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.

Diversifying microRNA sequence and function

Key Points

  • MicroRNAs (miRNAs) are small non-coding RNAs that guide post-transcriptional gene regulation to shape the rate at which genetic information is converted into proteins. Due to this, miRNAs contribute to the establishment of gene expression patterns that are required for normal development and physiology in plants and animals.

  • RNase III enzymes, together with specific double-stranded RNA-binding partner proteins, produce miRNAs from genomically encoded precursor miRNAs (pre-miRNAs). In rare cases, nucleases from other cellular pathways can replace RNase III enzymes in the production of miRNAs.

  • After the assembly of miRNA duplexes, these small RNAs are loaded into proteins from the Argonaute (AGO) protein family. AGO proteins organize small RNAs into subdomains, including the seed sequence, which mediates target RNA binding. The mechanisms by which miRNAs function include endonucleolytic cleavage, translational repression and mRNA turnover.

  • Recent evidence suggests that small RNA stability can be influenced by miRNA sequence motifs, chemical modifications and interactions with target mRNAs.

  • miRNAs are annotated as single sequences, but recent high-throughput efforts to catalogue small RNAs from various organisms, tissues and cell types reveal that most miRNAs comprise multiple isoforms. Several mechanisms have been shown to diversify miRNA sequence and function.

  • The advent of next-generation sequencing technology has revealed the miRNAs of key model organisms, but the extent to which each miRNA contributes to the regulation of targets in the transcriptome of a given cell type remains unclear. The biochemical and biophysical properties of miRNA silencing complexes provide a quantitative framework for their reciprocal function and their targets, according to their abundance and relative stoichiometry inside the cell.

Abstract

MicroRNAs (miRNAs) regulate the expression of most genes in animals, but we are only now beginning to understand how they are generated, assembled into functional complexes and destroyed. Various mechanisms have now been identified that regulate miRNA stability and that diversify miRNA sequences to create distinct isoforms. The production of different isoforms of individual miRNAs in specific cells and tissues may have broader implications for miRNA-mediated gene expression control. Rigorously testing the many discrepant models for how miRNAs function using quantitative biochemical measurements made in vivo and in vitro remains a major challenge for the future.

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

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: MicroRNA biogenesis.
Figure 2: Small RNA turnover by tailing and trimming.
Figure 3: Mechanisms and consequences of microRNA isoforms.
Figure 4: microRNA function in plants and animals.
Figure 5: A quantitative framework for microRNA function.

References

  1. 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 

  2. Wightman, B., Ha, I. & Ruvkun, G. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75, 855–862 (1993). References 1 and 2 report the discovery of the first miRNA, lin-4, and propose that it regulates mRNA expression post-transcriptionally.

    Article  CAS  PubMed  Google Scholar 

  3. Griffiths-Jones, S., Grocock, R. J., van Dongen, S., Bateman, A. & Enright, A. J. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 34, D140–D144 (2006).

    Article  CAS  PubMed  Google Scholar 

  4. Chiang, H. R. et al. Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev. 24, 992–1009 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Friedman, R. C., Farh, K. K., Burge, C. B. & Bartel, D. P. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 19, 92–105 (2009). Shows that more than half of all protein-coding genes in mammals have been evolutionarily selected to maintain pairing with miRNAs, indicating that most of the protein-coding transcriptome is regulated by miRNAs.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  7. Jones-Rhoades, M. W., Bartel, D. P. & Bartel, B. MicroRNAs and their regulatory roles in plants. Annu. Rev. Plant Biol. 57, 19–53 (2006).

    Article  CAS  PubMed  Google Scholar 

  8. Grimson, A. et al. Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature 455, 1193–1197 (2008).

    Article  CAS  PubMed  Google Scholar 

  9. Molnar, A., Schwach, F., Studholme, D. J., Thuenemann, E. C. & Baulcombe, D. C. miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii. Nature 447, 1126–1129 (2007).

    Article  CAS  PubMed  Google Scholar 

  10. Kim, V. N., Han, J. & Siomi, M. C. Biogenesis of small RNAs in animals. Nature Rev. Mol. Cell Biol. 10, 126–139 (2009).

    Article  CAS  Google Scholar 

  11. Axtell, M. J., Westholm, J. O. & Lai, E. C. Vive la différence: biogenesis and evolution of microRNAs in plants and animals. Genome Biol. 12, 221 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Siomi, H. & Siomi, M. C. Posttranscriptional regulation of microRNA biogenesis in animals. Mol. Cell 38, 323–332 (2010).

    Article  CAS  PubMed  Google Scholar 

  13. Carthew, R. W. & Sontheimer, E. J. Origins and mechanisms of miRNAs and siRNAs. Cell 136, 642–655 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Yang, J. S. & Lai, E. C. Alternative miRNA biogenesis pathways and the interpretation of core miRNA pathway mutants. Mol. Cell 43, 892–903 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Cai, X., Hagedorn, C. H. & Cullen, B. R. Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA 10, 1957–1966 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Xie, Z. et al. Expression of Arabidopsis MIRNA genes. Plant Physiol. 138, 2145–2154 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Ozsolak, F. et al. Chromatin structure analyses identify miRNA promoters. Genes Dev. 22, 3172–3183 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Corcoran, D. L. et al. Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data. PLoS ONE 4, e5279 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Rodriguez, A., Griffiths-Jones, S., Ashurst, J. L. & Bradley, A. Identification of mammalian microRNA host genes and transcription units. Genome Res. 14, 1902–1910 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Baskerville, S. & Bartel, D. P. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11, 241–247 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Aboobaker, A. A., Tomancak, P., Patel, N., Rubin, G. M. & Lai, E. C. Drosophila microRNAs exhibit diverse spatial expression patterns during embryonic development. Proc. Natl Acad. Sci. USA 102, 18017–18022 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Kim, Y. K. & Kim, V. N. Processing of intronic microRNAs. EMBO J. 26, 775–783 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Ballarino, M. et al. Coupled RNA processing and transcription of intergenic primary microRNAs. Mol. Cell. Biol. 29, 5632–5638 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Kataoka, N., Fujita, M. & Ohno, M. Functional association of the Microprocessor complex with the spliceosome. Mol. Cell. Biol. 29, 3243–3254 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Lee, Y. et al. The nuclear RNase III Drosha initiates microRNA processing. Nature 425, 415–419 (2003).

