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Wu S, Tong X, Li C, Lu K, Tan D, Hu H, Liu H, Dai F. Genome-wide identification and expression profiling of the C2H2-type zinc finger protein genes in the silkworm Bombyx mori. PeerJ 2019; 7:e7222. [PMID: 31316872 PMCID: PMC6613534 DOI: 10.7717/peerj.7222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 05/30/2019] [Indexed: 12/29/2022] Open
Abstract
Cys2-His2 zinc finger (C2H2-ZF) proteins comprise the largest class of putative eukaryotic transcription factors. The zinc finger motif array is highly divergent, indicating that most proteins will have distinctive binding sites and perform different functions. However, the binding sites and functions of the majority of C2H2-ZF proteins remain unknown. In this study, we identified 327 C2H2-ZF protein genes in the silkworm, 290 in the monarch butterfly, 243 in the fruit fly, 107 in elegans, 673 in mouse, and 1,082 in human. The C2H2-ZF protein genes of the silkworm were classified into three main grouping clades according to a phylogenetic classification, and 312 of these genes could be mapped onto 27 chromosomes. Most silkworm C2H2-ZF protein genes exhibited specific expression in larval tissues. Furthermore, several C2H2-ZF protein genes had sex-specific expression during metamorphosis. In addition, we found that some C2H2-ZF protein genes are involved in metamorphosis and female reproduction by using expression clustering and gene annotation analysis. Among them, five genes were selected, BGIBMGA002091 (CTCF), BGIBMGA006492 (fru), BGIBMGA006230 (wor), BGIBMGA004640 (lola), and BIGBMGA004569, for quantitative real-time PCR analysis from larvae to adult ovaries. The results showed that the five genes had different expression patterns in ovaries, among which BGIBMGA002091 (CTCF) gene expression level was the highest, and its expression level increased rapidly in late pupae and adult stages. These findings provide a basis for further investigation of the functions of C2H2-ZF protein genes in the silkworm, and the results offer clues for further research into the development of metamorphosis and female reproduction in the silkworm.
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Affiliation(s)
- SongYuan Wu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chong Qing, China.,College of Plant Protection, Southwest University, Chong Qing, China
| | - Xiaoling Tong
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chong Qing, China
| | - ChunLin Li
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chong Qing, China
| | - KunPeng Lu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chong Qing, China
| | - Duan Tan
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chong Qing, China
| | - Hai Hu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chong Qing, China
| | - Huai Liu
- College of Plant Protection, Southwest University, Chong Qing, China
| | - FangYin Dai
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, College of Biotechnology, Southwest University, Chong Qing, China
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Ha DT, Ghosh S, Ahn CH, Segal DJ, Kim MS. Pathogen-specific DNA sensing with engineered zinc finger proteins immobilized on a polymer chip. Analyst 2019; 143:4009-4016. [PMID: 30043772 DOI: 10.1039/c8an00395e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A specific double-stranded DNA sensing system is of great interest for diagnostic and other biomedical applications. Zinc finger domains, which recognize double-stranded DNA, can be engineered to form custom DNA-binding proteins for the recognition of specific DNA sequences. As a proof of concept, a sequence-enabled reassembly of a TEM-1 β-lactamase system (SEER-LAC) was previously demonstrated to develop zinc finger protein (ZFP) arrays for the detection of a double-stranded bacterial DNA sequence. Here, we implemented the SEER-LAC system to demonstrate the direct detection of pathogen-specific DNA sequences present in E. coli O157:H7 on a lab-on-a-chip. ZFPs custom-designed to detect Shiga toxin in E. coli O157:H7 were immobilized on a cyclic olefin copolymer (COC) chip, which can function as a non-PCR based molecular diagnostic device. Pathogen-specific double-stranded DNA was directly detected by using engineered ZFPs immobilized on the COC chip with high specificity, providing a detection limit of 10 fmol of target DNA in a colorimetric assay. Therefore, in this study, we demonstrated the great potential of ZFP arrays on the COC chip for further development of a simple and novel lab-on-a-chip technology for the detection of pathogens.
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Affiliation(s)
- Dat Thinh Ha
- Department of Chemistry, Western Kentucky University, Bowling Green, Kentucky 42101, USA.
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Xie SS, Qiu XY, Zhu LY, Zhu CS, Liu CY, Wu XM, Zhu L, Zhang DY. Assembly of TALE-based DNA scaffold for the enhancement of exogenous multi-enzymatic pathway. J Biotechnol 2019; 296:69-74. [DOI: 10.1016/j.jbiotec.2019.03.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 03/11/2019] [Accepted: 03/14/2019] [Indexed: 10/27/2022]
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In Vivo Genome Editing as a Therapeutic Approach. Int J Mol Sci 2018; 19:ijms19092721. [PMID: 30213032 PMCID: PMC6163904 DOI: 10.3390/ijms19092721] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/08/2018] [Accepted: 09/10/2018] [Indexed: 12/13/2022] Open
Abstract
Genome editing has been well established as a genome engineering tool that enables researchers to establish causal linkages between genetic mutation and biological phenotypes, providing further understanding of the genetic manifestation of many debilitating diseases. More recently, the paradigm of genome editing technologies has evolved to include the correction of mutations that cause diseases via the use of nucleases such as zinc-finger nucleases (ZFN), transcription activator-like effector nucleases (TALENs), and more recently, Cas9 nuclease. With the aim of reversing disease phenotypes, which arise from somatic gene mutations, current research focuses on the clinical translatability of correcting human genetic diseases in vivo, to provide long-term therapeutic benefits and potentially circumvent the limitations of in vivo cell replacement therapy. In this review, in addition to providing an overview of the various genome editing techniques available, we have also summarized several in vivo genome engineering strategies that have successfully demonstrated disease correction via in vivo genome editing. The various benefits and challenges faced in applying in vivo genome editing in humans will also be discussed.
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Kim MS, Kim J. Multiplexed detection of pathogen-specific DNA using engineered zinc finger proteins without target amplification. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2016; 8:6696-6700. [PMID: 28127406 PMCID: PMC5258119 DOI: 10.1039/c6ay02102f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Multiplexed detection of pathogen-specific DNA sequences in a simple and reliable way is in great demand for clinical and biomedical applications. However, there is still a lack of available DNA detection methods that are simple and pathogen-selective for point-of-care (POC) testing. Here, we report a novel zinc finger protein (ZFP)-based chemiluminescent method for direct detection of pathogenic double-stranded DNA (dsDNA) in a multiplexed platform. ZFPs are custom-designed to identify unique pathogenic DNA sequences. ZFP-based chemiluminescent detection of dsDNA provides sufficient sensitivity (≤50 fmol) and high specificity without target DNA amplification. Our study addresses the potential of developing a simple and selective pathogen detection method in a multiplexed fashion needed for POC application.
