Curated Optogenetic Publication Database

Abstract: The robustness and broad applicability of an optogenetic tool depends heavily on the properties of the underlying photoreceptor protein and its cognate binding partner-the light-responsive 'core'. Current red light optogenetic systems for mammalian cells rely on phytochrome-based photoreceptors: large (70-kDa) proteins that act as dimers, enforcing dimerization on attached proteins. Naturally occurring or engineered binding partners can function effectively, but large size, complex interaction, background binding, weak affinity and modest dynamic range remain limiting. Here we developed a small (17-kDa) monomeric biliverdin-binding photoreceptor, FenixS, and a highly selective, high-affinity binder, Ash1 (6 kDa) using structure-based design and directed evolution. Negligible OFF-state binding and a >1,200-fold increase in binding affinity upon 700-nm illumination yield a high-performance, ultralow background core for diverse applications. A FenixS-Ash1-based optogenetic tool for red light activation of transcription in mammalian cells performs robustly without biliverdin supplementation, with head-to-head comparisons confirming its control of gene expression versus established tools.

Abstract: Dynamic fibroblast growth factor (FGF)/extracellular signal-regulated kinase (ERK) signaling plays key roles in development, regeneration, and disease. We recently developed a zebrafish-optimized optogenetic tool, bOpto-FGF, that enables reversible activation of FGF/ERK signaling in response to blue light (∼455 nm) by fusing a zebrafish receptor tyrosine kinase domain to a blue-light-dimerizing light oxygen voltage-sensing domain. Previously, this tool was introduced into zebrafish embryos by mRNA injection. Here, we develop Tg(ubi:bOpto-FGF), a novel transgenic zebrafish ubiquitously expressing bOpto-FGF, to streamline experimental workflows. We demonstrate robust blue-light-mediated activation of FGF/ERK signaling and FGF target gene expression in early gastrulation-stage Tg(ubi:bOpto-FGF) embryos. Light-mediated signaling activation at this stage is more spatially uniform in transgenics compared to mRNA-injected embryos, and ectopic signaling in response to continuous light exposure is activated within 3 min and maintained for at least 75 min. Furthermore, Tg(ubi:bOpto-FGF) heterozygotes are light responsive from late blastula stages through at least 24 h postfertilization. Finally, we demonstrate light-mediated spatially localized FGF/ERK signaling activation within 1 min in the head, trunk, and tail at 1 day postfertilization. This transgenic line provides a powerful and convenient new strategy for spatiotemporal manipulation of FGF/ERK signaling in the vertebrate zebrafish model.

Abstract: Microbial cell factories promise sustainable biomanufacturing, yet balancing cellular growth and product synthesis remains a fundamental productivity bottleneck. While traditional static metabolic engineering fails to precisely orchestrate metabolic flux across temporal and spatial dimensions, optogenetic approaches offer unprecedented spatiotemporal control and programmability. This study developed an integrated framework combining dual-mode optogenetic switches with a machine learning-guided optimization strategy to achieve precise temporal orchestration of metabolic pathways. Using Saccharomyces cerevisiae (strain BY4742, which exhibits minimal endogenous 2,3-butanediol (2,3-BDO) production) as the model host, the 2,3-BDO biosynthetic pathway was constructed. The deployment of dual light-responsive modules for protein degradation and stabilization, together with systematic optimization of illumination conditions, enabled dynamic coordination of the growth and production phases, increasing the 2,3-BDO titre to 3.52 times that of the static control in shake flasks. To extend beyond empirical optimization, a convolutional neural network (CNN) was integrated with a differential evolution (DE) algorithm to identify the optimal dynamic illumination schedule, resulting in a further 15.60% increase in the predicted and experimentally validated 2,3-BDO titre. The optimized strategy was subsequently validated in a 5-L photobioreactor, where dynamic optogenetic regulation combined with optimized fermentation conditions yielded 23.95 g L-1 2,3-BDO under fed-batch conditions. This study establishes a machine learning-assisted optogenetic framework for dynamic metabolic regulation and provides an effective strategy for improving microbial biomanufacturing.

