Targeting miRNA for Therapeutics Using a Micronome Based Method for Identification of miRNA-mRNA Pairs and Validation of Key Regulator miRNA

  • Parveen Bansal
  • Ashish Kumar
  • Sudhir Chandna
  • Malika Arora
  • Renu Bansal
Part of the Methods in Molecular Biology book series (MIMB, volume 1823)


MicroRNAs are 18–22 bp long non-coding sequences and play a critical role in diverse biological processes, through modulation of gene expression at the post-transcriptional level by binding at the 3′-untranslated region of target mRNA. Consequent upon the discovery of structural and functional features of miRNA targeting, several molecular methods have been developed to identify miRNA targets. However, these methods suffer several drawbacks, including technical challenges, requirement of high cell volumes, inability to differentiate between direct and indirect targets, cell/tissue as well as experimental-specificity and imprecise binding site information. Alternatively in silico approach enables the exploration of the potential miRNA-mRNA pairs to investigate signature miRNA and proteins involved in the signaling of various diseases. Here, we describe micronome-based standard method for identification of miRNA-mRNA pairs as well as validation of key regulator miRNA.


MicroRNA Search Tool for Retrieval of Interacting Genes/Proteins (STRING) miRNA Target Protein–protein Interaction RNase protection assay mirTARbase 


  1. 1.
    Farazi TA, Hoell JI, Morozov P, Tuschl T (2013) MicroRNAs in human cancer. In: MicroRNA cancer regulation. Springer, Dordrecht, p 1–20Google Scholar
  2. 2.
    Liu Z, Sall A, Yang D (2008) MicroRNA: an emerging therapeutic target and intervention tool. Int J Mol Sci 9(6):978–999CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Drakaki A, Iliopoulos D (2009) MicroRNA gene networks in oncogenesis. Curr Genomics 10(1):35–41CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Chi SW, Zang JB, Mele A, Darnell RB (2009) Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460:479–486CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Murakami Y, Tanahashi T, Okada R, Toyoda H, Kumada T, Enomoto M et al (2014) Comparison of hepatocellular carcinoma miRNA expression profiling as evaluated by next generation sequencing and microarray. PLoS One 9:e106314 1-9CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Kelly AD, Hill KE, Correll M, Hu L, Wang YE, Rubio R et al (2013) Next-generation sequencing and microarray-based interrogation of microRNAs from formalin-fixed, paraffin-embedded tissue: preliminary assessment of cross-platform concordance. Genomics 1:8–14CrossRefGoogle Scholar
  7. 7.
    Yoon S, De Micheli G (2006) Computational identification of microRNAs and their targets. Birth Defects Res C Embryo Today 78:118–128CrossRefPubMedGoogle Scholar
  8. 8.
    Bar M, Wyman SK, Fritz BR, Qi J, Garg KS, Parkin RK et al (2008) MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries. Stem Cells 26:2496–2505CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Li L, Xu J, Yang D, Tan X, Wang H (2010) Computational approaches for microRNA studies: a review. Mamm Genome 21:1–12CrossRefPubMedGoogle Scholar
  10. 10.
    Akhtar MM, Micolucci L, Islam MS, Olivieri F, Procopio AD (2016) Bioinformatic tools for microRNA dissection. Nucleic Acids Res 44:24–44CrossRefPubMedGoogle Scholar
  11. 11.
    Christopher AF, Kaur RP, Kaur G, Kaur A, Gupta V, Bansal P (2016) MicroRNA therapeutics: discovering novel targets and developing specific therapy. Perspect Clin Res 7(2):68–74CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Christopher AF, Gupta M, Bansal P (2016) Micronome revealed miR-19a/b as key regulator of SOCS3 during cancer related inflammation of oral squamous cell carcinoma. Gene 594(1):30–40CrossRefPubMedGoogle Scholar
  13. 13.
    Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Cepas JH et al (2015) STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res 43:D447–D452CrossRefPubMedGoogle Scholar
  14. 14.
    Hsu SD, Lin FM, Wu WC, Liang C, Huang WC, Chan WL et al (2011) miRTarBase: a database curates experimentally validated microRNA–target interactions. Nucleic Acids Res 39:D163–D169CrossRefPubMedGoogle Scholar
  15. 15.
    Vergoulis T, Vlachos IS, George PA, Maragkakis GM, Reczko M, Gerangelos S et al (2012) TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support. Nucleic Acids Res 40:D222–D229CrossRefPubMedGoogle Scholar
  16. 16.
    Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T et al (2009) miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res 37:D105–D110CrossRefPubMedGoogle Scholar
  17. 17.
    Jiang Q, Wang Y, Hao Y, Juan L, Teng M, Zhang X et al (2009) miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res 37:D98–D104CrossRefPubMedGoogle Scholar
  18. 18.
    Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ranage D et al (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498–2504CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Agarwal V, Bell GW, Nam J, Bartel DP (2015) Predicting effective microRNA target sites in mammalian mRNAs. E Life 4:e05005 1-38Google Scholar
  20. 20.
    Shirdel EA, Xie W, Mak TW, Jurisica I (2011) Navigating the micronome–using multiple microRNA prediction databases to identify signalling pathway-associated microRNAs. PLoS One 6:e17429 1-17CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Assenov Y, Ramírez F, Schelhorn SE, Lengauer T, Albrecht M (2008) Computing topological parameters of biological networks. Bioinformatics 24:282–284CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Parveen Bansal
    • 1
  • Ashish Kumar
    • 2
  • Sudhir Chandna
    • 3
  • Malika Arora
    • 4
  • Renu Bansal
    • 5
  1. 1.University Centre of Excellence in ResearchBaba Farid University of Health SciencesFaridkotIndia
  2. 2.Texas Biomedical Research InstituteSan AntonioUSA
  3. 3.Division of Natural Radiation Response MechanismsInstitute of Nuclear Medicine and Allied SciencesTimarpurIndia
  4. 4.Multidisciplinary Research Unit, Indian Council of Medical ResearchGGSMCHFaridkotIndia
  5. 5.Department of MicrobiologyGGSMCHFaridkotIndia

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