    Article  CAS  PubMed  Google Scholar 

  27. Denli, A. M., Tops, B. B., Plasterk, R. H., Ketting, R. F. & Hannon, G. J. Processing of primary microRNAs by the Microprocessor complex. Nature 432, 231–235 (2004).

    Article  CAS  PubMed  Google Scholar 

  28. Gregory, R. I. et al. The Microprocessor complex mediates the genesis of microRNAs. Nature 432, 235–240 (2004).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  30. Han, J. et al. The Drosha–DGCR8 complex in primary microRNA processing. Genes Dev. 18, 3016–3027 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Han, J. et al. Molecular basis for the recognition of primary microRNAs by the Drosha–DGCR8 complex. Cell 125, 887–901 (2006).

    Article  CAS  PubMed  Google Scholar 

  32. Wu, H., Xu, H., Miraglia, L. J. & Crooke, S. T. Human RNase III is a 160-kDa protein involved in preribosomal RNA processing. J. Biol. Chem. 275, 36957–36965 (2000).

    Article  CAS  PubMed  Google Scholar 

  33. Billy, E., Brondani, V., Zhang, H., Muller, U. & Filipowicz, W. Specific interference with gene expression induced by long, double-stranded RNA in mouse embryonal teratocarcinoma cell lines. Proc. Natl Acad. Sci. USA 98, 14428–14433 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Provost, P. et al. Ribonuclease activity and RNA binding of recombinant human Dicer. EMBO J. 21, 5864–5874 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Okada, C. et al. A high-resolution structure of the pre-microRNA nuclear export machinery. Science 326, 1275–1279 (2009).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  40. Bohnsack, M. T., Czaplinski, K. & Gorlich, D. Exportin 5 is a Ran GTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs. RNA 10, 185–191 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Zeng, Y. & Cullen, B. R. Structural requirements for pre-microRNA binding and nuclear export by Exportin 5. Nucleic Acids Res. 32, 4776–4785 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Bernstein, E., Caudy, A. A., Hammond, S. M. & Hannon, G. J. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409, 363–366 (2001).

    Article  CAS  PubMed  Google Scholar 

  43. Hutvágner, G. et al. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293, 834–838 (2001).

    Article  PubMed  Google Scholar 

  44. Grishok, A. et al. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106, 23–34 (2001).

    Article  CAS  PubMed  Google Scholar 

  45. Ketting, R. F. et al. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev. 15, 2654–2659 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  47. Zhang, H., Kolb, F. A., Brondani, V., Billy, E. & Filipowicz, W. Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. EMBO J. 21, 5875–5885 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Zhang, H., Kolb, F. A., Jaskiewicz, L., Westhof, E. & Filipowicz, W. Single processing center models for human Dicer and bacterial RNase III. Cell 118, 57–68 (2004).

    Article  CAS  PubMed  Google Scholar 

  49. Pase, L. et al. miR-451 regulates zebrafish erythroid maturation in vivo via its target gata2. Blood 113, 1794–1804 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Cheloufi, S., Dos Santos, C. O., Chong, M. M. & Hannon, G. J. A dicer-independent miRNA biogenesis pathway that requires Ago catalysis. Nature 465, 584–589 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Yang, J. S. et al. Conserved vertebrate mir-451 provides a platform for Dicer-independent, Ago2-mediated microRNA biogenesis. Proc. Natl Acad. Sci. USA 107, 15163–15168 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  52. Saito, K., Ishizuka, A., Siomi, H. & Siomi, M. C. Processing of pre-microRNAs by the Dicer-1–Loquacious complex in Drosophila cells. PLoS Biol. 3, e235 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Forstemann, K. et al. Normal microRNA maturation and germ-line stem cell maintenance requires Loquacious, a double-stranded RNA-binding domain protein. PLoS Biol. 3, e236 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Jiang, F. et al. Dicer-1 and R3D1-L catalyze microRNA maturation in Drosophila. Genes Dev. 19, 1674–1679 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Fukunaga, R. et al. Dicer partner proteins tune the length of mature miRNAs in flies and mammals. Cell 151, 533–546 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Cenik, E. S. et al. Phosphate and R2D2 restrict the substrate specificity of Dicer-2, an ATP-driven ribonuclease. Mol. Cell 42, 172–184 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Chendrimada, T. P. et al. TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature 436, 740–744 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Haase, A. D. et al. TRBP, a regulator of cellular PKR and HIV-1 virus expression, interacts with Dicer and functions in RNA silencing. EMBO Rep. 6, 961–967 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Lee, Y. et al. The role of PACT in the RNA silencing pathway. EMBO J. 25, 522–532 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Lee, H. Y. & Doudna, J. A. TRBP alters human precursor microRNA processing in vitro. RNA 18, 2012–2019 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Czech, B. & Hannon, G. J. Small RNA sorting: matchmaking for Argonautes. Nature Rev. Genet. 12, 19–31 (2011).

    Article  CAS  PubMed  Google Scholar 

  62. Kawamata, T. & Tomari, Y. Making RISC. Trends Biochem. Sci. 35, 368–376 (2010).

    Article  CAS  PubMed  Google Scholar 

  63. Bartel, D. P. MicroRNAs: target recognition and regulatory functions. Cell 136, 215–233 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. 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).

    Article  PubMed  PubMed Central  Google Scholar 

  66. Gu, S., Jin, L., Zhang, F., Sarnow, P. & Kay, M. A. Biological basis for restriction of microRNA targets to the 3′ untranslated region in mammalian mRNAs. Nature Struct. Mol. Biol. 16, 144–150 (2009).

