Skip to main content
Log in

A novel method to monitor the expression of microRNAs

  • Research
  • Published:
Molecular Biotechnology Aims and scope Submit manuscript

Abstract

The microRNAs (miRNAs) are an extensive class of small noncoding RNAs (18–25 nucleotides) with important roles in the regulation of gene expression. Although a large number of miRNAs have been identified in a variety of eukaryotic systems, the function of the vast majority of these molecules remains unknown. To study the functions of miRNAs, it is crucial to determine their spatial and temporal expression patterns. Although there are some existing methods that can analyze the expression of miRNAs, it is not an easy task for routine gene-expression studies. In this study, we have established a simple method to detect the expression of mature miRNAs. Total RNA was polyadenylated by poly(A) polymerase, and then cDNA was synthesized by a specific reverse transcriptase (RT) primer and reverse transcriptase using the poly(A)-tailed total RNA as templates. The expression of several mature miRNAs was assayed by this method. The expression profile of two miRNAs, determined by the polymerase chain reaction (PCR) assay, was identical to that determined by Northern blotting. All these data show that the poly(A)-tailed RT-PCR is a convenient method to detect the expression of miRNAs.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  1. Bartel, D. P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281–297.

    Article  PubMed  CAS  Google Scholar 

  2. Lee, Y., Jeon, K., Lee, J. T., Kim, S., and Kim, V. N. (2002) MicroRNA maturation: stepwise processing and subcellular localization. EMBO J. 21, 4663–4670.

    Article  PubMed  CAS  Google Scholar 

  3. Lee, Y., Ahn, C., Han, J. et al. (2003) The nuclear RNase III Drosha initiates microRNA processing. Nature 425, 415–419.

    Article  PubMed  CAS  Google Scholar 

  4. Lund, E., Guttinger, S., Calado, A., Dahlberg, J. E., and Kutay, U. (2004) Nuclear export of microRNA precursors. Science 303, 95–98.

    Article  PubMed  CAS  Google Scholar 

  5. Yi, R., Qin, Y., Macara, I. G., and Cullen, B. R. (2003) Exportin 5 mediates the nuclear export of premicroRNAs and short hairpin RNAs. Genes & Dev. 17, 3011–3016.

    Article  CAS  Google Scholar 

  6. Hutvagner, G., McLachlan J., Pasquinelli, A. E., Balint, E., Tuschl, T., and Zamore, P. D. (2001) A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293, 834–838.

    Article  PubMed  CAS  Google Scholar 

  7. Ketting, R. F., Fischer, S. E., Bernstein, E., Sijen, T., Hannon, G. J., and Plasterk, R. H. (2001) Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes & Dev. 15, 2654–2659.

    Article  CAS  Google Scholar 

  8. Wightman, B., Ha, I., and Ruvkun, G. (1993) Post-transcriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75, 855–862.

    Article  PubMed  CAS  Google Scholar 

  9. Moss, E. G., Lee, R. C., and Ambros, V. (1997) The cold shock domain protein LIN-28 controls developmental timing in C. elegans and is regulated by the lin-4 RNA. Cell 88, 637–646.

    Article  PubMed  CAS  Google Scholar 

  10. Reinhart, B. J., Slack, F. J., Basson, M., et al. (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403, 901–06.

    Article  PubMed  CAS  Google Scholar 

  11. Johnston, R. J. and Hobert, O. (2003) A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature 426, 845–849.

    Article  PubMed  CAS  Google Scholar 

  12. Brennecke, J., Hipfner, D. R., Stark, A., Russell, R. B., and Cohen, S. M. (2003) Bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 113, 25–36.

    Article  PubMed  CAS  Google Scholar 

  13. Xu, P., Vernooy, S. Y., Guo, M., and Hay, B. A. (2003) The Drosophila microRNA Mir-14 suppresses cell death and is required for normal fat metabolism. Curr. Biol. 13, 790–795.

