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Seem K, Kaur S, Kumar S, Mohapatra T. Epigenome editing for targeted DNA (de)methylation: a new perspective in modulating gene expression. Crit Rev Biochem Mol Biol 2024:1-30. [PMID: 38440883 DOI: 10.1080/10409238.2024.2320659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/15/2024] [Indexed: 03/06/2024]
Abstract
Traditionally, it has been believed that inheritance is driven as phenotypic variations resulting from changes in DNA sequence. However, this paradigm has been challenged and redefined in the contemporary era of epigenetics. The changes in DNA methylation, histone modification, non-coding RNA biogenesis, and chromatin remodeling play crucial roles in genomic functions and regulation of gene expression. More importantly, some of these changes are inherited to the next generations as a part of epigenetic memory and play significant roles in gene expression. The sum total of all changes in DNA bases, histone proteins, and ncRNA biogenesis constitutes the epigenome. Continuous progress in deciphering epigenetic regulations and the existence of heritable epigenetic/epiallelic variations associated with trait of interest enables to deploy epigenome editing tools to modulate gene expression. DNA methylation marks can be utilized in epigenome editing for the manipulation of gene expression. Initially, genome/epigenome editing technologies relied on zinc-finger protein or transcriptional activator-like effector protein. However, the discovery of clustered regulatory interspaced short palindromic repeats CRISPR)/deadCRISPR-associated protein 9 (dCas9) enabled epigenome editing to be more specific/efficient for targeted DNA (de)methylation. One of the major concerns has been the off-target effects, wherein epigenome editing may unintentionally modify gene/regulatory element which may cause unintended change/harmful effects. Moreover, epigenome editing of germline cell raises several ethical/safety issues. This review focuses on the recent developments in epigenome editing tools/techniques, technological limitations, and future perspectives of this emerging technology in therapeutics for human diseases as well as plant improvement to achieve sustainable developmental goals.
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Affiliation(s)
- Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Trilochan Mohapatra
- Protection of Plant Varieties and Farmers' Rights Authority, New Delhi, India
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Ochiai H, Yamamoto T. Construction and Evaluation of Zinc Finger Nucleases. Methods Mol Biol 2023; 2637:1-25. [PMID: 36773134 DOI: 10.1007/978-1-0716-3016-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Zinc finger nucleases (ZFNs) are programmable nucleases that have contributed significantly to past genome-editing research. They are now utilized much less owing to the advent of transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats and CRISPR-associated protein system (CRISPR-Cas). These new methods allow for easier generation of reagents that target genomic sequences of interest and are less labor-intensive than ZFNs at targeting desired sequences. However, fundamental ZFN patents have expired, enabling a wide range of their distribution for clinical and industrial applications. This article introduces a ZFN construction protocol that uses bacterial one-hybrid (B1H) selection and single-strand annealing (SSA) assay.
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Affiliation(s)
- Hiroshi Ochiai
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan.
- Genome Editing Innovation Center, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan.
| | - Takashi Yamamoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- Genome Editing Innovation Center, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
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3
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Mikhailov N, Hämäläinen RH. Modulating Mitochondrial DNA Heteroplasmy with Mitochondrially Targeted Endonucleases. Ann Biomed Eng 2022:10.1007/s10439-022-03051-7. [PMID: 36001180 DOI: 10.1007/s10439-022-03051-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/09/2022] [Indexed: 11/01/2022]
Abstract
Mitochondria, mainly known as energy factories of eukaryotic cells, also exert several additional signaling and metabolic functions and are today recognized as major cellular biosynthetic and signaling hubs. Mitochondria possess their own genome (mitochondrial DNA-mtDNA), that encodes proteins essential for oxidative phosphorylation, and mutations in it are an important contributor to human disease. The mtDNA mutations often exist in heteroplasmic conditions, with both healthy and mutant versions of the mtDNA residing in patients' cells and the level of mutant mtDNA may vary between different tissues and organs and affect the clinical outcome of the disease. Thus, shifting the ratio between healthy and mutant mtDNA in patients' cells provides an intriguing therapeutic option for mtDNA diseases. In this review we describe current strategies for modulating mitochondrial heteroplasmy levels with engineered endonucleases including mitochondrially targeted TALENs and Zinc finger nucleases (ZFNs) and discuss their therapeutic potential. These gene therapy tools could in the future provide therapeutic help both for patients with mitochondrial disease as well as in preventing the transfer of pathogenic mtDNA mutations from a mother to her offspring.
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Affiliation(s)
- Nikita Mikhailov
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Riikka H Hämäläinen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland.
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Abstract
Therapeutic gene editing with the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas system offers significant improvements in specificity and programmability compared with previous methods. CRISPR editing strategies can be used ex vivo and in vivo with many theoretic disease applications. Off-target effects of CRISPR-mediated gene editing are an important outcome to be aware of, minimize, and detect. The current methods of regulatory approval for personalized therapies are complex and may be proved inefficient as these therapies are implemented more widely. The role of pathologists and laboratory medicine practitioners is vital to the clinical implementation of therapeutic gene editing.