    Article  CAS  Google Scholar 

  67. Forman, J. J. & Coller, H. A. The code within the code: microRNAs target coding regions. Cell Cycle 9, 1533–1541 (2010).

    Article  CAS  PubMed  Google Scholar 

  68. Farh, K. K. et al. The widespread impact of mammalian microRNAs on mRNA repression and evolution. Science 310, 1817–1821 (2005).

    Article  CAS  PubMed  Google Scholar 

  69. Stark, A., Brennecke, J., Bushati, N., Russell, R. B. & Cohen, S. M. Animal microRNAs confer robustness to gene expression and have a significant impact on 3′UTR evolution. Cell 123, 1133–1146 (2005).

    Article  CAS  PubMed  Google Scholar 

  70. 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).

    Article  CAS  PubMed  Google Scholar 

  71. Krutzfeldt, J. et al. Silencing of microRNAs in vivo with 'antagomirs'. Nature 438, 685–689 (2005).

    Article  CAS  PubMed  Google Scholar 

  72. Ameres, S. L. et al. Target RNA-directed trimming and tailing of small silencing RNAs. Science 328, 1534–1539 (2010). References 71, 72, 94 and 96 show that target-RNA binding can alter miRNA stability in mammals, flies and worms. References 72 and 94 help explain how the presence or absence of targets may destabilize miRNAs.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Baccarini, A. et al. Kinetic analysis reveals the fate of a microRNA following target regulation in mammalian cells. Curr. Biol. 21, 369–376 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Xie, J. et al. Long-term, efficient inhibition of microRNA function in mice using rAAV vectors. Nature Methods 9, 403–409 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Yan, K. S. et al. Structure and conserved RNA binding of the PAZ domain. Nature 426, 468–474 (2003).

    Article  CAS  PubMed  Google Scholar 

  76. Lingel, A., Simon, B., Izaurralde, E. & Sattler, M. Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain. Nature 426, 465–469 (2003).

    Article  CAS  PubMed  Google Scholar 

  77. Lingel, A., Simon, B., Izaurralde, E. & Sattler, M. NMR assignment of the Drosophila Argonaute2 PAZ domain. J. Biomol. NMR 29, 421–422 (2004).

    Article  CAS  PubMed  Google Scholar 

  78. Lingel, A., Simon, B., Izaurralde, E. & Sattler, M. Nucleic acid 3′-end recognition by the Argonaute2 PAZ domain. Nature Struct. Mol. Biol. 11, 576–577 (2004).

    Article  CAS  Google Scholar 

  79. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Hsu, S.-H. et al. Essential metabolic, anti-inflammatory, and anti-tumorigenic functions of miR-122 in liver. J. Clin. Invest. 122, 2871–2883 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Tsai, W.-C. et al. MicroRNA-122 plays a critical role in liver homeostasis and hepatocarcinogenesis. J. Clin. Invest. 122, 2884–2897 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Libri, V., Miesen, P., van Rij, R. P. & Buck, A. H. Regulation of microRNA biogenesis and turnover by animals and their viruses. Cell. Mol. Life Sci. http://dx.doi.org/10.1007/s00018-012-1257-1 (2013).

  83. tenOever, B. R. RNA viruses and the host microRNA machinery. Nature Rev. Microbiol. 11, 169–180 (2013).

    Article  CAS  Google Scholar 

  84. Pelisson, A., Sarot, E., Payen-Groschene, G. & Bucheton, A. A novel repeat-associated small interfering RNA-mediated silencing pathway downregulates complementary sense gypsy transcripts in somatic cells of the Drosophila ovary. J. Virol. 81, 1951–1960 (2007).

    Article  CAS  PubMed  Google Scholar 

  85. Horwich, M. D. et al. The Drosophila RNA methyltransferase, DmHen1, modifies germline piRNAs and single-stranded siRNAs in RISC. Curr. Biol. 17, 1265–1272 (2007).

    Article  CAS  PubMed  Google Scholar 

  86. Ameres, S. L., Hung, J. H., Xu, J., Weng, Z. & Zamore, P. D. Target RNA-directed tailing and trimming purifies the sorting of endo-siRNAs between the two Drosophila Argonaute proteins. RNA 17, 54–63 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Park, W., Li, J., Song, R., Messing, J. & Chen, X. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr. Biol. 12, 1484–1495 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Yu, B. et al. Methylation as a crucial step in plant microRNA biogenesis. Science 307, 932–935 (2005). Reports, for the first time, 2′- O -methyl modification of small RNAs, which is a stabilizing chemical modification that is added to all plant and some animal small RNA classes.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Li, J., Yang, Z., Yu, B., Liu, J. & Chen, X. Methylation protects miRNAs and siRNAs from a 3′-end uridylation activity in Arabidopsis. Curr. Biol. 15, 1501–1507 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Yang, Z., Ebright, Y. W., Yu, B. & Chen, X. HEN1 recognizes 21–24 nt small RNA duplexes and deposits a methyl group onto the 2′ OH of the 3′ terminal nucleotide. Nucleic Acids Res. 34, 667–675 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Abe, M. et al. WAVY LEAF1, an ortholog of Arabidopsis HEN1, regulates shoot development by maintaining microRNA and trans-acting small interfering RNA accumulation in rice. Plant Physiol. 154, 1335–1346 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Huang, Y. et al. Structural insights into mechanisms of the small RNA methyltransferase HEN1. Nature 461, 823–827 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Vilkaitis, G., Plotnikova, A. & Klimasauskas, S. Kinetic and functional analysis of the small RNA methyltransferase HEN1: the catalytic domain is essential for preferential modification of duplex RNA. RNA 16, 1935–1942 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Chatterjee, S. & Grosshans, H. Active turnover modulates mature microRNA activity in Caenorhabditis elegans. Nature 461, 546–549 (2009).

    Article  CAS  PubMed  Google Scholar 

  95. Song, E. et al. Sustained small interfering RNA-mediated human immunodeficiency virus type 1 inhibition in primary macrophages. J. Virol. 77, 7174–7181 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Chatterjee, S., Fasler, M., Bussing, I. & Grosshans, H. Target-mediated protection of endogenous microRNAs in C. elegans. Dev. Cell 20, 388–396 (2011).

