1
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Tan LL, Heng E, Leong CY, Ng V, Yang LK, Seow DCS, Koduru L, Kanagasundaram Y, Ng SB, Peh G, Lim YH, Wong FT. Application of Cas12j for Streptomyces Editing. Biomolecules 2024; 14:486. [PMID: 38672502 DOI: 10.3390/biom14040486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/09/2024] [Accepted: 04/14/2024] [Indexed: 04/28/2024] Open
Abstract
In recent years, CRISPR-Cas toolboxes for Streptomyces editing have rapidly accelerated natural product discovery and engineering. However, Cas efficiencies are oftentimes strain-dependent, and the commonly used Streptococcus pyogenes Cas9 (SpCas9) is notorious for having high levels of off-target toxicity effects. Thus, a variety of Cas proteins is required for greater flexibility of genetic manipulation within a wider range of Streptomyces strains. This study explored the first use of Acidaminococcus sp. Cas12j, a hypercompact Cas12 subfamily, for genome editing in Streptomyces and its potential in activating silent biosynthetic gene clusters (BGCs) to enhance natural product synthesis. While the editing efficiencies of Cas12j were not as high as previously reported efficiencies of Cas12a and Cas9, Cas12j exhibited higher transformation efficiencies compared to SpCas9. Furthermore, Cas12j demonstrated significantly improved editing efficiencies compared to Cas12a in activating BGCs in Streptomyces sp. A34053, a strain wherein both SpCas9 and Cas12a faced limitations in accessing the genome. Overall, this study expanded the repertoire of Cas proteins for genome editing in actinomycetes and highlighted not only the potential of recently characterized Cas12j in Streptomyces but also the importance of having an extensive genetic toolbox for improving the editing success of these beneficial microbes.
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Affiliation(s)
- Lee Ling Tan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos #07-06, Singapore 138673, Singapore
| | - Elena Heng
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos #07-06, Singapore 138673, Singapore
| | - Chung Yan Leong
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #02-01, Singapore 138669, Singapore
| | - Veronica Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #02-01, Singapore 138669, Singapore
| | - Lay Kien Yang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #02-01, Singapore 138669, Singapore
| | - Deborah Chwee San Seow
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #02-01, Singapore 138669, Singapore
| | - Lokanand Koduru
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos #07-06, Singapore 138673, Singapore
| | - Yoganathan Kanagasundaram
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #02-01, Singapore 138669, Singapore
| | - Siew Bee Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #02-01, Singapore 138669, Singapore
| | - Guangrong Peh
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, Neuros #07-01, Singapore 138665, Singapore
| | - Yee Hwee Lim
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, Neuros #07-01, Singapore 138665, Singapore
| | - Fong Tian Wong
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos #07-06, Singapore 138673, Singapore
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 8 Biomedical Grove, Neuros #07-01, Singapore 138665, Singapore
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2
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Vasilev R, Gunitseva N, Shebanova R, Korzhenkov A, Vlaskina A, Evteeva M, Polushkina I, Nikitchina N, Toshchakov S, Kamenski P, Patrushev M, Mazunin I. Targeted Modification of Mammalian DNA by a Novel Type V Cas12a Endonuclease from Ruminococcus bromii. Int J Mol Sci 2022; 23:ijms23169289. [PMID: 36012553 PMCID: PMC9409102 DOI: 10.3390/ijms23169289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 11/25/2022] Open
Abstract
Type V Cas12a nucleases are DNA editors working in a wide temperature range and using expanded protospacer-adjacent motifs (PAMs). Though they are widely used, there is still a demand for discovering new ones. Here, we demonstrate a novel ortholog from Ruminococcus bromii sp. entitled RbCas12a, which is able to efficiently cleave target DNA templates, using the particularly high accessibility of PAM 5′-YYN and a relatively wide temperature range from 20 °C to 42 °C. In comparison to Acidaminococcus sp. (AsCas12a) nuclease, RbCas12a is capable of processing DNA more efficiently, and can be active upon being charged by spacer-only RNA at lower concentrations in vitro. We show that the human-optimized RbCas12a nuclease is also active in mammalian cells, and can be applied for efficient deletion incorporation into the human genome. Given the advantageous properties of RbCas12a, this enzyme shows potential for clinical and biotechnological applications within the field of genome editing.
