Optogenetics is a modern research technology, which allows the control of cellular behavior with light and genetically encoded light-sensitive proteins. Originally developed to control neuronal activity with cellular and millisecond-temporal precision.

Recent advances in this field have opened new landscapes for the use of optogenetics to study and regulate function in various cells and tissues. The key components of optogenetics are light-sensitive proteins, techniques for delivering their genes to specific cells, targeted illumination, and compatible readouts for reporting on changes in cell, tissue and animal behavior. The majority of light-sensitive protein domains derive from plants or cyanobacteria. When appropriately coupled to a protein of interest, they allow regulation of the protein’s intracellular localization, clustering state, interaction with binding partners, or (in the case of enzymes) catalytic activity, using light of defined wavelengths (Figure1).

A wide range of gene delivery techniques such as transfection, viral transduction or creation of transgenic animal lineshave been used to introduce genes coding the light-sensitive proteins to the target cells. Specific promoters or recombinase-based conditional systems (e.g. the Cre system) enable restriction of their expression to cells of interest. The well-defined temporal and spatial control of the illumination light is critical for precise control of cellular activity via optogenetics. Widefield illumination coupled with an ultrafast shutter, fast switching of an LED or laser scanning microscopy can be used for this purpose. Readout techniques for measuring the effects induced by illumination of the photosensitive proteins depend on the nature of the induced changes and may vary from electrophysiology to behavioral tests, including fluorescence-based methods.

Approaches to controlling protein activity using optogenetics. In all panels, photoreceptors are depicted in blue, their binding partners in green and proteins of interest in gray. (A) Light-induced protein dimerization can be used to recruit a protein of interest to a specific intracellular location, where it can pursue its function. (B) Light-dependent oligomerization (clustering) can induce active functional signaling hubs or inhibit protein function. (C) Light-induced dimerization can also be adopted to sequester a protein of interest away from its site of action. (D) Photo-uncaging based on LOV domains can be used to directly control protein activity with light.
Daniel Krueger et al. Development 2019;

The number of optogenetic applications has explosively increased in recent years. An important emerging optogenetic application is the control of gene expression and cell signaling, which has enabled scientists not only to shed light on developmental processes, but also to develop new directions in systems and synthetic biology. Optogenetic tools have been successfully used to study different aspects of cell migration to address the open questions in the field of development. It has been also shown that optogenetics can be applied to dissect the interplay between cell-cell interaction, force transmission and tissue geometry during tissue morphogenesis. In addition, this technique has proved to be a reliable method for controlling the process of cell differentiation. 

In summary, optogenetics provides unprecedented control over the timescale of a perturbation, its spatial range, and its quantitative parameters. Because of these advantages, it has been become a powerful tool in many fields of biology. 


Erika Pastrana

“Optogenetics: controlling cell function with light,” Nature Methods 2011

Daniel Krueger, Emiliano Izquierdo, Ranjith Viswanathan, Jonas Hartmann, Cristina Pallares Cartes, Stefano De Renzis

“Principles and applications of optogenetics in developmental biology”, Development, 2019 

Khammash group papers:

Marc Rullan, Dirk Benzinger, Gregor W. Schmidt, Andreas Milias-Argeitis, Mustafa Khammash.

“An Optogenetic Platform for Real-Time, Single-Cell Interrogation of Stochastic Transcriptional Regulation,” Molecular Cell, 2018.

Dirk Benzinger and Mustafa Hani Khammash

“Pulsatile inputs achieve tunable attenuation of gene expression variability and graded multi-​gene regulation, ” Nature Communications, 2018.

Armin Baumschlager, Stephanie K. Aoki and Mustafa Khammash

“Dynamic Blue Light-Inducible T7 RNA Polymerases (Opto-T7RNAPs) for Precise Spatiotemporal Gene Expression Control,” ACS Synthetic Biology, 2017. 

A. Milias-Argeitis, M. Rullan, S. Aoki, P. Buchmann, and M. Khammash

“Automated optogenetic feedback control for precise and robust regulation of gene expression and cell growth,” Nature Communications, 2016. 

J. Ruess, F. Parise, A. Milias-Argeitis, M. Khammash, and J. Lygeros

“Iterative experiment design guides the characterization of a light-inducible gene expression circuit,” Proceedings of the National Academy of Sciences, 2015. 

A. Milias-ArgeitisS. SummersJ. Stewart-Ornstein, I. ZuletaD. PincusH. El-SamadM. Khammash, and J. Lygeros

“In silico feedback for in vivo regulation of a gene expression circuit,” Nature Biotechnology, 2011.