Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Opinion
  • Published:

Revisiting the principles of microRNA target recognition and mode of action

Abstract

MicroRNAs (miRNAs) are fundamental regulatory elements of animal and plant gene expression. Although rapid progress in our understanding of miRNA biogenesis has been achieved by experimentation, computational approaches have also been influential in determining the general principles that are thought to govern miRNA target recognition and mode of action. We discuss how these principles are being progressively challenged by genetic and biochemical studies. In addition, we discuss the role of target-site-specific endonucleolytic cleavage, which is the hallmark of experimental RNA interference and a mechanism that is used by plant miRNAs and a few animal miRNAs. Generally thought to be merely a degradation mechanism, we propose that this might also be a biogenesis mechanism for biologically functional, non-coding RNA fragments.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Seed and non-seed matches.
Figure 2: microRNA–target complementarity does not necessarily predict the regulatory output of interactions.
Figure 3: Possible functions of slicing and the resulting mRNA cleavage fragments.

Similar content being viewed by others

References

  1. Eulalio, A., Huntzinger, E. & Izaurralde, E. Getting to the root of miRNA-mediated gene silencing. Cell 132, 9–14 (2008).

    CAS  PubMed  Google Scholar 

  2. Vasudevan, S., Tong, Y. & Steitz, J. A. Switching from repression to activation: microRNAs can up-regulate translation. Science 318, 1931–1934 (2007).

    CAS  PubMed  Google Scholar 

  3. Vaucheret, H. Post-transcriptional small RNA pathways in plants: mechanisms and regulations. Genes Dev. 20, 759–771 (2006).

    CAS  PubMed  Google Scholar 

  4. Leung, A. K. & Sharp, P. A. microRNAs: a safeguard against turmoil? Cell 130, 581–585 (2007).

    CAS  PubMed  Google Scholar 

  5. Lee, Y. et al. MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 23, 4051–4060 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Borchert, G. M., Lanier, W. & Davidson, B. L. RNA polymerase III transcribes human microRNAs. Nature Struct. Mol. Biol. 13, 1097–1101 (2006).

    CAS  Google Scholar 

  7. Kim, V. N. MicroRNA biogenesis: coordinated cropping and dicing. Nature Rev. Mol. Cell Biol. 6, 376–385 (2005).

    CAS  Google Scholar 

  8. Kurihara, Y. & Watanabe, Y. Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proc. Natl Acad. Sci. USA 101, 12753–12758 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Okamura, K., Hagen, J. W., Duan, H., Tyler, D. M. & Lai, E. C. The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. Cell 130, 89–100 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Tomari, Y., Matranga, C., Haley, B., Martinez, N. & Zamore, P. D. A protein sensor for siRNA asymmetry. Science 306, 1377–1380 (2004).

    CAS  PubMed  Google Scholar 

  11. Song, J. J., Smith, S. K., Hannon, G. J. & Joshua-Tor, L. Crystal structure of Argonaute and its implications for RISC slicer activity. Science 305, 1434–1437 (2004).

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  13. Reinhart, B. J. et al. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403, 901–906 (2000).

    CAS  PubMed  Google Scholar 

  14. Lewis, B. P., Shih, I. H., Jones-Rhoades, M. W., Bartel, D. P. & Burge, C. B. Prediction of mammalian microRNA targets. Cell 115, 787–798 (2003).

    CAS  PubMed  Google Scholar 

  15. John, B. et al. Human microRNA targets. PLoS Biol. 2, e363 (2004).

    PubMed  PubMed Central  Google Scholar 

  16. Sethupathy, P., Corda, B. & Hatzigeorgiou, A. G. TarBase: a comprehensive database of experimentally supported animal microRNA targets. RNA 12, 192–197 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Grimson, A. et al. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol. Cell 27, 91–105 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Lim, L. P. et al. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433, 769–773 (2005).

    CAS  PubMed  Google Scholar 

  19. Lytle, J. R., Yario, T. A. & Steitz, J. A. Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5′ UTR as in the 3′ UTR. Proc. Natl Acad. Sci. USA 104, 9667–9672 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Duursma, A. M., Kedde, M., Schrier, M., le Sage, C. & Agami, R. miR-148 targets human DNMT3b protein coding region. RNA 14, 872–877 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Lal, A. et al. p16INK4a translation suppressed by miR-24. PLoS ONE 3, e1864 (2008).

