Source 1primary paper2021MED
Toolkit/phase-separation-engineered optogenetic synthetic transcription factors
phase-separation-engineered optogenetic synthetic transcription factors
Also known as: light-inducible transcription factors, optogenetic synthetic transcription factors
Taxonomy: Mechanism Branch / Architecture. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
Phase-separation-engineered optogenetic synthetic transcription factors are light-inducible transcription factor constructs modified with intrinsically disordered domains to promote liquid-liquid phase separation. In a 2021 study, this design increased transcriptional activation in mammalian cells and in mice after in situ transfection.
Usefulness & Problems
Why this is useful
These constructs are useful for increasing the activity of optogenetic synthetic transcription factors using a design principle based on intrinsically disordered domain addition. The reported benefit is stronger light-controlled transcriptional activation across multiple mammalian cell lines and in mice.
Problem solved
This approach addresses the problem of limited activation strength in light-inducible synthetic transcription factors. The cited study indicates that introducing intrinsically disordered domains can boost transcription factor performance through phase-separation engineering.
Problem links
limited performance of widely used light-inducible gene switches
LiteratureIt addresses limited performance of widely used light-inducible gene switches by boosting transcriptional output. The paper frames this as a way to mitigate practical constraints from low tissue penetrance and possible phototoxicity of light.
Source:
It addresses limited performance of widely used light-inducible gene switches by boosting transcriptional output. The paper frames this as a way to mitigate practical constraints from low tissue penetrance and possible phototoxicity of light.
need to increase transcriptional output despite low tissue penetrance and possible phototoxicity of light stimulus
LiteratureIt addresses limited performance of widely used light-inducible gene switches by boosting transcriptional output. The paper frames this as a way to mitigate practical constraints from low tissue penetrance and possible phototoxicity of light.
Source:
It addresses limited performance of widely used light-inducible gene switches by boosting transcriptional output. The paper frames this as a way to mitigate practical constraints from low tissue penetrance and possible phototoxicity of light.
Published Workflows
Objective: Engineer light-inducible synthetic transcription factors with improved transcriptional activation despite limitations of existing light-inducible gene switches.
Why it works: The abstract states that adding intrinsically disordered regions causes synthetic transcription factors to form droplets at target promoters, and that these droplets increase gene expression.
promoter-proximal liquid-liquid phase separationdroplet formation at target promoters via intrinsically disordered region incorporationoptogenetic engineeringquantitative mathematical modelingtransfection-based testing
Stages
- 1.Engineering phase-separating transcription factor designs(library_design)
This stage creates transcription factor designs intended to overcome limited performance of existing light-inducible gene switches.
Selection: Incorporation of intrinsically disordered regions to achieve liquid-liquid phase separation in constitutive and optogenetic synthetic transcription factors.
- 2.Model-supported mechanistic characterization(functional_characterization)
This stage tests whether the engineered phase-separation mechanism occurs and whether it improves transcriptional output.
Selection: Demonstration that engineered transcription factor droplets form at target promoters and increase gene expression.
- 3.Cross-context validation in mammalian cells and mice(confirmatory_validation)
This stage confirms that the engineered transcription factor improvement is not restricted to a single mammalian cell context.
Selection: Observation of increased performance in multiple mammalian cell lines and in mice following in situ transfection.
Taxonomy & Function
Primary hierarchy
Mechanism Branch
Architecture: A reusable architecture pattern for arranging parts into an engineered system.
Techniques
No technique tags yet.
Target processes
recombinationtranscriptionInput: Light
Implementation Constraints
cofactor dependency: cofactor requirement unknownencoding mode: genetically encodedimplementation constraint: context specific validationimplementation constraint: spectral hardware requirementoperating role: regulator
Implementation involves engineering light-inducible synthetic transcription factors by introducing intrinsically disordered domains to promote phase separation. The available evidence indicates use in mammalian cells and in mice after in situ transfection, but it does not specify the exact photoreceptor system, wavelengths, promoter targeting strategy, or delivery details.
The supplied evidence supports improved transcriptional activation, but it does not provide detailed quantitative performance metrics, kinetics, reversibility, or comparisons among specific intrinsically disordered domains. Evidence for recombination control, precise construct architectures, and independent replication is not provided in the supplied material.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
The performance increase from phase-separation-engineered synthetic transcription factors was observed in multiple mammalian cell lines and in mice following in situ transfection.
The performance increase from phase-separation-engineered synthetic transcription factors was observed in multiple mammalian cell lines and in mice following in situ transfection.
The performance increase from phase-separation-engineered synthetic transcription factors was observed in multiple mammalian cell lines and in mice following in situ transfection.
The performance increase from phase-separation-engineered synthetic transcription factors was observed in multiple mammalian cell lines and in mice following in situ transfection.
The performance increase from phase-separation-engineered synthetic transcription factors was observed in multiple mammalian cell lines and in mice following in situ transfection.
The performance increase from phase-separation-engineered synthetic transcription factors was observed in multiple mammalian cell lines and in mice following in situ transfection.
The performance increase from phase-separation-engineered synthetic transcription factors was observed in multiple mammalian cell lines and in mice following in situ transfection.
The performance increase from phase-separation-engineered synthetic transcription factors was observed in multiple mammalian cell lines and in mice following in situ transfection.
Introducing intrinsically disordered domains is a simple and effective means to boost synthetic transcription factor activity.
Introducing intrinsically disordered domains is a simple and effective means to boost synthetic transcription factor activity.
Introducing intrinsically disordered domains is a simple and effective means to boost synthetic transcription factor activity.
Introducing intrinsically disordered domains is a simple and effective means to boost synthetic transcription factor activity.
Introducing intrinsically disordered domains is a simple and effective means to boost synthetic transcription factor activity.