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Affiliation(s)
- Moon-Soo Kim
- Department of Chemistry, Western Kentucky University, Bowling Green, KY 42101 USA
| | - Juhwa Kim
- Department of Chemistry, Western Kentucky University, Bowling Green, KY 42101 USA
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6
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Taheri-Ghahfarokhi A, Malaver-Ortega LF, Sumer H. Genome Modification of Pluripotent Cells by Using Transcription Activator-Like Effector Nucleases (TALENs). Methods Mol Biol 2015; 1330:253-267. [PMID: 26621602 DOI: 10.1007/978-1-4939-2848-4_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Interest is increasing in transcription activator-like effector nucleases (TALENs) as a tool to introduce targeted double-strand breaks into the large genomes of human and animal cell lines. The produced DNA lesions stimulate DNA repair pathways, error-prone but dominant non-homologous end joining (NHEJ) and accurate but less occurring homology-directed repair (HDR), and as a result targeted genes can be modified. Here, we describe a modified Golden-Gate cloning method for generating TALENs and also details for targeting genes in mouse embryonic stem cells. The protocol described here can be used for modifying the genome of a broad range of pluripotent cell lines.
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Affiliation(s)
| | - Luis F Malaver-Ortega
- Monash Institute for Medical Research, Monash University, Clayton, VIC, 3168, Australia
- Australian Animal Health Laboratories, CSIRO Biosecurity Flagship, East Geelong, VIC, 3219, Australia
| | - Huseyin Sumer
- Department of Chemistry and Biotechnology, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, VIC, 3122, Australia
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7
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Gupta A, Christensen RG, Bell HA, Goodwin M, Patel RY, Pandey M, Enuameh MS, Rayla AL, Zhu C, Thibodeau-Beganny S, Brodsky MH, Joung JK, Wolfe SA, Stormo GD. An improved predictive recognition model for Cys(2)-His(2) zinc finger proteins. Nucleic Acids Res 2014; 42:4800-12. [PMID: 24523353 PMCID: PMC4005693 DOI: 10.1093/nar/gku132] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 01/21/2014] [Accepted: 01/22/2014] [Indexed: 11/17/2022] Open
Abstract
Cys(2)-His(2) zinc finger proteins (ZFPs) are the largest family of transcription factors in higher metazoans. They also represent the most diverse family with regards to the composition of their recognition sequences. Although there are a number of ZFPs with characterized DNA-binding preferences, the specificity of the vast majority of ZFPs is unknown and cannot be directly inferred by homology due to the diversity of recognition residues present within individual fingers. Given the large number of unique zinc fingers and assemblies present across eukaryotes, a comprehensive predictive recognition model that could accurately estimate the DNA-binding specificity of any ZFP based on its amino acid sequence would have great utility. Toward this goal, we have used the DNA-binding specificities of 678 two-finger modules from both natural and artificial sources to construct a random forest-based predictive model for ZFP recognition. We find that our recognition model outperforms previously described determinant-based recognition models for ZFPs, and can successfully estimate the specificity of naturally occurring ZFPs with previously defined specificities.
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Affiliation(s)
- Ankit Gupta
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Ryan G. Christensen
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Heather A. Bell
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Mathew Goodwin
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Ronak Y. Patel
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Manishi Pandey
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Metewo Selase Enuameh
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Amy L. Rayla
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Cong Zhu
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Stacey Thibodeau-Beganny
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Michael H. Brodsky
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - J. Keith Joung
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Scot A. Wolfe
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Gary D. Stormo
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA, Department of Biochemistry and Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609, USA, Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA and Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
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8
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Engineering nucleases for gene targeting: safety and regulatory considerations. N Biotechnol 2013; 31:18-27. [PMID: 23851284 DOI: 10.1016/j.nbt.2013.07.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 06/24/2013] [Accepted: 07/03/2013] [Indexed: 12/26/2022]
Abstract
Nuclease-based gene targeting (NBGT) represents a significant breakthrough in targeted genome editing since it is applicable from single-celled protozoa to human, including several species of economic importance. Along with the fast progress in NBGT and the increasing availability of customized nucleases, more data are available about off-target effects associated with the use of this approach. We discuss how NBGT may offer a new perspective for genetic modification, we address some aspects crucial for a safety improvement of the corresponding techniques and we also briefly relate the use of NBGT applications and products to the regulatory oversight.
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Enuameh MS, Asriyan Y, Richards A, Christensen RG, Hall VL, Kazemian M, Zhu C, Pham H, Cheng Q, Blatti C, Brasefield JA, Basciotta MD, Ou J, McNulty JC, Zhu LJ, Celniker SE, Sinha S, Stormo GD, Brodsky MH, Wolfe SA. Global analysis of Drosophila Cys₂-His₂ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants. Genome Res 2013; 23:928-40. [PMID: 23471540 PMCID: PMC3668361 DOI: 10.1101/gr.151472.112] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Cys2-His2 zinc finger proteins (ZFPs) are the largest group of transcription factors in higher metazoans. A complete characterization of these ZFPs and their associated target sequences is pivotal to fully annotate transcriptional regulatory networks in metazoan genomes. As a first step in this process, we have characterized the DNA-binding specificities of 129 zinc finger sets from Drosophila using a bacterial one-hybrid system. This data set contains the DNA-binding specificities for at least one encoded ZFP from 70 unique genes and 23 alternate splice isoforms representing the largest set of characterized ZFPs from any organism described to date. These recognition motifs can be used to predict genomic binding sites for these factors within the fruit fly genome. Subsets of fingers from these ZFPs were characterized to define their orientation and register on their recognition sequences, thereby allowing us to define the recognition diversity within this finger set. We find that the characterized fingers can specify 47 of the 64 possible DNA triplets. To confirm the utility of our finger recognition models, we employed subsets of Drosophila fingers in combination with an existing archive of artificial zinc finger modules to create ZFPs with novel DNA-binding specificity. These hybrids of natural and artificial fingers can be used to create functional zinc finger nucleases for editing vertebrate genomes.
