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Farahani PE, Reed EH, Underhill EJ, Aoki K, Toettcher JE. Signaling, Deconstructed: Using Optogenetics to Dissect and Direct Information Flow in Biological Systems. Annu Rev Biomed Eng 2021; 23:61-87. [PMID: 33722063 PMCID: PMC10436267 DOI: 10.1146/annurev-bioeng-083120-111648] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cells receive enormous amounts of information from their environment. How they act on this information-by migrating, expressing genes, or relaying signals to other cells-comprises much of the regulatory and self-organizational complexity found across biology. The "parts list" involved in cell signaling is generally well established, but how do these parts work together to decode signals and produce appropriate responses? This fundamental question is increasingly being addressed with optogenetic tools: light-sensitive proteins that enable biologists to manipulate the interaction, localization, and activity state of proteins with high spatial and temporal precision. In this review, we summarize how optogenetics is being used in the pursuit of an answer to this question, outlining the current suite of optogenetic tools available to the researcher and calling attention to studies that increase our understanding of and improve our ability to engineer biology.
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Affiliation(s)
- Payam E Farahani
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Ellen H Reed
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
- International Research Collaboration Center (IRCC), National Institutes of Natural Sciences, Tokyo 105-0001, Japan
| | - Evan J Underhill
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Kazuhiro Aoki
- International Research Collaboration Center (IRCC), National Institutes of Natural Sciences, Tokyo 105-0001, Japan
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
- International Research Collaboration Center (IRCC), National Institutes of Natural Sciences, Tokyo 105-0001, Japan
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52
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Oh TJ, Fan H, Skeeters SS, Zhang K. Steering Molecular Activity with Optogenetics: Recent Advances and Perspectives. Adv Biol (Weinh) 2021; 5:e2000180. [PMID: 34028216 PMCID: PMC8218620 DOI: 10.1002/adbi.202000180] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/14/2020] [Indexed: 12/24/2022]
Abstract
Optogenetics utilizes photosensitive proteins to manipulate the localization and interaction of molecules in living cells. Because light can be rapidly switched and conveniently confined to the sub-micrometer scale, optogenetics allows for controlling cellular events with an unprecedented resolution in time and space. The past decade has witnessed an enormous progress in the field of optogenetics within the biological sciences. The ever-increasing amount of optogenetic tools, however, can overwhelm the selection of appropriate optogenetic strategies. Considering that each optogenetic tool may have a distinct mode of action, a comparative analysis of the current optogenetic toolbox can promote the further use of optogenetics, especially by researchers new to this field. This review provides such a compilation that highlights the spatiotemporal accuracy of current optogenetic systems. Recent advances of optogenetics in live cells and animal models are summarized, the emerging work that interlinks optogenetics with other research fields is presented, and exciting clinical and industrial efforts to employ optogenetic strategy toward disease intervention are reported.
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Affiliation(s)
- Teak-Jung Oh
- 600 South Mathews Avenue, 314 B Roger Adams Laboratory, Urbana, IL, 61801, USA
| | - Huaxun Fan
- 600 South Mathews Avenue, 314 B Roger Adams Laboratory, Urbana, IL, 61801, USA
| | - Savanna S Skeeters
- 600 South Mathews Avenue, 314 B Roger Adams Laboratory, Urbana, IL, 61801, USA
| | - Kai Zhang
- 600 South Mathews Avenue, 314 B Roger Adams Laboratory, Urbana, IL, 61801, USA
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53
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Forlani G, Di Ventura B. A light way for nuclear cell biologists. J Biochem 2021; 169:273-286. [PMID: 33245128 PMCID: PMC8053400 DOI: 10.1093/jb/mvaa139] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 11/12/2020] [Indexed: 12/11/2022] Open
Abstract
The nucleus is a very complex organelle present in eukaryotic cells. Having the crucial task to safeguard, organize and manage the genetic information, it must tightly control its molecular constituents, its shape and its internal architecture at any given time. Despite our vast knowledge of nuclear cell biology, much is yet to be unravelled. For instance, only recently we came to appreciate the existence of a dynamic nuclear cytoskeleton made of actin filaments that regulates processes such as gene expression, DNA repair and nuclear expansion. This suggests further exciting discoveries ahead of us. Modern cell biologists embrace a new methodology relying on precise perturbations of cellular processes that require a reversible, highly spatially confinable, rapid, inexpensive and tunEable external stimulus: light. In this review, we discuss how optogenetics, the state-of-the-art technology that uses genetically encoded light-sensitive proteins to steer biological processes, can be adopted to specifically investigate nuclear cell biology.
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Affiliation(s)
- Giada Forlani
- Spemann Graduate School of Biology and Medicine (SGBM)
- Centers for Biological Signalling Studies BIOSS and CIBSS
- Faculty of Biology, Institute of Biology II, Albert Ludwigs University of Freiburg, Freiburg, Germany
| | - Barbara Di Ventura
- Centers for Biological Signalling Studies BIOSS and CIBSS
- Faculty of Biology, Institute of Biology II, Albert Ludwigs University of Freiburg, Freiburg, Germany
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54
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Seong J, Lin MZ. Optobiochemistry: Genetically Encoded Control of Protein Activity by Light. Annu Rev Biochem 2021; 90:475-501. [PMID: 33781076 DOI: 10.1146/annurev-biochem-072420-112431] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Optobiochemical control of protein activities allows the investigation of protein functions in living cells with high spatiotemporal resolution. Over the last two decades, numerous natural photosensory domains have been characterized and synthetic domains engineered and assembled into photoregulatory systems to control protein function with light. Here, we review the field of optobiochemistry, categorizing photosensory domains by chromophore, describing photoregulatory systems by mechanism of action, and discussing protein classes frequently investigated using optical methods. We also present examples of how spatial or temporal control of proteins in living cells has provided new insights not possible with traditional biochemical or cell biological techniques.
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Affiliation(s)
- Jihye Seong
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, South Korea;
| | - Michael Z Lin
- Department of Neurobiology, Stanford University, Stanford, California 94305, USA; .,Department of Bioengineering, Stanford University, Stanford, California 94305, USA.,Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, USA
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55
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Kataoka M, Nagata T. Expanding horizons of biosciences by light-control. Biophys Physicobiol 2021; 18:13-15. [PMID: 33708459 PMCID: PMC7929697 DOI: 10.2142/biophysico.bppb-v18.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 01/28/2021] [Indexed: 12/01/2022] Open
Affiliation(s)
- Mikio Kataoka
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Takashi Nagata
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
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56
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Tian X, Zhou B. Strategies for site-specific recombination with high efficiency and precise spatiotemporal resolution. J Biol Chem 2021; 296:100509. [PMID: 33676891 PMCID: PMC8050033 DOI: 10.1016/j.jbc.2021.100509] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 01/04/2023] Open
Abstract
Site-specific recombinases (SSRs) are invaluable genome engineering tools that have enormously boosted our understanding of gene functions and cell lineage relationships in developmental biology, stem cell biology, regenerative medicine, and multiple diseases. However, the ever-increasing complexity of biomedical research requires the development of novel site-specific genetic recombination technologies that can manipulate genomic DNA with high efficiency and fine spatiotemporal control. Here, we review the latest innovative strategies of the commonly used Cre-loxP recombination system and its combinatorial strategies with other site-specific recombinase systems. We also highlight recent progress with a focus on the new generation of chemical- and light-inducible genetic systems and discuss the merits and limitations of each new and established system. Finally, we provide the future perspectives of combining various recombination systems or improving well-established site-specific genetic tools to achieve more efficient and precise spatiotemporal genetic manipulation.
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Affiliation(s)
- Xueying Tian
- Key Laboratory of Regenerative Medicine of Ministry of Education, College of Life Science and Technology, Jinan University, Guangzhou, China.
| | - Bin Zhou
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, China; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
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57
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Duplus-Bottin H, Spichty M, Triqueneaux G, Place C, Mangeot PE, Ohlmann T, Vittoz F, Yvert G. A single-chain and fast-responding light-inducible Cre recombinase as a novel optogenetic switch. eLife 2021; 10:61268. [PMID: 33620312 PMCID: PMC7997657 DOI: 10.7554/elife.61268] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 02/22/2021] [Indexed: 11/20/2022] Open
Abstract
Optogenetics enables genome manipulations with high spatiotemporal resolution, opening exciting possibilities for fundamental and applied biological research. Here, we report the development of LiCre, a novel light-inducible Cre recombinase. LiCre is made of a single flavin-containing protein comprising the AsLOV2 photoreceptor domain of Avena sativa fused to a Cre variant carrying destabilizing mutations in its N-terminal and C-terminal domains. LiCre can be activated within minutes of illumination with blue light without the need of additional chemicals. When compared to existing photoactivatable Cre recombinases based on two split units, LiCre displayed faster and stronger activation by light as well as a lower residual activity in the dark. LiCre was efficient both in yeast, where it allowed us to control the production of β-carotene with light, and human cells. Given its simplicity and performances, LiCre is particularly suited for fundamental and biomedical research, as well as for controlling industrial bioprocesses. In a biologist’s toolkit, the Cre protein holds a special place. Naturally found in certain viruses, this enzyme recognises and modifies specific genetic sequences, creating changes that switch on or off whatever gene is close by. Genetically engineering cells or organisms so that they carry Cre and its target sequences allows scientists to control the activation of a given gene, often in a single tissue or organ. However, this relies on the ability to activate the Cre protein ‘on demand’ once it is in the cells of interest. One way to do so is to split the enzyme into two pieces, which can then reassemble when exposed to blue light. Yet, this involves the challenging step of introducing both parts separately into a tissue. Instead, Duplus-Bottin et al. engineered LiCre, a new system where a large section of the Cre protein is fused to a light sensor used by oats to detect their environment. LiCre is off in the dark, but it starts to recognize and modify Cre target sequences when exposed to blue light. Duplus-Bottin et al. then assessed how LiCre compares to the two-part Cre system in baker's yeast and human kidney cells. This showed that the new protein is less ‘incorrectly’ active in the dark, and can switch on faster under blue light. The improved approach could give scientists a better tool to study the role of certain genes at precise locations and time points, but also help them to harness genetic sequences for industry or during gene therapy.
