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He Y, Han Y, Ma Y, Liu S, Fan T, Liang Y, Tang X, Zheng X, Wu Y, Zhang T, Qi Y, Zhang Y. Expanding plant genome editing scope and profiles with CRISPR-FrCas9 systems targeting palindromic TA sites. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38713743 DOI: 10.1111/pbi.14363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 03/14/2024] [Accepted: 04/02/2024] [Indexed: 05/09/2024]
Abstract
CRISPR-Cas9 is widely used for genome editing, but its PAM sequence requirements limit its efficiency. In this study, we explore Faecalibaculum rodentium Cas9 (FrCas9) for plant genome editing, especially in rice. FrCas9 recognizes a concise 5'-NNTA-3' PAM, targeting more abundant palindromic TA sites in plant genomes than the 5'-NGG-3' PAM sites of the most popular SpCas9. FrCas9 shows cleavage activities at all tested 5'-NNTA-3' PAM sites with editing outcomes sharing the same characteristics of a typical CRISPR-Cas9 system. FrCas9 induces high-efficiency targeted mutagenesis in stable rice lines, readily generating biallelic mutants with expected phenotypes. We augment FrCas9's ability to generate larger deletions through fusion with the exonuclease, TREX2. TREX2-FrCas9 generates much larger deletions than FrCas9 without compromise in editing efficiency. We demonstrate TREX2-FrCas9 as an efficient tool for genetic knockout of a microRNA gene. Furthermore, FrCas9-derived cytosine base editors (CBEs) and adenine base editors (ABE) are developed to produce targeted C-to-T and A-to-G base edits in rice plants. Whole-genome sequencing-based off-target analysis suggests that FrCas9 is a highly specific nuclease. Expression of TREX2-FrCas9 in plants, however, causes detectable guide RNA-independent off-target mutations, mostly as single nucleotide variants (SNVs). Together, we have established an efficient CRISPR-FrCas9 system for targeted mutagenesis, large deletions, C-to-T base editing, and A-to-G base editing in plants. The simple palindromic TA motif in the PAM makes the CRISPR-FrCas9 system a promising tool for genome editing in plants with an expanded targeting scope.
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Affiliation(s)
- Yao He
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 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, China
| | - Yangshuo Han
- 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, China
| | - Yanqin Ma
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 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, China
| | - Tingting Fan
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yanling Liang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 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, China
| | - Xuelian Zheng
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 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, China
| | - 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, Agricultural College of Yangzhou University, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 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, Agricultural College of Yangzhou University, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, China
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Yong Zhang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 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, China
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2
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Tang N, Wu Z, Gao Y, Chen W, Wang Z, Su M, Ji W, Ji Q. Molecular Basis and Genome Editing Applications of a Compact Eubacterium ventriosum CRISPR-Cas9 System. ACS Synth Biol 2024; 13:269-281. [PMID: 38061052 DOI: 10.1021/acssynbio.3c00501] [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: 01/23/2024]
Abstract
CRISPR-Cas9 systems have been widely harnessed for diverse genome editing applications because of their ease of use and high efficiency. However, the large molecular sizes and strict PAM requirements of commonly used CRISPR-Cas9 systems restrict their broad applications in therapeutics. Here, we report the molecular basis and genome editing applications of a novel compact type II-A Eubacterium ventriosum CRISPR-Cas9 system (EvCas9) with 1107 residues and distinct 5'-NNGDGN-3' (where D represents A, T, or G) PAM specificity. We determine the cryo-EM structure of EvCas9 in a complex with an sgRNA and a target DNA, revealing the detailed PAM recognition and sgRNA and target DNA association mechanisms. Additionally, we demonstrate the robust genome editing capacity of EvCas9 in bacteria and human cells with superior fidelity compared to SaCas9 and SpCas9, and we engineer it to be efficient base editors by fusing a cytidine or adenosine deaminase. Collectively, our results facilitate further understanding of CRISPR-Cas9 working mechanisms and expand the compact CRISPR-Cas9 toolbox.