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Affiliation(s)
- Metewo Selase Enuameh
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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10
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Sizova I, Greiner A, Awasthi M, Kateriya S, Hegemann P. Nuclear gene targeting in Chlamydomonas using engineered zinc-finger nucleases. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 73:873-82. [PMID: 23137232 DOI: 10.1111/tpj.12066] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 10/31/2012] [Accepted: 11/02/2012] [Indexed: 05/18/2023]
Abstract
The unicellular green alga Chlamydomonas reinhardtii is a versatile model for fundamental and biotechnological research. A wide range of tools for genetic manipulation have been developed for this alga, but specific modification of nuclear genes is still not routinely possible. Here, we present a nuclear gene targeting strategy for Chlamydomonas that is based on the application of zinc-finger nucleases (ZFNs). Our approach includes (i) design of gene-specific ZFNs using available online tools, (ii) evaluation of the designed ZFNs in a Chlamydomonas in situ model system, (iii) optimization of ZFN activity by modification of the nuclease domain, and (iv) application of the most suitable enzymes for mutagenesis of an endogenous gene. Initially, we designed a set of ZFNs to target the COP3 gene that encodes the light-activated ion channel channelrhodopsin-1. To evaluate the designed ZFNs, we constructed a model strain by inserting a non-functional aminoglycoside 3'-phosphotransferase VIII (aphVIII) selection marker interspaced with a short COP3 target sequence into the nuclear genome. Upon co-transformation of this recipient strain with the engineered ZFNs and an aphVIII DNA template, we were able to restore marker activity and select paromomycin-resistant (Pm-R) clones with expressing nucleases. Of these Pm-R clones, 1% also contained a modified COP3 locus. In cases where cells were co-transformed with a modified COP3 template, the COP3 locus was specifically modified by homologous recombination between COP3 and the supplied template DNA. We anticipate that this ZFN technology will be useful for studying the functions of individual genes in Chlamydomonas.
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Affiliation(s)
- Irina Sizova
- Institute of Biology, Experimental Biophysics, Humboldt Universität Berlin, Berlin, Germany
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11
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Petolino JF, Davies JP. Designed transcriptional regulators for trait development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 201-202:128-36. [PMID: 23352411 DOI: 10.1016/j.plantsci.2012.12.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Revised: 12/05/2012] [Accepted: 12/07/2012] [Indexed: 05/21/2023]
Abstract
Development is largely controlled by proteins that regulate gene expression at the level of transcription. These regulatory proteins, the genes that control them, and the genes that they control, are organized in a hierarchical structure of complex interactions. Altering the expression of genes encoding regulatory proteins controlling critical nodes in this hierarchy has potential for dramatic phenotypic modification. Constitutive over-expression of genes encoding regulatory proteins in transgenic plants has resulted in agronomically interesting phenotypes along with developmental abnormalities. For trait development, the magnitude and timing of expression of genes encoding key regulatory proteins will need to be precisely controlled and targeted to specific cells and tissues at certain developmental timepoints. Such control is made possible by designed transcriptional regulators which are fusions of engineered DNA binding proteins and activator or repressor domains. Expression of genes encoding such designed transcriptional regulators enable the selective modulation of endogenous gene expression. Genes encoding proteins controlling regulatory networks are prime targets for up- or down-regulation via such designed transcriptional regulators.
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MESH Headings
- Adaptation, Physiological
- Crops, Agricultural/genetics
- Crops, Agricultural/metabolism
- Crops, Agricultural/physiology
- DNA, Plant/genetics
- DNA, Plant/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Droughts
- Gene Expression Regulation, Plant
- Genes, Plant
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/metabolism
- Plants, Genetically Modified/physiology
- Protein Interaction Mapping
- Protein Structure, Tertiary
- Regulatory Elements, Transcriptional
- Regulatory Sequences, Nucleic Acid
- Temperature
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcriptional Activation
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Chen S, Oikonomou G, Chiu CN, Niles BJ, Liu J, Lee DA, Antoshechkin I, Prober DA. A large-scale in vivo analysis reveals that TALENs are significantly more mutagenic than ZFNs generated using context-dependent assembly. Nucleic Acids Res 2013; 41:2769-78. [PMID: 23303782 PMCID: PMC3575824 DOI: 10.1093/nar/gks1356] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Zinc-finger nucleases (ZFNs) and TAL effector nucleases (TALENs) have been shown to induce targeted mutations, but they have not been extensively tested in any animal model. Here, we describe a large-scale comparison of ZFN and TALEN mutagenicity in zebrafish. Using deep sequencing, we found that TALENs are significantly more likely to be mutagenic and induce an average of 10-fold more mutations than ZFNs. We observed a strong correlation between somatic and germ-line mutagenicity, and identified germ line mutations using ZFNs whose somatic mutations rates are well below the commonly used threshold of 1%. Guidelines that have previously been proposed to predict optimal ZFN and TALEN target sites did not predict mutagenicity in vivo. However, we observed a significant negative correlation between TALEN mutagenicity and the number of CpG repeats in TALEN target sites, suggesting that target site methylation may explain the poor mutagenicity of some TALENs in vivo. The higher mutation rates and ability to target essentially any sequence make TALENs the superior technology for targeted mutagenesis in zebrafish, and likely other animal models.
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Affiliation(s)
- Shijia Chen
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
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13
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Zhu C, Gupta A, Hall VL, Rayla AL, Christensen RG, Dake B, Lakshmanan A, Kuperwasser C, Stormo GD, Wolfe SA. Using defined finger-finger interfaces as units of assembly for constructing zinc-finger nucleases. Nucleic Acids Res 2013; 41:2455-65. [PMID: 23303772 PMCID: PMC3575815 DOI: 10.1093/nar/gks1357] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Zinc-finger nucleases (ZFNs) have been used for genome engineering in a wide variety of organisms; however, it remains challenging to design effective ZFNs for many genomic sequences using publicly available zinc-finger modules. This limitation is in part because of potential finger–finger incompatibility generated on assembly of modules into zinc-finger arrays (ZFAs). Herein, we describe the validation of a new set of two-finger modules that can be used for building ZFAs via conventional assembly methods or a new strategy—finger stitching—that increases the diversity of genomic sequences targetable by ZFNs. Instead of assembling ZFAs based on units of the zinc-finger structural domain, our finger stitching method uses units that span the finger–finger interface to ensure compatibility of neighbouring recognition helices. We tested this approach by generating and characterizing eight ZFAs, and we found their DNA-binding specificities reflected the specificities of the component modules used in their construction. Four pairs of ZFNs incorporating these ZFAs generated targeted lesions in vivo, demonstrating that stitching yields ZFAs with robust recognition properties.
