1
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Liang Z, Huang C, Xia Y, Ye Z, Fan S, Zeng J, Guo S, Ma X, Sun L, Huo YX. Identification of functional sgRNA mutants lacking canonical secondary structure using high-throughput FACS screening. Cell Rep 2024; 43:114290. [PMID: 38823012 DOI: 10.1016/j.celrep.2024.114290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/22/2024] [Accepted: 05/13/2024] [Indexed: 06/03/2024] Open
Abstract
Coexpressing multiple identical single guide RNAs (sgRNAs) in CRISPR-dependent engineering triggers genetic instability and phenotype loss. To provide sgRNA derivatives for efficient DNA digestion, we design a high-throughput digestion-activity-dependent positive screening strategy and astonishingly obtain functional nonrepetitive sgRNA mutants with up to 48 out of the 61 nucleotides mutated, and these nonrepetitive mutants completely lose canonical secondary sgRNA structure in simulation. Cas9-sgRNA complexes containing these noncanonical sgRNAs maintain wild-type level of digestion activities in vivo, indicating that the Cas9 protein is compatible with or is able to adjust the secondary structure of sgRNAs. Using these noncanonical sgRNAs, we achieve multiplex genetic engineering for gene knockout and base editing in microbial cell factories. Libraries of strains with rewired metabolism are constructed, and overproducers of isobutanol or 1,3-propanediol are identified by biosensor-based fluorescence-activated cell sorting (FACS). This work sheds light on the remarkable flexibility of the secondary structure of functional sgRNA.
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Affiliation(s)
- Zeyu Liang
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Chaoyong Huang
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Yan Xia
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Zhaojin Ye
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Shunhua Fan
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Junwei Zeng
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Shuyuan Guo
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Xiaoyan Ma
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; Beijing Institute of Technology (Tangshan) Translational Research Center, Hebei 063611, China
| | - Lichao Sun
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; Beijing Institute of Technology (Tangshan) Translational Research Center, Hebei 063611, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; Beijing Institute of Technology (Tangshan) Translational Research Center, Hebei 063611, China.
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2
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Fan T, Cheng Y, Wu Y, Liu S, Tang X, He Y, Liao S, Zheng X, Zhang T, Qi Y, Zhang Y. High performance TadA-8e derived cytosine and dual base editors with undetectable off-target effects in plants. Nat Commun 2024; 15:5103. [PMID: 38877035 PMCID: PMC11178825 DOI: 10.1038/s41467-024-49473-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 06/06/2024] [Indexed: 06/16/2024] Open
Abstract
Cytosine base editors (CBEs) and adenine base editors (ABEs) enable precise C-to-T and A-to-G edits. Recently, ABE8e, derived from TadA-8e, enhances A-to-G edits in mammalian cells and plants. Interestingly, TadA-8e can also be evolved to confer C-to-T editing. This study compares engineered CBEs derived from TadA-8e in rice and tomato cells, identifying TadCBEa, TadCBEd, and TadCBEd_V106W as efficient CBEs with high purity and a narrow editing window. A dual base editor, TadDE, promotes simultaneous C-to-T and A-to-G editing. Multiplexed base editing with TadCBEa and TadDE is demonstrated in transgenic rice, with no off-target effects detected by whole genome and transcriptome sequencing, indicating high specificity. Finally, two crop engineering applications using TadDE are shown: introducing herbicide resistance alleles in OsALS and creating synonymous mutations in OsSPL14 to resist OsMIR156-mediated degradation. Together, this study presents TadA-8e derived CBEs and a dual base editor as valuable additions to the plant editing toolbox.
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Affiliation(s)
- Tingting Fan
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Yanhao Cheng
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, ML, 20742, USA
| | - Yuechao Wu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China
| | - Shishi Liu
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Xu Tang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Yao He
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Shanyue Liao
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Xuelian Zheng
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China.
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, ML, 20742, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, ML, 20850, USA.
| | - Yong Zhang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, 400715, China.