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Affiliation(s)
- Elan Hahn
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Medical Sciences Building, Room 6231, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.
| | - Matthew Hiemenz
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California 90027, USA; Department of Pathology, Keck School of Medicine of USC, Los Angeles, California 90033, USA
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Amritha PP, Shah JM. Can genetic engineering-based methods for gene function identification be eclipsed by genome editing in plants? A comparison of methodologies. Mol Genet Genomics 2021; 296:485-500. [PMID: 33751237 DOI: 10.1007/s00438-021-01769-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 02/10/2021] [Indexed: 10/22/2022]
Abstract
Finding and explaining the functions of genes in plants have promising applications in crop improvement and bioprospecting and hence, it is important to compare various techniques available for gene function identification in plants. Today, the most popular technology among researchers to identify the functions of genes is the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9)-based genome editing method. But by no means can we say that CRISPR/Cas9 is the go-to method for all purposes. It comes with its own baggage. Researchers will agree and have lived through at least seven more technologies deployed to find the functions of genes, which come under three umbrellas: 1. genetic engineering, 2. transient expression, and 3. chemical/physical mutagenesis. Each of the methods evolved when the previous one ran into an insurmountable problem. In this review, we compare the eight technologies against one another on 14 parameters. This review lays bare the pros and cons, and similarities and dissimilarities of various methods. Every method comes with its advantages and disadvantages. For example, the CRISPR/Cas9-based genome editing is an excellent method for modifying gene sequences, creating allelic versions of genes, thereby aiding the understanding of gene function. But it comes with the baggage of unwanted or off-target mutations. Then, we have methods based on random or targeted knockout of the gene, knockdown, and overexpression of the gene. Targeted disruption of genes is required for complete knockout of gene function, which may not be accomplished by editing. We have also discussed the strategies to overcome the shortcomings of the targeted gene-knockout and the CRISPR/Cas9-based methods. This review serves as a comprehensive guide towards the understanding and comparison of various technologies available for gene function identification in plants and hence, it will find application for crop improvement and bioprospecting related research.
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Affiliation(s)
- P P Amritha
- Department of Plant Science, Central University of Kerala, Periya, Kasaragod, Kerala, 671320, India
| | - Jasmine M Shah
- Department of Plant Science, Central University of Kerala, Periya, Kasaragod, Kerala, 671320, India.
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Hosseini N, Khanahmad H, Esfahani BN, Bandehpour M, Shariati L, Zahedi N, Kazemi B. Targeting of cholera toxin A ( ctxA) gene by zinc finger nuclease: pitfalls of using gene editing tools in prokaryotes. Res Pharm Sci 2020; 15:182-190. [PMID: 32582358 PMCID: PMC7306252 DOI: 10.4103/1735-5362.283818] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/22/2019] [Accepted: 04/29/2020] [Indexed: 01/14/2023] Open
Abstract
Background and purpose: The study was launched to use zinc finger nuclease (ZFN) technology to disrupt the cholera toxin gene (ctxA) for inhibiting CT toxin production in Vibrio cholera (V. cholera). Experimental approach: An engineered ZFN was designed to target the catalytic site of the ctxA gene. The coding sequence of ZFN was cloned to pKD46, pTZ57R T/A vector, and E2-crimson plasmid and transformed to Escherichia coli (E. coli) Top10 and V. cholera. The efficiency of ZFN was evaluated by colony counting. Findings/Results: No expression was observed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and western blotting in transformed E. coli. The ctxA gene sequencing did not show any mutation. Polymerase chain reaction on pKD46-ZFN plasmid had negative results. Transformation of E. coli Top10 with T/A vectors containing whole ZFN sequence led to 7 colonies all of which contained bacteria with self-ligated vector. Transformation with left array ZFN led to 24 colonies of which 6 contained bacteria with self-ligated vector and 18 of them contained bacteria with vector/left array. Transformation of V. cholera with E2-crimson vectors containing whole ZFN did not produce any colonies. Transformation with left array vectors led to 17 colonies containing bacteria with vector/left array. Left array protein band was captured using western blot assay. Conclusions and implications: ZFN might have off target on bacterial genome causing lethal double-strand DNA break due to lack of non-homologous end joining (NHEJ) mechanism. It is recommended to develop ZFNs against bacterial genes, engineered packaging host with NHEJ repair system is essential.
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Affiliation(s)
- Nafiseh Hosseini
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, I.R. Iran
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Bahram Nasr Esfahani
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Mojgan Bandehpour
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, I.R. Iran
| | - Laleh Shariati
- Biosensor Research Center, Department of Biomaterials, Nanotechnology and Tissue Engineering, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Nushin Zahedi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Bahram Kazemi
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, I.R. Iran.,Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, I.R. Iran
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Ashmore-Harris C, Fruhwirth GO. The clinical potential of gene editing as a tool to engineer cell-based therapeutics. Clin Transl Med 2020; 9:15. [PMID: 32034584 PMCID: PMC7007464 DOI: 10.1186/s40169-020-0268-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/29/2020] [Indexed: 12/13/2022] Open
Abstract
The clinical application of ex vivo gene edited cell therapies first began a decade ago with zinc finger nuclease editing of autologous CD4+ T-cells. Editing aimed to disrupt expression of the human immunodeficiency virus co-receptor gene CCR5, with the goal of yielding cells resistant to viral entry, prior to re-infusion into the patient. Since then the field has substantially evolved with the arrival of the new editing technologies transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR), and the potential benefits of gene editing in the arenas of immuno-oncology and blood disorders were quickly recognised. As the breadth of cell therapies available clinically continues to rise there is growing interest in allogeneic and off-the-shelf approaches and multiplex editing strategies are increasingly employed. We review here the latest clinical trials utilising these editing technologies and consider the applications on the horizon.
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Affiliation(s)
- Candice Ashmore-Harris
- Imaging Therapy and Cancer Group, Dept of Imaging Chemistry & Biology, School of Biomedical Engineering & Imaging Sciences, St Thomas' Hospital, King's College London (KCL), London, SE1 7EH, UK
- Centre for Stem Cells & Regenerative Medicine, School of Basic and Medical Biosciences, Guy's Hospital, KCL, London, SE1 9RT, UK
| | - Gilbert O Fruhwirth
- Imaging Therapy and Cancer Group, Dept of Imaging Chemistry & Biology, School of Biomedical Engineering & Imaging Sciences, St Thomas' Hospital, King's College London (KCL), London, SE1 7EH, UK.