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Affiliation(s)
- Cong Zhu
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA 63108 and Molecular Oncology Research Institute (MORI), Tufts University School of Medicine, Boston, MA, USA 02111
| | - Ankit Gupta
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA 63108 and Molecular Oncology Research Institute (MORI), Tufts University School of Medicine, Boston, MA, USA 02111
| | - Victoria L. Hall
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA 63108 and Molecular Oncology Research Institute (MORI), Tufts University School of Medicine, Boston, MA, USA 02111
| | - Amy L. Rayla
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA 63108 and Molecular Oncology Research Institute (MORI), Tufts University School of Medicine, Boston, MA, USA 02111
| | - Ryan G. Christensen
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA 63108 and Molecular Oncology Research Institute (MORI), Tufts University School of Medicine, Boston, MA, USA 02111
| | - Benjamin Dake
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA 63108 and Molecular Oncology Research Institute (MORI), Tufts University School of Medicine, Boston, MA, USA 02111
| | - Abirami Lakshmanan
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA 63108 and Molecular Oncology Research Institute (MORI), Tufts University School of Medicine, Boston, MA, USA 02111
| | - Charlotte Kuperwasser
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA 63108 and Molecular Oncology Research Institute (MORI), Tufts University School of Medicine, Boston, MA, USA 02111
| | - Gary D. Stormo
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA 63108 and Molecular Oncology Research Institute (MORI), Tufts University School of Medicine, Boston, MA, USA 02111
| | - Scot A. Wolfe
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA 63108 and Molecular Oncology Research Institute (MORI), Tufts University School of Medicine, Boston, MA, USA 02111
- *To whom correspondence should be addressed. Tel: +1 508 856 3953; Fax: +1 508 856 5460;
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14
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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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15
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Bhakta MS, Henry IM, Ousterout DG, Das KT, Lockwood SH, Meckler JF, Wallen MC, Zykovich A, Yu Y, Leo H, Xu L, Gersbach CA, Segal DJ. Highly active zinc-finger nucleases by extended modular assembly. Genome Res 2012; 23:530-8. [PMID: 23222846 PMCID: PMC3589541 DOI: 10.1101/gr.143693.112] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Zinc-finger nucleases (ZFNs) are important tools for genome engineering. Despite intense interest by many academic groups, the lack of robust noncommercial methods has hindered their widespread use. The modular assembly (MA) of ZFNs from publicly available one-finger archives provides a rapid method to create proteins that can recognize a very broad spectrum of DNA sequences. However, three- and four-finger arrays often fail to produce active nucleases. Efforts to improve the specificity of the one-finger archives have not increased the success rate above 25%, suggesting that the MA method might be inherently inefficient due to its insensitivity to context-dependent effects. Here we present the first systematic study on the effect of array length on ZFN activity. ZFNs composed of six-finger MA arrays produced mutations at 15 of 21 (71%) targeted loci in human and mouse cells. A novel drop-out linker scheme was used to rapidly assess three- to six-finger combinations, demonstrating that shorter arrays could improve activity in some cases. Analysis of 268 array variants revealed that half of MA ZFNs of any array composition that exceed an ab initio B-score cutoff of 15 were active. These results suggest that, when used appropriately, MA ZFNs are able to target more DNA sequences with higher success rates than other current methods.
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Affiliation(s)
- Mital S Bhakta
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
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16
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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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17
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Kim Y, Kim SH, Ferracane D, Katzenellenbogen JA, Schroeder CM. Specific labeling of zinc finger proteins using noncanonical amino acids and copper-free click chemistry. Bioconjug Chem 2012; 23:1891-901. [PMID: 22871171 DOI: 10.1021/bc300262h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Zinc finger proteins (ZFPs) play a key role in transcriptional regulation and serve as invaluable tools for gene modification and genetic engineering. Development of efficient strategies for labeling metalloproteins such as ZFPs is essential for understanding and controlling biological processes. In this work, we engineered ZFPs containing cysteine-histidine (Cys2-His2) motifs by metabolic incorporation of the unnatural amino acid azidohomoalanine (AHA), followed by specific protein labeling via click chemistry. We show that cyclooctyne promoted [3 + 2] dipolar cycloaddition with azides, known as copper-free click chemistry, provides rapid and specific labeling of ZFPs at high yields as determined by mass spectrometry analysis. We observe that the DNA-binding activity of ZFPs labeled by conventional copper-mediated click chemistry was completely abolished, whereas ZFPs labeled by copper-free click chemistry retain their sequence-specific DNA-binding activity under native conditions, as determined by electrophoretic mobility shift assays, protein microarrays, and kinetic binding assays based on Förster resonance energy transfer (FRET). Our work provides a general framework to label metalloproteins such as ZFPs by metabolic incorporation of unnatural amino acids followed by copper-free click chemistry.
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Affiliation(s)
- Younghoon Kim
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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18
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Gupta A, Christensen RG, Rayla AL, Lakshmanan A, Stormo GD, Wolfe SA. An optimized two-finger archive for ZFN-mediated gene targeting. Nat Methods 2012; 9:588-90. [PMID: 22543349 PMCID: PMC3443678 DOI: 10.1038/nmeth.1994] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 04/07/2012] [Indexed: 11/17/2022]
Abstract
The widespread use of zinc finger nucleases (ZFNs) for genome engineering is hampered by the fact that only a subset of sequences can be efficiently recognized using published finger archives. We describe a set of validated two-finger modules that complement existing finger archives and expand the range of ZFN-accessible sequences by three-fold. Using this archive, we successfully introduce lesions at 9 of 11 target sites in the zebrafish genome.
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Affiliation(s)
- Ankit Gupta
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, USA
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19
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Towards artificial metallonucleases for gene therapy: recent advances and new perspectives. Future Med Chem 2011; 3:1935-66. [DOI: 10.4155/fmc.11.139] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The process of DNA targeting or repair of mutated genes within the cell, induced by specifically positioned double-strand cleavage of DNA near the mutated sequence, can be applied for gene therapy of monogenic diseases. For this purpose, highly specific artificial metallonucleases are developed. They are expected to be important future tools of modern genetics. The present state of art and strategies of research are summarized, including protein engineering and artificial ‘chemical’ nucleases. From the results, we learn about the basic role of the metal ions and the various ligands, and about the DNA binding and cleavage mechanism. The results collected provide useful guidance for engineering highly controlled enzymes for use in gene therapy.