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3
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Cowan QT, Gu S, Gu W, Ranzau BL, Simonson TS, Komor AC. Development of multiplexed orthogonal base editor (MOBE) systems. Nat Biotechnol 2024:10.1038/s41587-024-02240-0. [PMID: 38773305 DOI: 10.1038/s41587-024-02240-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 04/10/2024] [Indexed: 05/23/2024]
Abstract
Base editors (BEs) enable efficient, programmable installation of point mutations while avoiding the use of double-strand breaks. Simultaneous application of two or more different BEs, such as an adenine BE (which converts A·T base pairs to G·C) and a cytosine BE (which converts C·G base pairs to T·A), is not feasible because guide RNA crosstalk results in non-orthogonal editing, with all BEs modifying all target loci. Here we engineer both adenine BEs and cytosine BEs that can be orthogonally multiplexed by using RNA aptamer-coat protein systems to recruit the DNA-modifying enzymes directly to the guide RNAs. We generate four multiplexed orthogonal BE systems that enable rates of precise co-occurring edits of up to 7.1% in the same DNA strand without enrichment or selection strategies. The addition of a fluorescent enrichment strategy increases co-occurring edit rates up to 24.8% in human cells. These systems are compatible with expanded protospacer adjacent motif and high-fidelity Cas9 variants, function well in multiple cell types, have equivalent or reduced off-target propensities compared with their parental systems and can model disease-relevant point mutation combinations.
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Affiliation(s)
- Quinn T Cowan
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Sifeng Gu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Wanjun Gu
- Department of Medicine, Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, University of California San Diego, La Jolla, CA, USA
| | - Brodie L Ranzau
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Tatum S Simonson
- Department of Medicine, Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, University of California San Diego, La Jolla, CA, USA
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.
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4
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Patange S, Maragh S. Fire Burn and Cauldron Bubble: What Is in Your Genome Editing Brew? Biochemistry 2023; 62:3500-3511. [PMID: 36306429 PMCID: PMC10734218 DOI: 10.1021/acs.biochem.2c00431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/28/2022] [Indexed: 11/28/2022]
Abstract
Genome editing is a rapidly evolving biotechnology with the potential to transform many sectors of industry such as agriculture, biomanufacturing, and medicine. This technology is enabled by an ever-growing portfolio of biomolecular reagents that span the central dogma, from DNA to RNA to protein. In this paper, we draw from our unique perspective as the National Metrology Institute of the United States to bring attention to the importance of understanding and reporting genome editing formulations accurately and promoting concepts to verify successful delivery into cells. Achieving the correct understanding may be hindered by the way units, quantities, and stoichiometries are reported in the field. We highlight the variability in how editing formulations are reported in the literature and examine how a reference molecule could be used to verify the delivery of a reagent into cells. We provide recommendations on how more accurate reporting of editing formulations and more careful verification of the steps in an editing experiment can help set baseline expectations of reagent performance, toward the aim of enabling genome editing studies to be more reproducible. We conclude with a future outlook on technologies that can further our control and enable our understanding of genome editing outcomes at the single-cell level.
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Affiliation(s)
- Simona Patange
- Biosystems and Biomaterials
Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Samantha Maragh
- Biosystems and Biomaterials
Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
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5
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Zhang A, Shan T, Sun Y, Chen Z, Hu J, Hu Z, Ming Z, Zhu Z, Li X, He J, Liu S, Jiang L, Dong X, Wu Y, Wang Y, Liu Y, Li C, Wan J. Directed evolution rice genes with randomly multiplexed sgRNAs assembly of base editors. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2597-2610. [PMID: 37571976 PMCID: PMC10651138 DOI: 10.1111/pbi.14156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 07/21/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023]
Abstract
CRISPR-based directed evolution is an effective breeding biotechnology to improve agronomic traits in plants. However, its gene diversification is still limited using individual single guide RNA. We described here a multiplexed orthogonal base editor (MoBE), and a randomly multiplexed sgRNAs assembly strategy to maximize gene diversification. MoBE could induce efficiently orthogonal ABE (<36.6%), CBE (<36.0%), and A&CBE (<37.6%) on different targets, while the sgRNA assembling strategy randomized base editing events on various targets. With respective 130 and 84 targets from each strand of the 34th exon of rice acetyl-coenzyme A carboxylase (OsACC), we observed the target-scaffold combination types up to 27 294 in randomly dual and randomly triple sgRNA libraries. We further performed directed evolution of OsACC using MoBE and randomly dual sgRNA libraries in rice, and obtained single or linked mutations of stronger herbicide resistance. These strategies are useful for in situ directed evolution of functional genes and may accelerate trait improvement in rice.
