Although several Cre-regulated CRISPR/Cas platforms exist, a CRISPR/Cas-controlled Cre-system remains a challenge. Here, we present a genetic switch we term SWITCHER based on a floxed wild-type Cre-construct representing a CRISPR-inducible and self-limiting kill switch. By leveraging CRISPR/Cas12a-mediated crRNA-array maturation, we showcase SWITCHER's dual role-not just as a recombinase but as a CRISPR switch, capable of orchestrating distinct Cas12a/crRNA-encoded programs.

CZ OPENSCREEN Institute of Molecular Genetics of the Czech Academy of Sciences Vídeňská 1083 142 20 Prague 4 Czech Republic

ETH Zurich Institute of Microbiology Vladimir Prelog Weg 1 5 10 8093 Zurich Switzerland

Laboratory of Cell Differentiation Institute of Molecular Genetics of the Czech Academy of Sciences Vídeňská 1083 142 20 Prague 4 Czech Republic

Laboratory of Leukocyte Signalling Institute of Molecular Genetics of the Czech Academy of Sciences Vídeňská 1083 142 20 Prague 4 Czech Republic

Military Health Institute Ministry of Defence of the Czech Republic U Vojenské nemocnice 1200 169 02 Prague 6 Czech Republic

Zobrazit více v PubMed

Zetsche, B. et al. Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array. PubMed PMC

Campa, C. C., Weisbach, N. R., Santinha, A. J., Incarnato, D. & Platt, R. J. Multiplexed genome engineering by Cas12a and CRISPR arrays encoded on single transcripts. PubMed

Hans, S. et al. Cre-Controlled CRISPR mutagenesis provides fast and easy conditional gene inactivation in zebrafish. PubMed PMC

Platt, R. J. et al. CRISPR-Cas9 knockin mice for genome editing and cancer modeling. PubMed PMC

Back, S. et al. Neuron-Specific Genome Modification in the Adult Rat Brain Using CRISPR-Cas9 Transgenic Rats. PubMed PMC

Carullo, N. V. N. et al. A Cre-Dependent CRISPR/dCas9 System for Gene Expression Regulation in Neurons. PubMed PMC

Chylinski, K. et al. CRISPR-Switch regulates sgRNA activity by Cre recombination for sequential editing of two loci. PubMed PMC

Chow, R. D., Kim, H. R. & Chen, S. Programmable sequential mutagenesis by inducible Cpf1 crRNA array inversion. PubMed PMC

Janbandhu, V. C., Moik, D. & Fassler, R. Cre recombinase induces DNA damage and tetraploidy in the absence of loxP sites. PubMed PMC

Feil, R., Wagner, J., Metzger, D. & Chambon, P. Regulation of Cre recombinase activity by mutated estrogen receptor ligand-binding domains. PubMed

Kristianto, J., Johnson, M. G., Zastrow, R. K., Radcliff, A. B. & Blank, R. D. Spontaneous recombinase activity of Cre-ERT2 in vivo. PubMed PMC

Alvarez-Aznar, A. et al. Tamoxifen-independent recombination of reporter genes limits lineage tracing and mosaic analysis using CreER(T2) lines. PubMed PMC

Tian, X. et al. Generation of a self-cleaved inducible Cre recombinase for efficient temporal genetic manipulation. PubMed PMC

Trovato, F. et al. Modelling genetic mosaicism of neurodevelopmental disorders in vivo by a Cre-amplifying fluorescent reporter. PubMed PMC

Rajaee, M. & Ow, D. W. A new location to split Cre recombinase for protein fragment complementation. PubMed PMC

Mashiko, D. et al. Generation of mutant mice by pronuclear injection of circular plasmid expressing Cas9 and single guided RNA. PubMed PMC

Suzuki, K. et al. In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration. PubMed PMC

Breinig, M. et al. Multiplexed orthogonal genome editing and transcriptional activation by Cas12a. PubMed

Kucherlapati, R. S., Eves, E. M., Song, K. Y., Morse, B. S. & Smithies, O. Homologous recombination between plasmids in mammalian cells can be enhanced by treatment of input DNA. PubMed PMC

Ayares, D., Spencer, J., Schwartz, F., Morse, B. & Kucherlapati, R. Homologous recombination between autonomously replicating plasmids in mammalian cells. PubMed PMC

Tang, K. et al. Cas12a-knock-in mice for multiplexed genome editing, disease modelling and immune-cell engineering. PubMed

Hebert, J. D. et al. Efficient and multiplexed somatic genome editing with Cas12a mice. Nat. Biomed. Eng 10.1038/s41551-025-01407-7 (2025). PubMed

Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. PubMed PMC

Zetsche, B. et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. PubMed PMC

Chavez, A. et al. Highly efficient Cas9-mediated transcriptional programming. PubMed PMC

Ran, F. A. et al. Genome engineering using the CRISPR-Cas9 system. PubMed PMC

Guo, L. Y. et al. Multiplexed genome regulation in vivo with hyper-efficient Cas12a. PubMed PMC

Concordet, J. P. & Haeussler, M. CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens. PubMed PMC

Wick, R. R., Judd, L. M. & Holt, K. E. Performance of neural network basecalling tools for Oxford Nanopore sequencing. PubMed PMC

Robinson, J. T. et al. Integrative genomics viewer. PubMed PMC

Bloh, K. et al. Deconvolution of Complex DNA Repair (DECODR): establishing a novel deconvolution algorithm for comprehensive analysis of CRISPR-edited sanger sequencing data. PubMed PMC