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20
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Conrado RJ, Wu GC, Boock JT, Xu H, Chen SY, Lebar T, Turnšek J, Tomšič N, Avbelj M, Gaber R, Koprivnjak T, Mori J, Glavnik V, Vovk I, Benčina M, Hodnik V, Anderluh G, Dueber JE, Jerala R, DeLisa MP. DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency. Nucleic Acids Res 2011; 40:1879-89. [PMID: 22021385 PMCID: PMC3287197 DOI: 10.1093/nar/gkr888] [Citation(s) in RCA: 205] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Synthetic scaffolds that permit spatial and temporal organization of enzymes in living cells are a promising post-translational strategy for controlling the flow of information in both metabolic and signaling pathways. Here, we describe the use of plasmid DNA as a stable, robust and configurable scaffold for arranging biosynthetic enzymes in the cytoplasm of Escherichia coli. This involved conversion of individual enzymes into custom DNA-binding proteins by genetic fusion to zinc-finger domains that specifically bind unique DNA sequences. When expressed in cells that carried a rationally designed DNA scaffold comprising corresponding zinc finger binding sites, the titers of diverse metabolic products, including resveratrol, 1,2-propanediol and mevalonate were increased as a function of the scaffold architecture. These results highlight the utility of DNA scaffolds for assembling biosynthetic enzymes into functional metabolic structures. Beyond metabolism, we anticipate that DNA scaffolds may be useful in sequestering different types of enzymes for specifying the output of biological signaling pathways or for coordinating other assembly-line processes such as protein folding, degradation and post-translational modifications.
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Affiliation(s)
- Robert J Conrado
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
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21
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Zhu C, Smith T, McNulty J, Rayla AL, Lakshmanan A, Siekmann AF, Buffardi M, Meng X, Shin J, Padmanabhan A, Cifuentes D, Giraldez AJ, Look AT, Epstein JA, Lawson ND, Wolfe SA. Evaluation and application of modularly assembled zinc-finger nucleases in zebrafish. Development 2011; 138:4555-64. [PMID: 21937602 PMCID: PMC3177320 DOI: 10.1242/dev.066779] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2011] [Indexed: 12/20/2022]
Abstract
Zinc-finger nucleases (ZFNs) allow targeted gene inactivation in a wide range of model organisms. However, construction of target-specific ZFNs is technically challenging. Here, we evaluate a straightforward modular assembly-based approach for ZFN construction and gene inactivation in zebrafish. From an archive of 27 different zinc-finger modules, we assembled more than 70 different zinc-finger cassettes and evaluated their specificity using a bacterial one-hybrid assay. In parallel, we constructed ZFNs from these cassettes and tested their ability to induce lesions in zebrafish embryos. We found that the majority of zinc-finger proteins assembled from these modules have favorable specificities and nearly one-third of modular ZFNs generated lesions at their targets in the zebrafish genome. To facilitate the application of ZFNs within the zebrafish community we constructed a public database of sites in the zebrafish genome that can be targeted using this archive. Importantly, we generated new germline mutations in eight different genes, confirming that this is a viable platform for heritable gene inactivation in vertebrates. Characterization of one of these mutants, gata2a, revealed an unexpected role for this transcription factor in vascular development. This work provides a resource to allow targeted germline gene inactivation in zebrafish and highlights the benefit of a definitive reverse genetic strategy to reveal gene function.
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Affiliation(s)
- Cong Zhu
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Tom Smith
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Joseph McNulty
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Amy L. Rayla
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Abirami Lakshmanan
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Arndt F. Siekmann
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Matthew Buffardi
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Xiangdong Meng
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jimann Shin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Arun Padmanabhan
- Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-6058, USA
| | - Daniel Cifuentes
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Antonio J. Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - A. Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan A. Epstein
- Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-6058, USA
| | - Nathan D. Lawson
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Scot A. Wolfe
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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22
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Lam KN, van Bakel H, Cote AG, van der Ven A, Hughes TR. Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays. Nucleic Acids Res 2011; 39:4680-90. [PMID: 21321018 PMCID: PMC3113560 DOI: 10.1093/nar/gkq1303] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 12/02/2010] [Accepted: 12/06/2010] [Indexed: 01/31/2023] Open
Abstract
C2H2 zinc fingers (C2H2-ZFs) are the most prevalent type of vertebrate DNA-binding domain, and typically appear in tandem arrays (ZFAs), with sequential C2H2-ZFs each contacting three (or more) sequential bases. C2H2-ZFs can be assembled in a modular fashion, providing one explanation for their remarkable evolutionary success. Given a set of modules with defined three-base specificities, modular assembly also presents a way to construct artificial proteins with specific DNA-binding preferences. However, a recent survey of a large number of three-finger ZFAs engineered by modular assembly reported high failure rates (∼70%), casting doubt on the generality of modular assembly. Here, we used protein-binding microarrays to analyze 28 ZFAs that failed in the aforementioned study. Most (17) preferred specific sequences, which in all but one case resembled the intended target sequence. Like natural ZFAs, the engineered ZFAs typically yielded degenerate motifs, binding dozens to hundreds of related individual sequences. Thus, the failure of these proteins in previous assays is not due to lack of sequence-specific DNA-binding activity. Our findings underscore the relevance of individual C2H2-ZF sequence specificities within tandem arrays, and support the general ability of modular assembly to produce ZFAs with sequence-specific DNA-binding activity.
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Affiliation(s)
- Kathy N. Lam
- Department of Molecular Genetics and Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Harm van Bakel
- Department of Molecular Genetics and Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Atina G. Cote
- Department of Molecular Genetics and Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Anton van der Ven
- Department of Molecular Genetics and Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Timothy R. Hughes
- Department of Molecular Genetics and Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
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23
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Cermak T, Doyle EL, Christian M, Wang L, Zhang Y, Schmidt C, Baller JA, Somia NV, Bogdanove AJ, Voytas DF. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res 2011; 39:e82. [PMID: 21493687 PMCID: PMC3130291 DOI: 10.1093/nar/gkr218] [Citation(s) in RCA: 1456] [Impact Index Per Article: 112.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
TALENs are important new tools for genome engineering. Fusions of transcription activator-like (TAL) effectors of plant pathogenic Xanthomonas spp. to the FokI nuclease, TALENs bind and cleave DNA in pairs. Binding specificity is determined by customizable arrays of polymorphic amino acid repeats in the TAL effectors. We present a method and reagents for efficiently assembling TALEN constructs with custom repeat arrays. We also describe design guidelines based on naturally occurring TAL effectors and their binding sites. Using software that applies these guidelines, in nine genes from plants, animals and protists, we found candidate cleavage sites on average every 35 bp. Each of 15 sites selected from this set was cleaved in a yeast-based assay with TALEN pairs constructed with our reagents. We used two of the TALEN pairs to mutate HPRT1 in human cells and ADH1 in Arabidopsis thaliana protoplasts. Our reagents include a plasmid construct for making custom TAL effectors and one for TAL effector fusions to additional proteins of interest. Using the former, we constructed de novo a functional analog of AvrHah1 of Xanthomonas gardneri. The complete plasmid set is available through the non-profit repository AddGene and a web-based version of our software is freely accessible online.
