[53]  C. Bracken,et al.  Experimental strategies for microRNA target identification , 2011, Nucleic acids research.

[54]  L. Paillard,et al.  AU-rich elements and associated factors: are there unifying principles? , 2006, Nucleic acids research.

[55]  Yvonne Tay,et al.  A Pattern-Based Method for the Identification of MicroRNA Binding Sites and Their Corresponding Heteroduplexes , 2006, Cell.

[56]  Enrico Macii,et al.  miREE: miRNA recognition elements ensemble , 2011, BMC Bioinformatics.

[57]  Sanghamitra Bandyopadhyay,et al.  TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples , 2009, Bioinform..

[58]  Colin N. Dewey,et al.  A Genome-Wide Map of Conserved MicroRNA Targets in C. elegans , 2006, Current Biology.

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

[60]  Hyeyoung Min,et al.  Got target?: computational methods for microRNA target prediction and their extension , 2010, Experimental & Molecular Medicine.

[61]  Ola Snøve,et al.  Weighted sequence motifs as an improved seeding step in microRNA target prediction algorithms. , 2005, RNA.

[62]  U. A. Ørom,et al.  Experimental identification of microRNA targets. , 2010, Gene.

[63]  J. Castle,et al.  Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs , 2005, Nature.

[64]  Yu-Ping Wang,et al.  MiRTif: a support vector machine-based microRNA target interaction filter , 2008, BMC Bioinformatics.

[65]  Doron Betel,et al.  The microRNA.org resource: targets and expression , 2007, Nucleic Acids Res..

[66]  Anders Krogh,et al.  MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action. , 2011, RNA.

[67]  Benedikt Brors,et al.  Microarray-based approach identifies microRNAs and their target functional patterns in polycystic kidney disease , 2008, BMC Genomics.

[68]  Stijn van Dongen,et al.  miRBase: tools for microRNA genomics , 2007, Nucleic Acids Res..

[69]  Jun Yu,et al.  A Brief Review on the Mechanisms of miRNA Regulation , 2009, Genom. Proteom. Bioinform..