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Pathak BP, Pruett E, Guan H, Srivastava V. Utility of I-SceI and CCR5-ZFN nucleases in excising selectable marker genes from transgenic plants. BMC Res Notes 2019; 12:272. [PMID: 31088537 PMCID: PMC6518718 DOI: 10.1186/s13104-019-4304-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/04/2019] [Indexed: 11/21/2022] Open
Abstract
Objectives Removal of selection marker genes from transgenic plants is highly desirable for their regulatory approval and public acceptance. This study evaluated the use of two nucleases, the yeast homing endonuclease, I-SceI, and the designed zinc finger nuclease, CCR5-ZFN, in excising marker genes from plants using rice and Arabidopsis as the models. Results In an in vitro culture assay, both nucleases were effective in precisely excising the DNA fragments marked by the nuclease target sites. However, rice cultures were found to be refractory to transformation with the I-SceI and CCR5-ZFN overexpressing constructs. The inducible I-SceI expression was also problematic in rice as the progeny of the transgenic lines expressing the heat-inducible I-SceI did not inherit the functional gene. On the other hand, heat-inducible I-SceI expression in Arabidopsis was effective in creating somatic excisions in transgenic plants but ineffective in generating heritable excisions. The inducible expression of CCR5-ZFN in rice, although transmitted stably to the progeny, appeared ineffective in creating detectable excisions. Therefore, toxicity of these nucleases in plant cells poses major bottleneck in their application in plant biotechnology, which could be avoided by expressing them transiently in cultures in vitro. Electronic supplementary material The online version of this article (10.1186/s13104-019-4304-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bhuvan P Pathak
- Dept. of Crop, Soil & Environmental Sciences, University of Arkansas, Fayetteville, AR, USA.,Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, USA
| | - Eliott Pruett
- Dept. of Crop, Soil & Environmental Sciences, University of Arkansas, Fayetteville, AR, USA.,Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, USA
| | - Huazhong Guan
- Dept. of Crop, Soil & Environmental Sciences, University of Arkansas, Fayetteville, AR, USA.,Fujian Provincial Key Laboratory of Crop Breeding, Fujian Agricultural & Forestry University, Fuzhou, China
| | - Vibha Srivastava
- Dept. of Crop, Soil & Environmental Sciences, University of Arkansas, Fayetteville, AR, USA. .,Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, USA. .,Dept. of Horticulture, University of Arkansas, Fayetteville, AR, USA.
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Khan A, Pan X, Najeeb U, Tan DKY, Fahad S, Zahoor R, Luo H. Coping with drought: stress and adaptive mechanisms, and management through cultural and molecular alternatives in cotton as vital constituents for plant stress resilience and fitness. Biol Res 2018; 51:47. [PMID: 30428929 PMCID: PMC6234603 DOI: 10.1186/s40659-018-0198-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/07/2018] [Indexed: 12/18/2022] Open
Abstract
Increased levels of greenhouse gases in the atmosphere and associated climatic variability is primarily responsible for inducing heat waves, flooding and drought stress. Among these, water scarcity is a major limitation to crop productivity. Water stress can severely reduce crop yield and both the severity and duration of the stress are critical. Water availability is a key driver for sustainable cotton production and its limitations can adversely affect physiological and biochemical processes of plants, leading towards lint yield reduction. Adaptation of crop husbandry techniques suitable for cotton crop requires a sound understanding of environmental factors, influencing cotton lint yield and fiber quality. Various defense mechanisms e.g. maintenance of membrane stability, carbon fixation rate, hormone regulation, generation of antioxidants and induction of stress proteins have been found play a vital role in plant survival under moisture stress. Plant molecular breeding plays a functional role to ascertain superior genes for important traits and can offer breeder ready markers for developing ideotypes. This review highlights drought-induced damage to cotton plants at structural, physiological and molecular levels. It also discusses the opportunities for increasing drought tolerance in cotton either through modern gene editing technology like clustered regularly interspaced short palindromic repeat (CRISPR/Cas9), zinc finger nuclease, molecular breeding as well as through crop management, such as use of appropriate fertilization, growth regulator application and soil amendments.
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Affiliation(s)
- Aziz Khan
- The Key Laboratory of Oasis Eco-agriculture, Xinjiang Production and Construction Group, Shihezi University, Shihezi, 832003 People’s Republic of China
- Key Laboratory of Plant Genetic and Breeding, College of Agriculture, Guangxi University, Nanning, 530005 People’s Republic of China
| | - Xudong Pan
- The Key Laboratory of Oasis Eco-agriculture, Xinjiang Production and Construction Group, Shihezi University, Shihezi, 832003 People’s Republic of China
| | - Ullah Najeeb
- Queensland Alliance for Agriculture and Food Innovation, Centre for Plant Science, The University of Queensland, Toowoomba, QLD 4350 Australia
- Plant Breeding Institute, Sydney Institute of Agriculture, School of Life and Environmental Faculty of Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Daniel Kean Yuen Tan
- Plant Breeding Institute, Sydney Institute of Agriculture, School of Life and Environmental Faculty of Science, The University of Sydney, Sydney, NSW 2006 Australia
| | - Shah Fahad
- Department of Plant Sciences and Technology, Huazhong Agriculture University, Wuhan, 430000 People’s Republic of China
- Department of Agronomy, The University of Swabi, Swabi, Pakistan
- College of Life Science, Linyi University, Linyi, 276000 Shandong China
| | - Rizwan Zahoor
- Key Laboratory of Crop Growth Regulation, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095 People’s Republic of China
| | - Honghai Luo
- The Key Laboratory of Oasis Eco-agriculture, Xinjiang Production and Construction Group, Shihezi University, Shihezi, 832003 People’s Republic of China
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Sivalingam J, Kenanov D, Ng WH, Lee SS, Phan TT, Maurer-Stroh S, Kon OL. Integrated Multimodal Evaluation of Genotoxicity in ZFN-Modified Primary Human Cells. Methods Mol Biol 2018; 1867:141-164. [PMID: 30155821 DOI: 10.1007/978-1-4939-8799-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Iatrogenic adverse events in clinical trials of retroviral vector-mediated gene-corrected cells have prioritized the urgent need for more comprehensive and stringent assessment of potentially genotoxic off-target alterations and the biosafety of cells intended for therapeutic applications. Genome editing tools such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced palindromic repeats (CRISPR)-Cas9 nuclease systems are being investigated as safer and efficient alternatives for site-directed genome modification. Using site-specific integration into the AAVS1 locus of primary human cells as an example, we present an integrated approach to multimodal investigation of off-target alterations and an evaluation of potential genotoxicity induced by ZFN-mediated integration of a therapeutic transgene.
