SpringerLink
Log in

The MicroRNA: Overview of the RNA Gene That Modulates Gene Functions

  • Protocol
MicroRNA Protocols

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 342))

Abstract

MicroRNAs (miRNAs), widely distributed, small regulatory RNA genes, target both messenger RNA (mRNA) degradation and suppression of protein translation based on sequence complementarity between the miRNA and its targeted mRNA. Different names have been used to describe various types of miRNA. During evolution, RNA retroviruses or transgenes invaded the eukaryotic genome and inserted itself in the noncoding regions of DNA, conceivably acting as transposon-like jum** genes, providing defense from viral invasion and fine-tuning of gene expression as a secondary level of gene modulation in eukaryotes. When a transposon is inserted in the intron, it becomes an intronic miRNA, taking advantage of the protein synthesis machinery, i.e., mRNA transcription and splicing, as a means for processing and maturation. Recently, miRNAs have been found to play an important, but not life-threatening, role in embryonic development. They might play a pivotal role in diverse biological systems in various organisms, facilitating a quick response and accurate plotting of body physiology and structures. Based on these unique properties, manufactured intronic miRNAs have been developed for in vitro evaluation of gene function, in vivo gene therapy, and generation of transgenic animal models. The biogenesis and identification of miRNAs, potential applications, and future directions for research are presented in this chapter, hopefully providing a guideline for further miRNA and gene function studies.

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

Access this chapter

Log in via an institution

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Protocol
GBP 34.95
Price includes VAT (United Kingdom)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
GBP 103.50
Price includes VAT (United Kingdom)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
GBP 129.99
Price includes VAT (United Kingdom)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free ship** worldwide - see info
Hardcover Book
GBP 129.99
Price includes VAT (United Kingdom)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free ship** worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Holley, R. W. (1965) Structure of an alanine transfer ribonucleic acid. JAMA 194, 868–871.

    Article  CAS  PubMed  Google Scholar 

  2. Maxwell, E. S. and Fournier, M. J. (1995) The small nucleolar RNAs. Annu. Rev. Biochem. 64, 897–934.

    Article  CAS  PubMed  Google Scholar 

  3. Tycowski, K. T., Shu, M. D., and Steitz, J. A. (1996) A mammalian gene with introns instead of exons generating stable RNA products. Nature 379, 464–466.

    Article  CAS  PubMed  Google Scholar 

  4. Filipowicz, W. (2000) Imprinted expression of small nucleolar RNAs in brain: time for RNomics. Proc. Natl. Acad. Sci. USA 97, 14,035–14,037.

    Article  CAS  PubMed  Google Scholar 

  5. Allmang, C., Kufel, J., Chanfreau, G., Mitchell, P., Petfalski, E., and Tollervey, D. (1999) Functions of the exosome in rRNA, snoRNA and snRNA synthesis. EMBO J. 18, 5399–5410.

    Article  CAS  PubMed  Google Scholar 

  6. van Hoof, A. and Parker, R. (1999) The exosome: a proteasome for RNA? Cell 99, 347–350.

    Article  PubMed  Google Scholar 

  7. Frank, D. N., Roiha, H., and Guthrie, C. (1994) Architecture of the U5 small nuclear RNA. Mol. Cell. Biol. 14, 2180–2190.

    CAS  PubMed  Google Scholar 

  8. Stavianopoulos, J. G., Karkus, J. D., and Charguff, E. (1971). Nucleic acid polymerase of the develo** chicken embryos: a DNA Polymerase preferring a hybrid template. Proc. Natl. Acad. Sci. USA 68, 2207–2211.

    Article  Google Scholar 

  9. Stavianopoulos, J. G., Karkus, J. D., and Charguff, E. (1972) Mechanism of DNA replica-tion by highly purified DNA polymerase of chicken embryos. Proc. Natl. Acad. Sci. USA 69, 2609–2613.

    Article  Google Scholar 

  10. Wank, H. and Schroeder, R. (1996) Antibiotic-induced oligomerisation of group I intron RNA. J. Mol. Biol. 258, 53–61.

