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Li J, Fan G, Sakari M, Tsukahara T. Improvement of C-to-U RNA editing using an artificial MS2-APOBEC system. Biotechnol J 2024; 19:e2300321. [PMID: 38010373 DOI: 10.1002/biot.202300321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 11/29/2023]
Abstract
RNA cytidine deamination (C-to-U editing) has been achieved using the MS2-apolipoprotein B-editing catalytic polypeptide-like (APOBEC)1 editing system. Here, we fused the cytidine deaminase (CDA) enzymes APOBEC3A and APOBEC3G with the MS2 system and examined their RNA editing efficiencies in transfected HEK 293T cells. Given the single-stranded RNA preferences of APOBEC3A and APOBEC3G, we designed unconventional guide RNAs that induced a loop at the target sequence, allowing the target to form a single-stranded structure. Because APOBEC3A and APOBEC3G have different base preferences (5'-TC and 5'-CC, respectively), we introduced the D317W mutation into APOBEC3G to convert its base preference to that of APOBEC3A. Upon co-transfection with a guide RNA that induced the formation of a 14 nt loop on the target sequence, MS2-fused APOBEC3A and APOBEC3G showed high editing efficiency. While the D317W mutation of APOBEC3G led to a slight improvement in editing efficiency, the difference was not statistically significant. These findings indicate that APOBEC3A and APOBEC3G can induce C-to-U RNA editing when transfected with a loop guide RNA. Moreover, the editing efficiency of APOBEC3G can be enhanced by site-specific mutation to alter the base preference. Overall, our results demonstrate that the MS2 system can fuse and catalyze reactions with different enzymes, suggesting that it holds an even greater potential for RNA editing than is utilized currently.
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Affiliation(s)
- Jiarui Li
- Bioscience, Biotechnology and Biomedical Engineering Research Area, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa, Japan
| | - Guangyao Fan
- Bioscience, Biotechnology and Biomedical Engineering Research Area, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa, Japan
- School of Medicine, Shaoxing University, Shaoxing, China
| | - Matomo Sakari
- Bioscience, Biotechnology and Biomedical Engineering Research Area, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa, Japan
| | - Toshifumi Tsukahara
- Bioscience, Biotechnology and Biomedical Engineering Research Area, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa, Japan
- GeCoRT Co. Ltd., Nishi-ku, Yokohama, Japan
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2
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Liu Y, Jing P, Zhou Y, Zhang J, Shi J, Zhang M, Yang H, Fei J. The effects of length and sequence of gRNA on Cas13b and Cas13d activity in vitro and in vivo. Biotechnol J 2023; 18:e2300002. [PMID: 37148478 DOI: 10.1002/biot.202300002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 04/15/2023] [Accepted: 05/03/2023] [Indexed: 05/08/2023]
Abstract
Cas13 are the only CRISPR/Cas systems found so far, which target RNA strand while preserving chromosomal integrity. Cas13b or Cas13d cleaves RNA by the crRNA guidance. However, the effect of the characteristics of the spacer sequences, such as the length and sequence preference, on the activity of Cas13b and Cas13d remains unclear. Our study shows that neither Cas13b nor Cas13d has a particular preference for the sequence composition of gRNA, including the sequence of crRNA and its flanking sites on target RNA. However, the crRNA, complementary to the middle part of the target RNA, seems to show higher cleavage efficiency for both Cas13b and Cas13d. As for the length of crRNAs, the most appropriate crRNA length for Cas13b is 22-25 nt and crRNA as short as 15 nt is still functional. Whereas, Cas13d requires longer crRNA, and 22-30 nt crRNA can achieve good effect. Both Cas13b and Cas13d show the ability to process precursor crRNAs. Our study suggests that Cas13b may have a stronger precursor processing ability than Cas13d. There are few in vivo studies on the application of Cas13b or Cas13d in mammals. With the methods of transgenic mice and hydrodynamic injection via tail vein, our study showed that both of them had high knock-down efficiency against target RNA in vivo. These results indicate that Cas13b and Cas13d have great potential for in vivo RNA operation and disease treatment without damaging genomic DNA.