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Affiliation(s)
- Na Tang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zhaowei Wu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Weizhong Chen
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zixiao Wang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Mengjiao Su
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wenxin Ji
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Quanjiang Ji
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
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3
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Chen F, Wang D, Lu T, Li S. Identification of a novel type II-C Cas9 from the fish pathogen Flavobacterium psychrophilum. Front Microbiol 2023; 14:1181303. [PMID: 37396349 PMCID: PMC10309648 DOI: 10.3389/fmicb.2023.1181303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/26/2023] [Indexed: 07/04/2023] Open
Abstract
Flavobacterium psychrophilum is the causative agent of rainbow trout fry syndrome and bacterial cold-water disease in salmonid fish worldwide. As an important fish pathogen, F. psychrophilum is frequently exposed to multiple invading genetic elements in natural environments. Endonuclease Cas9 provides bacteria with adaptive interference against invading genetic elements. Previous studies revealed that several F. psychrophilum strains harbored a type II-C Cas9 called Fp1Cas9, but little is known about the potential role of this endonuclease against invading genetic elements. In this work, we identified a gene encoding a novel type II-C Cas9 called Fp2Cas9 from F. psychrophilum strain CN46. Through bacterial RNA sequencing, we demonstrated active transcription of both Fp2Cas9 and pre-crRNAs in strain CN46. Bioinformatics analysis further revealed that the transcription of Fp2Cas9 and pre-crRNAs was driven by a newly integrated promoter sequence and a promoter element embedded within each CRISPR repeat, respectively. To formally demonstrate that Fp2Cas9 and associated crRNAs yielded functional interference in strain CN46, a plasmid interference assay was performed, resulting in adaptive immunity to target DNA sequences in Flavobacterium bacteriophages. Phylogenetic analysis demonstrated that Fp2Cas9 was present only in several F. psychrophilum isolates. Phylogenetic analysis revealed that this novel endonuclease was probably acquired through horizontal gene transfer from the CRISPR-Cas9 system in an unidentified Flavobacterium species. Comparative genomics analysis further showed that the Fp2Cas9 was integrated into the type II-C CRISPR-Cas locus in strain CN38 instead of the original Fp1Cas9. Taken together, our results shed light on the origin and evolution of Fp2Cas9 gene and demonstrated that this novel endonuclease provided adaptive interference against bacteriophage infections.
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Affiliation(s)
- Fuguang Chen
- Department of Aquatic Animal Health, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, China
| | - Di Wang
- Department of Aquatic Animal Health, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, China
| | - Tongyan Lu
- Department of Aquatic Animal Health, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, China
| | - Shaowu Li
- Department of Aquatic Animal Health, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, China
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Esquerra-Ruvira B, Baquedano I, Ruiz R, Fernandez A, Montoliu L, Mojica FJM. Identification of the EH CRISPR-Cas9 system on a metagenome and its application to genome engineering. Microb Biotechnol 2023. [PMID: 37097160 DOI: 10.1111/1751-7915.14266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/04/2023] [Accepted: 04/12/2023] [Indexed: 04/26/2023] Open
Abstract
Non-coding RNAs (crRNAs) produced from clustered regularly interspaced short palindromic repeats (CRISPR) loci and CRISPR-associated (Cas) proteins of the prokaryotic CRISPR-Cas systems form complexes that interfere with the spread of transmissible genetic elements through Cas-catalysed cleavage of foreign genetic material matching the guide crRNA sequences. The easily programmable targeting of nucleic acids enabled by these ribonucleoproteins has facilitated the implementation of CRISPR-based molecular biology tools for in vivo and in vitro modification of DNA and RNA targets. Despite the diversity of DNA-targeting Cas nucleases so far identified, native and engineered derivatives of the Streptococcus pyogenes SpCas9 are the most widely used for genome engineering, at least in part due to their catalytic robustness and the requirement of an exceptionally short motif (5'-NGG-3' PAM) flanking the target sequence. However, the large size of the SpCas9 variants impairs the delivery of the tool to eukaryotic cells and smaller alternatives are desirable. Here, we identify in a metagenome a new CRISPR-Cas9 system associated with a smaller Cas9 protein (EHCas9) that targets DNA sequences flanked by 5'-NGG-3' PAMs. We develop a simplified EHCas9 tool that specifically cleaves DNA targets and is functional for genome editing applications in prokaryotes and eukaryotic cells.
