351
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Wolter F, Puchta H. In planta gene targeting can be enhanced by the use of CRISPR/Cas12a. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1083-1094. [PMID: 31381206 DOI: 10.1111/tpj.14488] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 07/08/2019] [Accepted: 07/29/2019] [Indexed: 05/20/2023]
Abstract
The controlled change of plant genomes by homologous recombination (HR) is still difficult to achieve. We previously developed the in planta gene targeting (ipGT) technology which depends on the simultaneous activation of the target locus by a double-strand break and the excision of the target vector. Whereas the use of SpCas9 resulted in low ipGT frequencies in Arabidopsis, we were recently able to improve the efficiency by using egg cell-specific expression of the potent but less broadly applicable SaCas9 nuclease. In this study, we now tested whether we could improve ipGT further, by either performing it in cells with enhanced intrachromosomal HR efficiencies or by the use of Cas12a, a different kind of CRISPR/Cas nuclease with an alternative cutting mechanism. We could show before that plants possess three kinds of DNA ATPase complexes, which all lead to instabilities of homologous genomic repeats if lost by mutation. As these proteins act in independent pathways, we tested ipGT in double mutants in which intrachromosomal HR is enhanced 20-80-fold. However, we were not able to obtain higher ipGT frequencies, indicating that mechanisms for gene targeting (GT) and chromosomal repeat-induced HR differ. However, using LbCas12a, the GT frequencies were higher than with SaCas9, despite a lower non-homologous end-joining (NHEJ) induction efficiency, demonstrating the particular suitability of Cas12a to induce HR. As SaCas9 has substantial restrictions due to its longer GC rich PAM sequence, the use of LbCas12a with its AT-rich PAM broadens the range of ipGT drastically, particularly when targeting in CG-deserts like promoters and introns.
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Affiliation(s)
- Felix Wolter
- Botanical Institute, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany
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352
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Wierson WA, Simone BW, WareJoncas Z, Mann C, Welker JM, Kar B, Emch MJ, Friedberg I, Gendron WA, Barry MA, Clark KJ, Dobbs DL, McGrail MA, Ekker SC, Essner JJ. Expanding the CRISPR Toolbox with ErCas12a in Zebrafish and Human Cells. CRISPR J 2019; 2:417-433. [PMID: 31742435 PMCID: PMC6919245 DOI: 10.1089/crispr.2019.0026] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
CRISPR and CRISPR-Cas effector proteins enable the targeting of DNA double-strand breaks to defined loci based on a variable length RNA guide specific to each effector. The guide RNAs are generally similar in size and form, consisting of a ∼20 nucleotide sequence complementary to the DNA target and an RNA secondary structure recognized by the effector. However, the effector proteins vary in protospacer adjacent motif requirements, nuclease activities, and DNA binding kinetics. Recently, ErCas12a, a new member of the Cas12a family, was identified in Eubacterium rectale. Here, we report the first characterization of ErCas12a activity in zebrafish and expand on previously reported activity in human cells. Using a fluorescent reporter system, we show that CRISPR-ErCas12a elicits strand annealing mediated DNA repair more efficiently than CRISPR-Cas9. Further, using our previously reported gene targeting method that utilizes short homology, GeneWeld, we demonstrate the use of CRISPR-ErCas12a to integrate reporter alleles into the genomes of both zebrafish and human cells. Together, this work provides methods for deploying an additional CRISPR-Cas system, thus increasing the flexibility researchers have in applying genome engineering technologies.