    Article  CAS  PubMed  Google Scholar 

  97. Bail, S. et al. Differential regulation of microRNA stability. RNA 16, 1032–1039 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Berezikov, E. et al. Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Res. 21, 203–215 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Ruby, J. G. et al. Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res. 17, 1850–1864 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Wu, H. et al. miRNA profiling of naïve, effector and memory CD8 T cells. PLoS ONE 2, e1020 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Morin, R. D. et al. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res. 18, 610–621 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Seitz, H., Ghildiyal, M. & Zamore, P. D. Argonaute loading improves the 5′ precision of both microRNAs and their miRNA* strands in flies. Curr. Biol. 18, 147–151 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Rajagopalan, R., Vaucheret, H., Trejo, J. & Bartel, D. P. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev. 20, 3407–3425 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Westholm, J. O., Ladewig, E., Okamura, K., Robine, N. & Lai, E. C. Common and distinct patterns of terminal modifications to mirtrons and canonical microRNAs. RNA 18, 177–192 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Czech, B. et al. Hierarchical rules for Argonaute loading in Drosophila. Mol. Cell 36, 445–456 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Okamura, K., Liu, N. & Lai, E. C. Distinct mechanisms for microRNA strand selection by Drosophila Argonautes. Mol. Cell 36, 431–444 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Ghildiyal, M., Xu, J., Seitz, H., Weng, Z. & Zamore, P. D. Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. RNA 16, 43–56 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Ruby, J. G. et al. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127, 1193–1207 (2006).

    Article  CAS  PubMed  Google Scholar 

  109. Babiarz, J. E., Ruby, J. G., Wang, Y., Bartel, D. P. & Blelloch, R. Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. Genes Dev. 22, 2773–2785 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Glazov, E. A. et al. A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Res. 18, 957–964 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Ebhardt, H. A. et al. Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications. Nucleic Acids Res. 37, 2461–2470 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Blow, M. J. et al. RNA editing of human microRNAs. Genome Biol. 7, R27 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Landgraf, P. et al. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129, 1401–1414 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Kawahara, Y. et al. Redirection of silencing targets by adenosine-to-inosine editing of miRNAs. Science 315, 1137–1140 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Hundley, H. A. & Bass, B. L. ADAR editing in double-stranded UTRs and other noncoding RNA sequences. Trends Biochem. Sci. 35, 377–383 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Knight, S. W. & Bass, B. L. The role of RNA editing by ADARs in RNAi. Mol. Cell 10, 809–817 (2002).

    Article  CAS  PubMed  Google Scholar 

  117. Habig, J. W., Aruscavage, P. J. & Bass, B. L. In C. elegans, high levels of dsRNA allow RNAi in the absence of RDE-4. PLoS ONE 3, e4052 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Wu, D., Lamm, A. T. & Fire, A. Z. Competition between ADAR and RNAi pathways for an extensive class of RNA targets. Nature Struct. Mol. Biol. 18, 1094–1101 (2011).

    Article  CAS  Google Scholar 

  119. Liu, N. et al. The exoribonuclease Nibbler controls 3′ end processing of microRNAs in Drosophila. Curr. Biol. 21, 1888–1893 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Han, B. W., Hung, J. H., Weng, Z., Zamore, P. D. & Ameres, S. L. The 3′-to-5′ exoribonuclease Nibbler shapes the 3′ ends of microRNAs bound to Drosophila Argonaute1. Curr. Biol. 21, 1878–1887 (2011). References119 and 120 describe the enzyme responsible for generating much of the 3′ heterogeneity observed in D. melanogaster miRNAs, revealing that exonucleolytic trimming of miRNAs after assembly into AGO proteins promotes the formation of active complexes.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Ketting, R. F., Haverkamp, T. H., van Luenen, H. G. & Plasterk, R. H. Mut-7 of C. elegans, required for transposon silencing and RNA interference, is a homolog of Werner syndrome helicase and RNaseD. Cell 99, 133–141 (1999).

    Article  CAS  PubMed  Google Scholar 

  122. Ketting, R. F. & Plasterk, R. H. A genetic link between co-suppression and RNA interference in C. elegans. Nature 404, 296–298 (2000).

    Article  CAS  PubMed  Google Scholar 

  123. Grishok, A., Tabara, H. & Mello, C. C. Genetic requirements for inheritance of RNAi in C. elegans. Science 287, 2494–2497 (2000).

    Article  CAS  PubMed  Google Scholar 

  124. Sijen, T. & Plasterk, R. H. Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi. Nature 426, 310–314 (2003).

    Article  CAS  PubMed  Google Scholar 

  125. Rissland, O. S., Mikulasova, A. & Norbury, C. J. Efficient RNA polyuridylation by noncanonical poly(A) polymerases. Mol. Cell. Biol. 27, 3612–3624 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Dreyfus, M. & Regnier, P. The poly(A) tail of mRNAs: bodyguard in eukaryotes, scavenger in bacteria. Cell 111, 611–613 (2002).

    Article  CAS  PubMed  Google Scholar 

  127. Scott, D. D. & Norbury, C. J. RNA decay via 3′ uridylation. Biochim Biophys Acta 1829, 654–665 (2013).

    Article  CAS  PubMed  Google Scholar 

  128. Heo, I. et al. TUT4 in concert with Lin28 suppresses microRNA biogenesis through pre-microRNA uridylation. Cell 138, 696–708 (2009).

    Article  CAS  PubMed  Google Scholar 

  129. Hagan, J. P., Piskounova, E. & Gregory, R. I. Lin28 recruits the TUTase Zcchc11 to inhibit let-7 maturation in mouse embryonic stem cells. Nature Struct. Mol. Biol. 16, 1021–1025 (2009). References 128 and 129 report that LIN28-bound pre-miRNAs act as substrates for the TNTase ZCCHC11, thereby establishing the mechanism for inhibition of pre-miRNA processing by uridylation.