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Affiliation(s)
- Belen Esquerra-Ruvira
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Ignacio Baquedano
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Raul Ruiz
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Almudena Fernandez
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER-ISCIII), Madrid, Spain
| | - Lluis Montoliu
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER-ISCIII), Madrid, Spain
| | - Francisco J M Mojica
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies "Ramón Margalef", University of Alicante, Alicante, Spain
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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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Meng X, Wu TG, Lou QY, Niu KY, Jiang L, Xiao QZ, Xu T, Zhang L. Optimization of CRISPR-Cas system for clinical cancer therapy. Bioeng Transl Med 2023; 8:e10474. [PMID: 36925702 PMCID: PMC10013785 DOI: 10.1002/btm2.10474] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/24/2022] [Accepted: 12/07/2022] [Indexed: 12/25/2022] Open
Abstract
Cancer is a genetic disease caused by alterations in genome and epigenome and is one of the leading causes for death worldwide. The exploration of disease development and therapeutic strategies at the genetic level have become the key to the treatment of cancer and other genetic diseases. The functional analysis of genes and mutations has been slow and laborious. Therefore, there is an urgent need for alternative approaches to improve the current status of cancer research. Gene editing technologies provide technical support for efficient gene disruption and modification in vivo and in vitro, in particular the use of clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems. Currently, the applications of CRISPR-Cas systems in cancer rely on different Cas effector proteins and the design of guide RNAs. Furthermore, effective vector delivery must be met for the CRISPR-Cas systems to enter human clinical trials. In this review article, we describe the mechanism of the CRISPR-Cas systems and highlight the applications of class II Cas effector proteins. We also propose a synthetic biology approach to modify the CRISPR-Cas systems, and summarize various delivery approaches facilitating the clinical application of the CRISPR-Cas systems. By modifying the CRISPR-Cas system and optimizing its in vivo delivery, promising and effective treatments for cancers using the CRISPR-Cas system are emerging.
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Affiliation(s)
- Xiang Meng
- College & Hospital of Stomatology Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province Hefei People's Republic of China
| | - Tian-Gang Wu
- College & Hospital of Stomatology Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province Hefei People's Republic of China
| | - Qiu-Yue Lou
- Anhui Provincial Center for Disease Control and Prevention Hefei People's Republic of China
| | - Kai-Yuan Niu
- Clinical Pharmacology, William Harvey Research Institute (WHRI), Barts and The London School of Medicine and Dentistry Queen Mary University of London (QMUL) Heart Centre (G23) London UK.,Department of Otolaryngology The Third Affiliated Hospital of Anhui Medical University Hefei China
| | - Lei Jiang
- College & Hospital of Stomatology Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province Hefei People's Republic of China
| | - Qing-Zhong Xiao
- Clinical Pharmacology, William Harvey Research Institute (WHRI), Barts and The London School of Medicine and Dentistry Queen Mary University of London (QMUL) Heart Centre (G23) London UK
| | - Tao Xu
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products Anhui Medical University Hefei China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province Hefei China
| | - Lei Zhang
- College & Hospital of Stomatology Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province Hefei People's Republic of China.,Department of Periodontology Anhui Stomatology Hospital Affiliated to Anhui Medical University Hefei China
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7
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Yan F, Wang J, Zhang S, Lu Z, Li S, Ji Z, Song C, Chen G, Xu J, Feng J, Zhou X, Zhou H. CRISPR/FnCas12a-mediated efficient multiplex and iterative genome editing in bacterial plant pathogens without donor DNA templates. PLoS Pathog 2023; 19:e1010961. [PMID: 36626407 PMCID: PMC9870152 DOI: 10.1371/journal.ppat.1010961] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/23/2023] [Accepted: 12/27/2022] [Indexed: 01/11/2023] Open
Abstract
CRISPR-based genome editing technology is revolutionizing prokaryotic research, but it has been rarely studied in bacterial plant pathogens. Here, we have developed a targeted genome editing method with no requirement of donor templates for convenient and efficient gene knockout in Xanthomonas oryzae pv. oryzae (Xoo), one of the most important bacterial pathogens on rice, by employing the heterologous CRISPR/Cas12a from Francisella novicida and NHEJ proteins from Mycobacterium tuberculosis. FnCas12a nuclease generated both small and large DNA deletions at the target sites as well as it enabled multiplex genome editing, gene cluster deletion, and plasmid curing in the Xoo PXO99A strain. Accordingly, a non-TAL effector-free polymutant strain PXO99AD25E, which lacks all 25 xop genes involved in Xoo pathogenesis, has been engineered through iterative genome editing. Whole-genome sequencing analysis indicated that FnCas12a did not have a noticeable off-target effect. In addition, we revealed that these strategies are also suitable for targeted genome editing in another bacterial plant pathogen Pseudomonas syringae pv. tomato (Pst). We believe that our bacterial genome editing method will greatly expand the CRISPR study on microorganisms and advance our understanding of the physiology and pathogenesis of Xoo.