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Affiliation(s)
- Hélène Duplus-Bottin
- Laboratory of Biology and Modeling of the Cell, Universite de Lyon, Ecole Normale Superieure de Lyon, CNRS, UMR5239, Universite Claude Bernard Lyon 1, Lyon, France
| | - Martin Spichty
- Laboratory of Biology and Modeling of the Cell, Universite de Lyon, Ecole Normale Superieure de Lyon, CNRS, UMR5239, Universite Claude Bernard Lyon 1, Lyon, France
| | - Gérard Triqueneaux
- Laboratory of Biology and Modeling of the Cell, Universite de Lyon, Ecole Normale Superieure de Lyon, CNRS, UMR5239, Universite Claude Bernard Lyon 1, Lyon, France
| | - Christophe Place
- Laboratory of Physics, Universite de Lyon, Ecole Normale Superieure de Lyon, CNRS, UMR5672, Universite Claude Bernard Lyon 1, Lyon, France
| | - Philippe Emmanuel Mangeot
- CIRI-Centre International de Recherche en Infectiologie, Universite Claude Bernard Lyon 1, Universite de Lyon, Inserm, U1111, CNRS, UMR5308, Ecole Normale Superieure de Lyon, Lyon, France
| | - Théophile Ohlmann
- CIRI-Centre International de Recherche en Infectiologie, Universite Claude Bernard Lyon 1, Universite de Lyon, Inserm, U1111, CNRS, UMR5308, Ecole Normale Superieure de Lyon, Lyon, France
| | - Franck Vittoz
- Laboratory of Physics, Universite de Lyon, Ecole Normale Superieure de Lyon, CNRS, UMR5672, Universite Claude Bernard Lyon 1, Lyon, France
| | - Gaël Yvert
- Laboratory of Biology and Modeling of the Cell, Universite de Lyon, Ecole Normale Superieure de Lyon, CNRS, UMR5239, Universite Claude Bernard Lyon 1, Lyon, France
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58
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Yoshimi K, Yamauchi Y, Tanaka T, Shimada T, Sato M, Mashimo T. Photoactivatable Cre knock-in mice for spatiotemporal control of genetic engineering in vivo. J Transl Med 2021; 101:125-135. [PMID: 32892213 DOI: 10.1038/s41374-020-00482-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 11/09/2022] Open
Abstract
Although the Cre-loxP recombination system has been extensively used to analyze gene function in vivo, spatiotemporal control of Cre activity is a critical limitation for easy and precise recombination. Here, we established photoactivatable-Cre (PA-Cre) knock-in (KI) mice at a safe harbor locus for the spatial and temporal regulation of Cre recombinase activity. The mice showed whole-body Cre recombination activity following light exposure for only 1 h. Almost no leaks of Cre recombination activity were detected in the KI mice under natural light conditions. Spot irradiation could induce locus-specific recombination noninvasively, enabling us to compare phenotypes on the left and right sides in the same mouse. Furthermore, long-term irradiation using an implanted wireless LED substantially improved Cre recombination activity, especially in the brain. These results demonstrate that PA-Cre KI mice can facilitate the spatiotemporal control of genetic engineering and provide a useful resource to elucidate gene function in vivo with Cre-loxP.
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Affiliation(s)
- Kazuto Yoshimi
- Laboratory Animal Research Center, Division of Animal Genetics, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
- Center for Experimental Medicine and Systems Biology, Division of Genome Engineering, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Yuko Yamauchi
- Laboratory Animal Research Center, Division of Animal Genetics, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | | | | | - Moritoshi Sato
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan
| | - Tomoji Mashimo
- Laboratory Animal Research Center, Division of Animal Genetics, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan.
- Center for Experimental Medicine and Systems Biology, Division of Genome Engineering, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan.
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan.
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59
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Shaaya M, Fauser J, Karginov AV. Optogenetics: The Art of Illuminating Complex Signaling Pathways. Physiology (Bethesda) 2021; 36:52-60. [PMID: 33325819 DOI: 10.1152/physiol.00022.2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Dissection of cell signaling requires tools that can mimic spatiotemporal dynamics of individual pathways in living cells. Optogenetic methods enable manipulation of signaling processes with precise timing and local control. In this review, we describe recent optogenetic approaches for regulation of cell signaling, highlight their advantages and limitations, and discuss examples of their application.
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Affiliation(s)
- Mark Shaaya
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of Medicine, Chicago, Illinois
| | - Jordan Fauser
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of Medicine, Chicago, Illinois
| | - Andrei V Karginov
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of Medicine, Chicago, Illinois.,University of Illinois Cancer Center, The University of Illinois at Chicago, Chicago, Illinois
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60
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Efficient photoactivatable Dre recombinase for cell type-specific spatiotemporal control of genome engineering in the mouse. Proc Natl Acad Sci U S A 2020; 117:33426-33435. [PMID: 33318209 DOI: 10.1073/pnas.2003991117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Precise genetic engineering in specific cell types within an intact organism is intriguing yet challenging, especially in a spatiotemporal manner without the interference caused by chemical inducers. Here we engineered a photoactivatable Dre recombinase based on the identification of an optimal split site and demonstrated that it efficiently regulated transgene expression in mouse tissues spatiotemporally upon blue light illumination. Moreover, through a double-floxed inverted open reading frame strategy, we developed a Cre-activated light-inducible Dre (CALID) system. Taking advantage of well-defined cell-type-specific promoters or a well-established Cre transgenic mouse strain, we demonstrated that the CALID system was able to activate endogenous reporter expression for either bulk or sparse labeling of CaMKIIα-positive excitatory neurons and parvalbumin interneurons in the brain. This flexible and tunable system could be a powerful tool for the dissection and modulation of developmental and genetic complexity in a wide range of biological systems.
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61
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Figueroa D, Rojas V, Romero A, Larrondo LF, Salinas F. The rise and shine of yeast optogenetics. Yeast 2020; 38:131-146. [PMID: 33119964 DOI: 10.1002/yea.3529] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 12/11/2022] Open
Abstract
Optogenetics refers to the control of biological processes with light. The activation of cellular phenomena by defined wavelengths has several advantages compared with traditional chemically inducible systems, such as spatiotemporal resolution, dose-response regulation, low cost, and moderate toxic effects. Optogenetics has been successfully implemented in yeast, a remarkable biological platform that is not only a model organism for cellular and molecular biology studies, but also a microorganism with diverse biotechnological applications. In this review, we summarize the main optogenetic systems implemented in the budding yeast Saccharomyces cerevisiae, which allow orthogonal control (by light) of gene expression, protein subcellular localization, reconstitution of protein activity, and protein sequestration by oligomerization. Furthermore, we review the application of optogenetic systems in the control of metabolic pathways, heterologous protein production and flocculation. We then revise an example of a previously described yeast optogenetic switch, named FUN-LOV, which allows precise and strong activation of the target gene. Finally, we describe optogenetic systems that have not yet been implemented in yeast, which could therefore be used to expand the panel of available tools in this biological chassis. In conclusion, a wide repertoire of optogenetic systems can be used to address fundamental biological questions and broaden the biotechnological toolkit in yeast.
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Affiliation(s)
- David Figueroa
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,ANID - Millennium Science Initiative - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile
| | - Vicente Rojas
- ANID - Millennium Science Initiative - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Andres Romero
- ANID - Millennium Science Initiative - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Luis F Larrondo
- ANID - Millennium Science Initiative - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Francisco Salinas
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,ANID - Millennium Science Initiative - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile
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62
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The art of lineage tracing: From worm to human. Prog Neurobiol 2020; 199:101966. [PMID: 33249090 DOI: 10.1016/j.pneurobio.2020.101966] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 11/03/2020] [Accepted: 11/22/2020] [Indexed: 12/20/2022]
Abstract
Reconstructing the genealogy of every cell that makes up an organism remains a long-standing challenge in developmental biology. Besides its relevance for understanding the mechanisms underlying normal and pathological development, resolving the lineage origin of cell types will be crucial to create these types on-demand. Multiple strategies have been deployed towards the problem of lineage tracing, ranging from direct observation to sophisticated genetic approaches. Here we discuss the achievements and limitations of past and current technology. Finally, we speculate about the future of lineage tracing and how to reach the next milestones in the field.
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63
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Benedetti L, Marvin JS, Falahati H, Guillén-Samander A, Looger LL, De Camilli P. Optimized Vivid-derived Magnets photodimerizers for subcellular optogenetics in mammalian cells. eLife 2020; 9:e63230. [PMID: 33174843 PMCID: PMC7735757 DOI: 10.7554/elife.63230] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/10/2020] [Indexed: 12/28/2022] Open
Abstract
Light-inducible dimerization protein modules enable precise temporal and spatial control of biological processes in non-invasive fashion. Among them, Magnets are small modules engineered from the Neurospora crassa photoreceptor Vivid by orthogonalizing the homodimerization interface into complementary heterodimers. Both Magnets components, which are well-tolerated as protein fusion partners, are photoreceptors requiring simultaneous photoactivation to interact, enabling high spatiotemporal confinement of dimerization with a single excitation wavelength. However, Magnets require concatemerization for efficient responses and cell preincubation at 28°C to be functional. Here we overcome these limitations by engineering an optimized Magnets pair requiring neither concatemerization nor low temperature preincubation. We validated these 'enhanced' Magnets (eMags) by using them to rapidly and reversibly recruit proteins to subcellular organelles, to induce organelle contacts, and to reconstitute OSBP-VAP ER-Golgi tethering implicated in phosphatidylinositol-4-phosphate transport and metabolism. eMags represent a very effective tool to optogenetically manipulate physiological processes over whole cells or in small subcellular volumes.