    Article  CAS  Google Scholar 

  130. Heo, I. et al. Lin28 mediates the terminal uridylation of let-7 precursor microRNA. Mol. Cell 32, 276–284 (2008).

    Article  CAS  PubMed  Google Scholar 

  131. Joo, C., Fareh, M. & Kim, V. N. Bringing single-molecule spectroscopy to macromolecular protein complexes. Trends Biochem. Sci. 38, 30–37 (2013).

    Article  CAS  PubMed  Google Scholar 

  132. Chang, H.-M., Triboulet, R., Thornton, J. E. & Gregory, R. I. A role for the Perlman syndrome exonuclease Dis3l2 in the Lin28–let-7 pathway. Nature 497, 244–248 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  133. Heo, I. et al. Mono-uridylation of pre-microRNA as a key step in the biogenesis of group II let-7 microRNAs. Cell 151, 521–532 (2012). Reveals that monouridylation of specific pre-miRNAs enhances Dicer-mediated processing by restoring a canonical two nucleotide 3′ overhang, which is required for efficient substrate recognition by Dicer.

    Article  CAS  PubMed  Google Scholar 

  134. Jones, M. R. et al. Zcchc11-dependent uridylation of microRNA directs cytokine expression. Nature Cell Biol. 11, 1157–1163 (2009).

    Article  CAS  PubMed  Google Scholar 

  135. Katoh, T. et al. Selective stabilization of mammalian microRNAs by 3′ adenylation mediated by the cytoplasmic poly(A) polymerase GLD-2. Genes Dev. 23, 433–438 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  136. Burroughs, A. M. et al. A comprehensive survey of 3′ animal miRNA modification events and a possible role for 3′ adenylation in modulating miRNA targeting effectiveness. Genome Res. 20, 1398–1410 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  137. Lu, S., Sun, Y. H. & Chiang, V. L. Adenylation of plant miRNAs. Nucleic Acids Res. 37, 1878–1885 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. Zhao, Y. et al. The Arabidopsis nucleotidyl transferase HESO1 uridylates unmethylated small RNAs to trigger their degradation. Curr. Biol. 22, 689–694 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  139. Ren, G., Chen, X. & Yu, B. Uridylation of miRNAs by HEN1 SUPPRESSOR1 in Arabidopsis. Curr. Biol. 22, 695–700 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  140. Ibrahim, F. et al. Uridylation of mature miRNAs and siRNAs by the MUT68 nucleotidyltransferase promotes their degradation in Chlamydomonas. Proc. Natl Acad. Sci. USA http://dx.doi.org/10.1073/pnas.0912632107 (2010).

  141. Ibrahim, F., Rohr, J., Jeong, W.-J., Hesson, J. & Cerutti, H. Untemplated oligoadenylation promotes degradation of RISC-cleaved transcripts. Science 314, 1893 (2006).

    Article  CAS  PubMed  Google Scholar 

  142. Shen, B. & Goodman, H. M. Uridine addition after microRNA-directed cleavage. Science 306, 997 (2004).

    Article  CAS  PubMed  Google Scholar 

  143. Tang, G., Reinhart, B. J., Bartel, D. P. & Zamore, P. D. A biochemical framework for RNA silencing in plants. Genes Dev. 17, 49–63 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  144. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  145. Haley, B. & Zamore, P. D. Kinetic analysis of the RNAi enzyme complex. Nature Struct. Mol. Biol. 11, 599–606 (2004).

    Article  CAS  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  147. Wee, L., Flores-Jasso, C. F., Salomon, W. & Zamore, P. D. Argonaute divides its RNA guide into domains with distinct functions and RNA-binding properties. Cell 151, 1055–1067 (2012). Reports detailed kinetic analyses of AGO-directed small RNA–target RNA interactions in flies and mice. Establishes the biochemical basis for siRNA and miRNA function, which is determined by the relative abundance of small RNAs and their targets.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  148. 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).

    Article  CAS  PubMed  Google Scholar 

  149. Parker, J. S., Roe, S. M. & Barford, D. Structural insights into mRNA recognition from a PIWI domain–siRNA guide complex. Nature 434, 663–666 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. Wang, Y. et al. Structure of an Argonaute silencing complex with a seed-containing guide DNA and target RNA duplex. Nature 456, 921–926 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  151. Parker, J. S., Parizotto, E. A., Wang, M., Roe, S. M. & Barford, D. Enhancement of the seed-target recognition step in RNA silencing by a PIWI/MID domain protein. Mol. Cell 33, 204–214 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  152. Schirle, N. T. & MacRae, I. J. The crystal structure of human Argonaute2. Science 336, 1037–1040 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  153. Elkayam, E. et al. The structure of human Argonaute-2 in complex with miR-20a. Cell 150, 100–110 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  154. Nakanishi, K., Weinberg, D. E., Bartel, D. P. & Patel, D. J. Structure of yeast Argonaute with guide RNA. Nature 486, 368–374 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  155. Wang, Y. et al. Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes. Nature 461, 754–761 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  156. Chi, S. W., Hannon, G. J. & Darnell, R. B. An alternative mode of microRNA target recognition. Nature Struct. Mol. Biol. 19, 321–327 (2012).

    Article  CAS  Google Scholar 

  157. Long, D. et al. Potent effect of target structure on microRNA function. Nature Struct. Mol. Biol. 14, 287–294 (2007).

    Article  CAS  Google Scholar 

  158. Nielsen, C. B. et al. Determinants of targeting by endogenous and exogenous microRNAs and siRNAs. RNA 13, 1894–1910 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  159. 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).

    Article  CAS  PubMed  Google Scholar 

  160. Tafer, H. et al. The impact of target site accessibility on the design of effective siRNAs. Nature Biotech. 26, 578–583 (2008).

    Article  CAS  Google Scholar 

  161. Obernosterer, G., Tafer, H. & Martinez, J. Target site effects in the RNA interference and microRNA pathways. Biochem. Soc. Trans. 36, 1216–1219 (2008).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  163. 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).

