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Mammalian microRNAs predominantly act to decrease target mRNA levels

Abstract

MicroRNAs (miRNAs) are endogenous 22-nucleotide RNAs that mediate important gene-regulatory events by pairing to the mRNAs of protein-coding genes to direct their repression. Repression of these regulatory targets leads to decreased translational efficiency and/or decreased mRNA levels, but the relative contributions of these two outcomes have been largely unknown, particularly for endogenous targets expressed at low-to-moderate levels. Here, we use ribosome profiling to measure the overall effects on protein production and compare these to simultaneously measured effects on mRNA levels. For both ectopic and endogenous miRNA regulatory interactions, lowered mRNA levels account for most (≥84%) of the decreased protein production. These results show that changes in mRNA levels closely reflect the impact of miRNAs on gene expression and indicate that destabilization of target mRNAs is the predominant reason for reduced protein output.

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Figure 1: Ribosome profiling in human cells captured features of translation.
Figure 2: MicroRNAs downregulated gene expression mostly through mRNA destabilization, with a small effect on translational efficiency.
Figure 3: Ribosome changes from miRNA targeting corresponded to mRNA changes.
Figure 4: Ribosome and mRNA changes were uniform along the length of the ORFs.

Accession codes

Primary accessions

Gene Expression Omnibus

Data deposits

Small-RNA sequencing data and array data were deposited in the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) under accession number GSE22004.

References

  1. 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  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

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

    ADS  Article  Google Scholar 

  4. Liu, J. et al. Argonaute2 is the catalytic engine of mammalian RNAi. Science 305, 1437–1441 (2004)

    ADS  CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  6. 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)

    CAS  Article  Google Scholar 

  7. Olsen, P. H. & Ambros, V. The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. Dev. Biol. 216, 671–680 (1999)

    CAS  Article  Google Scholar 

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

    ADS  CAS  Article  Google Scholar 

  9. Krützfeldt, J. et al. Silencing of microRNAs in vivo with ‘antagomirs’. Nature 438, 685–689 (2005)

    ADS  Article  Google Scholar 

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

    ADS  CAS  Article  Google Scholar 

  11. 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)

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

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

    ADS  CAS  Article  Google Scholar 

  14. 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  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

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

    ADS  CAS  Article  Google Scholar 

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

    ADS  CAS  Article  Google Scholar 

  18. 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  Google Scholar 

  19. 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)

    ADS  CAS  Article  Google Scholar 

  20. Sachs, M. S. et al. Toeprint analysis of the positioning of translation apparatus components at initiation and termination codons of fungal mRNAs. Methods 26, 105–114 (2002)

    CAS  Article  Google Scholar 

  21. Johnnidis, J. B. et al. Regulation of progenitor cell proliferation and granulocyte function by microRNA-223. Nature 451, 1125–1129 (2008)

    ADS  CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

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

    ADS  CAS  Article  Google Scholar 

  24. 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)

    ADS  CAS  Article  Google Scholar 

  25. Chendrimada, T. P. et al. MicroRNA silencing through RISC recruitment of eIF6. Nature 447, 823–828 (2007)

    ADS  CAS  Article  Google Scholar 

  26. 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  Article  Google Scholar 

  27. Coller, J. & Parker, R. Eukaryotic mRNA decapping. Annu. Rev. Biochem. 73, 861–890 (2004)

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  29. Mendez, R. & Richter, J. D. Translational control by CPEB: a means to the end. Nature Rev. Mol. Cell Biol. 2, 521–529 (2001)

    CAS  Article  Google Scholar 

  30. Nottrott, S., Simard, M. J. & Richter, J. D. Human let-7a miRNA blocks protein production on actively translating polyribosomes. Nature Struct. Mol. Biol. 13, 1108–1114 (2006)

    CAS  Article  Google Scholar 

  31. Filipowicz, W., Bhattacharyya, S. N. & Sonenberg, N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nature Rev. Genet. 9, 102–114 (2008)

    CAS  Article  Google Scholar 

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

    ADS  CAS  Article  Google Scholar 

  33. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009)

    Article  Google Scholar 

  34. Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods 5, 621–628 (2008)

    CAS  Article  Google Scholar 

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Acknowledgements

We thank F. Camargo, C. Jan, J. Kim and C. Petersen for advice and discussions, R. Green and O. Rissland for comments on the manuscript, and the Whitehead Institute’s Genome Technology Core for sequencing and microarray profiling. This work was supported by grants from the NIH (D.P.B. and J.S.W.). H.G. was supported by the Agency for Science, Technology and Research, Singapore. N.T.I. was supported by a Ruth L. Kirschstein National Research Service Award (GM080853). D.P.B and J.S.W. are investigators of the Howard Hughes Medical Institute.

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H.G. performed the experiments and analysed the data, with input from the other authors. H.G., J.S.W., and D.P.B. contributed to the design of the study, and all authors contributed to preparation of the manuscript.

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Correspondence to David P. Bartel.

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Guo, H., Ingolia, N., Weissman, J. et al. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466, 835–840 (2010). https://doi.org/10.1038/nature09267

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