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Affiliation(s)
- Wesley A. Wierson
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa
| | - Brandon W. Simone
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Zachary WareJoncas
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Carla Mann
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa
| | - Jordan M. Welker
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa
| | - Bibekananda Kar
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Michael J. Emch
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Iddo Friedberg
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, Iowa
| | - William A.C. Gendron
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Michael A. Barry
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Karl J. Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Drena L. Dobbs
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa
| | - Maura A. McGrail
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa
| | - Stephen C. Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Jeffrey J. Essner
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa
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353
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Manghwar H, Lindsey K, Zhang X, Jin S. CRISPR/Cas System: Recent Advances and Future Prospects for Genome Editing. TRENDS IN PLANT SCIENCE 2019; 24:1102-1125. [PMID: 31727474 DOI: 10.1016/j.tplants.2019.09.006] [Citation(s) in RCA: 208] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 08/30/2019] [Accepted: 09/12/2019] [Indexed: 05/20/2023]
Abstract
Genome editing (GE) has revolutionized biological research through the new ability to precisely edit the genomes of living organisms. In recent years, various GE tools have been explored for editing simple and complex genomes. The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system has widely been used in GE due to its high efficiency, ease of use, and accuracy. It can be used to add desirable and remove undesirable alleles simultaneously in a single event. Here, we discuss various applications of CRISPR/Cas9 in a range of important crops, compare it with other GE tools, and review its mechanism, limitations, and future possibilities. Various newly emerging CRISPR/Cas systems, including base editing (BE), xCas9, and Cas12a (Cpf1), are also considered.
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Affiliation(s)
- Hakim Manghwar
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China
| | - Keith Lindsey
- Department of Biosciences, Durham University, Durham DH1 3LE, UK
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China.
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China.
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354
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Li J, Hong S, Chen W, Zuo E, Yang H. Advances in detecting and reducing off-target effects generated by CRISPR-mediated genome editing. J Genet Genomics 2019; 46:513-521. [PMID: 31911131 DOI: 10.1016/j.jgg.2019.11.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/05/2019] [Accepted: 11/14/2019] [Indexed: 12/26/2022]
Abstract
CRISPR-mediated genome editing is a revolutionary technology for genome manipulation that uses the CRISPR-Cas systems and base editors. Currently, poor efficiency and off-target problems have impeded the application of CRISPR systems. The on-target efficiency has been improved in several advanced versions of CRISPR systems, whereas the off-target detection still remains a key challenge. Here, we outline the different versions of CRISPR systems and off-target detection strategies, discuss the merits and limitations of off-target detection methods, and provide potential implications for further gene editing research.
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Affiliation(s)
- Jinjing Li
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China; Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Shunyan Hong
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China; Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Wanjin Chen
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China; Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China.
| | - Erwei Zuo
- Lingnan Guangdong Laboratory of Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
| | - Hui Yang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
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355
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Hematopoietic stem cell gene therapy: The optimal use of lentivirus and gene editing approaches. Blood Rev 2019; 40:100641. [PMID: 31761379 DOI: 10.1016/j.blre.2019.100641] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/06/2019] [Accepted: 11/11/2019] [Indexed: 12/26/2022]
Abstract
Due to pioneering in vitro investigations on gene modification, gene engineering platforms have incredibly improved to a safer and more powerful tool for the treatment of multiple blood and immune disorders. Likewise, several clinical trials have been initiated combining autologous hematopoietic stem cell transplantation (auto-HSCT) with gene therapy (GT) tools. As several GT modalities such as lentivirus and gene editing tools have a long developmental path ahead to diminish its negative side effects, it is hard to decide which modality is optimal for treating a specific disease. Gene transfer by lentiviruses is the platform of choice for loss-of-mutation diseases, whereas gene correction/addition or gene disruption by gene editing tools, mainly CRISPR/Cas9, is likely to be more efficient in diseases where tight regulation is needed. Therefore, in this review, we compiled pertinent information about lentiviral gene transfer and CRISPR/Cas9 gene editing, their evolution to a safer platform for HSCT, and their applications on other types of gene disorders based on the etiology of the disease and cell fitness.
