Method for Detection of miRNAs in Non-Model Organisms with Unreported Database

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


Non-model organisms are studied very frequently, as a simple accessible and convenient system to investigate the role of miRNAs in particular aspect of biology or disease. However, the unavailability of the annotated genome and hence miRNA database of these non-model organisms pose a major constraint for using them more efficiently. Here, we describe a new method to identify miRNAs in non-model organisms without complex sequencing strategies and using miRNAs from close relative organisms as proxy/reference sequences.


miRNA Non-model organisms 


  1. 1.
    Cai X, Hagedorn CH, Cullen BR (2004) Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA 10(12):1957–1966CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, Kim VN (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J 23(20):4051–4060CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Gregory RI, Yan KP, Amuthan G, Chendrimada T, Doratotaj B, Cooch N, Shiekhattar R (2004) The microprocessor complex mediates the genesis of microRNAs. Nature 432(7014):235–240CrossRefGoogle Scholar
  4. 4.
    Denli AM, Tops BB, Plasterk RH, Ketting RF, Hannon GJ (2004) Processing of primary microRNAs by the microprocessor complex. Nature 432(7014):231–235CrossRefPubMedGoogle Scholar
  5. 5.
    Han J, Lee Y, Yeom KH, Kim YK, Jin H, Kim VN (2004) The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev 18(24):3016–3027CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Yi R, Qin Y, Macara IG, Cullen BR (2003) Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev 17(24):3011–3016CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Bohnsack MT, Czaplinski K, GÖRLICH D (2004) Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs. RNA 10(2):185–191CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Lund E, Güttinger S, Calado A, Dahlberg JE, Kutay U (2004) Nuclear export of microRNA precursors. Science 303(5654):95–98CrossRefGoogle Scholar
  9. 9.
    Zeng Y, Cullen BR (2004) Structural requirements for pre-microRNA binding and nuclear export by Exportin 5. Nucleic acids Res 32(16):4776–4785CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Bernstein E, Caudy AA, Hammond SM, Hannon GJ (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409(6818):363–366CrossRefGoogle Scholar
  11. 11.
    Grishok A, Pasquinelli AE, Conte D, Li N, Parrish S, Ha I et al (2001) Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106(1):23–34CrossRefPubMedGoogle Scholar
  12. 12.
    Hutvágner G, McLachlan J, Pasquinelli AE, Bálint É, Tuschl T, Zamore PD (2001) A cellular function for the RNA-interference enzyme dicer in the maturation of the let-7 small temporal RNA. Science 293(5531):834–838CrossRefGoogle Scholar
  13. 13.
    Chendrimada TP, Gregory RI, Kumaraswamy E, Norman J, Cooch N, Nishikura K, Shiekhattar R (2005) TRBP recruits the dicer complex to Ago2 for microRNA processing and gene silencing. Nature 436(7051):740–744CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Saito K, Ishizuka A, Siomi H, Siomi MC (2005) Processing of pre-microRNAs by the Dicer-1–loquacious complex in drosophila cells. PLoS Biol 3(7):e235CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Tomari Y, Zamore PD (2005) Perspective: machines for RNAi. Genes Dev 19(5):517–529CrossRefPubMedGoogle Scholar
  16. 16.
    Meister G, Landthaler M, Patkaniowska A, Dorsett Y, Teng G, Tuschl T (2004) Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol Cell 15(2):185–197CrossRefPubMedGoogle Scholar
  17. 17.
    Rand TA, Petersen S, Du F, Wang X (2005) Argonaute2 cleaves the anti-guide strand of siRNA during RISC activation. Cell 23(4):621–629CrossRefGoogle Scholar
  18. 18.
    Kayvan E, Mazhar H, Sassan A (2013) Identification of microRNAs from Plutella xylostella larvae associated with parasitization by Diadegma semiclausum. Insect Biochem Mol Biol 43(4):309–318CrossRefGoogle Scholar
  19. 19.
    Wu WQ, Ren Q, Li C, Wang Y, Sang M, Yi Z et al (2013) Characterization and comparative profiling of MicroRNAs in a sexual dimorphism insect, Eupolyphaga sinensis Walker. PLoS One 8(4):e59016 1–8CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Kumar A, Ghosh S, Chandana S (2015) Evidence for microRNA-31 dependent Bim-Bax interaction preceding mitochondrial Bax translocation during radiation-induced apoptosis. Sci Rep 5:1–14Google 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 Research, Baba 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 Research, GGSMCHFaridkotIndia
  5. 5.Department of MicrobiologyGGSMCHFaridkotIndia

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