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Affiliation(s)
- Jaichandran Sivalingam
- Division of Medical Sciences, Laboratory of Applied Human Genetics, Humphrey Oei Institute of Cancer Research, National Cancer Centre, Singapore, Republic of Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore.
- Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore, Republic of Singapore.
| | - Dimitar Kenanov
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Republic of Singapore.
| | - Wai Har Ng
- Division of Medical Sciences, Laboratory of Applied Human Genetics, Humphrey Oei Institute of Cancer Research, National Cancer Centre, Singapore, Republic of Singapore
| | - Sze Sing Lee
- Division of Medical Sciences, Laboratory of Applied Human Genetics, Humphrey Oei Institute of Cancer Research, National Cancer Centre, Singapore, Republic of Singapore
| | - Toan Thang Phan
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
- CellResearch Corporation, Singapore, Republic of Singapore
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, Republic of Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Republic of Singapore
| | - Oi Lian Kon
- Division of Medical Sciences, Laboratory of Applied Human Genetics, Humphrey Oei Institute of Cancer Research, National Cancer Centre, Singapore, Republic of Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
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Mohanta TK, Bashir T, Hashem A, Abd Allah EF, Bae H. Genome Editing Tools in Plants. Genes (Basel) 2017; 8:E399. [PMID: 29257124 PMCID: PMC5748717 DOI: 10.3390/genes8120399] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/08/2017] [Accepted: 12/15/2017] [Indexed: 12/23/2022] Open
Abstract
Genome editing tools have the potential to change the genomic architecture of a genome at precise locations, with desired accuracy. These tools have been efficiently used for trait discovery and for the generation of plants with high crop yields and resistance to biotic and abiotic stresses. Due to complex genomic architecture, it is challenging to edit all of the genes/genomes using a particular genome editing tool. Therefore, to overcome this challenging task, several genome editing tools have been developed to facilitate efficient genome editing. Some of the major genome editing tools used to edit plant genomes are: Homologous recombination (HR), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), pentatricopeptide repeat proteins (PPRs), the CRISPR/Cas9 system, RNA interference (RNAi), cisgenesis, and intragenesis. In addition, site-directed sequence editing and oligonucleotide-directed mutagenesis have the potential to edit the genome at the single-nucleotide level. Recently, adenine base editors (ABEs) have been developed to mutate A-T base pairs to G-C base pairs. ABEs use deoxyadeninedeaminase (TadA) with catalytically impaired Cas9 nickase to mutate A-T base pairs to G-C base pairs.
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Affiliation(s)
| | - Tufail Bashir
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea.
| | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
- Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, Agriculture Research Center, Giza 12619, Egypt.
| | - Elsayed Fathi Abd Allah
- Plant Production Department, College of Food and Agriculture Science, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Hanhong Bae
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea.
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Sanagala R, Moola AK, Bollipo Diana RK. A review on advanced methods in plant gene targeting. J Genet Eng Biotechnol 2017; 15:317-321. [PMID: 30647669 PMCID: PMC6296621 DOI: 10.1016/j.jgeb.2017.07.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 06/29/2017] [Accepted: 07/03/2017] [Indexed: 12/26/2022]
Abstract
Plant genetic engineering is one of the most significant tools implemented in the modern molecular crop breeding techniques. The conventional approaches of plant genetic transformation include Agrobacterium tumefaciens, particle bombardment, DNA uptake into protoplast. The transgenic events derived by these methods carry the transgenes that are integrated at random sites in the plant genome. Novel techniques that mediate integration of foreign genes at specific pre-determined locations circumvent many problems associated with the existing methods of gene transfer. The recent years have witnessed the emergence of gene targeting techniques by employing zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindrome repeats (CRISPR). The present review focuses on the various approaches and their performance of plant gene targeting and suggests future directions in the important areas of plant molecular biology.
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Affiliation(s)
- Raghavendrarao Sanagala
- National Research Centre on Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Campus, New Delhi 110012, India
- Department of Botany, Bharathidasan University, Tiruchirappalli, Tamil Nadu 620024, India
| | - Anil Kumar Moola
- Department of Botany, Bharathidasan University, Tiruchirappalli, Tamil Nadu 620024, India
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Guha TK, Wai A, Hausner G. Programmable Genome Editing Tools and their Regulation for Efficient Genome Engineering. Comput Struct Biotechnol J 2017; 15:146-60. [PMID: 28179977 DOI: 10.1016/j.csbj.2016.12.006] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/24/2016] [Accepted: 12/27/2016] [Indexed: 12/26/2022] Open
Abstract
Targeted genome editing has become a powerful genetic tool for studying gene function or for modifying genomes by correcting defective genes or introducing genes. A variety of reagents have been developed in recent years that can generate targeted double-stranded DNA cuts which can be repaired by the error-prone, non-homologous end joining repair system or via the homologous recombination-based double-strand break repair pathway provided a suitable template is available. These genome editing reagents require components for recognizing a specific DNA target site and for DNA-cleavage that generates the double-stranded break. In order to reduce potential toxic effects of genome editing reagents, it might be desirable to control the in vitro or in vivo activity of these reagents by incorporating regulatory switches that can reduce off-target activities and/or allow for these reagents to be turned on or off. This review will outline the various genome editing tools that are currently available and describe the strategies that have so far been employed for regulating these editing reagents. In addition, this review will examine potential regulatory switches/strategies that can be employed in the future in order to provide temporal control for these reagents.