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Affiliation(s)
- Ruslan Vasilev
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
- Correspondence: (R.V.); (I.M.)
| | - Natalia Gunitseva
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Regina Shebanova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
| | - Aleksei Korzhenkov
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Anna Vlaskina
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Marta Evteeva
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Irina Polushkina
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Natalia Nikitchina
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
- UMR7156–Molecular Genetics, Genomics, Microbiology, University of Strasbourg and Centre National de la Recherche Scientifique (CNRS), 67000 Strasbourg, France
| | - Stepan Toshchakov
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Piotr Kamenski
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Maxim Patrushev
- Kurchatov Genomics Center, National Research Center “Kurchatov Institute”, 123098 Moscow, Russia
| | - Ilya Mazunin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
- Medical Genomics LLC, 119192 Moscow, Russia
- Correspondence: (R.V.); (I.M.)
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3
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Li R, Klingbeil O, Monducci D, Young MJ, Rodriguez DJ, Bayyat Z, Dempster JM, Kesar D, Yang X, Zamanighomi M, Vakoc CR, Ito T, Sellers WR. Comparative optimization of combinatorial CRISPR screens. Nat Commun 2022; 13:2469. [PMID: 35513429 PMCID: PMC9072436 DOI: 10.1038/s41467-022-30196-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 04/21/2022] [Indexed: 12/14/2022] Open
Abstract
Combinatorial CRISPR technologies have emerged as a transformative approach to systematically probe genetic interactions and dependencies of redundant gene pairs. However, the performance of different functional genomic tools for multiplexing sgRNAs vary widely. Here, we generate and benchmark ten distinct pooled combinatorial CRISPR libraries targeting paralog pairs to optimize digenic knockout screens. Libraries composed of dual Streptococcus pyogenes Cas9 (spCas9), orthogonal spCas9 and Staphylococcus aureus (saCas9), and enhanced Cas12a from Acidaminococcus were evaluated. We demonstrate a combination of alternative tracrRNA sequences from spCas9 consistently show superior effect size and positional balance between the sgRNAs as a robust combinatorial approach to profile genetic interactions of multiple genes.
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Affiliation(s)
- Ruitong Li
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Olaf Klingbeil
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | | | | | - Zaid Bayyat
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Devishi Kesar
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Xiaoping Yang
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | | | - Takahiro Ito
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Scorpion Therapeutics, Boston, MA, USA.
| | - William R Sellers
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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4
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DeWeirdt PC, Sanson KR, Sangree AK, Hegde M, Hanna RE, Feeley MN, Griffith AL, Teng T, Borys SM, Strand C, Joung JK, Kleinstiver BP, Pan X, Huang A, Doench JG. Optimization of AsCas12a for combinatorial genetic screens in human cells. Nat Biotechnol 2021; 39:94-104. [PMID: 32661438 PMCID: PMC7854777 DOI: 10.1038/s41587-020-0600-6] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 06/09/2020] [Indexed: 02/07/2023]
Abstract
Cas12a RNA-guided endonucleases are promising tools for multiplexed genetic perturbations because they can process multiple guide RNAs expressed as a single transcript, and subsequently cleave target DNA. However, their widespread adoption has lagged behind Cas9-based strategies due to low activity and the lack of a well-validated pooled screening toolkit. In the present study, we describe the optimization of enhanced Cas12a from Acidaminococcus (enAsCas12a) for pooled, combinatorial genetic screens in human cells. By assaying the activity of thousands of guides, we refine on-target design rules and develop a comprehensive set of off-target rules to predict and exclude promiscuous guides. We also identify 38 direct repeat variants that can substitute for the wild-type sequence. We validate our optimized AsCas12a toolkit by screening for synthetic lethalities in OVCAR8 and A375 cancer cells, discovering an interaction between MARCH5 and WSB2. Finally, we show that enAsCas12a delivers similar performance to Cas9 in genome-wide dropout screens but at greatly reduced library size, which will facilitate screens in challenging models.
