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Feola M, Pulicani S, Tkach D, Boyne A, Hong R, Mayer L, Duclert A, Duchateau P, Juillerat A. Comprehensive analysis of the editing window of C-to-T TALE base editors. Sci Rep 2024; 14:12870. [PMID: 38834632 PMCID: PMC11150444 DOI: 10.1038/s41598-024-63203-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/27/2024] [Indexed: 06/06/2024] Open
Abstract
One of the most recent advances in the genome editing field has been the addition of "TALE Base Editors", an innovative platform for cell therapy that relies on the deamination of cytidines within double strand DNA, leading to the formation of an uracil (U) intermediate. These molecular tools are fusions of transcription activator-like effector domains (TALE) for specific DNA sequence binding, split-DddA deaminase halves that will, upon catalytic domain reconstitution, initiate the conversion of a cytosine (C) to a thymine (T), and an uracil glycosylase inhibitor (UGI). We developed a high throughput screening strategy capable to probe key editing parameters in a precisely defined genomic context in cellulo, excluding or minimizing biases arising from different microenvironmental and/or epigenetic contexts. Here we aimed to further explore how target composition and TALEB architecture will impact the editing outcomes. We demonstrated how the nature of the linker between TALE array and split DddAtox head allows us to fine tune the editing window, also controlling possible bystander activity. Furthermore, we showed that both the TALEB architecture and spacer length separating the two TALE DNA binding regions impact the target TC editing dependence by the surrounding bases, leading to more restrictive or permissive editing profiles.
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2
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Huang J, Sun Y, Liao Y, He F. Rapid detection of nucleic acid sequences of pathogenic bacteria based on a series piezoelectric quartz crystal sensor with transcription activator-like effectors. Biosens Bioelectron 2024; 243:115747. [PMID: 37866323 DOI: 10.1016/j.bios.2023.115747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 10/03/2023] [Accepted: 10/07/2023] [Indexed: 10/24/2023]
Abstract
Accurate and rapid detection of pathogenic bacteria is of great importance in the field of clinical diagnosis and food safety. Current methods for pathogenic bacteria detection have some problems in accurate, rapid and universal application. Here we proposed a pathogenic bacteria series piezoelectric quartz crystal (SPQC) sensor for achieving highly specific and sensitive detection of pathogenic bacteria. The universal sequences of common clinical pathogens screened by our group were used as detection targets. A new TALEs nuclease was synthesized as a recognition element, which recognizes double-stranded DNA at the level of a single base mismatch in the range of 17-19 bases. Targets could be specifically recognized by TALEs, resulting in the change of electrode surface, which would be further amplified by hybridization chain reaction and silver staining technique. Finally, the changes would be detected by SPQC system. This strategy was demonstrated to have excellent performance, enabling sensitive detection of targets with a detection limit of 25 cfu/mL in less than 3 h. What's more, the identification of single base mismatch could be achieved when the target ranging in length between 17 and 19 bases. The proposed method is rapid, accurate and easy universal application and expected to be applied in clinical diagnosis and food safety.
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Affiliation(s)
- Ji Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Yifan Sun
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Yusheng Liao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Fengjiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China.
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3
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Pradhan S, Apaydin S, Bucevičius J, Gerasimaitė R, Kostiuk G, Lukinavičius G. Sequence-specific DNA labelling for fluorescence microscopy. Biosens Bioelectron 2023; 230:115256. [PMID: 36989663 DOI: 10.1016/j.bios.2023.115256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/04/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023]
Abstract
The preservation of nucleus structure during microscopy imaging is a top priority for understanding chromatin organization, genome dynamics, and gene expression regulation. In this review, we summarize the sequence-specific DNA labelling methods that can be used for imaging in fixed and/or living cells without harsh treatment and DNA denaturation: (i) hairpin polyamides, (ii) triplex-forming oligonucleotides, (iii) dCas9 proteins, (iv) transcription activator-like effectors (TALEs) and (v) DNA methyltransferases (MTases). All these techniques are capable of identifying repetitive DNA loci and robust probes are available for telomeres and centromeres, but visualizing single-copy sequences is still challenging. In our futuristic vision, we see gradual replacement of the historically important fluorescence in situ hybridization (FISH) by less invasive and non-destructive methods compatible with live cell imaging. Combined with super-resolution fluorescence microscopy, these methods will open the possibility to look into unperturbed structure and dynamics of chromatin in living cells, tissues and whole organisms.
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Abstract
Transcription activator-like effector (TALE) nuclease (TALEN) is the second-generation genome editing tool consisting of TALE protein containing customizable DNA-binding repeats and nuclease domain of FokI enzyme. Each DNA-binding repeat recognizes one base of double-strand DNA, and functional TALEN can be created by a simple modular assembly of these repeats. To easily and efficiently assemble the highly repetitive DNA-binding repeat arrays, various construction systems such as Golden Gate assembly, serial ligation, and ligation-independent cloning have been reported. In this chapter, we summarize the updated situation of these systems and publicly available reagents and protocols, enabling optimal selection of best suited systems for every researcher who wants to utilize TALENs in various research fields.
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Affiliation(s)
- Tetsushi Sakuma
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan.
| | - Takashi Yamamoto
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan.
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Nabeel Asim M, Ali Ibrahim M, Fazeel A, Dengel A, Ahmed S. DNA-MP: a generalized DNA modifications predictor for multiple species based on powerful sequence encoding method. Brief Bioinform 2023; 24:6931721. [PMID: 36528802 DOI: 10.1093/bib/bbac546] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 11/06/2022] [Accepted: 11/12/2022] [Indexed: 12/23/2022] Open
Abstract
Accurate prediction of deoxyribonucleic acid (DNA) modifications is essential to explore and discern the process of cell differentiation, gene expression and epigenetic regulation. Several computational approaches have been proposed for particular type-specific DNA modification prediction. Two recent generalized computational predictors are capable of detecting three different types of DNA modifications; however, type-specific and generalized modifications predictors produce limited performance across multiple species mainly due to the use of ineffective sequence encoding methods. The paper in hand presents a generalized computational approach "DNA-MP" that is competent to more precisely predict three different DNA modifications across multiple species. Proposed DNA-MP approach makes use of a powerful encoding method "position specific nucleotides occurrence based 117 on modification and non-modification class densities normalized difference" (POCD-ND) to generate the statistical representations of DNA sequences and a deep forest classifier for modifications prediction. POCD-ND encoder generates statistical representations by extracting position specific distributional information of nucleotides in the DNA sequences. We perform a comprehensive intrinsic and extrinsic evaluation of the proposed encoder and compare its performance with 32 most widely used encoding methods on $17$ benchmark DNA modifications prediction datasets of $12$ different species using $10$ different machine learning classifiers. Overall, with all classifiers, the proposed POCD-ND encoder outperforms existing $32$ different encoders. Furthermore, combinedly over 5-fold cross validation benchmark datasets and independent test sets, proposed DNA-MP predictor outperforms state-of-the-art type-specific and generalized modifications predictors by an average accuracy of 7% across 4mc datasets, 1.35% across 5hmc datasets and 10% for 6ma datasets. To facilitate the scientific community, the DNA-MP web application is available at https://sds_genetic_analysis.opendfki.de/DNA_Modifications/.
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Affiliation(s)
- Muhammad Nabeel Asim
- Department of Computer Science, Technical University of Kaiserslautern, Kaiserslautern 67663, Germany.,German Research Center for Artificial Intelligence GmbH, Kaiserslautern 67663, Germany
| | - Muhammad Ali Ibrahim
- Department of Computer Science, Technical University of Kaiserslautern, Kaiserslautern 67663, Germany.,German Research Center for Artificial Intelligence GmbH, Kaiserslautern 67663, Germany
| | - Ahtisham Fazeel
- Department of Computer Science, Technical University of Kaiserslautern, Kaiserslautern 67663, Germany.,German Research Center for Artificial Intelligence GmbH, Kaiserslautern 67663, Germany
| | - Andreas Dengel
- Department of Computer Science, Technical University of Kaiserslautern, Kaiserslautern 67663, Germany.,German Research Center for Artificial Intelligence GmbH, Kaiserslautern 67663, Germany
| | - Sheraz Ahmed
- German Research Center for Artificial Intelligence GmbH, Kaiserslautern 67663, Germany
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Improving cassava bacterial blight resistance by editing the epigenome. Nat Commun 2023; 14:85. [PMID: 36604425 PMCID: PMC9816117 DOI: 10.1038/s41467-022-35675-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 12/15/2022] [Indexed: 01/07/2023] Open
Abstract
Pathogens rely on expression of host susceptibility (S) genes to promote infection and disease. As DNA methylation is an epigenetic modification that affects gene expression, blocking access to S genes through targeted methylation could increase disease resistance. Xanthomonas phaseoli pv. manihotis, the causal agent of cassava bacterial blight (CBB), uses transcription activator-like20 (TAL20) to induce expression of the S gene MeSWEET10a. In this work, we direct methylation to the TAL20 effector binding element within the MeSWEET10a promoter using a synthetic zinc-finger DNA binding domain fused to a component of the RNA-directed DNA methylation pathway. We demonstrate that this methylation prevents TAL20 binding, blocks transcriptional activation of MeSWEET10a in vivo and that these plants display decreased CBB symptoms while maintaining normal growth and development. This work therefore presents an epigenome editing approach useful for crop improvement.
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Martinez MG, Smekalova E, Combe E, Gregoire F, Zoulim F, Testoni B. Gene Editing Technologies to Target HBV cccDNA. Viruses 2022; 14:v14122654. [PMID: 36560658 PMCID: PMC9787400 DOI: 10.3390/v14122654] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Hepatitis B virus (HBV) remains a significant cause of mortality and morbidity worldwide, since chronic HBV infection is associated with elevated risk of cirrhosis and hepatocellular carcinoma. Current licensed therapies against HBV efficiently suppress viral replication; however, they do not have significant effects on the intrahepatic covalently closed circular DNA (cccDNA) of the viral minichromosome responsible for viral persistence. Thus, life-long treatment is required to avoid viral rebound. There is a significant need for novel therapies that can reduce, silence or eradicate cccDNA, thus preventing HBV reemergence after treatment withdrawal. In this review, we discuss the latest developments and applications of gene editing and related approaches for directly targeting HBV DNA and, more specifically, cccDNA in infected hepatocytes.
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Affiliation(s)
| | | | - Emmanuel Combe
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), 69008 Lyon, France
| | | | - Fabien Zoulim
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), 69008 Lyon, France
- Hospices Civils de Lyon (HCL), 69002 Lyon, France
- Université Claude-Bernard Lyon 1 (UCBL1), 69008 Lyon, France
| | - Barbara Testoni
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), 69008 Lyon, France
- Université Claude-Bernard Lyon 1 (UCBL1), 69008 Lyon, France
- Correspondence:
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Boyne A, Yang M, Pulicani S, Feola M, Tkach D, Hong R, Duclert A, Duchateau P, Juillerat A. Efficient multitool/multiplex gene engineering with TALE-BE. Front Bioeng Biotechnol 2022; 10:1033669. [PMID: 36440442 PMCID: PMC9684181 DOI: 10.3389/fbioe.2022.1033669] [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: 08/31/2022] [Accepted: 09/30/2022] [Indexed: 11/11/2022] Open
Abstract
TALE base editors are a recent addition to the genome editing toolbox. These molecular tools are fusions of a transcription activator-like effector domain (TALE), split-DddA deaminase halves, and an uracil glycosylase inhibitor (UGI) that have the distinct ability to directly edit double strand DNA, converting a cytosine (C) to a thymine (T). To dissect the editing rules of TALE-BE, we combined the screening of dozens of TALE-BE targeting nuclear genomic loci with a medium/high throughput strategy based on precise knock-in of TALE-BE target site collections into the cell genome. This latter approach allowed us to gain in depth insight of the editing rules in cellulo, while excluding confounding factors such as epigenetic and microenvironmental differences among different genomic loci. Using the knowledge gained, we designed TALE-BE targeting CD52 and achieved very high frequency of gene knock-out (up to 80% of phenotypic CD52 knock out). We further demonstrated that TALE-BE generate only insignificant levels of Indels and byproducts. Finally, we combined two molecular tools, a TALE-BE and a TALEN, for multiplex genome engineering, generating high levels of double gene knock-out (∼75%) without creation of translocations between the two targeted sites.
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Affiliation(s)
- Alex Boyne
- Cellectis Inc., New York, NY, United States
| | - Ming Yang
- Cellectis Inc., New York, NY, United States
| | | | | | | | | | | | | | - Alexandre Juillerat
- Cellectis Inc., New York, NY, United States
- *Correspondence: Alexandre Juillerat,
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9
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Stewart ZA. Xenotransplantation: The Contribution of CRISPR/Cas9 Gene Editing Technology. CURRENT TRANSPLANTATION REPORTS 2022. [DOI: 10.1007/s40472-022-00380-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Genetic Kidney Diseases (GKDs) Modeling Using Genome Editing Technologies. Cells 2022; 11:cells11091571. [PMID: 35563876 PMCID: PMC9105797 DOI: 10.3390/cells11091571] [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: 03/31/2022] [Revised: 04/29/2022] [Accepted: 05/04/2022] [Indexed: 02/05/2023] Open
Abstract
Genetic kidney diseases (GKDs) are a group of rare diseases, affecting approximately about 60 to 80 per 100,000 individuals, for which there is currently no treatment that can cure them (in many cases). GKDs usually leads to early-onset chronic kidney disease, which results in patients having to undergo dialysis or kidney transplant. Here, we briefly describe genetic causes and phenotypic effects of six GKDs representative of different ranges of prevalence and renal involvement (ciliopathy, glomerulopathy, and tubulopathy). One of the shared characteristics of GKDs is that most of them are monogenic. This characteristic makes it possible to use site-specific nuclease systems to edit the genes that cause GKDs and generate in vitro and in vivo models that reflect the genetic abnormalities of GKDs. We describe and compare these site-specific nuclease systems (zinc finger nucleases (ZFNs), transcription activator-like effect nucleases (TALENs) and regularly clustered short palindromic repeat-associated protein (CRISPR-Cas9)) and review how these systems have allowed the generation of cellular and animal GKDs models and how they have contributed to shed light on many still unknown fields in GKDs. We also indicate the main obstacles limiting the application of these systems in a more efficient way. The information provided here will be useful to gain an accurate understanding of the technological advances in the field of genome editing for GKDs, as well as to serve as a guide for the selection of both the genome editing tool and the gene delivery method most suitable for the successful development of GKDs models.
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11
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Gardiner J, Ghoshal B, Wang M, Jacobsen SE. CRISPR-Cas-mediated transcriptional control and epi-mutagenesis. PLANT PHYSIOLOGY 2022; 188:1811-1824. [PMID: 35134247 PMCID: PMC8968285 DOI: 10.1093/plphys/kiac033] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/13/2022] [Indexed: 05/24/2023]
Abstract
Tools for sequence-specific DNA binding have opened the door to new approaches in investigating fundamental questions in biology and crop development. While there are several platforms to choose from, many of the recent advances in sequence-specific targeting tools are focused on developing Clustered Regularly Interspaced Short Palindromic Repeats- CRISPR Associated (CRISPR-Cas)-based systems. Using a catalytically inactive Cas protein (dCas), this system can act as a vector for different modular catalytic domains (effector domains) to control a gene's expression or alter epigenetic marks such as DNA methylation. Recent trends in developing CRISPR-dCas systems include creating versions that can target multiple copies of effector domains to a single site, targeting epigenetic changes that, in some cases, can be inherited to the next generation in the absence of the targeting construct, and combining effector domains and targeting strategies to create synergies that increase the functionality or efficiency of the system. This review summarizes and compares DNA targeting technologies, the effector domains used to target transcriptional control and epi-mutagenesis, and the different CRISPR-dCas systems used in plants.
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Affiliation(s)
| | | | - Ming Wang
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, USA
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12
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Erkes A, Mücke S, Reschke M, Boch J, Grau J. Epigenetic features improve TALE target prediction. BMC Genomics 2021; 22:914. [PMID: 34965853 PMCID: PMC8717664 DOI: 10.1186/s12864-021-08210-z] [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: 06/17/2021] [Accepted: 11/25/2021] [Indexed: 11/20/2022] Open
Abstract
Background The yield of many crop plants can be substantially reduced by plant-pathogenic Xanthomonas bacteria. The infection strategy of many Xanthomonas strains is based on transcription activator-like effectors (TALEs), which are secreted into the host cells and act as transcriptional activators of plant genes that are beneficial for the bacteria.The modular DNA binding domain of TALEs contains tandem repeats, each comprising two hyper-variable amino acids. These repeat-variable diresidues (RVDs) bind to their target box and determine the specificity of a TALE.All available tools for the prediction of TALE targets within the host plant suffer from many false positives. In this paper we propose a strategy to improve prediction accuracy by considering the epigenetic state of the host plant genome in the region of the target box. Results To this end, we extend our previously published tool PrediTALE by considering two epigenetic features: (i) chromatin accessibility of potentially bound regions and (ii) DNA methylation of cytosines within target boxes. Here, we determine the epigenetic features from publicly available DNase-seq, ATAC-seq, and WGBS data in rice.We benchmark the utility of both epigenetic features separately and in combination, deriving ground-truth from RNA-seq data of infections studies in rice. We find an improvement for each individual epigenetic feature, but especially the combination of both.Having established an advantage in TALE target predicting considering epigenetic features, we use these data for promoterome and genome-wide scans by our new tool EpiTALE, leading to several novel putative virulence targets. Conclusions Our results suggest that it would be worthwhile to collect condition-specific chromatin accessibility data and methylation information when studying putative virulence targets of Xanthomonas TALEs. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-021-08210-z).
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Affiliation(s)
- Annett Erkes
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany.
| | - Stefanie Mücke
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Maik Reschke
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Jens Boch
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Jan Grau
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany.
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Bhardwaj A, Nain V. TALENs-an indispensable tool in the era of CRISPR: a mini review. J Genet Eng Biotechnol 2021; 19:125. [PMID: 34420096 PMCID: PMC8380213 DOI: 10.1186/s43141-021-00225-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 08/08/2021] [Indexed: 12/26/2022]
Abstract
BACKGROUND Genome of an organism has always fascinated life scientists. With the discovery of restriction endonucleases, scientists were able to make targeted manipulations (knockouts) in any gene sequence of any organism, by the technique popularly known as genome engineering. Though there is a range of genome editing tools, but this era of genome editing is dominated by the CRISPR/Cas9 tool due to its ease of design and handling. But, when it comes to clinical applications, CRISPR is not usually preferred. In this review, we will elaborate on the structural and functional role of designer nucleases with emphasis on TALENs and CRISPR/Cas9 genome editing system. We will also present the unique features of TALENs and limitations of CRISPRs which makes TALENs a better genome editing tool than CRISPRs. MAIN BODY Genome editing is a robust technology used to make target specific DNA modifications in the genome of any organism. With the discovery of robust programmable endonucleases-based designer gene manipulating tools such as meganucleases (MN), zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats associated protein (CRISPR/Cas9), the research in this field has experienced a tremendous acceleration giving rise to a modern era of genome editing with better precision and specificity. Though, CRISPR-Cas9 platform has successfully gained more attention in the scientific world, TALENs and ZFNs are unique in their own ways. Apart from high-specificity, TALENs are proven to target the mitochondrial DNA (mito-TALEN), where gRNA of CRISPR is difficult to import. This review talks about genome editing goals fulfilled by TALENs and drawbacks of CRISPRs. CONCLUSIONS This review provides significant insights into the pros and cons of the two most popular genome editing tools TALENs and CRISPRs. This mini review suggests that, TALENs provides novel opportunities in the field of therapeutics being highly specific and sensitive toward DNA modifications. In this article, we will briefly explore the special features of TALENs that makes this tool indispensable in the field of synthetic biology. This mini review provides great perspective in providing true guidance to the researchers working in the field of trait improvement via genome editing.