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Kumar S, Worden A, Novak S, Lee R, Petolino JF. A trait stacking system via intra-genomic homologous recombination. Planta 2016; 244:1157-1166. [PMID: 27663725 DOI: 10.1007/s00425-016-2595-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/05/2016] [Indexed: 05/24/2023]
Abstract
MAIN CONCLUSION A gene targeting method has been developed, which allows the conversion of 'breeding stacks', containing unlinked transgenes into a 'molecular stack' and thereby circumventing the breeding challenges associated with transgene segregation. A gene targeting method has been developed for converting two unlinked trait loci into a single locus transgene stack. The method utilizes intra-genomic homologous recombination (IGHR) between stably integrated target and donor loci which share sequence homology and nuclease cleavage sites whereby the donor contains a promoterless herbicide resistance transgene. Upon crossing with a zinc finger nuclease (ZFN)-expressing plant, double-strand breaks (DSB) are created in both the stably integrated target and donor loci. DSBs flanking the donor locus result in intra-genomic mobilization of a promoterless selectable marker-containing donor sequence, which can be utilized as a template for homology-directed repair of a concomitant DSB at the target locus resulting in a functional selectable marker via nuclease-mediated cassette exchange (NMCE). The method was successfully demonstrated in maize using a glyphosate tolerance gene as a donor whereby up to 3.3 % of the resulting progeny embryos cultured on selection medium regenerated plants with the donor sequence integrated into the target locus. The process could be extended to multiple cycles of trait stacking by virtue of a unique intron sequence homology for NMCE between the target and the donor loci. This is the first report that describes NMCE via IGHR, thereby enabling trait stacking using conventional crossing.
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Affiliation(s)
- Sandeep Kumar
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN, 46268, USA.
| | - Andrew Worden
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN, 46268, USA
| | - Stephen Novak
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN, 46268, USA
| | - Ryan Lee
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN, 46268, USA
| | - Joseph F Petolino
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN, 46268, USA
- Biotechnology Department, Ivy Tech Community College, 9301 East 59th Street, Indianapolis, IN, 46216, USA
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15
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Qin Z, Li Y, Su B, Cheng Q, Ye Z, Perera DA, Fobes M, Shang M, Dunham RA. Editing of the Luteinizing Hormone Gene to Sterilize Channel Catfish, Ictalurus punctatus, Using a Modified Zinc Finger Nuclease Technology with Electroporation. Mar Biotechnol (NY) 2016; 18:255-263. [PMID: 26846523 DOI: 10.1007/s10126-016-9687-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/30/2015] [Indexed: 06/05/2023]
Abstract
Channel catfish (Ictalurus punctatus) is the most important freshwater aquaculture species in the USA. Genetically enhanced fish that are sterile could both profit the catfish industry and reduce potential environmental and ecological risks. As the first step to generate sterile channel catfish, three sets of zinc finger nuclease (ZFN) plasmids targeting the luteinizing hormone (LH) gene were designed and electroporated into one-cell embryos, different concentrations were introduced, and the Cel-I assay was conducted to detect mutations. Channel catfish carrying the mutated LH gene were sterile, as confirmed by DNA sequencing and mating experiments. The overall mutation rate was 19.7 % for 66 channel catfish, and the best treatment was ZFN set 1 at the concentration 25 μg/ml. To our knowledge, this is the first instance of gene editing of fish via plasmid introduction instead of mRNA microinjection. The introduction of the ZFN plasmids may have reduced mosaicism, as mutated individuals were gene edited in every tissue evaluated. Apparently, the plasmids were eventually degraded without integration, as they were not detectable in mutated individuals using PCR. Carp pituitary extract failed to induce spawning and restoration of fertility, indicating the need for developing other hormone therapies to achieve reversal of sterility upon demand. This is the first sterilization achieved using ZFN technology in an aquaculture species and the first successful gene editing of channel catfish. Our results will help understand the roles of the LH gene, purposeful sterilization of teleost fishes, and is a step towards control of domestic, hybrid, exotic, invasive, and transgenic fishes.
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Affiliation(s)
- Zhenkui Qin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Yun Li
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
- Laboratory of Fisheries Physiology and Reproduction-Breeding, Fisheries College, Ocean University of China, Qingdao, 266003, China
| | - Baofeng Su
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
- Key Laboratory of Freshwater Aquatic Biotechnology and Genetic Breeding, Ministry of Agriculture, Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China
| | - Qi Cheng
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Zhi Ye
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Dayan A Perera
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
- Research and Development Corporation, Gus R. Douglass Land-Grant Institute, West Virginia State University, Institute, WV, 25112, USA
| | - Michael Fobes
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Mei Shang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
- Key Laboratory of Freshwater Aquatic Biotechnology and Genetic Breeding, Ministry of Agriculture, Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, 150070, China
| | - Rex A Dunham
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA.
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16
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Abstract
Enrichment of desired mitochondrial DNA (mtDNA) haplotypes, in both experimental systems and the clinic, is an end sought by many. Through use of a designer nuclease platform optimized for delivery to mitochondria-the mitochondrially targeted zinc finger-nuclease (mtZFN)-it is possible to discriminate between mtDNA haplotypes with specificity to the order of a single nucleotide substitution. Site-specific cleavage of DNA produces a shift in the heteroplasmic ratio in favor of the untargeted haplotype. Here, we describe protocols for assembly of paired, conventional tail-tail mtZFN constructs and experimental approaches to assess mtZFN activity in mammalian cell cultures.
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Affiliation(s)
- Payam A Gammage
- MRC Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK.
| | - Lindsey Van Haute
- MRC Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK.
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17
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Abstract
Animal models of tumor initiation and tumor progression are essential components toward understanding cancer and designing/validating future therapies. Zebrafish is a powerful model for studying tumorigenesis and has been successfully exploited in drug discovery. According to the zebrafish reference genome, 82 % of disease-associated genes in the Online Mendelian Inheritance in Man (OMIM) database have clear zebrafish orthologues. Using a variety of large-scale random mutagenesis methods developed to date, zebrafish can provide a unique opportunity to identify gene mutations that may be associated with cancer predisposition. On the other hand, newer technologies enabling targeted mutagenesis can facilitate reverse cancer genetic studies and open the door for complex genetic analysis of tumorigenesis. In this chapter, we will describe the various technologies for conducting genome editing in zebrafish with special emphasis on the approaches to inactivate genes.
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Affiliation(s)
- John M Parant
- Department of Pharmacology and Toxicology, UAB Comprehensive Cancer Center, University of Alabama at Birmingham School of Medicine, Birmingham, AL, 35294, USA.
| | - Jing-Ruey Joanna Yeh
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, 02129, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.
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18
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De Silva Feelixge HS, Stone D, Pietz HL, Roychoudhury P, Greninger AL, Schiffer JT, Aubert M, Jerome KR. Detection of treatment-resistant infectious HIV after genome-directed antiviral endonuclease therapy. Antiviral Res 2016; 126:90-8. [PMID: 26718067 DOI: 10.1016/j.antiviral.2015.12.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 12/11/2015] [Accepted: 12/18/2015] [Indexed: 02/08/2023]
Abstract
Incurable chronic viral infections are a major cause of morbidity and mortality worldwide. One potential approach to cure persistent viral infections is via the use of targeted endonucleases. Nevertheless, a potential concern for endonuclease-based antiviral therapies is the emergence of treatment resistance. Here we detect for the first time an endonuclease-resistant infectious virus that is found with high frequency after antiviral endonuclease therapy. While testing the activity of HIV pol-specific zinc finger nucleases (ZFNs) alone or in combination with three prime repair exonuclease 2 (Trex2), we identified a treatment-resistant and infectious mutant virus that was derived from a ZFN-mediated disruption of reverse transcriptase (RT). Although gene disruption of HIV protease, RT and integrase could inhibit viral replication, a chance single amino acid insertion within the thumb domain of RT produced a virus that could actively replicate. The endonuclease-resistant virus could replicate in primary CD4(+) T cells, but remained susceptible to treatment with antiretroviral RT inhibitors. When secondary ZFN-derived mutations were introduced into the mutant virus's RT or integrase domains, replication could be abolished. Our observations suggest that caution should be exercised during endonuclease-based antiviral therapies; however, combination endonuclease therapies may prevent the emergence of resistance.
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19
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Butler JR, Ladowski JM, Martens GR, Tector M, Tector AJ. Recent advances in genome editing and creation of genetically modified pigs. Int J Surg 2015; 23:217-222. [PMID: 26231992 DOI: 10.1016/j.ijsu.2015.07.684] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 07/08/2015] [Accepted: 07/17/2015] [Indexed: 11/26/2022]
Abstract
The field of xenotransplantation is benefiting greatly from recent advances in genetic engineering. The efficiency and pace with which new model animals are being created has dramatically sped progress towards clinical relevance. Endonuclease-driven genome editing now allows for the efficient generation of targeted genetic alterations. Herein we review the available methods of genetic engineering that have been successfully employed to create genetically modified pigs.
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Affiliation(s)
- James R Butler
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Joseph M Ladowski
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Gregory R Martens
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Matthew Tector
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - A Joseph Tector
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA.
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20
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Hatada S, Subramanian A, Mandefro B, Ren S, Kim HW, Tang J, Funari V, Baloh RH, Sareen D, Arumugaswami V, Svendsen CN. Low-Dose Irradiation Enhances Gene Targeting in Human Pluripotent Stem Cells. Stem Cells Transl Med 2015; 4:998-1010. [PMID: 26185257 DOI: 10.5966/sctm.2015-0050] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/27/2015] [Indexed: 11/16/2022] Open
Abstract
UNLABELLED Human pluripotent stem cells (hPSCs) are now being used for both disease modeling and cell therapy; however, efficient homologous recombination (HR) is often crucial to develop isogenic control or reporter lines. We showed that limited low-dose irradiation (LDI) using either γ-ray or x-ray exposure (0.4 Gy) significantly enhanced HR frequency, possibly through induction of DNA repair/recombination machinery including ataxia-telangiectasia mutated, histone H2A.X and RAD51 proteins. LDI could also increase HR efficiency by more than 30-fold when combined with the targeting tools zinc finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats. Whole-exome sequencing confirmed that the LDI administered to hPSCs did not induce gross genomic alterations or affect cellular viability. Irradiated and targeted lines were karyotypically normal and made all differentiated lineages that continued to express green fluorescent protein targeted at the AAVS1 locus. This simple method allows higher throughput of new, targeted hPSC lines that are crucial to expand the use of disease modeling and to develop novel avenues of cell therapy. SIGNIFICANCE The simple and relevant technique described in this report uses a low level of radiation to increase desired gene modifications in human pluripotent stem cells by an order of magnitude. This higher efficiency permits greater throughput with reduced time and cost. The low level of radiation also greatly increased the recombination frequency when combined with developed engineered nucleases. Critically, the radiation did not lead to increases in DNA mutations or to reductions in overall cellular viability. This novel technique enables not only the rapid production of disease models using human stem cells but also the possibility of treating genetically based diseases by correcting patient-derived cells.