    Article  CAS  PubMed  Google Scholar 

  164. Huang, J. et al. Derepression of microRNA-mediated protein translation inhibition by apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G (APOBEC3G) and its family members. J. Biol. Chem. 282, 33632–33640 (2007).

    Article  CAS  PubMed  Google Scholar 

  165. Mishima, Y. et al. Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization. Genes Dev. 23, 619–632 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  166. Elcheva, I., Goswami, S., Noubissi, F. K. & Spiegelman, V. S. CRD-BP protects the coding region of βTrCP1 mRNA from miR-183-mediated degradation. Mol. Cell 35, 240–246 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  167. Goswami, S. et al. MicroRNA-340-mediated degradation of microphthalmia-associated transcription factor mRNA is inhibited by the coding region determinant-binding protein. J. Biol. Chem. 285, 20532–20540 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  168. Jafarifar, F., Yao, P., Eswarappa, S. M. & Fox, P. L. Repression of VEGFA by CA-rich element-binding microRNAs is modulated by hnRNP L. EMBO J. 30, 1324–1334 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  169. Toledano, H., D'Alterio, C., Czech, B., Levine, E. & Jones, D. L. The let-7–Imp axis regulates ageing of the Drosophila testis stem-cell niche. Nature 485, 605–610 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  170. Shin, C. et al. Expanding the microRNA targeting code: functional sites with centered pairing. Mol. Cell 38, 789–802 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  171. Llave, C., Xie, Z., Kasschau, K. D. & Carrington, J. C. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297, 2053–2056 (2002).

    Article  CAS  PubMed  Google Scholar 

  172. Dunoyer, P., Lecellier, C. H., Parizotto, E. A., Himber, C. & Voinnet, O. Probing the microRNA and small interfering RNA pathways with virus-encoded suppressors of RNA silencing. Plant Cell 16, 1235–1250 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  173. Souret, F. F., Kastenmayer, J. P. & Green, P. J. AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets. Mol. Cell 15, 173–183 (2004).

    Article  CAS  PubMed  Google Scholar 

  174. German, M. A. et al. Global identification of microRNA–target RNA pairs by parallel analysis of RNA ends. Nature Biotech. 26, 941–946 (2008).

    Article  CAS  Google Scholar 

  175. Addo-Quaye, C., Eshoo, T. W., Bartel, D. P. & Axtell, M. J. Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr. Biol. 18, 758–762 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  176. 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).

    Article  CAS  PubMed  Google Scholar 

  177. Lanet, E. et al. Biochemical evidence for translational repression by Arabidopsis microRNAs. Plant Cell 21, 1762–1768 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  178. Brodersen, P. et al. Widespread translational inhibition by plant miRNAs and siRNAs. Science 320, 1185–1190 (2008). References 177 and 178 propose that, despite the large number of extensively complementary cleavage targets for plant miRNAs, translational repression may be a widespread mechanism by which plant miRNAs repress gene expression.

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  181. Karginov, F. V. et al. Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases. Mol. Cell 38, 781–788 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  182. Bagga, S. et al. Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell 122, 553–563 (2005).

    Article  CAS  PubMed  Google Scholar 

  183. Jing, Q. et al. Involvement of microRNA in AU-rich element-mediated mRNA instability. Cell 120, 623–634 (2005).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  186. Rehwinkel, J. et al. Genome-wide analysis of mRNAs regulated by Drosha and Argonaute proteins in Drosophila melanogaster. Mol. Cell. Biol. 26, 2965–2975 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  187. Wu, L., Fan, J. & Belasco, J. G. MicroRNAs direct rapid deadenylation of mRNA. Proc. Natl Acad. Sci. USA 103, 4034–4039 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  190. Guo, H., Ingolia, N. T., Weissman, J. S. & Bartel, D. P. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466, 835–840 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  191. Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. & Weissman, J. S. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324, 218–223 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  192. Hendrickson, D. G. et al. Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. PLoS Biol. 7, e1000238 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  193. Bazzini, A. A., Lee, M. T. & Giraldez, A. J. Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science 336, 233–237 (2012). Proposes, together with reference 190, that animal miRNAs predominantly function by triggering mRNA decay. Reference 193 also suggests that translational repression may precede mRNA decay.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  194. Rehwinkel, J., Behm-Ansmant, I., Gatfield, D. & Izaurralde, E. A crucial role for GW182 and the DCP1:DCP2 decapping complex in miRNA-mediated gene silencing. RNA 11, 1640–1647 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  195. Behm-Ansmant, I. et al. mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes. Genes Dev. 20, 1885–1898 (2006).

    Article  PubMed  PubMed Central  Google Scholar 

  196. Braun, J. E., Huntzinger, E., Fauser, M. & Izaurralde, E. GW182 proteins directly recruit cytoplasmic deadenylase complexes to miRNA targets. Mol. Cell 44, 120–133 (2011).

    Article  CAS  PubMed  Google Scholar 

  197. Thermann, R. & Hentze, M. W. Drosophila miR2 induces pseudo-polysomes and inhibits translation initiation. Nature 447, 875–878 (2007).

    Article  CAS  PubMed  Google Scholar 

  198. Iwasaki, S., Kawamata, T. & Tomari, Y. Drosophila Argonaute1 and Argonaute2 employ distinct mechanisms for translational repression. Mol. Cell 34, 58–67 (2009).

    Article  PubMed  Google Scholar 

  199. Mathonnet, G. et al. MicroRNA inhibition of translation initiation in vitro by targeting the cap-binding complex eIF4F. Science 317, 1764–1767 (2007).

    Article  CAS  PubMed  Google Scholar 

  200. Zdanowicz, A. et al. Drosophila miR2 primarily targets the m7GpppN cap structure for translational repression. Mol. Cell 35, 881–888 (2009).