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Affiliation(s)
- Lorena Benedetti
- Department of Neuroscience and Cell Biology, Yale University School of MedicineNew HavenUnited States
- Howard Hughes Medical Institute, Yale University School of MedicineNew HavenUnited States
| | - Jonathan S Marvin
- Howard Hughes Medical Institute, Janelia Research CampusAshburnUnited States
| | - Hanieh Falahati
- Department of Neuroscience and Cell Biology, Yale University School of MedicineNew HavenUnited States
- Howard Hughes Medical Institute, Yale University School of MedicineNew HavenUnited States
| | - Andres Guillén-Samander
- Department of Neuroscience and Cell Biology, Yale University School of MedicineNew HavenUnited States
- Howard Hughes Medical Institute, Yale University School of MedicineNew HavenUnited States
| | - Loren L Looger
- Howard Hughes Medical Institute, Janelia Research CampusAshburnUnited States
| | - Pietro De Camilli
- Department of Neuroscience and Cell Biology, Yale University School of MedicineNew HavenUnited States
- Howard Hughes Medical Institute, Yale University School of MedicineNew HavenUnited States
- Kavli Institute for Neuroscience, Yale University School of MedicineNew HavenUnited States
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of MedicineNew HavenUnited States
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64
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Shaaya M, Fauser J, Zhurikhina A, Conage-Pough JE, Huyot V, Brennan M, Flower CT, Matsche J, Khan S, Natarajan V, Rehman J, Kota P, White FM, Tsygankov D, Karginov AV. Light-regulated allosteric switch enables temporal and subcellular control of enzyme activity. eLife 2020; 9:e60647. [PMID: 32965214 PMCID: PMC7577742 DOI: 10.7554/elife.60647] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/22/2020] [Indexed: 12/24/2022] Open
Abstract
Engineered allosteric regulation of protein activity provides significant advantages for the development of robust and broadly applicable tools. However, the application of allosteric switches in optogenetics has been scarce and suffers from critical limitations. Here, we report an optogenetic approach that utilizes an engineered Light-Regulated (LightR) allosteric switch module to achieve tight spatiotemporal control of enzymatic activity. Using the tyrosine kinase Src as a model, we demonstrate efficient regulation of the kinase and identify temporally distinct signaling responses ranging from seconds to minutes. LightR-Src off-kinetics can be tuned by modulating the LightR photoconversion cycle. A fast cycling variant enables the stimulation of transient pulses and local regulation of activity in a selected region of a cell. The design of the LightR module ensures broad applicability of the tool, as we demonstrate by achieving light-mediated regulation of Abl and bRaf kinases as well as Cre recombinase.
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Affiliation(s)
- Mark Shaaya
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of MedicineChicagoUnited States
| | - Jordan Fauser
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of MedicineChicagoUnited States
| | - Anastasia Zhurikhina
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of MedicineAtlantaUnited States
| | - Jason E Conage-Pough
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of TechnologyCambridgeUnited States
- Center for Precision Cancer Medicine, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biological Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Vincent Huyot
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of MedicineChicagoUnited States
| | - Martin Brennan
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of MedicineChicagoUnited States
| | - Cameron T Flower
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of TechnologyCambridgeUnited States
- Center for Precision Cancer Medicine, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biological Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
- Program in Computational and Systems Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Jacob Matsche
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of MedicineChicagoUnited States
| | - Shahzeb Khan
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of MedicineChicagoUnited States
| | - Viswanathan Natarajan
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of MedicineChicagoUnited States
| | - Jalees Rehman
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of MedicineChicagoUnited States
- University of Illinois Cancer Center, The University of Illinois at ChicagoChicagoUnited States
- Division of Cardiology, Department of Medicine, The University of Illinois, College of MedicineChicagoUnited States
| | - Pradeep Kota
- Marsico Lung Institute, Cystic Fibrosis Center and Department of Medicine, University of North CarolinaChapel HillUnited States
| | - Forest M White
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of TechnologyCambridgeUnited States
- Center for Precision Cancer Medicine, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biological Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
- Program in Computational and Systems Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Denis Tsygankov
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of MedicineAtlantaUnited States
| | - Andrei V Karginov
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of MedicineChicagoUnited States
- University of Illinois Cancer Center, The University of Illinois at ChicagoChicagoUnited States
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65
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Lu X, Shen Y, Campbell RE. Engineering Photosensory Modules of Non-Opsin-Based Optogenetic Actuators. Int J Mol Sci 2020; 21:E6522. [PMID: 32906617 PMCID: PMC7555876 DOI: 10.3390/ijms21186522] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 11/17/2022] Open
Abstract
Optogenetic (photo-responsive) actuators engineered from photoreceptors are widely used in various applications to study cell biology and tissue physiology. In the toolkit of optogenetic actuators, the key building blocks are genetically encodable light-sensitive proteins. Currently, most optogenetic photosensory modules are engineered from naturally-occurring photoreceptor proteins from bacteria, fungi, and plants. There is a growing demand for novel photosensory domains with improved optical properties and light-induced responses to satisfy the needs of a wider variety of studies in biological sciences. In this review, we focus on progress towards engineering of non-opsin-based photosensory domains, and their representative applications in cell biology and physiology. We summarize current knowledge of engineering of light-sensitive proteins including light-oxygen-voltage-sensing domain (LOV), cryptochrome (CRY2), phytochrome (PhyB and BphP), and fluorescent protein (FP)-based photosensitive domains (Dronpa and PhoCl).
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Affiliation(s)
- Xiaocen Lu
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; (X.L.); (Y.S.)
| | - Yi Shen
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; (X.L.); (Y.S.)
| | - Robert E. Campbell
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; (X.L.); (Y.S.)
- Department of Chemistry, The University of Tokyo, Tokyo 113-0033, Japan
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66
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Abstract
The human genome consists of more than 20000 genes and is essential for all biological phenomena. To understand these biological phenomena, including diseases, and to be able to modify them, approaches that enable optical control of the genome may be useful. Recently, we developed an optogenetic tool, named photoactivatable Cas9 (PA-Cas9). We divided Cas9 nuclease from the CRISPR-Cas9 system into two fragments and connected photo-inducible dimerization proteins, named Magnet system, to the fragments, leading to the development of PA-Cas9 of which nuclease activity is switchable with light. PA-Cas9 allows direct editing of DNA sequences by light stimulation. Additionally, we developed a light-inducible, RNA-guided programmable system for endogenous gene activation based on the CRISPR-Cas9 system. We demonstrated that this optogenetic tool allows rapid and reversible targeted gene activation by light. Using this tool, we exemplified optical control of neuronal differentiation of human induced pluripotent stem cells (iPSCs). The CRISPR-Cas9-based, photoactivatable transcription system offers a simple and versatile approach to precise gene activation. In addition to the CRISPR-Cas9-based optogenetic tools, we developed a photoactivatable Cre-loxP system. This tool allows optical control of DNA recombination reaction in an internal organ even by external, noninvasive illumination using LED light source. To date, genome engineering technology and optogenetics technology have emerged separately as different applications. Our studies described above merge these emerging research fields together.
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Affiliation(s)
- Moritoshi Sato
- Graduate School of Arts and Sciences, The University of Tokyo
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67
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A non-invasive far-red light-induced split-Cre recombinase system for controllable genome engineering in mice. Nat Commun 2020; 11:3708. [PMID: 32709899 PMCID: PMC7381682 DOI: 10.1038/s41467-020-17530-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 07/03/2020] [Indexed: 12/19/2022] Open
Abstract
The Cre-loxP recombination system is a powerful tool for genetic manipulation. However, there are widely recognized limitations with chemically inducible Cre-loxP systems, and the UV and blue-light induced systems have phototoxicity and minimal capacity for deep tissue penetration. Here, we develop a far-red light-induced split Cre-loxP system (FISC system) based on a bacteriophytochrome optogenetic system and split-Cre recombinase, enabling optogenetical regulation of genome engineering in vivo solely by utilizing a far-red light (FRL). The FISC system exhibits low background and no detectable photocytotoxicity, while offering efficient FRL-induced DNA recombination. Our in vivo studies showcase the strong organ-penetration capacity of FISC system, markedly outperforming two blue-light-based Cre systems for recombination induction in the liver. Demonstrating its strong clinical relevance, we successfully deploy a FISC system using adeno-associated virus (AAV) delivery. Thus, the FISC system expands the optogenetic toolbox for DNA recombination to achieve spatiotemporally controlled, non-invasive genome engineering in living systems. Current light-inducible Cre-loxP systems have minimal capacity for deep tissue penetration. Here, the authors present a far-red light-induced split Cre-loxP system for in vivo genome engineering.
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68
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Morikawa K, Furuhashi K, de Sena-Tomas C, Garcia-Garcia AL, Bekdash R, Klein AD, Gallerani N, Yamamoto HE, Park SHE, Collins GS, Kawano F, Sato M, Lin CS, Targoff KL, Au E, Salling MC, Yazawa M. Photoactivatable Cre recombinase 3.0 for in vivo mouse applications. Nat Commun 2020; 11:2141. [PMID: 32358538 PMCID: PMC7195411 DOI: 10.1038/s41467-020-16030-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/31/2020] [Indexed: 11/09/2022] Open
Abstract
Optogenetic genome engineering tools enable spatiotemporal control of gene expression and provide new insight into biological function. Here, we report the new version of genetically encoded photoactivatable (PA) Cre recombinase, PA-Cre 3.0. To improve PA-Cre technology, we compare light-dimerization tools and optimize for mammalian expression using a CAG promoter, Magnets, and 2A self-cleaving peptide. To prevent background recombination caused by the high sequence similarity in the dimerization domains, we modify the codons for mouse gene targeting and viral production. Overall, these modifications significantly reduce dark leak activity and improve blue-light induction developing our new version, PA-Cre 3.0. As a resource, we have generated and validated AAV-PA-Cre 3.0 as well as two mouse lines that can conditionally express PA-Cre 3.0. Together these new tools will facilitate further biological and biomedical research.