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Affiliation(s)
- Seigo Hatada
- Board of Governors, Regenerative Medicine Institute, Department of Biomedical Sciences, iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Genomics Core Facility, Department of Surgery, and Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Aparna Subramanian
- Board of Governors, Regenerative Medicine Institute, Department of Biomedical Sciences, iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Genomics Core Facility, Department of Surgery, and Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Berhan Mandefro
- Board of Governors, Regenerative Medicine Institute, Department of Biomedical Sciences, iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Genomics Core Facility, Department of Surgery, and Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Songyang Ren
- Board of Governors, Regenerative Medicine Institute, Department of Biomedical Sciences, iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Genomics Core Facility, Department of Surgery, and Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Ho Won Kim
- Board of Governors, Regenerative Medicine Institute, Department of Biomedical Sciences, iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Genomics Core Facility, Department of Surgery, and Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jie Tang
- Board of Governors, Regenerative Medicine Institute, Department of Biomedical Sciences, iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Genomics Core Facility, Department of Surgery, and Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Vincent Funari
- Board of Governors, Regenerative Medicine Institute, Department of Biomedical Sciences, iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Genomics Core Facility, Department of Surgery, and Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Robert H Baloh
- Board of Governors, Regenerative Medicine Institute, Department of Biomedical Sciences, iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Genomics Core Facility, Department of Surgery, and Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dhruv Sareen
- Board of Governors, Regenerative Medicine Institute, Department of Biomedical Sciences, iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Genomics Core Facility, Department of Surgery, and Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Vaithilingaraja Arumugaswami
- Board of Governors, Regenerative Medicine Institute, Department of Biomedical Sciences, iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Genomics Core Facility, Department of Surgery, and Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Clive N Svendsen
- Board of Governors, Regenerative Medicine Institute, Department of Biomedical Sciences, iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Genomics Core Facility, Department of Surgery, and Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, California, USA
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21
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Kumar S, AlAbed D, Worden A, Novak S, Wu H, Ausmus C, Beck M, Robinson H, Minnicks T, Hemingway D, Lee R, Skaggs N, Wang L, Marri P, Gupta M. A modular gene targeting system for sequential transgene stacking in plants. J Biotechnol 2015; 207:12-20. [PMID: 25913173 DOI: 10.1016/j.jbiotec.2015.04.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 03/14/2015] [Accepted: 04/03/2015] [Indexed: 11/16/2022]
Abstract
A modular, selection-based method was developed for site-specific integration of transgenes into a genomic locus to create multigene stacks. High-frequency gene targeting was obtained using zinc finger nuclease (ZFN)-mediated double-strand break (DSB) formation at a pre-defined target genomic location using a unique intron directly downstream of a promoter driving a selectable marker gene to facilitate homology between target and donor sequences. In this system, only insertion into the target locus leads to a functional selectable marker, and regeneration from random insertions of the promoterless donor construct are reduced on selection media. A new stack of transgenes can potentially be loaded with each successive cycle of gene targeting by exchanging the selectable marker gene using the intron homology. This system was tested in maize using the pat selectable marker gene, whereby up to 30% of the plants regenerated on Bialaphos-containing medium were observed to have the donor construct integrated into the target locus. Unlike previous gene targeting methods that utilize defective or partial genes for selecting targeted events, the present method exchanges fully functional genes with every cycle of targeting, thereby allowing the recycling of selectable marker genes, hypothetically for multiple generations of gene targeting.
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Affiliation(s)
- Sandeep Kumar
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268, USA.
| | - Diaa AlAbed
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268, USA
| | - Andrew Worden
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268, USA
| | - Stephen Novak
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268, USA
| | - Huixia Wu
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268, USA
| | - Carla Ausmus
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268, USA
| | - Margaret Beck
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268, USA
| | - Heather Robinson
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268, USA
| | - Tatyana Minnicks
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268, USA
| | - Daren Hemingway
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268, USA
| | - Ryan Lee
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268, USA
| | - Nicole Skaggs
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268, USA
| | - Lizhen Wang
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268, USA
| | - Pradeep Marri
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268, USA
| | - Manju Gupta
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268, USA
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22
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Park SY, Zheng X, Kim YG. Characterization of functional, noncovalently assembled zinc finger nucleases. Biochem Biophys Res Commun 2014; 453:289-95. [PMID: 25304177 DOI: 10.1016/j.bbrc.2014.09.140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 09/09/2014] [Indexed: 11/25/2022]
Abstract
Zinc finger nuclease (ZFN) is a chimeric restriction enzyme made of a C2H2-type zinc finger protein (ZFP) and the FokI nuclease domain (FN). ZFN technology has been considered as a powerful tool for genome editing. Here, we report a new type of ZFN system based on the coiled-coil interaction used as a noncovalent assembler. Like conventional ZFNs, noncovalently assembled ZFNs (ncZFNs) structurally have two domains, a ZFP and a FN. Each domain carries one of antiparallel heterodimeric leucine zippers, respectively, to form an ncZFN through leucine zipper assembly. The characterization of ncZFNs revealed that they behave as fully functional sequence-specific endonucleases, comparable to those of conventional ZFNs. Interestingly, some ncZFNs displayed augmented off-target cleavage, possibly by degenerate DNA binding of the ZFP domain of ncZFNs based on our data. We postulate that DNA cleavage of ncZFN(s) seems to be more sensitive to the ZFP binding to lesser-optimal sites. Facile design of ncZFNs through the mix-and-assemble approach could be applicable to other DNA binding proteins for evaluation of sequence-specificity. In addition, our work establishes that the coiled-coil interaction could be used as the peptide-based noncovalent assembler for the formation of a noncovalently-linked functional multidomain protein.
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Affiliation(s)
- So-Young Park
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - Xu Zheng
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - Yang-Gyun Kim
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Republic of Korea.