Abstract: Opto-CRISPR (optically controlled CRISPR/Cas) represents a major advancement in precision neurology by enabling localized gene editing within the nervous system at precise times and locations. While preclinical studies still rely largely on classical CRISPR/Cas systems, opto-CRISPR offers unprecedented opportunities to safely treat neurological diseases at their genetic roots. It achieves this by spatiotemporally correcting pathogenic mutations, halting toxic protein accumulation, repairing neurons, rebuilding neural circuitry, and accelerating drug discovery through highly realistic disease models. This review discusses this emerging field and its transformative potential for translational neuropharmacology, focusing on therapies for neurodevelopmental and neurodegenerative disorders. Opto-CRISPR is classified into four generations: Generation 1 (light-controlled Cas protein systems), Generation 2 (light-activated guide RNA systems), Generation 3 (light-controlled inhibitor systems), and Generation 4 (NIR upconversion and epigenetic multiplexing). Their working mechanisms, applications, advantages, and limitations are comprehensively described. We also critically discuss how opto-CRISPR offers distinct advantages over traditional biologics and remote modalities (e.g., small-molecule drugs, monoclonal antibodies, antisense oligonucleotides, viral-mediated gene therapy, magnetogenetics, and sonogenetics) in neuropharmacology. Finally, we address current challenges and the therapeutic outlook for the clinical translation of opto-CRISPR.

Abstract: Pulsatile actomyosin networks emerge as a widespread mechanism driving tissue morphogenesis. Compared with myosin-II pulses, F-actin pulses are largely unexplored. By studying Drosophila oogenesis, we report that basal pulsatile actomyosin networks consist of F-actin bundle and meshwork architectures, implicating the existence of different F-actin microstructures and corresponding nucleators. Here, Rac1 and the Scar/WAVE-Arp2/3 complex (branched F-actin nucleator), exhibiting constant levels, are necessary to support F-actin pulsation, whereas pulses of Dia (unbranched F-actin nucleator) trigger F-actin pulsation. The pulsatile F-actin networks recruit the F-actin turnover regulator cofilin, thus generating cofilin pulses. Cofilin at relatively low concentration can cooperate with F-actin nucleators to amplify F-actin and enhance its pulsation, while cofilin at relatively high concentration might trigger the F-actin disassembly to attenuate its pulsation. These two different effects of cofilin on F-actin pulsation were confirmed by Zdk-cofilin optogenetics. Rac1 signaling, Dia, and cofilin are also crucial for F-actin pulses in border cell migration. Our findings thus reveal a coordinated regulation of F-actin pulses conferring actomyosin contractility in morphogenesis and cell migration.

Abstract: Flocculation is a key technological trait in lager brewing, governing fermentation performance, yeast recovery, and beer quality. In the allo-aneuploid hybrid yeast Saccharomyces pastorianus, the genetic basis of flocculation remains poorly resolved due to its complex dual sub-genome architecture. Here, we systematically re-annotated and functionally characterized the complete FLO gene repertoire of the Group II strain CBS 1483. Thirteen FLO genes were identified, including allelic variants and a previously uncharacterized adhesin, Flo12, containing a Hyphal_reg_CWP domain instead of the canonical PA14 lectin-binding domain. Structural modeling revealed strong conservation of Ca²+-binding residues in PA14 domains, alongside repeat-region diversification likely contributing to functional variability. Using optogenetic expression in a FLO-null background, we demonstrated that SpcI-FLO9-1 and SpcI-FLO9-2_1 are the strongest drivers of flocculation, exhibiting NewFlo-like sugar sensitivity. Transcriptomic analysis during 17°P wort fermentation showed dynamic induction of these genes coinciding with flocculation onset. Surprisingly, deletion of both loci in CBS 1483 did not abolish but only delayed sedimentation in wort, accompanied by improved maltose utilization and attenuation. These findings reveal functional redundancy and compensatory mechanisms within the FLO network of lager yeast, highlighting the genetic complexity underlying flocculation, and providing a molecular framework to inform yeast selection, strain development, and optimization of the lager fermentation processes.IMPORTANCEFlocculation, the process by which yeast cells aggregate and settle, is essential for producing clear, high-quality lager beer, and for efficient yeast recovery during brewing. However, the genetic basis of this trait in lager yeast has remained poorly understood because these strains possess unusually complex hybrid genomes. In this study, we systematically identified and characterized the complete set of flocculation genes in the industrial lager yeast Saccharomyces pastorianus CBS 1483. We demonstrated that lager yeast flocculation is not controlled by a single dominant gene, but instead emerges from the combined action of several moderately active adhesion proteins that are expressed at low levels during fermentation. Surprisingly, deleting the two strongest candidate genes only delayed, rather than eliminated, sedimentation, revealing a robust compensatory network that preserves brewing performance. These findings refine the current understanding of yeast flocculation and provide a molecular framework for developing brewing strains with improved fermentation efficiency, product consistency, and flavor quality.