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Affiliation(s)
- Kumi Morikawa
- Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, USA.,Department of Rehabilitation and Regenerative Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA.,Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Kazuhiro Furuhashi
- Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, USA.,Columbia Center for Translational Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Carmen de Sena-Tomas
- Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, USA.,Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Alvaro L Garcia-Garcia
- Department of Psychiatry, Division of Systems Neuroscience, New York State Psychiatric Institute, Columbia University, New York, NY, 10032, USA
| | - Ramsey Bekdash
- Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, USA.,Department of Rehabilitation and Regenerative Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA.,Department of Pharmacology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Alison D Klein
- Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, USA.,Department of Rehabilitation and Regenerative Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Nicholas Gallerani
- Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, USA.,Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Hannah E Yamamoto
- Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, USA.,Department of Rehabilitation and Regenerative Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA.,Barnard College, New York, NY, 10027, USA
| | - Seon-Hye E Park
- Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, USA.,Department of Rehabilitation and Regenerative Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA.,Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, 75390-911, USA
| | - Grant S Collins
- Department of Cell Biology and Anatomy, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA
| | - Fuun Kawano
- Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, USA.,Department of Rehabilitation and Regenerative Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA.,Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Moritoshi Sato
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Saitama, Japan
| | - Chyuan-Sheng Lin
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA.,Transgenic Mouse Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA
| | - Kimara L Targoff
- Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, USA.,Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Edmund Au
- Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, USA.,Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA.,Columbia Translational Neuroscience Initiative Scholar, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Michael C Salling
- Department of Cell Biology and Anatomy, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA.,Department of Anesthesiology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Masayuki Yazawa
- Columbia Stem Cell Initiative, Columbia University, New York, NY, 10032, USA. .,Department of Rehabilitation and Regenerative Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA. .,Department of Pharmacology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA. .,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Saitama, Japan.
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69
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Luan H, Kuzin A, Odenwald WF, White BH. Cre-assisted fine-mapping of neural circuits using orthogonal split inteins. eLife 2020; 9:e53041. [PMID: 32286225 PMCID: PMC7217698 DOI: 10.7554/elife.53041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/11/2020] [Indexed: 01/18/2023] Open
Abstract
Existing genetic methods of neuronal targeting do not routinely achieve the resolution required for mapping brain circuits. New approaches are thus necessary. Here, we introduce a method for refined neuronal targeting that can be applied iteratively. Restriction achieved at the first step can be further refined in a second step, if necessary. The method relies on first isolating neurons within a targeted group (i.e. Gal4 pattern) according to their developmental lineages, and then intersectionally limiting the number of lineages by selecting only those in which two distinct neuroblast enhancers are active. The neuroblast enhancers drive expression of split Cre recombinase fragments. These are fused to non-interacting pairs of split inteins, which ensure reconstitution of active Cre when all fragments are expressed in the same neuroblast. Active Cre renders all neuroblast-derived cells in a lineage permissive for Gal4 activity. We demonstrate how this system can facilitate neural circuit-mapping in Drosophila.
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Affiliation(s)
- Haojiang Luan
- Laboratory of Molecular Biology, National Institute of Mental Health, NIHBethesdaUnited States
| | - Alexander Kuzin
- Neural Cell-Fate Determinants Section, National Institute of Neurological Disorders and Stroke, NIHBethesdaUnited States
| | - Ward F Odenwald
- Neural Cell-Fate Determinants Section, National Institute of Neurological Disorders and Stroke, NIHBethesdaUnited States
| | - Benjamin H White
- Laboratory of Molecular Biology, National Institute of Mental Health, NIHBethesdaUnited States
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70
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RecV recombinase system for in vivo targeted optogenomic modifications of single cells or cell populations. Nat Methods 2020; 17:422-429. [PMID: 32203389 PMCID: PMC7135964 DOI: 10.1038/s41592-020-0774-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 02/11/2020] [Indexed: 11/11/2022]
Abstract
Brain circuits comprise vast numbers of intricately interconnected neurons with diverse molecular, anatomical and physiological properties. To allow “user-defined” targeting of individual neurons for structural and functional studies, we created light-inducible site-specific DNA recombinases (SSRs) based on Cre, Dre and Flp (RecVs). RecVs can induce genomic modifications by one-photon or two-photon light induction in vivo. They can produce targeted, sparse and strong labeling of individual neurons by modifying multiple loci within mouse and zebrafish genomes. In combination with other genetic strategies, they allow intersectional targeting of different neuronal classes. In the mouse cortex they enable sparse labeling and whole-brain morphological reconstructions of individual neurons. Furthermore, these enzymes allow single-cell two-photon targeted genetic modifications and can be used in combination with functional optical indicators with minimal interference. In summary, RecVs enable spatiotemporally-precise optogenomic modifications that can facilitate detailed single-cell analysis of neural circuits by linking genetic identity, morphology, connectivity and function.
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71
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Takao T, Hiraoka Y, Kawabe K, Yamada D, Ming L, Tanaka K, Sato M, Takarada T. Establishment of a tTA-dependent photoactivatable Cre recombinase knock-in mouse model for optogenetic genome engineering. Biochem Biophys Res Commun 2020; 526:213-217. [PMID: 32204914 DOI: 10.1016/j.bbrc.2020.03.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 03/03/2020] [Indexed: 12/20/2022]
Abstract
The Cre-loxP recombination system is widely used to generate genetically modified mice for biomedical research. Recently, a highly efficient photoactivatable Cre (PA-Cre) based on reassembly of split Cre fragments has been established. This technology enables efficient DNA recombination that is activated upon blue light illumination with spatiotemporal precision. In this study, we generated a tTA-dependent photoactivatable Cre-loxP recombinase knock-in mouse model (TRE-PA-Cre mice) using a CRISPR/Cas9 system. These mice were crossed with ROSA26-tdTomato mice (Cre reporter mouse) to visualize DNA recombination as marked by tdTomato expression. We demonstrated that external noninvasive LED blue light illumination allows efficient DNA recombination in the liver of TRE-PA-Cre:ROSA26-tdTomato mice transfected with tTA expression vectors using hydrodynamic tail vein injection. The TRE-PA-Cre mouse established here promises to be useful for optogenetic genome engineering in a noninvasive, spatiotemporal, and cell-type specific manner in vivo.
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Affiliation(s)
- Tomoka Takao
- Department of Regenerative Science, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Yuichi Hiraoka
- Laboratory of Molecular Neuroscience, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Bunkyo-ku, Tokyo, 113-8510, Japan; Laboratory of Genome Editing for Biomedical Research, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Kenji Kawabe
- Department of Regenerative Science, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Daisuke Yamada
- Department of Regenerative Science, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Lu Ming
- Department of Regenerative Science, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Kohichi Tanaka
- Laboratory of Molecular Neuroscience, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Moritoshi Sato
- Graduate School of Arts and Sciences, The University of Tokyo, Komaba, Meguro-ku, Tokyo, Japan
| | - Takeshi Takarada
- Department of Regenerative Science, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan.
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72
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Light-mediated control of Gene expression in mammalian cells. Neurosci Res 2020; 152:66-77. [DOI: 10.1016/j.neures.2019.12.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 01/07/2023]
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73
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Abstract
Optogenetic tools can provide direct and programmable control of gene expression. Light-inducible recombinases, in particular, offer a powerful method for achieving precise spatiotemporal control of DNA modification. However, to-date this technology has been largely limited to eukaryotic systems. Here, we develop optogenetic recombinases for Escherichia coli that activate in response to blue light. Our approach uses a split recombinase coupled with photodimers, where blue light brings the split protein together to form a functional recombinase. We tested both Cre and Flp recombinases, Vivid and Magnet photodimers, and alternative protein split sites in our analysis. The optimal configuration, Opto-Cre-Vvd, exhibits strong blue light-responsive excision and low ambient light sensitivity. For this system we characterize the effect of light intensity and the temporal dynamics of light-induced recombination. These tools expand the microbial optogenetic toolbox, offering the potential for precise control of DNA excision with light-inducible recombinases in bacteria.
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Affiliation(s)
- Michael B Sheets
- Department of Biomedical Engineering , Boston University , Boston , Massachusetts 02215 , United States
- Biological Design Center , Boston University , Boston , Massachusetts 02215 , United States
| | - Wilson W Wong
- Department of Biomedical Engineering , Boston University , Boston , Massachusetts 02215 , United States
- Biological Design Center , Boston University , Boston , Massachusetts 02215 , United States
| | - Mary J Dunlop
- Department of Biomedical Engineering , Boston University , Boston , Massachusetts 02215 , United States
- Biological Design Center , Boston University , Boston , Massachusetts 02215 , United States
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74
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Delaney SL, Gendreau JL, D'Souza M, Feng AY, Ho AL. Optogenetic Modulation for the Treatment of Traumatic Brain Injury. Stem Cells Dev 2020; 29:187-197. [DOI: 10.1089/scd.2019.0187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
| | | | | | - Austin Y. Feng
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, Georgia
| | - Allen L. Ho
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, Georgia
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75
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Huang D, Ren J, Li R, Guan C, Feng Z, Bao B, Wang W, Zhou C. Tooth Regeneration: Insights from Tooth Development and Spatial-Temporal Control of Bioactive Drug Release. Stem Cell Rev Rep 2020; 16:41-55. [PMID: 31834583 PMCID: PMC6987083 DOI: 10.1007/s12015-019-09940-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Tooth defect and tooth loss are common clinical diseases in stomatology. Compared with the traditional oral restoration treatment, tooth regeneration has unique advantages and is currently the focus of oral biomedical research. It is known that dozens of cytokines/growth factors and other bioactive factors are expressed in a spatial-temporal pattern during tooth development. On the other hand, the technology for spatial-temporal control of drug release has been intensively studied and well developed recently, making control release of these bioactive factors mimicking spatial-temporal pattern more feasible than ever for the purpose of tooth regeneration. This article reviews the research progress on the tooth development and discusses the future of tooth regeneration in the context of spatial-temporal release of developmental factors.