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Affiliation(s)
- Peter C DeWeirdt
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kendall R Sanson
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Annabel K Sangree
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mudra Hegde
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ruth E Hanna
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Marissa N Feeley
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Audrey L Griffith
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Teng Teng
- Tango Therapeutics, Cambridge, MA, USA
| | - Samantha M Borys
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christine Strand
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - J Keith Joung
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Benjamin P Kleinstiver
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - John G Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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5
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Murugan K, Seetharam AS, Severin AJ, Sashital DG. CRISPR-Cas12a has widespread off-target and dsDNA-nicking effects. J Biol Chem 2020; 295:5538-5553. [PMID: 32161115 PMCID: PMC7186167 DOI: 10.1074/jbc.ra120.012933] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/04/2020] [Indexed: 12/26/2022] Open
Abstract
Cas12a (Cpf1) is an RNA-guided endonuclease in the bacterial type V-A CRISPR-Cas anti-phage immune system that can be repurposed for genome editing. Cas12a can bind and cut dsDNA targets with high specificity in vivo, making it an ideal candidate for expanding the arsenal of enzymes used in precise genome editing. However, this reported high specificity contradicts Cas12a's natural role as an immune effector against rapidly evolving phages. Here, we employed high-throughput in vitro cleavage assays to determine and compare the native cleavage specificities and activities of three different natural Cas12a orthologs (FnCas12a, LbCas12a, and AsCas12a). Surprisingly, we observed pervasive sequence-specific nicking of randomized target libraries, with strong nicking of DNA sequences containing up to four mismatches in the Cas12a-targeted DNA-RNA hybrid sequences. We also found that these nicking and cleavage activities depend on mismatch type and position and vary with Cas12a ortholog and CRISPR RNA sequence. Our analysis further revealed robust nonspecific nicking of dsDNA when Cas12a is activated by binding to a target DNA. Together, our findings reveal that Cas12a has multiple nicking activities against dsDNA substrates and that these activities vary among different Cas12a orthologs.
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Affiliation(s)
- Karthik Murugan
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011; Molecular, Cellular, and Developmental Biology Interdepartmental Program, Iowa State University, Ames, Iowa 50011
| | - Arun S Seetharam
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, Iowa 50011
| | - Andrew J Severin
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, Iowa 50011
| | - Dipali G Sashital
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011; Molecular, Cellular, and Developmental Biology Interdepartmental Program, Iowa State University, Ames, Iowa 50011.
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6
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Dai Y, Somoza RA, Wang L, Welter JF, Li Y, Caplan AI, Liu CC. Exploring the Trans-Cleavage Activity of CRISPR-Cas12a (cpf1) for the Development of a Universal Electrochemical Biosensor. Angew Chem Int Ed Engl 2019; 58:17399-17405. [PMID: 31568601 PMCID: PMC6938695 DOI: 10.1002/anie.201910772] [Citation(s) in RCA: 302] [Impact Index Per Article: 60.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/23/2019] [Indexed: 12/18/2022]
Abstract
An accurate, rapid, and cost-effective biosensor for the quantification of disease biomarkers is vital for the development of early-diagnostic point-of-care systems. The recent discovery of the trans-cleavage property of CRISPR type V effectors makes CRISPR a potential high-accuracy bio-recognition tool. Herein, a CRISPR-Cas12a (cpf1) based electrochemical biosensor (E-CRISPR) is reported, which is more cost-effective and portable than optical-transduction-based biosensors. Through optimizing the in vitro trans-cleavage activity of Cas12a, E-CRIPSR was used to detect viral nucleic acids, including human papillomavirus 16 (HPV-16) and parvovirus B19 (PB-19), with a picomolar sensitivity. An aptamer-based E-CRISPR cascade was further designed for the detection of transforming growth factor β1 (TGF-β1) protein in clinical samples. As demonstrated, E-CRISPR could enable the development of portable, accurate, and cost-effective point-of-care diagnostic systems.
