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A guide to the optogenetic regulation of endogenous molecules

Nature Methods volume 18, pages 1027–1037 (2021)Cite this article

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Abstract

Genetically encoded tools for the regulation of endogenous molecules (RNA, DNA elements and protein) are needed to study and control biological processes with minimal interference caused by protein overexpression and overactivation of signaling pathways. Here we focus on light-controlled optogenetic tools (OTs) that allow spatiotemporally precise regulation of gene expression and protein function. To control endogenous molecules, OTs combine light-sensing modules from natural photoreceptors with specific protein or nucleic acid binders. We discuss OT designs and group OTs according to the principles of their regulation. We outline characteristics of OT performance, discuss considerations for their use in vivo and review available OTs and their applications in cells and in vivo. Finally, we provide a brief outlook on the development of OTs.

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Fig. 1: Structural domains in OTs and principles of OT regulation.
Fig. 2: Examples of OTs for the regulation of endogenous proteins.
Fig. 3: Selected applications of OTs for regulation of endogenous proteins.
Fig. 4: Examples of OTs for the regulation of endogenous genes.
Fig. 5: Select applications of OTs for regulation of endogenous genes.

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Acknowledgements

This work was supported by grants EY030705 (to D.M.S.) and GM122567 from the US National Institutes of Health, 322226 from the Academy of Finland and 21-64-00025 from the Russian Science Foundation (all to V.V.V.).

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Authors and Affiliations

  1. Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA

    Kyrylo Yu. Manoilov, Vladislav V. Verkhusha & Daria M. Shcherbakova

  2. Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland

    Vladislav V. Verkhusha

  3. Science Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia

    Vladislav V. Verkhusha

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Peer review information Nature Methods thanks Barbara Di Ventura, Moritoshi Sato and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Nina Vogt was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

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Manoilov, K.Y., Verkhusha, V.V. & Shcherbakova, D.M. A guide to the optogenetic regulation of endogenous molecules. Nat Methods 18, 1027–1037 (2021). https://doi.org/10.1038/s41592-021-01240-1

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