Abstract: Embryonic myeloid (EM) cells are the first immune-cell population to emerge during development and must disperse throughout the embryo to act as the first line of defence against infection. Although EM cells migrate directionally toward wounds, how they navigate through unwounded tissues during early colonization remains unclear. Here we show that EM cell dispersion in Xenopus embryos is driven, at least in part, by cell-on-cell migration, an important yet underappreciated phenomenon, guided by dynamic tissue flows. We have established a new ex vivo EM cell migration system that allows for live imaging, computational analyses and optogenetic manipulation. We find that local ectodermal tissue flows repolarize EM cell protrusions and bias their directional migration. Disrupting these flows, both ex vivo and in vivo, either genetically or mechanically, impairs EM cell dispersion. Our findings reveal that mechanical cues generated by surrounding tissue flows coordinate immune-cell migration during development, highlighting an overlooked mechanism by which collective tissue dynamics guide individual cell behaviour.

Abstract: Transcription involves initiation, pausing, elongation, and termination. Suppressor of Ty5 (SPT5) regulates promoter-proximal pausing and elongation, but how it orchestrates both steps during dynamic developmental changes in gene expression remains unclear. Here, using rapid optogenetic depletion in Drosophila embryos, we uncover different consequences of SPT5 removal at different developmental stages. In early embryos, SPT5 depletion causes a shift of RNA polymerase II (Pol II) from the canonical pausing site to the +1 nucleosome, which is strongly positioned. In late embryos, SPT5 depletion similarly reduces pausing at the canonical site, but the transcriptional machinery can overcome the +1 nucleosome-which appears more labile at this time point-moving into the gene body. This results in lethality and both up- and downregulation of expression, depending on the balance between Pol II entering the gene body and defective elongation. This is intensified for genes naturally increasing or decreasing their expression, indicating that SPT5 contributes to fine-tuning dynamic expression changes.

Abstract: Optogenetic dimerization modules are widely used to regulate protein function, yet their behaviour within folded enzymes remains incompletely understood. Here, we engineered vesicular stomatitis virus by inserting an intramolecularly tethered light-inducible dimerizer into the viral RNA-dependent RNA polymerase [large (L) protein], enabling assessment of its effects on early viral transcription and viral replication. Blue light illumination enhanced viral replication, but reduced temperature produced a similar increase in viral replication even in the absence of light. In addition, a thermally stabilized dimerizer variant supported robust replication under dark conditions. These observations suggest that early viral transcription and viral replication are influenced by the structural and biophysical properties of the inserted dimerizer and their temperature dependence, rather than by light alone. Structural modelling suggested that permissive insertion sites are located within or adjacent to regions with low predicted Local Distance Difference Test (pLDDT) scores, whereas non-permissive insertions showed greater predicted local structural deviations, particularly in the capping domain. Although these analyses are based on predicted structures, the observed structural differences are consistent with the functional differences among insertion sites. Together, our results show that intramolecular optogenetic modules enable light- and temperature-dependent modulation of early viral transcription and replication. While the structural analyses are based on predicted models, they provide a useful framework for identifying permissive insertion sites and generate testable hypotheses regarding how the structural and biophysical properties of the inserted dimerizer may influence polymerase function.