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Affiliation(s)
- Tomas Cermak
- Department of Genetics, Cell Biology & Development and Center for Genome Engineering, 321 Church Street SE, University of Minnesota, Minneapolis, MN 55455, USA
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24
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He Z, Mei G, Zhao C, Chen Y. Potential application of FoldX force field based protein modeling in zinc finger nucleases design. SCIENCE CHINA-LIFE SCIENCES 2011; 54:442-9. [PMID: 21455692 DOI: 10.1007/s11427-011-4159-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2010] [Accepted: 12/16/2010] [Indexed: 10/18/2022]
Abstract
Engineered sequence-specific zinc finger nucleases (ZFNs) make the highly efficient modification of eukaryotic genomes possible. However, most current strategies for developing zinc finger nucleases with customized sequence specificities require the construction of numerous tandem arrays of zinc finger proteins (ZFPs), and subsequent largescale in vitro validation of their DNA binding affinities and specificities via bacterial selection. The labor and expertise required in this complex process limits the broad adoption of ZFN technology. An effective computational assisted design strategy will lower the complexity of the production of a pair of functional ZFNs. Here we used the FoldX force field to build 3D models of 420 ZFP-DNA complexes based on zinc finger arrays developed by the Zinc Finger Consortium using OPEN (oligomerized pool engineering). Using nonlinear and linear regression analysis, we found that the calculated protein-DNA binding energy in a modeled ZFP-DNA complex strongly correlates to the failure rate of the zinc finger array to show significant ZFN activity in human cells. In our models, less than 5% of the three-finger arrays with calculated protein-DNA binding energies lower than -13.132 kcal mol(-1) fail to form active ZFNs in human cells. By contrast, for arrays with calculated protein-DNA binding energies higher than -5 kcal mol(-1), as many as 40% lacked ZFN activity in human cells. Therefore, we suggest that the FoldX force field can be useful in reducing the failure rate and increasing efficiency in the design of ZFNs.
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Affiliation(s)
- ZuYong He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006, China
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25
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Kim MS, Stybayeva G, Lee JY, Revzin A, Segal DJ. A zinc finger protein array for the visual detection of specific DNA sequences for diagnostic applications. Nucleic Acids Res 2011; 39:e29. [PMID: 21134909 PMCID: PMC3061069 DOI: 10.1093/nar/gkq1214] [Citation(s) in RCA: 27] [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: 07/22/2010] [Revised: 11/06/2010] [Accepted: 11/10/2010] [Indexed: 11/13/2022] Open
Abstract
The visual detection of specific double-stranded DNA sequences possesses great potential for the development of diagnostics. Zinc finger domains provide a powerful scaffold for creating custom DNA-binding proteins that recognize specific DNA sequences. We previously demonstrated sequence-enabled reassembly of TEM-1 β-lactamase (SEER-LAC), a system consisting of two inactive fragments of β-lactamase each linked to engineered zinc finger proteins (ZFPs). Here the SEER-LAC system was applied to develop ZFP arrays that function as simple devices to identify bacterial double-stranded DNA sequences. The ZFP arrays provided a quantitative assay with a detection limit of 50 fmol of target DNA. The method could distinguish target DNA from non-target DNA within 5 min. The ZFP arrays provided sufficient sensitivity and high specificity to recognize specific DNA sequences. These results suggest that ZFP arrays have the potential to be developed into a simple and rapid point-of-care (POC) diagnostic for the multiplexed detection of pathogens.
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Affiliation(s)
- Moon-Soo Kim
- Genome Center, Department of Pharmacology and Department of Biomedical Engineering, 451 Health Sciences Drive, University of California, Davis, CA 95616, USA
| | - Gulnaz Stybayeva
- Genome Center, Department of Pharmacology and Department of Biomedical Engineering, 451 Health Sciences Drive, University of California, Davis, CA 95616, USA
| | - Ji Youn Lee
- Genome Center, Department of Pharmacology and Department of Biomedical Engineering, 451 Health Sciences Drive, University of California, Davis, CA 95616, USA
| | - Alexander Revzin
- Genome Center, Department of Pharmacology and Department of Biomedical Engineering, 451 Health Sciences Drive, University of California, Davis, CA 95616, USA
| | - David J. Segal
- Genome Center, Department of Pharmacology and Department of Biomedical Engineering, 451 Health Sciences Drive, University of California, Davis, CA 95616, USA
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26
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Yanover C, Bradley P. Extensive protein and DNA backbone sampling improves structure-based specificity prediction for C2H2 zinc fingers. Nucleic Acids Res 2011; 39:4564-76. [PMID: 21343182 PMCID: PMC3113574 DOI: 10.1093/nar/gkr048] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Sequence-specific DNA recognition by gene regulatory proteins is critical for proper cellular functioning. The ability to predict the DNA binding preferences of these regulatory proteins from their amino acid sequence would greatly aid in reconstruction of their regulatory interactions. Structural modeling provides one route to such predictions: by building accurate molecular models of regulatory proteins in complex with candidate binding sites, and estimating their relative binding affinities for these sites using a suitable potential function, it should be possible to construct DNA binding profiles. Here, we present a novel molecular modeling protocol for protein-DNA interfaces that borrows conformational sampling techniques from de novo protein structure prediction to generate a diverse ensemble of structural models from small fragments of related and unrelated protein-DNA complexes. The extensive conformational sampling is coupled with sequence space exploration so that binding preferences for the target protein can be inferred from the resulting optimized DNA sequences. We apply the algorithm to predict binding profiles for a benchmark set of eleven C2H2 zinc finger transcription factors, five of known and six of unknown structure. The predicted profiles are in good agreement with experimental binding data; furthermore, examination of the modeled structures gives insight into observed binding preferences.
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Affiliation(s)
- Chen Yanover
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
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27
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Gupta A, Meng X, Zhu LJ, Lawson ND, Wolfe SA. Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases. Nucleic Acids Res 2011; 39:381-92. [PMID: 20843781 PMCID: PMC3017618 DOI: 10.1093/nar/gkq787] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 08/16/2010] [Accepted: 08/19/2010] [Indexed: 01/12/2023] Open
Abstract
Zinc finger nucleases (ZFNs) facilitate tailor-made genomic modifications in vivo through the creation of targeted double-stranded breaks. They have been employed to modify the genomes of plants and animals, and cell-based therapies utilizing ZFNs are undergoing clinical trials. However, many ZFNs display dose-dependent toxicity presumably due to the generation of undesired double-stranded breaks at off-target sites. To evaluate the parameters influencing the functional specificity of ZFNs, we compared the in vivo activity of ZFN variants targeting the zebrafish kdrl locus, which display both high on-target activity and dose-dependent toxicity. We evaluated their functional specificity by assessing lesion frequency at 141 potential off-target sites using Illumina sequencing. Only a minority of these off-target sites accumulated lesions, where the thermodynamics of zinc finger-DNA recognition appear to be a defining feature of active sites. Surprisingly, we observed that both the specificity of the incorporated zinc fingers and the choice of the engineered nuclease domain could independently influence the fidelity of these ZFNs. The results of this study have implications for the assessment of likely off-target sites within a genome and point to both zinc finger-dependent and -independent characteristics that can be tailored to create ZFNs with greater precision.