    PubMed  PubMed Central  Google Scholar 

  22. Miranda, K. C. et al. A pattern-based method for the identification of microRNA binding sites and their corresponding heteroduplexes. Cell 126, 1203–1217 (2006).

    CAS  PubMed  Google Scholar 

  23. Lewis, B. P., Burge, C. B. & Bartel, D. P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15–20 (2005).

    CAS  PubMed  Google Scholar 

  24. Stark, A. et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450, 219–232 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Forman, J. J., Legesse-Miller, A. & Coller, H. A. A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence. Proc. Natl Acad. Sci. USA 105, 14879–14884 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Tay, Y., Zhang, J., Thomson, A. M., Lim, B. & Rigoutsos, I. MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature 455, 1124–1128 (2008).

    CAS  PubMed  Google Scholar 

  27. Lai, E. C. Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation. Nature Genet. 30, 363–364 (2002).

    CAS  PubMed  Google Scholar 

  28. Mallory, A. C. et al. MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5′ region. EMBO J. 23, 3356–3364 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Brennecke, J., Stark, A., Russell, R. B. & Cohen, S. M. Principles of microRNA–target recognition. PLoS Biol. 3, e85 (2005).

    PubMed  PubMed Central  Google Scholar 

  30. Doench, J. G. & Sharp, P. A. Specificity of microRNA target selection in translational repression. Genes Dev. 18, 504–511 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Selbach, M. et al. Widespread changes in protein synthesis induced by microRNAs. Nature 455, 58–63 (2008).

    CAS  PubMed  Google Scholar 

  32. Baek, D. et al. The impact of microRNAs on protein output. Nature 455, 64–71 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Ha, I., Wightman, B. & Ruvkun, G. A bulged lin-4/lin-14 RNA duplex is sufficient for Caenorhabditis elegans lin-14 temporal gradient formation. Genes Dev. 10, 3041–3050 (1996).

    CAS  PubMed  Google Scholar 

  34. Stern-Ginossar, N. et al. Host immune system gene targeting by a viral miRNA. Science 317, 376–381 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Orom, U. A., Nielsen, F. C. & Lund, A. H. MicroRNA-10a binds the 5′UTR of ribosomal protein mRNAs and enhances their translation. Mol. Cell 30, 460–471 (2008).

    PubMed  Google Scholar 

  36. Easow, G., Teleman, A. A. & Cohen, S. M. Isolation of microRNA targets by miRNP immunopurification. RNA 13, 1198–1204 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  38. Didiano, D. & Hobert, O. Perfect seed pairing is not a generally reliable predictor for miRNA–target interactions. Nature Struct. Mol. Biol. 13, 849–851 (2006).

    CAS  Google Scholar 

  39. Schwab, R. et al. Specific effects of microRNAs on the plant transcriptome. Dev. Cell 8, 517–527 (2005).

    CAS  PubMed  Google Scholar 

  40. Parizotto, E. A., Dunoyer, P., Rahm, N., Himber, C. & Voinnet, O. In vivo investigation of the transcription, processing, endonucleolytic activity, and functional relevance of the spatial distribution of a plant miRNA. Genes Dev. 18, 2237–2242 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Palatnik, J. F. et al. Sequence and expression differences underlie functional specialization of Arabidopsis microRNAs miR159 and miR319. Dev. Cell 13, 115–125 (2007).

    CAS  PubMed  Google Scholar 

  42. Chuck, G., Meeley, R., Irish, E., Sakai, H. & Hake, S. The maize tasselseed4 microRNA controls sex determination and meristem cell fate by targeting Tasselseed6/indeterminate spikelet1. Nature Genet. 39, 1517–1521 (2007).

    CAS  PubMed  Google Scholar 

  43. Ori, N. et al. Regulation of LANCEOLATE by miR319 is required for compound-leaf development in tomato. Nature Genet. 39, 787–791 (2007).

