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Rationally designed logic integration of regulatory signals in mammalian cells

Nature Nanotechnology volume 5, pages 666–670 (2010)Cite this article

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Abstract

Molecular-level information processing1,2 is essential for ‘smart’ in vivo nanosystems. Natural molecular computing, such as the regulation of messenger RNA (mRNA) synthesis by special proteins called transcription factors3,4, has inspired engineered systems5,6,7,8,9,10,11,12,13,14,15 that can control the levels of mRNA with certain combinations of transcription factors. Here, we show an alternative approach to achieving general-purpose control of mRNA and protein levels by logic integration of transcription factor input signals in mammalian cells. The transcription factors regulate synthetic genes coding for small regulatory RNAs (called microRNAs), which, in turn, control the mRNA of interest (the output) via an RNA interference pathway. The simplicity of these modular interactions makes it possible, in theory, to implement any arbitrary logic relation between the transcription factors and the output16. We construct, test and optimize increasingly complex circuits with up to three transcription factor inputs, establishing a platform for in vivo molecular computing.

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Figure 1: Design elements of the synthetic circuits.
Figure 2: Experimental implementation of two-input regulatory programs.
Figure 3: Experimental implementation of a three-input regulatory program.

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Acknowledgements

The authors would like to thank anonymous reviewers for thoughtful comments. M.L. is a recipient of Deutsche Forschungs Gemeinschaft scholarship. The research was funded by the Bauer Fellows program and by the NIGMS grant GM068763 for National Centres of Systems Biology. M.L. acknowledges her father R. Leisner, who passed away as this manuscript was prepared for submission: ‘One learns most from those one loves’ (Goethe).

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Author notes

  1. Leonidas Bleris & Yaakov Benenson

    Present address: Present address: Electrical Engineering Department, University of Texas at Dallas, NSERL 4.708, 800 West Campbell Road, Richardson, Texas, 75080 USA (L.B.); Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel, CH-4048 Switzerland (Y.B.),

Authors and Affiliations

  1. FAS Centre for Systems Biology, Harvard University, 52 Oxford Street, Cambridge, 02138, Massachussetts, USA

    Madeleine Leisner, Leonidas Bleris, Jason Lohmueller, Zhen Xie & Yaakov Benenson

  2. Department of Biological and Biomedical Sciences, Harvard Medical School, 25 Shattuck Street, Boston, 02115, Massachussetts, USA

    Jason Lohmueller

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  1. Madeleine Leisner
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Contributions

Y.B. designed the research and supervised the project. M.L., L.B., J.L., Z.X. and Y.B. performed the research. M.L., Y.B., J.L. and L.B. wrote the manuscript.

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Correspondence to Yaakov Benenson.

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Leisner, M., Bleris, L., Lohmueller, J. et al. Rationally designed logic integration of regulatory signals in mammalian cells. Nature Nanotech 5, 666–670 (2010). https://doi.org/10.1038/nnano.2010.135

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