    Article  CAS  PubMed  Google Scholar 

  201. Fabian, M. R. et al. Mammalian miRNA RISC recruits CAF1 and PABP to affect PABP-dependent deadenylation. Mol. Cell 35, 868–880 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  202. Djuranovic, S., Nahvi, A. & Green, R. miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science 336, 237–240 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  203. Bruno, I. G. et al. Identification of a microRNA that activates gene expression by repressing nonsense-mediated RNA decay. Mol. Cell 42, 500–510 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  204. Place, R. F., Li, L. C., Pookot, D., Noonan, E. J. & Dahiya, R. MicroRNA-373 induces expression of genes with complementary promoter sequences. Proc. Natl Acad. Sci. USA 105, 1608–1613 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  205. Li, L. C. et al. Small dsRNAs induce transcriptional activation in human cells. Proc. Natl Acad. Sci. USA 103, 17337–17342 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  206. Schwartz, J. C. et al. Antisense transcripts are targets for activating small RNAs. Nature Struct. Mol. Biol. 15, 842–848 (2008).

    Article  CAS  Google Scholar 

  207. Jangra, R. K., Yi, M. & Lemon, S. M. DDX6 (Rck/p54) is required for efficient hepatitis C virus replication but not for internal ribosome entry site-directed translation. J. Virol. 84, 6810–6824 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  208. Jopling, C. L., Yi, M., Lancaster, A. M., Lemon, S. M. & Sarnow, P. Modulation of hepatitis C virus RNA abundance by a liver-specific microRNA. Science 309, 1577–1581 (2005).

    Article  CAS  PubMed  Google Scholar 

  209. Lanford, R. E. et al. Therapeutic silencing of microRNA-122 in primates with chronic hepatitis C virus infection. Science 327, 198–201 (2010).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  211. Vasudevan, S. & Steitz, J. A. AU-rich-element-mediated upregulation of translation by FXR1 and Argonaute 2. Cell 128, 1105–1118 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  212. 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).

    Article  CAS  PubMed  Google Scholar 

  213. Li, X., Cassidy, J. J., Reinke, C. A., Fischboeck, S. & Carthew, R. W. A microRNA imparts robustness against environmental fluctuation during development. Cell 137, 273–282 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  214. Miska, E. A. et al. Most Caenorhabditis elegans microRNAs are individually not essential for development or viability. PLoS Genet. 3, e215 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  215. Seitz, H. Redefining microRNA targets. Curr. Biol. 19, 870–873 (2009). Hypothesizes that in animals many endogenous miRNA target site-containing transcripts ('titrating' targets) may function to titrate miRNA activity rather than serving as targets for regulation.

    Article  CAS  PubMed  Google Scholar 

  216. Meister, G., Landthaler, M., Dorsett, Y. & Tuschl, T. Sequence-specific inhibition of microRNA- and siRNA-induced RNA silencing. RNA 10, 544–550 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  217. Hutvagner, G., Simard, M. J., Mello, C. C. & Zamore, P. D. Sequence-specific inhibition of small RNA function. PLoS Biol. 2, e98 (2004).

    Article  PubMed  PubMed Central  Google Scholar 

  218. Ebert, M. S., Neilson, J. R. & Sharp, P. A. MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells. Nature Methods 4, 721–726 (2007).

    Article  CAS  PubMed  Google Scholar 

  219. Loya, C. M., Lu, C. S., Van Vactor, D. & Fulga, T. A. Transgenic microRNA inhibition with spatiotemporal specificity in intact organisms. Nature Methods 6, 897–903 (2009). References 216–219 describe strategies to competitively inhibit miRNAs for loss-of-function studies.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  220. Ebert, M. S. & Sharp, P. A. MicroRNA sponges: progress and possibilities. RNA 16, 2043–2050 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  221. Franco-Zorrilla, J. M. et al. Target mimicry provides a new mechanism for regulation of microRNA activity. Nature Genet. 39, 1033–1037 (2007).

    Article  CAS  PubMed  Google Scholar 

  222. Todesco, M., Rubio-Somoza, I., Paz-Ares, J. & Weigel, D. A collection of target mimics for comprehensive analysis of microRNA function in Arabidopsis thaliana. PLoS Genet. 6, e1001031 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  223. Salmena, L., Poliseno, L., Tay, Y., Kats, L. & Pandolfi, P. P. A ceRNA hypothesis: the Rosetta stone of a hidden RNA language? Cell 146, 353–358 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  224. Tay, Y. et al. Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. Cell 147, 344–357 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  225. Poliseno, L. et al. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 465, 1033–1038 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  226. Karreth, F. A. et al. In vivo identification of tumor-suppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma. Cell 147, 382–395 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  227. Cesana, M. et al. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 147, 358–369 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  228. Sumazin, P. et al. An extensive microRNA-mediated network of RNA–RNA interactions regulates established oncogenic pathways in glioblastoma. Cell 147, 370–381 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  229. Lim, L. P. et al. The microRNAs of Caenorhabditis elegans. Genes Dev. 17, 991–1008 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  230. Chang, J. et al. miR-122, a mammalian liver-specific microRNA, is processed from hcr mRNA and may downregulate the high affinity cationic amino acid transporter CAT-1. RNA Biol. 1, 106–113 (2004).

    Article  CAS  PubMed  Google Scholar 

  231. Mullokandov, G. et al. High-throughput assessment of microRNA activity and function using microRNA sensor and decoy libraries. Nature Methods 9, 840–846 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  232. Care, A. et al. MicroRNA-133 controls cardiac hypertrophy. Nature Med. 13, 613–618 (2007).

    Article  CAS  PubMed  Google Scholar 

  233. Gentner, B. et al. Stable knockdown of microRNA in vivo by lentiviral vectors. Nature Methods 6, 63–66 (2009).

    Article  CAS  PubMed  Google Scholar 

  234. Haraguchi, T., Ozaki, Y. & Iba, H. Vectors expressing efficient RNA decoys achieve the long-term suppression of specific microRNA activity in mammalian cells. Nucleic Acids Res. 37, e43 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  235. Cazalla, D., Yario, T. & Steitz, J. Down-regulation of a host microRNA by a herpesvirus saimiri noncoding RNA. Science 328, 1563–1566 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  236. Marcinowski, L. et al. Degradation of cellular mir-27 by a novel, highly abundant viral transcript is important for efficient virus replication in vivo. PLoS Pathog. 8, e1002510 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  237. Libri, V. et al. Murine cytomegalovirus encodes a miR-27 inhibitor disguised as a target. Proc. Natl Acad. Sci. USA 109, 279–284 (2012).