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Affiliation(s)
- Delan Huang
- Guanghua School of Stomatology, Hospital of Stomatology, and Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Jianhan Ren
- Guanghua School of Stomatology, Hospital of Stomatology, and Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Runze Li
- Guanghua School of Stomatology, Hospital of Stomatology, and Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Chenyu Guan
- Guanghua School of Stomatology, Hospital of Stomatology, and Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Zhicai Feng
- Guanghua School of Stomatology, Hospital of Stomatology, and Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Baicheng Bao
- Guanghua School of Stomatology, Hospital of Stomatology, and Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Weicai Wang
- Guanghua School of Stomatology, Hospital of Stomatology, and Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Chen Zhou
- Guanghua School of Stomatology, Hospital of Stomatology, and Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
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76
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Parag-Sharma K, O’Banion CP, Henry EC, Musicant AM, Cleveland JL, Lawrence DS, Amelio AL. Engineered BRET-Based Biologic Light Sources Enable Spatiotemporal Control over Diverse Optogenetic Systems. ACS Synth Biol 2020; 9:1-9. [PMID: 31834783 PMCID: PMC7875091 DOI: 10.1021/acssynbio.9b00277] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Light-inducible optogenetic systems offer precise spatiotemporal control over a myriad of biologic processes. Unfortunately, current systems are inherently limited by their dependence on external light sources for their activation. Further, the utility of laser/LED-based illumination strategies are often constrained by the need for invasive surgical procedures to deliver such devices and local heat production, photobleaching and phototoxicity that compromises cell and tissue viability. To overcome these limitations, we developed a novel BRET-activated optogenetics (BEACON) system that employs biologic light to control optogenetic tools. BEACON is driven by self-illuminating bioluminescent-fluorescent proteins that generate "spectrally tuned" biologic light via bioluminescence resonance energy transfer (BRET). Notably, BEACON robustly activates a variety of commonly used optogenetic systems in a spatially restricted fashion, and at physiologically relevant time scales, to levels that are achieved by conventional laser/LED light sources.
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Affiliation(s)
- Kshitij Parag-Sharma
- Graduate Curriculum in Cell Biology and Physiology, Biological and Biomedical Sciences Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Colin P. O’Banion
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Neuronal Signal Transduction, Max Planck Florida Institute for Neuroscience, Jupiter, Florida 33458, United States
| | - Erin C. Henry
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Division of Oral and Craniofacial Health Sciences, UNC Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Adele M. Musicant
- Graduate Curriculum in Genetics and Molecular Biology, Biological and Biomedical Sciences Graduate Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - John L. Cleveland
- Department of Tumor Biology, Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States
| | - David S. Lawrence
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Molecular Therapeutics Program, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Antonio L. Amelio
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Cancer Cell Biology Program, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Biomedical Research Imaging Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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77
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Kwon E, Heo WD. Optogenetic tools for dissecting complex intracellular signaling pathways. Biochem Biophys Res Commun 2020; 527:331-336. [PMID: 31948753 DOI: 10.1016/j.bbrc.2019.12.132] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 12/20/2019] [Indexed: 01/15/2023]
Abstract
Intracellular signaling forms complicated networks that involve dynamic alterations of the protein-protein interactions occurring inside a cell. To dissect these complex networks, light-inducible optogenetic technologies have offered a novel approach for modulating the function of intracellular machineries in space and time. Optogenetic approaches combine genetic and optical methods to initiate and control protein functions within live cells. In this review, we provide an overview of the optical strategies that can be used to manipulate intracellular signaling proteins and secondary messengers at the molecular level. We briefly address how an optogenetic actuator can be engineered to enhance homo- or hetero-interactions, survey various optical tools and targeting strategies for controlling cell-signaling pathways, examine their extension to in vivo systems and discuss the future prospects for the field.
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Affiliation(s)
- Eury Kwon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Won Do Heo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea; Center for Cognition and Sociality, Institute for Basic Science, Daejeon, Republic of Korea.
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78
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Abstract
Cre-mediated recombination has become a powerful tool to confine gene deletions (conditional knockouts) or overexpression of genes (conditional knockin/overexpression). By spatiotemporal restriction of genetic manipulations, major problems of classical knockouts such as embryonic lethality or pleiotropy can be circumvented. Furthermore, Cre-mediated recombination has broad applications in the analysis of the cellular behavior of subpopulations and cell types as well as for genetic fate mapping. This chapter gives an overview about applications for the Cre/LoxP system and their execution.
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Affiliation(s)
- Claudius F Kratochwil
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Filippo M Rijli
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
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79
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Teng CS, Cavin L, Maxson RE, Sánchez-Villagra MR, Crump JG. Resolving homology in the face of shifting germ layer origins: Lessons from a major skull vault boundary. eLife 2019; 8:e52814. [PMID: 31869306 PMCID: PMC6927740 DOI: 10.7554/elife.52814] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/13/2019] [Indexed: 12/13/2022] Open
Abstract
The vertebrate skull varies widely in shape, accommodating diverse strategies of feeding and predation. The braincase is composed of several flat bones that meet at flexible joints called sutures. Nearly all vertebrates have a prominent 'coronal' suture that separates the front and back of the skull. This suture can develop entirely within mesoderm-derived tissue, neural crest-derived tissue, or at the boundary of the two. Recent paleontological findings and genetic insights in non-mammalian model organisms serve to revise fundamental knowledge on the development and evolution of this suture. Growing evidence supports a decoupling of the germ layer origins of the mesenchyme that forms the calvarial bones from inductive signaling that establishes discrete bone centers. Changes in these relationships facilitate skull evolution and may create susceptibility to disease. These concepts provide a general framework for approaching issues of homology in cases where germ layer origins have shifted during evolution.
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Affiliation(s)
- Camilla S Teng
- Department of Stem Cell Biology and Regenerative MedicineUniversity of Southern CaliforniaLos AngelesUnited States
- Department of Biochemistry, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
| | - Lionel Cavin
- Department of Earth SciencesNatural History Museum of GenevaGenevaSwitzerland
| | - Robert E Maxson
- Department of Biochemistry, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
| | | | - J Gage Crump
- Department of Stem Cell Biology and Regenerative MedicineUniversity of Southern CaliforniaLos AngelesUnited States
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80
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Meador K, Wysoczynski CL, Norris AJ, Aoto J, Bruchas MR, Tucker CL. Achieving tight control of a photoactivatable Cre recombinase gene switch: new design strategies and functional characterization in mammalian cells and rodent. Nucleic Acids Res 2019; 47:e97. [PMID: 31287871 PMCID: PMC6753482 DOI: 10.1093/nar/gkz585] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/05/2019] [Accepted: 06/24/2019] [Indexed: 01/31/2023] Open
Abstract
A common mechanism for inducibly controlling protein function relies on reconstitution of split protein fragments using chemical or light-induced dimerization domains. A protein is split into fragments that are inactive on their own, but can be reconstituted after dimerization. As many split proteins retain affinity for their complementary half, maintaining low activity in the absence of an inducer remains a challenge. Here, we systematically explore methods to achieve tight regulation of inducible proteins that are effective despite variation in protein expression level. We characterize a previously developed split Cre recombinase (PA-Cre2.0) that is reconstituted upon light-induced CRY2-CIB1 dimerization, in cultured cells and in vivo in rodent brain. In culture, PA-Cre2.0 shows low background and high induced activity over a wide range of expression levels, while in vivo the system also shows low background and sensitive response to brief light inputs. The consistent activity stems from fragment compartmentalization that shifts localization toward the cytosol. Extending this work, we exploit nuclear compartmentalization to generate light-and-chemical regulated versions of Cre recombinase. This work demonstrates in vivo functionality of PA-Cre2.0, describes new approaches to achieve tight inducible control of Cre DNA recombinase, and provides general guidelines for further engineering and application of split protein fragments.
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Affiliation(s)
- Kyle Meador
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Christina L Wysoczynski
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Aaron J Norris
- Department of Anesthesiology, Division of Basic Research, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Jason Aoto
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Michael R Bruchas
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98195, USA
| | - Chandra L Tucker
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
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81
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Light Control of the Tet Gene Expression System in Mammalian Cells. Cell Rep 2019; 25:487-500.e6. [PMID: 30304687 DOI: 10.1016/j.celrep.2018.09.026] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 07/27/2018] [Accepted: 09/07/2018] [Indexed: 11/22/2022] Open
Abstract
Gene expression and its network structure are dynamically altered in multicellular systems during morphological, functional, and pathological changes. To precisely analyze the functional roles of dynamic gene expression changes, tools that manipulate gene expression at fine spatiotemporal resolution are needed. The tetracycline (Tet)-controlled gene expression system is a reliable drug-inducible method, and it is used widely in many mammalian cultured cells and model organisms. Here, we develop a photoactivatable (PA)-Tet-OFF/ON system for precise temporal control of gene expression at single-cell resolution. By integrating the cryptochrome 2-cryptochrome-interacting basic helix-loop-helix 1 (Cry2-CIB1) light-inducible binding switch, expression of the gene of interest is tightly regulated under the control of light illumination and drug application in our PA-Tet-OFF/ON system. This system has a large dynamic range of downstream gene expression and rapid activation/deactivation kinetics. We also demonstrate the optogenetic regulation of exogenous gene expression in vivo, such as in developing and adult mouse brains.
