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Towards a molecular understanding of microRNA-mediated gene silencing

Nature Reviews Genetics volume 16, pages 421–433 (2015)Cite this article

Subjects

Key Points

  • MicroRNAs (miRNAs) silence gene expression by repressing translation and accelerating target mRNA degradation.

  • The current consensus is that miRNAs inhibit cap-dependent translation at initiation, but the precise molecular mechanism remains to be elucidated.

  • Degradation of miRNA targets is the dominant effect of miRNAs at steady state in cultured mammalian cells.

  • The degradation of miRNA targets is catalysed by enzymes involved in the 5′-to-3′ mRNA decay pathway. In this pathway, mRNAs are first deadenylated, then decapped and finally degraded from the 5′ end.

  • The GW182 proteins play a central part in silencing. They bridge the interaction between Argonaute proteins and downstream effector complexes, such as the cytoplasmic deadenylase complexes PAN2–PAN3 and CCR4–NOT.

  • Structural studies have revealed that GW182 proteins interact with their partners by inserting tryptophan residues into hydrophobic pockets exposed on the surface of Argonaute proteins, PAN3 and NOT9.

  • Current models for miRNA-mediated translational repression invoke displacement of eukaryotic translation initiation factor 4A1 (eIF4A1) or its paralogue eIF4A2, or the recruitment of the translational repressor and decapping activator DEAD box protein 6 (DDX6).

  • Remaining open questions include how miRNA-induced silencing complexes (miRISCs) displace eIF4A1 and eIF4A2, and how DDX6 represses translation.

Abstract

MicroRNAs (miRNAs) are a conserved class of small non-coding RNAs that assemble with Argonaute proteins into miRNA-induced silencing complexes (miRISCs) to direct post-transcriptional silencing of complementary mRNA targets. Silencing is accomplished through a combination of translational repression and mRNA destabilization, with the latter contributing to most of the steady-state repression in animal cell cultures. Degradation of the mRNA target is initiated by deadenylation, which is followed by decapping and 5′-to-3′ exonucleolytic decay. Recent work has enhanced our understanding of the mechanisms of silencing, making it possible to describe in molecular terms a continuum of direct interactions from miRNA target recognition to mRNA deadenylation, decapping and 5′-to-3′ degradation. Furthermore, an intricate interplay between translational repression and mRNA degradation is emerging.

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Figure 1: Overview of miRNA-mediated gene silencing in animals.
Figure 2: Structural insight into the interaction of AGO proteins with GW182 proteins.
Figure 3: Assembly and interaction of the PAN2–PAN3 complex with GW182 proteins.
Figure 4: Assembly and interaction of the CCR4–NOT complex with GW182 proteins.
Figure 5: Structure-based model of miRNA-mediated silencing.

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References

  1. Ameres, S. L. & Zamore, P. D. Diversifying microRNA sequence and function. Nat. Rev. Mol. Cell Biol. 14, 475–488 (2013).

    CAS  PubMed  Google Scholar 

  2. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Hesse, M. & Arenz, C. MicroRNA maturation and human disease. Methods Mol. Biol. 1095, 11–25 (2013).

    Google Scholar 

  4. Ipsaro, J. J. & Joshua-Tor, L. From guide to target: molecular insights into eukaryotic RNA-interference machinery. Nat. Struct. Mol. Biol. 22, 20–28 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  5. Huntzinger, E. & Izaurralde, E. Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nat. Rev. Genet. 12, 99–110 (2011).

    CAS  PubMed  Google Scholar 

  6. Fabian, M. R. & Sonenberg, N. The mechanics of miRNA-mediated gene silencing: a look under the hood of miRISC. Nat. Struct. Mol. Biol. 19, 586–593 (2012).

    CAS  PubMed  Google Scholar 

  7. Ha, M. & Kim, V. N. Regulation of microRNA biogenesis. Nat. Rev. Mol. Cell Biol. 15, 509–524 (2014).

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  10. 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).