    Article  PubMed  Google Scholar 

  238. Salzman, J., Gawad, C., Wang, P. L., Lacayo, N. & Brown, P. O. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS ONE 7, e30733 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  239. Hansen, T. B. et al. Natural RNA circles function as efficient microRNA sponges. Nature 495, 384–388 (2013).

    Article  CAS  PubMed  Google Scholar 

  240. Memczak, S. et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495, 333–338 (2013).

    Article  CAS  PubMed  Google Scholar 

  241. Hwang, H. W., Wentzel, E. A. & Mendell, J. T. A hexanucleotide element directs microRNA nuclear import. Science 315, 97–100 (2007).

    Article  CAS  PubMed  Google Scholar 

  242. Gantier, M. P. et al. Analysis of microRNA turnover in mammalian cells following Dicer1 ablation. Nucleic Acids Res. 39, 5692–5703 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  243. van Rooij, E. et al. Control of stress-dependent cardiac growth and gene expression by a microRNA. Science 316, 575–579 (2007).

    Article  CAS  PubMed  Google Scholar 

  244. Rissland, O. S., Hong, S. J. & Bartel, D. P. MicroRNA destabilization enables dynamic regulation of the miR-16 family in response to cell-cycle changes. Mol. Cell 43, 993–1004 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  245. Zhang, Z. et al. Uracils at nucleotide position 9–11 are required for the rapid turnover of miR-29 family. Nucleic Acids Res. 39, 4387–4395 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

The authors thank the members of the Zamore and Ameres laboratories for helpful discussions and comments. The Ameres laboratory is funded by the Austrian Academy of Sciences and the Austrian Federal Ministry of Economy, Family and Youth (BMFWJ).

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Stefan L. Ameres or Phillip D. Zamore.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Related links

PowerPoint slides

Glossary

Argonaute

(AGO). Proteins that are guided to mRNA targets by small silencing RNAs. AGO proteins can also serve as scaffolds to bind secondary silencing factors such as the GW-repeat-containing protein GW182.

Primary miRNAs

(pri-miRNAs). Polyadenylated, 7-methylguanosine-capped RNA polymerase II transcripts containing a stem–loop structure that serves as a substrate for the RNase III enzyme Drosha in animals and Dicer-like 1 (DCL1) in plants. They are processed to liberate a precursor miRNA and two unstable, single-stranded by-products.

Ribonuclease III

(RNAse III). Double-stranded RNA-specific endoribonuclease that generates products with two nucleotide 3′ overhangs, a 5′ phosphate and a 3′ hydroxyl group.

dsRNA-binding protein

Proteins containing double-stranded RNA-binding domains, which are 70 amino acid motifs that bind to RNA helices via their 2′ hydroxyl group and phosphate backbone.

Precursor miRNAs

(pre-miRNAs). Stem–loop RNAs comprising a single-stranded loop that connects two partially complementary sequences. These sequences pair to form a predominantly double-stranded stem. Pre-miRNAs typically have a 5′ phosphate and a two nucleotide 3′ overhang, allowing them to serve as substrates for Dicer.

Drosha

The nuclear RNase III endonuclease in animals that cleaves the base of a stem–loop structure contained in primary microRNAs (pri-miRNAs) to produce a precursor miRNA. Collaborates with mammalian DGCR8 (or Pasha in other animals), which is its double-stranded RNA-binding protein partner.

Dicer

An RNase III endonuclease that is predominantly found in the cytoplasm of animal cells and the nucleus of plant and some fungal cells. Dicer proteins liberate mature microRNA–microRNA* duplexes from pre-microRNAs and siRNA duplexes from long double-stranded RNAs.

siRNAs

The 21 nucleotide small RNAs that mediate RNA interference in plants, animals and some fungi. Typically produced by Dicer processing of long double-stranded RNA (dsRNA) precursors encoded in the genome (endo-siRNAs) or from exogenous dsRNA sources (exo-siRNAs) such as viruses.

RNA-induced silencing complex

(RISC). A ribonucleoprotein complex that consists of a small RNA guide strand bound to an Argonaute protein. RISC mediates all RNA silencing pathways, and it can also include auxiliary proteins that extend or modify its function.

Seed sequence

A nucleotide motif in the 5′ domain of all small silencing RNAs, which is organized by Argonaute to determine target-RNA recognition.

PIWI-interacting RNAs

(piRNAs). Small silencing RNAs, 25–35 nucleotides long, that bind PIWI clade Argonaute proteins in animals and silence germline transposons. They are thought to derive from single-stranded RNA precursors and do not require RNase III enzymes for their maturation.

Exoribonuclease

Enzymes that successively remove nucleotides from either the 3′ (3′-to-5′ exoribonuclease) or the 5′ end (5′-to-3′ exoribonuclease) of RNA. They catalyse phosphodiester bond cleavage using water (releasing nucleotide monophosphates) or inorganic phosphate (releasing nucleotide diphosphates) as a nucleophile.

Isomirs

microRNA variants containing sequences that deviate from miRBase-annotated or most frequently observed species.

Mirtrons

Intron-derived precursor microRNAs excised from primary miRNAs by the splicing machinery and a lariat-debranching enzyme instead of Drosha.

Terminal nucleotidyl transferases

(TNTases). Template-independent polymerases that add nucleotides to the 3′ ends of nucleic acids.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Ameres, S., Zamore, P. Diversifying microRNA sequence and function. Nat Rev Mol Cell Biol 14, 475–488 (2013). https://doi.org/10.1038/nrm3611

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nrm3611

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