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82
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Savery D, Maniou E, Culshaw LH, Greene NDE, Copp AJ, Galea GL. Refinement of inducible gene deletion in embryos of pregnant mice. Birth Defects Res 2019; 112:196-204. [PMID: 31793758 PMCID: PMC7003956 DOI: 10.1002/bdr2.1628] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/22/2019] [Accepted: 11/21/2019] [Indexed: 01/04/2023]
Abstract
CreERT2‐mediated gene recombination is widely applied in developmental biology research. Activation of CreERT2 is typically achieved by injection of tamoxifen in an oily vehicle into the peritoneal cavity of mid‐gestation pregnant mice. This can be technically challenging and adversely impacts welfare. Here we characterize three refinements to this technique: Pipette feeding (not gavage) of tamoxifen, ex vivo CreERT2 activation in whole embryo culture and injection of cell‐permeable TAT‐Cre into Cre‐negative cultured embryos. We demonstrate that pipette feeding of tamoxifen solution to the mother on various days of gestation reliably activates embryonic CreERT2, illustrated here using β‐ActinCreERT2, Sox2CreERT2, TCreERT2, and Nkx1.2CreERT2. Pipette feeding of tamoxifen induces dose‐dependent recombination of Rosa26mTmG reporters when administered at E8.5. Activation of two neuromesodermal progenitor‐targeting Cre drivers, TCreERT2, and Nkx1.2CreERT2, produces comparable neuroepithelial lineage tracing. Dose‐dependent CreERT2 activation can also be achieved by brief exposure to 4OH‐tamoxifen in whole embryo culture, allowing temporal control of gene deletion and eliminating the need to treat pregnant mice. Rosa26mTmG reporter recombination can also be achieved regionally by injecting TAT‐Cre into embryonic tissues at the start of culture. This allows greater spatial control over Cre activation than can typically be achieved with endogenous CreERT2, for example by injecting TAT‐Cre on one side of the midline. We hope that our description and application of these techniques will stimulate refinement of experimental methods involving CreERT2 activation for gene deletion and lineage tracing studies. Improved temporal (ex vivo treatment) and spatial (TAT‐Cre injection) control of recombination will also allow previously intractable questions to be addressed.
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Affiliation(s)
- Dawn Savery
- Developmental Biology and Cancer, UCL GOS Institute of Child Health, London, UK
| | - Eirini Maniou
- Developmental Biology and Cancer, UCL GOS Institute of Child Health, London, UK
| | - Lucy H Culshaw
- Developmental Biology and Cancer, UCL GOS Institute of Child Health, London, UK
| | - Nicholas D E Greene
- Developmental Biology and Cancer, UCL GOS Institute of Child Health, London, UK
| | - Andrew J Copp
- Developmental Biology and Cancer, UCL GOS Institute of Child Health, London, UK
| | - Gabriel L Galea
- Developmental Biology and Cancer, UCL GOS Institute of Child Health, London, UK.,Comparative Bioveterinary Sciences, Royal Veterinary College, London, UK
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83
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Weinberg BH, Cho JH, Agarwal Y, Pham NTH, Caraballo LD, Walkosz M, Ortega C, Trexler M, Tague N, Law B, Benman WKJ, Letendre J, Beal J, Wong WW. High-performance chemical- and light-inducible recombinases in mammalian cells and mice. Nat Commun 2019; 10:4845. [PMID: 31649244 PMCID: PMC6813296 DOI: 10.1038/s41467-019-12800-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 09/30/2019] [Indexed: 11/10/2022] Open
Abstract
Site-specific DNA recombinases are important genome engineering tools. Chemical- and light-inducible recombinases, in particular, enable spatiotemporal control of gene expression. However, inducible recombinases are scarce due to the challenge of engineering high performance systems, thus constraining the sophistication of genetic circuits and animal models that can be created. Here we present a library of >20 orthogonal inducible split recombinases that can be activated by small molecules, light and temperature in mammalian cells and mice. Furthermore, we engineer inducible split Cre systems with better performance than existing systems. Using our orthogonal inducible recombinases, we create a genetic switchboard that can independently regulate the expression of 3 different cytokines in the same cell, a tripartite inducible Flp, and a 4-input AND gate. We quantitatively characterize the inducible recombinases for benchmarking their performances, including computation of distinguishability of outputs. This library expands capabilities for multiplexed mammalian gene expression control.
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Affiliation(s)
- Benjamin H Weinberg
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Jang Hwan Cho
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Yash Agarwal
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - N T Hang Pham
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Leidy D Caraballo
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Maciej Walkosz
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Charina Ortega
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Micaela Trexler
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Nathan Tague
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Billy Law
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - William K J Benman
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Justin Letendre
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Jacob Beal
- Raytheon BBN Technologies, Cambridge, MA, 02138, USA.
| | - Wilson W Wong
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, 02215, USA.
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84
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Sasaki Y, Oshikawa M, Bharmoria P, Kouno H, Hayashi‐Takagi A, Sato M, Ajioka I, Yanai N, Kimizuka N. Near‐Infrared Optogenetic Genome Engineering Based on Photon‐Upconversion Hydrogels. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201911025] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Yoichi Sasaki
- Department of Chemistry and Biochemistry Graduate School of Engineering Center for Molecular Systems (CMS) Kyushu University 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
| | - Mio Oshikawa
- Center for Brain Integration Research (CBIR) Tokyo Medical and Dental University (TMDU) 1-5-45 Yushima, Bunkyo-ku Tokyo 113–8510 Japan
| | - Pankaj Bharmoria
- Department of Chemistry and Biochemistry Graduate School of Engineering Center for Molecular Systems (CMS) Kyushu University 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
| | - Hironori Kouno
- Department of Chemistry and Biochemistry Graduate School of Engineering Center for Molecular Systems (CMS) Kyushu University 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
| | - Akiko Hayashi‐Takagi
- Laboratory of Medical Neuroscience Institute for Molecular and Cellular Regulation Gunma University Maebashi-city Gunma 371-8512 Japan
- PRESTO JST Honcho 4-1-8 Kawaguchi Saitama 332-0012 Japan
| | - Moritoshi Sato
- Graduate School of Arts and Sciences The University of Tokyo, Komaba, Meguro-ku Tokyo 153-8902 Japan
| | - Itsuki Ajioka
- Center for Brain Integration Research (CBIR) Tokyo Medical and Dental University (TMDU) 1-5-45 Yushima, Bunkyo-ku Tokyo 113–8510 Japan
- PRESTO JST Honcho 4-1-8 Kawaguchi Saitama 332-0012 Japan
| | - Nobuhiro Yanai
- Department of Chemistry and Biochemistry Graduate School of Engineering Center for Molecular Systems (CMS) Kyushu University 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
- PRESTO JST Honcho 4-1-8 Kawaguchi Saitama 332-0012 Japan
| | - Nobuo Kimizuka
- Department of Chemistry and Biochemistry Graduate School of Engineering Center for Molecular Systems (CMS) Kyushu University 744 Moto-oka, Nishi-ku Fukuoka 819-0395 Japan
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85
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Sasaki Y, Oshikawa M, Bharmoria P, Kouno H, Hayashi-Takagi A, Sato M, Ajioka I, Yanai N, Kimizuka N. Near-Infrared Optogenetic Genome Engineering Based on Photon-Upconversion Hydrogels. Angew Chem Int Ed Engl 2019; 58:17827-17833. [PMID: 31544993 DOI: 10.1002/anie.201911025] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Indexed: 12/16/2022]
Abstract
Photon upconversion (UC) from near-infrared (NIR) light to visible light has enabled optogenetic manipulations in deep tissues. However, materials for NIR optogenetics have been limited to inorganic UC nanoparticles. Herein, NIR-light-triggered optogenetics using biocompatible, organic TTA-UC hydrogels is reported. To achieve triplet sensitization even in highly viscous hydrogel matrices, a NIR-absorbing complex is covalently linked with energy-pooling acceptor chromophores, which significantly elongates the donor triplet lifetime. The donor and acceptor are solubilized in hydrogels formed from biocompatible Pluronic F127 micelles, and heat treatment endows the excited triplets in the hydrogel with remarkable oxygen tolerance. Combined with photoactivatable Cre recombinase technology, NIR-light stimulation successfully performs genome engineering resulting in the formation of dendritic-spine-like structures of hippocampal neurons.
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Affiliation(s)
- Yoichi Sasaki
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Mio Oshikawa
- Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Pankaj Bharmoria
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Hironori Kouno
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Akiko Hayashi-Takagi
- Laboratory of Medical Neuroscience, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi-city, Gunma, 371-8512, Japan.,PRESTO, JST, Honcho 4-1-8, Kawaguchi, Saitama, 332-0012, Japan
| | - Moritoshi Sato
- Graduate School of Arts and Sciences, The University of Tokyo, Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Itsuki Ajioka
- Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.,PRESTO, JST, Honcho 4-1-8, Kawaguchi, Saitama, 332-0012, Japan
| | - Nobuhiro Yanai
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan.,PRESTO, JST, Honcho 4-1-8, Kawaguchi, Saitama, 332-0012, Japan
| | - Nobuo Kimizuka
- Department of Chemistry and Biochemistry, Graduate School of Engineering, Center for Molecular Systems (CMS), Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan
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86
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Allen ME, Zhou W, Thangaraj J, Kyriakakis P, Wu Y, Huang Z, Ho P, Pan Y, Limsakul P, Xu X, Wang Y. An AND-Gated Drug and Photoactivatable Cre- loxP System for Spatiotemporal Control in Cell-Based Therapeutics. ACS Synth Biol 2019; 8:2359-2371. [PMID: 31592660 PMCID: PMC8135225 DOI: 10.1021/acssynbio.9b00175] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
While engineered chimeric antigen receptor (CAR) T cells have shown promise in detecting and eradicating cancer cells within patients, it remains difficult to identify a set of truly cancer-specific CAR-targeting cell surface antigens to prevent potentially fatal on-target off-tumor toxicity against other healthy tissues within the body. To help address this issue, we present a novel tamoxifen-gated photoactivatable split-Cre recombinase optogenetic system, called TamPA-Cre, that features high spatiotemporal control to limit CAR T cell activity to the tumor site. We created and optimized a novel genetic AND gate switch by integrating the features of tamoxifen-dependent nuclear localization and blue-light-inducible heterodimerization of Magnet protein domains (nMag, pMag) into split Cre recombinase. By fusing the cytosol-localizing mutant estrogen receptor ligand binding domain (ERT2) to the N-terminal half of split Cre(2-59aa)-nMag, the TamPA-Cre protein ERT2-CreN-nMag is physically separated from its nuclear-localized binding partner, NLS-pMag-CreC(60-343aa). Without tamoxifen to drive nuclear localization of ERT2-CreN-nMag, the typically high background of the photoactivation system was significantly suppressed. Upon blue light stimulation following tamoxifen treatment, the TamPA-Cre system exhibits sensitivity to low intensity, short durations of blue light exposure to induce robust Cre-loxP recombination efficiency. We finally demonstrate that this TamPA-Cre system can be applied to specifically control localized CAR expression and subsequently T cell activation. As such, we posit that CAR T cell activity can be confined to a solid tumor site by applying an external stimulus, with high precision of control in both space and time, such as light.