    Article  CAS  PubMed  Google Scholar 

  11. van der Krol, A. R., Mur, L. A., Beld, M., Mol, J. N., and Stuitje, A. R. (1990) Flavonoid genes in petunia: addition of a limited number of gene copies may lead to a suppression of gene expression. Plant Cell 2, 291–299.

    Article  PubMed  Google Scholar 

  12. Napoli, C., Lemieux, C., and Jorgensen, R. A. (1990) Introduction of a chimeric chalcone synthase gene into Petunia results in reversible co-suppression of homologous genes in trans. Plant Cell 2, 279–289.

    Article  CAS  PubMed  Google Scholar 

  13. Matzke, M. A., Primig, M. J., Trnovsky, J., and Matzke, A. J. M. (1989) Reversible methy-lation and inactivation of marker genes in sequentially transformed tobacco plants. EMBO J. 8, 643–649.

    CAS  PubMed  Google Scholar 

  14. Fire, A., Xu, S., Montgomery, M. K., et al. (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806–811.

    Article  CAS  PubMed  Google Scholar 

  15. Shi, Y. (2003) Mammalian RNAi for the masses. Trends Genet. 19, 9–12.

    Article  PubMed  Google Scholar 

  16. Sui, G., Soohoo, C., el Affar, B., et al. (2002) A DNA vector-based RNAi technology to suppress gene expression in mammalian cells. Proc. Natl. Acad. Sci. USA 99, 5515–5520.

    Article  CAS  PubMed  Google Scholar 

  17. Elbashir, S. M., Lendeckel, W., and Tuschl, T. (2001) RNA interference is mediated by 21-and 22-nucleotide RNAs. Genes Dev. 15, 188–200.

    Article  CAS  PubMed  Google Scholar 

  18. Pasquinelli, A. E., Reinhart, B. J., Slack, F., et al. (2000) Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408, 86–89.

    Article  CAS  PubMed  Google Scholar 

  19. Reinhart, B. J. and Bartel, D. P. (2002) Small RNAs correspond to centromere heterochro-matic repeats. Science 297, 1831.

    Article  CAS  PubMed  Google Scholar 

  20. Kuwabara, T., Hsieh, J., Nakashima, K., Taira, K., and Gage, F. H. (2004) A small modula-tory dsRNA specifies the fate of adult neural stem cells. Cell 116, 779–793.

    Article  CAS  PubMed  Google Scholar 

  21. Lee, R. C., Feinbaum, R. L., and Ambros, V. (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843–854.

    Article  CAS  PubMed  Google Scholar 

  22. 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  CAS  PubMed  Google Scholar 

  23. Lagos-Quintana, M., Rauhut, R., Meyer, J., Borkhardt, A., and Tuschl, T. (2003) New microRNAs from mouse and human. RNA 9, 175–179.

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  25. Lund, E., Guttinger, S., Calado, A., Dahlberg, J. E., and Kutay, U. (2003) Nuclear export of microRNA precursors. Science 303, 95–98.

    Article  PubMed  Google Scholar 

  26. Ying, S. Y. and Lin, S. L. (2005) Intronic microRNAs (miRNAs). Biochem. Biophys. Res. Commun. 326, 515–520.

    Article  CAS  PubMed  Google Scholar 

  27. Lee, Y. S., Nakahara, K., Pham, J. W., et al. (2004) Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell 117, 69–81.

    Article  CAS  PubMed  Google Scholar 

  28. Tang, G. (2005) siRNA and miRNA: an insight into RISCs. Trends Biochem. Sci. 30, 106–114.

    Article  CAS  PubMed  Google Scholar 

  29. Lambowitz, A. M. and Zimmerly, S. (2004) Mobile group II introns. Annu. Rev. Genet. 38, 1–35.

    Article  CAS  PubMed  Google Scholar 

  30. Coghlan, A. and Wolfe, K. H. (2004) Origins of recently gained introns in Caenorhabditis. Proc. Natl. Acad. Sci. USA 101, 11,362–11,367.

