1
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Bisht D, Salave S, Desai N, Gogoi P, Rana D, Biswal P, Sarma G, Benival D, Kommineni N, Desai D. Genome editing and its role in vaccine, diagnosis, and therapeutic advancement. Int J Biol Macromol 2024; 269:131802. [PMID: 38670178 DOI: 10.1016/j.ijbiomac.2024.131802] [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: 11/05/2023] [Revised: 02/25/2024] [Accepted: 03/15/2024] [Indexed: 04/28/2024]
Abstract
Genome editing involves precise modification of specific nucleotides in the genome using nucleases like CRISPR/Cas, ZFN, or TALEN, leading to increased efficiency of homologous recombination (HR) for gene editing, and it can result in gene disruption events via non-homologous end joining (NHEJ) or homology-driven repair (HDR). Genome editing, particularly CRISPR-Cas9, revolutionizes vaccine development by enabling precise modifications of pathogen genomes, leading to enhanced vaccine efficacy and safety. It allows for tailored antigen optimization, improved vector design, and deeper insights into host genes' impact on vaccine responses, ultimately enhancing vaccine development and manufacturing processes. This review highlights different types of genome editing methods, their associated risks, approaches to overcome the shortcomings, and the diverse roles of genome editing.
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Affiliation(s)
- Deepanker Bisht
- ICAR- Indian Veterinary Research Institute, Izatnagar 243122, Bareilly, India
| | - Sagar Salave
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, Gujarat, India
| | - Nimeet Desai
- Indian Institute of Technology Hyderabad, Kandi 502285, Telangana, India
| | - Purnima Gogoi
- School of Medicine and Public Health, University of Wisconsin and Madison, Madison, WI 53726, USA
| | - Dhwani Rana
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, Gujarat, India
| | - Prachurya Biswal
- College of Veterinary and Animal Sciences, Bihar Animal Sciences University, Kishanganj 855115, Bihar, India
| | - Gautami Sarma
- College of Veterinary & Animal Sciences, G. B. Pant University of Agriculture and Technology, Pantnagar 263145, U.S. Nagar, Uttarakhand, India
| | - Derajram Benival
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, Gujarat, India.
| | | | - Dhruv Desai
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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2
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Yarnall MTN, Ioannidi EI, Schmitt-Ulms C, Krajeski RN, Lim J, Villiger L, Zhou W, Jiang K, Garushyants SK, Roberts N, Zhang L, Vakulskas CA, Walker JA, Kadina AP, Zepeda AE, Holden K, Ma H, Xie J, Gao G, Foquet L, Bial G, Donnelly SK, Miyata Y, Radiloff DR, Henderson JM, Ujita A, Abudayyeh OO, Gootenberg JS. Drag-and-drop genome insertion of large sequences without double-strand DNA cleavage using CRISPR-directed integrases. Nat Biotechnol 2023; 41:500-512. [PMID: 36424489 PMCID: PMC10257351 DOI: 10.1038/s41587-022-01527-4] [Citation(s) in RCA: 110] [Impact Index Per Article: 110.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 09/23/2022] [Indexed: 11/26/2022]
Abstract
Programmable genome integration of large, diverse DNA cargo without DNA repair of exposed DNA double-strand breaks remains an unsolved challenge in genome editing. We present programmable addition via site-specific targeting elements (PASTE), which uses a CRISPR-Cas9 nickase fused to both a reverse transcriptase and serine integrase for targeted genomic recruitment and integration of desired payloads. We demonstrate integration of sequences as large as ~36 kilobases at multiple genomic loci across three human cell lines, primary T cells and non-dividing primary human hepatocytes. To augment PASTE, we discovered 25,614 serine integrases and cognate attachment sites from metagenomes and engineered orthologs with higher activity and shorter recognition sequences for efficient programmable integration. PASTE has editing efficiencies similar to or exceeding those of homology-directed repair and non-homologous end joining-based methods, with activity in non-dividing cells and in vivo with fewer detectable off-target events. PASTE expands the capabilities of genome editing by allowing large, multiplexed gene insertion without reliance on DNA repair pathways.
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Affiliation(s)
- Matthew T N Yarnall
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Eleonora I Ioannidi
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
- ETH Zürich, Zürich, Switzerland
| | - Cian Schmitt-Ulms
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rohan N Krajeski
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Justin Lim
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lukas Villiger
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Wenyuan Zhou
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kaiyi Jiang
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sofya K Garushyants
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Liyang Zhang
- Integrated DNA Technologies, Coralville, IA, USA
| | | | | | | | | | | | - Hong Ma
- University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jun Xie
- University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Guangping Gao
- University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Greg Bial
- Yecuris Corporation, Tualatin, OR, USA
| | | | | | | | | | | | - Omar O Abudayyeh
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Jonathan S Gootenberg
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
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3
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Nambiar TS, Baudrier L, Billon P, Ciccia A. CRISPR-based genome editing through the lens of DNA repair. Mol Cell 2022; 82:348-388. [PMID: 35063100 PMCID: PMC8887926 DOI: 10.1016/j.molcel.2021.12.026] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/18/2021] [Accepted: 12/20/2021] [Indexed: 01/22/2023]
Abstract
Genome editing technologies operate by inducing site-specific DNA perturbations that are resolved by cellular DNA repair pathways. Products of genome editors include DNA breaks generated by CRISPR-associated nucleases, base modifications induced by base editors, DNA flaps created by prime editors, and integration intermediates formed by site-specific recombinases and transposases associated with CRISPR systems. Here, we discuss the cellular processes that repair CRISPR-generated DNA lesions and describe strategies to obtain desirable genomic changes through modulation of DNA repair pathways. Advances in our understanding of the DNA repair circuitry, in conjunction with the rapid development of innovative genome editing technologies, promise to greatly enhance our ability to improve food production, combat environmental pollution, develop cell-based therapies, and cure genetic and infectious diseases.