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Affiliation(s)
- Yuhui Liu
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Ping Jing
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Yi Zhou
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Jingyu Zhang
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Jiahao Shi
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Mengjie Zhang
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Hua Yang
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Jian Fei
- School of Life Science and Technology, Tongji University, Shanghai, China
- Shanghai Engineering Research Center for Model Organisms, SMOC, Shanghai, China
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3
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Reshetnikov VV, Chirinskaite AV, Sopova JV, Ivanov RA, Leonova EI. Cas-Based Systems for RNA Editing in Gene Therapy of Monogenic Diseases: In Vitro and in Vivo Application and Translational Potential. Front Cell Dev Biol 2022; 10:903812. [PMID: 35784464 PMCID: PMC9245891 DOI: 10.3389/fcell.2022.903812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/05/2022] [Indexed: 12/12/2022] Open
Abstract
Rare genetic diseases reduce quality of life and can significantly shorten the lifespan. There are few effective treatment options for these diseases, and existing therapeutic strategies often represent only supportive or palliative care. Therefore, designing genetic-engineering technologies for the treatment of genetic diseases is urgently needed. Rapid advances in genetic editing technologies based on programmable nucleases and in the engineering of gene delivery systems have made it possible to conduct several dozen successful clinical trials; however, the risk of numerous side effects caused by off-target double-strand breaks limits the use of these technologies in the clinic. Development of adenine-to-inosine (A-to-I) and cytosine-to-uracil (C-to-U) RNA-editing systems based on dCas13 enables editing at the transcriptional level without double-strand breaks in DNA. In this review, we discuss recent progress in the application of these technologies in in vitro and in vivo experiments. The main strategies for improving RNA-editing tools by increasing their efficiency and specificity are described as well. These data allow us to outline the prospects of base-editing systems for clinical application.
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Affiliation(s)
- Vasiliy V. Reshetnikov
- Department of Biotechnology, Sirius University of Science and Technology, Sochi, Russia
- Department of Molecular Genetics, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Angelina V. Chirinskaite
- Center of Transgenesis and Genome Editing, St. Petersburg State University, St. Petersburg, Russia
| | - Julia V. Sopova
- Center of Transgenesis and Genome Editing, St. Petersburg State University, St. Petersburg, Russia
- Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Roman A. Ivanov
- Department of Biotechnology, Sirius University of Science and Technology, Sochi, Russia
| | - Elena I. Leonova
- Center of Transgenesis and Genome Editing, St. Petersburg State University, St. Petersburg, Russia
- Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia
- *Correspondence: Elena I. Leonova,
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4
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Abstract
Editing mutated genes is a potential way for the treatment of genetic diseases. G-to-A mutations are common in mammals and can be treated by adenosine-to-inosine (A-to-I) editing, a type of substitutional RNA editing. The molecular mechanism of A-to-I editing involves the hydrolytic deamination of adenosine to an inosine base; this reaction is mediated by RNA-specific deaminases, adenosine deaminases acting on RNA (ADARs), family protein. Here, we review recent findings regarding the application of ADARs to restoring the genetic code along with different approaches involved in the process of artificial RNA editing by ADAR. We have also addressed comparative studies of various isoforms of ADARs. Therefore, we will try to provide a detailed overview of the artificial RNA editing and the role of ADAR with a focus on the enzymatic site directed A-to-I editing.
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Affiliation(s)
- Sonali Bhakta
- Area of Bioscience and Biotechnology, School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomicity, Ishikawa, 923-1292, Japan
| | - Toshifumi Tsukahara
- Area of Bioscience and Biotechnology, School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomicity, Ishikawa, 923-1292, Japan
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5
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Perčulija V, Lin J, Zhang B, Ouyang S. Functional Features and Current Applications of the RNA-Targeting Type VI CRISPR-Cas Systems. Adv Sci (Weinh) 2021; 8:2004685. [PMID: 34254038 PMCID: PMC8209922 DOI: 10.1002/advs.202004685] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/26/2021] [Indexed: 05/14/2023]
Abstract
CRISPR-Cas systems are a form of prokaryotic adaptive immunity that employs RNA-guided endonucleases (Cas effectors) to cleave foreign genetic elements. Due to their simplicity, targeting programmability, and efficiency, single-effector CRISPR-Cas systems have great potential for application in research, biotechnology, and therapeutics. While DNA-targeting Cas effectors such as Cas9 and Cas12a have become indispensable tools for genome editing in the past decade, the more recent discovery of RNA-targeting CRISPR-Cas systems has opened the door for implementation of CRISPR-Cas technology in RNA manipulation. With an increasing number of studies reporting their application in transcriptome engineering, viral interference, nucleic acid detection, and RNA imaging, type VI CRISPR-Cas systems and the associated Cas13 effectors particularly hold promise as RNA-targeting or RNA-binding tools. However, even though previous structural and biochemical characterization provided a firm basis for leveraging type VI CRISPR-Cas systems into such tools, the lack of comprehension of certain mechanisms underlying their functions hinders more sophisticated and conventional use. This review will summarize current knowledge on structural and mechanistic properties of type VI CRISPR-Cas systems, give an overview on the reported applications, and discuss functional features that need further investigation in order to improve performance of Cas13-based tools.
