A Guide to in silico Identification of miRNAs and their Targets
DOI:
https://doi.org/10.24154/jhs.v10i1.166Keywords:
miRNA, Bioinformatics, miRNA Targets, Structure, software ToolsAbstract
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.References
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
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Copyright (c) 2015 V Radhika, Kanupriya ., R Rashmi, C Aswath (Author)
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