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Affiliation(s)
- Yifan Dai
- Department of Chemical and Biomolecular Engineering, Electronics Design Center, Case Western Reserve University; Cleveland, Ohio, 44106 (USA)
| | - Rodrigo A Somoza
- Department of Biology, Skeletal Research Center & Center for Multimodal Evaluation of Engineered Cartilage, Case Western Reserve University, Cleveland, Ohio, 44106 (USA)
| | - Liu Wang
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, 44106 (USA)
| | - Jean F Welter
- Department of Biology, Skeletal Research Center & Center for Multimodal Evaluation of Engineered Cartilage, Case Western Reserve University, Cleveland, Ohio, 44106 (USA)
| | - Yan Li
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, 44106 (USA)
| | - Arnold I Caplan
- Department of Biology, Skeletal Research Center & Center for Multimodal Evaluation of Engineered Cartilage, Case Western Reserve University, Cleveland, Ohio, 44106 (USA)
| | - Chung Chiun Liu
- Department of Chemical and Biomolecular Engineering, Electronics Design Center, Case Western Reserve University; Cleveland, Ohio, 44106 (USA)
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7
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Maule G, Casini A, Montagna C, Ramalho AS, De Boeck K, Debyser Z, Carlon MS, Petris G, Cereseto A. Allele specific repair of splicing mutations in cystic fibrosis through AsCas12a genome editing. Nat Commun 2019; 10:3556. [PMID: 31391465 PMCID: PMC6685978 DOI: 10.1038/s41467-019-11454-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 07/05/2019] [Indexed: 12/19/2022] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the CFTR gene. The 3272-26A>G and 3849+10kbC>T CFTR mutations alter the correct splicing of the CFTR gene, generating new acceptor and donor splice sites respectively. Here we develop a genome editing approach to permanently correct these genetic defects, using a single crRNA and the Acidaminococcus sp. BV3L6, AsCas12a. This genetic repair strategy is highly precise, showing very strong discrimination between the wild-type and mutant sequence and a complete absence of detectable off-targets. The efficacy of this gene correction strategy is verified in intestinal organoids and airway epithelial cells derived from CF patients carrying the 3272-26A>G or 3849+10kbC>T mutations, showing efficient repair and complete functional recovery of the CFTR channel. These results demonstrate that allele-specific genome editing with AsCas12a can correct aberrant CFTR splicing mutations, paving the way for a permanent splicing correction in genetic diseases.
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Affiliation(s)
- Giulia Maule
- Centre for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Antonio Casini
- Centre for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Claudia Montagna
- Centre for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Anabela S Ramalho
- Department of Development and Regeneration, CF Centre, Woman and Child, KU Leuven, Herestraat 49, Leuven, 3000, Belgium
| | - Kris De Boeck
- Department of Development and Regeneration, CF Centre, Woman and Child, KU Leuven, Herestraat 49, Leuven, 3000, Belgium
- Pediatric Pulmonology, Department of Pediatrics, University Hospital Leuven, Herestraat 49, Leuven, 3000, Belgium
| | - Zeger Debyser
- Laboratory for Molecular Virology and Drug Discovery, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, Leuven, 3000, Belgium
| | - Marianne S Carlon
- Laboratory for Molecular Virology and Drug Discovery, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49, Leuven, 3000, Belgium.
| | - Gianluca Petris
- Centre for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy.
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Anna Cereseto
- Centre for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Trento, Italy.
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8
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Wang W, Hou J, Zheng N, Wang X, Zhang J. Keeping our eyes on CRISPR: the "Atlas" of gene editing. Cell Biol Toxicol 2019; 35:285-288. [PMID: 31165372 DOI: 10.1007/s10565-019-09480-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 05/16/2019] [Indexed: 12/22/2022]
Affiliation(s)
- William Wang
- Zhongshan Hospital Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Center for Tumor Diagnosis and Therapy, Jinshan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiayuan Hou
- Zhongshan Hospital Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Center for Tumor Diagnosis and Therapy, Jinshan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Nannan Zheng
- Zhongshan Hospital Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Center for Tumor Diagnosis and Therapy, Jinshan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiangdong Wang
- Zhongshan Hospital Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Center for Tumor Diagnosis and Therapy, Jinshan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Jiaqiang Zhang
- Department of Anaesthesiology, Centre for Clinical Single Cell Biomedicine, Henan provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, China.
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9
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Abstract
The CRISPR effector protein Cas12a has been used for a wide variety of applications such as in vivo gene editing and regulation or in vitro DNA sensing. Here, we add programmability to Cas12a-based DNA processing by combining it with strand displacement-based reaction circuits. We first establish a viable strategy for augmenting Cas12a guide RNAs (gRNAs) at their 5' end and then use such 5' extensions to construct strand displacement gRNAs (SD gRNAs) that can be activated by single-stranded RNA trigger molecules. These SD gRNAs are further engineered to exhibit a digital and orthogonal response to different trigger RNA inputs-including full length mRNAs-and to function as multi-input logic gates. We also demonstrate that SD gRNAs can be designed to work inside bacterial cells. Using such in vivo SD gRNAs and a DNase inactive version of Cas12a (dCas12a), we demonstrate logic gated transcriptional control of gene expression in E. coli.