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356
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Hason M, Bartůněk P. Zebrafish Models of Cancer-New Insights on Modeling Human Cancer in a Non-Mammalian Vertebrate. Genes (Basel) 2019; 10:genes10110935. [PMID: 31731811 PMCID: PMC6896156 DOI: 10.3390/genes10110935] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/11/2019] [Accepted: 11/11/2019] [Indexed: 12/26/2022] Open
Abstract
Zebrafish (Danio rerio) is a valuable non-mammalian vertebrate model widely used to study development and disease, including more recently cancer. The evolutionary conservation of cancer-related programs between human and zebrafish is striking and allows extrapolation of research outcomes obtained in fish back to humans. Zebrafish has gained attention as a robust model for cancer research mainly because of its high fecundity, cost-effective maintenance, dynamic visualization of tumor growth in vivo, and the possibility of chemical screening in large numbers of animals at reasonable costs. Novel approaches in modeling tumor growth, such as using transgene electroporation in adult zebrafish, could improve our knowledge about the spatial and temporal control of cancer formation and progression in vivo. Looking at genetic as well as epigenetic alterations could be important to explain the pathogenesis of a disease as complex as cancer. In this review, we highlight classic genetic and transplantation models of cancer in zebrafish as well as provide new insights on advances in cancer modeling. Recent progress in zebrafish xenotransplantation studies and drug screening has shown that zebrafish is a reliable model to study human cancer and could be suitable for evaluating patient-derived xenograft cell invasiveness. Rapid, large-scale evaluation of in vivo drug responses and kinetics in zebrafish could undoubtedly lead to new applications in personalized medicine and combination therapy. For all of the above-mentioned reasons, zebrafish is approaching a future of being a pre-clinical cancer model, alongside the mouse. However, the mouse will continue to be valuable in the last steps of pre-clinical drug screening, mostly because of the highly conserved mammalian genome and biological processes.
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357
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Engineered amphiphilic peptides enable delivery of proteins and CRISPR-associated nucleases to airway epithelia. Nat Commun 2019; 10:4906. [PMID: 31659165 PMCID: PMC6817825 DOI: 10.1038/s41467-019-12922-y] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 09/30/2019] [Indexed: 12/20/2022] Open
Abstract
The delivery of biologic cargoes to airway epithelial cells is challenging due to the formidable barriers imposed by its specialized and differentiated cells. Among cargoes, recombinant proteins offer therapeutic promise but the lack of effective delivery methods limits their development. Here, we achieve protein and SpCas9 or AsCas12a ribonucleoprotein (RNP) delivery to cultured human well-differentiated airway epithelial cells and mouse lungs with engineered amphiphilic peptides. These shuttle peptides, non-covalently combined with GFP protein or CRISPR-associated nuclease (Cas) RNP, allow rapid entry into cultured human ciliated and non-ciliated epithelial cells and mouse airway epithelia. Instillation of shuttle peptides combined with SpCas9 or AsCas12a RNP achieves editing of loxP sites in airway epithelia of ROSAmT/mG mice. We observe no evidence of short-term toxicity with a widespread distribution restricted to the respiratory tract. This peptide-based technology advances potential therapeutic avenues for protein and Cas RNP delivery to refractory airway epithelial cells. Delivering biological cargo to airway epithelial cells is very challenging. Here, the authors use engineered amphiphilic peptides to shuttle proteins and CRISPR RNPs into airway cells in vivo.
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358
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Jiang W, Singh J, Allen A, Li Y, Kathiresan V, Qureshi O, Tangprasertchai N, Zhang X, Parameshwaran HP, Rajan R, Qin PZ. CRISPR-Cas12a Nucleases Bind Flexible DNA Duplexes without RNA/DNA Complementarity. ACS OMEGA 2019; 4:17140-17147. [PMID: 31656887 PMCID: PMC6811856 DOI: 10.1021/acsomega.9b01469] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/25/2019] [Indexed: 05/03/2023]
Abstract
Cas12a (also known as "Cpf1") is a class 2 type V-A CRISPR-associated nuclease that can cleave double-stranded DNA at specific sites. The Cas12a effector enzyme comprises a single protein and a CRISPR-encoded small RNA (crRNA) and has been used for genome editing and manipulation. Work reported here examined in vitro interactions between the Cas12a effector enzyme and DNA duplexes with varying states of base-pairing between the two strands. The data revealed that in the absence of complementarity between the crRNA guide and the DNA target-strand, Cas12a binds duplexes with unpaired segments. These off-target duplexes were bound at the Cas12a site responsible for RNA-guided double-stranded DNA binding but were not cleaved due to the lack of RNA/DNA hybrid formation. Such promiscuous binding was attributed to increased DNA flexibility induced by the unpaired segment present next to the protospacer-adjacent-motif. The results suggest that target discrimination of Cas12a can be influenced by flexibility of the DNA. As such, in addition to the linear sequence, flexibility and other physical properties of the DNA should be considered in Cas12a-based genome engineering applications.
