Browse the toolkit beneath workflows. The mechanism branch runs mechanism -> architecture -> component, while the technique branch runs from high-level approaches down to concrete methods.
23 items matching 1 filter
Mechanism Branch
Layer 1
Mechanisms
Top-level concepts: biophysical action modes such as heterodimerization, photocleavage, or RNA binding.
Layer 2
Architectures
Arrangements that realize or deploy mechanisms, including switches, construct patterns, and delivery strategies.
Layer 3
Components
Low-level parts and sequence-defined elements used inside architectures, including protein domains and RNA elements.
Technique Branch
Layer 1
Approaches
High-level engineering practices such as computational design, directed evolution, sequence verification, and functional assay.
Layer 2
Methods
Concrete methods used to design, build, verify, or characterize engineered systems.
Showing 1-23 of 23
FUN-LOV is a fungal light-oxygen-voltage optogenetic switch for yeast built from Neurospora crassa photoreceptors WC-1 and VVD. It uses the photon-regulated interaction of these components to drive light-dependent target gene activation, including GPD1 and ADH1 expression in a wine yeast strain.
The CcaS/CcaR system is a green/red light-responsive two-component optogenetic switch used to control transcription in Synechococcus sp. PCC 7002. In the cited work, its output was tuned through genetic modification of the pCpcG2 promoter and its transcriptional response kinetics were quantified by qRT-PCR.
TAEL is an engineered optogenetic transcription factor optimized for zebrafish in which blue light induces TAEL dimerization, binding to the C120 promoter element, and activation of downstream transcription. TAEL 2.0 is an improved transgenic implementation that enables inducible expression at late embryonic and larval stages and produces faster, higher reporter expression than the original system.
CRISPR activation and interference (CRISPRa/CRISPRi) is a CRISPR-based gene regulation method that uses Nab2- or Egr3-targeted single-guide RNAs to modulate transcription. In the cited 2022 study, these tools were used in Neuro2a cells to mimic bidirectional cocaine-associated expression changes in Nab2 and Egr3.
We demonstrate the toxicity of CRISPRa vectors expressing the activation domains (ADs) of the transcription factors p65 and HSF1, components of the synergistic activation mediator (SAM) CRISPRa system.
The synthetic optogenetic transcription device is a multi-component light-responsive signaling cascade that links melanopsin signal transduction to the nuclear factor of activated T cells (NFAT) control circuit to drive light-inducible transgene expression. It was reported to enable remote regulation of implanted transgenic cells in mice and to enhance blood-glucose homeostasis.
The bidirectional promoter system is an engineered EL222-based optogenetic construct pattern for Escherichia coli that enables blue light-mediated transcriptional activation and repression from a bidirectional promoter architecture. It uses the blue light-dependent DNA-binding protein EL222 to provide rapid and reversible control of gene expression.
TAEL 2.0 is a modified version of the TAEL/C120 optogenetic transcription system in which both the TAEL transcriptional activator and the C120 regulatory element were altered. In zebrafish embryos, blue light induces TAEL dimerization, binding to the C120 element, and transcriptional activation to drive light-inducible gene expression.
The supplied web research summary states that the anchor review names CRISPR-Combo as a system enabling simultaneous genome editing and gene activation in plants.
The supplied web research summary identifies dCas9-SunTag as explicitly supported and central to plant locus-specific activation and methylation targeting in the review's epigenome-editing module.
In these technologies, genetically encoded molecules integrate molecular events resulting from neuronal activity with light/drug-dependent events.
BcWCL1 PASΔ is a PAS-domain-deleted variant of the Botrytis cinerea blue-light photoreceptor BcWCL1 that functions in yeast as a blue-light-activated transcription switch. The reported activity depends on the BcWCL1 N-terminal region, which supports light-stimulated self-dimerization and contains a functional 9aaTAD-family transcriptional activation domain.
Synthetic Notch (synNotch) receptors are modular engineered receptors expressed in mammalian cells that detect signals presented by neighboring cells or ligand-bearing materials and activate prescribed transcriptional programs. In the cited work, synNotch was used as a programmable material-to-cell signaling interface for spatial control of cell phenotypes in multicellular constructs.
HEAL is a compact, inducible, multi-component dCas12f-based CRISPR activation system for programmable transcriptional activation in vivo. It uses sgRNA-embedded MS2 aptamers to recruit transactivators through MS2 coat protein binding at CRISPR-targeted DNA sites.
The CRY2-CIB1 light-inducible transcription system is a multi-component optogenetic switch built from Arabidopsis cryptochrome 2 (CRY2) and CIB1 that drives protein expression by stimulating transcription in response to light. In mammalian cells, it uses light-triggered CRY2-CIB1 interaction to regulate gene expression and can also produce light-dependent redistribution of CRY2-tethered proteins within the nucleus.
The light-controlled Bicoid transcription factor is an engineered optogenetic version of the Drosophila developmental transcription factor Bicoid used in embryos to acutely modulate Bicoid activity and measure downstream gap-gene responses in vivo. It was applied with fast light stimuli and real-time transcriptional reporters to probe the kinetics of Bicoid-dependent gene regulation.
LOV-LexA is a light-gated LexA-based expression system for Drosophila that fuses the bacterial LexA transcription factor to a plant-derived LOV photosensitive domain and a fluorescent protein. Blue light uncages a nuclear localization signal, drives nuclear translocation, and initiates LexAop transgene expression with spatial and temporal control.
The optimized Enhanced Magnet transcription factor is a light-responsive split transcription factor developed in Saccharomyces cerevisiae using Enhanced Magnet dimerization modules. It was rationally designed and tested to improve light-sensitive gene expression.
The UVB-inducible expression system is a UVB-responsive split transcription factor engineered from the Arabidopsis thaliana UVB receptor UVR8 and the COP1 WD40 domain. In mammalian cells, UVB illumination triggers transcriptional activation and provides one wavelength-specific channel for multichromatic gene control.
Opto-T7RNAP is an engineered blue light-inducible T7 RNA polymerase transcription system developed in Escherichia coli. It enables light-controlled transcription with spatiotemporal precision and is intended to function independently of endogenous cellular regulation.
Using inducible lentiviral vectors, we could not identify an activator expression window for effective SAM-based CRISPRa without measurable toxicity.
This review synthesizes genome-guided interventions (CRISPRa and mtDNA editing)... combined with mtDNA base editors...
We demonstrate the toxicity of CRISPRa vectors expressing the activation domains (ADs) of the transcription factors p65 and HSF1, components of the synergistic activation mediator (SAM) CRISPRa system.