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Affiliation(s)
- Molly E. Allen
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, United States
- Institute of Engineering in Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, United States
| | - Wei Zhou
- Chongqing Cancer Hospital, 181 Hanyu Road, Shapingba District, Chongqing 400030, China
| | - Jeyan Thangaraj
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, United States
- Institute of Engineering in Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, United States
| | - Phillip Kyriakakis
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, United States
| | - Yiqian Wu
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, United States
- Institute of Engineering in Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, United States
| | - Ziliang Huang
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, United States
- Institute of Engineering in Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, United States
| | - Phuong Ho
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, United States
- Institute of Engineering in Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, United States
| | - Yijia Pan
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, United States
- Institute of Engineering in Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, United States
| | - Praopim Limsakul
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, United States
- Institute of Engineering in Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, United States
| | - Xiangdong Xu
- Department of Pathology, Veterans Affairs San Diego Healthcare System, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, United States
| | - Yingxiao Wang
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, United States
- Institute of Engineering in Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0412, United States
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87
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Hu W, Li Q, Li B, Ma K, Zhang C, Fu X. Optogenetics sheds new light on tissue engineering and regenerative medicine. Biomaterials 2019; 227:119546. [PMID: 31655444 DOI: 10.1016/j.biomaterials.2019.119546] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 10/09/2019] [Accepted: 10/14/2019] [Indexed: 01/23/2023]
Abstract
Optogenetics has demonstrated great potential in the fields of tissue engineering and regenerative medicine, from basic research to clinical applications. Spatiotemporal encoding during individual development has been widely identified and is considered a novel strategy for regeneration. A as a noninvasive method with high spatiotemporal resolution, optogenetics are suitable for this strategy. In this review, we discuss roles of dynamic signal coding in cell physiology and embryonic development. Several optogenetic systems are introduced as ideal optogenetic tools, and their features are compared. In addition, potential applications of optogenetics for tissue engineering are discussed, including light-controlled genetic engineering and regulation of signaling pathways. Furthermore, we present how emerging biomaterials and photoelectric technologies have greatly promoted the clinical application of optogenetics and inspired new concepts for optically controlled therapies. Our summation of currently available data conclusively demonstrates that optogenetic tools are a promising method for elucidating and simulating developmental processes, thus providing vast prospects for tissue engineering and regenerative medicine applications.
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Affiliation(s)
- Wenzhi Hu
- Wound Healing and Cell Biology Laboratory, Institute of Basic Medicine Science, College of Life Science, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, PR China; Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center, Chinese PLA General Hospital, 100048, Beijing, PR China
| | - Qiankun Li
- Wound Healing and Cell Biology Laboratory, Institute of Basic Medicine Science, College of Life Science, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, PR China; Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center, Chinese PLA General Hospital, 100048, Beijing, PR China
| | - Bingmin Li
- Wound Healing and Cell Biology Laboratory, Institute of Basic Medicine Science, College of Life Science, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, PR China; Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center, Chinese PLA General Hospital, 100048, Beijing, PR China
| | - Kui Ma
- Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center, Chinese PLA General Hospital, 100048, Beijing, PR China
| | - Cuiping Zhang
- Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center, Chinese PLA General Hospital, 100048, Beijing, PR China.
| | - Xiaobing Fu
- Wound Healing and Cell Biology Laboratory, Institute of Basic Medicine Science, College of Life Science, Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, PR China; Key Laboratory of Tissue Repair and Regeneration of PLA and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Fourth Medical Center, Chinese PLA General Hospital, 100048, Beijing, PR China.
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88
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Ye H, Fussenegger M. Optogenetic Medicine: Synthetic Therapeutic Solutions Precision-Guided by Light. Cold Spring Harb Perspect Med 2019; 9:a034371. [PMID: 30291146 PMCID: PMC6719591 DOI: 10.1101/cshperspect.a034371] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Gene- and cell-based therapies are well recognized as central pillars of next-generation medicine, but controllability remains a critical issue for clinical applications. In this context, optogenetics is opening up exciting new opportunities for precision-guided medicine by using illumination with light of appropriate intensity and wavelength as a trigger signal to achieve pinpoint spatiotemporal control of cellular activities, such as transgene expression. In this review, we highlight recent advances in optogenetics, focusing on devices for biomedical applications. We introduce the construction and applications of optogenetic-based biomedical tools to treat neurological diseases, diabetes, heart diseases, and cancer, as well as bioelectronic implants that combine light-interfaced electronic devices and optogenetic systems into portable personalized precision bioelectronic medical tools. Optogenetics-based technology promises the capability to achieve traceless, remotely controlled precision dosing of an enormous range of therapeutic outputs. Finally, we discuss the prospects for optogenetic medicine, as well as some emerging challenges.
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Affiliation(s)
- Haifeng Ye
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 200241 Shanghai, China
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland
- University of Basel, Faculty of Science, CH-4058 Basel, Switzerland
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89
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Tichy AM, Gerrard EJ, Legrand JMD, Hobbs RM, Janovjak H. Engineering Strategy and Vector Library for the Rapid Generation of Modular Light-Controlled Protein-Protein Interactions. J Mol Biol 2019; 431:3046-3055. [PMID: 31150735 DOI: 10.1016/j.jmb.2019.05.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 05/20/2019] [Accepted: 05/21/2019] [Indexed: 01/22/2023]
Abstract
Optogenetics enables the spatio-temporally precise control of cell and animal behavior. Many optogenetic tools are driven by light-controlled protein-protein interactions (PPIs) that are repurposed from natural light-sensitive domains (LSDs). Applying light-controlled PPIs to new target proteins is challenging because it is difficult to predict which of the many available LSDs, if any, will yield robust light regulation. As a consequence, fusion protein libraries need to be prepared and tested, but methods and platforms to facilitate this process are currently not available. Here, we developed a genetic engineering strategy and vector library for the rapid generation of light-controlled PPIs. The strategy permits fusing a target protein to multiple LSDs efficiently and in two orientations. The public and expandable library contains 29 vectors with blue, green or red light-responsive LSDs, many of which have been previously applied ex vivo and in vivo. We demonstrate the versatility of the approach and the necessity for sampling LSDs by generating light-activated caspase-9 (casp9) enzymes. Collectively, this work provides a new resource for optical regulation of a broad range of target proteins in cell and developmental biology.
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Affiliation(s)
- Alexandra-Madelaine Tichy
- Australian Regenerative Medicine Institute (ARMI), Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton/Melbourne, VIC 3800, Australia; European Molecular Biology Laboratory Australia (EMBL Australia), Monash University, Clayton/Melbourne, VIC 3800, Australia; Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria
| | - Elliot J Gerrard
- Australian Regenerative Medicine Institute (ARMI), Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton/Melbourne, VIC 3800, Australia; European Molecular Biology Laboratory Australia (EMBL Australia), Monash University, Clayton/Melbourne, VIC 3800, Australia; Commonwealth Scientific and Industrial Research Organisation, Synthetic Biology Future Science Platform, Monash University, Clayton/Melbourne, VIC 3800, Australia
| | - Julien M D Legrand
- Australian Regenerative Medicine Institute (ARMI), Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton/Melbourne, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton/Melbourne, VIC 3800, Australia
| | - Robin M Hobbs
- Australian Regenerative Medicine Institute (ARMI), Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton/Melbourne, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton/Melbourne, VIC 3800, Australia
| | - Harald Janovjak
- Australian Regenerative Medicine Institute (ARMI), Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton/Melbourne, VIC 3800, Australia; European Molecular Biology Laboratory Australia (EMBL Australia), Monash University, Clayton/Melbourne, VIC 3800, Australia; Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria.
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90
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Safari F, Zare K, Negahdaripour M, Barekati-Mowahed M, Ghasemi Y. CRISPR Cpf1 proteins: structure, function and implications for genome editing. Cell Biosci 2019; 9:36. [PMID: 31086658 PMCID: PMC6507119 DOI: 10.1186/s13578-019-0298-7] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 04/20/2019] [Indexed: 12/19/2022] Open
Abstract
CRISPR and CRISPR-associated (Cas) protein, as components of microbial adaptive immune system, allows biologists to edit genomic DNA in a precise and specific way. CRISPR-Cas systems are classified into two main classes and six types. Cpf1 is a putative type V (class II) CRISPR effector, which can be programmed with a CRISPR RNA to bind and cleave complementary DNA targets. Cpf1 has recently emerged as an alternative for Cas9, due to its distinct features such as the ability to target T-rich motifs, no need for trans-activating crRNA, inducing a staggered double-strand break and potential for both RNA processing and DNA nuclease activity. In this review, we attempt to discuss the evolutionary origins, basic architectures, and molecular mechanisms of Cpf1 family proteins, as well as crRNA designing and delivery strategies. We will also describe the novel Cpf1 variants, which have broadened the versatility and feasibility of this system in genome editing, transcription regulation, epigenetic modulation, and base editing. Finally, we will be reviewing the recent studies on utilization of Cpf1as a molecular tool for genome editing.