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Affiliation(s)
- Lukas Oesinghaus
- Physics Department E14, Technical University Munich, 85748, Garching, Germany
| | - Friedrich C Simmel
- Physics Department E14, Technical University Munich, 85748, Garching, Germany.
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10
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Strohkendl I, Saifuddin FA, Rybarski JR, Finkelstein IJ, Russell R. Kinetic Basis for DNA Target Specificity of CRISPR-Cas12a. Mol Cell 2018; 71:816-824.e3. [PMID: 30078724 PMCID: PMC6679935 DOI: 10.1016/j.molcel.2018.06.043] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 06/13/2018] [Accepted: 06/26/2018] [Indexed: 12/26/2022]
Abstract
Class 2 CRISPR-Cas nucleases are programmable genome editing tools with promising applications in human health and disease. However, DNA cleavage at off-target sites that resemble the target sequence is a pervasive problem that remains poorly understood mechanistically. Here, we use quantitative kinetics to dissect the reaction steps of DNA targeting by Acidaminococcus sp Cas12a (also known as Cpf1). We show that Cas12a binds DNA tightly in two kinetically separable steps. Protospacer-adjacent motif (PAM) recognition is followed by rate-limiting R-loop propagation, leading to inevitable DNA cleavage of both strands. Despite functionally irreversible binding, Cas12a discriminates strongly against mismatches along most of the DNA target sequence. This result implies substantial reversibility during R-loop formation-a late transition state-and defies common descriptions of a "seed" region. Our results provide a quantitative basis for the DNA cleavage patterns measured in vivo and observations of greater reported target specificity for Cas12a than for the Cas9 nuclease.
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Affiliation(s)
- Isabel Strohkendl
- Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Fatema A Saifuddin
- Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - James R Rybarski
- Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Rick Russell
- Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
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11
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Jeon Y, Choi YH, Jang Y, Yu J, Goo J, Lee G, Jeong YK, Lee SH, Kim IS, Kim JS, Jeong C, Lee S, Bae S. Direct observation of DNA target searching and cleavage by CRISPR-Cas12a. Nat Commun 2018; 9:2777. [PMID: 30018371 PMCID: PMC6050341 DOI: 10.1038/s41467-018-05245-x] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/20/2018] [Indexed: 12/24/2022] Open
Abstract
Cas12a (also called Cpf1) is a representative type V-A CRISPR effector RNA-guided DNA endonuclease, which provides an alternative to type II CRISPR-Cas9 for genome editing. Previous studies have revealed that Cas12a has unique features distinct from Cas9, but the detailed mechanisms of target searching and DNA cleavage by Cas12a are still unclear. Here, we directly observe this entire process by using single-molecule fluorescence assays to study Cas12a from Acidaminococcus sp. (AsCas12a). We determine that AsCas12a ribonucleoproteins search for their on-target site by a one-dimensional diffusion along elongated DNA molecules and induce cleavage in the two DNA strands in a well-defined order, beginning with the non-target strand. Furthermore, the protospacer-adjacent motif (PAM) for AsCas12a makes only a limited contribution of DNA unwinding during R-loop formation and shows a negligible role in the process of DNA cleavage, in contrast to the Cas9 PAM.
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Affiliation(s)
- Yongmoon Jeon
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul, 02792, South Korea
| | - You Hee Choi
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea
| | - Yunsu Jang
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea
| | - Jihyeon Yu
- Department of Chemistry, Hanyang University, Seoul, 04763, South Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Jiyoung Goo
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul, 02792, South Korea
- KHU-KIST Department of Converging Science and Technology, Kyunghee University, Seoul, 02447, South Korea
| | - Gyejun Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul, 02792, South Korea
- KHU-KIST Department of Converging Science and Technology, Kyunghee University, Seoul, 02447, South Korea
| | - You Kyeong Jeong
- Department of Chemistry, Hanyang University, Seoul, 04763, South Korea
| | - Seung Hwan Lee
- Center for Genome Engineering, Institute for Basic Science, Seoul, 08826, South Korea
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Chungcheongbuk-do, 28116, South Korea
| | - In-San Kim
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul, 02792, South Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, South Korea
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science, Seoul, 08826, South Korea
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
| | - Cherlhyun Jeong
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul, 02792, South Korea.