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Affiliation(s)
- Vanja Perčulija
- The Key Laboratory of Innate Immune Biology of Fujian ProvinceProvincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhou350117China
- International College of Chinese StudiesFujian Normal UniversityFuzhou350117China
| | - Jinying Lin
- The Key Laboratory of Innate Immune Biology of Fujian ProvinceProvincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhou350117China
| | - Bo Zhang
- The Key Laboratory of Innate Immune Biology of Fujian ProvinceProvincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhou350117China
| | - Songying Ouyang
- The Key Laboratory of Innate Immune Biology of Fujian ProvinceProvincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhou350117China
- Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and Technology (Qingdao)Qingdao266237China
- National Laboratory of BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing100101China
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6
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Xu Y, Peng X, Zheng Y, Jin C, Lu X, Han D, Fu H, Chen C, Wu N. Inactivation of Latent HIV-1 Proviral DNA Using Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 Treatment and the Assessment of Off-Target Effects. Front Microbiol 2021; 12:629153. [PMID: 34122355 PMCID: PMC8187572 DOI: 10.3389/fmicb.2021.629153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 04/28/2021] [Indexed: 11/29/2022] Open
Abstract
Viral DNA integrated in host cells is a major barrier to completely curing HIV-1. However, genome editing using the recently developed technique of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 has the potential to eradicate HIV-1. The present study aimed to use a lentiviral vector-based CRISPR/Cas9 system combined with dual-small/single guide RNAs (sgRNAs) to attack HIV-1 DNA in the latency reactivation model J-Lat 10.6 cell line and to assess off-target effects using whole-genome sequencing (WGS). We designed 12 sgRNAs targeting HIV-1 DNA, and selected high-efficiency sgRNAs for further pairwise combinations after a preliminary evaluation of the editing efficiency. Three combinations of dual-sgRNAs/Cas9 with high editing efficiency were screened successfully from multiple combinations. Among these combinations, the incidences of insertions and deletions in the sgRNA-targeted regions reached 76% and above, and no credible off-target sites were detected using WGS. The results provided comprehensive basic experimental evidence and methodological recommendations for future personalized HIV-1 treatment using CRISPR/Cas9 genome editing technology.
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Affiliation(s)
- Yufan Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaorong Peng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yanghao Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Changzhong Jin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiangyun Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Dating Han
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Haijing Fu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Chaoyu Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Nanping Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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7
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Liu Y, Zhou C, Huang S, Dang L, Wei Y, He J, Zhou Y, Mao S, Tao W, Zhang Y, Yang H, Huang X, Chi T. A Cas-embedding strategy for minimizing off-target effects of DNA base editors. Nat Commun 2020; 11:6073. [PMID: 33247095 DOI: 10.1038/s41467-020-19690-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/19/2020] [Indexed: 12/26/2022] Open
Abstract
DNA base editors, typically comprising editing enzymes fused to the N-terminus of nCas9, display off-target effects on DNA and/or RNA, which have remained an obstacle to their clinical applications. Off-target edits are typically countered via rationally designed point mutations, but the approach is tedious and not always effective. Here, we report that the off-target effects of both A > G and C > T editors can be dramatically reduced without compromising the on-target editing simply by inserting the editing enzymes into the middle of nCas9 at tolerant sites identified using a transposon-based genetic screen. Furthermore, employing this Cas-embedding strategy, we have created a highly specific editor capable of efficient C > T editing at methylated and GC-rich sequences. DNA base editors can display off-target effects on DNA and RNA. Here the authors embed the base editing enzymes in the middle of nCas9 to reduce these without impacting on-target editing.
