A Guide to in silico Identification of miRNAs and their Targets

V. Radhika, Kanupriya, R. Rashmi, C. Aswath


MicroRNAs (miRNA) are non-coding RNA molecules that play a critical role in gene regulation including translational repression in animals and mRNA cleavage in plants. MicroRNAs control various cellular, metabolic and physiological processes in living organisms. In this paper, we provide an overview on the significance of miRNA, nomenclature, their biogenesis and the pipelines for prediction of miRNA and their targets. These tools are important for identification of conserved miRNAs in crops where miRNAs have not been previously discovered. The newlyidentified miRNAs and their targets play an important role in understanding regulation of growth, development and gene silencing in various life forms.


miRNA, Bioinformatics, miRNA Targets, Structure, software Tools.

Full Text:



An, J., Lai, J., Lehman, M.L. and Nelson, C.C. 2013. miRDeep: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res., 41:727-37

Bonnet, E., He, Y., Billiau, K. and Peer, Y.V. 2010. TAPIR, a web server for the prediction of plant microRNA targets, including target mimics. Bioinformatics, 26:1566-1568

Dai, X. and Zhao, P.X. 2011. psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res., 39:155-159

Griffiths-Jones, S. 2006. miRBase: the microRNA sequence database. Methods Mol. Biol., 342:129–138

Kanupriya, C., Radhika V. and Ravishankar, K.V. 2013. ‘Mining of miRNAs in pomegranate (Punica granatum L.) by pyrosequencing of part of the genome.’ J. Hort’l. Sci. Biotech., 88:735-742

Lee, J., Kim, D., Park, J.H., Choi, I. and Shin, C. 2013. miRAuto: An automated user-friendly microRNA prediction tool utilizing plant small RNA sequencing data. Molecules and Cells, 35:342-347

Llave, C., Kasschau, K.D., Rector, M. and Carrington, J.C. 2002. Endogeneous and silencing-associated small RNAs in plants. Pl. Cell, 14:1605–1619

Markham, N.R. and Zuker, M. 2008. UNAFold: software for nucleic acid folding and hybridization. Methods Mol. Biol., 453:3-31

Mhuantong, W. and Wichadakul, D. 2009. MicroPC (ìPC): A comprehensive resource for predicting and comparing plant microRNAs. BMC Genomics, 10:366

Milev, I., Yahubyan, G., Minkov, I. and Baev, V. 2011. miRTour: Plant miRNA and target prediction tool. Bioinformation, 6:248-249

Numnark, S., Mhuantong, W., Ingsriswang, S. and Wichadakul, D. 2012. C-mii: a tool for plant miRNA and target identification. BMC Genomics, 13:7-16

Reddy, D.C.L., Radhika, V., Bhardwaj, A., Khandagalek, S. and Aswath, C. 2012. miRNAs in brinjal (Solanum melongena) mined through an in silico approach. J. Hort’l. Sci. Biotech., 87:186-192

Rhoades, M.W., Reinhart, B.J., Lim, L.P., Burge, C.B., Bartel, B. and Bartel, D.P. 2002. Prediction of plant microRNA targets. Cell, 110:513–520

Wu, Y., Wei, B., Liu, H., Li, T. and Rayner, S. 2011. MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences. BMC Bioinformatics, 12:107

Zuker, M. and Stiegler, P. 1981. Optimal computer folding of large RNA sequences using thermodynamic and auxiliary information. Nucl Acid Res, 9:133-148

Copyright (c) 2016 Journal of Horticultural Science