Abstract: Optogenetics, a biotechnology that combines optical and genetic strategies to regulate cellular and tissue functions with high spatial and temporal precision, serves as a powerful tool-level regulatory technology widely employed to investigate cellular processes and elucidate disease mechanisms. Nanotechnology-driven optogenetics, which incorporates nanomaterials/nanostructures to improve the efficacy and broaden the applications of optogenetic systems, synergistically integrates the precision, tunability, and multifunctionality of nanotechnology with the spatiotemporal control inherent to optogenetics. The development not only enhances the flexibility and efficiency of optogenetic technology but also advances the field toward therapeutic-grade interventions. In this review, we summarize recent advances in nanotechnology-driven optogenetics, with a particular emphasis on three key areas: (1) nanostructured light sources for the precise activation of optogenetic systems, which include both externally light-stimulated systems and systems that operate independently of external light sources; (2) nanotechnology-enabled targeted delivery of light-sensitive proteins and genetic constructs to ensure efficient modulation of optogenetic pathways, which specifically involves the nanotechnology-assisted gene, protein, and recombinase enzyme delivery approaches; and (3) nanotechnology-driven therapeutic applications of optogenetics, including CAR T cell immunotherapy, cancer treatment, neurological interventions, and cardiac therapies. We further discuss the current challenges facing this emerging field and outline future research directions. This review aims not only to highlight recent breakthroughs but also to position nanotechnology-driven optogenetics as a promising tool for next-generation precision medicine.

Abstract: Engineered yeast-living drugs offer significant potential for oral protein therapy but remain limited by poor intestinal retention and lack of precise spatiotemporal control over therapeutic delivery. Here, we developed an ingestible hydrogel-encapsulated optogenetic yeast system controlled by a wearable electronic device for programmable interleukin-10 (IL-10) delivery in inflammatory bowel disease (IBD). We engineered Pichia pastoris with an EL222-based blue-light-inducible circuit achieving rapid, stringent IL-10 secretion (50% saturated concentration within just 1 h upon induction). The yeast was encapsulated in a photo-crosslinkable HAMA hydrogel that was gelated within 60 s upon blue-light exposure, exhibiting robust mechanical stability and tissue adhesion. A lightweight (2.27 g) wearable Bluetooth-controlled electronic device delivered targeted blue light transdermally, enabling simultaneous in situ hydrogel crosslinking and optogenetic activation in yeast cells. This system significantly extended the time yeast stays in the mouse gut, with reporter gene expression lasting over 5 h, while the unencapsulated control group lasted less than 2 h. In DSS-induced colitis mice, our strategy reduced proinflammatory cytokines (IL-1β, IL-6, and TNF-α) by >60%, restored intestinal barrier integrity, and normalized gut microbiota diversity to near-healthy levels, which performed significantly better than in other groups. This integrated "extracorporeal instruction-intracorporeal response" paradigm establishes a digitally programmable platform for precision live biotherapeutics. However, limited blue-light tissue penetration remains a key constraint; future work should focus on near-infrared photosensitive systems, programmable-degradation hydrogels, and wireless closed‑loop feedback to advance clinical translation.

Abstract: Endoplasmic reticulum-plasma membrane (ER-PM) contact sites are dynamic membrane interfaces that regulate essential cellular processes, including calcium signaling and lipid homeostasis. Emerging evidence suggests that contact-site geometry and organization critically influence these functions, yet existing tools cannot systematically manipulate individual geometric parameters while providing high-fidelity visualization in living cells. Here, we develop complementary chemical and optical platforms for inducible ER-PM contact-site reconstitution. A nontoxic, reversible abscisic acid-inducible system based on the plant-derived ABIcs/PYLcs pair and a rapidly reversible optogenetic iLID/SspB system enable robust visualization and dose-dependent control of contact-site assembly and disassembly. Increasing inducer dose selectively increases contact-site density and total contact area per cell without substantially changing the average size of individual contact sites. In contrast, systematic variation of tether length or tether abundance selectively increases average contact-site size and total contact area without altering contact-site density, providing orthogonal strategies to modulate contact-site density and size. Importantly, engineered contact sites recruit ER-PM contact-site-associated proteins, including MAPPER, Kv2.1, and Stromal Interaction Molecule 1 (STIM1), demonstrating key organizational features of native ER-PM contacts. MAPPER recruitment is maintained across tether lengths tested, whereas Kv2.1/STIM1 recruitment depends strongly on tether length, with longer tethers promoting recruitment by increasing intermembrane spacing. In contrast, varying tether abundance has little effect on protein recruitment, revealing distinct roles for intermembrane spacing and tether density in organizing ER-PM contact sites. Together, this work establishes a quantitative platform for engineering ER-PM contact sites with defined geometric properties and provides a framework for investigating how membrane contact-site architecture regulates cellular function.

