Abstract
One of the longstanding challenges in synthetic biology is rational design of complex regulatory circuitry with multiple biological inputs, complex internal processing, and physiologically active outputs. We have previously proposed how to address this challenge in the case of transcription factor inputs. Here we describe the methods used to construct these synthetic circuits, capable of performing logic integration of transcription factor inputs using microRNA expression vectors and RNA interference (RNAi). The circuits operate in mammalian cells and they can serve as starting point for more complex synthetic information processing networks in these cells.
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References
Benenson, Y. (2009) Biocomputers: from test tubes to live cells, Molecular Biosystems 5, 675–685.
Benenson, Y. (2009) RNA-based computation in live cells, Current Opinion in Biotechnology 20, 471–478.
Weiss, R., Homsy, G. E., and Knight, T. F. (1999) Toward in vivo digital circuits, In Evolution as Computation: DIMACS Workshop (Landweber, L. F., and Winfree, E., Eds.), pp 275–295, Springer.
Gardner, T. S., Cantor, C. R., and Collins, J. J. (2000) Construction of a genetic toggle switch in Escherichia coli, Nature 403, 339–342.
Elowitz, M. B., and Leibler, S. (2000) A synthetic oscillatory network of transcriptional regulators, Nature 403, 335–338.
Isaacs, F. J., Dwyer, D. J., and Collins, J. J. (2006) RNA synthetic biology, Nature Biotechnology 24, 545–554.
Canton, B., Labno, A., and Endy, D. (2008) Refinement and standardization of synthetic biological parts and devices, Nature Biotechnology 26, 787–793.
Weber, W., and Fussenegger, M. (2002) Artificial mammalian gene regulation networks – novel approaches for gene therapy and bioengineering, Journal of Biotechnology 98, 161–187.
Guet, C. C., Elowitz, M. B., Hsing, W. H., and Leibler, S. (2002) Combinatorial synthesis of genetic networks, Science 296, 1466–1470.
Cox, R. S., Surette, M. G., and Elowitz, M. B. (2007) Programming gene expression with combinatorial promoters, Molecular Systems Biology 3, 11.
Ellis, T., Wang, X., and Collins, J. J. (2009) Diversity-based, model-guided construction of synthetic gene networks with predicted functions, Nature Biotechnology 27, 465–471.
Kramer, B. P., Fischer, C., and Fussenegger, M. (2004) BioLogic gates enable logical transcription control in mammalian cells, Biotechnology and Bioengineering 87, 478–484.
Rinaudo, K., Bleris, L., Maddamsetti, R., Subramanian, S., Weiss, R., and Benenson, Y. (2007) A universal RNAi-based logic evaluator that operates in mammalian cells, Nature Biotechnology 25, 795–801.
Xie, Z., Liu, S. J., Bleris, L., and Benenson, Y. (2010) Logic integration of mRNA signals by an RNAi-based molecular computer, Nucleic Acids Research 38, 2692–2701.
Leisner, M., Bleris, L., Lohmueller, J., Xie, Z., and Benenson, Y. (2010) Rationally designed logic integration of regulatory signals in mammalian cells, Nature Nanotechnology 5, 666–670.
Shapiro, E., and Benenson, Y. (2006) Bringing DNA computers to life, Scientific American 294, 44–51.
Baker, D., Group, B. F., Church, G., Collins, J., Endy, D., Jacobson, J., Keasling, J., Modrich, P., Smolke, C., and Weiss, R. (2006) Engineering life: Building a fab for biology, Scientific American 294, 44–51.
Benenson, Y. (2011) Engineering RNAi circuits, Methods in Enzymology 497, 187-205.
Chang, K., Elledge, S. J., and Hannon, G. J. (2006) Lessons from Nature: microRNA-based shRNA libraries, Nature Methods 3, 707–714.
Stegmeier, F., Hu, G., Rickles, R. J., Hannon, G. J., and Elledge, S. J. (2005) A lentiviral microRNA-based system for single-copy polymerase II-regulated RNA interference in mammalian cells, Proceedings of the National Academy of Sciences of the United States of America 102, 13212–13217.
Zhang, Z. L., Xie, Z., Zou, X. L., Casaretto, J., Ho, T. H. D., and Shen, Q. X. J. (2004) A rice WRKY gene encodes a transcriptional repressor of the gibberellin signaling pathway in aleurone cells, Plant Physiology 134, 1500–1513.
Wagner, E. J., Baines, A., Albrecht, T., Brazas, R. M., and Garcia-Blanco, M. A. (2004) Imaging alternative splicing in living cells, Methods in Molecular Biology, 29–46.
Shu, X. K., Royant, A., Lin, M. Z., Aguilera, T. A., Lev-Ram, V., Steinbach, P. A., and Tsien, R. Y. (2009) Mammalian Expression of Infrared Fluorescent Proteins Engineered from a Bacterial Phytochrome, Science 324, 804–807.
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Leisner, M., Bleris, L., Lohmueller, J., Xie, Z., Benenson, Y. (2012). MicroRNA Circuits for Transcriptional Logic. In: Weber, W., Fussenegger, M. (eds) Synthetic Gene Networks. Methods in Molecular Biology, vol 813. Humana Press. https://doi.org/10.1007/978-1-61779-412-4_10
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DOI: https://doi.org/10.1007/978-1-61779-412-4_10
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