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Affiliation(s)
- Fatemeh Safari
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Khadijeh Zare
- Department of Basic Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Manica Negahdaripour
- Pharmaceutical Sciences Research Center, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mazyar Barekati-Mowahed
- Department of Physiology & Biophysics, School of Medicine, Case Western Reserve University, Ohio, USA
| | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
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91
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Brown W, Deiters A. Light-activation of Cre recombinase in zebrafish embryos through genetic code expansion. Methods Enzymol 2019; 624:265-281. [PMID: 31370934 DOI: 10.1016/bs.mie.2019.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cre recombinase-mediated DNA recombination is an established method for conditional control of gene expression in animal models. Regulation of its activity has been accomplished to impart spatial and/or temporal control over recombination of the target gene. In this chapter, optical control of Cre recombinase in developing zebrafish embryos through genetic code expansion is discussed. This method takes advantage of an evolved aminoacyl tRNA synthetase and tRNA pair that can incorporate an unnatural amino acid (UAA) into proteins in response to an amber stop codon (TAG). Genetic code expansion is used to replace a lysine residue critical to Cre recombinase function with a photocaged analogue of lysine, successfully blocking DNA recombination until irradiation with 405nm light. Use of optically controlled Cre recombinase for cell-lineage tracing experiments in zebrafish embryos is highlighted, demonstrating the ability to target small populations of cells at different developmental time points for recombination. Optically controlled Cre recombinase showed no background activity and precise activation upon irradiation, making it a useful new tool for studying development and disease in the zebrafish embryo.
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Affiliation(s)
- Wes Brown
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, United States.
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92
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Hernández-Candia CN, Wysoczynski CL, Tucker CL. Advances in optogenetic regulation of gene expression in mammalian cells using cryptochrome 2 (CRY2). Methods 2019; 164-165:81-90. [PMID: 30905749 DOI: 10.1016/j.ymeth.2019.03.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/05/2019] [Accepted: 03/14/2019] [Indexed: 11/19/2022] Open
Abstract
Synthetic regulation of gene expression provides a powerful approach to reprogram molecular and cellular processes and test the function of specific genes and gene products. In the last decade, optogenetic systems that allow light-dependent gene regulation have become valuable tools, providing tight spatiotemporal control of protein levels. Here we discuss and build on recent optogenetic approaches for regulating gene expression in mammalian cells using cryptochrome 2 (CRY2), a photoreceptor protein from Arabidopsis. We provide detailed protocols for using light to manipulate activity of a CRY2-based engineered photoactivatable Cre DNA recombinase, and to induce or disrupt transcription factor function. In addition, we provide instructions and software for building an inexpensive Rasberry-Pi-based programable LED device for optogenetic experiments, delivering pulsed light with customized control of illumination duration, frequency, and intensity.
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Affiliation(s)
| | - Christina L Wysoczynski
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Chandra L Tucker
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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93
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Photodimerization systems for regulating protein-protein interactions with light. Curr Opin Struct Biol 2019; 57:1-8. [PMID: 30818200 DOI: 10.1016/j.sbi.2019.01.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/08/2019] [Accepted: 01/28/2019] [Indexed: 12/17/2022]
Abstract
Optogenetic dimerizers are modular domains that can be utilized in a variety of versatile ways to modulate cellular biochemistry. Because of their modularity, many applications using these tools can be easily transferred to new targets without extensive engineering. While a number of photodimerizer systems are currently available, the field remains nascent, with new optimizations for existing systems and new approaches to regulating biological function continuing to be introduced at a steady pace.
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94
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Lugagne JB, Dunlop MJ. Cell-machine interfaces for characterizing gene regulatory network dynamics. ACTA ACUST UNITED AC 2019; 14:1-8. [PMID: 31579842 DOI: 10.1016/j.coisb.2019.01.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Gene regulatory networks and the dynamic responses they produce offer a wealth of information about how biological systems process information about their environment. Recently, researchers interested in dissecting these networks have been outsourcing various parts of their experimental workflow to computers. Here we review how, using microfluidic or optogenetic tools coupled with fluorescence imaging, it is now possible to interface cells and computers. These platforms enable scientists to perform informative dynamic stimulations of genetic pathways and monitor their reaction. It is also possible to close the loop and regulate genes in real time, providing an unprecedented view of how signals propagate through the network. Finally, we outline new tools that can be used within the framework of cell-machine interfaces.
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Affiliation(s)
- Jean-Baptiste Lugagne
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.,Biological Design Center, Boston University, Boston, MA, USA
| | - Mary J Dunlop
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.,Biological Design Center, Boston University, Boston, MA, USA
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95
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Noninvasive optical activation of Flp recombinase for genetic manipulation in deep mouse brain regions. Nat Commun 2019; 10:314. [PMID: 30659191 PMCID: PMC6338782 DOI: 10.1038/s41467-018-08282-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 12/22/2018] [Indexed: 01/04/2023] Open
Abstract
Spatiotemporal control of gene expression or labeling is a valuable strategy for identifying functions of genes within complex neural circuits. Here, we develop a highly light-sensitive and efficient photoactivatable Flp recombinase (PA-Flp) that is suitable for genetic manipulation in vivo. The highly light-sensitive property of PA-Flp is ideal for activation in deep mouse brain regions by illumination with a noninvasive light-emitting diode. In addition, PA-Flp can be extended to the Cre-lox system through a viral vector as Flp-dependent Cre expression platform, thereby activating both Flp and Cre. Finally, we demonstrate that PA-Flp–dependent, Cre-mediated Cav3.1 silencing in the medial septum increases object-exploration behavior in mice. Thus, PA-Flp is a noninvasive, highly efficient, and easy-to-use optogenetic module that offers a side-effect-free and expandable genetic manipulation tool for neuroscience research. Most approaches to control gene expression in vivo require generation of knock-in mouse lines and often lack spatiotemporal control. Here the authors develop a photo-activatable Flp recombinase system and demonstrate its use by controlling object-exploration behavior in mice through Cav3.1 silencing.
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96
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Selectable marker recycling in the nonconventional yeast Xanthophyllomyces dendrorhous by transient expression of Cre on a genetically unstable vector. Appl Microbiol Biotechnol 2018; 103:963-971. [DOI: 10.1007/s00253-018-9496-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/29/2018] [Accepted: 10/29/2018] [Indexed: 10/27/2022]
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97
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Ueda Y, Sato M. Cell membrane dynamics induction using optogenetic tools. Biochem Biophys Res Commun 2018; 506:387-393. [DOI: 10.1016/j.bbrc.2017.11.091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 11/13/2017] [Indexed: 10/25/2022]
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98
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Luke GA, Ryan MD. "Therapeutic applications of the 'NPGP' family of viral 2As". Rev Med Virol 2018; 28:e2001. [PMID: 30094875 DOI: 10.1002/rmv.2001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/29/2018] [Accepted: 07/01/2018] [Indexed: 12/15/2022]
Abstract
Oligopeptide "2A" and "2A-like" sequences ("2As"; 18-25aa) are found in a range of RNA virus genomes controlling protein biogenesis through "recoding" of the host-cell translational apparatus. Insertion of multiple 2As within a single open reading frame (ORF) produces multiple proteins; hence, 2As have been used in a very wide range of biotechnological and biomedical applications. During translation, these 2A peptide sequences mediate a eukaryote-specific, self-"cleaving" event, termed "ribosome skipping" with very high efficiency. A particular advantage of using 2As is the ability to simultaneously translate a number of proteins at an equal level in all eukaryotic systems although, naturally, final steady-state levels depend upon other factors-notably protein stability. By contrast, the use of internal ribosome entry site elements for co-expression results in an unbalanced expression due to the relative inefficiency of internal initiation. For example, a 1:1 ratio is of particular importance for the biosynthesis of the heavy-chain and light-chain components of antibodies: highly valuable as therapeutic proteins. Furthermore, each component of these "artificial polyprotein" systems can be independently targeted to different sub-cellular sites. The potential of this system was vividly demonstrated by concatenating multiple gene sequences, linked via 2A sequences, into a single, long, ORF-a polycistronic construct. Here, ORFs comprising the biosynthetic pathways for violacein (five gene sequences) and β-carotene (four gene sequences) were concatenated into a single cistron such that all components were co-expressed in the yeast Pichia pastoris. In this review, we provide useful information on 2As to serve as a guide for future utilities of this co-expression technology in basic research, biotechnology, and clinical applications.
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Affiliation(s)
- Garry A Luke
- Centre for Biomolecular Sciences, School of Biology, University of St Andrews, St Andrews, UK
| | - Martin D Ryan
- Centre for Biomolecular Sciences, School of Biology, University of St Andrews, St Andrews, UK
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99
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Johnson HE, Toettcher JE. Illuminating developmental biology with cellular optogenetics. Curr Opin Biotechnol 2018; 52:42-48. [PMID: 29505976 PMCID: PMC6082700 DOI: 10.1016/j.copbio.2018.02.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 02/11/2018] [Indexed: 01/28/2023]
Abstract
In developmental biology, localization is everything. The same stimulus-cell signaling event or expression of a gene-can have dramatically different effects depending on the time, spatial position, and cell types in which it is applied. Yet the field has long lacked the ability to deliver localized perturbations with high specificity in vivo. The advent of optogenetic tools, capable of delivering highly localized stimuli, is thus poised to profoundly expand our understanding of development. We describe the current state-of-the-art in cellular optogenetic tools, review the first wave of major studies showcasing their application in vivo, and discuss major obstacles that must be overcome if the promise of developmental optogenetics is to be fully realized.
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Affiliation(s)
- Heath E Johnson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States.
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100
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Krishnamurthy VV, Zhang K. Chemical physics in living cells — Using light to visualize and control intracellular signal transduction. CHINESE J CHEM PHYS 2018. [DOI: 10.1063/1674-0068/31/cjcp1806152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Vishnu V. Krishnamurthy
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Kai Zhang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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