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8
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Huang X, Lv J, Li Y, Mao S, Li Z, Jing Z, Sun Y, Zhang X, Shen S, Wang X, Di M, Ge J, Huang X, Zuo E, Chi T. Programmable C-to-U RNA editing using the human APOBEC3A deaminase. EMBO J 2020; 39:e104741. [PMID: 33058229 PMCID: PMC7667879 DOI: 10.15252/embj.2020104741] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 09/07/2020] [Accepted: 09/18/2020] [Indexed: 12/12/2022] Open
Abstract
Programmable RNA cytidine deamination has recently been achieved using a bifunctional editor (RESCUE-S) capable of deaminating both adenine and cysteine. Here, we report the development of "CURE", the first cytidine-specific C-to-U RNA Editor. CURE comprises the cytidine deaminase enzyme APOBEC3A fused to dCas13 and acts in conjunction with unconventional guide RNAs (gRNAs) designed to induce loops at the target sites. Importantly, CURE does not deaminate adenosine, enabling the high-specificity versions of CURE to create fewer missense mutations than RESCUE-S at the off-targets transcriptome-wide. The two editing approaches exhibit overlapping editing motif preferences, with CURE and RESCUE-S being uniquely able to edit UCC and AC motifs, respectively, while they outperform each other at different subsets of the UC targets. Finally, a nuclear-localized version of CURE, but not that of RESCUE-S, can efficiently edit nuclear RNAs. Thus, CURE and RESCUE are distinct in design and complementary in utility.
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Affiliation(s)
- Xinxin Huang
- School of Life Sciences and TechnologyShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Junjun Lv
- School of Life Sciences and TechnologyShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yongqin Li
- School of Life Sciences and TechnologyShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Shaoshuai Mao
- School of Life Sciences and TechnologyShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhifang Li
- Shenzhen BranchGuangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Zhengyu Jing
- School of Life Sciences and TechnologyShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yidi Sun
- Institute of NeuroscienceState Key Laboratory of NeuroscienceKey Laboratory of Primate NeurobiologyCAS Center for Excellence in Brain Science and Intelligence TechnologyShanghai Research Center for Brain Science and Brain‐Inspired IntelligenceShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Xiaoming Zhang
- School of Life Sciences and TechnologyShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Shengxi Shen
- School of Life Sciences and TechnologyShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xinxin Wang
- School of Life Sciences and TechnologyShanghaiTech UniversityShanghaiChina
| | - Minghui Di
- School of Life Sciences and TechnologyShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jianyang Ge
- School of Life Sciences and TechnologyShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xingxu Huang
- School of Life Sciences and TechnologyShanghaiTech UniversityShanghaiChina
| | - Erwei Zuo
- Shenzhen BranchGuangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Tian Chi
- School of Life Sciences and TechnologyShanghaiTech UniversityShanghaiChina
- Department of ImmunobiologyYale University School of MedicineNew HavenCTUSA
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9
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Liu Y, Mao S, Huang S, Li Y, Chen Y, Di M, Huang X, Lv J, Wang X, Ge J, Shen S, Zhang X, Liu D, Huang X, Chi T. REPAIRx, a specific yet highly efficient programmable A > I RNA base editor. EMBO J 2020; 39:e104748. [PMID: 33058207 DOI: 10.15252/embj.2020104748] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/27/2020] [Accepted: 06/03/2020] [Indexed: 12/26/2022] Open
Abstract
Programmable A > I RNA editing is a valuable tool for basic research and medicine. A variety of editors have been created, but a genetically encoded editor that is both precise and efficient has not been described to date. The trade-off between precision and efficiency is exemplified in the state of the art editor REPAIR, which comprises the ADAR2 deaminase domain fused to dCas13b. REPAIR is highly efficient, but also causes significant off-target effects. Mutations that weaken the deaminase domain can minimize the undesirable effects, but this comes at the expense of on-target editing efficiency. We have now overcome this dilemma by using a multipronged approach: We have chosen an alternative Cas protein (CasRx), inserted the deaminase domain into the middle of CasRx, and redirected the editor to the nucleus. The new editor created, dubbed REPAIRx, is precise yet highly efficient, outperforming various previous versions on both mRNA and nuclear RNA targets. Thus, REPAIRx markedly expands the RNA editing toolkit and illustrates a novel strategy for base editor optimization.
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Affiliation(s)
- Yajing Liu
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China.,Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shaoshuai Mao
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China.,Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Shisheng Huang
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yongqin Li
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China.,Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Yuxin Chen
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Minghui Di
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xinxin Huang
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Junjun Lv
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xinxin Wang
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China
| | - Jianyang Ge
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China
| | - Shengxi Shen
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoming Zhang
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Dahai Liu
- Department of Basic Medicine and Biomedical Engineering, School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Xingxu Huang
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China
| | - Tian Chi
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
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