    PubMed  PubMed Central  Google Scholar 

  11. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Subtelny, A. O., Eichhorn, S. W., Chen, G. R., Sive, H. & Bartel, D. P. Poly(A)-tail profiling reveals an embryonic switch in translational control. Nature 508, 66–71 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Eichhorn, S. W. et al. mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues. Mol. Cell 56, 104–115 (2014). References 11 and 13 used ribosome profiling to investigate the contribution of translational repression and mRNA degradation to miRNA-mediated gene silencing. The studies conclude that mRNA degradation is the dominant effect of miRISCs at steady state in several cellular systems.

    CAS  PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  15. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  19. Eulalio, A. et al. Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing. Genes Dev. 21, 2558–2570 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Chen, C. Y., Zheng D., Xia Z. & Shyu A. B. Ago–TNRC6 triggers microRNA-mediated decay by promoting two deadenylation steps. Nat. Struct. Mol. Biol. 16, 1160–1166 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Eulalio, A. et al. Deadenylation is a widespread effect of miRNA regulation. RNA 15, 21–32 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Piao, X., Zhang, X., Wu, L. & Belasco, J. G. CCR4–NOT deadenylates mRNA associated with RNA-induced silencing complexes in human cells. Mol. Cell. Biol. 30, 1486–1494 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Huntzinger, E. et al. The interactions of GW182 proteins with PABP and deadenylases are required for both translational repression and degradation of miRNA targets. Nucleic Acids Res. 41, 978–994 (2013).

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  26. Chekulaeva, M. et al. miRNA repression involves GW182-mediated recruitment of CCR4–NOT through conserved W-containing motifs. Nat. Struct. Mol. Biol. 18, 1218–1226 (2011).

    CAS  PubMed  Google Scholar 

  27. Fabian, M. R. et al. miRNA-mediated deadenylation is orchestrated by GW182 through two conserved motifs that interact with CCR4–NOT. Nat. Struct. Mol. Biol. 18, 1211–1217 (2011). References 25–27 provide evidence for direct interactions between GW182 proteins and subunits of the PAN2–PAN3 and CCR4–NOT complexes, demonstrating that the miRISCs recruit the cellular mRNA degradation machinery directly to the mRNA target.

    CAS  PubMed  Google Scholar 

  28. Christie, M., Boland, A., Huntzinger, E., Weichenrieder, O. & Izaurralde, E. Structure of the PAN3 pseudokinase reveals the basis for interactions with the PAN2 deadenylase and the GW182 proteins. Mol. Cell 51, 360–373 (2013).

    CAS  PubMed  Google Scholar 

  29. Chen, Y. et al. A DDX6–NOT1 complex and W-binding pockets in CNOT9 reveal direct links between miRNA target recognition and silencing. Mol. Cell 54, 737–750 (2014).

    CAS  PubMed  Google Scholar 

  30. Mathys, H. et al. Structural and biochemical insights to the role of the CCR4–NOT complex and DDX6 ATPase in microRNA repression. Mol. Cell 54, 751–765 (2014). References 28–30 present crystal structures of PAN3 and NOT9 bound to W residues, revealing the location of W-binding pockets in these proteins. These W-binding pockets mediate binding to GW182 proteins. References 29 and 30 also present the structure of DDX6 bound to the NOT1 MIF4G domain, therefore providing a missing direct link between deadenylation and decapping.

    CAS  PubMed  Google Scholar 

  31. Wahle, E. & Winkler, G. S. RNA decay machines: deadenylation by the Ccr4–Not and Pan2–Pan3 complexes. Biochim. Biophys. Acta 1829, 561–570 (2013).

    CAS  PubMed  Google Scholar 

  32. Jonas, S. & Izaurralde, E. The role of disordered protein regions in the assembly of decapping complexes and RNP granules. Genes Dev. 27, 2628–2641 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Braun, J. E. et al. A direct interaction between DCP1 and XRN1 couples mRNA decapping to 5′ exonucleolytic degradation. Nat. Struct. Mol. Biol. 19, 1324–1331 (2012).

    CAS  PubMed  Google Scholar 

  34. Chang, H., Lim, J., Ha, M. & Kim, V. N. TAIL-seq: genome-wide determination of poly(A) tail length and 3′ end modifications. Mol. Cell 53, 1044–1052 (2014).

    CAS  PubMed  Google Scholar 

  35. Wakiyama, M., Takimoto, K., Ohara, O. & Yokoyama, S. Let-7 microRNA-mediated mRNA deadenylation and translational repression in a mammalian cell-free system. Genes Dev. 21, 1857–1862 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Wu, E. et al. Pervasive and cooperative deadenylation of 3′ UTRs by embryonic microRNA families. Mol. Cell 40, 558–570 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Fukaya, T. & Tomari, Y. PABP is not essential for microRNA-mediated translational repression and deadenylation in vitro. EMBO J. 30, 4998–5009 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Fukaya, T. & Tomari, Y. MicroRNAs mediate gene silencing via multiple different pathways in Drosophila. Mol. Cell 48, 825–836 (2012).

    CAS  PubMed  Google Scholar 

  39. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Ricci, E. P. et al. miRNA repression of translation in vitro takes place during 43S ribosomal scanning. Nucleic Acids Res. 41, 586–598 (2013).

    CAS  PubMed  Google Scholar 

  41. Moretti, F., Kaiser, C., Zdanowicz-Specht, A. & Hentze, M. W. PABP and the poly(A) tail augment microRNA repression by facilitated miRISC binding. Nat. Struct. Mol. Biol. 19, 603–608 (2012).

    CAS  PubMed  Google Scholar 

  42. Muddashetty, R. S. et al. Reversible inhibition of PSD-95 mRNA translation by miR-125a, FMRP phosphorylation, and mGluR signaling. Mol. Cell 42, 673–688 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  43. Schratt, G. M. et al. A brain-specific microRNA regulates dendritic spine development. Nature 439, 283–289 (2006).

    CAS  PubMed  Google Scholar 

  44. Meister, G. et al. Identification of novel Argonaute-associated proteins. Curr. Biol. 15, 2149–2155 (2005).

    CAS  PubMed  Google Scholar 

  45. Jakymiw, A. et al. Disruption of GW bodies impairs mammalian RNA interference. Nat. Cell Biol. 7, 1267–1274 (2005).

    PubMed  Google Scholar 

  46. Liu, J. et al. A role for the P-body component GW182 in microRNA function. Nat. Cell Biol. 7, 1261–1266 (2005).

    PubMed  PubMed Central  Google Scholar 

  47. Zhang, L. et al. Systematic identification of C. elegans miRISC proteins, miRNAs, and mRNA targets by their interactions with GW182 proteins AIN-1 and AIN-2. Mol. Cell 28, 598–613 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  48. Eulalio, A., Huntzinger, E. & Izaurralde, E. GW182 interaction with Argonaute is essential for miRNA-mediated translational repression and mRNA decay. Nat. Struct. Mol. Biol. 15, 346–353 (2008).

    CAS  PubMed  Google Scholar 

  49. Ding, X. C. & Großhans, H. Repression of C. elegans microRNA targets at the initiation level of translation requires GW182 proteins. EMBO J. 28, 213–222 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. Eulalio, A., Tritschler, F. & Izaurralde, E. The GW182 protein family in animal cells: new insights into domains required for miRNA mediated gene silencing. RNA 15, 1433–1442 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  51. Eulalio, A., Helms, S., Fritzsch, C., Fauser, M. & Izaurralde, E. A. C-terminal silencing domain in GW182 is essential for miRNA function. RNA 15, 1067–1077 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  52. Chekulaeva, M., Filipowicz, W. & Parker, R. Multiple independent domains of dGW182 function in miRNA-mediated repression in Drosophila. RNA 15, 794–803 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  53. Lazzaretti, D., Tournier, I. & Izaurralde, E. The C-terminal domains of human TNRC6A, B and C silence bound transcripts independently of the Argonaute proteins. RNA 15, 1059–1066 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  54. Zipprich, J. T., Bhattacharyya, S., Mathys, H. & Filipowicz, W. Importance of the C-terminal domain of the human GW182 protein TNRC6C for translational repression. RNA 15, 781–793 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  55. Lian, S. L. et al. The C-terminal half of human Ago2 binds to multiple GW-rich regions of GW182 and requires GW182 to mediate silencing. RNA 15, 804–813 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  56. Takimoto, K., Wakiyama, M. & Yokoyama, S. Mammalian GW182 contains multiple Argonaute binding sites and functions in microRNA-mediated translational repression. RNA 15, 1078–1089 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  57. Till, S. et al. A conserved motif in Argonaute-interacting proteins mediates functional interactions through the Argonaute PIWI domain. Nat. Struct. Mol. Biol. 14, 897–903 (2007).

    CAS  PubMed  Google Scholar 

  58. El-Shami, M. et al. Reiterated WG/GW motifs form functionally and evolutionarily conserved ARGONAUTE-binding platforms in RNAi-related components. Genes Dev. 21, 2539–2544 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  60. Pfaff, J. et al. Structural features of Argonaute-GW182 protein interactions. Proc. Natl Acad. Sci. USA 110, E3770–E3779 (2013).

    CAS  PubMed  Google Scholar 

  61. Schirle, N. T., Sheu-Gruttadauria, J. & MacRae, I. J. Structural basis for microRNA targeting. Science 346, 608–613 (2014). References 59 and 61 report the crystal structure of human AGO2 in complex with a miRNA mimic and a free W residue, thereby revealing the location of W-binding pockets in the AGO proteins.

    CAS  PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  63. Miyoshi, K., Okada, T. N., Siomi, H. & Siomi, M. C. Characterization of miRNA–RISC loading complex and miRNA–RISC formed in the Drosophila miRNA pathway. RNA 15, 1282–1291 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  64. Siddiqui, N. et al. Poly(A) nuclease interacts with the C-terminal domain of polyadenylate-binding protein domain from poly(A)-binding protein. J. Biol. Chem. 282, 25067–25075 (2007).

    CAS  PubMed  Google Scholar 

  65. Wolf, J. et al. Structural basis for Pan3 binding to Pan2 and its function in mRNA recruitment and deadenylation. EMBO J. 33, 1514–1526 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  66. Schäfer, I. B., Rode, M., Bonneau, F., Schüssler, S. & Conti, E. The structure of the Pan2–Pan3 core complex reveals cross-talk between deadenylase and pseudokinase. Nat. Struct. Mol. Biol. 21, 591–598 (2014).

    PubMed  Google Scholar 

  67. Jonas, S. et al. An asymmetric PAN3 dimer recruits a single PAN2 exonuclease to mediate mRNA deadenylation and decay. Nat. Struct. Mol. Biol. 21, 599–608 (2014).

    CAS  PubMed  Google Scholar 

  68. Yamashita, A. et al. Concerted action of poly(A) nucleases and decapping enzyme in mammalian mRNA turnover. Nat. Struct. Mol. Biol. 12, 1054–1063 (2005).

    CAS  PubMed  Google Scholar 

  69. Cooke, A., Prigge, A. & Wickens, M. Translational repression by deadenylases. J. Biol. Chem. 285, 28506–28513 (2010). This report demonstrates that the CCR4–NOT complex can repress translation independently of deadenylation in Xenopus laevis oocytes.

    CAS  PubMed  PubMed Central  Google Scholar 

  70. Zekri, L., Kuzuogˇlu-Öztürk, D. & Izaurralde, E. GW182 proteins cause PABP dissociation from silenced miRNA targets in the absence of deadenylation. EMBO J. 32, 1052–1065 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  71. Bawankar, P., Loh, B., Wohlbold, L., Schmidt, S. & Izaurralde, E. NOT10 and C2orf29/NOT11 form a conserved module of the CCR4–NOT complex that docks onto the NOT1 N-terminal domain. RNA Biol. 10, 228–244 (2013). References 26, 70 and 71 confirmed in D. melanogaster and human cells that other subunits of the CCR4–NOT complex can repress translation independently of deadenylation.

    CAS  PubMed  PubMed Central  Google Scholar 

  72. Petit, A. P. et al. The structural basis for the interaction between the CAF1 nuclease and the NOT1 scaffold of the human CCR4–NOT deadenylase complex. Nucleic Acids Res. 40, 11058–11072 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  73. Basquin, J. et al. Architecture of the nuclease module of the yeast Ccr4–Not complex: the Not1–Caf1–Ccr4 interaction. Mol. Cell 48, 207–218 (2012).

    CAS  PubMed  Google Scholar 

  74. Presnyak, V. & Coller, J. The DHH1/RCKp54 family of helicases: an ancient family of proteins that promote translational silencing. Biochim. Biophys. Acta 1829, 817–823 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  75. Zekri, L., Huntzinger, E., Heimstädt, S. & Izaurralde, E. The silencing domain of GW182 interacts with PABPC1 to promote translational repression and degradation of miRNA targets and is required for target release. Mol. Cell. Biol. 29, 6220–6231 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  76. Jinek, M., Fabian, M. R., Coyle, S. M., Sonenberg, N. & Doudna, J. A. Structural insights into the human GW182-PABC interaction in microRNA-mediated deadenylation. Nat. Struct. Mol. Biol. 17, 238–240 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  77. Kozlov, G., Safaee, N., Rosenauer, A. & Gehring, K. Structural basis of binding of P-body associated protein GW182 and Ataxin-2 by the MLLE domain of poly(A)-binding protein. J. Biol. Chem. 285, 13599–13606 (2010). References 76 and 77 present structures of the PAM2 motif of human TNRC6C bound to the PABPC C-terminal MLLE domain, providing structural evidence for a direct interaction between these proteins.

    CAS  PubMed  PubMed Central  Google Scholar 

  78. Huntzinger, E., Braun, E. J., Heimstädt, S., Zekri, L. & Izaurralde, E. Two PABPC-binding sites in GW182 proteins promote miRNA-mediated gene silencing. EMBO J. 29, 4146–4160 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  79. Derry, M. C., Yanagiya, A., Martineau, Y. & Sonenberg, N. Regulation of poly(A)-binding protein through PABP-interacting proteins. Cold Spring Harb. Symp. Quant. Biol. 71, 537–543 (2006).

    CAS  PubMed  Google Scholar 

  80. Walters, R. W., Bradrick, S. S. & Gromeier, M. Poly(A)-binding protein modulates mRNA susceptibility to cap-dependent miRNA-mediated repression. RNA 16, 239–250 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  81. Beilharz, T. H. et al. microRNA-mediated messenger RNA deadenylation contributes to translational repression in mammalian cells. PLoS ONE. 4, e6783 (2009).

    PubMed  PubMed Central  Google Scholar 

  82. Mishima, Y. et al. Translational inhibition by deadenylation-independent mechanisms is central to microRNA-mediated silencing in zebrafish. Proc. Natl Acad. Sci. USA 109, 1104–1109 (2012).

    CAS  PubMed  Google Scholar 

  83. Kuzuoglu-Öztürk, D., Huntzinger, E., Schmidt, S. & Izaurralde, E. The Caenorhabditis elegans GW182 protein AIN-1 interacts with PAB-1 and subunits of the PAN2–PAN3 and CCR4–NOT deadenylase complexes. Nucleic Acids Res. 40, 5651–5665 (2012).

    PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  85. Pillai, R. S. et al. Inhibition of translational initiation by Let-7 microRNA in human cells. Science 309, 1573–1576 (2005).

    CAS  PubMed  Google Scholar 

  86. Mathonnet, G. et al. MicroRNA inhibition of translation initiation in vitro by targeting the cap-binding complex eIF4F. Science 17, 1764–1767 (2007).

    Google Scholar 

  87. Humphreys, D. T., Westman, B. J., Martin, D. I. & Preiss, T. MicroRNAs control translation initiation by inhibiting eukaryotic initiation factor 4E/cap and poly(A) tail function. Proc. Natl Acad. Sci. USA 102, 16961–16966 (2005).

    CAS  PubMed  Google Scholar 

  88. Thermann, R. & Hentze, M. W. Drosophila miR2 induces pseudo-polysomes and inhibits translation initiation. Nature 447, 875–858 (2007).

    CAS  PubMed  Google Scholar 

  89. Mishima, Y. et al. Differential regulation of germline mRNAs in soma and germ cells by zebrafish miR-430. Curr. Biol. 16, 2135–2142 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  91. Béthune, J., Artus-Revel, C. G. & Filipowicz, W. Kinetic analysis reveals successive steps leading to miRNA-mediated silencing in mammalian cells. EMBO Rep. 13, 716–723 (2012).

    PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  93. Meijer, H. A. et al. Translational repression and eIF4A2 activity are critical for microRNA-mediated gene regulation. Science 340, 82–85 (2013).

    CAS  PubMed  Google Scholar 

  94. Hu, W., Sweet, T. J., Chamnongpol, S., Baker, K. E. & Coller, J. Co-translational mRNA decay in Saccharomyces cerevisiae. Nature 461, 225–229 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  95. Fukaya, T., Iwakawa, H. O. & Tomari, Y. MicroRNAs block assembly of eIF4F translation initiation complex in Drosophila. Mol. Cell 56, 67–78 (2014).

    CAS  PubMed  Google Scholar 

  96. Wu, P. H., Isaji, M. & Carthew, R. W. Functionally diverse microRNA effector complexes are regulated by extracellular signaling. Mol. Cell 52, 113–123 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  97. Su, H. et al. Mammalian hyperplastic discs homolog EDD regulates miRNA-mediated gene silencing. Mol. Cell 43, 97–109 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  98. Nicklas, S. et al. The RNA helicase DDX6 regulates cell-fate specification in neural stem cells via miRNAs. Nucleic Acids Res. 45, 2638–2654 (2015).

    Google Scholar 

  99. Jackson, R. J., Hellen, C. U. & Pestova, T. V. The mechanism of eukaryotic translation initiation and principles of its regulation. Nat. Rev. Mol. Cell Biol. 11, 113–127 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  100. Fukao, A. et al. MicroRNAs trigger dissociation of eIF4AI and eIF4AII from target mRNAs in humans. Mol. Cell 56, 79–89 (2014). References 95 and 100 reveal eIF4A1 and eIF4A2 displacement as a mechanism by which miRISCs inhibit translation initiation.

    CAS  PubMed  Google Scholar 

  101. Rouya, C. et al. Human DDX6 effects miRNA-mediated gene silencing via direct binding to NOT1. RNA 20, 1398–1409 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  102. Petersen, C. P., Bordeleau, M. E., Pelletier, J. & Sharp, P. A. Short RNAs repress translation after initiation in mammalian cells. Mol. Cell 21, 533–542 (2006).

    CAS  PubMed  Google Scholar 

  103. Ryu, I., Park, J. H., An, S., Kwon, O. S. & Jang, S. K. eIF4GI facilitates the microRNA-mediated gene silencing. PLoS ONE 8, e55725 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  104. Chu, C. Y. & Rana, T. M. Translation repression in human cells by microRNA-induced gene silencing requires RCK/p54. PLoS Biol. 4, e210 (2006).

    PubMed  PubMed Central  Google Scholar 

  105. Schütz, P. et al. Crystal structure of the yeast eIF4A–eIF4G complex: an RNA-helicase controlled by protein–protein interactions. Proc. Natl Acad. Sci. USA 105, 9564–9569 (2008).

    PubMed  Google Scholar 

  106. Tritschler, F. et al. Structural basis for the mutually exclusive anchoring of P body components EDC3 and Tral to the DEAD box protein DDX6/Me31B. Mol. Cell 33, 661–668 (2009).

    CAS  PubMed  Google Scholar 

  107. Fromm, S. A. et al. The structural basis of Edc3- and Scd6-mediated activation of the Dcp1:Dcp2 mRNA decapping complex. EMBO J. 31, 279–290 (2012).

    CAS  PubMed  Google Scholar 

  108. She, M. et al. Structural basis of Dcp2 recognition and activation by Dcp1. Mol. Cell 29, 337–349 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  109. Rolland, T. et al. A proteome-scale map of the human interactome network. Cell 159, 1212–1226 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  110. Kamenska, A. et al. Human 4E-T represses translation of bound mRNAs and enhances microRNA-mediated silencing. Nucleic Acids Res. 42, 3298–3313 (2014).

    CAS  PubMed  Google Scholar 

  111. Zheng, D. et al. Deadenylation is prerequisite for P-body formation and mRNA decay in mammalian cells. J. Cell Biol. 182, 89–101 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  112. Horman, S. R. et al. Akt-mediated phosphorylation of argonaute 2 downregulates cleavage and upregulates translational repression of microRNA targets. Mol. Cell 50, 356–367 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  113. Braun, J. E., Huntzinger, E. & Izaurralde, E. The role of GW182 proteins in miRNA-mediated gene silencing. Adv. Exp. Med. Biol. 768, 147–163 (2013).

    CAS  PubMed  Google Scholar 

  114. Eulalio, A., Behm-Ansmant, I., Schweizer, D. & Izaurralde, E. P-body formation is a consequence, not the cause of RNA-mediated gene silencing. Mol. Cell. Biol. 27, 3970–3981 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  115. Eulalio, A. et al. The RRM domain in GW182 proteins contributes to miRNA-mediated gene silencing. Nucleic Acids Res. 37, 2974–2983 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

Research from the authors' laboratory is supported by the Max Planck Society and by the Gottfried Wilhelm Leibniz Program of the Deutsche Forschungsgemeinschaft (DFG) awarded to E.I.

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  1. Max Planck Institute for Developmental Biology, Spemannstrasse 35, Tübingen, D-72076, Germany

    Stefanie Jonas & Elisa Izaurralde

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  1. Stefanie Jonas
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  2. Elisa Izaurralde
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Correspondence to Elisa Izaurralde.

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Glossary

Deadenylation

Shortening of mRNA poly(A) tails. In eukaryotes, this process is catalysed by the consecutive but partially redundant action of two cytoplasmic deadenylase complexes: PAN2–PAN3 and CCR4–NOT.

Decapping

Hydrolysis of the 5′ cap structure on the mRNA. A major decapping enzyme in eukaryotes is decapping protein 2 (DCP2), which hydrolyses the cap structure, releasing 7-methyl-GDP and a 5′ monophosphorylated mRNA. This 5′ monophosphorylated mRNA is a substrate for 5′-to-3′ exoribonuclease 1 (XRN1), which rapidly degrades decapped mRNA.

Ribosome profiling

A method that allows the determination of the position of ribosomes on cellular mRNAs with high sequence resolution. Briefly, cells are treated with cycloheximide to stabilize ribosomes on mRNAs, then lysed and treated with nucleases to degrade mRNA regions not protected by ribosomes. Translating ribosomes protect RNA fragments of about 30 nucleotides in length (known as ribosome-protected fragments) that can be sequenced, generating millions of mRNA sequence tags.

Cooperativity

The changes that occur when the binding of a ligand to a binding site on one molecule increases (or decreases) the affinity for binding to a second ligand on another binding site on the same molecule.

Avidity

The phenomenon by which individual binding events increase the likelihood of other interactions occurring, for example, by increasing the local concentration of each binding partner in proximity to the binding site.

Cap-dependent translation

Initiation of translation that requires the ternary eukaryotic translation initiation factor 4F (eIF4F) complex, which consists of the cap-binding protein eIF4E, the adaptor protein eIF4G and the DEAD box RNA helicase eIF4A. This complex interacts with the cap structure at the 5′ end of an mRNA molecule and recruits the 43S pre-initiation complex.

Cap structure

Eukaryotic mRNA is modified by the addition of an m7G(5′)ppp(5′)N structure (7-methylguanosine attached, via its 5′ hydroxyl group, by a triphosphate group to the 5′ hydroxyl group of the first encoded nucleoside) at the 5′ terminus. Capping is essential for several important steps of gene expression, including mRNA stabilization, splicing, mRNA export from the nucleus and translation initiation.

Ribosome scanning

The 5′-to-3′ migration of the 43S pre-initiation complex towards the initiation codon. The 43S pre-initiation complex comprises a 40S ribosomal subunit, eukaryotic translation initiation factor 3 (eIF3), eIF1 and eIF1A, the ternary eIF2–GTP–Met-tRNAMeti complex and most likely eIF5.

Internal ribosome entry sites

(IRESs). Structured RNA elements, usually present in the 5′ untranslated region, that allow cap-independent association of ribosomes with mRNAs.

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Jonas, S., Izaurralde, E. Towards a molecular understanding of microRNA-mediated gene silencing. Nat Rev Genet 16, 421–433 (2015). https://doi.org/10.1038/nrg3965

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