    CAS  PubMed  Google Scholar 

  44. Jones-Rhoades, M. W. & Bartel, D. P. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell 14, 787–799 (2004).

    CAS  PubMed  Google Scholar 

  45. Didiano, D. & Hobert, O. Molecular architecture of a miRNA-regulated 3′ UTR. RNA 14, 1297–1317 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Ameres, S. L., Martinez, J. & Schroeder, R. Molecular basis for target RNA recognition and cleavage by human RISC. Cell 130, 101–112 (2007).

    CAS  PubMed  Google Scholar 

  47. Wang, Y., Sheng, G., Juranek, S., Tuschl, T. & Patel, D. J. Structure of the guide-strand-containing argonaute silencing complex. Nature 456, 209–213 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  48. Kertesz, M., Iovino, N., Unnerstall, U., Gaul, U. & Segal, E. The role of site accessibility in microRNA target recognition. Nature Genet. 39, 1278–1284 (2007).

    CAS  PubMed  Google Scholar 

  49. Vella, M. C., Choi, E. Y., Lin, S. Y., Reinert, K. & Slack, F. J. The C. elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 3′UTR. Genes Dev. 18, 132–137 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. Martinez, J. & Tuschl, T. RISC is a 5′ phosphomonoester-producing RNA endonuclease. Genes Dev. 18, 975–980 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  51. Hutvagner, G. & Zamore, P. D. A microRNA in a multiple-turnover RNAi enzyme complex. Science 297, 2056–2060 (2002).

    CAS  PubMed  Google Scholar 

  52. Kasschau, K. D. et al. P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA function. Dev. Cell 4, 205–217 (2003).

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  54. Davis, E. et al. RNAi-mediated allelic trans-interaction at the imprinted Rtl1/Peg11 locus. Curr. Biol. 15, 743–749 (2005).

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  57. Brodersen, P. et al. Widespread translational inhibition by plant miRNAs and siRNAs. Science 320, 1185–1190 (2008).

    CAS  PubMed  Google Scholar 

  58. Fahlgren, N. et al. High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS ONE 2, e219 (2007).

    PubMed  PubMed Central  Google Scholar 

  59. Umbach, J. L. et al. MicroRNAs expressed by herpes simplex virus 1 during latent infection regulate viral mRNAs. Nature 454, 780–783 (2008).

    CAS  PubMed  Google Scholar 

  60. Wu, L., Fan, J. & Belasco, J. G. Importance of translation and nonnucleolytic Ago proteins for on-target RNA interference. Curr. Biol. 18, 1327–1332 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  61. Moore, M. J. From birth to death: the complex lives of eukaryotic mRNAs. Science 309, 1514–1518 (2005).

    CAS  PubMed  Google Scholar 

  62. Kong, Y. W. et al. The mechanism of micro-RNA-mediated translation repression is determined by the promoter of the target gene. Proc. Natl Acad. Sci. USA 105, 8866–8871 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  63. Rhoades, M. W. et al. Prediction of plant microRNA targets. Cell 110, 513–520 (2002).

    CAS  PubMed  Google Scholar 

  64. Dugas, D. V. & Bartel, B. Sucrose induction of Arabidopsis miR398 represses two Cu/Zn superoxide dismutases. Plant Mol. Biol. 67, 403–417 (2008).

    CAS  PubMed  Google Scholar 

  65. Saetrom, P. et al. Distance constraints between microRNA target sites dictate efficacy and cooperativity. Nucleic Acids Res. 35, 2333–2342 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  66. Giraldez, A. J. et al. Zebrafish miR-430 promotes deadenylation and clearance of maternal mRNAs. Science 312, 75–79 (2006).

    CAS  PubMed  Google Scholar 

  67. Sieber, P., Wellmer, F., Gheyselinck, J., Riechmann, J. L. & Meyerowitz, E. M. Redundancy and specialization among plant microRNAs: role of the MIR164 family in developmental robustness. Development 134, 1051–1060 (2007).

    CAS  PubMed  Google Scholar 

  68. Allen, E., Xie, Z., Gustafson, A. M. & Carrington, J. C. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121, 207–221 (2005).