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Affiliation(s)
- Ankit Gupta
- Program in Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Xiangdong Meng
- Program in Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Lihua J. Zhu
- Program in Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Nathan D. Lawson
- Program in Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Scot A. Wolfe
- Program in Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
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28
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Sander JD, Reyon D, Maeder ML, Foley JE, Thibodeau-Beganny S, Li X, Regan MR, Dahlborg EJ, Goodwin MJ, Fu F, Voytas DF, Joung JK, Dobbs D. Predicting success of oligomerized pool engineering (OPEN) for zinc finger target site sequences. BMC Bioinformatics 2010; 11:543. [PMID: 21044337 PMCID: PMC3098093 DOI: 10.1186/1471-2105-11-543] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 11/02/2010] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Precise and efficient methods for gene targeting are critical for detailed functional analysis of genomes and regulatory networks and for potentially improving the efficacy and safety of gene therapies. Oligomerized Pool ENgineering (OPEN) is a recently developed method for engineering C2H2 zinc finger proteins (ZFPs) designed to bind specific DNA sequences with high affinity and specificity in vivo. Because generation of ZFPs using OPEN requires considerable effort, a computational method for identifying the sites in any given gene that are most likely to be successfully targeted by this method is desirable. RESULTS Analysis of the base composition of experimentally validated ZFP target sites identified important constraints on the DNA sequence space that can be effectively targeted using OPEN. Using alternate encodings to represent ZFP target sites, we implemented Naïve Bayes and Support Vector Machine classifiers capable of distinguishing "active" targets, i.e., ZFP binding sites that can be targeted with a high rate of success, from those that are "inactive" or poor targets for ZFPs generated using current OPEN technologies. When evaluated using leave-one-out cross-validation on a dataset of 135 experimentally validated ZFP target sites, the best Naïve Bayes classifier, designated ZiFOpT, achieved overall accuracy of 87% and specificity+ of 90%, with an ROC AUC of 0.89. When challenged with a completely independent test set of 140 newly validated ZFP target sites, ZiFOpT performance was comparable in terms of overall accuracy (88%) and specificity+ (92%), but with reduced ROC AUC (0.77). Users can rank potentially active ZFP target sites using a confidence score derived from the posterior probability returned by ZiFOpT. CONCLUSION ZiFOpT, a machine learning classifier trained to identify DNA sequences amenable for targeting by OPEN-generated zinc finger arrays, can guide users to target sites that are most likely to function successfully in vivo, substantially reducing the experimental effort required. ZiFOpT is freely available and incorporated in the Zinc Finger Targeter web server (http://bindr.gdcb.iastate.edu/ZiFiT).
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Affiliation(s)
- Jeffry D Sander
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
- Department of Genetics, Development and Cell Biology, Interdepartmental Graduate Program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011, USA
| | - Deepak Reyon
- Department of Genetics, Development and Cell Biology, Interdepartmental Graduate Program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011, USA
| | - Morgan L Maeder
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan E Foley
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Stacey Thibodeau-Beganny
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Xiaohong Li
- Department of Genetics, Cell Biology & Development, Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Maureen R Regan
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Elizabeth J Dahlborg
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Mathew J Goodwin
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Fengli Fu
- Department of Genetics, Development and Cell Biology, Interdepartmental Graduate Program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011, USA
| | - Daniel F Voytas
- Department of Genetics, Cell Biology & Development, Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - J Keith Joung
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129, USA
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
- Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA 02115, USA
| | - Drena Dobbs
- Department of Genetics, Development and Cell Biology, Interdepartmental Graduate Program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011, USA
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29
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Urnov FD, Rebar EJ, Holmes MC, Zhang HS, Gregory PD. Genome editing with engineered zinc finger nucleases. Nat Rev Genet 2010; 11:636-46. [PMID: 20717154 DOI: 10.1038/nrg2842] [Citation(s) in RCA: 1440] [Impact Index Per Article: 102.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Reverse genetics in model organisms such as Drosophila melanogaster, Arabidopsis thaliana, zebrafish and rats, efficient genome engineering in human embryonic stem and induced pluripotent stem cells, targeted integration in crop plants, and HIV resistance in immune cells - this broad range of outcomes has resulted from the application of the same core technology: targeted genome cleavage by engineered, sequence-specific zinc finger nucleases followed by gene modification during subsequent repair. Such 'genome editing' is now established in human cells and a number of model organisms, thus opening the door to a range of new experimental and therapeutic possibilities.
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Affiliation(s)
- Fyodor D Urnov
- Sangamo BioSciences Inc., Richmond, California 94804, USA
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30
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Guo J, Gaj T, Barbas CF. Directed evolution of an enhanced and highly efficient FokI cleavage domain for zinc finger nucleases. J Mol Biol 2010; 400:96-107. [PMID: 20447404 PMCID: PMC2885538 DOI: 10.1016/j.jmb.2010.04.060] [Citation(s) in RCA: 156] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 04/27/2010] [Accepted: 04/28/2010] [Indexed: 10/19/2022]
Abstract
Zinc finger nucleases (ZFNs) are powerful tools for gene therapy and genetic engineering. The high specificity and affinity of these chimeric enzymes are based on custom-designed zinc finger proteins (ZFPs). To improve the performance of existing ZFN technology, we developed an in vivo evolution-based approach to improve the efficacy of the FokI cleavage domain (FCD). After multiple rounds of cycling mutagenesis and DNA shuffling, a more efficient nuclease variant (Sharkey) was generated. In vivo analyses indicated that Sharkey is >15-fold more active than wild-type FCD on a diverse panel of cleavage sites. Further, a mammalian cell-based assay showed a three to sixfold improvement in targeted mutagenesis for ZFNs containing derivatives of the Sharkey cleavage domain. We also identified mutations that impart sequence specificity to the FCD that might be utilized in future studies to further refine ZFNs through cooperative specificity. In addition, Sharkey was observed to enhance the cleavage profiles of previously published and newly selected heterodimer ZFN architectures. This enhanced and highly efficient cleavage domain will aid in a variety of ZFN applications in medicine and biology.