    Google Scholar 

  31. Harper, P. S. (1989) Myotonic Dystrophy (Saunders, London, ed. 2).

    Google Scholar 

  32. Liquori, C. L., Ricker, K., Moseley, M. L., et al. (2001) Myotonic dystrophy type 2 caused by a CCTG expansion in intron 1 of ZNF9. Science 293, 864–867.

    Article  CAS  PubMed  Google Scholar 

  33. Lin, S. L., Chang, D., Wu, D. Y., and Ying, S. Y. (2003) A novel RNA splicing-mediated gene silencing mechanism potential for genome evolution. Biochem. Biophys. Res. Commun. 310, 754–760.

    Article  CAS  PubMed  Google Scholar 

  34. Lee, Y., Kim, M., Han, J., et al. (2004) MicroRNA genes are transcribed by RNA polymer-ase II. EMBO J. 23, 4051–4060.

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  36. Schwarz, D. S., Hutvagner, G., Du, T., Xu, Z., Aronin, N., and Zamore, P. D. (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115, 199–208.

    Article  CAS  PubMed  Google Scholar 

  37. Khvorova, A., Reynolds, A., and Jayasena, S. D. (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115, 209–216.

    Article  CAS  PubMed  Google Scholar 

  38. Jones, L., Hamilton, A. J., Voinnet, O., Thomas, C. L., Maule, A. J., and Baulcombe, D. C. (1999). RNA-DNA interactions and DNA methylation in post-transcriptional gene silencing. Plant Cell 11, 2291–2301.

    Article  CAS  PubMed  Google Scholar 

  39. Vaistij, F. E., Jones, L., and Baulcombe, D. C. (2002). Spreading of RNA targeting and DNA methylation in RNA silencing requires transcription of the target gene and a puta-tive RNA-dependent RNA polymerase. Plant Cell 14, 857–867.

    Article  CAS  PubMed  Google Scholar 

  40. Béclin, C., Boutet, S., Waterhouse, P., and Vaucheret H. (2002). A branched pathway for transgene-induced RNA silencing in plants. Curr. Biol. 12, 684–688.

    Article  PubMed  Google Scholar 

  41. Okamura, K., Ishizuka, A., Siomi, H., and Siomi, M.C. (2004) Distinct roles for Argonaute proteins in small RNA-directed RNA cleavage pathways. Genes Dev. 18, 1655–1666.

    Article  CAS  PubMed  Google Scholar 

  42. Kidner, C. A. and Martienssen, R. A. (2005) The role of ARGONAUTE1 (AGO1) in meri-stem formation and identity. Dev. Biol. 280, 504–517.

    Article  CAS  PubMed  Google Scholar 

  43. Liu, J., Valencia-Sanchez, M. A., Hannon, G. J., and Parker, R. (2005) MicroRNA-depen-dent localization of targeted mRNAs to mammalian P-bodies. Nat. Cell. Biol. 7, 719–723.

    Article  CAS  PubMed  Google Scholar 

  44. Meister, G., Landthaler, M., Patkaniowska,, A., Dorsett,, Y., Teng, G., and Tuschl, T. (2004) Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol. Cell. 15, 185–197.

    Article  CAS  PubMed  Google Scholar 

  45. Takamizawa, J., Konishi, H., Yanagisawa, K., et al. (2004) Reduced expression of the let-7 microRNAs in human lung cancers in association with shortened postoperative survival. Cancer Res. 64, 3753–2756.

    Article  CAS  PubMed  Google Scholar 

  46. Karube, Y., Tanaka, H., Osada, H., et al. (2005) Reduced expression of Dicer associated with poor prognosis in lung cancer patients. Cancer Sci. 96, 111–115.

    Article  CAS  PubMed  Google Scholar 

  47. Xu, P., Guo, M., and Hay, B. A. (2004) MicroRNAs and the regulation of cell death. Trends Genet. 20, 617–624.

    Article  CAS  PubMed  Google Scholar 

  48. **, P., Alisch, R. S., and Warren, S. T. (2004) RNA and microRNAs in fragile X mental retardation. Nat. Cell Biol. 6, 1048–1053.