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Affiliation(s)
- Fang Yan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jingwen Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sujie Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China,Scientific Observing and Experimental Station of Crop Pests in Guilin, Ministry of Agriculture and Rural Affairs, Guilin, China
| | - Zhenwan Lu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China,Scientific Observing and Experimental Station of Crop Pests in Guilin, Ministry of Agriculture and Rural Affairs, Guilin, China
| | - Shaofang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiyuan Ji
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Congfeng Song
- Key Laboratory of Monitoring and Management of Plant Diseases and Insects, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Gongyou Chen
- State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jin Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Feng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China,State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Huanbin Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China,Scientific Observing and Experimental Station of Crop Pests in Guilin, Ministry of Agriculture and Rural Affairs, Guilin, China,* E-mail:
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Xu R, Qin R, Xie H, Li J, Liu X, Zhu M, Sun Y, Yu Y, Lu P, Wei P. Genome editing with type II-C CRISPR-Cas9 systems from Neisseria meningitidis in rice. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:350-359. [PMID: 34582079 PMCID: PMC8753361 DOI: 10.1111/pbi.13716] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 05/05/2023]
Abstract
Two type II-C Cas9 orthologs (Nm1Cas9 and Nm2Cas9) were recently identified from Neisseria meningitidis and have been extensively used in mammalian cells, but whether these NmCas9 orthologs or other type II-C Cas9 proteins can mediate genome editing in plants remains unclear. In this study, we developed and optimized targeted mutagenesis systems from NmCas9s for plants. Efficient genome editing at the target with N4 GATT and N4 CC protospacer adjacent motifs (PAMs) was achieved with Nm1Cas9 and Nm2Cas9 respectively. These results indicated that a highly active editing system could be developed from type II-C Cas9s with distinct PAM preferences, thus providing a reliable strategy to extend the scope of genome editing in plants. Base editors (BEs) were further developed from the NmCas9s. The editing efficiency of adenine BEs (ABEs) of TadA*-7.10 and cytosine BEs (CBEs) of rat APOBEC1 (rAPO1) or human APOBEC3a (hA3A) were extremely limited, whereas ABEs of TadA-8e and CBEs of Petromyzon marinus cytidine deaminase 1 (PmCDA1) exhibited markedly improved performance on the same targets. In addition, we found that fusion of a single-stranded DNA-binding domain from the human Rad51 protein enhanced the base editing capability of rAPO1-CBEs of NmCas9s. Together, our results suggest that the engineering of NmCas9s or other type II-C Cas9s can provide useful alternatives for crop genome editing.