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23
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Zhang W, Chen H, Zheng X, Wang D, Ji H, Xia H, Mao Q. Targeted genome correction by a single adenoviral vector simultaneously carrying an inducible zinc finger nuclease and a donor template. J Biotechnol 2014; 188:1-6. [PMID: 25116362 DOI: 10.1016/j.jbiotec.2014.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Revised: 07/28/2014] [Accepted: 08/01/2014] [Indexed: 01/24/2023]
Abstract
Zinc finger nuclease (ZFN) technology, which can be used to induce targeted genome correction in the presence of a DNA donor template, is becoming an attractive strategy for treating monogenic diseases. This strategy requires efficient delivery of ZFN and donor template into cells, ideally, in a single viral vector to achieve efficient genome editing and to avoid unwanted mutagenesis. In this study, we successfully produced a single adenoviral (Ad) vector with high titer that carried a ZFN expression cassette and a donor template simultaneously. We then demonstrated that this single Ad system could mediate efficient site-specific genome correction in vitro and ex vivo. The gene correction efficiency of the single Ad was significantly higher than that of the double Ad system. This novel vector will be a promising ZFN and donor delivery system for treatment of monogenic diseases.
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Affiliation(s)
- Weifeng Zhang
- Co-Innovation Center for Qinba Regions' Sustainable Development, College of Life Sciences, Shaanxi Normal University, Xi'an 710062, Shaanxi, PR China
| | - Hao Chen
- Co-Innovation Center for Qinba Regions' Sustainable Development, College of Life Sciences, Shaanxi Normal University, Xi'an 710062, Shaanxi, PR China
| | - Xiaojing Zheng
- Co-Innovation Center for Qinba Regions' Sustainable Development, College of Life Sciences, Shaanxi Normal University, Xi'an 710062, Shaanxi, PR China
| | - Dongyang Wang
- Co-Innovation Center for Qinba Regions' Sustainable Development, College of Life Sciences, Shaanxi Normal University, Xi'an 710062, Shaanxi, PR China
| | - Haiyan Ji
- Co-Innovation Center for Qinba Regions' Sustainable Development, College of Life Sciences, Shaanxi Normal University, Xi'an 710062, Shaanxi, PR China
| | - Haibin Xia
- Co-Innovation Center for Qinba Regions' Sustainable Development, College of Life Sciences, Shaanxi Normal University, Xi'an 710062, Shaanxi, PR China.
| | - Qinwen Mao
- Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
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24
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Abstract
For a century, Drosophila has been a favored organism for genetic research. However, the array of materials and methods available to the Drosophila worker has expanded dramatically in the last decade. The most common gene targeting tools, zinc finger nucleases, TALENs, and RNA-guided CRISPR/Cas9, have all been adapted for use in Drosophila, both for simple mutagenesis and for gene editing via homologous recombination. For each tool, there exist a number of web sites, design applications, and delivery methods. The successful application of any of these tools also requires an understanding of methods for detecting successful genome modifications. This article provides an overview of the available gene targeting tools and their application in Drosophila. In lieu of simply providing a protocol for gene targeting, we direct the researcher to resources that will allow access to the latest research in this rapidly evolving field.
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Affiliation(s)
- Kelly J Beumer
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112-5650, United States.
| | - Dana Carroll
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112-5650, United States
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25
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Tee KL, Wong TS. Polishing the craft of genetic diversity creation in directed evolution. Biotechnol Adv 2013; 31:1707-21. [PMID: 24012599 DOI: 10.1016/j.biotechadv.2013.08.021] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 08/31/2013] [Accepted: 08/31/2013] [Indexed: 12/25/2022]
Abstract
Genetic diversity creation is a core technology in directed evolution where a high quality mutant library is crucial to its success. Owing to its importance, the technology in genetic diversity creation has seen rapid development over the years and its application has diversified into other fields of scientific research. The advances in molecular cloning and mutagenesis since 2008 were reviewed. Specifically, new cloning techniques were classified based on their principles of complementary overhangs, homologous sequences, overlapping PCR and megaprimers and the advantages, drawbacks and performances of these methods were highlighted. New mutagenesis methods developed for random mutagenesis, focused mutagenesis and DNA recombination were surveyed. The technical requirements of these methods and the mutational spectra were compared and discussed with references to commonly used techniques. The trends of mutant library preparation were summarised. Challenges in genetic diversity creation were discussed with emphases on creating "smart" libraries, controlling the mutagenesis spectrum and specific challenges in each group of mutagenesis methods. An outline of the wider applications of genetic diversity creation includes genome engineering, viral evolution, metagenomics and a study of protein functions. The review ends with an outlook for genetic diversity creation and the prospective developments that can have future impact in this field.
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Affiliation(s)
- Kang Lan Tee
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, England, United Kingdom
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26
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Anand P, Schug A, Wenzel W. Structure based design of protein linkers for zinc finger nuclease. FEBS Lett 2013; 587:3231-5. [PMID: 23994524 DOI: 10.1016/j.febslet.2013.08.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 08/05/2013] [Accepted: 08/12/2013] [Indexed: 12/18/2022]
Abstract
Zinc finger nucleases are a promising tool to edit DNA in many biological applications, in particular for gene knockout. Despite many efforts the number of genes that can be effectively targeted with ZFNs remains severely limited, as available constructs cannot address arbitrary gene sequences. Here, we develop a novel concept to significantly enhance the number of DNA sequences that can be targeted by ZFN. Using an efficient computational model, we provide an extensive library of possible linker molecules between individual zinc finger motifs in the construct that can skip up to 10 base pairs between adjacent zinc finger recognition sites in the DNA sequence, which increases the number of genes that can be efficiently targeted by more than an order of magnitude.
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Affiliation(s)
- Priya Anand
- Institute of Nanotechnology, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
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