51
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Baker EG, Bartlett GJ, Porter Goff KL, Woolfson DN. Miniprotein Design: Past, Present, and Prospects. Acc Chem Res 2017; 50:2085-2092. [PMID: 28832117 DOI: 10.1021/acs.accounts.7b00186] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The design and study of miniproteins, that is, polypeptide chains <40 amino acids in length that adopt defined and stable 3D structures, is resurgent. Miniproteins offer possibilities for reducing the complexity of larger proteins and so present new routes to studying sequence-to-structure and sequence-to-stability relationships in proteins generally. They also provide modules for protein design by pieces and, with this, prospects for building more-complex or even entirely new protein structures. In addition, miniproteins are useful scaffolds for templating functional domains, for example, those involved in protein-protein interactions, catalysis, and biomolecular binding, leading to potential applications in biotechnology and medicine. Here we select examples from almost four decades of miniprotein design, development, and dissection. Simply because of the word limit for this Account, we focus on miniproteins that are cooperatively folded monomers in solution and not stabilized by cross-linking or metal binding. In these cases, the optimization of noncovalent interactions is even more critical for the maintenance of the folded states than in larger proteins. Our chronology and catalogue highlights themes in miniproteins, which we explore further and begin to put on a firmer footing through an analysis of the miniprotein structures that have been deposited in the Protein Data Bank (PDB) thus far. Specifically, and compared with larger proteins, miniproteins generally have a lower proportion of residues in regular secondary structure elements (α helices, β strands, and polyproline-II helices) and, concomitantly, more residues in well-structured loops. This allows distortions of the backbone enabling mini-hydrophobic cores to be made. This also contrasts with larger proteins, which can achieve hydrophobic cores through tertiary contacts between distant regions of sequence. On average, miniproteins have a higher proportion of aromatic residues than larger proteins, and specifically electron-rich Trp and Tyr, which are often found in combination with Pro and Arg to render networks of CH-π or cation-π interactions. Miniproteins also have a higher proportion of the long-chain charged amino acids (Arg, Glu, and Lys), which presumably reflects salt-bridge formation and their greater surface area-to-volume ratio. Together, these amino-acid preferences appear to support greater densities of noncovalent interactions in miniproteins compared with larger proteins. We anticipate that with recent developments such as parametric protein design, it will become increasingly routine to use computation to generate and evaluate models for miniproteins in silico ahead of experimental studies. This could include accessing new structures comprising secondary structure elements linked in previously unseen configurations. The improved understanding of the noncovalent interactions that stabilize the folded states of such miniproteins that we are witnessing through both in-depth bioinformatics analyses and experimental testing will feed these computational protein designs. With this in mind, we can expect a new and exciting era for miniprotein design, study, and application.
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Affiliation(s)
- Emily G. Baker
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Gail J. Bartlett
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | | | - Derek N. Woolfson
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
- School
of Biochemistry, University of Bristol, Biomedical Sciences Building, University
Walk, Bristol BS8 1TD, U.K
- BrisSynBio
and the Bristol BioDesign Institute, University of Bristol, Life Sciences
Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
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52
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Kim MS, Kini AG. Engineering and Application of Zinc Finger Proteins and TALEs for Biomedical Research. Mol Cells 2017; 40:533-541. [PMID: 28835021 PMCID: PMC5582299 DOI: 10.14348/molcells.2017.0139] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 08/10/2017] [Accepted: 08/11/2017] [Indexed: 12/13/2022] Open
Abstract
Engineered DNA-binding domains provide a powerful technology for numerous biomedical studies due to their ability to recognize specific DNA sequences. Zinc fingers (ZF) are one of the most common DNA-binding domains and have been extensively studied for a variety of applications, such as gene regulation, genome engineering and diagnostics. Another novel DNA-binding domain known as a transcriptional activator-like effector (TALE) has been more recently discovered, which has a previously undescribed DNA-binding mode. Due to their modular architecture and flexibility, TALEs have been rapidly developed into artificial gene targeting reagents. Here, we describe the methods used to design these DNA-binding proteins and their key applications in biomedical research.
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Affiliation(s)
- Moon-Soo Kim
- Department of Chemistry, Western Kentucky University, 1906 College Heights Blvd., Bowling Green, KY 42101,
USA
| | - Anu Ganesh Kini
- Department of Chemistry, Western Kentucky University, 1906 College Heights Blvd., Bowling Green, KY 42101,
USA
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53
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George KL, Horne WS. Heterogeneous-Backbone Foldamer Mimics of Zinc Finger Tertiary Structure. J Am Chem Soc 2017; 139:7931-7938. [PMID: 28509549 DOI: 10.1021/jacs.7b03114] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A variety of oligomeric backbones with compositions deviating from biomacromolecules can fold in defined ways. Termed "foldamers," these agents have diverse potential applications. A number of protein-inspired secondary structures (e.g., helices, sheets) have been produced from unnatural backbones, yet examples of tertiary folds combining several secondary structural elements in a single entity are rare. One promising strategy to address this challenge is the systematic backbone alteration of natural protein sequences, through which a subset of the native side chains is displayed on an unnatural building block to generate a heterogeneous backbone. A drawback to this approach is that substitution at more than one or two sites often comes at a significant energetic cost to fold stability. Here we report heterogeneous-backbone foldamers that mimic the zinc finger domain, a ubiquitous and biologically important metal-binding tertiary motif, and do so with a folded stability that is superior to the natural protein on which their design is based. A combination of UV-vis spectroscopy, isothermal titration calorimetry, and multidimensional NMR reveals that suitably designed oligomers with >20% modified backbones can form native-like tertiary folds with metal-binding environments identical to the prototype sequence (the third finger of specificity factor 1) and enhanced thermodynamic stability. These results expand the scope of heterogeneous-backbone foldamer design to a new tertiary structure class and show that judiciously applied backbone modification can be accompanied by improvement to fold stability.
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Affiliation(s)
- Kelly L George
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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54
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Genomic targeting of epigenetic probes using a chemically tailored Cas9 system. Proc Natl Acad Sci U S A 2017; 114:681-686. [PMID: 28069948 DOI: 10.1073/pnas.1615723114] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent advances in the field of programmable DNA-binding proteins have led to the development of facile methods for genomic localization of genetically encodable entities. Despite the extensive utility of these tools, locus-specific delivery of synthetic molecules remains limited by a lack of adequate technologies. Here we combine the flexibility of chemical synthesis with the specificity of a programmable DNA-binding protein by using protein trans-splicing to ligate synthetic elements to a nuclease-deficient Cas9 (dCas9) in vitro and subsequently deliver the dCas9 cargo to live cells. The versatility of this technology is demonstrated by delivering dCas9 fusions that include either the small-molecule bromodomain and extra-terminal family bromodomain inhibitor JQ1 or a peptide-based PRC1 chromodomain ligand, which are capable of recruiting endogenous copies of their cognate binding partners to targeted genomic binding sites. We expect that this technology will allow for the genomic localization of a wide array of small molecules and modified proteinaceous materials.