Abstract: Inducing tumor cell pyroptosis represents a promising anticancer strategy; however, uncontrolled pyroptosis not only restricts the production of viral delivery vectors but also poses a risk of systemic damage, thereby limiting the translational application of pyroptosis-based therapies. The development of genetic tools that enable precise spatiotemporal control over pyroptosis remains challenging. To address this, we developed PyroRACS, a bioorthogonal optogenetic inducer for precise pyroptosis induction. PyroRACS utilizes an engineered red-light-activatable Cre-ON genetic switch (RACS) to drive the expression of the gasdermin D N-terminal domain, enabling tunable initiation of pyroptosis without relying on endogenous signaling pathways. We validated robust pyroptosis induction by PyroRACS in multiple cell lines. PyroRACS exhibited high controllability by selectively ablating cancer cells in vitro with precise spatiotemporal resolution. Moreover, its superior controllability enabled the production of the adenovirus vector and allowed "all-in-one" delivery of PyroRACS. In a tumor-bearing mouse model, spatially restricted induction of pyroptosis by PyroRACS resulted in effective tumor suppression, with no detectable systemic toxicity observed under the tested conditions. Collectively, PyroRACS provides a novel optogenetic tool for precise manipulation of pyroptosis, facilitating fundamental research and advancing pyroptosis-based precision oncology therapeutics.

Abstract: The complexity of the eukaryotic cell cycle complicates experiment design and data interpretation, limiting our understanding of how cells coordinate cell cycle processes. Traditional perturbation methods, including knockouts, deletions, and arrest-inducing chemicals, are limited by compensatory feedback interactions or pleiotropic side effects. Inducible synthetic systems offer greater specificity but often rely on external inducers, making rapid reversibility difficult. Here, we developed OPTO-Cln2, an optogenetic tool for light-controlled and reversible regulation of G1 progression in budding yeast. Using time-lapse microscopy, we show that OPTO-Cln2-strains rapidly switch between normal and altered G1 progression. Combining OPTO-Cln2 with a readout of TORC1 and PKA activity, we find that oscillatory signaling dynamics is coordinated with G1 progression. Finally, we show that OPTO-Cln2 enables at least two cycles of synchronous arrest and release in liquid cultures. This system provides a powerful approach for studying cell cycle dynamics and the coordination of cell growth with division.

Abstract: Microbial coculture can integrate advantages and overcome the metabolic imbalance of individual species. Programming strain interactions represents a common routine for synthetic microbial communities with distinct species, which causes difficulties and redundant workloads in interaction construction before being available as chassis hosts. This study explores yeast-bacterium consortium without engineered interactions for the co-inducible relayed synthesis of natural products. The Komagataella phaffii-Escherichia coli consortium is explored for co-growth under selected conditions. Low-level glucose- and blue light-responsive transcriptional systems are rebuilt separately for each host, allowing single-signal co-induced activation of compound synthesis in coculture. Pathway redirection, genome mining, and rewiring of key targets for acyl donor degradation result in efficient production of the reporter molecule simvastatin (26.2 mg l-1) through living consortium cultured on simple carbon source. Inducible biosynthesis of another reporter compound (2S)-naringenin (165.6 mg l-1) further validates the extendibility of this community. The described platform represents a breakthrough in engineering microbial consortium for biosynthesis.

Abstract: Primordial germ cells (PGCs) are the first cells specified in the Drosophila embryo and are precursors to the germline. Their formation requires suppression of somatic fates, achieved by degrading the receptor tyrosine kinase Torso at the posterior pole through the ubiquitin ligase adaptor germ cell-less (GCL). Although Torso is known to antagonize PGC formation, the underlying mechanisms remained unclear. Here, we combine optogenetic Ras activation and Ras effector loop mutants to show that Ras suppresses PGC formation independently of the canonical Raf/MEK/ERK pathway. We identify an unexpected early role for Torso in activating phosphoinositide 3-kinase (PI3K), generating membrane domains enriched in phosphatidylinositol (3,4,5)-trisphosphate (PIP3). Elevated PI3K activity disrupts PGC formation, while reduced PI3K activity creates ectopic PGCs. We demonstrate that GCL remodels the posterior pole membrane by suppressing Torso-dependent PI3K activation. Clearing PIP3 enables myosin II enrichment, allowing for PGC formation. Together, our findings reveal how antagonistic Torso and GCL activities establish the soma-germline boundary by organizing cortical lipids.