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Affiliation(s)
- Rongfang Xu
- College of AgronomyAnhui Agricultural UniversityHefeiChina
- Key Laboratory of Rice Genetic Breeding of Anhui ProvinceRice Research InstituteAnhui Academy of Agricultural SciencesHefeiChina
| | - Ruiying Qin
- Key Laboratory of Rice Genetic Breeding of Anhui ProvinceRice Research InstituteAnhui Academy of Agricultural SciencesHefeiChina
| | - Hongjun Xie
- Key Laboratory of Indica Rice Genetics and Breeding in the middle and Lower Reaches of Yangtze River ValleyMinistry of AgricultureHunan Rice Research InstituteChangshaChina
| | - Juan Li
- Key Laboratory of Rice Genetic Breeding of Anhui ProvinceRice Research InstituteAnhui Academy of Agricultural SciencesHefeiChina
| | - Xiaoshuang Liu
- College of AgronomyAnhui Agricultural UniversityHefeiChina
- Key Laboratory of Rice Genetic Breeding of Anhui ProvinceRice Research InstituteAnhui Academy of Agricultural SciencesHefeiChina
| | - Mingdong Zhu
- Key Laboratory of Indica Rice Genetics and Breeding in the middle and Lower Reaches of Yangtze River ValleyMinistry of AgricultureHunan Rice Research InstituteChangshaChina
| | - Yang Sun
- State Key Laboratory of Crop Stress Adaptation and ImprovementKey Laboratory of Plant Stress BiologySchool of Life SciencesHenan UniversityKaifengChina
| | - Yinghong Yu
- Key Laboratory of Indica Rice Genetics and Breeding in the middle and Lower Reaches of Yangtze River ValleyMinistry of AgricultureHunan Rice Research InstituteChangshaChina
| | - Pingli Lu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major DiseasesCollege of Life SciencesAnhui Normal UniversityWuhuChina
| | - Pengcheng Wei
- College of AgronomyAnhui Agricultural UniversityHefeiChina
- Key Laboratory of Rice Genetic Breeding of Anhui ProvinceRice Research InstituteAnhui Academy of Agricultural SciencesHefeiChina
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Liu Z, Chen S, Xie W, Song Y, Li J, Lai L, Li Z. Versatile and efficient in vivo genome editing with compact Streptococcus pasteurianus Cas9. Mol Ther 2022; 30:256-267. [PMID: 34174445 PMCID: PMC8753289 DOI: 10.1016/j.ymthe.2021.06.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/01/2021] [Accepted: 06/21/2021] [Indexed: 01/07/2023] Open
Abstract
Compact CRISPR-Cas9 systems that can be packaged into an adeno-associated virus (AAV) show promise for gene therapy. However, the requirement of protospacer adjacent motifs (PAMs) restricts the target scope. To expand this repertoire, we revisited and optimized a small Cas9 ortholog derived from Streptococcus pasteurianus (SpaCas9) for efficient genome editing in vivo. We found that SpaCas9 enables potent targeting of 5'-NNGYRA-3' PAMs, which are distinct from those recognized by currently used small Cas9s; the Spa-cytosine base editor (CBE) and Spa-adenine base editor (ABE) systems efficiently generated robust C-to-T and A-to-G conversions both in vitro and in vivo. In addition, by exploiting natural variation in the PAM-interacting domain, we engineered three SpaCas9 variants to further expand the targeting scope of compact Cas9 systems. Moreover, mutant mice with efficient disruption of the Tyr gene were successfully generated by microinjection of SpaCas9 mRNA and the corresponding single guide RNA (sgRNA) into zygotes. Notably, all-in-one AAV delivery of SpaCas9 targeting the Pcsk9 gene in adult mouse liver produced efficient genome-editing events and reduced its serum cholesterol. Thus, with distinct PAMs and a small size, SpaCas9 will broaden the CRISPR-Cas9 toolsets for efficient gene modifications and therapeutic applications.
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Affiliation(s)
- Zhiquan Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun 130062, China
| | - Siyu Chen
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun 130062, China
| | - Wanhua Xie
- The Precise Medicine Center, Shenyang Medical College, Shenyang 110000, China
| | - Yuning Song
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun 130062, China
| | - Jinze Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun 130062, China
| | - Liangxue Lai
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun 130062, China; CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Guangzhou Regenerative Medicine and Health Guang Dong Laboratory (GRMH-GDL), Guangzhou 510005, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | - Zhanjun Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Animal Science, Jilin University, Changchun 130062, China.