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55
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Lv YH, Li XQ, Yue CW, Wang M. Application of genome editing technologies in gastrointestinal cancers. Shijie Huaren Xiaohua Zazhi 2016; 24:4772-4780. [DOI: 10.11569/wcjd.v24.i36.4772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Genome editing is a site-directed modification technology for gene targeting and a powerful tool to edit the target DNA by site-specific DNA knockout or knockin. Genome editing has achieved a considerable success from lower microbes to human in the past years and may play a very important role in tumor staging, precision medicine as well as prognosis evaluation in gastrointestinal cancers. This review discusses the mechanisms of different genome-editing strategies and describes each of the common nuclease-based platforms, including transcription activator-like effector nucleases, zinc finger nucleases and the CRISPR/Cas9 system. We also summarize the progress made in applying genome editing to the research of gastrointestinal cancers.
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56
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Liu J, Shui SL. Delivery methods for site-specific nucleases: Achieving the full potential of therapeutic gene editing. J Control Release 2016; 244:83-97. [DOI: 10.1016/j.jconrel.2016.11.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 10/30/2016] [Accepted: 11/07/2016] [Indexed: 12/20/2022]
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57
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Hossain MA, Shen Y, Knudson I, Thakur S, Stees JR, Qiu Y, Pace BS, Peterson KR, Bungert J. Activation of Fetal γ-globin Gene Expression via Direct Protein Delivery of Synthetic Zinc-finger DNA-Binding Domains. MOLECULAR THERAPY-NUCLEIC ACIDS 2016; 5:e378. [PMID: 27754490 DOI: 10.1038/mtna.2016.85] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 08/29/2016] [Indexed: 12/20/2022]
Abstract
Reactivation of γ-globin expression has been shown to ameliorate disease phenotypes associated with mutations in the adult β-globin gene, including sickle cell disease. Specific mutations in the promoter of the γ-globin genes are known to prevent repression of the genes in the adult and thus lead to hereditary persistence of fetal hemoglobin. One such hereditary persistence of fetal hemoglobin is associated with a sequence located 567 bp upstream of the Gγ-globin gene which assembles a GATA-containing repressor complex. We generated two synthetic zinc-finger DNA-binding domains (ZF-DBDs) targeting this sequence. The -567Gγ ZF-DBDs associated with high affinity and specificity with the target site in the γ-globin gene promoter. We delivered the -567Gγ ZF-DBDs directly to primary erythroid cells. Exposure of these cells to the recombinant -567Gγ ZF-DBDs led to increased expression of the γ-globin gene. Direct protein delivery of ZF-DBDs that compete with transcription regulatory proteins will have broad implications for modulating gene expression in analytical or therapeutic settings.
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Affiliation(s)
- Mir A Hossain
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Yong Shen
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Isaac Knudson
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Shaleen Thakur
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Jared R Stees
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Yi Qiu
- Department of Anatomy and Cell Biology, College of Medicine, UF Health Cancer Center, Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Betty S Pace
- Department of Pediatrics, Augusta University, Augusta, Georgia, USA
| | - Kenneth R Peterson
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Jörg Bungert
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
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Abstract
Genome targeting has quickly developed as one of the most promising fields in science. By using programmable DNA-binding platforms and nucleases, scientists are now able to accurately edit the genome. These DNA-binding tools have recently also been applied to engineer the epigenome for gene expression modulation. Such epigenetic editing constructs have firmly demonstrated the causal role of epigenetics in instructing gene expression. Another focus of epigenome engineering is to understand the order of events of chromatin remodeling in gene expression regulation. Groundbreaking approaches in this field are beginning to yield novel insights into the function of individual chromatin marks in the context of maintaining cellular phenotype and regulating transient gene expression changes. This review focuses on recent advances in the field of epigenetic editing and highlights its promise for sustained gene expression reprogramming.
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59
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Robinson-Hamm JN, Gersbach CA. Gene therapies that restore dystrophin expression for the treatment of Duchenne muscular dystrophy. Hum Genet 2016; 135:1029-40. [PMID: 27542949 PMCID: PMC5006996 DOI: 10.1007/s00439-016-1725-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 08/08/2016] [Indexed: 12/18/2022]
Abstract
Duchenne muscular dystrophy is one of the most common inherited genetic diseases and is caused by mutations to the DMD gene that encodes the dystrophin protein. Recent advances in genome editing and gene therapy offer hope for the development of potential therapeutics. Truncated versions of the DMD gene can be delivered to the affected tissues with viral vectors and show promising results in a variety of animal models. Genome editing with the CRISPR/Cas9 system has recently been used to restore dystrophin expression by deleting one or more exons of the DMD gene in patient cells and in a mouse model that led to functional improvement of muscle strength. Exon skipping with oligonucleotides has been successful in several animal models and evaluated in multiple clinical trials. Next-generation oligonucleotide formulations offer significant promise to build on these results. All these approaches to restoring dystrophin expression are encouraging, but many hurdles remain. This review summarizes the current state of these technologies and summarizes considerations for their future development.
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Affiliation(s)
- Jacqueline N Robinson-Hamm
- Department of Biomedical Engineering, Duke University, Room 1427, Fitzpatrick CIEMAS, 101 Science Drive, Box 90281, Durham, NC, 27708-0281, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Room 1427, Fitzpatrick CIEMAS, 101 Science Drive, Box 90281, Durham, NC, 27708-0281, USA.
- Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA.
- Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC, 27710, USA.
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60
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Hossain MA, Barrow JJ, Shen Y, Haq MI, Bungert J. Artificial zinc finger DNA binding domains: versatile tools for genome engineering and modulation of gene expression. J Cell Biochem 2016; 116:2435-44. [PMID: 25989233 DOI: 10.1002/jcb.25226] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 05/11/2015] [Indexed: 02/01/2023]
Abstract
Genome editing and alteration of gene expression by synthetic DNA binding activities gained a lot of momentum over the last decade. This is due to the development of new DNA binding molecules with enhanced binding specificity. The most commonly used DNA binding modules are zinc fingers (ZFs), TALE-domains, and the RNA component of the CRISPR/Cas9 system. These binding modules are fused or linked to either nucleases that cut the DNA and induce DNA repair processes, or to protein domains that activate or repress transcription of genes close to the targeted site in the genome. This review focuses on the structure, design, and applications of ZF DNA binding domains (ZFDBDs). ZFDBDs are relatively small and have been shown to penetrate the cell membrane without additional tags suggesting that they could be delivered to cells without a DNA or RNA intermediate. Advanced algorithms that are based on extensive knowledge of the mode of ZF/DNA interactions are used to design the amino acid composition of ZFDBDs so that they bind to unique sites in the genome. Off-target binding has been a concern for all synthetic DNA binding molecules. Thus, increasing the specificity and affinity of ZFDBDs will have a significant impact on their use in analytical or therapeutic settings.
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Affiliation(s)
- Mir A Hossain
- Department of Biochemistry and Molecular Biology, College of Medicine, Cancer Center, Genetics Institute, University of Florida, Gainesville, Florida, 32610
| | - Joeva J Barrow
- Department of Biochemistry and Molecular Biology, College of Medicine, Cancer Center, Genetics Institute, University of Florida, Gainesville, Florida, 32610
| | - Yong Shen
- Department of Biochemistry and Molecular Biology, College of Medicine, Cancer Center, Genetics Institute, University of Florida, Gainesville, Florida, 32610
| | - Md Imdadul Haq
- Department of Biochemistry and Molecular Biology, College of Medicine, Cancer Center, Genetics Institute, University of Florida, Gainesville, Florida, 32610
| | - Jörg Bungert
- Department of Biochemistry and Molecular Biology, College of Medicine, Cancer Center, Genetics Institute, University of Florida, Gainesville, Florida, 32610
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61
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Editing the epigenome: technologies for programmable transcription and epigenetic modulation. Nat Methods 2016; 13:127-37. [PMID: 26820547 DOI: 10.1038/nmeth.3733] [Citation(s) in RCA: 284] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 12/16/2015] [Indexed: 02/08/2023]
Abstract
Gene regulation is a complex and tightly controlled process that defines cell identity, health and disease, and response to pharmacologic and environmental signals. Recently developed DNA-targeting platforms, including zinc finger proteins, transcription activator-like effectors (TALEs) and the clustered, regularly interspaced, short palindromic repeats (CRISPR)-Cas9 system, have enabled the recruitment of transcriptional modulators and epigenome-modifying factors to any genomic site, leading to new insights into the function of epigenetic marks in gene expression. Additionally, custom transcriptional and epigenetic regulation is facilitating refined control over cell function and decision making. The unique properties of the CRISPR-Cas9 system have created new opportunities for high-throughput genetic screens and multiplexing targets to manipulate complex gene expression patterns. This Review summarizes recent technological developments in this area and their application to biomedical challenges. We also discuss remaining limitations and necessary future directions for this field.
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62
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Abstract
The field of genome engineering has created new possibilities for gene therapy, including improved animal models of disease, engineered cell therapies, and in vivo gene repair. The most significant challenge for the clinical translation of genome engineering is the development of safe and effective delivery vehicles. A large body of work has applied genome engineering to genetic modification in vitro, and clinical trials have begun using cells modified by genome editing. Now, promising preclinical work is beginning to apply these tools in vivo. This article summarizes the development of genome engineering platforms, including meganucleases, zinc finger nucleases, TALENs, and CRISPR/Cas9, and their flexibility for precise genetic modifications. The prospects for the development of safe and effective viral and nonviral delivery vehicles for genome editing are reviewed, and promising advances in particular therapeutic applications are discussed.
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Affiliation(s)
- Christopher E Nelson
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708
- Center for Genomic & Computational Biology, Duke University, Durham, North Carolina 27708
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708
- Center for Genomic & Computational Biology, Duke University, Durham, North Carolina 27708
- Department of Orthopaedic Surgery, Duke University, Durham, North Carolina 27708;
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63
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Rodríguez J, Mosquera J, García-Fandiño R, Vázquez ME, Mascareñas JL. A designed DNA binding motif that recognizes extended sites and spans two adjacent major grooves. Chem Sci 2016; 7:3298-3303. [PMID: 27252825 PMCID: PMC4885664 DOI: 10.1039/c6sc00045b] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 02/01/2016] [Indexed: 12/28/2022] Open
Abstract
We report the rational design of a DNA-binding peptide construct composed of the DNA-contacting regions of two transcription factors (GCN4 and GAGA) linked through an AT-hook DNA anchor. The resulting chimera, which represents a new, non-natural DNA binding motif, binds with high affinity and selectivity to a long composite sequence of 13 base pairs (TCAT-AATT-GAGAG).
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Affiliation(s)
- Jéssica Rodríguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
15782 Santiago de Compostela
, Spain
.
; Fax: +34 981 595 012
; Tel: +34 981576541-14405
| | - Jesús Mosquera
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
15782 Santiago de Compostela
, Spain
.
; Fax: +34 981 595 012
; Tel: +34 981576541-14405
| | - Rebeca García-Fandiño
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
15782 Santiago de Compostela
, Spain
.
; Fax: +34 981 595 012
; Tel: +34 981576541-14405
| | - M. Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
15782 Santiago de Compostela
, Spain
.
; Fax: +34 981 595 012
; Tel: +34 981576541-14405
| | - José L. Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
15782 Santiago de Compostela
, Spain
.
; Fax: +34 981 595 012
; Tel: +34 981576541-14405
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64
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Kubik G, Summerer D. TALEored Epigenetics: A DNA-Binding Scaffold for Programmable Epigenome Editing and Analysis. Chembiochem 2016; 17:975-80. [DOI: 10.1002/cbic.201600072] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Grzegorz Kubik
- Technische Universität Dortmund; Fakultät für Chemie und Chemische Biologie; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Daniel Summerer
- Technische Universität Dortmund; Fakultät für Chemie und Chemische Biologie; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
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65
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Piatek A, Mahfouz MM. Targeted genome regulation via synthetic programmable transcriptional regulators. Crit Rev Biotechnol 2016; 37:429-440. [DOI: 10.3109/07388551.2016.1165180] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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66
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Perdigão P, Gaj T, Santa-Marta M, Barbas CF, Goncalves J. Reactivation of Latent HIV-1 Expression by Engineered TALE Transcription Factors. PLoS One 2016; 11:e0150037. [PMID: 26933881 PMCID: PMC4774903 DOI: 10.1371/journal.pone.0150037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/08/2016] [Indexed: 11/22/2022] Open
Abstract
The presence of replication-competent HIV-1 -which resides mainly in resting CD4+ T cells--is a major hurdle to its eradication. While pharmacological approaches have been useful for inducing the expression of this latent population of virus, they have been unable to purge HIV-1 from all its reservoirs. Additionally, many of these strategies have been associated with adverse effects, underscoring the need for alternative approaches capable of reactivating viral expression. Here we show that engineered transcriptional modulators based on customizable transcription activator-like effector (TALE) proteins can induce gene expression from the HIV-1 long terminal repeat promoter, and that combinations of TALE transcription factors can synergistically reactivate latent viral expression in cell line models of HIV-1 latency. We further show that complementing TALE transcription factors with Vorinostat, a histone deacetylase inhibitor, enhances HIV-1 expression in latency models. Collectively, these findings demonstrate that TALE transcription factors are a potentially effective alternative to current pharmacological routes for reactivating latent virus and that combining synthetic transcriptional activators with histone deacetylase inhibitors could lead to the development of improved therapies for latent HIV-1 infection.
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Affiliation(s)
- Pedro Perdigão
- Research Institute for Medicines (iMed ULisboa), Faculdadede Farmácia, Universidade de Lisboa, Lisboa, Portugal
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Departments of Chemistry, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Thomas Gaj
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Departments of Chemistry, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Mariana Santa-Marta
- Research Institute for Medicines (iMed ULisboa), Faculdadede Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Carlos F. Barbas
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Departments of Chemistry, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Joao Goncalves
- Research Institute for Medicines (iMed ULisboa), Faculdadede Farmácia, Universidade de Lisboa, Lisboa, Portugal
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67
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Limsirichai P, Gaj T, Schaffer DV. CRISPR-mediated Activation of Latent HIV-1 Expression. Mol Ther 2016; 24:499-507. [PMID: 26607397 PMCID: PMC4786916 DOI: 10.1038/mt.2015.213] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 11/20/2015] [Indexed: 01/02/2023] Open
Abstract
Complete eradication of HIV-1 infection is impeded by the existence of cells that harbor chromosomally integrated but transcriptionally inactive provirus. These cells can persist for years without producing viral progeny, rendering them refractory to immune surveillance and antiretroviral therapy and providing a permanent reservoir for the stochastic reactivation and reseeding of HIV-1. Strategies for purging this latent reservoir are thus needed to eradicate infection. Here, we show that engineered transcriptional activation systems based on CRISPR/Cas9 can be harnessed to activate viral gene expression in cell line models of HIV-1 latency. We further demonstrate that complementing Cas9 activators with latency-reversing compounds can enhance latent HIV-1 transcription and that epigenome modulation using CRISPR-based acetyltransferases can also promote viral gene activation. Collectively, these results demonstrate that CRISPR systems are potentially effective tools for inducing latent HIV-1 expression and that their use, in combination with antiretroviral therapy, could lead to improved therapies for HIV-1 infection.
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Affiliation(s)
- Prajit Limsirichai
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Thomas Gaj
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California, USA
| | - David V Schaffer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA
- Department of Cell and Molecular Biology, University of California, Berkeley, Berkeley, California, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, California, USA
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Hsia J, Holtz WJ, Maharbiz MM, Arcak M, Keasling JD. Modular Synthetic Inverters from Zinc Finger Proteins and Small RNAs. PLoS One 2016; 11:e0149483. [PMID: 26886888 PMCID: PMC4757538 DOI: 10.1371/journal.pone.0149483] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 01/31/2016] [Indexed: 12/18/2022] Open
Abstract
Synthetic zinc finger proteins (ZFPs) can be created to target promoter DNA sequences, repressing transcription. The binding of small RNA (sRNA) to ZFP mRNA creates an ultrasensitive response to generate higher effective Hill coefficients. Here we combined three “off the shelf” ZFPs and three sRNAs to create new modular inverters in E. coli and quantify their behavior using induction fold. We found a general ordering of the effects of the ZFPs and sRNAs on induction fold that mostly held true when combining these parts. We then attempted to construct a ring oscillator using our new inverters. Our chosen parts performed insufficiently to create oscillations, but we include future directions for improvement upon our work presented here.
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Affiliation(s)
- Justin Hsia
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, United States of America
- * E-mail:
| | - William J. Holtz
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, United States of America
- Joint BioEnergy Institute, Emeryville, California, United States of America
| | - Michel M. Maharbiz
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, United States of America
| | - Murat Arcak
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, United States of America
| | - Jay D. Keasling
- Joint BioEnergy Institute, Emeryville, California, United States of America
- Department of Bioengineering, University of California, Berkeley, California, United States of America
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, United States of America
- Biological Systems & Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
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69
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Maeder ML, Gersbach CA. Genome-editing Technologies for Gene and Cell Therapy. Mol Ther 2016; 24:430-46. [PMID: 26755333 PMCID: PMC4786923 DOI: 10.1038/mt.2016.10] [Citation(s) in RCA: 410] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 01/07/2016] [Indexed: 12/11/2022] Open
Abstract
Gene therapy has historically been defined as the addition of new genes to human cells. However, the recent advent of genome-editing technologies has enabled a new paradigm in which the sequence of the human genome can be precisely manipulated to achieve a therapeutic effect. This includes the correction of mutations that cause disease, the addition of therapeutic genes to specific sites in the genome, and the removal of deleterious genes or genome sequences. This review presents the mechanisms of different genome-editing strategies and describes each of the common nuclease-based platforms, including zinc finger nucleases, transcription activator-like effector nucleases (TALENs), meganucleases, and the CRISPR/Cas9 system. We then summarize the progress made in applying genome editing to various areas of gene and cell therapy, including antiviral strategies, immunotherapies, and the treatment of monogenic hereditary disorders. The current challenges and future prospects for genome editing as a transformative technology for gene and cell therapy are also discussed.
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Affiliation(s)
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA.,Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina, USA
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70
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Abstract
The development of a facile genome engineering technology based on transcription activator-like effector nucleases (TALENs) has led to significant advances in diverse areas of science and medicine. In this review, we provide a broad overview of the development of TALENs and the use of this technology in basic science, biotechnology, and biomedical applications. This includes the discovery of DNA recognition by TALEs, engineering new TALE proteins to diverse targets, general advances in nuclease-based editing strategies, and challenges that are specific to various applications of the TALEN technology. We review examples of applying TALENs for studying gene function and regulation, generating disease models, and developing gene therapies. The current status of genome editing and future directions for other uses of these technologies are also discussed.
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Affiliation(s)
- David G Ousterout
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Room 136 Hudson Hall, Box 90281, Durham, NC, 27708-0281, USA. .,Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA. .,Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC, 27710, USA.
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71
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Thakore PI, Gersbach CA. Design, Assembly, and Characterization of TALE-Based Transcriptional Activators and Repressors. Methods Mol Biol 2016; 1338:71-88. [PMID: 26443215 DOI: 10.1007/978-1-4939-2932-0_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Transcription activator-like effectors (TALEs) are modular DNA-binding proteins that can be fused to a variety of effector domains to regulate the epigenome. Nucleotide recognition by TALE monomers follows a simple cipher, making this a powerful and versatile method to activate or repress gene expression. Described here are methods to design, assemble, and test TALE transcription factors (TALE-TFs) for control of endogenous gene expression. In this protocol, TALE arrays are constructed by Golden Gate cloning and tested for activity by transfection and quantitative RT-PCR. These methods for engineering TALE-TFs are useful for studies in reverse genetics and genomics, synthetic biology, and gene therapy.
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Affiliation(s)
- Pratiksha I Thakore
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Room 136 Hudson Hall, Box 90281, Durham, NC, 27708-0281, USA. .,Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA. .,Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC, 27710, USA.
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72
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Barrière Y, Courtial A, Chateigner-Boutin AL, Denoue D, Grima-Pettenati J. Breeding maize for silage and biofuel production, an illustration of a step forward with the genome sequence. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:310-329. [PMID: 26566848 DOI: 10.1016/j.plantsci.2015.08.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 08/04/2015] [Accepted: 08/13/2015] [Indexed: 05/21/2023]
Abstract
The knowledge of the gene families mostly impacting cell wall digestibility variations would significantly increase the efficiency of marker-assisted selection when breeding maize and grass varieties with improved silage feeding value and/or with better straw fermentability into alcohol or methane. The maize genome sequence of the B73 inbred line was released at the end of 2009, opening up new avenues to identify the genetic determinants of quantitative traits. Colocalizations between a large set of candidate genes putatively involved in secondary cell wall assembly and QTLs for cell wall digestibility (IVNDFD) were then investigated, considering physical positions of both genes and QTLs. Based on available data from six RIL progenies, 59 QTLs corresponding to 38 non-overlapping positions were matched up with a list of 442 genes distributed all over the genome. Altogether, 176 genes colocalized with IVNDFD QTLs and most often, several candidate genes colocalized at each QTL position. Frequent QTL colocalizations were found firstly with genes encoding ZmMYB and ZmNAC transcription factors, and secondly with genes encoding zinc finger, bHLH, and xylogen regulation factors. In contrast, close colocalizations were less frequent with genes involved in monolignol biosynthesis, and found only with the C4H2, CCoAOMT5, and CCR1 genes. Close colocalizations were also infrequent with genes involved in cell wall feruloylation and cross-linkages. Altogether, investigated colocalizations between candidate genes and cell wall digestibility QTLs suggested a prevalent role of regulation factors over constitutive cell wall genes on digestibility variations.
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Affiliation(s)
- Yves Barrière
- INRA, UR889, Unité de Génétique et d'Amélioration des Plantes Fourragères, 86600 Lusignan, France.
| | - Audrey Courtial
- LRSV, Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Paul Sabatier Toulouse III / CNRS, Auzeville, BP 42617, 31326 Castanet-Tolosan, France; INRA, US1258, Centre National de Ressources Génomiques Végétales, CS 52627, 31326 Castanet-Tolosan, France
| | | | - Dominique Denoue
- INRA, UR889, Unité de Génétique et d'Amélioration des Plantes Fourragères, 86600 Lusignan, France
| | - Jacqueline Grima-Pettenati
- LRSV, Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Paul Sabatier Toulouse III / CNRS, Auzeville, BP 42617, 31326 Castanet-Tolosan, France
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73
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Blackburn MC, Petrova E, Correia BE, Maerkl SJ. Integrating gene synthesis and microfluidic protein analysis for rapid protein engineering. Nucleic Acids Res 2015; 44:e68. [PMID: 26704969 PMCID: PMC4838357 DOI: 10.1093/nar/gkv1497] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 12/09/2015] [Indexed: 11/15/2022] Open
Abstract
The capability to rapidly design proteins with novel functions will have a significant impact on medicine, biotechnology and synthetic biology. Synthetic genes are becoming a commodity, but integrated approaches have yet to be developed that take full advantage of gene synthesis. We developed a solid-phase gene synthesis method based on asymmetric primer extension (APE) and coupled this process directly to high-throughput, on-chip protein expression, purification and characterization (via mechanically induced trapping of molecular interactions, MITOMI). By completely circumventing molecular cloning and cell-based steps, APE-MITOMI reduces the time between protein design and quantitative characterization to 3–4 days. With APE-MITOMI we synthesized and characterized over 400 zinc-finger (ZF) transcription factors (TF), showing that although ZF TFs can be readily engineered to recognize a particular DNA sequence, engineering the precise binding energy landscape remains challenging. We also found that it is possible to engineer ZF–DNA affinity precisely and independently of sequence specificity and that in silico modeling can explain some of the observed affinity differences. APE-MITOMI is a generic approach that should facilitate fundamental studies in protein biophysics, and protein design/engineering.
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Affiliation(s)
- Matthew C Blackburn
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Ekaterina Petrova
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Bruno E Correia
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Sebastian J Maerkl
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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74
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Vijaya Chandra SH, Makhija H, Peter S, Myint Wai CM, Li J, Zhu J, Ren Z, D'Alcontres MS, Siau JW, Chee S, Ghadessy FJ, Dröge P. Conservative site-specific and single-copy transgenesis in human LINE-1 elements. Nucleic Acids Res 2015; 44:e55. [PMID: 26673710 PMCID: PMC4824084 DOI: 10.1093/nar/gkv1345] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 11/17/2015] [Indexed: 12/22/2022] Open
Abstract
Genome engineering of human cells plays an important role in biotechnology and molecular medicine. In particular, insertions of functional multi-transgene cassettes into suitable endogenous sequences will lead to novel applications. Although several tools have been exploited in this context, safety issues such as cytotoxicity, insertional mutagenesis and off-target cleavage together with limitations in cargo size/expression often compromise utility. Phage λ integrase (Int) is a transgenesis tool that mediates conservative site-specific integration of 48 kb DNA into a safe harbor site of the bacterial genome. Here, we show that an Int variant precisely recombines large episomes into a sequence, term edattH4X, found in 1000 human Long INterspersed Elements-1 (LINE-1). We demonstrate single-copy transgenesis through attH4X-targeting in various cell lines including hESCs, with the flexibility of selecting clones according to transgene performance and downstream applications. This is exemplified with pluripotency reporter cassettes and constitutively expressed payloads that remain functional in LINE1-targeted hESCs and differentiated progenies. Furthermore, LINE-1 targeting does not induce DNA damage-response or chromosomal aberrations, and neither global nor localized endogenous gene expression is substantially affected. Hence, this simple transgene addition tool should become particularly useful for applications that require engineering of the human genome with multi-transgenes.
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Affiliation(s)
| | - Harshyaa Makhija
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Sabrina Peter
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Cho Mar Myint Wai
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Jinming Li
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Tonghe GuangZhou 510515, People's Republic of China State Key Laboratory of Organ Failure Research, Division of Nephrology, Nanfang Hospital, Tonghe, Guangzhou 510515, People's Republic of China
| | - Jindong Zhu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Tonghe GuangZhou 510515, People's Republic of China State Key Laboratory of Organ Failure Research, Division of Nephrology, Nanfang Hospital, Tonghe, Guangzhou 510515, People's Republic of China
| | - Zhonglu Ren
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Tonghe GuangZhou 510515, People's Republic of China State Key Laboratory of Organ Failure Research, Division of Nephrology, Nanfang Hospital, Tonghe, Guangzhou 510515, People's Republic of China
| | | | - Jia Wei Siau
- p53Lab, Agency for Science Technology and Research, Singapore 138673
| | - Sharon Chee
- p53Lab, Agency for Science Technology and Research, Singapore 138673
| | | | - Peter Dröge
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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75
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Cress BF, Trantas EA, Ververidis F, Linhardt RJ, Koffas MAG. Sensitive cells: enabling tools for static and dynamic control of microbial metabolic pathways. Curr Opin Biotechnol 2015; 36:205-14. [DOI: 10.1016/j.copbio.2015.09.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/31/2015] [Accepted: 09/17/2015] [Indexed: 12/31/2022]
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76
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Liu J, Gaj T, Yang Y, Wang N, Shui S, Kim S, Kanchiswamy CN, Kim JS, Barbas CF. Efficient delivery of nuclease proteins for genome editing in human stem cells and primary cells. Nat Protoc 2015; 10:1842-59. [DOI: 10.1038/nprot.2015.117] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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77
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Abstract
Advances in genome engineering technologies have made the precise control over genome sequence and regulation possible across a variety of disciplines. These tools can expand our understanding of fundamental biological processes and create new opportunities for therapeutic designs. The rapid evolution of these methods has also catalyzed a new era of genomics that includes multiple approaches to functionally characterize and manipulate the regulation of genomic information. Here, we review the recent advances of the most widely adopted genome engineering platforms and their application to functional genomics. This includes engineered zinc finger proteins, TALEs/TALENs, and the CRISPR/Cas9 system as nucleases for genome editing, transcription factors for epigenome editing, and other emerging applications. We also present current and potential future applications of these tools, as well as their current limitations and areas for future advances.
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Affiliation(s)
- Isaac B Hilton
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA; Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina 27710, USA
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78
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Redesigning Recombinase Specificity for Safe Harbor Sites in the Human Genome. PLoS One 2015; 10:e0139123. [PMID: 26414179 PMCID: PMC4587366 DOI: 10.1371/journal.pone.0139123] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 09/09/2015] [Indexed: 11/19/2022] Open
Abstract
Site-specific recombinases (SSRs) are valuable tools for genetic engineering due to their ability to manipulate DNA in a highly specific manner. Engineered zinc-finger and TAL effector recombinases, in particular, are two classes of SSRs composed of custom-designed DNA-binding domains fused to a catalytic domain derived from the resolvase/invertase family of serine recombinases. While TAL effector and zinc-finger proteins can be assembled to recognize a wide range of possible DNA sequences, recombinase catalytic specificity has been constrained by inherent base requirements present within each enzyme. In order to further expand the targeted recombinase repertoire, we used a genetic screen to isolate enhanced mutants of the Bin and Tn21 recombinases that recognize target sites outside the scope of other engineered recombinases. We determined the specific base requirements for recombination by these enzymes and demonstrate their potential for genome engineering by selecting for variants capable of specifically recombining target sites present in the human CCR5 gene and the AAVS1 safe harbor locus. Taken together, these findings demonstrate that complementing functional characterization with protein engineering is a potentially powerful approach for generating recombinases with expanded targeting capabilities.
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79
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Deng S, Zhang T, Ji X, Wan Y, Xin P, Shan D, Zhang X. Detection of zinc finger protein (EGR1) based on electrogenerated chemiluminescence from singlet oxygen produced in a nanoclay-supported porphyrin environment. Anal Chem 2015; 87:9155-62. [PMID: 26301820 DOI: 10.1021/acs.analchem.5b01318] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Early growth response protein 1 (EGR1), as a characteristic example of zinc finger proteins, acts as a transcription factor in eukaryotic cells, mediating protein-protein interactions. Here, a novel electrochemiluminescence (ECL)-based protocol for EGR1 assay was developed with a new eco-friendly emitter: singlet oxygen produced in the vicinity of nanoclay-supported zinc proto-porphyrin IX (ZnPPIX). Its electrochemical reduction stimulates an intense monochromic CL irradiation at 644 nm from the dissolved oxygen as endogenous coreactant in the aqueous solution. This ECL derivation was rationalized via hyphenated spectroscopy and theoretical calculation. To promote hydrophilicity and solid-state immobilization of porphyrins, the lamellar artificial laponite was employed as a nanocarrier owning to its large specific area without the blackbody effect. The facile exfoliation of laponite produced quality monolayered nanosheets and facilitated the adsorption and flattening of PPIX upon the surface, resulting in a highly efficient ECL emission. Based on the release of Zn(2+) in zinc finger domains of EGR1 upon contact with the ECL-inactive PPIX, which was monitored by circular dichroism and UV-absorption, a sensitive Zn(2+)-selective electrode for the "signal-on" detection of EGR1 was prepared with a detection limit down to 0.48 pg mL(-1) and a linearity over 6 orders of magnitude. The proposed porphyrin-based ECL system thus infused fresh blood into the traditional ECL family, showing great promise in bioassays of structural Zn(II) proteins and zinc finger-binding nucleotides.
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Affiliation(s)
- Shengyuan Deng
- Sino-French Laboratory of Biomaterials and Bioanalytical Chemistry, School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing 210094, P. R. China
| | - Tingting Zhang
- Sino-French Laboratory of Biomaterials and Bioanalytical Chemistry, School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing 210094, P. R. China
| | - Xubo Ji
- Sino-French Laboratory of Biomaterials and Bioanalytical Chemistry, School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing 210094, P. R. China
| | - Ying Wan
- Sino-French Laboratory of Biomaterials and Bioanalytical Chemistry, School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing 210094, P. R. China.,Intelligent Microsystem Technology and Engineering Center, School of Mechanical Engineering, Nanjing University of Science and Technology , Nanjing 210094, P. R. China
| | - Peng Xin
- Sino-French Laboratory of Biomaterials and Bioanalytical Chemistry, School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing 210094, P. R. China
| | - Dan Shan
- Sino-French Laboratory of Biomaterials and Bioanalytical Chemistry, School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing 210094, P. R. China
| | - Xueji Zhang
- Sino-French Laboratory of Biomaterials and Bioanalytical Chemistry, School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing 210094, P. R. China
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80
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Negi S, Yoshioka M, Mima H, Mastumoto M, Suzuki M, Yokoyama M, Kano K, Sugiura Y. Efficient cleavage of DNA oligonucleotides by a non-FokI-type zinc finger nuclease containing one His₄-type finger domain derived from the first finger domain of Sp1. Bioorg Med Chem Lett 2015; 25:4074-7. [PMID: 26316464 DOI: 10.1016/j.bmcl.2015.08.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 08/12/2015] [Accepted: 08/14/2015] [Indexed: 12/28/2022]
Abstract
In this study, we sought to improve the hydrolytic activity of a His4-type single finger domain (f2), which was previously derived from the second finger domain (f2') of the Sp1 zinc finger protein (Sp1wt), which has 3 tandem finger domains (f1', f2', and f3'). To this end, 2 His4-type single finger domains were generated by mutating 2 Cys residues participating in Zn(II) coordination with the His residues in the first (f1') and third finger (f3') domains of Sp1wt. Circular dichroism spectroscopy results showed that the first and second His4-type zinc finger domains (f1 and f2) adopted folded ββα structures in the presence of Zn(II), but that the third His4-type zinc finger domain (f3) did not. Non-FokI-type zinc finger nucleases containing 3 or 4 finger domains were also prepared by combining a His4-type zinc finger domain with the Sp1wt scaffold. We studied their DNA-binding abilities and hydrolytic activities against DNA oligonucleotides by performing gel-mobility-shift assays. The results showed that f1 had higher hydrolytic activity for a DNA oligonucleotide with a GC box (5'-GGG GCG GGG-3'), compared with that of f2, although both His4-type single finger domains had similar DNA-binding affinities. The difference in the hydrolytic activity between f1 and f2 was ascribed not only to the zinc coordinate structure, but also to its folding structure and the stability of finger domain.
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Affiliation(s)
- Shigeru Negi
- Faculty of Pharmaceutical Science, Doshisha Women's University, 97-1 Minamihokotachi, Koudo, Kyotanabe, Kyoto 610-0395, Japan.
| | - Michiko Yoshioka
- Faculty of Pharmaceutical Science, Doshisha Women's University, 97-1 Minamihokotachi, Koudo, Kyotanabe, Kyoto 610-0395, Japan
| | - Hiroko Mima
- Faculty of Pharmaceutical Science, Doshisha Women's University, 97-1 Minamihokotachi, Koudo, Kyotanabe, Kyoto 610-0395, Japan
| | - Makoto Mastumoto
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan
| | - Michiko Suzuki
- Faculty of Pharmaceutical Science, Doshisha Women's University, 97-1 Minamihokotachi, Koudo, Kyotanabe, Kyoto 610-0395, Japan
| | - Mao Yokoyama
- Faculty of Pharmaceutical Science, Doshisha Women's University, 97-1 Minamihokotachi, Koudo, Kyotanabe, Kyoto 610-0395, Japan
| | - Koji Kano
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan
| | - Yukio Sugiura
- Faculty of Pharmaceutical Science, Doshisha Women's University, 97-1 Minamihokotachi, Koudo, Kyotanabe, Kyoto 610-0395, Japan
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81
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Modulation of Estrogen Response Element-Driven Gene Expressions and Cellular Proliferation with Polar Directions by Designer Transcription Regulators. PLoS One 2015; 10:e0136423. [PMID: 26295471 PMCID: PMC4546503 DOI: 10.1371/journal.pone.0136423] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 08/03/2015] [Indexed: 12/27/2022] Open
Abstract
Estrogen receptor α (ERα), as a ligand-dependent transcription factor, mediates 17β-estradiol (E2) effects. ERα is a modular protein containing a DNA binding domain (DBD) and transcription activation domains (AD) located at the amino- and carboxyl-termini. The interaction of the E2-activated ERα dimer with estrogen response elements (EREs) of genes constitutes the initial step in the ERE-dependent signaling pathway necessary for alterations of cellular features. We previously constructed monomeric transcription activators, or monotransactivators, assembled from an engineered ERE-binding module (EBM) using the ERα-DBD and constitutively active ADs from other transcription factors. Monotransactivators modulated cell proliferation by activating and repressing ERE-driven gene expressions that simulate responses observed with E2-ERα. We reasoned here that integration of potent heterologous repression domains (RDs) into EBM could generate monotransrepressors that alter ERE-bearing gene expressions and cellular proliferation in directions opposite to those observed with E2-ERα or monotransactivators. Consistent with this, monotransrepressors suppressed reporter gene expressions that emulate the ERE-dependent signaling pathway. Moreover, a model monotransrepressor regulated DNA synthesis, cell cycle progression and proliferation of recombinant adenovirus infected ER-negative cells through decreasing as well as increasing gene expressions with polar directions compared with E2-ERα or monotransactivator. Our results indicate that an ‘activator’ or a ‘repressor’ possesses both transcription activating/enhancing and repressing/decreasing abilities within a chromatin context. Offering a protein engineering platform to alter signal pathway-specific gene expressions and cell growth, our approach could also be used for the development of tools for epigenetic modifications and for clinical interventions wherein multigenic de-regulations are an issue.
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82
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Besold AN, Michel SLJ. Neural Zinc Finger Factor/Myelin Transcription Factor Proteins: Metal Binding, Fold, and Function. Biochemistry 2015; 54:4443-52. [DOI: 10.1021/bi501371a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Angelique N. Besold
- Department of Pharmaceutical
Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180, United States
| | - Sarah L. J. Michel
- Department of Pharmaceutical
Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180, United States
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83
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Kabadi AM, Thakore PI, Vockley CM, Ousterout DG, Gibson TM, Guilak F, Reddy TE, Gersbach CA. Enhanced MyoD-induced transdifferentiation to a myogenic lineage by fusion to a potent transactivation domain. ACS Synth Biol 2015; 4:689-99. [PMID: 25494287 PMCID: PMC4475448 DOI: 10.1021/sb500322u] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Genetic reprogramming holds great potential for disease modeling, drug screening, and regenerative medicine. Genetic reprogramming of mammalian cells is typically achieved by forced expression of natural transcription factors that control master gene networks and cell lineage specification. However, in many instances, the natural transcription factors do not induce a sufficiently robust response to completely reprogram cell phenotype. In this study, we demonstrate that protein engineering of the master transcription factor MyoD can enhance the conversion of human dermal fibroblasts and adult stem cells to a skeletal myocyte phenotype. Fusion of potent transcriptional activation domains to MyoD led to increased myogenic gene expression, myofiber formation, cell fusion, and global reprogramming of the myogenic gene network. This work supports a general strategy for synthetically enhancing the direct conversion between cell types that can be applied in both synthetic biology and regenerative medicine.
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Affiliation(s)
| | | | | | | | | | - Farshid Guilak
- Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina 27710, United States
| | | | - Charles A. Gersbach
- Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina 27710, United States
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84
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Sehnal D, Pravda L, Svobodová Vařeková R, Ionescu CM, Koča J. PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank. Nucleic Acids Res 2015; 43:W383-8. [PMID: 26013810 PMCID: PMC4489247 DOI: 10.1093/nar/gkv561] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/17/2015] [Indexed: 01/10/2023] Open
Abstract
Well defined biomacromolecular patterns such as binding sites, catalytic sites, specific protein or nucleic acid sequences, etc. precisely modulate many important biological phenomena. We introduce PatternQuery, a web-based application designed for detection and fast extraction of such patterns. The application uses a unique query language with Python-like syntax to define the patterns that will be extracted from datasets provided by the user, or from the entire Protein Data Bank (PDB). Moreover, the database-wide search can be restricted using a variety of criteria, such as PDB ID, resolution, and organism of origin, to provide only relevant data. The extraction generally takes a few seconds for several hundreds of entries, up to approximately one hour for the whole PDB. The detected patterns are made available for download to enable further processing, as well as presented in a clear tabular and graphical form directly in the browser. The unique design of the language and the provided service could pave the way towards novel PDB-wide analyses, which were either difficult or unfeasible in the past. The application is available free of charge at http://ncbr.muni.cz/PatternQuery.
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Affiliation(s)
- David Sehnal
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic Faculty of Informatics, Masaryk University Brno, Botanická 68a, 602 00 Brno, Czech Republic
| | - Lukáš Pravda
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Radka Svobodová Vařeková
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Crina-Maria Ionescu
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jaroslav Koča
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
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85
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Gaj T, Liu J. Direct protein delivery to mammalian cells using cell-permeable Cys2-His2 zinc-finger domains. J Vis Exp 2015:52814. [PMID: 25866937 PMCID: PMC4401377 DOI: 10.3791/52814] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Due to their modularity and ability to be reprogrammed to recognize a wide range of DNA sequences, Cys2-His2 zinc-finger DNA-binding domains have emerged as useful tools for targeted genome engineering. Like many other DNA-binding proteins, zinc-fingers also possess the innate ability to cross cell membranes. We recently demonstrated that this intrinsic cell-permeability could be leveraged for intracellular protein delivery. Genetic fusion of zinc-finger motifs leads to efficient transport of protein and enzyme cargo into a broad range of mammalian cell types. Unlike other protein transduction technologies, delivery via zinc-finger domains does not inhibit enzyme activity and leads to high levels of cytosolic delivery. Here a detailed step-by-step protocol is presented for the implementation of zinc-finger technology for protein delivery into mammalian cells. Key steps for achieving high levels of intracellular zinc-finger-mediated delivery are highlighted and strategies for maximizing the performance of this system are discussed.
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Affiliation(s)
- Thomas Gaj
- Departments of Chemistry and Cell and Molecular Biology, The Scripps Research Institute;
| | - Jia Liu
- Departments of Chemistry and Cell and Molecular Biology, The Scripps Research Institute; Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University
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86
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Improved cell-penetrating zinc-finger nuclease proteins for precision genome engineering. MOLECULAR THERAPY-NUCLEIC ACIDS 2015; 4:e232. [PMID: 25756962 PMCID: PMC4354341 DOI: 10.1038/mtna.2015.6] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 01/27/2015] [Indexed: 12/27/2022]
Abstract
Safe, efficient, and broadly applicable methods for delivering site-specific nucleases into cells are needed in order for targeted genome editing to reach its full potential for basic research and medicine. We previously reported that zinc-finger nuclease (ZFN) proteins have the innate capacity to cross cell membranes and induce genome modification via their direct application to human cells. Here, we show that incorporation of tandem nuclear localization signal (NLS) repeats into the ZFN protein backbone enhances cell permeability nearly 13-fold and that single administration of multi-NLS ZFN proteins leads to genome modification rates of up to 26% in CD4(+) T cells and 17% in CD34(+) hematopoietic stem/progenitor cells. In addition, we show that multi-NLS ZFN proteins attenuate off-target effects and that codelivery of ZFN protein pairs facilitates dual gene modification frequencies of 20-30% in CD4(+) T cells. These results illustrate the applicability of ZFN protein delivery for precision genome engineering.
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87
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Correction of dystrophin expression in cells from Duchenne muscular dystrophy patients through genomic excision of exon 51 by zinc finger nucleases. Mol Ther 2014; 23:523-32. [PMID: 25492562 PMCID: PMC4351462 DOI: 10.1038/mt.2014.234] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 11/28/2014] [Indexed: 01/22/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is caused by genetic mutations that result in the absence of dystrophin protein expression. Oligonucleotide-induced exon skipping can restore the dystrophin reading frame and protein production. However, this requires continuous drug administration and may not generate complete skipping of the targeted exon. In this study, we apply genome editing with zinc finger nucleases (ZFNs) to permanently remove essential splicing sequences in exon 51 of the dystrophin gene and thereby exclude exon 51 from the resulting dystrophin transcript. This approach can restore the dystrophin reading frame in ~13% of DMD patient mutations. Transfection of two ZFNs targeted to sites flanking the exon 51 splice acceptor into DMD patient myoblasts led to deletion of this genomic sequence. A clonal population was isolated with this deletion and following differentiation we confirmed loss of exon 51 from the dystrophin mRNA transcript and restoration of dystrophin protein expression. Furthermore, transplantation of corrected cells into immunodeficient mice resulted in human dystrophin expression localized to the sarcolemmal membrane. Finally, we quantified ZFN toxicity in human cells and mutagenesis at predicted off-target sites. This study demonstrates a powerful method to restore the dystrophin reading frame and protein expression by permanently deleting exons.
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88
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Reyes LM, Estrada JL, Wang ZY, Blosser RJ, Smith RF, Sidner RA, Paris LL, Blankenship RL, Ray CN, Miner AC, Tector M, Tector AJ. Creating class I MHC-null pigs using guide RNA and the Cas9 endonuclease. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2014; 193:5751-7. [PMID: 25339675 PMCID: PMC5922270 DOI: 10.4049/jimmunol.1402059] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Pigs are emerging as important large animal models for biomedical research, and they may represent a source of organs for xenotransplantation. The MHC is pivotal to the function of the immune system in health and disease, and it is particularly important in infection and transplant rejection. Pigs deficient in class I MHC could serve as important reagents to study viral immunity as well as allograft and xenograft rejection. In this study, we report the creation and characterization of class I MHC knockout pigs using the Cas9 nuclease and guide RNAs. Pig fetal fibroblasts were genetically engineered using Cas9 and guide RNAs, and class I MHC(-) cells were then used as nuclear donors for somatic cell nuclear transfer. We produced three piglets devoid of all cell surface class I proteins. Although these animals have reduced levels of CD4(-)CD8(+) T cells in peripheral blood, the pigs appear healthy and are developing normally. These pigs are a promising reagent for immunological research.
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Affiliation(s)
- Luz M Reyes
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Jose L Estrada
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Zheng Yu Wang
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Rachel J Blosser
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Rashod F Smith
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Richard A Sidner
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Leela L Paris
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Ross L Blankenship
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Caitlin N Ray
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Aaron C Miner
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202
| | | | - A Joseph Tector
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202; Indiana University Health Transplant Institute, Indianapolis, IN 46202
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89
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Kabadi AM, Ousterout DG, Hilton IB, Gersbach CA. Multiplex CRISPR/Cas9-based genome engineering from a single lentiviral vector. Nucleic Acids Res 2014; 42:e147. [PMID: 25122746 PMCID: PMC4231726 DOI: 10.1093/nar/gku749] [Citation(s) in RCA: 243] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 08/01/2014] [Accepted: 08/04/2014] [Indexed: 01/08/2023] Open
Abstract
Engineered DNA-binding proteins that manipulate the human genome and transcriptome have enabled rapid advances in biomedical research. In particular, the RNA-guided CRISPR/Cas9 system has recently been engineered to create site-specific double-strand breaks for genome editing or to direct targeted transcriptional regulation. A unique capability of the CRISPR/Cas9 system is multiplex genome engineering by delivering a single Cas9 enzyme and two or more single guide RNAs (sgRNAs) targeted to distinct genomic sites. This approach can be used to simultaneously create multiple DNA breaks or to target multiple transcriptional activators to a single promoter for synergistic enhancement of gene induction. To address the need for uniform and sustained delivery of multiplex CRISPR/Cas9-based genome engineering tools, we developed a single lentiviral system to express a Cas9 variant, a reporter gene and up to four sgRNAs from independent RNA polymerase III promoters that are incorporated into the vector by a convenient Golden Gate cloning method. Each sgRNA is efficiently expressed and can mediate multiplex gene editing and sustained transcriptional activation in immortalized and primary human cells. This delivery system will be significant to enabling the potential of CRISPR/Cas9-based multiplex genome engineering in diverse cell types.
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Affiliation(s)
- Ami M Kabadi
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - David G Ousterout
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Isaac B Hilton
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC 27710, USA
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90
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Rader C, Segal DJ, Shabat D. Carlos F. Barbas III (1964-2014): Visionary at the interface of chemistry and biology. ACS Chem Biol 2014; 9:1645-6. [PMID: 25123302 DOI: 10.1021/cb5005993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christoph Rader
- Department
of Cancer Biology and Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - David J. Segal
- Genome
Center, Department of Biochemistry and Molecular Medicine, and MIND
Institute, University of California, Davis, 451 Health Science Drive, Davis, California 95616, United States
| | - Doron Shabat
- Department
of Organic Chemistry, School of Chemistry, Raymond and Beverly Sackler
Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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91
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Gaj T, Liu J, Anderson KE, Sirk SJ, Barbas CF. Protein delivery using Cys2-His2 zinc-finger domains. ACS Chem Biol 2014; 9:1662-7. [PMID: 24936957 DOI: 10.1021/cb500282g] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The development of new methods for delivering proteins into cells is a central challenge for advancing both basic research and therapeutic applications. We previously reported that zinc-finger nuclease proteins are intrinsically cell-permeable due to the cell-penetrating activity of the Cys2-His2 zinc-finger domain. Here, we demonstrate that genetically fused zinc-finger motifs can transport proteins and enzymes into a wide range of primary and transformed mammalian cell types. We show that zinc-finger domains mediate protein uptake at efficiencies that exceed conventional protein transduction systems and do so without compromising enzyme activity. In addition, we demonstrate that zinc-finger proteins enter cells primarily through macropinocytosis and facilitate high levels of cytosolic delivery. These findings establish zinc-finger proteins as not only useful tools for targeted genome engineering but also effective reagents for protein delivery.
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Affiliation(s)
- Thomas Gaj
- The Skaggs
Institute for
Chemical Biology and the Departments of Chemistry and Cell and Molecular
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jia Liu
- The Skaggs
Institute for
Chemical Biology and the Departments of Chemistry and Cell and Molecular
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Kimberly E. Anderson
- The Skaggs
Institute for
Chemical Biology and the Departments of Chemistry and Cell and Molecular
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Shannon J. Sirk
- The Skaggs
Institute for
Chemical Biology and the Departments of Chemistry and Cell and Molecular
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Carlos F. Barbas
- The Skaggs
Institute for
Chemical Biology and the Departments of Chemistry and Cell and Molecular
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
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92
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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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93
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