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Affiliation(s)
- Wei Jiang
- Department of Chemistry andDepartment of
Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Jaideep Singh
- Department of Chemistry andDepartment of
Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Aleique Allen
- Department of Chemistry andDepartment of
Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Yue Li
- Department of Chemistry andDepartment of
Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Venkatesan Kathiresan
- Department of Chemistry andDepartment of
Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Omair Qureshi
- Department of Chemistry andDepartment of
Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Narin Tangprasertchai
- Department of Chemistry andDepartment of
Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Xiaojun Zhang
- Department of Chemistry andDepartment of
Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
| | - Hari Priya Parameshwaran
- Department
of Chemistry and Biochemistry, Price Family Foundation Institute of
Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Rakhi Rajan
- Department
of Chemistry and Biochemistry, Price Family Foundation Institute of
Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Peter Z. Qin
- Department of Chemistry andDepartment of
Biological Sciences, University of Southern
California, Los Angeles, California 90089, United States
- E-mail: . Phone: (213) 821-2461. Fax: (213) 740-2701
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359
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CRISPR technologies for stem cell engineering and regenerative medicine. Biotechnol Adv 2019; 37:107447. [PMID: 31513841 DOI: 10.1016/j.biotechadv.2019.107447] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/03/2019] [Accepted: 09/06/2019] [Indexed: 12/13/2022]
Abstract
CRISPR/Cas9 system exploits the concerted action of Cas9 nuclease and programmable single guide RNA (sgRNA), and has been widely used for genome editing. The Cas9 nuclease activity can be abolished by mutation to yield the catalytically deactivated Cas9 (dCas9). Coupling with the customizable sgRNA for targeting, dCas9 can be fused with transcription repressors to inhibit specific gene expression (CRISPR interference, CRISPRi) or fused with transcription activators to activate the expression of gene of interest (CRISPR activation, CRISPRa). Here we introduce the principles and recent advances of these CRISPR technologies, their delivery vectors and review their applications in stem cell engineering and regenerative medicine. In particular, we focus on in vitro stem cell fate manipulation and in vivo applications such as prevention of retinal and muscular degeneration, neural regeneration, bone regeneration, cartilage tissue engineering, as well as treatment of diseases in blood, skin and liver. Finally, the challenges to translate CRISPR to regenerative medicine and future perspectives are discussed and proposed.
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360
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Shelake RM, Pramanik D, Kim JY. Exploration of Plant-Microbe Interactions for Sustainable Agriculture in CRISPR Era. Microorganisms 2019; 7:E269. [PMID: 31426522 PMCID: PMC6723455 DOI: 10.3390/microorganisms7080269] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/08/2019] [Accepted: 08/14/2019] [Indexed: 12/16/2022] Open
Abstract
Plants and microbes are co-evolved and interact with each other in nature. Plant-associated microbes, often referred to as plant microbiota, are an integral part of plant life. Depending on the health effects on hosts, plant-microbe (PM) interactions are either beneficial or harmful. The role of microbiota in plant growth promotion (PGP) and protection against various stresses is well known. Recently, our knowledge of community composition of plant microbiome and significant driving factors have significantly improved. So, the use of plant microbiome is a reliable approach for a next green revolution and to meet the global food demand in sustainable and eco-friendly agriculture. An application of the multifaceted PM interactions needs the use of novel tools to know critical genetic and molecular aspects. Recently discovered clustered regularly interspaced short palindromic repeats (CRISPR)/Cas-mediated genome editing (GE) tools are of great interest to explore PM interactions. A systematic understanding of the PM interactions will enable the application of GE tools to enhance the capacity of microbes or plants for agronomic trait improvement. This review focuses on applying GE techniques in plants or associated microbiota for discovering the fundamentals of the PM interactions, disease resistance, PGP activity, and future implications in agriculture.
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Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
| | - Dibyajyoti Pramanik
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Plus Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea.
- Division of Life Science (CK1 Program), Gyeongsang National University, Jinju 660-701, Korea.
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361
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Zhang Y, Malzahn AA, Sretenovic S, Qi Y. The emerging and uncultivated potential of CRISPR technology in plant science. NATURE PLANTS 2019; 5:778-794. [PMID: 31308503 DOI: 10.1038/s41477-019-0461-5] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 05/24/2019] [Indexed: 05/18/2023]
Abstract
The application of clustered regularly interspaced short palindromic repeats (CRISPR) for genetic manipulation has revolutionized life science over the past few years. CRISPR was first discovered as an adaptive immune system in bacteria and archaea, and then engineered to generate targeted DNA breaks in living cells and organisms. During the cellular DNA repair process, various DNA changes can be introduced. The diverse and expanding CRISPR toolbox allows programmable genome editing, epigenome editing and transcriptome regulation in plants. However, challenges in plant genome editing need to be fully appreciated and solutions explored. This Review intends to provide an informative summary of the latest developments and breakthroughs of CRISPR technology, with a focus on achievements and potential utility in plant biology. Ultimately, CRISPR will not only facilitate basic research, but also accelerate plant breeding and germplasm development. The application of CRISPR to improve germplasm is particularly important in the context of global climate change as well as in the face of current agricultural, environmental and ecological challenges.
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Affiliation(s)
- Yingxiao Zhang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Aimee A Malzahn
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Simon Sretenovic
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA.
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362
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Abstract
The prokaryote-derived CRISPR-Cas genome editing systems have transformed our ability to manipulate, detect, image and annotate specific DNA and RNA sequences in living cells of diverse species. The ease of use and robustness of this technology have revolutionized genome editing for research ranging from fundamental science to translational medicine. Initial successes have inspired efforts to discover new systems for targeting and manipulating nucleic acids, including those from Cas9, Cas12, Cascade and Cas13 orthologues. Genome editing by CRISPR-Cas can utilize non-homologous end joining and homology-directed repair for DNA repair, as well as single-base editing enzymes. In addition to targeting DNA, CRISPR-Cas-based RNA-targeting tools are being developed for research, medicine and diagnostics. Nuclease-inactive and RNA-targeting Cas proteins have been fused to a plethora of effector proteins to regulate gene expression, epigenetic modifications and chromatin interactions. Collectively, the new advances are considerably improving our understanding of biological processes and are propelling CRISPR-Cas-based tools towards clinical use in gene and cell therapies.
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Affiliation(s)
- Adrian Pickar-Oliver
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA.
- Department of Surgery, Duke University Medical Center, Durham, NC, USA.
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363
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Liu J, Srinivasan S, Li CY, Ho IL, Rose J, Shaheen M, Wang G, Yao W, Deem A, Bristow C, Hart T, Draetta G. Pooled library screening with multiplexed Cpf1 library. Nat Commun 2019; 10:3144. [PMID: 31316073 PMCID: PMC6637147 DOI: 10.1038/s41467-019-10963-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 05/31/2019] [Indexed: 12/26/2022] Open
Abstract
Capitalizing on the inherent multiplexing capability of AsCpf1, we developed a multiplexed, high-throughput screening strategy that minimizes library size without sacrificing gene targeting efficiency. We demonstrated that AsCpf1 can be used for functional genomics screenings and that an AsCpf1-based multiplexed library performs similarly as compared to currently available monocistronic CRISPR/Cas9 libraries, with only one vector required for each gene. We construct the smallest whole-genome CRISPR knock-out library, Mini-human, for the human genome (n = 17,032 constructs targeting 16,977 protein-coding genes), which performs favorably compared to conventional Cas9 libraries.
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Affiliation(s)
- Jintan Liu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Houston, Houston, TX, 77030, USA.
| | - Sanjana Srinivasan
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Houston, Houston, TX, 77030, USA
| | - Chieh-Yuan Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Houston, Houston, TX, 77030, USA
| | - I-Lin Ho
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Houston, Houston, TX, 77030, USA
| | - Johnathon Rose
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Houston, Houston, TX, 77030, USA
| | - MennatAllah Shaheen
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Houston, Houston, TX, 77030, USA
| | - Gang Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Wantong Yao
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Angela Deem
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Chris Bristow
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Traver Hart
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Giulio Draetta
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Houston, Houston, TX, 77030, USA.
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364
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Puig-Saus C, Ribas A. Gene editing: Towards the third generation of adoptive T-cell transfer therapies. IMMUNO-ONCOLOGY TECHNOLOGY 2019; 1:19-26. [PMID: 35755321 PMCID: PMC9216344 DOI: 10.1016/j.iotech.2019.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
First-generation adoptive T-cell transfer (ACT) administering tumor-infiltrating lymphocytes (TILs), and second-generation ACT using autologous T cells genetically modified to express tumor-specific T-cell receptors (TCRs) or chimeric antigen receptors (CARs) have both shown promise for the treatment of several cancers, including melanoma, leukemia and lymphoma. However, these treatments require labor-intensive manufacturing of the cell product for each patient, frequently utilize lentiviral or retroviral vectors to genetically modify the T cells, and have limited antitumor efficacy in solid tumors. Gene editing is revolutionizing the field of gene therapy, and ACT is at the forefront of this revolution. Gene-editing technologies can be used to re-engineer the phenotype of T cells to increase their antitumor potency, to generate off-the-shelf ACT products, and to replace endogenous TCRs with tumor-specific TCRs or CARs using homology-directed repair (HDR) donor templates. Adeno-associated viral vectors or linear DNA have been used as HDR donor templates. Of note, non-viral delivery substantially reduces the time required to generate clinical-grade reagents for manufacture of T-cell products—a critical step for the translation of personalized T-cell therapies. These technological advances in the field using gene editing open the door to the third generation of ACT therapies. CRISPR-Cas9 allows the generation of tumor-specific T cells for adoptive T-cell transfer (ACT). Gene editing allows generation of off-the-shelf ACT products. Gene editing can tailor T-cell phenotype and increase antitumor potency. Non-viral gene editing is a requirement for personalized ACT. Personalized third-generation ACT: gene-edited neoantigen-specific T cells.
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Affiliation(s)
- Cristina Puig-Saus
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, USA
| | - Antoni Ribas
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, USA.,Division of Surgical Oncology, Department of Surgery, UCLA, Los Angeles, USA.,Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, USA.,Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, USA
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Abstract
Abstract
The development of clustered regularly interspaced short-palindromic repeat (CRISPR)-Cas systems for genome editing has transformed the way life science research is conducted and holds enormous potential for the treatment of disease as well as for many aspects of biotechnology. Here, I provide a personal perspective on the development of CRISPR-Cas9 for genome editing within the broader context of the field and discuss our work to discover novel Cas effectors and develop them into additional molecular tools. The initial demonstration of Cas9-mediated genome editing launched the development of many other technologies, enabled new lines of biological inquiry, and motivated a deeper examination of natural CRISPR-Cas systems, including the discovery of new types of CRISPR-Cas systems. These new discoveries in turn spurred further technological developments. I review these exciting discoveries and technologies as well as provide an overview of the broad array of applications of these technologies in basic research and in the improvement of human health. It is clear that we are only just beginning to unravel the potential within microbial diversity, and it is quite likely that we will continue to discover other exciting phenomena, some of which it may be possible to repurpose as molecular technologies. The transformation of mysterious natural phenomena to powerful tools, however, takes a collective effort to discover, characterize, and engineer them, and it has been a privilege to join the numerous researchers who have contributed to this transformation of CRISPR-Cas systems.