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Affiliation(s)
- Tarun S. Nambiar
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032
| | - Lou Baudrier
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N. W., Calgary, Alberta T2N 4N1, Canada
| | - Pierre Billon
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N. W., Calgary, Alberta T2N 4N1, Canada,Corresponding authors: ,
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032,Lead Contact,Corresponding authors: ,
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4
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Precise determination of input-output mapping for multimodal gene circuits using data from transient transfection. PLoS Comput Biol 2020; 16:e1008389. [PMID: 33253149 PMCID: PMC7728399 DOI: 10.1371/journal.pcbi.1008389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 12/10/2020] [Accepted: 09/23/2020] [Indexed: 11/19/2022] Open
Abstract
The mapping of molecular inputs to their molecular outputs (input/output, I/O mapping) is an important characteristic of gene circuits, both natural and synthetic. Experimental determination of such mappings for synthetic circuits is best performed using stably integrated genetic constructs. In mammalian cells, stable integration of complex circuits is a time-consuming process that hampers rapid characterization of multiple circuit variants. On the other hand, transient transfection is quick. However, it is an extremely noisy process and it is unclear whether the obtained data have any relevance to the input/output mapping of a circuit obtained in the case of a stable integration. Here we describe a data processing workflow, Peakfinder algorithm for flow cytometry data (PFAFF), that allows extracting precise input/output mapping from single-cell protein expression data gathered by flow cytometry after a transient transfection. The workflow builds on the numerically-proven observation that the multivariate modes of input and output expression of multi-channel flow cytometry datasets, pre-binned by the expression level of an independent transfection reporter gene, harbor cells with circuit gene copy numbers distributions that depend deterministically on the properties of a bin. We validate our method by simulating flow cytometry data for seven multi-node circuit architectures, including a complex bi-modal circuit, under stable integration and transient transfection scenarios. The workflow applied to the simulated transient transfection data results in similar conclusions to those reached with simulated stable integration data. This indicates that the input/output mapping derived from transient transfection data using our method is an excellent approximation of the ground truth. Thus, the method allows to determine input/output mapping of complex gene network using noisy transient transfection data. One of the key features of a gene circuit is its input/output behavior. A few earlier publications attempted to develop methods to extract this behavior using transient transfection of circuit components in mammalian cells. However, the hitherto developed methods are only suitable for circuit with monomodal output distribution. Moreover, the relationship between the extracted I/O mapping and the "ground truth" that would have obtained with stably-integrated circuits, has not been addressed. Here we explore cell populations easily identifiable in flow cytometry data, namely, the peaks of fluorescent readout distribution in cells binned by the common expression value of the transfection reporter, or marker, gene. Using numerical simulations, we find that the distribution of circuit copy number in these cells deterministically depends on marker fluorescence in the noise-dependent manner. Moreover, we find that this is true also in the case of bi-modal output distribution. Using the peaks of input and output distributions, we are able to reconstruct the I/O mapping of the circuit and relate it to the I/O mapping of the stably-integrated circuit. The reconstruction is enabled by a new computational method we call PFAFF. The method is extensively validated with forward-simulated flow cytometry data from stable and transient transfections, with up to seven different circuits. The results show excellent correlation between the I/O behavior extracted by PFAFF from simulated transient transfection data, and the data simulated for stably integrated circuit.
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5
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Gurumurthy CB, Perez-Pinera P. Technological advances in integrating multi-kilobase DNA sequences into genomes. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2018. [DOI: 10.1016/j.cobme.2018.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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6
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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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7
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Woodard LE, Galvan DL, Wilson MH. Site-Directed Genome Modification with Engineered Zinc Finger Proteins. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Lauren E. Woodard
- Department of Veterans Affairs; Nashville TN 37212 USA
- Vanderbilt University Medical Center; Department of Medicine, Department of Pharmacology; Nashville TN 37232 USA
| | - Daniel L. Galvan
- University of Texas at MD Anderson Cancer Center; Section of Nephrology; Houston TX 77030 USA
| | - Matthew H. Wilson
- Department of Veterans Affairs; Nashville TN 37212 USA
- Vanderbilt University Medical Center; Department of Medicine, Department of Pharmacology; Nashville TN 37232 USA
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8
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Chaikind B, Bessen JL, Thompson DB, Hu JH, Liu DR. A programmable Cas9-serine recombinase fusion protein that operates on DNA sequences in mammalian cells. Nucleic Acids Res 2016; 44:9758-9770. [PMID: 27515511 PMCID: PMC5175349 DOI: 10.1093/nar/gkw707] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 08/01/2016] [Accepted: 08/02/2016] [Indexed: 02/07/2023] Open
Abstract
We describe the development of ‘recCas9’, an RNA-programmed small serine recombinase that functions in mammalian cells. We fused a catalytically inactive dCas9 to the catalytic domain of Gin recombinase using an optimized fusion architecture. The resulting recCas9 system recombines DNA sites containing a minimal recombinase core site flanked by guide RNA-specified sequences. We show that these recombinases can operate on DNA sites in mammalian cells identical to genomic loci naturally found in the human genome in a manner that is dependent on the guide RNA sequences. DNA sequencing reveals that recCas9 catalyzes guide RNA-dependent recombination in human cells with an efficiency as high as 32% on plasmid substrates. Finally, we demonstrate that recCas9 expressed in human cells can catalyze in situ deletion between two genomic sites. Because recCas9 directly catalyzes recombination, it generates virtually no detectable indels or other stochastic DNA modification products. This work represents a step toward programmable, scarless genome editing in unmodified cells that is independent of endogenous cellular machinery or cell state. Current and future generations of recCas9 may facilitate targeted agricultural breeding, or the study and treatment of human genetic diseases.