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Affiliation(s)
- Ao Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjingChina
| | - Tiaofeng Shan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjingChina
| | - Yan Sun
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjingChina
| | - Zhipeng Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary StudiesNanjing Agricultural UniversityNanjingChina
| | - Jianjian Hu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjingChina
| | - Zhichao Hu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjingChina
| | - Ziheng Ming
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjingChina
| | - Zhitao Zhu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary StudiesNanjing Agricultural UniversityNanjingChina
| | - Xue Li
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary StudiesNanjing Agricultural UniversityNanjingChina
| | - Jun He
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjingChina
| | - Shijia Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjingChina
| | - Ling Jiang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjingChina
| | - Xiaoou Dong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjingChina
- Hainan Yazhou Bay Seed LaboratorySanyaChina
| | - Yufeng Wu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary StudiesNanjing Agricultural UniversityNanjingChina
| | - Yanpeng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome EditingInstitute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of SciencesBeijingChina
| | - Yuqiang Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjingChina
- Hainan Yazhou Bay Seed LaboratorySanyaChina
| | - Chao Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjingChina
- Hainan Yazhou Bay Seed LaboratorySanyaChina
| | - Jianmin Wan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Engineering Research Center for Plant Genome Editing, National Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjingChina
- Hainan Yazhou Bay Seed LaboratorySanyaChina
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop Science, Chinese Academy of Agricultural SciencesBeijingChina
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6
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Cazier A, Irvin OM, Chávez LS, Dalvi S, Abraham H, Wickramanayake N, Yellayi S, Blazeck J. A Rapid Antibody Enhancement Platform in Saccharomyces cerevisiae Using an Improved, Diversifying CRISPR Base Editor. ACS Synth Biol 2023; 12:3287-3300. [PMID: 37873982 PMCID: PMC10661033 DOI: 10.1021/acssynbio.3c00299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/02/2023] [Accepted: 10/03/2023] [Indexed: 10/25/2023]
Abstract
The yeast Saccharomyces cerevisiae is commonly used to interrogate and screen protein variants and to perform directed evolution studies to develop proteins with enhanced features. While several techniques have been described that help enable the use of yeast for directed evolution, there remains a need to increase their speed and ease of use. Here we present yDBE, a yeast diversifying base editor that functions in vivo and employs a CRISPR-dCas9-directed cytidine deaminase base editor to diversify DNA in a targeted, rapid, and high-breadth manner. To develop yDBE, we enhanced the mutation rate of an initial base editor by employing improved deaminase variants and characterizing several scaffolded guide constructs. We then demonstrate the ability of the yDBE platform to improve the affinity of a displayed antibody scFv, rapidly generating diversified libraries and isolating improved binders via cell sorting. By performing high-throughput sequencing analysis of the high-activity yDBE, we show that it enables a mutation rate of 2.13 × 10-4 substitutions/bp/generation over a window of 100 bp. As yDBE functions entirely in vivo and can be easily programmed to diversify nearly any such window of DNA, we posit that it can be a powerful tool for facilitating a variety of directed evolution experiments.
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Affiliation(s)
- Andrew
P. Cazier
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Olivia M. Irvin
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Lizmarie S. Chávez
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Saachi Dalvi
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Hannah Abraham
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Nevinka Wickramanayake
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Sreenivas Yellayi
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - John Blazeck
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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7
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Li K, Qin LY, Zhang ZX, Yan CX, Gu Y, Sun XM, Huang H. Powerful Microbial Base-Editing Toolbox: From Optimization Strategies to Versatile Applications. ACS Synth Biol 2023; 12:1586-1598. [PMID: 37224027 DOI: 10.1021/acssynbio.3c00141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Base editors (BE) based on CRISPR systems are practical gene-editing tools which continue to drive frontier advances of life sciences. BEs are able to efficiently induce point mutations at target sites without double-stranded DNA cleavage. Hence, they are widely employed in the fields of microbial genome engineering. As applications of BEs continue to expand, the demands for base-editing efficiency, fidelity, and versatility are also on the rise. In recent years, a series of optimization strategies for BEs have been developed. By engineering the core components of BEs or adopting different assembly methods, the performance of BEs has been well optimized. Moreover, series of newly established BEs have significantly expanded the base-editing toolsets. In this Review, we will summarize the current efforts for BE optimization, introduce several novel BEs with versatility, and look forward to the broadened applications for industrial microorganisms.
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Affiliation(s)
- Ke Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210046, People's Republic of China
| | - Ling-Yun Qin
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210046, People's Republic of China
| | - Zi-Xu Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210046, People's Republic of China
| | - Chun-Xiao Yan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210046, People's Republic of China
| | - Yang Gu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210046, People's Republic of China
| | - Xiao-Man Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210046, People's Republic of China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210046, People's Republic of China
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8
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Liang Y, Chen F, Wang K, Lai L. Base editors: development and applications in biomedicine. Front Med 2023; 17:359-387. [PMID: 37434066 DOI: 10.1007/s11684-023-1013-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/19/2023] [Indexed: 07/13/2023]
Abstract
Base editor (BE) is a gene-editing tool developed by combining the CRISPR/Cas system with an individual deaminase, enabling precise single-base substitution in DNA or RNA without generating a DNA double-strand break (DSB) or requiring donor DNA templates in living cells. Base editors offer more precise and secure genome-editing effects than other conventional artificial nuclease systems, such as CRISPR/Cas9, as the DSB induced by Cas9 will cause severe damage to the genome. Thus, base editors have important applications in the field of biomedicine, including gene function investigation, directed protein evolution, genetic lineage tracing, disease modeling, and gene therapy. Since the development of the two main base editors, cytosine base editors (CBEs) and adenine base editors (ABEs), scientists have developed more than 100 optimized base editors with improved editing efficiency, precision, specificity, targeting scope, and capacity to be delivered in vivo, greatly enhancing their application potential in biomedicine. Here, we review the recent development of base editors, summarize their applications in the biomedical field, and discuss future perspectives and challenges for therapeutic applications.
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Affiliation(s)
- Yanhui Liang
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China
| | - Fangbing Chen
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, Wuyi University, Jiangmen, 529020, China
| | - Kepin Wang
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, Wuyi University, Jiangmen, 529020, China
| | - Liangxue Lai
- China-New Zealand Joint Laboratory on Biomedicine and Health, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, 510530, China.
- Sanya Institute of Swine Resource, Hainan Provincial Research Centre of Laboratory Animals, Sanya, 572000, China.
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, Wuyi University, Jiangmen, 529020, China.
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9
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Zhou L, Yao S. Recent advances in therapeutic CRISPR-Cas9 genome editing: mechanisms and applications. MOLECULAR BIOMEDICINE 2023; 4:10. [PMID: 37027099 PMCID: PMC10080534 DOI: 10.1186/s43556-023-00115-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 01/04/2023] [Indexed: 04/08/2023] Open
Abstract
Recently, clustered regularly interspaced palindromic repeats (CRISPR)-Cas9 derived editing tools had significantly improved our ability to make desired changes in the genome. Wild-type Cas9 protein recognizes the target genomic loci and induced local double strand breaks (DSBs) in the guidance of small RNA molecule. In mammalian cells, the DSBs are mainly repaired by endogenous non-homologous end joining (NHEJ) pathway, which is error prone and results in the formation of indels. The indels can be harnessed to interrupt gene coding sequences or regulation elements. The DSBs can also be fixed by homology directed repair (HDR) pathway to introduce desired changes, such as base substitution and fragment insertion, when proper donor templates are provided, albeit in a less efficient manner. Besides making DSBs, Cas9 protein can be mutated to serve as a DNA binding platform to recruit functional modulators to the target loci, performing local transcriptional regulation, epigenetic remolding, base editing or prime editing. These Cas9 derived editing tools, especially base editors and prime editors, can introduce precise changes into the target loci at a single-base resolution and in an efficient and irreversible manner. Such features make these editing tools very promising for therapeutic applications. This review focuses on the evolution and mechanisms of CRISPR-Cas9 derived editing tools and their applications in the field of gene therapy.
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Affiliation(s)
- Lifang Zhou
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Shaohua Yao
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China.
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10
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Liu N, Zhou L, Lin G, Hu Y, Jiao Y, Wang Y, Liu J, Yang S, Yao S. HDAC inhibitors improve CRISPR-Cas9 mediated prime editing and base editing. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 29:36-46. [PMID: 35784015 PMCID: PMC9207553 DOI: 10.1016/j.omtn.2022.05.036] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 05/27/2022] [Indexed: 01/19/2023]
Abstract
Recent advances in CRISPR-Cas9 techniques, especially the discovery of base and prime editing, have significantly improved our ability to make precise changes in the genome. We hypothesized that modulating certain endogenous pathway cells could improve the action of those editing tools in mammalian cells. We established a reporter system in which a small fragment was integrated into the genome by prime editing (PE). With this system, we screened an in-house small-molecule library and identified a group of histone deacetylase inhibitors (HDACi) increasing prime editing. We also found that HDACi increased the efficiency of both cytosine base editing (CBE) and adenine base editing (ABE). Moreover, HDACi increased the purity of cytosine base editor products, which was accompanied by an upregulation of the acetylation of uracil DNA glycosylase (UNG) and UNG inhibitor (UGI) and an enhancement of their interaction. In summary, our work demonstrated that HDACi improves Cas9-mediated prime editing and base editing.
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Affiliation(s)
- Nan Liu
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu 610041, Sichuan, China
| | - Lifang Zhou
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu 610041, Sichuan, China
| | - Guifeng Lin
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu 610041, Sichuan, China
| | - Yun Hu
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu 610041, Sichuan, China
| | - Yaoge Jiao
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu 610041, Sichuan, China
| | - Yanhong Wang
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu 610041, Sichuan, China
| | - Jingming Liu
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu 610041, Sichuan, China
| | - Shengyong Yang
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu 610041, Sichuan, China
| | - Shaohua Yao
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu 610041, Sichuan, China
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11
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Liu B, Dong X, Cheng H, Zheng C, Chen Z, Rodríguez TC, Liang SQ, Xue W, Sontheimer EJ. A split prime editor with untethered reverse transcriptase and circular RNA template. Nat Biotechnol 2022; 40:1388-1393. [PMID: 35379962 DOI: 10.1038/s41587-022-01255-9] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 02/08/2022] [Indexed: 12/19/2022]
Abstract
Delivery and optimization of prime editors (PEs) have been hampered by their large size and complexity. Although split versions of genome-editing tools can reduce construct size, they require special engineering to tether the binding and catalytic domains. Here we report a split PE (sPE) in which the Cas9 nickase (nCas9) remains untethered from the reverse transcriptase (RT). The sPE showed similar efficiencies in installing precise edits as the parental unsplit PE3 and no increase in insertion-deletion (indel) byproducts. Delivery of sPE to the mouse liver with hydrodynamic injection to modify β-catenin drove tumor formation with similar efficiency as PE3. Delivery with two adeno-associated virus (AAV) vectors corrected the disease-causing mutation in a mouse model of type I tyrosinemia. Similarly, prime editing guide RNAs (pegRNAs) can be split into a single guide RNA (sgRNA) and a circular RNA RT template to increase flexibility and stability. Compared to previous sPEs, ours lacks inteins, protein-protein affinity modules and nuclease-sensitive pegRNA extensions, which increase construct complexity and might reduce efficiency. Our modular system will facilitate the delivery and optimization of PEs.
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Affiliation(s)
- Bin Liu
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Xiaolong Dong
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Haoyang Cheng
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Chunwei Zheng
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Zexiang Chen
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Tomás C Rodríguez
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Shun-Qing Liang
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Wen Xue
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Department of Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA.
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Department of Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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12
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Zhou J, Liu Y, Wei Y, Zheng S, Gou S, Chen T, Yang Y, Lan T, Chen M, Liao Y, Zhang Q, Tang C, Liu Y, Wu Y, Peng X, Gao M, Wang J, Zhang K, Lai L, Zou Q. Eliminating predictable DNA off-target effects of cytosine base editor by using dual guiders including sgRNA and TALE. Mol Ther 2022; 30:2443-2451. [PMID: 35443934 PMCID: PMC9263286 DOI: 10.1016/j.ymthe.2022.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 04/07/2022] [Accepted: 04/16/2022] [Indexed: 11/30/2022] Open
Abstract
Predictable DNA off-target effect is one of the major safety concerns for the application of cytosine base editors (CBEs). To eliminate Cas9-dependent DNA off-target effects, we designed a novel effective CBE system with dual guiders by combining CRISPR with transcription activator-like effector (TALE). In this system, Cas9 nickase (nCas9) and cytosine deaminase are guided to the same target site to conduct base editing by single-guide RNA (sgRNA) and TALE, respectively. However, if nCas9 is guided to a wrong site by sgRNA, it will not generate base editing due to the absence of deaminase. Similarly, when deaminase is guided to a wrong site by TALE, base editing will not occur due to the absence of single-stranded DNA. In this way, Cas9- and TALE-dependent DNA off-target effects could be completely eliminated. Furthermore, by fusing TALE with YE1, a cytidine deaminase with minimal Cas9-independent off-target effect, we established a novel CBE that could induce efficient C-to-T conversion without detectable Cas9- or TALE-dependent DNA off-target mutations.