    CAS  PubMed  Google Scholar 

  69. Brennecke, J. et al. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128, 1089–1103 (2007).

    CAS  PubMed  Google Scholar 

  70. Gunawardane, L. S. et al. A slicer-mediated mechanism for repeat-associated siRNA 5′ end formation in Drosophila. Science 315, 1587–1590 (2007).

    CAS  PubMed  Google Scholar 

  71. Lu, C. et al. Elucidation of the small RNA component of the transcriptome. Science 309, 1567–1569 (2005).

    CAS  PubMed  Google Scholar 

  72. Jenny, A. et al. A translation-independent role of oskar RNA in early Drosophila oogenesis. Development 133, 2827–2833 (2006).

    CAS  PubMed  Google Scholar 

  73. Pauler, F. M., Koerner, M. V. & Barlow, D. P. Silencing by imprinted noncoding RNAs: is transcription the answer? Trends Genet. 23, 284–292 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  74. Bao, N., Lye, K. W. & Barton, M. K. MicroRNA binding sites in Arabidopsis class III HD-ZIP mRNAs are required for methylation of the template chromosome. Dev. Cell 7, 653–662 (2004).

    CAS  PubMed  Google Scholar 

  75. Rinn, J. L. et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129, 1311–1323 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  76. Itaya, A. et al. A structured viroid RNA serves as a substrate for dicer-like cleavage to produce biologically active small RNAs but is resistant to RNA-induced silencing complex-mediated degradation. J. Virol. 81, 2980–2994 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  77. Kedde, M. et al. RNA-binding protein Dnd1 inhibits microRNA access to target mRNA. Cell 131, 1273–1286 (2007).

    CAS  PubMed  Google Scholar 

  78. Bhattacharyya, S. N., Habermacher, R., Martine, U., Closs, E. I. & Filipowicz, W. Relief of microRNA-mediated translational repression in human cells subjected to stress. Cell 125, 1111–1124 (2006).

    CAS  PubMed  Google Scholar 

  79. Mattick, J. S. RNA regulation: a new genetics? Nature Rev. Genet. 5, 316–323 (2004).

    CAS  PubMed  Google Scholar 

  80. Prasanth, K. V. & Spector, D. L. Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum. Genes Dev. 21, 11–42 (2007).

    CAS  PubMed  Google Scholar 

  81. Brockdorff, N. et al. The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus. Cell 71, 515–526 (1992).

    CAS  PubMed  Google Scholar 

  82. Wutz, A. & Jaenisch, R. A shift from reversible to irreversible X inactivation is triggered during ES cell differentiation. Mol. Cell 5, 695–705 (2000).

    CAS  PubMed  Google Scholar 

  83. Sleutels, F., Zwart, R. & Barlow, D. P. The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 415, 810–813 (2002).

    CAS  PubMed  Google Scholar 

  84. Nagano, T. et al. The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science 322, 1717–1720 (2008).

    CAS  PubMed  Google Scholar 

  85. Lai, E. C., Burks, C. & Posakony, J. W. The K box, a conserved 3′ UTR sequence motif, negatively regulates accumulation of enhancer of split complex transcripts. Development 125, 4077–4088 (1998).

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

The authors are supported by grants to O.V. from the European Research Council, 'Frontiers of RNAi' 210890 and from the Fondation Bettancourt pour les Sciences du Vivant, and to O.V. and P.B. from the European Union (MC-EIF-25064-2005). The authors thank S. Pfeffer, L. Navarro, B. Wulff and D. Gibbings for comments on the manuscript.

Author information

Authors and Affiliations

Authors

Related links

Related links

DATABASES

The miRNA Registry

let-7

lin-4

lsy-6

miR-10a

miR-24

miR-148

miR-164

miR-165

miR-172

miR-398

miR-430

miR-834

miR-H2-3p

FURTHER INFORMATION

Olivier Voinnet's homepage

Rights and permissions

Reprints and permissions

About this article

Cite this article

Brodersen, P., Voinnet, O. Revisiting the principles of microRNA target recognition and mode of action. Nat Rev Mol Cell Biol 10, 141–148 (2009). https://doi.org/10.1038/nrm2619

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nrm2619

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing