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Cardi T, Murovec J, Bakhsh A, Boniecka J, Bruegmann T, Bull SE, Eeckhaut T, Fladung M, Galovic V, Linkiewicz A, Lukan T, Mafra I, Michalski K, Kavas M, Nicolia A, Nowakowska J, Sági L, Sarmiento C, Yıldırım K, Zlatković M, Hensel G, Van Laere K. CRISPR/Cas-mediated plant genome editing: outstanding challenges a decade after implementation. TRENDS IN PLANT SCIENCE 2023; 28:1144-1165. [PMID: 37331842 DOI: 10.1016/j.tplants.2023.05.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/09/2023] [Accepted: 05/15/2023] [Indexed: 06/20/2023]
Abstract
The discovery of the CRISPR/Cas genome-editing system has revolutionized our understanding of the plant genome. CRISPR/Cas has been used for over a decade to modify plant genomes for the study of specific genes and biosynthetic pathways as well as to speed up breeding in many plant species, including both model and non-model crops. Although the CRISPR/Cas system is very efficient for genome editing, many bottlenecks and challenges slow down further improvement and applications. In this review we discuss the challenges that can occur during tissue culture, transformation, regeneration, and mutant detection. We also review the opportunities provided by new CRISPR platforms and specific applications related to gene regulation, abiotic and biotic stress response improvement, and de novo domestication of plants.
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Affiliation(s)
- Teodoro Cardi
- Consiglio Nazionale delle Ricerche (CNR), Institute of Biosciences and Bioresources (IBBR), Portici, Italy; CREA Research Centre for Vegetable and Ornamental Crops, Pontecagnano, Italy
| | - Jana Murovec
- University of Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | - Allah Bakhsh
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey; Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Justyna Boniecka
- Department of Genetics, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Toruń, Poland; Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Toruń, Poland
| | | | - Simon E Bull
- Molecular Plant Breeding, Institute of Agricultural Sciences, Eidgenössische Technische Hochschule (ETH) Zurich, Switzerland; Plant Biochemistry, Institute of Molecular Plant Biology, ETH, Zurich, Switzerland
| | - Tom Eeckhaut
- Flanders Research Institute for Agricultural, Fisheries and Food, Melle, Belgium
| | | | - Vladislava Galovic
- University of Novi Sad, Institute of Lowland Forestry and Environment (ILFE), Novi Sad, Serbia
| | - Anna Linkiewicz
- Molecular Biology and Genetics Department, Institute of Biological Sciences, Faculty of Biology and Environmental Sciences, Cardinal Stefan Wyszyński University, Warsaw, Poland
| | - Tjaša Lukan
- National Institute of Biology, Department of Biotechnology and Systems Biology, Ljubljana, Slovenia
| | - Isabel Mafra
- Rede de Química e Tecnologia (REQUIMTE) Laboratório Associado para a Química Verde (LAQV), Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Krzysztof Michalski
- Plant Breeding and Acclimatization Institute, National Research Institute, Błonie, Poland
| | - Musa Kavas
- Department of Molecular Biology and Genetics, Faculty of Science, Ondokuz Mayis University, Samsun, Turkey
| | - Alessandro Nicolia
- CREA Research Centre for Vegetable and Ornamental Crops, Pontecagnano, Italy
| | - Justyna Nowakowska
- Molecular Biology and Genetics Department, Institute of Biological Sciences, Faculty of Biology and Environmental Sciences, Cardinal Stefan Wyszyński University, Warsaw, Poland
| | - Laszlo Sági
- Centre for Agricultural Research, Loránd Eötvös Research Network, Martonvásár, Hungary
| | - Cecilia Sarmiento
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Kubilay Yıldırım
- Department of Molecular Biology and Genetics, Faculty of Science, Ondokuz Mayis University, Samsun, Turkey
| | - Milica Zlatković
- University of Novi Sad, Institute of Lowland Forestry and Environment (ILFE), Novi Sad, Serbia
| | - Goetz Hensel
- Heinrich-Heine-University, Institute of Plant Biochemistry, Centre for Plant Genome Engineering, Düsseldorf, Germany; Division of Molecular Biology, Centre of the Region Hana for Biotechnological and Agriculture Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Katrijn Van Laere
- Flanders Research Institute for Agricultural, Fisheries and Food, Melle, Belgium.
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Tang Y, Zhang Z, Yang Z, Wu J. CRISPR/Cas9 and Agrobacterium tumefaciens virulence proteins synergistically increase efficiency of precise genome editing via homology directed repair in plants. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:3518-3530. [PMID: 36919203 PMCID: PMC10797490 DOI: 10.1093/jxb/erad096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
CRISPR/Cas9 genome editing and Agrobacterium tumefaciens-mediated genetic transformation are widely-used plant biotechnology tools derived from bacterial immunity-related systems, each involving DNA modification. The Cas9 endonuclease introduces DNA double-strand breaks (DSBs), and the A. tumefaciens T-DNA is released by the VirD2 endonuclease assisted by VirDl and attached by VirE2, transferred to the plant nucleus and integrated into the genome. Here, we explored the potential for synergy between the two systems and found that Cas9 and three virulence (Vir) proteins achieve precise genome editing via the homology directed repair (HDR) pathway in tobacco and rice plants. Compared with Cas9T (Cas9, VirD1, VirE2) and CvD (Cas9-VirD2) systems, the HDR frequencies of a foreign GFPm gene in the CvDT system (Cas9-VirD2, VirD1, VirE2) increased 52-fold and 22-fold, respectively. Further optimization of the CvDT process with a donor linker (CvDTL) achieved a remarkable increase in the efficiency of HDR-mediated genome editing. Additionally, the HDR efficiency of the three rice endogenous genes ACETOLACTATE SYNTHASE (ALS), PHYTOENE DESATURASE (PDS), and NITROGEN TRANSPORTER 1.1 B (NRT1.1B) increased 24-, 32- and 16-fold, respectively, in the CvDTL system, compared with corresponding Cas9TL (Cas9T process with a donor linker). Our results suggest that collaboration between CRISPR/Cas9 and Agrobacterium-mediated genetic transformation can make great progress towards highly efficient and precise genome editing via the HDR pathway.
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Affiliation(s)
- Ye Tang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhennan Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhiyuan Yang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jiahe Wu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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3
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Zhou J, Luan X, Liu Y, Wang L, Wang J, Yang S, Liu S, Zhang J, Liu H, Yao D. Strategies and Methods for Improving the Efficiency of CRISPR/Cas9 Gene Editing in Plant Molecular Breeding. PLANTS (BASEL, SWITZERLAND) 2023; 12:1478. [PMID: 37050104 PMCID: PMC10097296 DOI: 10.3390/plants12071478] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
Following recent developments and refinement, CRISPR-Cas9 gene-editing technology has become increasingly mature and is being widely used for crop improvement. The application of CRISPR/Cas9 enables the generation of transgene-free genome-edited plants in a short period and has the advantages of simplicity, high efficiency, high specificity, and low production costs, which greatly facilitate the study of gene functions. In plant molecular breeding, the gene-editing efficiency of the CRISPR-Cas9 system has proven to be a key step in influencing the effectiveness of molecular breeding, with improvements in gene-editing efficiency recently becoming a focus of reported scientific research. This review details strategies and methods for improving the efficiency of CRISPR/Cas9 gene editing in plant molecular breeding, including Cas9 variant enzyme engineering, the effect of multiple promoter driven Cas9, and gRNA efficient optimization and expression strategies. It also briefly introduces the optimization strategies of the CRISPR/Cas12a system and the application of BE and PE precision editing. These strategies are beneficial for the further development and optimization of gene editing systems in the field of plant molecular breeding.
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Affiliation(s)
- Junming Zhou
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Xinchao Luan
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Yixuan Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Lixue Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Jiaxin Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Songnan Yang
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; (S.Y.); (J.Z.)
| | - Shuying Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Jun Zhang
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; (S.Y.); (J.Z.)
| | - Huijing Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Dan Yao
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
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A roadmap for translational cancer glycoimmunology at single cell resolution. J Exp Clin Cancer Res 2022; 41:143. [PMID: 35428302 PMCID: PMC9013178 DOI: 10.1186/s13046-022-02335-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/17/2022] [Indexed: 11/11/2022] Open
Abstract
Cancer cells can evade immune responses by exploiting inhibitory immune checkpoints. Immune checkpoint inhibitor (ICI) therapies based on anti-CTLA-4 and anti-PD-1/PD-L1 antibodies have been extensively explored over the recent years to unleash otherwise compromised anti-cancer immune responses. However, it is also well established that immune suppression is a multifactorial process involving an intricate crosstalk between cancer cells and the immune systems. The cancer glycome is emerging as a relevant source of immune checkpoints governing immunosuppressive behaviour in immune cells, paving an avenue for novel immunotherapeutic options. This review addresses the current state-of-the-art concerning the role played by glycans controlling innate and adaptive immune responses, while shedding light on available experimental models for glycoimmunology. We also emphasize the tremendous progress observed in the development of humanized models for immunology, the paramount contribution of advances in high-throughput single-cell analysis in this context, and the importance of including predictive machine learning algorithms in translational research. This may constitute an important roadmap for glycoimmunology, supporting careful adoption of models foreseeing clinical translation of fundamental glycobiology knowledge towards next generation immunotherapies.
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Tian W, Huang X, Ouyang X. Genome-wide prediction of activating regulatory elements in rice by combining STARR-seq with FACS. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2284-2297. [PMID: 36028476 PMCID: PMC9674312 DOI: 10.1111/pbi.13907] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/23/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Self-transcribing active regulatory region sequencing (STARR-seq) is widely used to identify enhancers at the whole-genome level. However, whether STARR-seq works as efficiently in plants as in animal systems remains unclear. Here, we determined that the traditional STARR-seq method can be directly applied to rice (Oryza sativa) protoplasts to identify enhancers, though with limited efficiency. Intriguingly, we identified not only enhancers but also constitutive promoters with this technique. To increase the performance of STARR-seq in plants, we optimized two procedures. We coupled fluorescence activating cell sorting (FACS) with STARR-seq to alleviate the effect of background noise, and we minimized PCR cycles and retained duplicates during prediction, which significantly increased the positive rate for activating regulatory elements (AREs). Using this method, we determined that AREs are associated with AT-rich regions and are enriched for a motif that the AP2/ERF family can recognize. Based on GC content preferences, AREs are clustered into two groups corresponding to promoters and enhancers. Either AT- or GC-rich regions within AREs could boost transcription. Additionally, disruption of AREs resulted in abnormal expression of both proximal and distal genes, which suggests that STARR-seq-revealed elements function as enhancers in vivo. In summary, our work provides a promising method to identify AREs in plants.
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Affiliation(s)
- Wei Tian
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life SciencesXiamen UniversityXiamenChina
| | - Xi Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life SciencesXiamen UniversityXiamenChina
| | - Xinhao Ouyang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life SciencesXiamen UniversityXiamenChina
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Biswas S, Bridgeland A, Irum S, Thomson MJ, Septiningsih EM. Optimization of Prime Editing in Rice, Peanut, Chickpea, and Cowpea Protoplasts by Restoration of GFP Activity. Int J Mol Sci 2022; 23:9809. [PMID: 36077206 PMCID: PMC9456013 DOI: 10.3390/ijms23179809] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/19/2022] [Accepted: 08/26/2022] [Indexed: 01/23/2023] Open
Abstract
Precise editing of the plant genome has long been desired for functional genomic research and crop breeding. Prime editing is a newly developed precise editing technology based on CRISPR-Cas9, which uses an engineered reverse transcriptase (RT), a catalytically impaired Cas9 endonuclease (nCas9), and a prime editing guide RNA (pegRNA). In addition, prime editing has a wider range of editing types than base editing and can produce nearly all types of edits. Although prime editing was first established in human cells, it has recently been applied to plants. As a relatively new technique, optimization will be needed to increase the editing efficiency in different crops. In this study, we successfully edited a mutant GFP in rice, peanut, chickpea, and cowpea protoplasts. In rice, up to 16 times higher editing efficiency was achieved with a dual pegRNA than the single pegRNA containing vectors. Edited-mutant GFP protoplasts have also been obtained in peanut, chickpea, and cowpea after transformation with the dual pegRNA vectors, albeit with much lower editing efficiency than in rice, ranging from 0.2% to 0.5%. These initial results promise to expedite the application of prime editing in legume breeding programs to accelerate crop improvement.
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Affiliation(s)
- Sudip Biswas
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Aya Bridgeland
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Samra Irum
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
- Department of Biological Sciences, International Islamic University, Islamabad 44000, Pakistan
| | - Michael J. Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
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Uetz P, Melnik S, Grünwald-Gruber C, Strasser R, Stoger E. CRISPR/Cas9-mediated knockout of a prolyl-4-hydroxylase subfamily in Nicotiana benthamiana using DsRed2 for plant selection. Biotechnol J 2022; 17:e2100698. [PMID: 35427441 DOI: 10.1002/biot.202100698] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 04/01/2022] [Accepted: 04/11/2022] [Indexed: 11/08/2022]
Abstract
The properties of host plants used for molecular farming can be modified by CRISPR/Cas9 genome editing to improve the quality and yield of recombinant proteins. However, it is often necessary to target multiple genes simultaneously, particularly when using host plants with large and complex genomes. This is the case for Nicotiana benthamiana, an allotetraploid relative of tobacco frequently used for transient protein expression. A multiplex genome editing system incorporating the DsRed2 fluorescent marker for the identification and selection of transgenic plants was established. As proof of principle, NbP4H4 was targeted encoding a prolyl-4-hydroxylase involved in protein O-linked glycosylation. Using preselected gRNAs with efficiencies confirmed by transient expression, transgenic plant lines with knockout mutations in all four NbP4H4 genes were obtained. Leaf fluorescence was then used to screen for the absence of the SpCas9 transgene in T1 plants, and transgene-free lines with homozygous or biallelic mutations were identified. The analysis of plant-produced recombinant IgA1 as a reporter protein revealed changes in the number of peptides containing hydroxyproline residues and pentoses in the knockout plants. The selection of efficient gRNAs combined with the DsRed2 marker reduces the effort needed to generate N. benthamiana mutants and simplifies the screening processes to obtain transgene-free progeny.
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Affiliation(s)
- Pia Uetz
- Institute of Plant Biotechnology and Cell Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Stanislav Melnik
- Institute of Plant Biotechnology and Cell Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Clemens Grünwald-Gruber
- Core Facility Mass Spectrometry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Richard Strasser
- Institute of Plant Biotechnology and Cell Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Eva Stoger
- Institute of Plant Biotechnology and Cell Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
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Zhong Y, Qu JZ, Liu X, Ding L, Liu Y, Bertoft E, Petersen BL, Hamaker BR, Hebelstrup KH, Blennow A. Different genetic strategies to generate high amylose starch mutants by engineering the starch biosynthetic pathways. Carbohydr Polym 2022; 287:119327. [DOI: 10.1016/j.carbpol.2022.119327] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/04/2022] [Accepted: 03/06/2022] [Indexed: 01/14/2023]
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Andreasson E, Kieu NP, Zahid MA, Carlsen FM, Marit L, Sandgrind S, Petersen BL, Zhu LH. Invited Mini-Review Research Topic: Utilization of Protoplasts to Facilitate Gene Editing in Plants: Schemes for In Vitro Shoot Regeneration From Tissues and Protoplasts of Potato and Rapeseed: Implications of Bioengineering Such as Gene Editing of Broad-Leaved Plants. Front Genome Ed 2022; 4:780004. [PMID: 35845346 PMCID: PMC9276966 DOI: 10.3389/fgeed.2022.780004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Schemes for efficient regenerationand recovery of shoots from in vitro tissues or single cells, such as protoplasts, are only available for limited numbers of plant species and genotypes and are crucial for establishing gene editing tools on a broader scale in agriculture and plant biology. Growth conditions, including hormone and nutrient composition as well as light regimes in key steps of known regeneration protocols, display significant variations, even between the genotypes within the same species, e.g., potato (Solanum tuberosum). As fresh plant material is a prerequisite for successful shoot regeneration, the plant material often needs to be refreshed for optimizing the growth and physiological state prior to genetic transformation. Utilization of protoplasts has become a more important approach for obtaining transgene-free edited plants by genome editing, CRISPR/Cas9. In this approach, callus formation from protoplasts is induced by one set of hormones, followed by organogenesis, i.e., shoot formation, which is induced by a second set of hormones. The requirements on culture conditions at these key steps vary considerably between the species and genotypes, which often require quantitative adjustments of medium compositions. In this mini-review, we outline the protocols and notes for clonal regeneration and cultivation from single cells, particularly protoplasts in potato and rapeseed. We focus mainly on different hormone treatment schemes and highlight the importance of medium compositions, e.g., sugar, nutrient, and light regimes as well as culture durations at the key regeneration steps. We believe that this review would provide important information and hints for establishing efficient regeneration strategies from other closely related and broad-leaved plant species in general.
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Affiliation(s)
- Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Lomma, Sweden
- *Correspondence: Erik Andreasson,
| | - Nam Phuong Kieu
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Muhammad Awais Zahid
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Frida Meijer Carlsen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Lenman Marit
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Sjur Sandgrind
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Bent Larsen Petersen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Li-Hua Zhu
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
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Mahto RK, Ambika, Singh C, Chandana BS, Singh RK, Verma S, Gahlaut V, Manohar M, Yadav N, Kumar R. Chickpea Biofortification for Cytokinin Dehydrogenase via Genome Editing to Enhance Abiotic-Biotic Stress Tolerance and Food Security. Front Genet 2022; 13:900324. [PMID: 35669196 PMCID: PMC9164125 DOI: 10.3389/fgene.2022.900324] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
Globally more than two billion people suffer from micronutrient malnutrition (also known as "hidden hunger"). Further, the pregnant women and children in developing nations are mainly affected by micronutrient deficiencies. One of the most important factors is food insecurity which can be mitigated by improving the nutritional values through biofortification using selective breeding and genetic enhancement techniques. Chickpea is the second most important legume with numerous economic and nutraceutical properties. Therefore, chickpea production needs to be increased from the current level. However, various kind of biotic and abiotic stresses hamper global chickpea production. The emerging popular targets for biofortification in agronomic crops include targeting cytokinin dehydrogenase (CKX). The CKXs play essential roles in both physiological and developmental processes and directly impact several agronomic parameters i.e., growth, development, and yield. Manipulation of CKX genes using genome editing tools in several crop plants reveal that CKXs are involved in regulation yield, shoot and root growth, and minerals nutrition. Therefore, CKXs have become popular targets for yield improvement, their overexpression and mutants can be directly correlated with the increased yield and tolerance to various stresses. Here, we provide detailed information on the different roles of CKX genes in chickpea. In the end, we discuss the utilization of genome editing tool clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9 (CRISPR/Cas9) to engineer CKX genes that can facilitate trait improvement. Overall, recent advancements in CKX and their role in plant growth, stresses and nutrient accumulation are highlighted, which could be used for chickpea improvement.
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Affiliation(s)
| | - Ambika
- Department of Genetics and Plant Breeding, UAS, Bangalore, India
| | - Charul Singh
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - B S. Chandana
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | | | - Shruti Verma
- NCoE-SAM, Department of Pediatrics, KSCH, Lady Hardinge Medical College, New Delhi, India
| | - Vijay Gahlaut
- Institute of Himalayan Bioresource Technology (CSIR), Palampur, India
| | - Murli Manohar
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Neelam Yadav
- Centre of Food Technology, University of Allahabad, Prayagraj, India
| | - Rajendra Kumar
- Indian Agricultural Research Institute (ICAR), New Delhi, India
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Carlsen FM, Johansen IE, Yang Z, Liu Y, Westberg IN, Kieu NP, Jørgensen B, Lenman M, Andreasson E, Nielsen KL, Blennow A, Petersen BL. Strategies for Efficient Gene Editing in Protoplasts of Solanum tuberosum Theme: Determining gRNA Efficiency Design by Utilizing Protoplast (Research). Front Genome Ed 2022; 3:795644. [PMID: 35128523 PMCID: PMC8811252 DOI: 10.3389/fgeed.2021.795644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Potato, Solanum tuberosum is a highly diverse tetraploid crop. Elite cultivars are extremely heterozygous with a high prevalence of small length polymorphisms (indels) and single nucleotide polymorphisms (SNPs) within and between cultivars, which must be considered in CRISPR/Cas gene editing strategies and designs to obtain successful gene editing. In the present study, in-depth sequencing of the gene encoding glucan water dikinase (GWD) 1 and the downy mildew resistant 6 (DMR6-1) genes in the potato cultivars Saturna and Wotan, respectively, revealed both indels and a 1.3–2.8 higher SNP prevalence when compared to the heterozygous diploid RH genome sequence as expected for a tetraploid compared to a diploid. This complicates guide RNA (gRNA) and diagnostic PCR designs. At the same time, high editing efficiencies at the cell pool (protoplast) level are pivotal for achieving full allelic knock-out in tetraploids. Furthermore, high editing efficiencies reduce the downstream cumbersome and delicate ex-plant regeneration. Here, CRISPR/Cas ribonucleoprotein particles (RNPs) were delivered transiently to protoplasts by polyethylene glycol (PEG) mediated transformation. For each of GWD1 and the DMR6-1, 6–10 gRNAs were designed to target regions comprising the 5′ and the 3′ end of the two genes. Similar to other studies including several organisms, editing efficiency of the individual RNPs varied significantly, and some generated specific indel patterns. RNP’s targeting the 5′ end of GWD1 yielded significantly higher editing efficiency as compared to targeting the 3′ end. For DMR6-1, such an effect was not seen. Simultaneously targeting each of the two target regions with two RNPs (multiplexing) yielded a clear positive synergistic effect on the total editing when targeting the 3′ end of the GWD1 gene only. Multiplexing of the two genes, residing on different chromosomes, yielded no or a slightly negative effect on editing from the single or combined gRNA/RNPs. These initial findings may instigate much larger studies needed for facilitating and optimizing precision breeding in plants.
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Affiliation(s)
- Frida Meijer Carlsen
- Department of Plant and Environmental Sciences, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Ida Elisabeth Johansen
- Department of Plant and Environmental Sciences, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
- Kartoffel Mel Centralen Amba, Brande, Denmark
| | - Zhang Yang
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ying Liu
- Department of Plant and Environmental Sciences, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Ida Nøhr Westberg
- Department of Plant and Environmental Sciences, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Nam Phuong Kieu
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Bodil Jørgensen
- Department of Plant and Environmental Sciences, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Marit Lenman
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Andreas Blennow
- Department of Plant and Environmental Sciences, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Bent Larsen Petersen
- Department of Plant and Environmental Sciences, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
- *Correspondence: Bent Larsen Petersen,
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12
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Decaestecker W, Bollier N, Buono RA, Nowack MK, Jacobs TB. Protoplast Preparation and Fluorescence-Activated Cell Sorting for the Evaluation of Targeted Mutagenesis in Plant Cells. Methods Mol Biol 2022; 2464:205-221. [PMID: 35258835 DOI: 10.1007/978-1-0716-2164-6_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Fluorescence-activated cell sorting (FACS) allows for the enrichment of specific plant cell populations after protoplasting. In this book chapter, we describe the transformation and protoplasting of an Arabidopsis thaliana cell suspension culture (PSB-D, derived from MM2d) that can be used for the evaluation of CRISPR vectors in a subpopulation of cells. We also describe the protoplasting of Arabidopsis thaliana cells from the roots and stomatal lineage for the evaluation of tissue-specific gene editing. These protocols allow us to rapidly and accurately quantify various CRISPR systems in plant cells.
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Affiliation(s)
- Ward Decaestecker
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Norbert Bollier
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Rafael Andrade Buono
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Moritz K Nowack
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Thomas B Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
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13
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Kiryushkin AS, Ilina EL, Guseva ED, Pawlowski K, Demchenko KN. Hairy CRISPR: Genome Editing in Plants Using Hairy Root Transformation. PLANTS (BASEL, SWITZERLAND) 2021; 11:51. [PMID: 35009056 PMCID: PMC8747350 DOI: 10.3390/plants11010051] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/15/2021] [Accepted: 12/20/2021] [Indexed: 05/27/2023]
Abstract
CRISPR/Cas-mediated genome editing is a powerful tool of plant functional genomics. Hairy root transformation is a rapid and convenient approach for obtaining transgenic roots. When combined, these techniques represent a fast and effective means of studying gene function. In this review, we outline the current state of the art reached by the combination of these approaches over seven years. Additionally, we discuss the origins of different Agrobacterium rhizogenes strains that are widely used for hairy root transformation; the components of CRISPR/Cas vectors, such as the promoters that drive Cas or gRNA expression, the types of Cas nuclease, and selectable and screenable markers; and the application of CRISPR/Cas genome editing in hairy roots. The modification of the already known vector pKSE401 with the addition of the rice translational enhancer OsMac3 and the gene encoding the fluorescent protein DsRed1 is also described.
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Affiliation(s)
- Alexey S. Kiryushkin
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (E.L.I.); (E.D.G.)
| | - Elena L. Ilina
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (E.L.I.); (E.D.G.)
| | - Elizaveta D. Guseva
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (E.L.I.); (E.D.G.)
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden
| | - Kirill N. Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (E.L.I.); (E.D.G.)
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14
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Goullée H, Taylor RL, Forrest ARR, Laing NG, Ravenscroft G, Clayton JS. Improved CRISPR/Cas9 gene editing in primary human myoblasts using low confluency cultures on Matrigel. Skelet Muscle 2021; 11:23. [PMID: 34551826 PMCID: PMC8456651 DOI: 10.1186/s13395-021-00278-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 09/08/2021] [Indexed: 11/23/2022] Open
Abstract
Background CRISPR/Cas9 is an invaluable tool for studying cell biology and the development of molecular therapies. However, delivery of CRISPR/Cas9 components into some cell types remains a major hurdle. Primary human myoblasts are a valuable cell model for muscle studies, but are notoriously difficult to transfect. There are currently no commercial lipofection protocols tailored for primary myoblasts, and most generic guidelines simply recommend transfecting healthy cells at high confluency. This study aimed to maximize CRISPR/Cas9 transfection and editing in primary human myoblasts. Methods Since increased cell proliferation is associated with increased transfection efficiency, we investigated two factors known to influence myoblast proliferation: cell confluency, and a basement membrane matrix, Matrigel. CRISPR/Cas9 editing was performed by delivering Cas9 ribonucleoprotein complexes via lipofection into primary human myoblasts, cultured in wells with or without a Matrigel coating, at low (~ 40%) or high (~ 80%) confluency. Results Cells transfected at low confluency on Matrigel-coated wells had the highest levels of transfection, and were most effectively edited across three different target loci, achieving a maximum editing efficiency of 93.8%. On average, editing under these conditions was >4-fold higher compared to commercial recommendations (high confluency, uncoated wells). Conclusion This study presents a simple, effective and economical method of maximizing CRISPR/Cas9-mediated gene editing in primary human myoblasts. This protocol could be a valuable tool for improving the genetic manipulation of cultured human skeletal muscle cells, and potentially be adapted for use in other cell types. Supplementary Information The online version contains supplementary material available at 10.1186/s13395-021-00278-1.
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Affiliation(s)
- Hayley Goullée
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, WA, Australia.,Harry Perkins Institute of Medical Research, 6 Verdun St, Nedlands, WA, 6009, Australia.,School of Biomedical Science, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, WA, Australia
| | - Rhonda L Taylor
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, WA, Australia.,Harry Perkins Institute of Medical Research, 6 Verdun St, Nedlands, WA, 6009, Australia.,School of Biomedical Science, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, WA, Australia
| | - Alistair R R Forrest
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, WA, Australia.,Harry Perkins Institute of Medical Research, 6 Verdun St, Nedlands, WA, 6009, Australia
| | - Nigel G Laing
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, WA, Australia.,Harry Perkins Institute of Medical Research, 6 Verdun St, Nedlands, WA, 6009, Australia
| | - Gianina Ravenscroft
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, WA, Australia.,Harry Perkins Institute of Medical Research, 6 Verdun St, Nedlands, WA, 6009, Australia
| | - Joshua S Clayton
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, WA, Australia. .,Harry Perkins Institute of Medical Research, 6 Verdun St, Nedlands, WA, 6009, Australia.
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15
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Acha G, Vergara R, Muñoz M, Mora R, Aguirre C, Muñoz M, Kalazich J, Prieto H. A Traceable DNA-Replicon Derived Vector to Speed Up Gene Editing in Potato: Interrupting Genes Related to Undesirable Postharvest Tuber Traits as an Example. PLANTS 2021; 10:plants10091882. [PMID: 34579415 PMCID: PMC8468489 DOI: 10.3390/plants10091882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 11/30/2022]
Abstract
In potato (Solanum tuberosum L.), protoplast techniques are limited to a few genotypes; thus, the use of regular regeneration procedures of multicellular explants causes us to face complexities associated to CRISPR/Cas9 gene editing efficiency and final identification of individuals. Geminivirus-based replicons contained in T-DNAs could provide an improvement to these procedures considering their cargo capability. We built a Bean yellow dwarf virus-derived replicon vector, pGEF-U, that expresses all the editing reagents under a multi-guide RNA condition, and the Green Fluorescent Protein (GFP) marker gene. Agrobacterium-mediated gene transfer experiments were carried out on ‘Yagana-INIA’, a relevant local variety with no previous regeneration protocol. Assays showed that pGEF-U had GFP transient expression for up to 10 days post-infiltration when leaf explants were used. A dedicated potato genome analysis tool allowed for the design of guide RNA pairs to induce double cuts of genes associated to enzymatic browning (StPPO1 and 2) and to cold-induced sweetening (StvacINV1 and StBAM1). Monitoring GFP at 7 days post-infiltration, explants led to vector validation as well as to selection for regeneration (34.3% of starting explants). Plant sets were evaluated for the targeted deletion, showing individuals edited for StPPO1 and StBAM1 genes (1 and 4 lines, respectively), although with a transgenic condition. While no targeted deletion was seen in StvacINV1 and StPPO2 plant sets, stable GFP-expressing calli were chosen for analysis; we observed different repair alternatives, ranging from the expected loss of large gene fragments to those showing punctual insertions/deletions at both cut sites or incomplete repairs along the target region. Results validate pGEF-U for gene editing coupled to regular regeneration protocols, and both targeted deletion and single site editings encourage further characterization of the set of plants already generated.
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Affiliation(s)
- Giovana Acha
- Programa de Doctorado en Biotecnología, Universidad de Santiago, Santiago 9170020, Chile;
| | - Ricardo Vergara
- Laboratorio de Biotecnología, Instituto de Investigaciones Agropecuarias-La Platina, Santiago 8831314, Chile; (M.M.); (R.M.); (C.A.)
- Correspondence: (R.V.); (H.P.); Tel.: +56-2-2577-9129 (R.V. & H.P.)
| | - Marisol Muñoz
- Laboratorio de Biotecnología, Instituto de Investigaciones Agropecuarias-La Platina, Santiago 8831314, Chile; (M.M.); (R.M.); (C.A.)
| | - Roxana Mora
- Laboratorio de Biotecnología, Instituto de Investigaciones Agropecuarias-La Platina, Santiago 8831314, Chile; (M.M.); (R.M.); (C.A.)
| | - Carlos Aguirre
- Laboratorio de Biotecnología, Instituto de Investigaciones Agropecuarias-La Platina, Santiago 8831314, Chile; (M.M.); (R.M.); (C.A.)
| | - Manuel Muñoz
- Instituto de Investigaciones Agropecuarias-Remehue, Osorno 5290000, Chile;
| | - Julio Kalazich
- Carrera de Agronomía, Campus Osorno, Universidad de Los Lagos, Osorno 5290000, Chile;
| | - Humberto Prieto
- Laboratorio de Biotecnología, Instituto de Investigaciones Agropecuarias-La Platina, Santiago 8831314, Chile; (M.M.); (R.M.); (C.A.)
- Correspondence: (R.V.); (H.P.); Tel.: +56-2-2577-9129 (R.V. & H.P.)
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16
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Badhan S, Ball AS, Mantri N. First Report of CRISPR/Cas9 Mediated DNA-Free Editing of 4CL and RVE7 Genes in Chickpea Protoplasts. Int J Mol Sci 2021; 22:E396. [PMID: 33401455 PMCID: PMC7795094 DOI: 10.3390/ijms22010396] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/28/2020] [Accepted: 12/29/2020] [Indexed: 12/13/2022] Open
Abstract
The current genome editing system Clustered Regularly Interspaced Short Palindromic Repeats Cas9 (CRISPR/Cas9) has already confirmed its proficiency, adaptability, and simplicity in several plant-based applications. Together with the availability of a vast amount of genome data and transcriptome data, CRISPR/Cas9 presents a massive opportunity for plant breeders and researchers. The successful delivery of ribonucleoproteins (RNPs), which are composed of Cas9 enzyme and a synthetically designed single guide RNA (sgRNA) and are used in combination with various transformation methods or lately available novel nanoparticle-based delivery approaches, allows targeted mutagenesis in plants species. Even though this editing technique is limitless, it has still not been employed in many plant species to date. Chickpea is the second most crucial winter grain crop cultivated worldwide; there are currently no reports on CRISPR/Cas9 gene editing in chickpea. Here, we selected the 4-coumarate ligase (4CL) and Reveille 7 (RVE7) genes, both associated with drought tolerance for CRISPR/Cas9 editing in chickpea protoplast. The 4CL represents a key enzyme involved in phenylpropanoid metabolism in the lignin biosynthesis pathway. It regulates the accumulation of lignin under stress conditions in several plants. The RVE7 is a MYB transcription factor which is part of regulating circadian rhythm in plants. The knockout of these selected genes in the chickpea protoplast using DNA-free CRISPR/Cas9 editing represents a novel approach for achieving targeted mutagenesis in chickpea. Results showed high-efficiency editing was achieved for RVE7 gene in vivo compared to the 4CL gene. This study will help unravel the role of these genes under drought stress and understand the complex drought stress mechanism pathways. This is the first study in chickpea protoplast utilizing CRISPR/Cas9 DNA free gene editing of drought tolerance associated genes.
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Affiliation(s)
| | | | - Nitin Mantri
- The Pangenomics Lab, School of Science, RMIT University, Melbourne 3000, Australia; (S.B.); (A.S.B.)
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17
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Bennett EP, Petersen BL, Johansen IE, Niu Y, Yang Z, Chamberlain CA, Met Ö, Wandall HH, Frödin M. INDEL detection, the 'Achilles heel' of precise genome editing: a survey of methods for accurate profiling of gene editing induced indels. Nucleic Acids Res 2020; 48:11958-11981. [PMID: 33170255 PMCID: PMC7708060 DOI: 10.1093/nar/gkaa975] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 10/05/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022] Open
Abstract
Advances in genome editing technologies have enabled manipulation of genomes at the single base level. These technologies are based on programmable nucleases (PNs) that include meganucleases, zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated 9 (Cas9) nucleases and have given researchers the ability to delete, insert or replace genomic DNA in cells, tissues and whole organisms. The great flexibility in re-designing the genomic target specificity of PNs has vastly expanded the scope of gene editing applications in life science, and shows great promise for development of the next generation gene therapies. PN technologies share the principle of inducing a DNA double-strand break (DSB) at a user-specified site in the genome, followed by cellular repair of the induced DSB. PN-elicited DSBs are mainly repaired by the non-homologous end joining (NHEJ) and the microhomology-mediated end joining (MMEJ) pathways, which can elicit a variety of small insertion or deletion (indel) mutations. If indels are elicited in a protein coding sequence and shift the reading frame, targeted gene knock out (KO) can readily be achieved using either of the available PNs. Despite the ease by which gene inactivation in principle can be achieved, in practice, successful KO is not only determined by the efficiency of NHEJ and MMEJ repair; it also depends on the design and properties of the PN utilized, delivery format chosen, the preferred indel repair outcomes at the targeted site, the chromatin state of the target site and the relative activities of the repair pathways in the edited cells. These variables preclude accurate prediction of the nature and frequency of PN induced indels. A key step of any gene KO experiment therefore becomes the detection, characterization and quantification of the indel(s) induced at the targeted genomic site in cells, tissues or whole organisms. In this survey, we briefly review naturally occurring indels and their detection. Next, we review the methods that have been developed for detection of PN-induced indels. We briefly outline the experimental steps and describe the pros and cons of the various methods to help users decide a suitable method for their editing application. We highlight recent advances that enable accurate and sensitive quantification of indel events in cells regardless of their genome complexity, turning a complex pool of different indel events into informative indel profiles. Finally, we review what has been learned about PN-elicited indel formation through the use of the new methods and how this insight is helping to further advance the genome editing field.
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Affiliation(s)
- Eric Paul Bennett
- Copenhagen Center for Glycomics, Department of Odontology and Molecular and Cellular Medicine, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Bent Larsen Petersen
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Ida Elisabeth Johansen
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Yiyuan Niu
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, China
| | - Zhang Yang
- Copenhagen Center for Glycomics, Department of Odontology and Molecular and Cellular Medicine, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | | | - Özcan Met
- Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hans H Wandall
- Copenhagen Center for Glycomics, Department of Odontology and Molecular and Cellular Medicine, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Morten Frödin
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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18
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Wang J, Chen H. A novel CRISPR/Cas9 system for efficiently generating Cas9-free multiplex mutants in Arabidopsis. ABIOTECH 2020; 1:6-14. [PMID: 36305009 PMCID: PMC9584096 DOI: 10.1007/s42994-019-00011-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/07/2019] [Indexed: 11/30/2022]
Abstract
The CRISPR/Cas9 genome-editing system has emerged as a popular powerful tool for biological research. However, the process of selecting efficiently edited Cas9-free plants is usually laborious and time consuming. Here, we demonstrated P2A to be the most efficient self-cleaving peptide for fusing Cas9 and GFP in Arabidopsis and then used Cas9-P2A-GFP to develop a novel CRISPR/Cas9 system. Additionally, a pair of isocaudomer restriction enzymes were selected to conveniently assemble multiple sgRNAs. In this system, the GFP fluorescence intensity in T1 transgenic plants indicates the expression level of the Cas9 protein, which correlates well with the editing efficiency. Furthermore, Cas9-free plants can be easily selected by examining GFP fluorescence in T2 transgenic plants. The efficient knockout of BRI1, BZR1 and BES1 demonstrated the robustness of our new system. Thus, we designed a novel CRISPR/Cas9 system that can generate Cas9-free multiplex mutants efficiently in Arabidopsis and possibly in other plant species.
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Affiliation(s)
- Jiajun Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Haodong Chen
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
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19
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High efficacy full allelic CRISPR/Cas9 gene editing in tetraploid potato. Sci Rep 2019; 9:17715. [PMID: 31776399 PMCID: PMC6881354 DOI: 10.1038/s41598-019-54126-w] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 08/29/2019] [Indexed: 12/20/2022] Open
Abstract
CRISPR/Cas9 editing efficacies in tetraploid potato were highly improved through the use of endogenous potato U6 promoters. Highly increased editing efficiencies in the Granular Bound Starch Synthase gene at the protoplast level were obtained by replacement of the Arabidopsis U6 promotor, driving expression of the CRISPR component, with endogenous potato U6 promotors. This translated at the ex-plant level into 35% full allelic gene editing. Indel Detection Amplicon Analysis was established as an efficient tool for fast assessment of gene editing in complex genomes, such as potato. Together, this warrants significant reduction of laborious cell culturing, ex-plant regeneration and screening procedures of plants with high complexity genomes.
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