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Affiliation(s)
- Jizeng Zhou
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China; School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China
| | - Yang Liu
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yuhui Wei
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Shuwen Zheng
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Shixue Gou
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Tao Chen
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Yang Yang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China
| | - Ting Lan
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Min Chen
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Yuan Liao
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Quanjun Zhang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China; Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, China
| | - Chengcheng Tang
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Yu Liu
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Yunqin Wu
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Xiaohua Peng
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Minghui Gao
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Junwei Wang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Kun Zhang
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China; School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China.
| | - Liangxue Lai
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China; CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China; Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences (2019RU015), Guangzhou, China.
| | - Qingjian Zou
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China.
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13
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Xiong X, Li Z, Liang J, Liu K, Li C, Li JF. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3565-3580. [PMID: 35286371 PMCID: PMC8989527 DOI: 10.1093/nar/gkac166] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/20/2022] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
CRISPR/Cas-derived base editing tools empower efficient alteration of genomic cytosines or adenines associated with essential genetic traits in plants and animals. Diversified target sequences and customized editing products call for base editors with distinct features regarding the editing window and target scope. Here we developed a toolkit of plant base editors containing AID10, an engineered human AID cytosine deaminase. When fused to the N-terminus or C-terminus of the conventional Cas9 nickase (nSpCas9), AID10 exhibited a broad or narrow activity window at the protospacer adjacent motif (PAM)-distal and -proximal protospacer, respectively, while AID10 fused to both termini conferred an additive activity window. We further replaced nSpCas9 with orthogonal or PAM-relaxed Cas9 variants to widen target scopes. Moreover, we devised dual base editors with AID10 located adjacently or distally to the adenine deaminase ABE8e, leading to juxtaposed or spaced cytosine and adenine co-editing at the same target sequence in plant cells. Furthermore, we expanded the application of this toolkit in plants for tunable knockdown of protein-coding genes via creating upstream open reading frame and for loss-of-function analysis of non-coding genes, such as microRNA sponges. Collectively, this toolkit increases the functional diversity and versatility of base editors in basic and applied plant research.
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Affiliation(s)
| | - Zhenxiang Li
- Correspondence may also be addressed to Zhenxiang Li.
| | - Jieping Liang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Kehui Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Chenlong Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jian-Feng Li
- To whom correspondence should be addressed. Tel: +86 20 39943513; Fax: +86 20 39943513;
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14
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Long J, Liu N, Tang W, Xie L, Qin F, Zhou L, Tao R, Wang Y, Hu Y, Jiao Y, Li L, Jiang L, Qu J, Chen Q, Yao S. A split cytosine deaminase architecture enables robust inducible base editing. FASEB J 2021; 35:e22045. [PMID: 34797942 DOI: 10.1096/fj.202100123r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 09/23/2021] [Accepted: 11/01/2021] [Indexed: 02/05/2023]
Abstract
Directed base substitution with base editing technology enables efficient and programmable conversion of C:G or A:T base pairs to T:A or G:C in the genome. Although this technology has shown great potentials in a variety of basic research, off-target editing is among one of the biggest challenges toward its way to clinical application. Base editing tools, especially the tools converting C to T, caused unpredictable off-target editing throughout the genome, which raise the concern that long-term application of these tools would induce genomic instability or even tumorigenesis. To overcome this challenge, we designed an inducible base editing tool that was active only in the presence of a clinically safe chemical, rapamycin. In the guidance of structural information, we designed four split-human APOBEC3A (A3A) -BE3 base editors in which these A3A deaminase enzymes were split at sites that were opposite to the protein-nucleotide interface. We showed that by inducible deaminase reconstruction with a rapamycin responsible interaction system (FRB and FKBP); three out of four split-A3A-derived base editors showed robust inducible base editing. However, in the absence of rapamycin, their editing ability was dramatically inhibited. Among these split editors, splicing at Aa85 of A3A generated the most efficient inducible editing. In addition, compared to the full-length base editor, the splitting did not obviously alter the editing window and motif preference, but slightly increased the product purity. We also expanded this strategy to another frequently used cytosine deaminase, rat APOBEC1 (rA1), and observed a similar induction response. In summary, these results demonstrated the concept that splitting deaminases is a practicable method for timely controlling of base editing tools.
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Affiliation(s)
- Jie Long
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Chengdu, China
| | - Nan Liu
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Chengdu, China
| | - Wenling Tang
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Chengdu, China
| | - Lifang Xie
- The College of Life Sciences, Sichuan University, Chengdu, China
| | - Fengming Qin
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Chengdu, China
| | - Lifang Zhou
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Chengdu, China
| | - Rui Tao
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Chengdu, China
| | - Yanhong Wang
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Chengdu, China
| | - Yun Hu
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Chengdu, China
| | - Yaoge Jiao
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Chengdu, China
| | - Li Li
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Chengdu, China
| | - Lurong Jiang
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Chengdu, China
| | - Junyan Qu
- Center of Infectious Disease, West China Hospital, Sichuan University, Chengdu, China
| | - Qiang Chen
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Chengdu, China
| | - Shaohua Yao
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Chengdu, China
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15
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Denes CE, Cole AJ, Aksoy YA, Li G, Neely GG, Hesselson D. Approaches to Enhance Precise CRISPR/Cas9-Mediated Genome Editing. Int J Mol Sci 2021; 22:8571. [PMID: 34445274 PMCID: PMC8395304 DOI: 10.3390/ijms22168571] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/30/2021] [Accepted: 08/06/2021] [Indexed: 12/17/2022] Open
Abstract
Modification of the human genome has immense potential for preventing or treating disease. Modern genome editing techniques based on CRISPR/Cas9 show great promise for altering disease-relevant genes. The efficacy of precision editing at CRISPR/Cas9-induced double-strand breaks is dependent on the relative activities of nuclear DNA repair pathways, including the homology-directed repair and error-prone non-homologous end-joining pathways. The competition between multiple DNA repair pathways generates mosaic and/or therapeutically undesirable editing outcomes. Importantly, genetic models have validated key DNA repair pathways as druggable targets for increasing editing efficacy. In this review, we highlight approaches that can be used to achieve the desired genome modification, including the latest progress using small molecule modulators and engineered CRISPR/Cas proteins to enhance precision editing.
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Affiliation(s)
- Christopher E. Denes
- The Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre and School of Life & Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (C.E.D.); (G.L.)
| | - Alexander J. Cole
- Centenary Institute, The University of Sydney, Sydney, NSW 2006, Australia;
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Yagiz Alp Aksoy
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia;
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2113, Australia
| | - Geng Li
- The Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre and School of Life & Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (C.E.D.); (G.L.)
| | - Graham Gregory Neely
- The Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre and School of Life & Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (C.E.D.); (G.L.)
- Centenary Institute, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Daniel Hesselson
- Centenary Institute, The University of Sydney, Sydney, NSW 2006, Australia;
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
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16
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Wang Y, Zhou L, Tao R, Liu N, Long J, Qin F, Tang W, Yang Y, Chen Q, Yao S. sgBE: a structure-guided design of sgRNA architecture specifies base editing window and enables simultaneous conversion of cytosine and adenosine. Genome Biol 2020; 21:222. [PMID: 32859244 PMCID: PMC7453718 DOI: 10.1186/s13059-020-02137-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 08/07/2020] [Indexed: 02/05/2023] Open
Abstract
We present a base editing system, in which base editors are attached to different sites of sgRNA scaffold (sgBE). Each independent sgBE has its own specific editing pattern for a given target site. Among tested sgBEs, sgBE-SL4, in which deaminase is attached to the last stem-loop of sgRNA, yields the highest editing efficiency in the window several nucleotides next to the one edited by BE3. sgBE enables the simultaneous editing of adenine and cytosine. Finally, in order to facilitate in vivo base editing, we extend our sgBE system to an AAV-compatible Cas9, SaCas9 (Staphylococcus aureus), and observe robust base editing.
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Affiliation(s)
- Yanhong Wang
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Lifang Zhou
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Rui Tao
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Nan Liu
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Jie Long
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Fengming Qin
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Wenling Tang
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Yang Yang
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Qiang Chen
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Shaohua Yao
- Laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China.
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