- KHU-KIST Department of Converging Science and Technology, Kyunghee University, Seoul, 02447, South Korea.
| | - Sanghwa Lee
- Advanced Photonics Research Institute, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea.
- Cell Logistics Research Center, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea.
| | - Sangsu Bae
- Department of Chemistry, Hanyang University, Seoul, 04763, South Korea.
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, South Korea.
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12
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Yamano T, Zetsche B, Ishitani R, Zhang F, Nishimasu H, Nureki O. Structural Basis for the Canonical and Non-canonical PAM Recognition by CRISPR-Cpf1. Mol Cell 2017; 67:633-645.e3. [PMID: 28781234 PMCID: PMC5957536 DOI: 10.1016/j.molcel.2017.06.035] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 06/07/2017] [Accepted: 06/30/2017] [Indexed: 12/26/2022]
Abstract
The RNA-guided Cpf1 (also known as Cas12a) nuclease associates with a CRISPR RNA (crRNA) and cleaves the double-stranded DNA target complementary to the crRNA guide. The two Cpf1 orthologs from Acidaminococcus sp. (AsCpf1) and Lachnospiraceae bacterium (LbCpf1) have been harnessed for eukaryotic genome editing. Cpf1 requires a specific nucleotide sequence, called a protospacer adjacent motif (PAM), for target recognition. Besides the canonical TTTV PAM, Cpf1 recognizes suboptimal C-containing PAMs. Here, we report four crystal structures of LbCpf1 in complex with the crRNA and its target DNA containing either TTTA, TCTA, TCCA, or CCCA as the PAM. These structures revealed that, depending on the PAM sequences, LbCpf1 undergoes conformational changes to form altered interactions with the PAM-containing DNA duplexes, thereby achieving the relaxed PAM recognition. Collectively, the present structures advance our mechanistic understanding of the PAM-dependent, crRNA-guided DNA cleavage by the Cpf1 family nucleases.
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Affiliation(s)
- Takashi Yamano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Bernd Zetsche
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hiroshi Nishimasu
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
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13
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Gao L, Cox DBT, Yan WX, Manteiga JC, Schneider MW, Yamano T, Nishimasu H, Nureki O, Crosetto N, Zhang F. Engineered Cpf1 variants with altered PAM specificities. Nat Biotechnol 2017. [PMID: 28581492 DOI: 10.1038/nbt.3900.engineered] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
The RNA-guided endonuclease Cpf1 is a promising tool for genome editing in eukaryotic cells. However, the utility of the commonly used Acidaminococcus sp. BV3L6 Cpf1 (AsCpf1) and Lachnospiraceae bacterium ND2006 Cpf1 (LbCpf1) is limited by their requirement of a TTTV protospacer adjacent motif (PAM) in the DNA substrate. To address this limitation, we performed a structure-guided mutagenesis screen to increase the targeting range of Cpf1. We engineered two AsCpf1 variants carrying the mutations S542R/K607R and S542R/K548V/N552R, which recognize TYCV and TATV PAMs, respectively, with enhanced activities in vitro and in human cells. Genome-wide assessment of off-target activity using BLISS indicated that these variants retain high DNA-targeting specificity, which we further improved by introducing an additional non-PAM-interacting mutation. Introducing the identified PAM-interacting mutations at their corresponding positions in LbCpf1 similarly altered its PAM specificity. Together, these variants increase the targeting range of Cpf1 by approximately threefold in human coding sequences to one cleavage site per ∼11 bp.
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Affiliation(s)
- Linyi Gao
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology Cambridge, Massachusetts, USA
| | - David B T Cox
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, Massachusetts, USA
| | - Winston X Yan
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, Massachusetts, USA
- Graduate Program in Biophysics, Harvard Medical School, Boston, Massachusetts, USA
| | - John C Manteiga
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Takashi Yamano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Nishimasu
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- JST, PRESTO, Tokyo, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Nicola Crosetto
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology Cambridge, Massachusetts, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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14
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Nishimasu H, Yamano T, Gao L, Zhang F, Ishitani R, Nureki O. Structural Basis for the Altered PAM Recognition by Engineered CRISPR-Cpf1. Mol Cell 2017; 67:139-147.e2. [PMID: 28595896 PMCID: PMC5957533 DOI: 10.1016/j.molcel.2017.04.019] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 04/13/2017] [Accepted: 04/25/2017] [Indexed: 12/27/2022]
Abstract
The RNA-guided Cpf1 nuclease cleaves double-stranded DNA targets complementary to the CRISPR RNA (crRNA), and it has been harnessed for genome editing technologies. Recently, Acidaminococcus sp. BV3L6 (AsCpf1) was engineered to recognize altered DNA sequences as the protospacer adjacent motif (PAM), thereby expanding the target range of Cpf1-mediated genome editing. Whereas wild-type AsCpf1 recognizes the TTTV PAM, the RVR (S542R/K548V/N552R) and RR (S542R/K607R) variants can efficiently recognize the TATV and TYCV PAMs, respectively. However, their PAM recognition mechanisms remained unknown. Here we present the 2.0 Å resolution crystal structures of the RVR and RR variants bound to a crRNA and its target DNA. The structures revealed that the RVR and RR variants primarily recognize the PAM-complementary nucleotides via the substituted residues. Our high-resolution structures delineated the altered PAM recognition mechanisms of the AsCpf1 variants, providing a basis for the further engineering of CRISPR-Cpf1.
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Affiliation(s)
- Hiroshi Nishimasu
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; JST, PRESTO, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
| | - Takashi Yamano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Linyi Gao
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
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15
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Tang X, Lowder LG, Zhang T, Malzahn AA, Zheng X, Voytas DF, Zhong Z, Chen Y, Ren Q, Li Q, Kirkland ER, Zhang Y, Qi Y. A CRISPR-Cpf1 system for efficient genome editing and transcriptional repression in plants. Nat Plants 2017; 3:17018. [PMID: 28211909 DOI: 10.1038/nplants.2017.18] [Citation(s) in RCA: 267] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/27/2017] [Indexed: 05/20/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cpf1 has emerged as an effective genome editing tool in animals. Here we compare the activity of Cpf1 from Acidaminococcus sp. BV3L6 (As) and Lachnospiraceae bacterium ND2006 (Lb) in plants, using a dual RNA polymerase II promoter expression system. LbCpf1 generated biallelic mutations at nearly 100% efficiency at four independent sites in rice T0 transgenic plants. Moreover, we repurposed AsCpf1 and LbCpf1 for efficient transcriptional repression in Arabidopsis, and demonstrated a more than tenfold reduction in miR159b transcription. Our data suggest promising applications of CRISPR-Cpf1 for editing plant genomes and modulating the plant transcriptome.
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Affiliation(s)
- Xu Tang
- Department of Biotechnology, School of Life Science and Technology, Centre for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Levi G Lowder
- Department of Biology, East Carolina University, Greenville, North Carolina 27834, USA
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Centre for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Aimee A Malzahn
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742, USA
| | - Xuelian Zheng
- Department of Biotechnology, School of Life Science and Technology, Centre for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Daniel F Voytas
- Department of Genetics, Cell Biology &Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Zhaohui Zhong
- Department of Biotechnology, School of Life Science and Technology, Centre for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yiyi Chen
- Department of Biotechnology, School of Life Science and Technology, Centre for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Qiurong Ren
- Department of Biotechnology, School of Life Science and Technology, Centre for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Qian Li
- Department of Biotechnology, School of Life Science and Technology, Centre for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Elida R Kirkland
- Department of Biology, East Carolina University, Greenville, North Carolina 27834, USA
| | - Yong Zhang
- Department of Biotechnology, School of Life Science and Technology, Centre for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850, USA
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16
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Watkins-Chow DE, Varshney GK, Garrett LJ, Chen Z, Jimenez EA, Rivas C, Bishop KS, Sood R, Harper UL, Pavan WJ, Burgess SM. Highly Efficient Cpf1-Mediated Gene Targeting in Mice Following High Concentration Pronuclear Injection. G3 (Bethesda) 2017; 7:719-722. [PMID: 28040780 PMCID: PMC5295614 DOI: 10.1534/g3.116.038091] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 12/20/2016] [Indexed: 01/12/2023]
Abstract
Cpf1 has emerged as an alternative to the Cas9 RNA-guided nuclease. Here we show that gene targeting rates in mice using Cpf1 can meet, or even surpass, Cas9 targeting rates (approaching 100% targeting), but require higher concentrations of mRNA and guide. We also demonstrate that coinjecting two guides with close targeting sites can result in synergistic genomic cutting, even if one of the guides has minimal cutting activity.