Abstract: Many molecular signals are known to be organized in subcellular regions termed microdomains. One example entails Rho GTPases, which control a range of cell behaviors through their functional patterning in spatiotemporal units. While fluorescent biosensors have allowed precise measurement of Rho GTPase activity in living cells, computational tools to delineate and track signaling microdomains in time-lapse image sequences of such biosensors do not exist. Here, we introduce a method that centers on the notion of activation time series coordination to identify signaling microdomains in space and time. After validating the algorithm with simulated microdomains, we show that our method identifies domains that support current hypotheses on the signaling architecture governing Rho GTPase organization and also respond to perturbation with optogenetics. A record of this paper's transparent peer review process is included in the supplemental information.

Abstract: Microtubules form dynamic cytoskeletal scaffolds essential for intracellular transport, organelle positioning, and spatial organization of signaling. Their architecture and function are continuously remodeled through the concerted actions of microtubule-associated proteins (MAPs), post-translational modifications (PTMs), and molecular motors. To precisely interrogate these processes in living systems, we developed a genetically encoded, single-component optogenetic platform for spatiotemporal control of microtubule organization and dynamics. By harnessing light-induced oligomerization to regulate microtubule association, this system supports reversible microtubule labeling and plus-end tracking, localized control of tubulin PTMs, optically regulated kinesin-driven cargo transport, and inducible microtubule severing within a unified design strategy. Using these tools, we reveal how local microtubule integrity governs lysosomal trafficking and endoplasmic reticulum (ER)-associated signaling dynamics. Collectively, this modular optogenetic toolkit bridges molecular design with cytoskeletal function, offering a versatile platform to dissect how dynamic cytoskeletal architectures coordinate intracellular organization, transport, and signaling.

Abstract: Regulation of gene transcription based on clustered regularly interspaced short palindromic repeats (CRISPR) is a powerful tool for constructing synthetic gene circuits in Saccharomyces cerevisiae. The current CRISPR-based regulatory approaches primarily focus on inhibiting the binding of dCas9 protein to single guide RNA (sgRNA) or blocking target site recognition. However, these regulation strategies are often at a single level, and their sensitivity still needs to be improved. In this study, the gene regulatory approaches at the translational and post-translational levels were integrated with optogenetic control patterns to attain very sensitive multi-level precision regulation of the dCas9 protein, thereby facilitating flexible regulation of transcription levels of target genes. This strategy was used to regulate the transcription levels of fluorescent proteins, resulting in up to 2.58-fold increase in the fluorescence intensity of mCherry compared to that without regulation. This CRISPR-based multi-level optogenetic system should be extremely helpful in understanding gene regulatory networks and in designing robust genetic circuits for synthetic biology.

Abstract: In cell biology, optical techniques can measure cells' internal states (biosensors) and stimulate cellular responses (optogenetics). Yet the design of all-optical experiments is often manual: a predetermined stimulus pattern is applied to cells, biosensors are measured over time, and data are processed offline. Here, we develop PyCLM, a Python-based suite enabling closed-loop measurement, image segmentation, and optogenetic control of thousands of cells per experiment. We showcase PyCLM on diverse applications, including performing feedback control on single cells and delivering developmental signaling patterns to Drosophila embryos. We compare single-cell versus tissue-scale optogenetic control of epithelial migration, revealing that fast and slow waves of receptor tyrosine kinase activity determine the direction of tissue movement, matching prior in vivo observations in zebrafish and mouse. PyCLM enables simple setup of dynamic experiments to probe cell and tissue properties and provides a first step toward real-time control of single-cell states at the tissue scale.

Abstract: Neurons acquire polarity by specifying one neurite as the axon, whereas the others become dendrites. But how this fundamental asymmetry is established remains unclear1. Neuronal polarization has been thought to rely primarily on growth cones that sense external cues2. Here we show that growth cones alone do not direct this process and that the soma acts as a central organizer of neuronal polarization. Using live imaging and genetic loss-of-function approaches in vivo, combined with optogenetic control and local cytoskeletal perturbations in cultured neurons, we uncover a soma-initiated oscillatory program that primes axon selection. Periodic actin branching that depends on the actin-related protein 2/3 (ARP2/3) complex at the soma remodels a global actomyosin network, thereby generating an actin wave that retracts neurites before propagating into a single neurite tip. Exposure to this wave relaxes local actomyosin contractility, which drives a transient microtubule-based protrusion and biases this neurite towards axon fate. As the cell exits this oscillatory stage, this neurite can overcome global inhibition and extend independently of ARP2/3, whereas actomyosin activity suppresses axon formation in the remaining neurites so that they subsequently become dendrites. This soma-driven mechanism ensures the emergence of a single axon independent of environmental cues and underpins the unidirectional information flow in neuronal circuits.