    Article  CAS  PubMed  Google Scholar 

  49. Gesellchen,V. and Boutros, M. (2004) Managing the genome: microRNAs in Drosophila. Differentiation 72, 74–80.

    Article  PubMed  Google Scholar 

  50. McManus, M. T. (2003) MicroRNAs and cancer. Semin. Cancer Biol. 13, 253–258.

    Article  CAS  PubMed  Google Scholar 

  51. Liu, C. G., Calin, G. A., Meloon, B., et al. (2004) An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proc. Natl. Acad. Sci. USA 101, 9740–8744.

    Article  CAS  PubMed  Google Scholar 

  52. Miska, E. A., Alvarez-Saavedra, E., Townsend, M., et al. (2004) Microarray analysis of microRNA expression in the develo** mammalian brain. Genome Biol. 5 R68.

    Article  PubMed  Google Scholar 

  53. Valoczi, A., Hornyik, C., Varga, N., Burgyan, J., Kauppinen, S., and Havelda, Z. (2004) Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modi-fied oligonucleotide probes. Nucleic Acids Res. 32, e175

    Article  PubMed  Google Scholar 

  54. Giraldez, A. J., Cinalli, R. M., Glasner, M. E., et al. (2005) MicroRNAs regulate brain mor-phogenesis in zebrafish. Science 308, 833–838.

    Article  CAS  PubMed  Google Scholar 

  55. Lai, E. C., Tomancak, P., Williams, R. W., and Rubin, G. M. (2003) Computational identi-fication of Drosophila microRNA genes. Genome Biol. 4, R42.

    Article  PubMed  Google Scholar 

  56. Brown, J. R. and Sanseau, P. (2005) A computational view of microRNAs and their tar-gets. Drug Discov. Today 10, 595–601.

    Article  CAS  PubMed  Google Scholar 

  57. Miyagishi, M., Matsumoto, S., and Taira, K. (2004) Generation of and shRNAi expres-sion library against the whole human transcripts. Virus Res. 102, 117–124.

    Article  CAS  PubMed  Google Scholar 

  58. Nagl, S. B. (2002) Computational function assignment for potential drug targets: from single genes to cellular systems. Curr. Drug Targets 3, 387–399.

    Article  CAS  PubMed  Google Scholar 

  59. Landthaler,, M., Yalcin, A., and Tuschl, T. (2004) The human DiGeorge syndrome critical region gene 8 and Its D. melanogaster homolog are required for miRNA biogenesis. Curr. Biol. 14, 2162–2167.

    Article  CAS  PubMed  Google Scholar 

  60. Pardridge, W. M. (2004) Intravenous, non-viral RNAi gene therapy of brain cancer. Expert Opin. Biol. Ther. 4, 1103–1113.

    Article  CAS  PubMed  Google Scholar 

  61. Zamore, P. D. (2004) Plant RNAi: How a viral silencing suppressor inactivates siRNA. Curr. Biol. 9, R198–200.

    Article  Google Scholar 

  62. Lecellier, C. H., Dunoyer, P., Arar,, K., et al. (2005) A cellular microRNA mediates anti-viral defense in human cells. Science 308, 557–561.

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Cell and Neurobiology, Keck School of Medicine, University of Southern California, Los Angeles, CA

    Shao-Yao Ying, Donald C. Chang, Joseph D. Miller & Shi-Lung Lin

Authors
  1. Shao-Yao Ying
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Donald C. Chang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Joseph D. Miller
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Shi-Lung Lin
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Cell and Neurobiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA

    Shao-Yao Ying

Rights and permissions

Reprints and permissions

Copyright information

© 2006 Humana Press Inc.

About this protocol

Cite this protocol

Ying, SY., Chang, D.C., Miller, J.D., Lin, SL. (2006). The MicroRNA: Overview of the RNA Gene That Modulates Gene Functions . In: Ying, SY. (eds) MicroRNA Protocols. Methods in Molecular Biology™, vol 342. Humana Press. https://doi.org/10.1385/1-59745-123-1:1

Download citation

  • DOI: https://doi.org/10.1385/1-59745-123-1:1

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-581-1

  • Online ISBN: 978-1-59745-123-9

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation