1
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Ichikawa DM, Abdin O, Alerasool N, Kogenaru M, Mueller AL, Wen H, Giganti DO, Goldberg GW, Adams S, Spencer JM, Razavi R, Nim S, Zheng H, Gionco C, Clark FT, Strokach A, Hughes TR, Lionnet T, Taipale M, Kim PM, Noyes MB. A universal deep-learning model for zinc finger design enables transcription factor reprogramming. Nat Biotechnol 2023; 41:1117-1129. [PMID: 36702896 PMCID: PMC10421740 DOI: 10.1038/s41587-022-01624-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 11/17/2022] [Indexed: 01/27/2023]
Abstract
Cys2His2 zinc finger (ZF) domains engineered to bind specific target sequences in the genome provide an effective strategy for programmable regulation of gene expression, with many potential therapeutic applications. However, the structurally intricate engagement of ZF domains with DNA has made their design challenging. Here we describe the screening of 49 billion protein-DNA interactions and the development of a deep-learning model, ZFDesign, that solves ZF design for any genomic target. ZFDesign is a modern machine learning method that models global and target-specific differences induced by a range of library environments and specifically takes into account compatibility of neighboring fingers using a novel hierarchical transformer architecture. We demonstrate the versatility of designed ZFs as nucleases as well as activators and repressors by seamless reprogramming of human transcription factors. These factors could be used to upregulate an allele of haploinsufficiency, downregulate a gain-of-function mutation or test the consequence of regulation of a single gene as opposed to the many genes that a transcription factor would normally influence.
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Affiliation(s)
- David M Ichikawa
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Osama Abdin
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Nader Alerasool
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Manjunatha Kogenaru
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA
| | - April L Mueller
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA
| | - Han Wen
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - David O Giganti
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA
| | - Gregory W Goldberg
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA
| | - Samantha Adams
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA
| | - Jeffrey M Spencer
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA
| | - Rozita Razavi
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Satra Nim
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Hong Zheng
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Courtney Gionco
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA
| | - Finnegan T Clark
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA
| | - Alexey Strokach
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Timothy R Hughes
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Timothee Lionnet
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA
| | - Mikko Taipale
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Philip M Kim
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.
| | - Marcus B Noyes
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA.
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA.
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2
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Sauvagère S, Siatka C. CRISPR-Cas: 'The Multipurpose Molecular Tool' for Gene Therapy and Diagnosis. Genes (Basel) 2023; 14:1542. [PMID: 37628594 PMCID: PMC10454384 DOI: 10.3390/genes14081542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
Since the discovery of the CRISPR-Cas engineering system in 2012, several approaches for using this innovative molecular tool in therapeutic strategies and even diagnosis have been investigated. The use of this tool requires a global approach to DNA damage processes and repair systems in cells. The diversity in the functions of various Cas proteins allows for the use of this technology in clinical applications and trials. Wide variants of Cas12 and Cas13 are exploited using the collateral effect in many diagnostic applications. Even though this tool is well known, its use still raises real-world ethical and regulatory questions.
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3
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Kuang C, Xiao Y, Hondmann D. Cleavage-free human genome editing. Mol Ther 2022; 30:268-282. [PMID: 34864205 PMCID: PMC8753458 DOI: 10.1016/j.ymthe.2021.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 08/17/2021] [Accepted: 11/30/2021] [Indexed: 01/07/2023] Open
Abstract
Most gene editing technologies introduce breaks or nicks into DNA, leading to the generation of mutagenic insertions and deletions by non-homologous end-joining repair. Here, we report a new, cleavage-free gene editing approach based on replication interrupted template-driven DNA modification (RITDM). The RITDM system makes use of sequence-specific DLR fusion molecules that are specifically designed to enable localized, temporary blockage of DNA replication fork progression, thereby exposing single-stranded DNA that can be bound by DNA sequence modification templates for precise editing. We evaluate the use of zinc-finger arrays for sequence recognition. We demonstrate that RITDM can be used for gene editing at endogenous genomic loci in human cells and highlight its safety profile of low indel frequencies and undetectable off-target side effects in RITDM-edited clones and pools of cells.
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Affiliation(s)
- Chenzhong Kuang
- Peter Biotherapeutics, Inc, 75 Kneeland Street, Boston, MA 02111, USA
| | - Yan Xiao
- Peter Biotherapeutics, Inc, 75 Kneeland Street, Boston, MA 02111, USA
| | - Dirk Hondmann
- Peter Biotherapeutics, Inc, 75 Kneeland Street, Boston, MA 02111, USA,Corresponding author: Dirk Hondmann, Peter Biotherapeutics, Inc, 75 Kneeland Street, Boston, MA 02111, USA.
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4
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Xun J, Zhang X, Guo S, Lu H, Chen J. Editing out HIV: application of gene editing technology to achieve functional cure. Retrovirology 2021; 18:39. [PMID: 34922576 PMCID: PMC8684261 DOI: 10.1186/s12977-021-00581-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 11/05/2021] [Indexed: 03/01/2023] Open
Abstract
Highly active antiretroviral therapy (HAART) successfully suppresses human immunodeficiency virus (HIV) replication and improves the quality of life of patients living with HIV. However, current HAART does not eradicate HIV infection because an HIV reservoir is established in latently infected cells and is not recognized by the immune system. The successful curative treatment of the Berlin and London patients following bone marrow transplantation inspired researchers to identify an approach for the functional cure of HIV. As a promising technology, gene editing-based strategies have attracted considerable attention and sparked much debate. Herein, we discuss the development of different gene editing strategies in the functional cure of HIV and highlight the potential for clinical applications prospects. ![]()
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Affiliation(s)
- Jingna Xun
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Shanghai, 201508, China.,State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Xinyu Zhang
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Shanghai, 201508, China
| | - Shuyan Guo
- Shanghai Foreign Language School, Shanghai International Studies University, Shanghai, China
| | - Hongzhou Lu
- Department of Infectious Diseases and Immunology, Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Shanghai, 201508, China
| | - Jun Chen
- Department of Infectious Diseases and Immunology, Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Shanghai, 201508, China.
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5
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Allen AG, Chung CH, Atkins A, Dampier W, Khalili K, Nonnemacher MR, Wigdahl B. Gene Editing of HIV-1 Co-receptors to Prevent and/or Cure Virus Infection. Front Microbiol 2018; 9:2940. [PMID: 30619107 PMCID: PMC6304358 DOI: 10.3389/fmicb.2018.02940] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/15/2018] [Indexed: 12/26/2022] Open
Abstract
Antiretroviral therapy has prolonged the lives of people living with human immunodeficiency virus type 1 (HIV-1), transforming the disease into one that can be controlled with lifelong therapy. The search for an HIV-1 vaccine has plagued researchers for more than three decades with little to no success from clinical trials. Due to these failures, scientists have turned to alternative methods to develop next generation therapeutics that could allow patients to live with HIV-1 without the need for daily medication. One method that has been proposed has involved the use of a number of powerful gene editing tools; Zinc Finger Nucleases (ZFN), Transcription Activator–like effector nucleases (TALENs), and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 to edit the co-receptors (CCR5 or CXCR4) required for HIV-1 to infect susceptible target cells efficiently. Initial safety studies in patients have shown that editing the CCR5 locus is safe. More in depth in vitro studies have shown that editing the CCR5 locus was able to inhibit infection from CCR5-utilizing virus, but CXCR4-utilizing virus was still able to infect cells. Additional research efforts were then aimed at editing the CXCR4 locus, but this came with other safety concerns. However, in vitro studies have since confirmed that CXCR4 can be edited without killing cells and can confer resistance to CXCR4-utilizing HIV-1. Utilizing these powerful new gene editing technologies in concert could confer cellular resistance to HIV-1. While the CD4, CCR5, CXCR4 axis for cell-free infection has been the most studied, there are a plethora of reports suggesting that the cell-to-cell transmission of HIV-1 is significantly more efficient. These reports also indicated that while broadly neutralizing antibodies are well suited with respect to blocking cell-free infection, cell-to-cell transmission remains refractile to this approach. In addition to stopping cell-free infection, gene editing of the HIV-1 co-receptors could block cell-to-cell transmission. This review aims to summarize what has been shown with regard to editing the co-receptors needed for HIV-1 entry and how they could impact the future of HIV-1 therapeutic and prevention strategies.
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Affiliation(s)
- Alexander G Allen
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States.,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Cheng-Han Chung
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States.,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Andrew Atkins
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States.,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States.,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States.,School of Biomedical Engineering and Health Systems, Drexel University, Philadelphia, PA, United States
| | - Kamel Khalili
- Department of Neuroscience, Center for Neurovirology, and Comprehensive NeuroAIDS Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States.,Center for Translational AIDS Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Michael R Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States.,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States.,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States.,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States.,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States
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6
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Leonard JL, Leonard DM, Wolfe SA, Liu J, Rivera J, Yang M, Leonard RT, Johnson JPS, Kumar P, Liebmann KL, Tutto AA, Mou Z, Simin KJ. The Dkk3 gene encodes a vital intracellular regulator of cell proliferation. PLoS One 2017; 12:e0181724. [PMID: 28738084 PMCID: PMC5524345 DOI: 10.1371/journal.pone.0181724] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 07/06/2017] [Indexed: 11/18/2022] Open
Abstract
Members of the Dickkopf (Dkk) family of Wnt antagonists interrupt Wnt-induced receptor assembly and participate in axial patterning and cell fate determination. One family member, DKK3, does not block Wnt receptor activation. Loss of Dkk3 expression in cancer is associated with hyperproliferation and dysregulated ß-catenin signaling, and ectopic expression of Dkk3 halts cancer growth. The molecular events mediating the DKK3-dependent arrest of ß-catenin-driven cell proliferation in cancer cells are unknown. Here we report the identification of a new intracellular gene product originating from the Dkk3 locus. This Dkk3b transcript originates from a second transcriptional start site located in intron 2 of the Dkk3 gene. It is essential for early mouse development and is a newly recognized regulator of ß-catenin signaling and cell proliferation. Dkk3b interrupts nuclear translocation ß-catenin by capturing cytoplasmic, unphosphorylated ß-catenin in an extra-nuclear complex with ß-TrCP. These data reveal a new regulator of one of the most studied signal transduction pathways in metazoans and provides a novel, completely untapped therapeutic target for silencing the aberrant ß-catenin signaling that drives hyperproliferation in many cancers.
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Affiliation(s)
- Jack L. Leonard
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail:
| | - Deborah M. Leonard
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Scot A. Wolfe
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jilin Liu
- Department of Cell and Molecular Physiology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jaime Rivera
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Michelle Yang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Ryan T. Leonard
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jacob P. S. Johnson
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Prashant Kumar
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Kate L. Liebmann
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Amanda A. Tutto
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Zhongming Mou
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Karl J. Simin
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
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7
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Zhu W, Xie K, Xu Y, Wang L, Chen K, Zhang L, Fang J. CRISPR/Cas9 produces anti-hepatitis B virus effect in hepatoma cells and transgenic mouse. Virus Res 2016; 217:125-32. [PMID: 27049051 DOI: 10.1016/j.virusres.2016.04.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/30/2016] [Accepted: 04/01/2016] [Indexed: 12/20/2022]
Abstract
Chronic infection of hepatitis B virus (HBV) is at risk of liver cirrhosis and hepatocellular carcinoma and remains one of the major public health problems worldwide. It is a major barrier of persistence HBV cccDNA under current antiviral therapy as novel strategies of disrupting HBV cccDNA is pressing. The (CRISPR)/Cas9 system is presently emerging in gene editing and we also apply it for targeting and deleting the conserved regions of HBV genome. Two homologous sequences of HBV S and X genes were carried with CRISPR/Cas9 endonuclease to build pCas9 constructs, which may mediate anti-HBV effects of in vitro and in vivo systems in this study. The results showed the better anti-HBV productions by pCas9-2 and without significant differences in between Huh7 and HepG2 cells. CRISPR/Cas9 direct cleavage and mutagenesis were further analyzed of in vitro system. In the M-TgHBV mouse model of HBV, injection of pCas9 constructs by hydrodynamics decreased HBsAg of sera and liver HBcAg. In conclusion, this designed CRISPR/Cas9 system can induce anti-HBV effects and potentially consider as a novel therapeutic agent against chronic HBV infection.
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Affiliation(s)
- Wei Zhu
- Laboratory of Molecular Medicine, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
| | - Kun Xie
- Laboratory of Molecular Medicine, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yuanjian Xu
- Laboratory of Molecular Medicine, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Le Wang
- Laboratory of Molecular Medicine, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Kaiming Chen
- Laboratory of Molecular Medicine, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Longzhen Zhang
- Laboratory of Molecular Medicine, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jianmin Fang
- Laboratory of Molecular Medicine, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
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8
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The Development and Use of Zinc-Finger Nucleases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016. [DOI: 10.1007/978-1-4939-3509-3_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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9
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Bolukbasi MF, Gupta A, Oikemus S, Derr AG, Garber M, Brodsky MH, Zhu LJ, Wolfe SA. DNA-binding-domain fusions enhance the targeting range and precision of Cas9. Nat Methods 2015; 12:1150-6. [PMID: 26480473 PMCID: PMC4679368 DOI: 10.1038/nmeth.3624] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 08/19/2015] [Indexed: 12/26/2022]
Abstract
The CRISPR-Cas9 system is commonly used in biomedical research; however, the precision of Cas9 is suboptimal for applications that involve editing a large population of cells (for example, gene therapy). Variations on the standard Cas9 system have yielded improvements in the precision of targeted DNA cleavage, but they often restrict the range of targetable sequences. It remains unclear whether these variants can limit lesions to a single site in the human genome over a large cohort of treated cells. Here we show that by fusing a programmable DNA-binding domain (pDBD) to Cas9 and attenuating Cas9's inherent DNA-binding affinity, we were able to produce a Cas9-pDBD chimera with dramatically improved precision and an increased targeting range. Because the specificity and affinity of this framework can be easily tuned, Cas9-pDBDs provide a flexible system that can be tailored to achieve extremely precise genome editing at nearly any genomic locus.
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Affiliation(s)
- Mehmet Fatih Bolukbasi
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Ankit Gupta
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Sarah Oikemus
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Alan G Derr
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Manuel Garber
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Michael H Brodsky
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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10
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Martins JT, Ramos ÓL, Pinheiro AC, Bourbon AI, Silva HD, Rivera MC, Cerqueira MA, Pastrana L, Malcata FX, González-Fernández Á, Vicente AA. Edible Bio-Based Nanostructures: Delivery, Absorption and Potential Toxicity. FOOD ENGINEERING REVIEWS 2015. [DOI: 10.1007/s12393-015-9116-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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11
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Persikov AV, Wetzel JL, Rowland EF, Oakes BL, Xu DJ, Singh M, Noyes MB. A systematic survey of the Cys2His2 zinc finger DNA-binding landscape. Nucleic Acids Res 2015; 43:1965-84. [PMID: 25593323 PMCID: PMC4330361 DOI: 10.1093/nar/gku1395] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cys2His2 zinc fingers (C2H2-ZFs) comprise the largest class of metazoan DNA-binding domains. Despite this domain's well-defined DNA-recognition interface, and its successful use in the design of chimeric proteins capable of targeting genomic regions of interest, much remains unknown about its DNA-binding landscape. To help bridge this gap in fundamental knowledge and to provide a resource for design-oriented applications, we screened large synthetic protein libraries to select binding C2H2-ZF domains for each possible three base pair target. The resulting data consist of >160 000 unique domain-DNA interactions and comprise the most comprehensive investigation of C2H2-ZF DNA-binding interactions to date. An integrated analysis of these independent screens yielded DNA-binding profiles for tens of thousands of domains and led to the successful design and prediction of C2H2-ZF DNA-binding specificities. Computational analyses uncovered important aspects of C2H2-ZF domain-DNA interactions, including the roles of within-finger context and domain position on base recognition. We observed the existence of numerous distinct binding strategies for each possible three base pair target and an apparent balance between affinity and specificity of binding. In sum, our comprehensive data help elucidate the complex binding landscape of C2H2-ZF domains and provide a foundation for efforts to determine, predict and engineer their DNA-binding specificities.
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Affiliation(s)
- Anton V Persikov
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Joshua L Wetzel
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA Department of Computer Science, Princeton University, Princeton, NJ 08544, USA
| | - Elizabeth F Rowland
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Benjamin L Oakes
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Denise J Xu
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Mona Singh
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA Department of Computer Science, Princeton University, Princeton, NJ 08544, USA
| | - Marcus B Noyes
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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12
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Abstract
Understanding how sequence-specific protein-DNA interactions direct cellular function is of great interest to the research community. High-throughput methods have been developed to determine DNA-binding specificities; one such technique, the bacterial one-hybrid (B1H) system, confers advantages including ease of use, sensitivity and throughput. In this review, we describe the evolution of the B1H system as a tool capable of screening large DNA libraries to investigate protein-DNA interactions of interest. We discuss how DNA-binding specificities produced by the B1H system have been used to predict regulatory targets. Additionally, we examine how this approach has been applied to characterize two common DNA-binding domain families-homeodomains and Cys2His2 zinc fingers-both in organism-wide studies and with synthetic approaches. In the case of the former, the B1H system has produced large catalogs of protein specificity and nuanced information about previously recovered DNA targets, thereby improving our understanding of these proteins' functions in vivo and increasing our capacity to predict similar interactions in other species. In the latter, synthetic screens of the same DNA-binding domains have further refined our models of specificity, through analyzing comprehensive libraries to uncover all proteins able to bind a complete set of targets, and, for instance, exploring how context-in the form of domain position within the parent protein-may affect specificity. Finally, we recognize the limitations of the B1H system and discuss its potential for use in the production of designer proteins and in studies of protein-protein interactions.
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13
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Abstract
The coupling of light-inducible protein-protein interactions with gene regulation systems has enabled the control of gene expression with light. In particular, heterodimer protein pairs from plants can be used to engineer a gene regulation system in mammalian cells that is reversible, repeatable, tunable, controllable in a spatiotemporal manner, and targetable to any DNA sequence. This system, Light-Inducible Transcription using Engineered Zinc finger proteins (LITEZ), is based on the blue light-induced interaction of GIGANTEA and the LOV domain of FKF1 that drives the localization of a transcriptional activator to the DNA-binding site of a highly customizable engineered zinc finger protein. This chapter provides methods for modifying LITEZ to target new DNA sequences, engineering a programmable LED array to illuminate cell cultures, and using the modified LITEZ system to achieve spatiotemporal control of transgene expression in mammalian cells.
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Affiliation(s)
- Lauren R Polstein
- Department of Biomedical Engineering, Duke University, Room 136 Hudson Hall, 90281, Durham, NC, 27708-0281, USA
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14
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The CRISPR/Cas9 System Facilitates Clearance of the Intrahepatic HBV Templates In Vivo. MOLECULAR THERAPY. NUCLEIC ACIDS 2014; 3:e186. [PMID: 25137139 PMCID: PMC4221598 DOI: 10.1038/mtna.2014.38] [Citation(s) in RCA: 290] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 06/30/2014] [Indexed: 02/07/2023]
Abstract
Persistence of hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) under current antiviral therapy is a major barrier to eradication of chronic hepatitis B (CHB). Curing CHB will require novel strategies for specific disruption of cccDNA. The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system is a newly developed tool for site-specific cleavage of DNA targets directed by a synthetic guide RNA (gRNA) base-paired to the target DNA sequence. To examine whether this system can cleave HBV genomes, we designed eight gRNAs against HBV of genotype A. With the HBV-specific gRNAs, the CRISPR/Cas9 system significantly reduced the production of HBV core and surface proteins in Huh-7 cells transfected with an HBV-expression vector. Among eight screened gRNAs, two effective ones were identified. Interestingly, one gRNA targeting the conserved HBV sequence acted against different genotypes. Using a hydrodynamics-HBV persistence mouse model, we further demonstrated that this system could cleave the intrahepatic HBV genome-containing plasmid and facilitate its clearance in vivo, resulting in reduction of serum surface antigen levels. These data suggest that the CRISPR/Cas9 system could disrupt the HBV-expressing templates both in vitro and in vivo, indicating its potential in eradicating persistent HBV infection.
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Lin SR, Yang HC, Kuo YT, Liu CJ, Yang TY, Sung KC, Lin YY, Wang HY, Wang CC, Shen YC, Wu FY, Kao JH, Chen DS, Chen PJ. The CRISPR/Cas9 System Facilitates Clearance of the Intrahepatic HBV Templates In Vivo. MOLECULAR THERAPY-NUCLEIC ACIDS 2014. [PMID: 25137139 DOI: 10.1038/mtna.2014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Persistence of hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) under current antiviral therapy is a major barrier to eradication of chronic hepatitis B (CHB). Curing CHB will require novel strategies for specific disruption of cccDNA. The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system is a newly developed tool for site-specific cleavage of DNA targets directed by a synthetic guide RNA (gRNA) base-paired to the target DNA sequence. To examine whether this system can cleave HBV genomes, we designed eight gRNAs against HBV of genotype A. With the HBV-specific gRNAs, the CRISPR/Cas9 system significantly reduced the production of HBV core and surface proteins in Huh-7 cells transfected with an HBV-expression vector. Among eight screened gRNAs, two effective ones were identified. Interestingly, one gRNA targeting the conserved HBV sequence acted against different genotypes. Using a hydrodynamics-HBV persistence mouse model, we further demonstrated that this system could cleave the intrahepatic HBV genome-containing plasmid and facilitate its clearance in vivo, resulting in reduction of serum surface antigen levels. These data suggest that the CRISPR/Cas9 system could disrupt the HBV-expressing templates both in vitro and in vivo, indicating its potential in eradicating persistent HBV infection.
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Affiliation(s)
- Su-Ru Lin
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Hung-Chih Yang
- 1] Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan [2] Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan [3] Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Ting Kuo
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chun-Jen Liu
- 1] Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan [2] Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan [3] Hepatitis Research Center, National Taiwan University Hospital, Taipei, Taiwan
| | - Ta-Yu Yang
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ku-Chun Sung
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - You-Yu Lin
- 1] Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan [2] Department of Life Science, National Taiwan University College of Life Science, Taipei, Taiwan
| | - Hurng-Yi Wang
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chih-Chiang Wang
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yueh-Chi Shen
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Fang-Yi Wu
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Jia-Horng Kao
- 1] Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan [2] Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan [3] Hepatitis Research Center, National Taiwan University Hospital, Taipei, Taiwan [4] Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Ding-Shinn Chen
- 1] Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan [2] Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan [3] Hepatitis Research Center, National Taiwan University Hospital, Taipei, Taiwan [4] Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Pei-Jer Chen
- 1] Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan [2] Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan [3] Hepatitis Research Center, National Taiwan University Hospital, Taipei, Taiwan [4] Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
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16
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Kabadi AM, Gersbach CA. Engineering synthetic TALE and CRISPR/Cas9 transcription factors for regulating gene expression. Methods 2014; 69:188-97. [PMID: 25010559 DOI: 10.1016/j.ymeth.2014.06.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 06/26/2014] [Accepted: 06/27/2014] [Indexed: 12/22/2022] Open
Abstract
Engineered DNA-binding proteins that can be targeted to specific sites in the genome to manipulate gene expression have enabled many advances in biomedical research. This includes generating tools to study fundamental aspects of gene regulation and the development of a new class of gene therapies that alter the expression of endogenous genes. Designed transcription factors have entered clinical trials for the treatment of human diseases and others are in preclinical development. High-throughput and user-friendly platforms for designing synthetic DNA-binding proteins present innovative methods for deciphering cell biology and designing custom synthetic gene circuits. We review two platforms for designing synthetic transcription factors for manipulating gene expression: Transcription activator-like effectors (TALEs) and the RNA-guided clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system. We present an overview of each technology and a guide for designing and assembling custom TALE- and CRISPR/Cas9-based transcription factors. We also discuss characteristics of each platform that are best suited for different applications.
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Affiliation(s)
- Ami M Kabadi
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, United States
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, United States; Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, United States; Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC 27710, United States.
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The functional significance of common polymorphisms in zinc finger transcription factors. G3-GENES GENOMES GENETICS 2014; 4:1647-55. [PMID: 24970883 PMCID: PMC4169156 DOI: 10.1534/g3.114.012195] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Variants that alter the DNA-binding specificity of transcription factors could affect the specificity for and expression of potentially many target genes, as has been observed in several tumor-derived mutations. Here we examined if such trans expression quantitative trait loci (trans-eQTLs) could similarly result from common genetic variants. We chose to focus on the Cys2-His2 class of zinc finger transcription factors because they are the most abundant superfamily of transcription factors in human and have well-characterized DNA binding interactions. We identified 430 SNPs that cause missense substitutions in the DNA-contacting residues. Fewer common missense SNPs were found at DNA-contacting residues compared with non-DNA-contacting residues (P = 0.00006), consistent with possible functional selection against SNPs at DNA-contacting positions. Functional predictions based on zinc finger transcription factor (ZNF) DNA binding preferences also suggested that many common substitutions could potentially alter binding specificity. However, Hardy-Weinberg Equilibrium analysis and examination of seven orthologs within the primate lineage failed to find evidence of trans-eQTLs associated with the DNA-contacting positions or evidence of a different selection pressure on a contemporary and evolutionary timescales. The overall conclusion was that common SNPs that alter the DNA-contacting residues of these factors are unlikely to produce strong trans-eQTLs, consistent with the observations by others that trans-eQTLs in humans tend to be few and weak. Some rare SNPs might alter specificity and remained rare due to purifying selection. The study also underscores the need for large-scale eQTLs mapping efforts that might provide experimental evidence for SNPs that alter the choice of transcription factor binding sites.
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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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19
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Abstract
Current technology enables the production of highly specific genome modifications with excellent efficiency and specificity. Key to this capability are targetable DNA cleavage reagents and cellular DNA repair pathways. The break made by these reagents can produce localized sequence changes through inaccurate nonhomologous end joining (NHEJ), often leading to gene inactivation. Alternatively, user-provided DNA can be used as a template for repair by homologous recombination (HR), leading to the introduction of desired sequence changes. This review describes three classes of targetable cleavage reagents: zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR/Cas RNA-guided nucleases (RGNs). As a group, these reagents have been successfully used to modify genomic sequences in a wide variety of cells and organisms, including humans. This review discusses the properties, advantages, and limitations of each system, as well as the specific considerations required for their use in different biological systems.
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Affiliation(s)
- Dana Carroll
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112;
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20
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Persikov AV, Rowland EF, Oakes BL, Singh M, Noyes MB. Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets. Nucleic Acids Res 2013; 42:1497-508. [PMID: 24214968 PMCID: PMC3919609 DOI: 10.1093/nar/gkt1034] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Cys2His2 zinc finger (ZF) is the most frequently found sequence-specific DNA-binding domain in eukaryotic proteins. The ZF's modular protein-DNA interface has also served as a platform for genome engineering applications. Despite decades of intense study, a predictive understanding of the DNA-binding specificities of either natural or engineered ZF domains remains elusive. To help fill this gap, we developed an integrated experimental-computational approach to enrich and recover distinct groups of ZFs that bind common targets. To showcase the power of our approach, we built several large ZF libraries and demonstrated their excellent diversity. As proof of principle, we used one of these ZF libraries to select and recover thousands of ZFs that bind several 3-nt targets of interest. We were then able to computationally cluster these recovered ZFs to reveal several distinct classes of proteins, all recovered from a single selection, to bind the same target. Finally, for each target studied, we confirmed that one or more representative ZFs yield the desired specificity. In sum, the described approach enables comprehensive large-scale selection and characterization of ZF specificities and should be a great aid in furthering our understanding of the ZF domain.
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Affiliation(s)
- Anton V Persikov
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Department of Computer Science, Princeton University, Princeton, NJ 08544, USA and Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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21
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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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22
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Wang L, Lin J, Zhang T, Xu K, Ren C, Zhang Z. Simultaneous screening and validation of effective zinc finger nucleases in yeast. PLoS One 2013; 8:e64687. [PMID: 23741369 PMCID: PMC3669427 DOI: 10.1371/journal.pone.0064687] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Accepted: 04/17/2013] [Indexed: 01/29/2023] Open
Abstract
Zinc finger nucleases (ZFNs) have been successfully used for genome modification in various cell types and species. However, construction of an effective ZFN remained challenging. Previous studies all focused on obtaining specific zinc finger proteins (ZFPs) first via bacterial 2-hybrid approach, and then fusing selected ZFPs to FokI nuclease domain. These assembled ZFNs have high rate of failing to cleave target sites in vivo. In this study, we developed a simultaneous screening and validation system to obtain effective ZFNs directly in yeast AH109. This system is based on Gal4 reporter system carrying a unique intermediate reporter plasmid with two 30-bp Gal4 homology arms and a ZFN target site. DNA double strand breaks introduced on target sequence by ZFNs were repaired by single strand annealing (SSA) mechanism, and the restored Gal4 drove reporter genes expression. Taking the advantage of OPEN (Oligomerized Pool ENgineering) selection, we constructed 3 randomized ZFNs libraries and 9 reporter strains for each target gene. We tested this system by taking goat α s1-casein as target gene following three-step selection. Consequently, 3 efficient pairs of ZFNs were obtained from positive colonies on selective medium. The ZFNs achieved a 15.9% disruption frequency in goat mammary epithelial cells. In conclusion, we created a novel system to obtain effective ZFNs directly with simultaneous screening and validation.
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Affiliation(s)
- Ling Wang
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China
| | - Juan Lin
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China
| | - Tingting Zhang
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China
| | - Kun Xu
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China
| | - Chonghua Ren
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China
| | - Zhiying Zhang
- College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi, China
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23
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Abstract
The specificity of protein-DNA interactions is most commonly modeled using position weight matrices (PWMs). First introduced in 1982, they have been adapted to many new types of data and many different approaches have been developed to determine the parameters of the PWM. New high-throughput technologies provide a large amount of data rapidly and offer an unprecedented opportunity to determine accurately the specificities of many transcription factors (TFs). But taking full advantage of the new data requires advanced algorithms that take into account the biophysical processes involved in generating the data. The new large datasets can also aid in determining when the PWM model is inadequate and must be extended to provide accurate predictions of binding sites. This article provides a general mathematical description of a PWM and how it is used to score potential binding sites, a brief history of the approaches that have been developed and the types of data that are used with an emphasis on algorithms that we have developed for analyzing high-throughput datasets from several new technologies. It also describes extensions that can be added when the simple PWM model is inadequate and further enhancements that may be necessary. It briefly describes some applications of PWMs in the discovery and modeling of in vivo regulatory networks.
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24
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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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