    Article  PubMed  CAS  Google Scholar 

  14. Poy, M. N., Eliasson, L., Krutzfeldt, J., et al. (2004) A pancreatic islet-specific microRNA regulates insulin secretion. Nature 432, 226–230.

    Article  PubMed  CAS  Google Scholar 

  15. Aukerman, M. J. and Sakai, H. (2003) Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes. Plant Cell 15, 2730–2741.

    Article  PubMed  CAS  Google Scholar 

  16. Chen, X. (2004) A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 303, 2022–2025.

    Article  PubMed  CAS  Google Scholar 

  17. Palatnik, J. F., Allen, E., Wu, X., Schommer, C., Schwab, R., Carrington, J. C., and Weigel, D. (2003) Control of leaf morphogenesis by microRNAs. Nature 425, 257–263.

    Article  PubMed  CAS  Google Scholar 

  18. Yekta, S., Shih, I. H., and Bartel, D. P. (2004) MicroRNA-directed cleavage of HOXB8 mRNA. Science 304, 594–596.

    Article  PubMed  CAS  Google Scholar 

  19. Lim, L. P., Glasner, M. E., Yekta, S., Burge, C. B., and Bartel, D. P. (2003) Vertebrate microRNA genes. Science 299, 1540.

    Article  PubMed  CAS  Google Scholar 

  20. Reinhart, B. J., Weinstein, E. G., Rhoades, M. W., Bartel, B., and Bartel, D. P. (2002) MicroRNAs in plants. Genes & Dev 16, 1616–1626.

    Article  CAS  Google Scholar 

  21. Ambros, V. (2003) MicroRNA pathways in flies and worms: growth, death, fat, stress, and timing. Cell 113, 673–676.

    Article  PubMed  CAS  Google Scholar 

  22. Zeng, Y. and Cullen, B. R. (2003) Sequence requirements for micro RNA processing and function in human cells. RNA 9, 112–123.

    Article  PubMed  CAS  Google Scholar 

  23. Schmittgen, T. D., Jiang, J., Liu, Q., and Yang, L. (2004) A high-throughput method to monitor the expression of microRNA precursors. Nucleic Acids Res. 32, e43.

    Article  PubMed  Google Scholar 

  24. Lau, N. C., Lim, L. P., Weinstein, E. G., and Bartel, D. P. (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294, 858–862.

    Article  PubMed  CAS  Google Scholar 

  25. Lagos-Quintana, M., Rauhut, R., Yalcin, A., Meyer, J., Lendeckel, W., and Tuschl, T. (2002) Identification of tissue-specific microRNAs from mouse. Curr. Biol. 12, 735–739.

    Article  PubMed  CAS  Google Scholar 

  26. Suh, M. R., Lee, Y., Kim, J. Y., et al. (2004) Human embryonic stem cells express a unique set of microRNAs. Dev. Biol. 270, 488–498.

    Article  PubMed  CAS  Google Scholar 

  27. Barad, O., Meiri, E., Avniel, A., et al. (2004) MicroRNA expression detected by oligonucleotide microarrays: system establishment and expression profiling in human tissues. Genome Res. 14, 2486–2494.

    Article  PubMed  CAS  Google Scholar 

  28. Allawi, H. T., Dahlberg, J. E., Olson, S., et al. (2004) Quantitation of microRNAs using a modified Invader assay. RNA 10, 1153–1161.

    Article  PubMed  CAS  Google Scholar 

  29. Grad, Y., Aach, J., Hayes, G. D., Reinhart, B. J., Church, G. M., Ruvkun, G., and Kim, J. (2003) Computational and experimental identification of C. elegans microRNAs. Mol. Cell. 11, 1253–1263.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Xiao-Fei Zheng.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Fu, HJ., Zhu, J., Yang, M. et al. A novel method to monitor the expression of microRNAs. Mol Biotechnol 32, 197–204 (2006). https://doi.org/10.1385/MB:32:3:197

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1385/MB:32:3:197

Index Entries

Navigation