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Cautereels C, Smets J, De Saeger J, Cool L, Zhu Y, Zimmermann A, Steensels J, Gorkovskiy A, Jacobs TB, Verstrepen KJ. Orthogonal LoxPsym sites allow multiplexed site-specific recombination in prokaryotic and eukaryotic hosts. Nat Commun 2024; 15:1113. [PMID: 38326330 PMCID: PMC10850332 DOI: 10.1038/s41467-024-44996-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024] Open
Abstract
Site-specific recombinases such as the Cre-LoxP system are routinely used for genome engineering in both prokaryotes and eukaryotes. Importantly, recombinases complement the CRISPR-Cas toolbox and provide the additional benefit of high-efficiency DNA editing without generating toxic DNA double-strand breaks, allowing multiple recombination events at the same time. However, only a handful of independent, orthogonal recombination systems are available, limiting their use in more complex applications that require multiple specific recombination events, such as metabolic engineering and genetic circuits. To address this shortcoming, we develop 63 symmetrical LoxP variants and test 1192 pairwise combinations to determine their cross-reactivity and specificity upon Cre activation. Ultimately, we establish a set of 16 orthogonal LoxPsym variants and demonstrate their use for multiplexed genome engineering in both prokaryotes (E. coli) and eukaryotes (S. cerevisiae and Z. mays). Together, this work yields a significant expansion of the Cre-LoxP toolbox for genome editing, metabolic engineering and other controlled recombination events, and provides insights into the Cre-LoxP recombination process.
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Affiliation(s)
- Charlotte Cautereels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Jolien Smets
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Jonas De Saeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
| | - Lloyd Cool
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
- Laboratory of Socioecology and Social Evolution, KU Leuven, Leuven, Belgium
| | - Yanmei Zhu
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Anna Zimmermann
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Jan Steensels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Anton Gorkovskiy
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium
| | - Thomas B Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark-Zwijnaarde 71, 9052, Ghent, Belgium
| | - Kevin J Verstrepen
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium.
- CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, 3001, Belgium.
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Bock C, Datlinger P, Chardon F, Coelho MA, Dong MB, Lawson KA, Lu T, Maroc L, Norman TM, Song B, Stanley G, Chen S, Garnett M, Li W, Moffat J, Qi LS, Shapiro RS, Shendure J, Weissman JS, Zhuang X. High-content CRISPR screening. NATURE REVIEWS. METHODS PRIMERS 2022; 2:9. [PMID: 37214176 PMCID: PMC10200264 DOI: 10.1038/s43586-022-00098-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
CRISPR screens are a powerful source of biological discovery, enabling the unbiased interrogation of gene function in a wide range of applications and species. In pooled CRISPR screens, various genetically encoded perturbations are introduced into pools of cells. The targeted cells proliferate under a biological challenge such as cell competition, drug treatment or viral infection. Subsequently, the perturbation-induced effects are evaluated by sequencing-based counting of the guide RNAs that specify each perturbation. The typical results of such screens are ranked lists of genes that confer sensitivity or resistance to the biological challenge of interest. Contributing to the broad utility of CRISPR screens, adaptations of the core CRISPR technology make it possible to activate, silence or otherwise manipulate the target genes. Moreover, high-content read-outs such as single-cell RNA sequencing and spatial imaging help characterize screened cells with unprecedented detail. Dedicated software tools facilitate bioinformatic analysis and enhance reproducibility. CRISPR screening has unravelled various molecular mechanisms in basic biology, medical genetics, cancer research, immunology, infectious diseases, microbiology and other fields. This Primer describes the basic and advanced concepts of CRISPR screening and its application as a flexible and reliable method for biological discovery, biomedical research and drug development - with a special emphasis on high-content methods that make it possible to obtain detailed biological insights directly as part of the screen.
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Affiliation(s)
- Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Institute of Artificial Intelligence, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Paul Datlinger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Florence Chardon
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Matthew B. Dong
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Systems Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Keith A. Lawson
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Tian Lu
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Department of Physics, Harvard University, Cambridge, MA, USA
| | - Laetitia Maroc
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Thomas M. Norman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bicna Song
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC, USA
- Department of Genomics and Precision Medicine, George Washington University, Washington, DC, USA
| | - Geoff Stanley
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Systems Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Mathew Garnett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Wei Li
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC, USA
- Department of Genomics and Precision Medicine, George Washington University, Washington, DC, USA
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Lei S. Qi
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
| | - Rebecca S. Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Jonathan S. Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Department of Physics, Harvard University, Cambridge, MA, USA
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