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Affiliation(s)
- Anuradha Bhardwaj
- Department of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, 201312, India
| | - Vikrant Nain
- Department of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, 201312, India.
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Kim YC, Kang Y, Yang EY, Cho MC, Schafleitner R, Lee JH, Jang S. Applications and Major Achievements of Genome Editing in Vegetable Crops: A Review. FRONTIERS IN PLANT SCIENCE 2021; 12:688980. [PMID: 34178006 PMCID: PMC8231707 DOI: 10.3389/fpls.2021.688980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/18/2021] [Indexed: 05/04/2023]
Abstract
The emergence of genome-editing technology has allowed manipulation of DNA sequences in genomes to precisely remove or replace specific sequences in organisms resulting in targeted mutations. In plants, genome editing is an attractive method to alter gene functions to generate improved crop varieties. Genome editing is thought to be simple to use and has a lower risk of off-target effects compared to classical mutation breeding. Furthermore, genome-editing technology tools can also be applied directly to crops that contain complex genomes and/or are not easily bred using traditional methods. Currently, highly versatile genome-editing tools for precise and predictable editing of almost any locus in the plant genome make it possible to extend the range of application, including functional genomics research and molecular crop breeding. Vegetables are essential nutrient sources for humans and provide vitamins, minerals, and fiber to diets, thereby contributing to human health. In this review, we provide an overview of the brief history of genome-editing technologies and the components of genome-editing tool boxes, and illustrate basic modes of operation in representative systems. We describe the current and potential practical application of genome editing for the development of improved nutritious vegetables and present several case studies demonstrating the potential of the technology. Finally, we highlight future directions and challenges in applying genome-editing systems to vegetable crops for research and product development.
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Affiliation(s)
- Young-Cheon Kim
- Division of Life Sciences, Jeonbuk National University, Jeonju, South Korea
| | - Yeeun Kang
- World Vegetable Center Korea Office, Wanju-gun, South Korea
| | - Eun-Young Yang
- National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Wanju-gun, South Korea
| | - Myeong-Cheoul Cho
- National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Wanju-gun, South Korea
| | | | - Jeong Hwan Lee
- Division of Life Sciences, Jeonbuk National University, Jeonju, South Korea
| | - Seonghoe Jang
- World Vegetable Center Korea Office, Wanju-gun, South Korea
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15
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Programmable tools for targeted analysis of epigenetic DNA modifications. Curr Opin Chem Biol 2021; 63:1-10. [PMID: 33588304 DOI: 10.1016/j.cbpa.2021.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/04/2021] [Accepted: 01/04/2021] [Indexed: 11/21/2022]
Abstract
Modifications of the cytosine 5-position are dynamic epigenetic marks of mammalian DNA with important regulatory roles in development and disease. Unraveling biological functions of such modified nucleobases is tightly connected with the potential of available methods for their analysis. Whereas genome-wide nucleobase quantification and mapping are first-line analyses, targeted analyses move into focus the more genomic sites with high biological significance are identified. We here review recent developments in an emerging field that addresses such targeted analyses via probes that combine a programmable, sequence-specific DNA-binding domain with the ability to directly recognize or cross-link an epigenetically modified nucleobase of interest. We highlight how such probes offer simple, high-resolution nucleobase analyses in vitro and enable in situ correlations between a nucleobase and other chromatin regulatory elements at user-defined loci on the single-cell level by imaging.
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The evolution and history of gene editing technologies. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 178:1-62. [PMID: 33685594 DOI: 10.1016/bs.pmbts.2021.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Scientific enquiry must be the driving force of research. This sentiment is manifested as the profound impact gene editing technologies are having in our current world. There exist three main gene editing technologies today: Zinc Finger Nucleases, TALENs and the CRISPR-Cas system. When these systems were being uncovered, none of the scientists set out to design tools to engineer genomes. They were simply trying to understand the mechanisms existing in nature. If it was not for this simple sense of wonder, we probably would not have these breakthrough technologies. In this chapter, we will discuss the history, applications and ethical issues surrounding these technologies, focusing on the now predominant CRISPR-Cas technology. Gene editing technologies, as we know them now, are poised to have an overwhelming impact on our world. However, it is impossible to predict the route they will take in the future or to comprehend the full impact of its repercussions.
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Abstract
Methylation of DNA at cytosine bases is an important DNA modification underlying normal development and disease states. Despite decades of research into the biological function of DNA methylation, most of the observations so far have relied primarily on associative data between observed changes in DNA methylation states and local changes in transcriptional activity or chromatin state processes. This is primarily due to the lack of molecular tools to precisely modify DNA methylation in the genome. Recent advances in genome editing technologies have allowed repurposing the CRISPR-Cas9 system for epigenome editing by fusing the catalytically dead Cas9 (dCas9) to epigenome modifying enzymes. Moreover, methods of recruiting multiple protein domains, including the SunTag system, have increased the efficacy of epigenome editing at target sites. Here, we describe an end-to-end protocol for efficient targeted removal of DNA methylation by recruiting multiple catalytic domain of TET1 enzymes to the target sites with the dCas9-SunTag system, including sgRNA design, molecular cloning, delivery of plasmid into mammalian cells, and targeted DNA methylation analysis.
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Affiliation(s)
- Trung Viet Nguyen
- ARC Center of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
- The Harry Perkins Institute of Medical Research, Perth, WA, Australia
| | - Ryan Lister
- ARC Center of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia.
- The Harry Perkins Institute of Medical Research, Perth, WA, Australia.
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18
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Gao Y, Gao K, Yang H. CRISPR/Cas: a potential gene-editing tool in the nervous system. CELL REGENERATION (LONDON, ENGLAND) 2020; 9:12. [PMID: 32761306 PMCID: PMC7406588 DOI: 10.1186/s13619-020-00044-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 04/01/2020] [Indexed: 02/07/2023]
Abstract
The rapidly developmental RNA-guided CRISPR/Cas system is a powerful tool for RNA and DNA editing in a variety of cells from different species and makes a great contribution to gene function research, disease model generation and gene therapy development in the past few years. The ease of use, low cost and high efficiency of CRISPR/Cas make it commonly used in various conditions. In this review, we introduce the CRISPR/Cas system and its diverse applications in nervous system briefly, which provides a better understanding for its potential application values.
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Affiliation(s)
- Yanxia Gao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Kexin Gao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Hui Yang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
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19
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Harnessing targeted DNA methylation and demethylation using dCas9. Essays Biochem 2020; 63:813-825. [PMID: 31724704 DOI: 10.1042/ebc20190029] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/23/2019] [Accepted: 10/24/2019] [Indexed: 12/15/2022]
Abstract
DNA methylation is an essential DNA modification that plays a crucial role in genome regulation during differentiation and development, and is disrupted in a range of disease states. The recent development of CRISPR/catalytically dead CRISPR/Cas9 (dCas9)-based targeted DNA methylation editing tools has enabled new insights into the roles and functional relevance of this modification, including its importance at regulatory regions and the role of aberrant methylation in various diseases. However, while these tools are advancing our ability to understand and manipulate this regulatory layer of the genome, they still possess a variety of limitations in efficacy, implementation, and targeting specificity. Effective targeted DNA methylation editing will continue to advance our fundamental understanding of the role of this modification in different genomic and cellular contexts, and further improvements may enable more accurate disease modeling and possible future treatments. In this review, we discuss strategies, considerations, and future directions for targeted DNA methylation editing.
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20
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Adenoviral Vectors Meet Gene Editing: A Rising Partnership for the Genomic Engineering of Human Stem Cells and Their Progeny. Cells 2020; 9:cells9040953. [PMID: 32295080 PMCID: PMC7226970 DOI: 10.3390/cells9040953] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/10/2020] [Accepted: 04/10/2020] [Indexed: 12/13/2022] Open
Abstract
Gene editing permits changing specific DNA sequences within the vast genomes of human cells. Stem cells are particularly attractive targets for gene editing interventions as their self-renewal and differentiation capabilities consent studying cellular differentiation processes, screening small-molecule drugs, modeling human disorders, and testing regenerative medicines. To integrate gene editing and stem cell technologies, there is a critical need for achieving efficient delivery of the necessary molecular tools in the form of programmable DNA-targeting enzymes and/or exogenous nucleic acid templates. Moreover, the impact that the delivery agents themselves have on the performance and precision of gene editing procedures is yet another critical parameter to consider. Viral vectors consisting of recombinant replication-defective viruses are under intense investigation for bringing about efficient gene-editing tool delivery and precise gene-editing in human cells. In this review, we focus on the growing role that adenoviral vectors are playing in the targeted genetic manipulation of human stem cells, progenitor cells, and their differentiated progenies in the context of in vitro and ex vivo protocols. As preamble, we provide an overview on the main gene editing principles and adenoviral vector platforms and end by discussing the possibilities ahead resulting from leveraging adenoviral vector, gene editing, and stem cell technologies.