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Affiliation(s)
- Jing Guo
- The Skaggs Institute for Chemical Biology and the Departments of Molecular Biology and Chemistry, The Scripps Research Institute, La Jolla, California, USA
| | - Thomas Gaj
- The Skaggs Institute for Chemical Biology and the Departments of Molecular Biology and Chemistry, The Scripps Research Institute, La Jolla, California, USA
| | - Carlos F. Barbas
- The Skaggs Institute for Chemical Biology and the Departments of Molecular Biology and Chemistry, The Scripps Research Institute, La Jolla, California, USA
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31
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Guo J, Gaj T, Barbas CF. Directed evolution of an enhanced and highly efficient FokI cleavage domain for zinc finger nucleases. J Mol Biol 2010. [PMID: 20447404 DOI: 10.1016/s13007-018-0305-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Zinc finger nucleases (ZFNs) are powerful tools for gene therapy and genetic engineering. The high specificity and affinity of these chimeric enzymes are based on custom-designed zinc finger proteins (ZFPs). To improve the performance of existing ZFN technology, we developed an in vivo evolution-based approach to improve the efficacy of the FokI cleavage domain (FCD). After multiple rounds of cycling mutagenesis and DNA shuffling, a more efficient nuclease variant (Sharkey) was generated. In vivo analyses indicated that Sharkey is >15-fold more active than wild-type FCD on a diverse panel of cleavage sites. Further, a mammalian cell-based assay showed a three to sixfold improvement in targeted mutagenesis for ZFNs containing derivatives of the Sharkey cleavage domain. We also identified mutations that impart sequence specificity to the FCD that might be utilized in future studies to further refine ZFNs through cooperative specificity. In addition, Sharkey was observed to enhance the cleavage profiles of previously published and newly selected heterodimer ZFN architectures. This enhanced and highly efficient cleavage domain will aid in a variety of ZFN applications in medicine and biology.
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Affiliation(s)
- Jing Guo
- The Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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32
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Jantz D, Berg JM. Probing the DNA-binding affinity and specificity of designed zinc finger proteins. Biophys J 2010; 98:852-60. [PMID: 20197039 DOI: 10.1016/j.bpj.2009.11.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Revised: 10/30/2009] [Accepted: 11/02/2009] [Indexed: 11/17/2022] Open
Abstract
Engineered transcription factors and endonucleases based on designed Cys(2)His(2) zinc finger domains have proven to be effective tools for the directed regulation and modification of genes. The introduction of this technology into both research and clinical settings necessitates the development of rapid and accurate means of evaluating both the binding affinity and binding specificity of designed zinc finger domains. Using a fluorescence anisotropy-based DNA-binding assay, we examined the DNA-binding properties of two engineered zinc finger proteins that differ by a single amino acid. We demonstrate that the protein with the highest affinity for a particular DNA site need not be the protein that binds that site with the highest degree of specificity. Moreover, by comparing the binding characteristics of the two proteins at varying salt concentrations, we show that the ionic strength makes significant and variable contributions to both affinity and specificity. These results have significant implications for zinc finger design as they highlight the importance of considering affinity, specificity, and environmental requirements in designing a DNA-binding domain for a particular application.
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Affiliation(s)
- Derek Jantz
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, USA
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33
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Sander JD, Maeder ML, Reyon D, Voytas DF, Joung JK, Dobbs D. ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool. Nucleic Acids Res 2010; 38:W462-8. [PMID: 20435679 PMCID: PMC2896148 DOI: 10.1093/nar/gkq319] [Citation(s) in RCA: 290] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
ZiFiT (Zinc Finger Targeter) is a simple and intuitive web-based tool that provides an interface to identify potential binding sites for engineered zinc finger proteins (ZFPs) in user-supplied DNA sequences. In this updated version, ZiFiT identifies potential sites for ZFPs made by both the modular assembly and OPEN engineering methods. In addition, ZiFiT now integrates additional tools and resources including scoring schemes for modular assembly, an interface with the Zinc Finger Database (ZiFDB) of engineered ZFPs, and direct querying of NCBI BLAST servers for identifying potential off-target sites within a host genome. Taken together, these features facilitate design of ZFPs using reagents made available to the academic research community by the Zinc Finger Consortium. ZiFiT is freely available on the web without registration at http://bindr.gdcb.iastate.edu/ZiFiT/.
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Affiliation(s)
- Jeffry D Sander
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129, USA.
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34
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Construction and testing of engineered zinc-finger proteins for sequence-specific modification of mtDNA. Nat Protoc 2010; 5:342-56. [PMID: 20134433 DOI: 10.1038/nprot.2009.245] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Engineered zinc-finger proteins (ZFPs) are hybrid proteins developed to direct various effector domains (EDs) of choice to predetermined DNA sequences. They are used to alter gene expression and to modify DNA in a sequence-specific manner in vivo and in vitro. Until now, ZFPs have mostly been used to target DNA sites in nuclear genomes. This protocol describes how to adapt engineered ZFP technology to specifically modify the mammalian mitochondrial genome. The first step describes how to construct mitochondrially targeted ZFPs (mtZFPs) so that they are efficiently imported into mammalian mitochondria. In the second step, methods to test the basic properties of mtZFPs in vitro are described. Finally, we outline how the mtZFPs can be transiently transfected into mammalian cells and their mitochondrial import tested by both immunofluorescence and biochemical methods. The protocol can be completed within a week, although time-consuming DNA cloning steps may extend this.
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35
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Abstract
The modular assembly (MA) method of generating engineered zinc finger proteins (ZFPs) was the first practical method for creating custom DNA-binding proteins. As such, MA has enabled a vast exploration of sequence-specific methods and reagents, ushering in the modern era of zinc finger-based applications that are described in this volume. The first zinc finger nuclease to cleave an endogenous site was created using MA, as was the first artificial transcription factor to enter phase II clinical trials. In recent years, other excellent methods have been developed that improved the affinity and specificity of the engineered ZFPs. However, MA is still used widely for many applications. This chapter will describe methods and give guidance for the creation of ZFPs using MA. Such ZFPs might be useful as starting materials to perform other methods described in this volume. Here, we also describe a single-strand annealing recombination assay for the initial testing of zinc finger nucleases.
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36
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Imanishi M, Nakamura A, Morisaki T, Futaki S. Positive and negative cooperativity of modularly assembled zinc fingers. Biochem Biophys Res Commun 2009; 387:440-3. [DOI: 10.1016/j.bbrc.2009.07.059] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Accepted: 07/08/2009] [Indexed: 11/15/2022]
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