Toolkit Items

dCas9*_PhlF is a bacterial CRISPR-based transcriptional switch comprising a non-toxic dCas9* variant with the R1335K PAM-binding mutation fused to the PhlF repressor. The fusion recovered DNA-binding-dependent repression and enabled sgRNA-programmed NOT gate behavior that depends on both an sgRNA target site and a PhlF operator.

The autorepression-based conditional gene expression system is a yeast genetic controller in which TetR represses both a gene of interest and its own expression, creating a negative-feedback autorepression loop. Addition of anhydrotetracycline relieves TetR-mediated repression to enable conditional control of protein dosage with reduced cell-to-cell variation.

The TetR autorepression loop is a yeast gene-control construct pattern in which TetR represses both its own expression and a gene of interest, creating a negative autoregulatory circuit. In the reported implementation, induction is achieved with anhydrotetracycline to reversibly control protein dosage.

TetR-Tup1 is a yeast transcriptional repression fusion used as a second repressor in a TetR-based conditional expression controller. In the reported system, it suppresses residual target-gene expression to reduce leakiness, while anhydrotetracycline relieves TetR-mediated repression to restore expression.

VosA is an NF-κB-like velvet domain protein from Aspergillus nidulans that functions as a transcriptional regulator. It binds more than 1,500 promoter sequences and represses the SclB regulatory network, including control of the sclB promoter and inhibition of premature brlA induction.

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.

Light-controlled nuclear localization is an optogenetic engineering method reported for constructing repressors of gene expression in yeasts. It uses light to regulate nuclear localization, thereby controlling transcriptional repression.

Engineered BUFFER logical operations are single-input transcriptional logic elements described in a collection of network-capable genetic programs. In the cited study, the BUFFER operation was implemented as a repressor-based logical operation and experimentally characterized as part of a framework for predictive design of more complex transcriptional circuits.

Engineered BUFFER (repressor) and engineered NOT (antirepressor) logical operations are single-input transcriptional logic elements developed as network-capable components for synthetic gene programs. They were experimentally characterized and used as foundational parts for predictive modeling of more complex compressed transcriptional logic circuits.

Opto-CRISPR-KDM1a is a light-inducible CRISPR epigenome editing system designed to recruit KDM1a in a controllable manner. In Neuro2A cells, it downregulated Egr3 and Nab2 transcripts and produced bidirectional expression changes reported to resemble cocaine-associated regulation.

The CRY2 and LOV-fused degron light-responsive repression/degradation system is a multi-component optogenetic platform reported in mammalian cells that uses light to simultaneously block transcription and deplete protein levels. It is based on Arabidopsis cryptochrome 2 (CRY2), which interacts with CIB1 upon illumination, together with a LOV-fused degron configuration.

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.

The prototype of these B12-dependent photoreceptors, the transcriptional repressor CarH, is widespread in bacteria and mediates light-dependent gene regulation in a photoprotective cellular response. CarH activity as a transcription factor relies on the modulation of its oligomeric state by 5'-deoxyadenosylcobalamin and light.

the Nature Communications article associated with DOI 10.1038/s41467-025-67201-w describes ... a ZIM3-dCas9 CRISPRi module ... useful for extracting explicit component provenance and benchmark context for ... pTET-DD-ZIM3.