Introducing intrinsically disordered domains is a simple and effective means to boost synthetic transcription factor activity.
Introducing intrinsically disordered domains is a simple and effective means to boost synthetic transcription factor activity.
Introducing intrinsically disordered domains is a simple and effective means to boost synthetic transcription factor activity.
Incorporation of intrinsically disordered regions enabled constitutive and optogenetic synthetic transcription factors to undergo liquid-liquid phase separation near promoters.
Incorporation of intrinsically disordered regions enabled constitutive and optogenetic synthetic transcription factors to undergo liquid-liquid phase separation near promoters.
Incorporation of intrinsically disordered regions enabled constitutive and optogenetic synthetic transcription factors to undergo liquid-liquid phase separation near promoters.
Incorporation of intrinsically disordered regions enabled constitutive and optogenetic synthetic transcription factors to undergo liquid-liquid phase separation near promoters.
Incorporation of intrinsically disordered regions enabled constitutive and optogenetic synthetic transcription factors to undergo liquid-liquid phase separation near promoters.
Incorporation of intrinsically disordered regions enabled constitutive and optogenetic synthetic transcription factors to undergo liquid-liquid phase separation near promoters.
Incorporation of intrinsically disordered regions enabled constitutive and optogenetic synthetic transcription factors to undergo liquid-liquid phase separation near promoters.
Incorporation of intrinsically disordered regions enabled constitutive and optogenetic synthetic transcription factors to undergo liquid-liquid phase separation near promoters.
Engineered transcription factor droplets formed at target promoters and increased gene expression up to fivefold.
gene expression increase 5 fold
Engineered transcription factor droplets formed at target promoters and increased gene expression up to fivefold.
gene expression increase 5 fold
Engineered transcription factor droplets formed at target promoters and increased gene expression up to fivefold.
gene expression increase 5 fold
Engineered transcription factor droplets formed at target promoters and increased gene expression up to fivefold.
gene expression increase 5 fold
Engineered transcription factor droplets formed at target promoters and increased gene expression up to fivefold.
gene expression increase 5 fold
Engineered transcription factor droplets formed at target promoters and increased gene expression up to fivefold.
gene expression increase 5 fold
Engineered transcription factor droplets formed at target promoters and increased gene expression up to fivefold.
gene expression increase 5 fold
Engineered transcription factor droplets formed at target promoters and increased gene expression up to fivefold.
gene expression increase 5 fold
Approval Evidence
1 source4 linked approval claimsfirst-pass slug phase-separation-engineered-optogenetic-synthetic-transcription-factors
To overcome these limitations, we engineer optogenetic synthetic transcription factors to undergo liquid-liquid phase separation in close spatial proximity to promoters.
Source:
cross context performancesupports
The performance increase from phase-separation-engineered synthetic transcription factors was observed in multiple mammalian cell lines and in mice following in situ transfection.
Source:
design principlesupports
Introducing intrinsically disordered domains is a simple and effective means to boost synthetic transcription factor activity.
Source:
engineering resultsupports
Incorporation of intrinsically disordered regions enabled constitutive and optogenetic synthetic transcription factors to undergo liquid-liquid phase separation near promoters.
Source:
mechanistic effectsupports
Engineered transcription factor droplets formed at target promoters and increased gene expression up to fivefold.
Source:
Comparisons
Source-stated alternatives
The source contrasts this engineered design with widely used gene switches that lack the reported phase-separation enhancement. It also mentions constitutive synthetic transcription factors as another class in which phase separation was achieved by adding intrinsically disordered regions.
Source:
The source contrasts this engineered design with widely used gene switches that lack the reported phase-separation enhancement. It also mentions constitutive synthetic transcription factors as another class in which phase separation was achieved by adding intrinsically disordered regions.
Source-backed strengths
The reported performance increase was observed in multiple mammalian cell lines, indicating activity across more than one cellular context. The effect was also demonstrated in mice following in situ transfection, supporting functionality beyond cultured cells.
Source:
Incorporation of intrinsically disordered regions enabled constitutive and optogenetic synthetic transcription factors to undergo liquid-liquid phase separation near promoters.
Compared with biomolecular liquid-liquid phase separation
The source contrasts this engineered design with widely used gene switches that lack the reported phase-separation enhancement. It also mentions constitutive synthetic transcription factors as another class in which phase separation was achieved by adding intrinsically disordered regions.
Shared frame: source-stated alternative in extracted literature
Strengths here: increased gene expression up to fivefold; observed performance increase in multiple mammalian cell lines and in mice following in situ transfection; described as a simple means to boost synthetic transcription factor activity.
Relative tradeoffs: light-inducible systems are limited by low tissue penetrance and possible phototoxicity of the light stimulus.
Source:
The source contrasts this engineered design with widely used gene switches that lack the reported phase-separation enhancement. It also mentions constitutive synthetic transcription factors as another class in which phase separation was achieved by adding intrinsically disordered regions.
Compared with synthetic transcription factor
The source contrasts this engineered design with widely used gene switches that lack the reported phase-separation enhancement. It also mentions constitutive synthetic transcription factors as another class in which phase separation was achieved by adding intrinsically disordered regions.
Shared frame: source-stated alternative in extracted literature
Strengths here: increased gene expression up to fivefold; observed performance increase in multiple mammalian cell lines and in mice following in situ transfection; described as a simple means to boost synthetic transcription factor activity.
Relative tradeoffs: light-inducible systems are limited by low tissue penetrance and possible phototoxicity of the light stimulus.
Source:
The source contrasts this engineered design with widely used gene switches that lack the reported phase-separation enhancement. It also mentions constitutive synthetic transcription factors as another class in which phase separation was achieved by adding intrinsically disordered regions.
Ranked Citations
- 1.