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MicroRNAs can generate thresholds in target gene expression

Nature Genetics volume 43, pages 854–859 (2011)Cite this article

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Abstract

MicroRNAs (miRNAs) are short, highly conserved noncoding RNA molecules that repress gene expression in a sequence-dependent manner. We performed single-cell measurements using quantitative fluorescence microscopy and flow cytometry to monitor a target gene's protein expression in the presence and absence of regulation by miRNA. We find that although the average level of repression is modest, in agreement with previous population-based measurements, the repression among individual cells varies dramatically. In particular, we show that regulation by miRNAs establishes a threshold level of target mRNA below which protein production is highly repressed. Near this threshold, protein expression responds sensitively to target mRNA input, consistent with a mathematical model of molecular titration. These results show that miRNAs can act both as a switch and as a fine-tuner of gene expression.

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Figure 1: Quantitative fluorescence microscopy reveals the miRNA-mediated gene expression threshold.
Figure 2: Biochemical model of miRNA-mediated gene regulation.
Figure 3: Modulating the threshold.
Figure 4: Comparison to model.
Figure 5: Thresholding in endogenous 3′ UTRs.

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Acknowledgements

This work was supported by the US National Institutes of Health (NIH) Director's Pioneer Award to A.v.O. (1DP1OD003936) and the NIH–National Cancer Institute (NCI) Physical Sciences Oncology Center at the Massachusetts Institute of Technology (U54CA143874); and by US Public Health Service grants R01-CA133404 , R01-GM34277 from the NIH, PO1-CA42063 from the NCI (to P.A.S.) and partially by Cancer Center Support (core) grant P30-CA14051 from the NCI. M.S.E. was supported by a Howard Hughes Medical Institute Predoctoral Fellowship and a Paul and Cleo Schimmel Scholarship. G.X.Y.Z. and J.S.T. were partially supported by Natural Sciences and Engineering Research Council of Canada Post Graduate Scholarships. We thank G. Neuert for help with cloning the reporter genes, Koch Institute flow cytometry staff for training and cell sorting and D. Bartel for helpful discussions.

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Author notes

  1. John S Tsang

    Present address: Present addresses: Howard Hughes Medical Institute and FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, USA (S.M.); Howard Hughes Medical Institute and Laboratory of Neural Circuits and Behavior, The Rockefeller University, New York, New York, USA (M.S.E.); Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford School of Medicine, Stanford, California, USA (G.X.Y.Z.); and Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA (J.S.T.).,

  2. Shankar Mukherji and Margaret S Ebert: These authors contributed equally to this work.

Authors and Affiliations

  1. Harvard–Massachusetts Institute of Technology Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Shankar Mukherji

  2. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Margaret S Ebert, Grace X Y Zheng, Phillip A Sharp & Alexander van Oudenaarden

  3. Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Margaret S Ebert, Phillip A Sharp & Alexander van Oudenaarden

  4. Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Grace X Y Zheng

  5. Graduate Program in Biophysics, Harvard University, Cambridge, Massachusetts, USA

    John S Tsang

  6. Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Alexander van Oudenaarden

Authors
  1. Shankar Mukherji
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  5. Phillip A Sharp
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  6. Alexander van Oudenaarden
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Contributions

M.S.E., J.S.T., P.A.S. and A.v.O. conceived the project. M.S.E., S.M. and G.X.Y.Z. performed the experiments. S.M. and M.S.E. processed the data and constructed the model, and S.M. quantitatively analyzed the model. S.M., M.S.E., A.v.O. and P.A.S. interpreted the results and wrote the paper.

Corresponding author

Correspondence to Alexander van Oudenaarden.

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The authors declare no competing financial interests.

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Supplementary Figures 1–6, Supplementary Table 1 and Supplementary Note. (PDF 2268 kb)

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Mukherji, S., Ebert, M., Zheng, G. et al. MicroRNAs can generate thresholds in target gene expression. Nat Genet 43, 854–859 (2011). https://doi.org/10.1038/ng.905

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