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366
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Wu N, Liu B, Du H, Zhao S, Li Y, Cheng X, Wang S, Lin J, Zhou J, Qiu G, Wu Z, Zhang J. The Progress of CRISPR/Cas9-Mediated Gene Editing in Generating Mouse/Zebrafish Models of Human Skeletal Diseases. Comput Struct Biotechnol J 2019; 17:954-962. [PMID: 31360334 PMCID: PMC6639410 DOI: 10.1016/j.csbj.2019.06.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/28/2019] [Accepted: 06/11/2019] [Indexed: 12/18/2022] Open
Abstract
Genetic factors play a substantial role in the etiology of skeletal diseases, which involve 1) defects in skeletal development, including intramembranous ossification and endochondral ossification; 2) defects in skeletal metabolism, including late bone growth and bone remodeling; 3) defects in early developmental processes related to skeletal diseases, such as neural crest cell (NCC) and cilia functions; 4) disturbance of the cellular signaling pathways which potentially affect bone growth. Efficient and high-throughput genetic methods have enabled the exploration and verification of disease-causing genes and variants. Animal models including mouse and zebrafish have been extensively used in functional mechanism studies of causal genes and variants. The conventional approaches of generating mutant animal models include spontaneous mutagenesis, random integration, and targeted integration via mouse embryonic stem cells. These approaches are costly and time-consuming. Recent development and application of gene-editing tools, especially the CRISPR/Cas9 system, has significantly accelerated the process of gene-editing in diverse organisms. Here we review both mice and zebrafish models of human skeletal diseases generated by CRISPR/Cas9 system, and their contributions to deciphering the underpins of disease mechanisms.
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Affiliation(s)
- Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
- Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Bowen Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Huakang Du
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Sen Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Yaqi Li
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Xi Cheng
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Shengru Wang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Jiachen Lin
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Junde Zhou
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | | | - Guixing Qiu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
- Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing 100730, China
- Central Laboratory & Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
- Central Laboratory & Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Correspondence to: Z. Wu, Central Laboratory & Medical Research Center, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, China.
| | - Jianguo Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
- Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing 100730, China
- Correspondence to: J. Zhang, Department of Orthopedic Surgery, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Medical Research Center of Orthopedics, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing 100730, China.
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367
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Tang J, Lee T, Sun T. Single-nucleotide editing: From principle, optimization to application. Hum Mutat 2019; 40:2171-2183. [PMID: 31131955 DOI: 10.1002/humu.23819] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/30/2019] [Accepted: 05/23/2019] [Indexed: 12/26/2022]
Abstract
Cytosine base editors (CBEs) and adenine base editors (ABEs), which are generally composed of an engineered deaminase and a catalytically impaired CRISPR-Cas9 variant, are new favorite tools for single base substitution in cells and organisms. In this review, we summarize the principle of base-editing systems and elaborate on the evolution of different platforms of CBEs and ABEs, including their deaminase, Cas9 variants, and editing outcomes. Moreover, we highlight their applications in mouse and human cells and discuss the challenges and prospects of base editors. The ABE- and CBE systems have been used in gene silencing, pathogenic gene correction, and functional genetic screening. Single base editing is becoming a new promising genetic tool in biomedical research and gene therapy.
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Affiliation(s)
- Jinling Tang
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
| | - Trevor Lee
- Department of Cell and Developmental Biology, Weill Medical College, Cornell University, New York, New York
| | - Tao Sun
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian, China
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368
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Chow RD, Wang G, Ye L, Codina A, Kim HR, Shen L, Dong MB, Errami Y, Chen S. In vivo profiling of metastatic double knockouts through CRISPR-Cpf1 screens. Nat Methods 2019; 16:405-408. [PMID: 30962622 PMCID: PMC6592845 DOI: 10.1038/s41592-019-0371-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 03/05/2019] [Indexed: 12/26/2022]
Abstract
The genetic interactions influencing metastatic potential have been challenging to investigate systematically. Here we developed MCAP (massively parallel CRISPR-Cpf1/Cas12a crRNA array profiling), an approach for combinatorial interrogation of double knockouts in vivo. We designed an MCAP library of 11,934 arrays targeting 325 pairwise combinations of genes implicated in metastasis. By assessing the metastatic potential of the double knockouts in mice, we unveiled a quantitative landscape of genetic interactions driving metastasis.
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Affiliation(s)
- Ryan D Chow
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.,System Biology Institute, Integrated Science & Technology Center, Yale University, West Haven, CT, USA.,Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA.,Yale MD-PhD Program, Yale University, New Haven, CT, USA
| | - Guangchuan Wang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.,System Biology Institute, Integrated Science & Technology Center, Yale University, West Haven, CT, USA.,Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA
| | - Lupeng Ye
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.,System Biology Institute, Integrated Science & Technology Center, Yale University, West Haven, CT, USA.,Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA
| | - Adan Codina
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.,System Biology Institute, Integrated Science & Technology Center, Yale University, West Haven, CT, USA.,Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA.,Yale Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT, USA
| | - Hyunu Ray Kim
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.,System Biology Institute, Integrated Science & Technology Center, Yale University, West Haven, CT, USA.,Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA
| | - Li Shen
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.,System Biology Institute, Integrated Science & Technology Center, Yale University, West Haven, CT, USA.,Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA
| | - Matthew B Dong
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.,System Biology Institute, Integrated Science & Technology Center, Yale University, West Haven, CT, USA.,Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA.,Yale MD-PhD Program, Yale University, New Haven, CT, USA.,Yale Immunobiology Program, The Anlyan Center for Medical Research & Education, New Haven, CT, USA
| | - Youssef Errami
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.,System Biology Institute, Integrated Science & Technology Center, Yale University, West Haven, CT, USA.,Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA. .,System Biology Institute, Integrated Science & Technology Center, Yale University, West Haven, CT, USA. .,Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA. .,Yale MD-PhD Program, Yale University, New Haven, CT, USA. .,Yale Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT, USA. .,Yale Immunobiology Program, The Anlyan Center for Medical Research & Education, New Haven, CT, USA. .,Yale Comprehensive Cancer Center, New Haven, CT, USA. .,Yale Stem Cell Center, New Haven, CT, USA.
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369
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Broad-spectrum enzymatic inhibition of CRISPR-Cas12a. Nat Struct Mol Biol 2019; 26:315-321. [PMID: 30936531 PMCID: PMC6449189 DOI: 10.1038/s41594-019-0208-z] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 02/27/2019] [Indexed: 12/15/2022]
Abstract
Cas12a (Cpf1) is a bacterial RNA-guided nuclease used widely for genome editing and diagnostic applications. In bacteria, Cas12a enzymes can be inhibited by bacteriophage-derived proteins, anti-CRISPRs (Acrs), to thwart clustered regularly interspaced short palindromic repeat (CRISPR) adaptive immune systems. How these inhibitors disable Cas12a by preventing programmed DNA cleavage is unknown. We show that three inhibitors (AcrVA1, AcrVA4 and AcrVA5) block Cas12a activity using functionally distinct mechanisms, including a previously unobserved enzymatic strategy. AcrVA4 and AcrVA5 inhibit double-stranded DNA (dsDNA) recognition with AcrVA4 driving Cas12a dimerization. In contrast, AcrVA1 is a multiple-turnover inhibitor that triggers cleavage of the target recognition sequence of the Cas12a-bound guide RNA to irreversibly inactivate the Cas12a complex. These distinct mechanisms equip bacteriophage with tools to evade CRISPR-Cas12a and support biotechnological applications where multiple-turnover enzymatic inhibition of Cas12a are desirable.
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