Abstract: We have developed an optogenetic tool called InLOV-an insulin receptor fused to a LOV domain-that enables activation of the insulin receptor signaling pathway via light-induced phosphorylation of its intracellular domains. Light activation of InLOV promotes insulin-induced neuronal plasticity in the mouse cerebellum and enhances cerebellar-driven self-motion behavior. Thus, InLOV enables optogenetic modulation of insulin receptor phosphorylation, opening new possibilities for disease modeling and therapeutic strategies for pathological insulin signaling in humans.

Abstract: The FKBP-based chemically induced dimerization (CID) technology is a fundamental tool for spatiotemporal precise modulation of protein functions in living cells, widely used in gene editing, protein function regulation, disease therapy, and drug development. However, its widespread application is limited by the inherent drawbacks including issues with immunosuppressive activity, stability, reversibility, and in vivo delivery. Recent years have seen remarkable progress in addressing these challenges: orthogonalization strategies eliminate immunosuppressive effects, fast-dissociating ligands and optogenetic systems enable reversible regulation, and protein engineering optimizes the FKBP/FRB domains to enhance stability and reduce immunogenicity. Moreover, integration with novel delivery technologies broadens its application scope greatly. This review summarizes the key optimization strategies and innovative applications of this technology in the cutting-edge biological research, aiming to reference the development of next-generation chemogenetic tools with higher precision, better safety, and greater application potential.

Abstract: Photoreceptor sensory histidine kinases (SHKs) couple light absorption to conformational changes regulating two-component signaling. Despite their importance and widespread use in optogenetics, the underlying structural signaling mechanisms remain poorly understood. Here, we engineered dimeric SHKs based on Pseudomonas putida short light-oxygen-voltage (LOV) proteins, determined their crystal structures, and investigated their signaling mechanisms. Regardless of illumination, the structures adopted a light-state like LOV-LOV dimer with symmetric/straight kinase modules. In contrast, small-angle x-ray scattering together with functional assays revealed pronounced light-dependent rearrangements in solution and allowed the assignment of the kinase-ON dark state to an asymmetric/kinked conformation, whereas the light state adopts a symmetric/straight structure. Comparative analyses of natural and engineered SHKs identified conserved motifs linking light-induced LOV domain rotation to kinase activity. The findings highlight the central role of dimer asymmetry and flexibility in SHK signaling, thereby not least informing the engineering of new light-responsive signaling systems.

Abstract: Cancer is increasingly recognized as a disease of the dysregulated epigenome; however, current epi-drugs are blunt, systemically toxic instruments. Catalytically dead CRISPR nucleases (dCas9) linked to chromatin effectors have now made it possible not only to write and erase epigenetic marks at specified loci without double-strand breaks but also to add an element of optogenetics, or reversible and light-encoded control over the timing and localization of the editors. In this review, the technological underpinnings of light-controlled CRISPR-dCas9 epigenome editing, which include architectures of dCas9 scaffold and guide, blue-to-near-infrared photoswitches, and high-gain epigenetic effector designs, are synthesized, and viral, non-viral, and stimuli-responsive delivery platforms, which have to be co-optimized with clinical light interfaces, are discussed. We then outline four functional routes by which opto-epigenome editors may be used therapeutically in cancer: tumor suppressor reactivation; oncogene and super-enhancer repression with metabolic rewiring; control of cancer stem cell differentiation; and immunomodulation of the tumor microenvironment. Lastly, a translational roadmap is defined in terms of preclinical model tiers, biomarker strategies, regulatory and manufacturing factors, and future directions, including NIR and bioluminescent actuation, implantable μLED devices, and AI-guided closed-loop illumination. Together, these aspects constitute design principles for advancing light-addressable epigenome editors toward first-in-human studies and for integrating them into combination regimens as a new class of precision cancer therapeutics.