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Affiliation(s)
- Brian Chaikind
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical institute, Harvard University, Cambridge, MA 02138 USA
| | - Jeffrey L Bessen
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical institute, Harvard University, Cambridge, MA 02138 USA
| | - David B Thompson
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Johnny H Hu
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - David R Liu
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138, USA .,Howard Hughes Medical institute, Harvard University, Cambridge, MA 02138 USA
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9
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Cheng JK, Lewis AM, Kim DS, Dyess T, Alper HS. Identifying and retargeting transcriptional hot spots in the human genome. Biotechnol J 2016; 11:1100-9. [PMID: 27311394 DOI: 10.1002/biot.201600015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 05/18/2016] [Accepted: 05/30/2016] [Indexed: 01/17/2023]
Abstract
Mammalian cell line development requires streamlined methodologies that will reduce both the cost and time to identify candidate cell lines. Improvements in site-specific genomic editing techniques can result in flexible, predictable, and robust cell line engineering. However, an outstanding question in the field is the specific site of integration. Here, we seek to identify productive loci within the human genome that will result in stable, high expression of heterologous DNA. Using an unbiased, random integration approach and a green fluorescent reporter construct, we identify ten single-integrant, recombinant human cell lines that exhibit stable, high-level expression. From these cell lines, eight unique corresponding integration loci were identified. These loci are concentrated in non-protein coding regions or intronic regions of protein coding genes. Expression mapping of the surrounding genes reveals minimal disruption of endogenous gene expression. Finally, we demonstrate that targeted de novo integration at one of the identified loci, the 12(th) exon-intron region of the GRIK1 gene on chromosome 21, results in superior expression and stability compared to the standard, illegitimate integration approach at levels approaching 4-fold. The information identified here along with recent advances in site-specific genomic editing techniques can lead to expedited cell line development.
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Affiliation(s)
- Joseph K Cheng
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, USA
| | - Amanda M Lewis
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, USA.,Biologics Development, Bristol-Myers Squibb, Devens, MA, USA
| | - Do Soon Kim
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, USA
| | - Timothy Dyess
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, USA
| | - Hal S Alper
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, USA. .,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA.
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10
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Zhao X, Chen M, Tan J. Knockdown of ZFR suppresses cell proliferation and invasion of human pancreatic cancer. Biol Res 2016; 49:26. [PMID: 27177590 PMCID: PMC4866406 DOI: 10.1186/s40659-016-0086-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 04/17/2016] [Indexed: 12/23/2022] Open
Abstract
Background Zinc finger RNA binding protein (ZFR) is involved in the regulation of growth and cancer development. However, little is known about ZFR function in pancreatic cancer. Methods Herein, to investigate whether ZFR is involved in tumor growth, Oncomine microarray data was firstly used to evaluate ZFR gene expression in human pancreatic tumors. Then short hairpin RNA (shRNA) targeting ZFR was designed and delivered into PANC-1 pancreatic cancer cells to knock down ZFR expression. Cell viability, cell proliferation and cell cycle analysis after ZFR knockdown were determined by MTT, colony forming and FACS, respectively. In addition, cell migration and invasion were assessed using the Transwell system. Results The expression of ZFR was significantly higher in pancreatic tumors than normal pancreas tissues by Oncomine database analysis. Knockdown of ZFR by shRNA-expressing lentivirus significantly decreased the viability and invasion ability of pancreatic cancer cells. Moreover, FACS analysis showed that knockdown of ZFR in PANC-1 cells caused a significant cell cycle arrest at G0/G1 phase. Furthermore, knockdown of ZFR decreased the levels of CDK2, CDK4, CyclinA and CyclinD1 and enhanced the expression of p27, which has evidenced by qRT-PCR and Western blot analysis. Conclusions Knockdown of ZFR might provide a novel alternative to targeted therapy of pancreatic cancer and deserves further investigation.
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Affiliation(s)
- Xiaolan Zhao
- Health Management Center, The First Affiliated Hospital of Third Military Medical University, NO. 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, China.
| | - Man Chen
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, 610083, China
| | - Jishan Tan
- Department of Laboratory Medicine, Chengdu Military General Hospital, Chengdu, 610083, China
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11
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Abstract
The fields of molecular genetics, biotechnology and synthetic biology are demanding ever more sophisticated molecular tools for programmed precise modification of cell genomic DNA and other DNA sequences. This review presents the current state of knowledge and development of one important group of DNA-modifying enzymes, the site-specific recombinases (SSRs). SSRs are Nature's 'molecular machines' for cut-and-paste editing of DNA molecules by inserting, deleting or inverting precisely defined DNA segments. We survey the SSRs that have been put to use, and the types of applications for which they are suitable. We also discuss problems associated with uses of SSRs, how these problems can be minimized, and how recombinases are being re-engineered for improved performance and novel applications.
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12
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Abstract
The development of a facile genome engineering technology based on transcription activator-like effector nucleases (TALENs) has led to significant advances in diverse areas of science and medicine. In this review, we provide a broad overview of the development of TALENs and the use of this technology in basic science, biotechnology, and biomedical applications. This includes the discovery of DNA recognition by TALEs, engineering new TALE proteins to diverse targets, general advances in nuclease-based editing strategies, and challenges that are specific to various applications of the TALEN technology. We review examples of applying TALENs for studying gene function and regulation, generating disease models, and developing gene therapies. The current status of genome editing and future directions for other uses of these technologies are also discussed.
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Affiliation(s)
- David G Ousterout
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Room 136 Hudson Hall, Box 90281, Durham, NC, 27708-0281, USA. .,Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA. .,Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC, 27710, USA.
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14
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Abstract
Advances in genome engineering technologies have made the precise control over genome sequence and regulation possible across a variety of disciplines. These tools can expand our understanding of fundamental biological processes and create new opportunities for therapeutic designs. The rapid evolution of these methods has also catalyzed a new era of genomics that includes multiple approaches to functionally characterize and manipulate the regulation of genomic information. Here, we review the recent advances of the most widely adopted genome engineering platforms and their application to functional genomics. This includes engineered zinc finger proteins, TALEs/TALENs, and the CRISPR/Cas9 system as nucleases for genome editing, transcription factors for epigenome editing, and other emerging applications. We also present current and potential future applications of these tools, as well as their current limitations and areas for future advances.
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Affiliation(s)
- Isaac B Hilton
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA; Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina 27710, USA
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15
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Gersbach CA, Gaj T, Barbas CF. Synthetic zinc finger proteins: the advent of targeted gene regulation and genome modification technologies. Acc Chem Res 2014; 47:2309-18. [PMID: 24877793 PMCID: PMC4139171 DOI: 10.1021/ar500039w] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
The understanding
of gene regulation and the structure and function
of the human genome increased dramatically at the end of the 20th
century. Yet the technologies for manipulating the genome have been
slower to develop. For instance, the field of gene therapy has been
focused on correcting genetic diseases and augmenting tissue repair
for more than 40 years. However, with the exception of a few very
low efficiency approaches, conventional genetic engineering methods
have only been able to add auxiliary genes to cells. This has been
a substantial obstacle to the clinical success of gene therapies and
has also led to severe unintended consequences in several cases. Therefore,
technologies that facilitate the precise modification of cellular
genomes have diverse and significant implications in many facets of
research and are essential for translating the products of the Genomic
Revolution into tangible benefits for medicine and biotechnology.