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21
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Targeted gene therapy into a safe harbor site in human hematopoietic progenitor cells. Gene Ther 2020; 27:435-450. [PMID: 32218505 DOI: 10.1038/s41434-020-0144-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 03/10/2020] [Accepted: 03/12/2020] [Indexed: 12/16/2022]
Abstract
Directed gene therapy mediated by nucleases has become a new alternative to lead targeted integration of therapeutic genes in specific regions in the genome. In this work, we have compared the efficiency of two nuclease types, TALEN and meganucleases (MN), to introduce an EGFP reporter gene in a specific site in a safe harbor locus on chromosome 21 in an intergenic region, named here SH6. The efficiency of targeted integration mediated by SH6v5-MN and SH6-TALEN in HEK-293H cells was up to 16.3 and 15.0%. A stable expression was observed both in the pool of transfected cells and in established pseudoclones, with no detection of off-target integrations by Southern blot. In human hematopoietic stem and progenitor CD34+ cells, the nucleofection process preserved the viability and clonogenic capacity of nucleofected cells, reaching up to 3.1% of specific integration of the transgene in colony forming cells when the SH6-TALEN was used, although no expression of the transgene could be found in these cells. Our results show the possibility to specifically integrate genes at the SH6 locus in CD34+ progenitor cells, although further improvements in the efficacy of the procedure are required before this approach could be used for the gene editing of hematopoietic stem cells in patients with hematopoietic diseases.
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22
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Liu L, Zhang Y, Liu M, Wei W, Yi C, Peng J. Structural Insights into the Specific Recognition of 5-methylcytosine and 5-hydroxymethylcytosine by TAL Effectors. J Mol Biol 2020; 432:1035-1047. [DOI: 10.1016/j.jmb.2019.11.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 11/12/2019] [Accepted: 11/27/2019] [Indexed: 01/02/2023]
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23
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Van Vu T, Sung YW, Kim J, Doan DTH, Tran MT, Kim JY. Challenges and Perspectives in Homology-Directed Gene Targeting in Monocot Plants. RICE (NEW YORK, N.Y.) 2019; 12:95. [PMID: 31858277 PMCID: PMC6923311 DOI: 10.1186/s12284-019-0355-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/04/2019] [Indexed: 05/18/2023]
Abstract
Continuing crop domestication/redomestication and modification is a key determinant of the adaptation and fulfillment of the food requirements of an exploding global population under increasingly challenging conditions such as climate change and the reduction in arable lands. Monocotyledonous crops are not only responsible for approximately 70% of total global crop production, indicating their important roles in human life, but also the first crops to be challenged with the abovementioned hurdles; hence, monocot crops should be the first to be engineered and/or de novo domesticated/redomesticated. A long time has passed since the first green revolution; the world is again facing the challenge of feeding a predicted 9.7 billion people in 2050, since the decline in world hunger was reversed in 2015. One of the major lessons learned from the first green revolution is the importance of novel and advanced trait-carrying crop varieties that are ideally adapted to new agricultural practices. New plant breeding techniques (NPBTs), such as genome editing, could help us succeed in this mission to create novel and advanced crops. Considering the importance of NPBTs in crop genetic improvement, we attempt to summarize and discuss the latest progress with major approaches, such as site-directed mutagenesis using molecular scissors, base editors and especially homology-directed gene targeting (HGT), a very challenging but potentially highly precise genome modification approach in plants. We therefore suggest potential approaches for the improvement of practical HGT, focusing on monocots, and discuss a potential approach for the regulation of genome-edited products.
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Affiliation(s)
- Tien Van Vu
- Division of Applied Life Science (BK21 Plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Km 02, Pham Van Dong Road, Co Nhue 1, Bac Tu Liem, Hanoi, 11917, Vietnam
| | - Yeon Woo Sung
- Division of Applied Life Science (BK21 Plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Jihae Kim
- Division of Applied Life Science (BK21 Plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Duong Thi Hai Doan
- Division of Applied Life Science (BK21 Plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Mil Thi Tran
- Division of Applied Life Science (BK21 Plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea.
- Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
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24
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Oh HS, Neuhausser WM, Eggan P, Angelova M, Kirchner R, Eggan KC, Knipe DM. Herpesviral lytic gene functions render the viral genome susceptible to novel editing by CRISPR/Cas9. eLife 2019; 8:e51662. [PMID: 31789594 PMCID: PMC6917492 DOI: 10.7554/elife.51662] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 12/01/2019] [Indexed: 01/29/2023] Open
Abstract
Herpes simplex virus (HSV) establishes lifelong latent infection and can cause serious human disease, but current antiviral therapies target lytic but not latent infection. We screened for sgRNAs that cleave HSV-1 DNA sequences efficiently in vitro and used these sgRNAs to observe the first editing of quiescent HSV-1 DNA. The sgRNAs targeted lytic replicating viral DNA genomes more efficiently than quiescent genomes, consistent with the open structure of lytic chromatin. Editing of latent genomes caused short indels while editing of replicating genomes produced indels, linear molecules, and large genomic sequence loss around the gRNA target site. The HSV ICP0 protein and viral DNA replication increased the loss of DNA sequences around the gRNA target site. We conclude that HSV, by promoting open chromatin needed for viral gene expression and by inhibiting the DNA damage response, makes the genome vulnerable to a novel form of editing by CRISPR-Cas9 during lytic replication.
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Affiliation(s)
- Hyung Suk Oh
- Department of MicrobiologyBlavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Werner M Neuhausser
- Department of Stem Cell and Regenerative BiologyHarvard UniversityCambridgeUnited States
- Harvard Stem Cell InstituteHarvard UniversityCambridgeUnited States
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and InfertilityBeth Israel Deaconess Medical Center, Harvard Medical SchoolBostonUnited States
| | - Pierce Eggan
- Department of Stem Cell and Regenerative BiologyHarvard UniversityCambridgeUnited States
- Harvard Stem Cell InstituteHarvard UniversityCambridgeUnited States
| | - Magdalena Angelova
- Department of MicrobiologyBlavatnik Institute, Harvard Medical SchoolBostonUnited States
| | - Rory Kirchner
- Department of BiostatisticsHarvard TH Chan School of Public HealthBostonUnited States
| | - Kevin C Eggan
- Department of Stem Cell and Regenerative BiologyHarvard UniversityCambridgeUnited States
- Harvard Stem Cell InstituteHarvard UniversityCambridgeUnited States
- Stanley Center for Psychiatric Research, Broad Institute of MIT and HarvardCambridgeUnited States
| | - David M Knipe
- Department of MicrobiologyBlavatnik Institute, Harvard Medical SchoolBostonUnited States
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25
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The diverse roles of DNA methylation in mammalian development and disease. Nat Rev Mol Cell Biol 2019; 20:590-607. [PMID: 31399642 DOI: 10.1038/s41580-019-0159-6] [Citation(s) in RCA: 1097] [Impact Index Per Article: 219.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2019] [Indexed: 12/22/2022]
Abstract
DNA methylation is of paramount importance for mammalian embryonic development. DNA methylation has numerous functions: it is implicated in the repression of transposons and genes, but is also associated with actively transcribed gene bodies and, in some cases, with gene activation per se. In recent years, sensitive technologies have been developed that allow the interrogation of DNA methylation patterns from a small number of cells. The use of these technologies has greatly improved our knowledge of DNA methylation dynamics and heterogeneity in embryos and in specific tissues. Combined with genetic analyses, it is increasingly apparent that regulation of DNA methylation erasure and (re-)establishment varies considerably between different developmental stages. In this Review, we discuss the mechanisms and functions of DNA methylation and demethylation in both mice and humans at CpG-rich promoters, gene bodies and transposable elements. We highlight the dynamic erasure and re-establishment of DNA methylation in embryonic, germline and somatic cell development. Finally, we provide insights into DNA methylation gained from studying genetic diseases.
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26
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Tsuji S, Imanishi M. Modified nucleobase-specific gene regulation using engineered transcription activator-like effectors. Adv Drug Deliv Rev 2019; 147:59-65. [PMID: 31513826 DOI: 10.1016/j.addr.2019.08.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 08/20/2019] [Accepted: 08/22/2019] [Indexed: 01/10/2023]
Abstract
Epigenetic modification, as typified by cytosine methylation, is a key aspect of gene regulation that affects many biological processes. However, the biological roles of individual methylated cytosines are poorly understood. Sequence-specific DNA recognition tools can be used to investigate the roles of individual instances of DNA methylation. Transcription activator-like effectors (TALEs), which are DNA-binding proteins, are promising candidate tools with designable sequence specificity and sensitivity to DNA methylation. In this review, we describe the bases of DNA recognition of TALEs, including methylated cytosine recognition, and the applications of TALEs for the study of methylated DNA. In addition, we discuss TALE-based epigenome editing and oxidized methylated cytosine recognition.
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27
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Kostyushev D, Brezgin S, Kostyusheva A, Zarifyan D, Goptar I, Chulanov V. Orthologous CRISPR/Cas9 systems for specific and efficient degradation of covalently closed circular DNA of hepatitis B virus. Cell Mol Life Sci 2019; 76:1779-1794. [PMID: 30673820 PMCID: PMC11105500 DOI: 10.1007/s00018-019-03021-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/16/2019] [Accepted: 01/17/2019] [Indexed: 12/11/2022]
Abstract
Covalently closed circular DNA (cccDNA) of hepatitis B virus (HBV) is the major cause of viral persistence and chronic hepatitis B. CRISPR/Cas9 nucleases can specifically target HBV cccDNA for decay, but off-target effects of nucleases in the human genome limit their clinical utility. CRISPR/Cas9 systems from four different species were co-expressed in cell lines with guide RNAs targeting conserved regions of the HBV genome. CRISPR/Cas9 systems from Streptococcus pyogenes (Sp) and Streptococcus thermophilus (St) targeting conserved regions of the HBV genome blocked HBV replication and, most importantly, resulted in degradation of over 90% of HBV cccDNA by 6 days post-transfection. Degradation of HBV cccDNA was impaired by inhibition of non-homologous end-joining pathway and resulted in an erroneous repair of HBV cccDNA. HBV cccDNA methylation also affected antiviral activity of CRISPR/Cas9. Single-nucleotide HBV genetic variants did not impact anti-HBV activity of St CRISPR/Cas9, suggesting its utility in targeting many HBV variants. However, two or more mismatches impaired or blocked CRISPR/Cas9 activity, indicating that host DNA will not likely be targeted. Deep sequencing revealed that Sp CRISPR/Cas9 induced off-target mutagenesis, whereas St CRISPR/Cas9 had no effect on the host genome. St CRISPR/Cas9 system represents the safest system with high anti-HBV activity.
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Affiliation(s)
- Dmitry Kostyushev
- Viral Hepatitis Laboratory, Central Research Institute of Epidemiology, 3A Novogireevskaya Street, Moscow, 111123, Russian Federation.
| | - Sergey Brezgin
- Viral Hepatitis Laboratory, Central Research Institute of Epidemiology, 3A Novogireevskaya Street, Moscow, 111123, Russian Federation
- Institute of Immunology, Federal Medical Biological Agency, Moscow, 115478, Russian Federation
| | - Anastasiya Kostyusheva
- Viral Hepatitis Laboratory, Central Research Institute of Epidemiology, 3A Novogireevskaya Street, Moscow, 111123, Russian Federation
| | - Dmitry Zarifyan
- Viral Hepatitis Laboratory, Central Research Institute of Epidemiology, 3A Novogireevskaya Street, Moscow, 111123, Russian Federation
| | - Irina Goptar
- Viral Hepatitis Laboratory, Central Research Institute of Epidemiology, 3A Novogireevskaya Street, Moscow, 111123, Russian Federation
- Izmerov Research Institute of Occupational Health, Moscow, 105275, Russian Federation
| | - Vladimir Chulanov
- Viral Hepatitis Laboratory, Central Research Institute of Epidemiology, 3A Novogireevskaya Street, Moscow, 111123, Russian Federation
- Sechenov University, Moscow, 119146, Russian Federation
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28
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Wang Q, Dai L, Wang Y, Deng J, Lin Y, Wang Q, Fang C, Ma Z, Wang H, Shi G, Cheng L, Liu Y, Chen S, Li J, Dong Z, Su X, Yang L, Zhang S, Jiang M, Huang M, Yang Y, Yu D, Zhou Z, Wei Y, Deng H. Targeted demethylation of the SARI promotor impairs colon tumour growth. Cancer Lett 2019; 448:132-143. [DOI: 10.1016/j.canlet.2019.01.040] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 10/27/2022]
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29
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Janssen JM, Chen X, Liu J, Gonçalves MAFV. The Chromatin Structure of CRISPR-Cas9 Target DNA Controls the Balance between Mutagenic and Homology-Directed Gene-Editing Events. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 16:141-154. [PMID: 30884291 PMCID: PMC6424062 DOI: 10.1016/j.omtn.2019.02.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 02/11/2019] [Accepted: 02/11/2019] [Indexed: 12/19/2022]
Abstract
Gene editing based on homology-directed repair (HDR) depends on donor DNA templates and programmable nucleases, e.g., RNA-guided CRISPR-Cas9 nucleases. However, next to inducing HDR involving the mending of chromosomal double-stranded breaks (DSBs) with donor DNA substrates, programmable nucleases also yield gene disruptions, triggered by competing non-homologous end joining (NHEJ) pathways. It is, therefore, imperative to identify parameters underlying the relationship between these two outcomes in the context of HDR-based gene editing. Here we implemented quantitative cellular systems, based on epigenetically regulated isogenic target sequences and donor DNA of viral, non-viral, and synthetic origins, to investigate gene-editing outcomes resulting from the interaction between different chromatin conformations and donor DNA structures. We report that, despite a significantly higher prevalence of NHEJ-derived events at euchromatin over Krüppel-associated box (KRAB)-impinged heterochromatin, HDR frequencies are instead generally less impacted by these alternative chromatin conformations. Hence, HDR increases in relation to NHEJ when open euchromatic target sequences acquire a closed heterochromatic state, with donor DNA structures determining, to some extent, the degree of this relative increase in HDR events at heterochromatin. Finally, restricting nuclease activity to HDR-permissive G2 and S phases of the cell cycle through a Cas9-Geminin construct yields lower, hence more favorable, NHEJ to HDR ratios, independently of the chromatin structure.
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Affiliation(s)
- Josephine M Janssen
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Xiaoyu Chen
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Jin Liu
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Manuel A F V Gonçalves
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands.
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30
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Abstract
DNA methylation plays important roles in determining cellular identity, disease, and environmental responses, but little is known about the mechanisms that drive methylation changes during cellular differentiation and tumorigenesis. Meanwhile, the causal relationship between DNA methylation and transcription remains incompletely understood. Recently developed targeted DNA methylation manipulation tools can address these gaps in knowledge, leading to new insights into how methylation governs gene expression. Here, we summarize technological developments in the DNA methylation editing field and discuss the remaining challenges facing current tools, as well as potential future directions.
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Affiliation(s)
- Yong Lei
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yung-Hsin Huang
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA.,Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Margaret A Goodell
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, 77030, USA. .,Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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31
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Landel C, Pritchett-Corning KR. Gene Editing Technologies and Use of Recombinant/Synthetic Nucleic Acids in Laboratory Animals. APPLIED BIOSAFETY 2018. [DOI: 10.1177/1535676018797353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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32
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Bogdanove AJ, Bohm A, Miller JC, Morgan RD, Stoddard BL. Engineering altered protein-DNA recognition specificity. Nucleic Acids Res 2018; 46:4845-4871. [PMID: 29718463 PMCID: PMC6007267 DOI: 10.1093/nar/gky289] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/03/2018] [Accepted: 04/06/2018] [Indexed: 02/07/2023] Open
Abstract
Protein engineering is used to generate novel protein folds and assemblages, to impart new properties and functions onto existing proteins, and to enhance our understanding of principles that govern protein structure. While such approaches can be employed to reprogram protein-protein interactions, modifying protein-DNA interactions is more difficult. This may be related to the structural features of protein-DNA interfaces, which display more charged groups, directional hydrogen bonds, ordered solvent molecules and counterions than comparable protein interfaces. Nevertheless, progress has been made in the redesign of protein-DNA specificity, much of it driven by the development of engineered enzymes for genome modification. Here, we summarize the creation of novel DNA specificities for zinc finger proteins, meganucleases, TAL effectors, recombinases and restriction endonucleases. The ease of re-engineering each system is related both to the modularity of the protein and the extent to which the proteins have evolved to be capable of readily modifying their recognition specificities in response to natural selection. The development of engineered DNA binding proteins that display an ideal combination of activity, specificity, deliverability, and outcomes is not a fully solved problem, however each of the current platforms offers unique advantages, offset by behaviors and properties requiring further study and development.
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Affiliation(s)
- Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Andrew Bohm
- Sackler School of Graduate Biomedical Sciences, Tufts University, 136 Harrison Avenue, Boston, MA 02111, USA
| | - Jeffrey C Miller
- Sangamo Therapeutics Inc. 501 Canal Blvd., Richmond, CA 94804, USA
| | - Richard D Morgan
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98019, USA
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33
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Nerys-Junior A, Braga-Dias LP, Pezzuto P, Cotta-de-Almeida V, Tanuri A. Comparison of the editing patterns and editing efficiencies of TALEN and CRISPR-Cas9 when targeting the human CCR5 gene. Genet Mol Biol 2018; 41:167-179. [PMID: 29583154 PMCID: PMC5901495 DOI: 10.1590/1678-4685-gmb-2017-0065] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/07/2017] [Indexed: 01/02/2023] Open
Abstract
The human C-C chemokine receptor type-5 (CCR5) is the major transmembrane
co-receptor that mediates HIV-1 entry into target CD4+ cells. Gene therapy to
knock-out the CCR5 gene has shown encouraging results in providing a functional
cure for HIV-1 infection. In gene therapy strategies, the initial region of the
CCR5 gene is a hotspot for producing functional gene knock-out. Such target gene
editing can be done using programmable endonucleases such as transcription
activator-like effector nucleases (TALEN) or clustered regularly interspaced
short palindromic repeats (CRISPR-Cas9). These two gene editing approaches are
the most modern and effective tools for precise gene modification. However,
little is known of potential differences in the efficiencies of TALEN and
CRISPR-Cas9 for editing the beginning of the CCR5 gene. To examine which of
these two methods is best for gene therapy, we compared the patterns and amount
of editing at the beginning of the CCR5 gene using TALEN and CRISPR-Cas9
followed by DNA sequencing. This comparison revealed that CRISPR-Cas9 mediated
the sorting of cells that contained 4.8 times more gene editing than TALEN+
transfected cells.
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Affiliation(s)
- Arildo Nerys-Junior
- Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Luciene P Braga-Dias
- Laboratório do Serviço de Biotecnologia e Desenvolvimento Animal, Instituto de Ciência e Tecnologia em Biomodelos, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Paula Pezzuto
- Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | | | - Amilcar Tanuri
- Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
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34
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Pham HT, Mesplède T. The latest evidence for possible HIV-1 curative strategies. Drugs Context 2018; 7:212522. [PMID: 29497452 PMCID: PMC5824924 DOI: 10.7573/dic.212522] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/25/2018] [Accepted: 01/26/2018] [Indexed: 01/01/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) infection remains a major health issue worldwide. In developed countries, antiretroviral therapy has extended its reach from treatment of people living with HIV-1 to post-exposure prophylaxis, treatment as prevention, and, more recently, pre-exposure prophylaxis. These healthcare strategies offer the epidemiological tools to curve the epidemic in rich settings and will be concomitantly implemented in developing countries. One of the remaining challenges is to identify an efficacious curative strategy. This review manuscript will focus on some of the current curative strategies aiming at providing a sterilizing or functional cure to HIV-1-positive individuals. These include the following: early treatment initiation in post-treatment controllers as a long-term HIV-1 remission strategy, latency reversal, gene editing with or without stem cell transplantation, and antibodies against either the viral envelope protein or the host integrin α4β7.
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Affiliation(s)
- Hanh Thi Pham
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada.,Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montréal, Québec, Canada
| | - Thibault Mesplède
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada.,Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montréal, Québec, Canada.,Division of Experimental Medicine, Faculty of Medicine, McGill University, Montréal, Québec, Canada.,Division of Infectious Diseases, Jewish General Hospital, McGill University, Montréal, Québec, Canada
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35
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Tsuji S, Futaki S, Imanishi M. Sequence-specific recognition of methylated DNA by an engineered transcription activator-like effector protein. Chem Commun (Camb) 2018; 52:14238-14241. [PMID: 27872906 DOI: 10.1039/c6cc06824c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A 5mC-selective TALE-repeat was created by screening a TALE repeat library containing randomized amino acids at repeat variable diresidues and their neighboring residues. The new repeat showed high 5mC discrimination ability. An artificial TALE containing the new repeat activated an endogenous gene in a genomic methylation status-dependent manner.
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Affiliation(s)
- Shogo Tsuji
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Shiroh Futaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Miki Imanishi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
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36
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Waryah CB, Moses C, Arooj M, Blancafort P. Zinc Fingers, TALEs, and CRISPR Systems: A Comparison of Tools for Epigenome Editing. Methods Mol Biol 2018. [PMID: 29524128 DOI: 10.1007/978-1-4939-7774-1_2] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The completion of genome, epigenome, and transcriptome mapping in multiple cell types has created a demand for precision biomolecular tools that allow researchers to functionally manipulate DNA, reconfigure chromatin structure, and ultimately reshape gene expression patterns. Epigenetic editing tools provide the ability to interrogate the relationship between epigenetic modifications and gene expression. Importantly, this information can be exploited to reprogram cell fate for both basic research and therapeutic applications. Three different molecular platforms for epigenetic editing have been developed: zinc finger proteins (ZFs), transcription activator-like effectors (TALEs), and the system of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) proteins. These platforms serve as custom DNA-binding domains (DBDs), which are fused to epigenetic modifying domains to manipulate epigenetic marks at specific sites in the genome. The addition and/or removal of epigenetic modifications reconfigures local chromatin structure, with the potential to provoke long-lasting changes in gene transcription. Here we summarize the molecular structure and mechanism of action of ZF, TALE, and CRISPR platforms and describe their applications for the locus-specific manipulation of the epigenome. The advantages and disadvantages of each platform will be discussed with regard to genomic specificity, potency in regulating gene expression, and reprogramming cell phenotypes, as well as ease of design, construction, and delivery. Finally, we outline potential applications for these tools in molecular biology and biomedicine and identify possible barriers to their future clinical implementation.
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Affiliation(s)
- Charlene Babra Waryah
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia
| | - Colette Moses
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia
- School of Human Sciences, The University of Western Australia, Perth, WA, Australia
| | - Mahira Arooj
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Pilar Blancafort
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia.
- School of Human Sciences, The University of Western Australia, Perth, WA, Australia.
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37
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Lowder LG, Malzahn A, Qi Y. Plant Gene Regulation Using Multiplex CRISPR-dCas9 Artificial Transcription Factors. Methods Mol Biol 2018; 1676:197-214. [PMID: 28986912 DOI: 10.1007/978-1-4939-7315-6_12] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Besides genome editing, the CRISPR-Cas9-based platform provides a new way of engineering artificial transcription factors (ATFs). Multiplex of guide RNA (gRNA) expression cassettes holds a great promise for many useful applications of CRISPR-Cas9. In this chapter, we provide a detailed protocol for building advanced multiplexed CRISPR-dCas9-Activator/repressor T-DNA vectors for carrying out transcriptional activation or repression experiments in plants. We specifically describe the assembly of multiplex T-DNA vectors that can express multiple gRNAs to activate a silenced gene, or to repress two independent miRNA genes simultaneously in Arabidopsis. We then describe a "higher-order" vector assembly method for increased multiplexing capacity. This higher-order assembly method in principle allows swift stacking of gRNAs cassettes that are only limited by the loading capacity of a cloning or expression vector.
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Affiliation(s)
- Levi G Lowder
- Department of Biology, East Carolina University, Howell Science Complex, Greenville, NC, 27858, USA
| | - Aimee Malzahn
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA.
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38
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Muñoz-López Á, Summerer D. Recognition of Oxidized 5-Methylcytosine Derivatives in DNA by Natural and Engineered Protein Scaffolds. CHEM REC 2017; 18:105-116. [PMID: 29251421 DOI: 10.1002/tcr.201700088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Indexed: 12/14/2022]
Abstract
Methylation of genomic cytosine to 5-methylcytosine is a central regulatory element of mammalian gene expression with important roles in development and disease. 5-methylcytosine can be actively reversed to cytosine via oxidation to 5-hydroxymethyl-, 5-formyl-, and 5-carboxylcytosine by ten-eleven-translocation dioxygenases and subsequent base excision repair or replication-dependent dilution. Moreover, the oxidized 5-methylcytosine derivatives are potential epigenetic marks with unique biological roles. Key to a better understanding of these roles are insights into the interactions of the nucleobases with DNA-binding protein scaffolds: Natural scaffolds involved in transcription, 5-methylcytosine-reading and -editing as well as general chromatin organization can be selectively recruited or repulsed by oxidized 5-methylcytosines, forming the basis of their biological functions. Moreover, designer protein scaffolds engineered for the selective recognition of oxidized 5-methylcytosines are valuable tools to analyze their genomic levels and distribution. Here, we review recent structural and functional insights into the molecular recognition of oxidized 5-methylcytosine derivatives in DNA by selected protein scaffolds.
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Affiliation(s)
- Álvaro Muñoz-López
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund
| | - Daniel Summerer
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund
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39
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Rathi P, Witte A, Summerer D. Engineering DNA Backbone Interactions Results in TALE Scaffolds with Enhanced 5-Methylcytosine Selectivity. Sci Rep 2017; 7:15067. [PMID: 29118409 PMCID: PMC5678105 DOI: 10.1038/s41598-017-15361-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/25/2017] [Indexed: 12/14/2022] Open
Abstract
Transcription activator-like effectors (TALEs) are DNA major-groove binding proteins widely used for genome targeting. TALEs contain an N-terminal region (NTR) and a central repeat domain (CRD). Repeats of the CRD selectively recognize each one DNA nucleobase, offering programmability. Moreover, repeats with selectivity for 5-methylcytosine (5mC) and its oxidized derivatives can be designed for analytical applications. However, both TALE domains also nonspecifically interact with DNA phosphates via basic amino acids. To enhance the 5mC selectivity of TALEs, we aimed to decrease the nonselective binding energy of TALEs. We substituted basic amino acids with alanine in the NTR and identified TALE mutants with increased selectivity. We then analysed conserved, DNA phosphate-binding KQ diresidues in CRD repeats and identified further improved mutants. Combination of mutations in the NTR and CRD was highly synergetic and resulted in TALE scaffolds with up to 4.3-fold increased selectivity in genomic 5mC analysis via affinity enrichment. Moreover, transcriptional activation in HEK293T cells by a TALE-VP64 construct based on this scaffold design exhibited a 3.5-fold increased 5mC selectivity. This provides perspectives for improved 5mC analysis and for the 5mC-conditional control of TALE-based editing constructs in vivo.
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Affiliation(s)
- Preeti Rathi
- Department of Chemistry and Chemical Biology, Technical University of Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Anna Witte
- Department of Chemistry and Chemical Biology, Technical University of Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Daniel Summerer
- Department of Chemistry and Chemical Biology, Technical University of Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany.
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40
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Malankhanova TB, Malakhova AA, Medvedev SP, Zakian SM. Modern Genome Editing Technologies in Huntington's Disease Research. J Huntingtons Dis 2017; 6:19-31. [PMID: 28128770 PMCID: PMC5389024 DOI: 10.3233/jhd-160222] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The development of new revolutionary technologies for directed gene editing has made it possible to thoroughly model and study NgAgo human diseases at the cellular and molecular levels. Gene editing tools like ZFN, TALEN, CRISPR-based systems, NgAgo and SGN can introduce different modifications. In gene sequences and regulate gene expression in different types of cells including induced pluripotent stem cells (iPSCs). These tools can be successfully used for Huntington's disease (HD) modeling, for example, to generate isogenic cell lines bearing different numbers of CAG repeats or to correct the mutation causing the disease. This review presents common genome editing technologies and summarizes the progress made in using them in HD and other hereditary diseases. Furthermore, we will discuss prospects and limitations of genome editing in understanding HD pathology.
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Affiliation(s)
- Tuyana B Malankhanova
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia.,State Research Institute of Circulation Pathology, Ministry of Healthcare of the Russian Federation, Novosibirsk, Russia.,Institute of Chemical Biology and Fundamental Medicine, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anastasia A Malakhova
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,State Research Institute of Circulation Pathology, Ministry of Healthcare of the Russian Federation, Novosibirsk, Russia.,Institute of Chemical Biology and Fundamental Medicine, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergey P Medvedev
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia.,State Research Institute of Circulation Pathology, Ministry of Healthcare of the Russian Federation, Novosibirsk, Russia.,Institute of Chemical Biology and Fundamental Medicine, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Suren M Zakian
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia.,State Research Institute of Circulation Pathology, Ministry of Healthcare of the Russian Federation, Novosibirsk, Russia.,Institute of Chemical Biology and Fundamental Medicine, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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41
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Gautron AS, Juillerat A, Guyot V, Filhol JM, Dessez E, Duclert A, Duchateau P, Poirot L. Fine and Predictable Tuning of TALEN Gene Editing Targeting for Improved T Cell Adoptive Immunotherapy. MOLECULAR THERAPY-NUCLEIC ACIDS 2017; 9:312-321. [PMID: 29246309 PMCID: PMC5684446 DOI: 10.1016/j.omtn.2017.10.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 10/11/2017] [Accepted: 10/11/2017] [Indexed: 12/25/2022]
Abstract
Using a TALEN-mediated gene-editing approach, we have previously described a process for the large-scale manufacturing of “off-the-shelf” CAR T cells from third-party donor T cells by disrupting the gene encoding TCRα constant chain (TRAC). Taking advantage of a previously described strategy to control TALEN targeting based on the exclusion capacities of non-conventional RVDs, we have developed highly efficient and specific nucleases targeting a key T cell immune checkpoint, PD-1, to improve engineered CAR T cells’ functionalities. Here, we demonstrate that this approach allows combined TRAC and PDCD1 TALEN processing at the desired locus while eliminating low-frequency off-site processing. Thus, by replacing few RVDs, we provide here an easy and rapid redesign of optimal TALEN combinations. We anticipate that this method can greatly benefit multiplex editing, which is of key importance especially for therapeutic applications where high editing efficiencies need to be associated with maximal specificity and safety.
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Affiliation(s)
| | | | - Valérie Guyot
- Cellectis SA, 8 Rue de la Croix Jarry, 75013 Paris, France
| | | | - Emilie Dessez
- Cellectis SA, 8 Rue de la Croix Jarry, 75013 Paris, France
| | | | | | - Laurent Poirot
- Cellectis SA, 8 Rue de la Croix Jarry, 75013 Paris, France
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42
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Deciphering TAL effectors for 5-methylcytosine and 5-hydroxymethylcytosine recognition. Nat Commun 2017; 8:901. [PMID: 29026078 PMCID: PMC5638953 DOI: 10.1038/s41467-017-00860-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 08/01/2017] [Indexed: 12/29/2022] Open
Abstract
DNA recognition by transcription activator-like effector (TALE) proteins is mediated by tandem repeats that specify nucleotides through repeat-variable diresidues. These repeat-variable diresidues form direct and sequence-specific contacts to DNA bases; hence, TALE-DNA interaction is sensitive to DNA chemical modifications. Here we conduct a thorough investigation, covering all theoretical repeat-variable diresidue combinations, for their recognition capabilities for 5-methylcytosine and 5-hydroxymethylcytosine, two important epigenetic markers in higher eukaryotes. We identify both specific and degenerate repeat-variable diresidues for 5-methylcytosine and 5-hydroxymethylcytosine. Utilizing these novel repeat-variable diresidues, we achieve methylation-dependent gene activation and genome editing in vivo; we also report base-resolution detection of 5hmC in an in vitro assay. Our work deciphers repeat-variable diresidues for 5-methylcytosine and 5-hydroxymethylcytosine, and provides tools for TALE-dependent epigenome recognition.Transcription activator-like effector proteins recognise specific DNA sequences via tandem repeats. Here the authors demonstrate TALEs can recognise the methylated bases 5mC and 5hmC, enabling them to detect epigenetic modifications.
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43
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Alzubi J, Pallant C, Mussolino C, Howe SJ, Thrasher AJ, Cathomen T. Targeted genome editing restores T cell differentiation in a humanized X-SCID pluripotent stem cell disease model. Sci Rep 2017; 7:12475. [PMID: 28963568 PMCID: PMC5622068 DOI: 10.1038/s41598-017-12750-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 09/15/2017] [Indexed: 12/18/2022] Open
Abstract
The generation of T cells from pluripotent stem cells (PSCs) is attractive for investigating T cell development and validating genome editing strategies in vitro. X-linked severe combined immunodeficiency (X-SCID) is an immune disorder caused by mutations in the IL2RG gene and characterised by the absence of T and NK cells in patients. IL2RG encodes the common gamma chain, which is part of several interleukin receptors, including IL-2 and IL-7 receptors. To model X-SCID in vitro, we generated a mouse embryonic stem cell (ESC) line in which a disease-causing human IL2RG gene variant replaces the endogenous Il2rg locus. We developed a stage-specific T cell differentiation protocol to validate genetic correction of the common G691A mutation with transcription activator-like effector nucleases. While all ESC clones could be differentiated to hematopoietic precursor cells, stage-specific analysis of T cell maturation confirmed early arrest of T cell differentiation at the T cell progenitor stage in X-SCID cells. In contrast, genetically corrected ESCs differentiated to CD4 + or CD8 + single-positive T cells, confirming correction of the cellular X-SCID phenotype. This study emphasises the value of PSCs for disease modelling and underlines the significance of in vitro models as tools to validate genome editing strategies before clinical application.
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Affiliation(s)
- Jamal Alzubi
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, Freiburg, Germany
| | - Celeste Pallant
- Institute of Child Health, University College London, London, United Kingdom.,GlaxoSmithKline plc., Stevenage, Hertfordshire, United Kingdom
| | - Claudio Mussolino
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, Freiburg, Germany
| | - Steven J Howe
- Institute of Child Health, University College London, London, United Kingdom.,GlaxoSmithKline plc., Stevenage, Hertfordshire, United Kingdom
| | - Adrian J Thrasher
- Institute of Child Health, University College London, London, United Kingdom.,Great Ormond Street Hospital, NHS Foundation Trust, London, United Kingdom
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg, Germany. .,Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, Freiburg, Germany. .,Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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44
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Chandrasekaran AP, Song M, Ramakrishna S. Genome editing: a robust technology for human stem cells. Cell Mol Life Sci 2017; 74:3335-3346. [PMID: 28405721 PMCID: PMC11107609 DOI: 10.1007/s00018-017-2522-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 04/05/2017] [Accepted: 04/07/2017] [Indexed: 12/20/2022]
Abstract
Human pluripotent stem cells comprise induced pluripotent and embryonic stem cells, which have tremendous potential for biological and therapeutic applications. The development of efficient technologies for the targeted genome alteration of stem cells in disease models is a prerequisite for utilizing stem cells to their full potential. Genome editing of stem cells is possible with the help of synthetic nucleases that facilitate site-specific modification of a gene of interest. Recent advances in genome editing techniques have improved the efficiency and speed of the development of stem cells for human disease models. Zinc finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated system are powerful tools for editing DNA at specific loci. Here, we discuss recent technological advances in genome editing with site-specific nucleases in human stem cells.
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Affiliation(s)
| | - Minjung Song
- Division of Bioindustry, Department of Food Biotechnology, College of Medical and Life Science, Silla University, Seoul, Republic of Korea.
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, Republic of Korea.
- College of Medicine, Hanyang University, Seoul, Republic of Korea.
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45
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Flade S, Jasper J, Gieß M, Juhasz M, Dankers A, Kubik G, Koch O, Weinhold E, Summerer D. The N6-Position of Adenine Is a Blind Spot for TAL-Effectors That Enables Effective Binding of Methylated and Fluorophore-Labeled DNA. ACS Chem Biol 2017; 12:1719-1725. [PMID: 28493677 DOI: 10.1021/acschembio.7b00324] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Transcription-activator-like effectors (TALEs) are programmable DNA binding proteins widely used for genome targeting. TALEs consist of multiple concatenated repeats, each selectively recognizing one nucleobase via a defined repeat variable diresidue (RVD). Effective use of TALEs requires knowledge about their binding ability to epigenetic and other modified nucleobases occurring in target DNA. However, aside from epigenetic cytosine-5 modifications, the binding ability of TALEs to modified DNA is unknown. We here study the binding of TALEs to the epigenetic nucleobase N6-methyladenine (6mA) found in prokaryotic and recently also eukaryotic genomes. We find that the natural, adenine (A)-binding RVD NI is insensitive to 6mA. Model-assisted structure-function studies reveal accommodation of 6mA by RVDs with altered hydrophobic surfaces and abilities of hydrogen bonding to the N6-amino group or N7 atom of A. Surprisingly, this tolerance of N6 substitution was transferrable to bulky N6-alkynyl substituents usable for click chemistry and even to a large rhodamine dye, establishing the N6 position of A as the first site of DNA that offers label introduction within TALE target sites without interference. These findings will guide future in vivo studies with TALEs and expand their applicability as DNA capture probes for analytical applications in vitro.
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Affiliation(s)
- Sarah Flade
- Department
of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Julia Jasper
- Department
of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Mario Gieß
- Department
of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Matyas Juhasz
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| | - Andreas Dankers
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| | - Grzegorz Kubik
- Department
of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Oliver Koch
- Department
of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Elmar Weinhold
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| | - Daniel Summerer
- Department
of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
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46
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Aushev M, Koller U, Mussolino C, Cathomen T, Reichelt J. Traceless Targeting and Isolation of Gene-Edited Immortalized Keratinocytes from Epidermolysis Bullosa Simplex Patients. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2017; 6:112-123. [PMID: 28765827 PMCID: PMC5527154 DOI: 10.1016/j.omtm.2017.06.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/30/2017] [Indexed: 12/20/2022]
Abstract
Epidermolysis bullosa simplex (EBS) is a blistering skin disease caused by dominant-negative mutations in either KRT5 or KRT14, resulting in impairment of keratin filament structure and epidermal fragility. Currently, nearly 200 mutations distributed across the entire length of these genes are known to cause EBS. Genome editing using programmable nucleases enables the development of ex vivo gene therapies for dominant-negative genetic diseases. A clinically feasible strategy involves the disruption of the mutant allele while leaving the wild-type allele unaffected. Our aim was to develop a traceless approach to efficiently disrupt KRT5 alleles using TALENs displaying unbiased monoallelic disruption events and devise a strategy that allows for subsequent screening and isolation of correctly modified keratinocyte clones without the need for selection markers. Here we report on TALENs that efficiently disrupt the KRT5 locus in immortalized patient-derived EBS keratinocytes. Inactivation of the mutant allele using a TALEN working at sub-optimal levels resulted in restoration of intermediate filament architecture. This approach can be used for the functional inactivation of any mutant keratin allele regardless of the position of the mutation within the gene and is furthermore applicable to the treatment of other inherited skin disorders.
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Affiliation(s)
- Magomet Aushev
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Biomedicine West Wing, Centre for Life, Times Square, Newcastle upon Tyne NE1 3BZ, UK
| | - Ulrich Koller
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses and Department of Dermatology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
| | - Claudio Mussolino
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany.,Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, Breisacherstrasse 115, 79106 Freiburg, Germany.,Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany.,Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, Breisacherstrasse 115, 79106 Freiburg, Germany.,Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Julia Reichelt
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses and Department of Dermatology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
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47
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Malzahn A, Lowder L, Qi Y. Plant genome editing with TALEN and CRISPR. Cell Biosci 2017; 7:21. [PMID: 28451378 PMCID: PMC5404292 DOI: 10.1186/s13578-017-0148-4] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 04/19/2017] [Indexed: 11/10/2022] Open
Abstract
Genome editing promises giant leaps forward in advancing biotechnology, agriculture, and basic research. The process relies on the use of sequence specific nucleases (SSNs) to make DNA double stranded breaks at user defined genomic loci, which are subsequently repaired by two main DNA repair pathways: non-homologous end joining (NHEJ) and homology directed repair (HDR). NHEJ can result in frameshift mutations that often create genetic knockouts. These knockout lines are useful for functional and reverse genetic studies but also have applications in agriculture. HDR has a variety of applications as it can be used for gene replacement, gene stacking, and for creating various fusion proteins. In recent years, transcription activator-like effector nucleases and clustered regularly interspaced palindromic repeats (CRISPR) and CRISPR associated protein 9 or CRISPR from Prevotella and Francisella 1 have emerged as the preferred SSNs for research purposes. Here, we review their applications in plant research, discuss current limitations, and predict future research directions in plant genome editing.
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Affiliation(s)
- Aimee Malzahn
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742 USA
| | - Levi Lowder
- Department of Biology, East Carolina University, Greenville, NC 27858 USA
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742 USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850 USA
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48
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Daer RM, Cutts JP, Brafman DA, Haynes KA. The Impact of Chromatin Dynamics on Cas9-Mediated Genome Editing in Human Cells. ACS Synth Biol 2017; 6:428-438. [PMID: 27783893 DOI: 10.1021/acssynbio.5b00299] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In order to efficiently edit eukaryotic genomes, it is critical to test the impact of chromatin dynamics on CRISPR/Cas9 function and develop strategies to adapt the system to eukaryotic contexts. So far, research has extensively characterized the relationship between the CRISPR endonuclease Cas9 and the composition of the RNA-DNA duplex that mediates the system's precision. Evidence suggests that chromatin modifications and DNA packaging can block eukaryotic genome editing by custom-built DNA endonucleases like Cas9; however, the underlying mechanism of Cas9 inhibition is unclear. Here, we demonstrate that closed, gene-silencing-associated chromatin is a mechanism for the interference of Cas9-mediated DNA editing. Our assays use a transgenic cell line with a drug-inducible switch to control chromatin states (open and closed) at a single genomic locus. We show that closed chromatin inhibits binding and editing at specific target sites and that artificial reversal of the silenced state restores editing efficiency. These results provide new insights to improve Cas9-mediated editing in human and other mammalian cells.
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Affiliation(s)
- René M. Daer
- School of Biological and
Health Systems Engineering, Arizona State University, 501 E. Tyler
Mall, ECG 344A, Tempe, Arizona 85287, United States
| | - Josh P. Cutts
- School of Biological and
Health Systems Engineering, Arizona State University, 501 E. Tyler
Mall, ECG 344A, Tempe, Arizona 85287, United States
| | - David A. Brafman
- School of Biological and
Health Systems Engineering, Arizona State University, 501 E. Tyler
Mall, ECG 344A, Tempe, Arizona 85287, United States
| | - Karmella A. Haynes
- School of Biological and
Health Systems Engineering, Arizona State University, 501 E. Tyler
Mall, ECG 344A, Tempe, Arizona 85287, United States
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Streubel J, Baum H, Grau J, Stuttman J, Boch J. Dissection of TALE-dependent gene activation reveals that they induce transcription cooperatively and in both orientations. PLoS One 2017; 12:e0173580. [PMID: 28301511 PMCID: PMC5354296 DOI: 10.1371/journal.pone.0173580] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/22/2017] [Indexed: 11/19/2022] Open
Abstract
Plant-pathogenic Xanthomonas bacteria inject transcription activator-like effector proteins (TALEs) into host cells to specifically induce transcription of plant genes and enhance susceptibility. Although the DNA-binding mode is well-understood it is still ambiguous how TALEs initiate transcription and whether additional promoter elements are needed to support this. To systematically dissect prerequisites for transcriptional initiation the activity of one TALE was compared on different synthetic Bs4 promoter fragments. In addition, a large collection of artificial TALEs spanning the OsSWEET14 promoter was compared. We show that the presence of a TALE alone is not sufficient to initiate transcription suggesting the requirement of additional supporting promoter elements. At the OsSWEET14 promoter TALEs can initiate transcription from various positions, in a synergistic manner of multiple TALEs binding in parallel to the promoter, and even by binding in reverse orientation. TALEs are known to shift the transcriptional start site, but our data show that this shift depends on the individual position of a TALE within a promoter context. Our results implicate that TALEs function like classical enhancer-binding proteins and initiate transcription in both orientations which has consequences for in planta target gene prediction and design of artificial activators.
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Affiliation(s)
- Jana Streubel
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
- Department of Plant Genetics, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Heidi Baum
- Department of Plant Genetics, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Jan Grau
- Institute of Computer Science, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Johannes Stuttman
- Department of Plant Genetics, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Jens Boch
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
- Department of Plant Genetics, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
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Kaya H, Numa H, Nishizawa-Yokoi A, Toki S, Habu Y. DNA Methylation Affects the Efficiency of Transcription Activator-Like Effector Nucleases-Mediated Genome Editing in Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:302. [PMID: 28348570 PMCID: PMC5346537 DOI: 10.3389/fpls.2017.00302] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 02/20/2017] [Indexed: 05/28/2023]
Abstract
Genome editing in plants becomes popular since the advent of sequence-specific nucleases (SSNs) that are simple to set up and efficient in various plant species. Although transcription activator-like effector nucleases (TALENs) are one of the most prevalent SSNs and have a potential to provide higher target specificity by their dimeric property, TALENs are sensitive to methylated cytosines that are present not only in transposons but also in active genes in plants. In mammalian cells, the methylation sensitivity of TALENs could be overcome by using a base-recognition module (N∗) that has a higher affinity to methylated cytosine. In contrast to mammals, plants carry DNA methylation at all cytosine contexts (CG, CHG, and CHH, where H represents A, C, or T) with various degrees and effectiveness of N∗ module in genome editing in plants has not been explored. In this study, we designed sets of TALENs with or without N∗ modules and examined their efficiency in genome editing of methylated regions in rice. Although improvement in genome editing efficiency was observed with N∗-TALENs designed to a stably methylated target, another target carrying cytosines with various levels of methylation showed resistance to both normal and N∗-TALENs. The results suggest that variability of cytosine methylation in target regions is an additional factor affecting the genome editing efficiency of TALENs.
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Affiliation(s)
- Hidetaka Kaya
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO)Tsukuba, Japan
| | - Hisataka Numa
- Advanced Analysis Center, National Agriculture and Food Research Organization (NARO)Tsukuba, Japan
| | - Ayako Nishizawa-Yokoi
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO)Tsukuba, Japan
| | - Seiichi Toki
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO)Tsukuba, Japan
| | - Yoshiki Habu
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO)Tsukuba, Japan
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