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Widespread changes in protein synthesis induced by microRNAs

Abstract

Animal microRNAs (miRNAs) regulate gene expression by inhibiting translation and/or by inducing degradation of target messenger RNAs. It is unknown how much translational control is exerted by miRNAs on a genome-wide scale. We used a new proteomic approach to measure changes in synthesis of several thousand proteins in response to miRNA transfection or endogenous miRNA knockdown. In parallel, we quantified mRNA levels using microarrays. Here we show that a single miRNA can repress the production of hundreds of proteins, but that this repression is typically relatively mild. A number of known features of the miRNA-binding site such as the seed sequence also govern repression of human protein synthesis, and we report additional target sequence characteristics. We demonstrate that, in addition to downregulating mRNA levels, miRNAs also directly repress translation of hundreds of genes. Finally, our data suggest that a miRNA can, by direct or indirect effects, tune protein synthesis from thousands of genes.

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Figure 1: Global analysis of changes in protein production induced by microRNAs.
Figure 2: miRNAs downregulate protein synthesis of hundreds of genes.
Figure 3: The miRNA seed explains a large fraction of downregulated protein synthesis.
Figure 4: miRNAs inhibit translation on a genome-wide scale.
Figure 5: Endogenous miRNA knockdown.

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Acknowledgements

We thank J. Cox and M. Mann for early access to the MaxQuant software package, N. D. Socci for discussions, S. Schmidt, G. Born and N. Huebner for the hybridizations at the MDC microarray facility, C. Sommer for technical assistance, M. Huska and M. Andrade-Navarro for setting up the pSILAC website, P. Sharp for a CXCR4 luciferase construct, M. Peter for the IMP-1 reporters, and the Bundesministerium für Bildung und Forschung for funding mass spectrometry instrumentation. R.K. gratefully acknowledges a DAAD scholarship for research stays at the MDC. pSILAC and microarray data can be queried at http://psilac.mdc-berlin.de.

Author Contributions M.S. and N.R. conceived, designed and supervised the experiments. B.S. and N.T. performed the wet lab experiments. M.S., Z.F., R.K. and N.R. analysed genome-wide data. M.S., R.K. and N.R. interpreted the data. M.S. and N.R. wrote the paper.

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Correspondence to Matthias Selbach or Nikolaus Rajewsky.

Supplementary information

Supplementary Information 1

The file contains Supplementary Methods, Supplementary Figures S1-S7 with Legends, Supplementary Table 1 and additional references. (PDF 2285 kb)

Supplementary Table 2

This table shows Gene ontology analysis of proteins which are predominately regulated at the level of translation. This file was originally omitted and was uploaded on 2nd April, 2009. (XLS 35 kb)

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Selbach, M., Schwanhäusser, B., Thierfelder, N. et al. Widespread changes in protein synthesis induced by microRNAs. Nature 455, 58–63 (2008). https://doi.org/10.1038/nature07228

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