Translational Repression and eIF4A2 Activity Are Critical for MicroRNA-Mediated Gene Regulation
MicroRNA Mechanism
MicroRNAs are small noncoding RNAs that regulate gene expression by binding complementary target messenger RNAs (mRNAs) and repressing their expression through repression of protein translation and mRNA degradation. Meijer et al. (p. 82) show that in a HeLa cell system mRNA degradation is a consequence of translational inhibition via the initiation factor eIF4A2.
Abstract
MicroRNAs (miRNAs) control gene expression through both translational repression and degradation of target messenger RNAs (mRNAs). However, the interplay between these processes and the precise molecular mechanisms involved remain unclear. Here, we show that translational inhibition is the primary event required for mRNA degradation. Translational inhibition depends on miRNAs impairing the function of the eIF4F initiation complex. We define the RNA helicase eIF4A2 as the key factor of eIF4F through which miRNAs function. We uncover a correlation between the presence of miRNA target sites in the 3′ untranslated region (3′UTR) of mRNAs and secondary structure in the 5′UTR and show that mRNAs with unstructured 5′UTRs are refractory to miRNA repression. These data support a linear model for miRNA-mediated gene regulation in which translational repression via eIF4A2 is required first, followed by mRNA destabilization.
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References and Notes
1
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 (2010).
2
Fabian M. R., et al., Mammalian miRNA RISC recruits CAF1 and PABP to affect PABP-dependent deadenylation. Mol. Cell 35, 868 (2009).
3
Djuranovic S., Nahvi A., Green R., miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science 336, 237 (2012).
4
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 (2012).
5
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 (2012).
6
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 (2012).
7
Mishima Y., et al., Translational inhibition by deadenylation-independent mechanisms is central to microRNA-mediated silencing in zebrafish. Proc. Natl. Acad. Sci. U.S.A. 109, 1104 (2012).
8
Wu L., Fan J., Belasco J. G., MicroRNAs direct rapid deadenylation of mRNA. Proc. Natl. Acad. Sci. U.S.A. 103, 4034 (2006).
9
Pillai R. S., et al., Inhibition of translational initiation by Let-7 MicroRNA in human cells. Science 309, 1573 (2005).
10
Thermann R., Hentze M. W., Drosophila miR2 induces pseudo-polysomes and inhibits translation initiation. Nature 447, 875 (2007).
11
Mathonnet G., et al., MicroRNA inhibition of translation initiation in vitro by targeting the cap-binding complex eIF4F. Science 317, 1764 (2007).
12
Zdanowicz A., et al., Drosophila miR2 primarily targets the m7GpppN cap structure for translational repression. Mol. Cell 35, 881 (2009).
13
Pestova T. V., Kolupaeva V. G., The roles of individual eukaryotic translation initiation factors in ribosomal scanning and initiation codon selection. Genes Dev. 16, 2906 (2002).
14
Boyerinas B., et al., Identification of let-7-regulated oncofetal genes. Cancer Res. 68, 2587 (2008).
15
Galicia-Vázquez G., Cencic R., Robert F., Agenor A. Q., Pelletier J., A cellular response linking eIF4AI activity to eIF4AII transcription. RNA 18, 1373 (2012).
16
Chekulaeva M., et al., miRNA repression involves GW182-mediated recruitment of CCR4-NOT through conserved W-containing motifs. Nat. Struct. Mol. Biol. 18, 1218 (2011).
17
Braun J. E., Huntzinger E., Fauser M., Izaurralde E., GW182 proteins directly recruit cytoplasmic deadenylase complexes to miRNA targets. Mol. Cell 44, 120 (2011).
18
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 (2011).
19
Cooke A., Prigge A., Wickens M., Translational repression by deadenylases. J. Biol. Chem. 285, 28506 (2010).
20
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 (2012).
21
Kong Y. W., et al., The mechanism of micro-RNA-mediated translation repression is determined by the promoter of the target gene. Proc. Natl. Acad. Sci. U.S.A. 105, 8866 (2008).
22
Ricci E. P., et al., Activation of a microRNA response in trans reveals a new role for poly(A) in translational repression. Nucleic Acids Res. 39, 5215 (2011).
23
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. U.S.A. 102, 16961 (2005).
24
Clark A. T., Robertson M. E., Conn G. L., Belsham G. J., Conserved nucleotides within the J domain of the encephalomyocarditis virus internal ribosome entry site are required for activity and for interaction with eIF4G. J. Virol. 77, 12441 (2003).
25
Kolupaeva V. G., Pestova T. V., Hellen C. U., Ribosomal binding to the internal ribosomal entry site of classical swine fever virus. RNA 6, 1791 (2000).
26
Totaro A., et al., The human Pat1b protein: A novel mRNA deadenylation factor identified by a new immunoprecipitation technique. Nucleic Acids Res. 39, 635 (2011).
27
di Penta A., et al., Dendritic LSm1/CBP80-mRNPs mark the early steps of transport commitment and translational control. J. Cell Biol. 184, 423 (2009).
28
Charlesworth A., Cox L. L., MacNicol A. M., Cytoplasmic polyadenylation element (CPE)- and CPE-binding protein (CPEB)-independent mechanisms regulate early class maternal mRNA translational activation in Xenopus oocytes. J. Biol. Chem. 279, 17650 (2004).
29
Pruitt K. D., Tatusova T., Brown G. R., Maglott D. R., NCBI Reference Sequences (RefSeq): Current status, new features and genome annotation policy. Nucleic Acids Res. 40, D130 (2012).
30
Benson D. A., Karsch-Mizrachi I., Lipman D. J., Ostell J., Sayers E. W., GenBank. Nucleic Acids Res. 39, D32 (2011).
31
Chatterjee S., Pal J. K., Role of 5′- and 3′-untranslated regions of mRNAs in human diseases. Biol. Cell 101, 251 (2009).
32
Friedman R. C., Farh K. K., Burge C. B., Bartel D. P., Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 19, 92 (2009).
33
Garcia D. M., et al., Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat. Struct. Mol. Biol. 18, 1139 (2011).
34
Zuker M., Stiegler P., Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 9, 133 (1981).
35
Gruber A. R., Lorenz R., Bernhart S. H., Neuböck R., Hofacker I. L., The Vienna RNA websuite. Nucleic Acids Res. 36, (Web Server issue), W70 (2008).
36
Petersen C. P., Bordeleau M. E., Pelletier J., Sharp P. A., Short RNAs repress translation after initiation in mammalian cells. Mol. Cell 21, 533 (2006).
37
Lewis B. P., Shih I. H., Jones-Rhoades M. W., Bartel D. P., Burge C. B., Prediction of mammalian microRNA targets. Cell 115, 787 (2003).
38
Mayr C., Hemann M. T., Bartel D. P., Disrupting the pairing between let-7 and Hmga2 enhances oncogenic transformation. Science 315, 1576 (2007).
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Published In
Science
Volume 340 | Issue 6128
5 April 2013
5 April 2013
Copyright
Copyright © 2013, American Association for the Advancement of Science.
Submission history
Received: 8 October 2012
Accepted: 31 January 2013
Published in print: 5 April 2013
Acknowledgments
We thank E. Smith, M. Stoneley, T. Pöyry, E. Jan, C. Jopling, T. Achsel, M. Hentze, and J. Pelletier for helpful comments and reagents. This work was funded by the MRC, UK. M.B. is an MRC Senior Fellow, and A.E.W. is a Biotechnology and Biological Sciences Research Council Professorial Fellow.
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