To address this need, in the 1990s, we embarked on a mission to develop
technologies for engineering protein–DNA interactions with
the aim of creating custom tools capable of targeting any DNA sequence.
Our goal has been to allow researchers to reach into genomes to specifically
regulate, knock out, or replace any gene. To realize these goals,
we initially focused on understanding and manipulating zinc finger
proteins. In particular, we sought to create a simple and straightforward
method that enables unspecialized laboratories to engineer custom
DNA-modifying proteins using only defined modular components, a web-based
utility, and standard recombinant DNA technology. Two significant
challenges we faced were (i) the development of zinc finger domains
that target sequences not recognized by naturally occurring zinc finger
proteins and (ii) determining how individual zinc finger domains could
be tethered together as polydactyl proteins to recognize unique locations
within complex genomes. We and others have since used this modular
assembly method to engineer artificial proteins and enzymes that activate,
repress, or create defined changes to user-specified genes in human
cells, plants, and other organisms. We have also engineered novel
methods for externally controlling protein activity and delivery,
as well as developed new strategies for the directed evolution of
protein and enzyme function. This Account summarizes our work in these
areas and highlights independent studies that have successfully used
the modular assembly approach to create proteins with novel function.
We also discuss emerging alternative methods for genomic targeting,
including transcription activator-like effectors (TALEs) and CRISPR/Cas
systems, and how they complement the synthetic zinc finger protein
technology.
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Affiliation(s)
- Charles A. Gersbach
- Department
of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Thomas Gaj
- The
Skaggs Institute for Chemical Biology and the Departments of Chemistry
and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Carlos F. Barbas
- The
Skaggs Institute for Chemical Biology and the Departments of Chemistry
and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, United States
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16
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Gaj T, Sirk SJ, Tingle RD, Mercer AC, Wallen MC, Barbas CF. Enhancing the specificity of recombinase-mediated genome engineering through dimer interface redesign. J Am Chem Soc 2014; 136:5047-56. [PMID: 24611715 PMCID: PMC3985937 DOI: 10.1021/ja4130059] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
Despite
recent advances in genome engineering made possible by
the emergence of site-specific endonucleases, there remains a need
for tools capable of specifically delivering genetic payloads into
the human genome. Hybrid recombinases based on activated catalytic
domains derived from the resolvase/invertase family of serine recombinases
fused to Cys2-His2 zinc-finger or TAL effector
DNA-binding domains are a class of reagents capable of achieving this.
The utility of these enzymes, however, has been constrained by their
low overall targeting specificity, largely due to the formation of
side-product homodimers capable of inducing off-target modifications.
Here, we combine rational design and directed evolution to re-engineer
the serine recombinase dimerization interface and generate a recombinase
architecture that reduces formation of these undesirable homodimers
by >500-fold. We show that these enhanced recombinases demonstrate
substantially improved targeting specificity in mammalian cells and
achieve rates of site-specific integration similar to those previously
reported for site-specific nucleases. Additionally, we show that enhanced
recombinases exhibit low toxicity and promote the delivery of the
human coagulation factor IX and α-galactosidase genes into endogenous
genomic loci with high specificity. These results provide a general
means for improving hybrid recombinase specificity by protein engineering
and illustrate the potential of these enzymes for basic research and
therapeutic applications.
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Affiliation(s)
- Thomas Gaj
- The Skaggs Institute for Chemical Biology and the Departments of Chemistry and Cell and Molecular Biology, The Scripps Research Institute , La Jolla, California 92037, United States
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17
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Sirk SJ, Gaj T, Jonsson A, Mercer AC, Barbas CF. Expanding the zinc-finger recombinase repertoire: directed evolution and mutational analysis of serine recombinase specificity determinants. Nucleic Acids Res 2014; 42:4755-66. [PMID: 24452803 PMCID: PMC3985619 DOI: 10.1093/nar/gkt1389] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The serine recombinases are a diverse family of modular enzymes that promote high-fidelity DNA rearrangements between specific target sites. Replacement of their native DNA-binding domains with custom-designed Cys2–His2 zinc-finger proteins results in the creation of engineered zinc-finger recombinases (ZFRs) capable of achieving targeted genetic modifications. The flexibility afforded by zinc-finger domains enables the design of hybrid recombinases that recognize a wide variety of potential target sites; however, this technology remains constrained by the strict recognition specificities imposed by the ZFR catalytic domains. In particular, the ability to fully reprogram serine recombinase catalytic specificity has been impeded by conserved base requirements within each recombinase target site and an incomplete understanding of the factors governing DNA recognition. Here we describe an approach to complement the targeting capacity of ZFRs. Using directed evolution, we isolated mutants of the β and Sin recombinases that specifically recognize target sites previously outside the scope of ZFRs. Additionally, we developed a genetic screen to determine the specific base requirements for site-specific recombination and showed that specificity profiling enables the discovery of unique genomic ZFR substrates. Finally, we conducted an extensive and family-wide mutational analysis of the serine recombinase DNA-binding arm region and uncovered a diverse network of residues that confer target specificity. These results demonstrate that the ZFR repertoire is extensible and highlights the potential of ZFRs as a class of flexible tools for targeted genome engineering.
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Affiliation(s)
- Shannon J Sirk
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA, Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA and Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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18
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Sakuma T, Woltjen K. Nuclease-mediated genome editing: At the front-line of functional genomics technology. Dev Growth Differ 2014; 56:2-13. [PMID: 24387662 DOI: 10.1111/dgd.12111] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 11/18/2013] [Accepted: 11/18/2013] [Indexed: 12/26/2022]
Abstract
Genome editing with engineered endonucleases is rapidly becoming a staple method in developmental biology studies. Engineered nucleases permit random or designed genomic modification at precise loci through the stimulation of endogenous double-strand break repair. Homology-directed repair following targeted DNA damage is mediated by co-introduction of a custom repair template, allowing the derivation of knock-out and knock-in alleles in animal models previously refractory to classic gene targeting procedures. Currently there are three main types of customizable site-specific nucleases delineated by the source mechanism of DNA binding that guides nuclease activity to a genomic target: zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR). Among these genome engineering tools, characteristics such as the ease of design and construction, mechanism of inducing DNA damage, and DNA sequence specificity all differ, making their application complementary. By understanding the advantages and disadvantages of each method, one may make the best choice for their particular purpose.
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Affiliation(s)
- Tetsushi Sakuma
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
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19
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20
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Elmer JJ, Christensen MD, Rege K. Applying horizontal gene transfer phenomena to enhance non-viral gene therapy. J Control Release 2013; 172:246-257. [PMID: 23994344 PMCID: PMC4258102 DOI: 10.1016/j.jconrel.2013.08.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 08/17/2013] [Accepted: 08/20/2013] [Indexed: 12/25/2022]
Abstract
Horizontal gene transfer (HGT) is widespread amongst prokaryotes, but eukaryotes tend to be far less promiscuous with their genetic information. However, several examples of HGT from pathogens into eukaryotic cells have been discovered and mimicked to improve non-viral gene delivery techniques. For example, several viral proteins and DNA sequences have been used to significantly increase cytoplasmic and nuclear gene delivery. Plant genetic engineering is routinely performed with the pathogenic bacterium Agrobacterium tumefaciens and similar pathogens (e.g. Bartonella henselae) may also be able to transform human cells. Intracellular parasites like Trypanosoma cruzi may also provide new insights into overcoming cellular barriers to gene delivery. Finally, intercellular nucleic acid transfer between host cells will also be briefly discussed. This article will review the unique characteristics of several different viruses and microbes and discuss how their traits have been successfully applied to improve non-viral gene delivery techniques. Consequently, pathogenic traits that originally caused diseases may eventually be used to treat many genetic diseases.
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Affiliation(s)
- Jacob J Elmer
- Department of Chemical Engineering, Villanova University, Villanova 19085, USA.
| | | | - Kaushal Rege
- Chemical Engineering, Arizona State University, Tempe 85287-6106, USA.
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21
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Gaj T, Sirk SJ, Barbas CF. Expanding the scope of site-specific recombinases for genetic and metabolic engineering. Biotechnol Bioeng 2013; 111:1-15. [PMID: 23982993 DOI: 10.1002/bit.25096] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 08/12/2013] [Accepted: 08/13/2013] [Indexed: 12/20/2022]
Abstract
Site-specific recombinases are tremendously valuable tools for basic research and genetic engineering. By promoting high-fidelity DNA modifications, site-specific recombination systems have empowered researchers with unprecedented control over diverse biological functions, enabling countless insights into cellular structure and function. The rigid target specificities of many sites-specific recombinases, however, have limited their adoption in fields that require highly flexible recognition abilities. As a result, intense effort has been directed toward altering the properties of site-specific recombination systems by protein engineering. Here, we review key developments in the rational design and directed molecular evolution of site-specific recombinases, highlighting the numerous applications of these enzymes across diverse fields of study.
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Affiliation(s)
- Thomas Gaj
- The Skaggs Institute for Chemical Biology and the Departments of Chemistry and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California, 92037
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22
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Abstract
Zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) comprise a powerful class of tools that are redefining the boundaries of biological research. These chimeric nucleases are composed of programmable, sequence-specific DNA-binding modules linked to a nonspecific DNA cleavage domain. ZFNs and TALENs enable a broad range of genetic modifications by inducing DNA double-strand breaks that stimulate error-prone nonhomologous end joining or homology-directed repair at specific genomic locations. Here, we review achievements made possible by site-specific nuclease technologies and discuss applications of these reagents for genetic analysis and manipulation. In addition, we highlight the therapeutic potential of ZFNs and TALENs and discuss future prospects for the field, including the emergence of clustered regulatory interspaced short palindromic repeat (CRISPR)/Cas-based RNA-guided DNA endonucleases.
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Affiliation(s)
- Thomas Gaj
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
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23
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78495111110.1016/j.tibtech.2013.04.004" />
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24
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Gaj T, Gersbach CA, Barbas CF. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 2013; 31:397-405. [PMID: 23664777 DOI: 10.1016/j.tibtech.2013.04.004] [Citation(s) in RCA: 2351] [Impact Index Per Article: 213.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 04/13/2013] [Accepted: 04/13/2013] [Indexed: 12/11/2022]
Abstract
Zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) comprise a powerful class of tools that are redefining the boundaries of biological research. These chimeric nucleases are composed of programmable, sequence-specific DNA-binding modules linked to a nonspecific DNA cleavage domain. ZFNs and TALENs enable a broad range of genetic modifications by inducing DNA double-strand breaks that stimulate error-prone nonhomologous end joining or homology-directed repair at specific genomic locations. Here, we review achievements made possible by site-specific nuclease technologies and discuss applications of these reagents for genetic analysis and manipulation. In addition, we highlight the therapeutic potential of ZFNs and TALENs and discuss future prospects for the field, including the emergence of clustered regulatory interspaced short palindromic repeat (CRISPR)/Cas-based RNA-guided DNA endonucleases.
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Affiliation(s)
- Thomas Gaj
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
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25
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Digiusto DL, Kiem HP. Current translational and clinical practices in hematopoietic cell and gene therapy. Cytotherapy 2013; 14:775-90. [PMID: 22799276 DOI: 10.3109/14653249.2012.694420] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Clinical trials over the last 15 years have demonstrated that cell and gene therapies for cancer, monogenic and infectious disease are feasible and can lead to long-term benefit for patients. However, these trials have been limited to proof-of-principle and were conducted on modest numbers of patients or over long periods of time. In order for these studies to move towards standard practice and commercialization, scalable technologies for the isolation, ex vivo manipulation and delivery of these cells to patients must be developed. Additionally, regulatory strategies and clinical protocols for the collection, creation and delivery of cell products must be generated. In this article we review recent progress in hematopoietic cell and gene therapy, describe some of the current issues facing the field and discuss clinical, technical and regulatory approaches used to navigate the road to product development.
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Affiliation(s)
- David L Digiusto
- Department of Virology and Laboratory for Cellular Medicine, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA.
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26
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Gaj T, Mercer AC, Sirk SJ, Smith HL, Barbas CF. A comprehensive approach to zinc-finger recombinase customization enables genomic targeting in human cells. Nucleic Acids Res 2013; 41:3937-46. [PMID: 23393187 PMCID: PMC3616721 DOI: 10.1093/nar/gkt071] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Zinc-finger recombinases (ZFRs) represent a potentially powerful class of tools for targeted genetic engineering. These chimeric enzymes are composed of an activated catalytic domain derived from the resolvase/invertase family of serine recombinases and a custom-designed zinc-finger DNA-binding domain. The use of ZFRs, however, has been restricted by sequence requirements imposed by the recombinase catalytic domain. Here, we combine substrate specificity analysis and directed evolution to develop a diverse collection of Gin recombinase catalytic domains capable of recognizing an estimated 3.77 × 107 unique DNA sequences. We show that ZFRs assembled from these engineered catalytic domains recombine user-defined DNA targets with high specificity, and that designed ZFRs integrate DNA into targeted endogenous loci in human cells. This study demonstrates the feasibility of generating customized ZFRs and the potential of ZFR technology for a diverse range of applications, including genome engineering, synthetic biology and gene therapy.
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Affiliation(s)
- Thomas Gaj
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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27
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Engineered Zinc Finger Nucleases for Targeted Genome Editing. SITE-DIRECTED INSERTION OF TRANSGENES 2013. [DOI: 10.1007/978-94-007-4531-5_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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28
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Bire S, Rouleux-Bonnin F. Transgene Site-Specific Integration: Problems and Solutions. SITE-DIRECTED INSERTION OF TRANSGENES 2013. [DOI: 10.1007/978-94-007-4531-5_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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29
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Lai WF. Nucleic acid delivery: roles in biogerontological interventions. Ageing Res Rev 2013; 12:310-5. [PMID: 22982112 DOI: 10.1016/j.arr.2012.08.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 08/29/2012] [Accepted: 08/30/2012] [Indexed: 12/27/2022]
Abstract
Prolongation of longevity is a history-long desire of humans. Driven by the genetic contribution to longevity and the remarkable plasticity of healthy lifespan as demonstrated in animal models, arduous efforts have been directed to aging and longevity research over the years. Today, our understanding of lifespan determination is much greater than it was in the past, but administrable interventions for longevity enhancement are still virtually absent. The aim of this article is to highlight the technical gap between basic biogerontological research and intervention development, and to explore the importance of nucleic acid (NA) delivery technologies in bridging the gap. It is hoped that this article can engender more awareness of the roles of NA delivery technologies in biogerontological interventions, particularly NA therapy.
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30
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Xu SY, Gupta YK. Natural zinc ribbon HNH endonucleases and engineered zinc finger nicking endonuclease. Nucleic Acids Res 2012; 41:378-90. [PMID: 23125367 PMCID: PMC3592412 DOI: 10.1093/nar/gks1043] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Many bacteriophage and prophage genomes encode an HNH endonuclease (HNHE) next to their cohesive end site and terminase genes. The HNH catalytic domain contains the conserved catalytic residues His-Asn-His and a zinc-binding site [CxxC]2. An additional zinc ribbon (ZR) domain with one to two zinc-binding sites ([CxxxxC], [CxxxxH], [CxxxC], [HxxxH], [CxxC] or [CxxH]) is frequently found at the N-terminus or C-terminus of the HNHE or a ZR domain protein (ZRP) located adjacent to the HNHE. We expressed and purified 10 such HNHEs and characterized their cleavage sites. These HNHEs are site-specific and strand-specific nicking endonucleases (NEase or nickase) with 3- to 7-bp specificities. A minimal HNH nicking domain of 76 amino acid residues was identified from Bacillus phage γ HNHE and subsequently fused to a zinc finger protein to generate a chimeric NEase with a new specificity (12–13 bp). The identification of a large pool of previously unknown natural NEases and engineered NEases provides more ‘tools’ for DNA manipulation and molecular diagnostics. The small modular HNH nicking domain can be used to generate rare NEases applicable to targeted genome editing. In addition, the engineered ZF nickase is useful for evaluation of off-target sites in vitro before performing cell-based gene modification.
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Affiliation(s)
- Shuang-yong Xu
- New England Biolabs, Inc, Research Department, 240 County Road, Ipswich, MA 01938, USA.
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31
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Lanza AM, Cheng JK, Alper HS. Emerging synthetic biology tools for engineering mammalian cell systems and expediting cell line development. Curr Opin Chem Eng 2012. [DOI: 10.1016/j.coche.2012.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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32
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Owens JB, Urschitz J, Stoytchev I, Dang NC, Stoytcheva Z, Belcaid M, Maragathavally KJ, Coates CJ, Segal DJ, Moisyadi S. Chimeric piggyBac transposases for genomic targeting in human cells. Nucleic Acids Res 2012; 40:6978-91. [PMID: 22492708 PMCID: PMC3413120 DOI: 10.1093/nar/gks309] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 03/23/2012] [Accepted: 03/25/2012] [Indexed: 11/14/2022] Open
Abstract
Integrating vectors such as viruses and transposons insert transgenes semi-randomly and can potentially disrupt or deregulate genes. For these techniques to be of therapeutic value, a method for controlling the precise location of insertion is required. The piggyBac (PB) transposase is an efficient gene transfer vector active in a variety of cell types and proven to be amenable to modification. Here we present the design and validation of chimeric PB proteins fused to the Gal4 DNA binding domain with the ability to target transgenes to pre-determined sites. Upstream activating sequence (UAS) Gal4 recognition sites harbored on recipient plasmids were preferentially targeted by the chimeric Gal4-PB transposase in human cells. To analyze the ability of these PB fusion proteins to target chromosomal locations, UAS sites were randomly integrated throughout the genome using the Sleeping Beauty transposon. Both N- and C-terminal Gal4-PB fusion proteins but not native PB were capable of targeting transposition nearby these introduced sites. A genome-wide integration analysis revealed the ability of our fusion constructs to bias 24% of integrations near endogenous Gal4 recognition sequences. This work provides a powerful approach to enhance the properties of the PB system for applications such as genetic engineering and gene therapy.
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Affiliation(s)
- Jesse B. Owens
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, Department of Information and Computer Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, Entomology Department, Texas A&M University, College Station, TX 77843 and Genome Center, Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - Johann Urschitz
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, Department of Information and Computer Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, Entomology Department, Texas A&M University, College Station, TX 77843 and Genome Center, Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - Ilko Stoytchev
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, Department of Information and Computer Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, Entomology Department, Texas A&M University, College Station, TX 77843 and Genome Center, Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - Nong C. Dang
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, Department of Information and Computer Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, Entomology Department, Texas A&M University, College Station, TX 77843 and Genome Center, Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - Zoia Stoytcheva
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, Department of Information and Computer Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, Entomology Department, Texas A&M University, College Station, TX 77843 and Genome Center, Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - Mahdi Belcaid
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, Department of Information and Computer Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, Entomology Department, Texas A&M University, College Station, TX 77843 and Genome Center, Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - Kommineni J. Maragathavally
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, Department of Information and Computer Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, Entomology Department, Texas A&M University, College Station, TX 77843 and Genome Center, Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - Craig J. Coates
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, Department of Information and Computer Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, Entomology Department, Texas A&M University, College Station, TX 77843 and Genome Center, Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - David J. Segal
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, Department of Information and Computer Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, Entomology Department, Texas A&M University, College Station, TX 77843 and Genome Center, Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - Stefan Moisyadi
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, Department of Information and Computer Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, Entomology Department, Texas A&M University, College Station, TX 77843 and Genome Center, Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
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33
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Perez-Pinera P, Ousterout DG, Gersbach CA. Advances in targeted genome editing. Curr Opin Chem Biol 2012; 16:268-77. [PMID: 22819644 DOI: 10.1016/j.cbpa.2012.06.007] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 06/16/2012] [Accepted: 06/20/2012] [Indexed: 01/19/2023]
Abstract
New technologies have recently emerged that enable targeted editing of genomes in diverse systems. This includes precise manipulation of gene sequences in their natural chromosomal context and addition of transgenes to specific genomic loci. This progress has been facilitated by advances in engineering targeted nucleases with programmable, site-specific DNA-binding domains, including zinc finger proteins and transcription activator-like effectors (TALEs). Recent improvements have enhanced nuclease performance, accelerated nuclease assembly, and lowered the cost of genome editing. These advances are driving new approaches to many areas of biotechnology, including biopharmaceutical production, agriculture, creation of transgenic organisms and cell lines, and studies of genome structure, regulation, and function. Genome editing is also being investigated in preclinical and clinical gene therapies for many diseases.
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Affiliation(s)
- Pablo Perez-Pinera
- Department of Biomedical Engineering, Duke University, Durham, NC 27708-0281, USA
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34
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Sun N, Abil Z, Zhao H. Recent advances in targeted genome engineering in mammalian systems. Biotechnol J 2012; 7:1074-87. [PMID: 22777886 DOI: 10.1002/biot.201200038] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 05/22/2012] [Accepted: 06/15/2012] [Indexed: 12/21/2022]
Abstract
Targeted genome engineering enables researchers to disrupt, insert, or replace a genomic sequence precisely at a predetermined locus. One well-established technology to edit a mammalian genome is known as gene targeting, which is based on the homologous recombination (HR) mechanism. However, the low HR frequency in mammalian cells (except for mice) prevents its wide application. To address this limitation, a custom-designed nuclease is used to introduce a site-specific DNA double-strand break (DSB) on the chromosome and the subsequent repair of the DSB by the HR mechanism or the non-homologous end joining mechanism results in efficient targeted genome modifications. Engineered homing endonucleases (also called meganucleases), zinc finger nucleases, and transcription activator-like effector nucleases represent the three major classes of custom-designed nucleases that have been successfully applied in many different organisms for targeted genome engineering. This article reviews the recent developments of these genome engineering tools and highlights a few representative applications in mammalian systems. Recent advances in gene delivery strategies of these custom-designed nucleases are also briefly discussed.
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Affiliation(s)
- Ning Sun
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 61801, USA
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35
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Taylor GK, Petrucci LH, Lambert AR, Baxter SK, Jarjour J, Stoddard BL. LAHEDES: the LAGLIDADG homing endonuclease database and engineering server. Nucleic Acids Res 2012; 40:W110-6. [PMID: 22570419 PMCID: PMC3394308 DOI: 10.1093/nar/gks365] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
LAGLIDADG homing endonucleases (LHEs) are DNA cleaving enzymes, also termed ‘meganucleases’ that are employed as gene-targeting reagents. This use of LHEs requires that their DNA specificity be altered to match sequences in genomic targets. The choice of the most appropriate LHE to target a particular gene is facilitated by the growing number of such enzymes with well-characterized activities and structures. ‘LAHEDES’ (The LAGLIDADG Homing Endonuclease Database and Engineering Server) provides both an online archive of LHEs with validated DNA cleavage specificities and DNA-binding interactions, as well as a tool for the identification of DNA sequences that might be targeted by various LHEs. Searches can be performed using four separate scoring algorithms and user-defined choices of LHE scaffolds. The webserver subsequently provides information regarding clusters of amino acids that should be interrogated during engineering and selection experiments. The webserver is fully open access and can be found at http://homingendonuclease.net.
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Affiliation(s)
- Gregory K Taylor
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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36
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Abstract
Many devastating human diseases are caused by mutations in a single gene that prevent a somatic cell from carrying out its essential functions, or by genetic changes acquired as a result of infectious disease or in the course of cell transformation. Targeted gene therapies have emerged as potential strategies for treatment of such diseases. These therapies depend upon rare-cutting endonucleases to cleave at specific sites in or near disease genes. Targeted gene correction provides a template for homology-directed repair, enabling the cell's own repair pathways to erase the mutation and replace it with the correct sequence. Targeted gene disruption ablates the disease gene, disabling its function. Gene targeting can also promote other kinds of genome engineering, including mutation, insertion, or gene deletion. Targeted gene therapies present significant advantages compared to approaches to gene therapy that depend upon delivery of stably expressing transgenes. Recent progress has been fueled by advances in nuclease discovery and design, and by new strategies that maximize efficiency of targeting and minimize off-target damage. Future progress will build on deeper mechanistic understanding of critical factors and pathways.
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Affiliation(s)
- Olivier Humbert
- Departments of Immunology and Biochemistry, University of Washington School of Medicine, Seattle, WA 98195, USA
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37
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Nomura W, Masuda A, Ohba K, Urabe A, Ito N, Ryo A, Yamamoto N, Tamamura H. Effects of DNA binding of the zinc finger and linkers for domain fusion on the catalytic activity of sequence-specific chimeric recombinases determined by a facile fluorescent system. Biochemistry 2012; 51:1510-7. [PMID: 22304662 DOI: 10.1021/bi201878x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Artificial zinc finger proteins (ZFPs) consist of Cys(2)-His(2)-type modules composed of ∼30 amino acids with a ββα structure that coordinates a zinc ion. ZFPs that recognize specific DNA target sequences can substitute for the binding domains of enzymes that act on DNA to create designer enzymes with programmable sequence specificity. The most studied of these engineered enzymes are zinc finger nucleases (ZFNs). ZFNs have been widely used to model organisms and are currently in human clinical trials with an aim of therapeutic gene editing. Difficulties with ZFNs arise from unpredictable mutations caused by nonhomologous end joining and off-target DNA cleavage and mutagenesis. A more recent strategy that aims to address the shortcomings of ZFNs involves zinc finger recombinases (ZFRs). A thorough understanding of ZFRs and methods for their modification promises powerful new tools for gene manipulation in model organisms as well as in gene therapy. In an effort to design efficient and specific ZFRs, the effects of the DNA binding affinity of the zinc finger domains and the linker sequence between ZFPs and recombinase catalytic domains have been assessed. A plasmid system containing ZFR target sites was constructed for evaluation of catalytic activities of ZFRs with variable linker lengths and numbers of zinc finger modules. Recombination efficiencies were evaluated by restriction enzyme analysis of isolated plasmids after reaction in Escherichia coli and changes in EGFP fluorescence in mammalian cells. The results provide information relevant to the design of ZFRs that will be useful for sequence-specific genome modification.
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Affiliation(s)
- Wataru Nomura
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan.
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Abstract
Transcription activator-like effectors (TALEs) are a class of naturally occurring DNA-binding proteins found in the plant pathogen Xanthomonas sp. The DNA-binding domain of each TALE consists of tandem 34-amino acid repeat modules that can be rearranged according to a simple cipher to target new DNA sequences. Customized TALEs can be used for a wide variety of genome engineering applications, including transcriptional modulation and genome editing. Here we describe a toolbox for rapid construction of custom TALE transcription factors (TALE-TFs) and nucleases (TALENs) using a hierarchical ligation procedure. This toolbox facilitates affordable and rapid construction of custom TALE-TFs and TALENs within 1 week and can be easily scaled up to construct TALEs for multiple targets in parallel. We also provide details for testing the activity in mammalian cells of custom TALE-TFs and TALENs using quantitative reverse-transcription PCR and Surveyor nuclease, respectively. The TALE toolbox described here will enable a broad range of biological applications.
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Perez-Pinera P, Ousterout DG, Brown MT, Gersbach CA. Gene targeting to the ROSA26 locus directed by engineered zinc finger nucleases. Nucleic Acids Res 2011; 40:3741-52. [PMID: 22169954 PMCID: PMC3333879 DOI: 10.1093/nar/gkr1214] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Targeted gene addition to mammalian genomes is central to biotechnology, basic research and gene therapy. For example, gene targeting to the ROSA26 locus by homologous recombination in embryonic stem cells is commonly used for mouse transgenesis to achieve ubiquitous and persistent transgene expression. However, conventional methods are not readily adaptable to gene targeting in other cell types. The emerging zinc finger nuclease (ZFN) technology facilitates gene targeting in diverse species and cell types, but an optimal strategy for engineering highly active ZFNs is still unclear. We used a modular assembly approach to build ZFNs that target the ROSA26 locus. ZFN activity was dependent on the number of modules in each zinc finger array. The ZFNs were active in a variety of cell types in a time- and dose-dependent manner. The ZFNs directed gene addition to the ROSA26 locus, which enhanced the level of sustained gene expression, the uniformity of gene expression within clonal cell populations and the reproducibility of gene expression between clones. These ZFNs are a promising resource for cell engineering, mouse transgenesis and pre-clinical gene therapy studies. Furthermore, this characterization of the modular assembly method provides general insights into the implementation of the ZFN technology.
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Affiliation(s)
- Pablo Perez-Pinera
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
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Prorocic MM, Wenlong D, Olorunniji FJ, Akopian A, Schloetel JG, Hannigan A, McPherson AL, Stark WM. Zinc-finger recombinase activities in vitro. Nucleic Acids Res 2011; 39:9316-28. [PMID: 21849325 PMCID: PMC3241657 DOI: 10.1093/nar/gkr652] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Zinc-finger recombinases (ZFRs) are chimaeric proteins comprising a serine recombinase catalytic domain linked to a zinc-finger DNA binding domain. ZFRs can be tailored to promote site-specific recombination at diverse 'Z-sites', which each comprise a central core sequence flanked by zinc-finger domain-binding motifs. Here, we show that purified ZFRs catalyse efficient high-specificity reciprocal recombination between pairs of Z-sites in vitro. No off-site activity was detected. Under different reaction conditions, ZFRs can catalyse Z-site-specific double-strand DNA cleavage. ZFR recombination activity in Escherichia coli and in vitro is highly dependent on the length of the Z-site core sequence. We show that this length effect is manifested at reaction steps prior to formation of recombinants (binding, synapsis and DNA cleavage). The design of the ZFR protein itself is also a crucial variable affecting activity. A ZFR with a very short (2 amino acids) peptide linkage between the catalytic and zinc-finger domains has high activity in vitro, whereas a ZFR with a very long linker was less recombination-proficient and less sensitive to variations in Z-site length. We discuss the causes of these phenomena, and their implications for practical applications of ZFRs.
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Affiliation(s)
- Marko M Prorocic
- Institute of Infection, Immunity and Inflammation, University of Glasgow, GBRC, Glasgow G12 8QQ, Scotland, UK
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