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Affiliation(s)
- Dawn E Watkins-Chow
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Gaurav K Varshney
- Functional and Chemical Genomics Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104
| | - Lisa J Garrett
- Embryonic Stem Cell and Transgenic Mouse Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Zelin Chen
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Erin A Jimenez
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Cecilia Rivas
- Embryonic Stem Cell and Transgenic Mouse Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Kevin S Bishop
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Raman Sood
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Ursula L Harper
- Genomics Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Shawn M Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
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17
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Kim HK, Song M, Lee J, Menon AV, Jung S, Kang YM, Choi JW, Woo E, Koh HC, Nam JW, Kim H. In vivo high-throughput profiling of CRISPR-Cpf1 activity. Nat Methods 2017; 14:153-159. [PMID: 27992409 DOI: 10.1038/nmeth.4104] [Citation(s) in RCA: 229] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 11/09/2016] [Indexed: 12/26/2022]
Abstract
CRISPR from Prevotella and Francisella 1 (Cpf1) is an effector endonuclease of the class 2 CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) gene editing system. We developed a method for evaluating Cpf1 activity, based on target sequence composition in mammalian cells, in a high-throughput manner. A library of >11,000 target sequence and guide RNA pairs was delivered into human cells using lentiviral vectors. Subsequent delivery of Cpf1 into this cell library induced insertions and deletions (indels) at the integrated synthetic target sequences, which allowed en masse evaluation of Cpf1 activity by using deep sequencing. With this approach, we determined protospacer-adjacent motif sequences of two Cpf1 nucleases, one from Acidaminococcus sp. BV3L6 (hereafter referred to as AsCpf1) and the other from Lachnospiraceae bacterium ND2006 (hereafter referred to as LbCpf1). We also defined target-sequence-dependent activity profiles of AsCpf1, which enabled the development of a web tool that predicts the indel frequencies for given target sequences (http://big.hanyang.ac.kr/cindel). Both the Cpf1 characterization profile and the in vivo high-throughput evaluation method will greatly facilitate Cpf1-based genome editing.
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Affiliation(s)
- Hui K Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, South Korea
- Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, South Korea
| | - Myungjae Song
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, South Korea
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea
| | - Jinu Lee
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, South Korea
| | - A Vipin Menon
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, South Korea
| | - Soobin Jung
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, South Korea
- Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, South Korea
| | - Young-Mook Kang
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, South Korea
| | - Jae W Choi
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, South Korea
| | - Euijeon Woo
- Drug Target Structure Research Center, Korea Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Hyun C Koh
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea
- Department of Pharmacology, College of Medicine, Hanyang University, Seoul, South Korea
| | - Jin-Wu Nam
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, South Korea
| | - Hyongbum Kim
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, South Korea
- Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul, South Korea
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, South Korea
- Graduate Program of Nano Science and Technology, Yonsei University, Seoul, South Korea
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18
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D'Auria G, Galán JC, Rodríguez-Alcayna M, Moya A, Baquero F, Latorre A. Complete genome sequence of Acidaminococcus intestini RYC-MR95, a Gram-negative bacterium from the phylum Firmicutes. J Bacteriol 2011; 193:7008-9. [PMID: 22123762 PMCID: PMC3232847 DOI: 10.1128/jb.06301-11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Acidaminococcus intestini belongs to the family Acidaminococcaceae, order Selenomonadales, class Negativicutes, phylum Firmicutes. Negativicutes show the double-membrane system of Gram-negative bacteria, although their chromosomal backbone is closely related to that of Gram-positive bacteria of the phylum Firmicutes. The complete genome of a clinical A. intestini strain is here presented.
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Affiliation(s)
- Giuseppe D'Auria
- Joint Unit of Research in Genomics and Health, Centre for Public Health Research-Cavanilles Institute for Biodiversity and Evolutionary Biology (University of Valencia), Valencia, Spain.
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