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10
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Molloy EM, Dell M, Hänsch VG, Dunbar KL, Feldmann R, Oberheide A, Seyfarth L, Kumpfmüller J, Horch T, Arndt H, Hertweck C. Enzyme‐Primed Native Chemical Ligation Produces Autoinducing Cyclopeptides in Clostridia. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Evelyn M. Molloy
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural, Product Research and Infection Biology HKI Beutenbergstr. 11a 07745 Jena Germany
| | - Maria Dell
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural, Product Research and Infection Biology HKI Beutenbergstr. 11a 07745 Jena Germany
| | - Veit G. Hänsch
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural, Product Research and Infection Biology HKI Beutenbergstr. 11a 07745 Jena Germany
| | - Kyle L. Dunbar
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural, Product Research and Infection Biology HKI Beutenbergstr. 11a 07745 Jena Germany
| | - Romy Feldmann
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural, Product Research and Infection Biology HKI Beutenbergstr. 11a 07745 Jena Germany
| | - Ansgar Oberheide
- Institute for Organic Chemistry and Macromolecular Chemistry Friedrich Schiller University Jena Humboldtstr. 10 07743 Jena Germany
| | - Lydia Seyfarth
- Institute for Organic Chemistry and Macromolecular Chemistry Friedrich Schiller University Jena Humboldtstr. 10 07743 Jena Germany
| | - Jana Kumpfmüller
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural, Product Research and Infection Biology HKI Beutenbergstr. 11a 07745 Jena Germany
| | - Therese Horch
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural, Product Research and Infection Biology HKI Beutenbergstr. 11a 07745 Jena Germany
| | - Hans‐Dieter Arndt
- Institute for Organic Chemistry and Macromolecular Chemistry Friedrich Schiller University Jena Humboldtstr. 10 07743 Jena Germany
| | - Christian Hertweck
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural, Product Research and Infection Biology HKI Beutenbergstr. 11a 07745 Jena Germany
- Faculty of Biological Sciences Friedrich Schiller University Jena 07743 Jena Germany
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11
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Molloy EM, Dell M, Hänsch VG, Dunbar KL, Feldmann R, Oberheide A, Seyfarth L, Kumpfmüller J, Horch T, Arndt HD, Hertweck C. Enzyme-Primed Native Chemical Ligation Produces Autoinducing Cyclopeptides in Clostridia. Angew Chem Int Ed Engl 2021; 60:10670-10679. [PMID: 33625794 PMCID: PMC8251862 DOI: 10.1002/anie.202016378] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Indexed: 12/14/2022]
Abstract
Clostridia coordinate many important processes such as toxin production, infection, and survival by density‐dependent communication (quorum sensing) using autoinducing peptides (AIPs). Although clostridial AIPs have been proposed to be (thio)lactone‐containing peptides, their true structures remain elusive. Here, we report the genome‐guided discovery of an AIP that controls endospore formation in Ruminiclostridium cellulolyticum. Through a combination of chemical synthesis and chemical complementation assays with a mutant strain, we reveal that the genuine chemical mediator is a homodetic cyclopeptide (cAIP). Kinetic analyses indicate that the mature cAIP is produced via a cryptic thiolactone intermediate that undergoes a rapid S→N acyl shift, in a manner similar to intramolecular native chemical ligation (NCL). Finally, by implementing a chemical probe in a targeted screen, we show that this novel enzyme‐primed, intramolecular NCL is a widespread feature of clostridial AIP biosynthesis.
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Affiliation(s)
- Evelyn M Molloy
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural, Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Maria Dell
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural, Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Veit G Hänsch
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural, Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Kyle L Dunbar
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural, Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Romy Feldmann
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural, Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Ansgar Oberheide
- Institute for Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstr. 10, 07743, Jena, Germany
| | - Lydia Seyfarth
- Institute for Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstr. 10, 07743, Jena, Germany
| | - Jana Kumpfmüller
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural, Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Therese Horch
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural, Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Hans-Dieter Arndt
- Institute for Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstr. 10, 07743, Jena, Germany
| | - Christian Hertweck
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural, Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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12
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Wang G, Li J. Review, analysis, and optimization of the CRISPR Streptococcus pyogenes Cas9 system. MEDICINE IN DRUG DISCOVERY 2021. [DOI: 10.1016/j.medidd.2021.100080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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13
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Collias D, Beisel CL. CRISPR technologies and the search for the PAM-free nuclease. Nat Commun 2021; 12:555. [PMID: 33483498 PMCID: PMC7822910 DOI: 10.1038/s41467-020-20633-y] [Citation(s) in RCA: 132] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/03/2020] [Indexed: 12/20/2022] Open
Abstract
The ever-expanding set of CRISPR technologies and their programmable RNA-guided nucleases exhibit remarkable flexibility in DNA targeting. However, this flexibility comes with an ever-present constraint: the requirement for a protospacer adjacent motif (PAM) flanking each target. While PAMs play an essential role in self/nonself discrimination by CRISPR-Cas immune systems, this constraint has launched a far-reaching expedition for nucleases with relaxed PAM requirements. Here, we review ongoing efforts toward realizing PAM-free nucleases through natural ortholog mining and protein engineering. We also address potential consequences of fully eliminating PAM recognition and instead propose an alternative nuclease repertoire covering all possible PAM sequences.
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Affiliation(s)
- Daphne Collias
- Department of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695-7905, USA
| | - Chase L Beisel
- Department of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695-7905, USA.
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz Centre for Infection Research (HZI), 97080, Würzburg, Germany.
- Medical Faculty, University of Würzburg, 97080, Würzburg, Germany.
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14
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SpCas9- and LbCas12a-Mediated DNA Editing Produce Different Gene Knockout Outcomes in Zebrafish Embryos. Genes (Basel) 2020; 11:genes11070740. [PMID: 32635161 PMCID: PMC7397077 DOI: 10.3390/genes11070740] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/04/2020] [Accepted: 06/09/2020] [Indexed: 12/26/2022] Open
Abstract
CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein) genome editing is a powerful technology widely used in current genetic research. In the most simple and straightforward way it can be applied for a gene knockout resulting from repair errors, induced by dsDNA cleavage by Cas nuclease. For decades, zebrafish (Danio rerio) has been known as a convenient model object of developmental biology. Both commonly used nucleases SpCas9 (Streptococcus pyogenes Cas9) and LbCas12a (Lachnospiraceae bacterium Cas12a) are extensively used in this model. Among them, LbCas12a is featured with higher specificity and efficiency of homology-directed editing in human cells and mouse. But the editing outcomes for these two nucleases in zebrafish are still not compared quantitatively. Therefore, to reveal possible advantages of one nuclease in comparison to the other in the context of gene knockout generation, we compare here the outcomes of repair of the DNA breaks introduced by these two commonly used nucleases in zebrafish embryos. To address this question, we microinjected the ribonucleoprotein complexes of the both nucleases with the corresponding guide RNAs in zebrafish zygotes and sequenced the target gene regions after three days of development. We found that LbCas12a editing resulted in longer deletions and more rare inserts, in comparison to those generated by SpCas9, while the editing efficiencies (percentage of mutated copies of the target gene to all gene copies in the embryo) of both nucleases were the same. On the other hand, overlapping of protospacers resulted in similarities in repair outcome, although they were cut by two different nucleases. Thus, our results indicate that the repair outcome depends both on the nuclease mode of action and on protospacer sequence.
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15
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Comprehensive Mining and Characterization of CRISPR-Cas Systems in Bifidobacterium. Microorganisms 2020; 8:microorganisms8050720. [PMID: 32408568 PMCID: PMC7284854 DOI: 10.3390/microorganisms8050720] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/01/2020] [Accepted: 05/08/2020] [Indexed: 12/12/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated cas) systems constitute the adaptive immune system in prokaryotes, which provides resistance against bacteriophages and invasive genetic elements. The landscape of applications in bacteria and eukaryotes relies on a few Cas effector proteins that have been characterized in detail. However, there is a lack of comprehensive studies on naturally occurring CRISPR-Cas systems in beneficial bacteria, such as human gut commensal Bifidobacterium species. In this study, we mined 954 publicly available Bifidobacterium genomes and identified CRIPSR-Cas systems in 57% of these strains. A total of five CRISPR-Cas subtypes were identified as follows: Type I-E, I-C, I-G, II-A, and II-C. Among the subtypes, Type I-C was the most abundant (23%). We further characterized the CRISPR RNA (crRNA), tracrRNA, and PAM sequences to provide a molecular basis for the development of new genome editing tools for a variety of applications. Moreover, we investigated the evolutionary history of certain Bifidobacterium strains through visualization of acquired spacer sequences and demonstrated how these hypervariable CRISPR regions can be used as genotyping markers. This extensive characterization will enable the repurposing of endogenous CRISPR-Cas systems in Bifidobacteria for genome engineering, transcriptional regulation, genotyping, and screening of rare variants.
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