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Liu X, Chen Q, Yin X, Wang X, Ran J, Yu W, Wang B. Study on chromatin regulation patterns of expression vectors in the PhiC31 integration site. Epigenetics 2024; 19:2337085. [PMID: 38595049 PMCID: PMC11008548 DOI: 10.1080/15592294.2024.2337085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 03/26/2024] [Indexed: 04/11/2024] Open
Abstract
The PhiC31 integration system allows for targeted and efficient transgene integration and expression by recognizing pseudo attP sites in mammalian cells and integrating the exogenous genes into the open chromatin regions of active chromatin. In order to investigate the regulatory patterns of efficient gene expression in the open chromatin region of PhiC31 integration, this study utilized Ubiquitous Chromatin Opening Element (UCOE) and activating RNA (saRNA) to modulate the chromatin structure in the promoter region of the PhiC31 integration vector. The study analysed the effects of DNA methylation and nucleosome occupancy changes in the integrated promoter on gene expression levels. The results showed that for the OCT4 promoter with moderate CG density, DNA methylation had a smaller impact on expression compared to changes in nucleosome positioning near the transcription start site, which was crucial for enhancing downstream gene expression. On the other hand, for the SOX2 promoter with high CG density, increased methylation in the CpG island upstream of the transcription start site played a key role in affecting high expression, but the positioning and clustering of nucleosomes also had an important influence. In conclusion, analysing the DNA methylation patterns, nucleosome positioning, and quantity distribution of different promoters can determine whether the PhiC31 integration site possesses the potential to further enhance expression or overcome transgene silencing effects by utilizing chromatin regulatory elements.
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Affiliation(s)
- Xueli Liu
- Key Technology Engineering Center for New Veterinary Vaccine and Industry of Yunnan Provincial Education Department, Kunming University, Kunming, Yunnan, China
- Pharmaceutical Department, Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Qina Chen
- Key Technology Engineering Center for New Veterinary Vaccine and Industry of Yunnan Provincial Education Department, Kunming University, Kunming, Yunnan, China
| | - Xudong Yin
- Key Technology Engineering Center for New Veterinary Vaccine and Industry of Yunnan Provincial Education Department, Kunming University, Kunming, Yunnan, China
| | - Xiao Wang
- Key Technology Engineering Center for New Veterinary Vaccine and Industry of Yunnan Provincial Education Department, Kunming University, Kunming, Yunnan, China
| | - Jinshan Ran
- Key Technology Engineering Center for New Veterinary Vaccine and Industry of Yunnan Provincial Education Department, Kunming University, Kunming, Yunnan, China
| | - Wei Yu
- Department of Pharmacy, 920th Hospital of Joint Logistics Support Force, PLA, Kunming, China
| | - Bin Wang
- Key Technology Engineering Center for New Veterinary Vaccine and Industry of Yunnan Provincial Education Department, Kunming University, Kunming, Yunnan, China
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de Oliveira MA, Florentino LH, Sales TT, Lima RN, Barros LRC, Limia CG, Almeida MSM, Robledo ML, Barros LMG, Melo EO, Bittencourt DM, Rehen SK, Bonamino MH, Rech E. Protocol for the establishment of a serine integrase-based platform for functional validation of genetic switch controllers in eukaryotic cells. PLoS One 2024; 19:e0303999. [PMID: 38781126 PMCID: PMC11115199 DOI: 10.1371/journal.pone.0303999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 05/04/2024] [Indexed: 05/25/2024] Open
Abstract
Serine integrases (Ints) are a family of site-specific recombinases (SSRs) encoded by some bacteriophages to integrate their genetic material into the genome of a host. Their ability to rearrange DNA sequences in different ways including inversion, excision, or insertion with no help from endogenous molecular machinery, confers important biotechnological value as genetic editing tools with high host plasticity. Despite advances in their use in prokaryotic cells, only a few Ints are currently used as gene editors in eukaryotes, partly due to the functional loss and cytotoxicity presented by some candidates in more complex organisms. To help expand the number of Ints available for the assembly of more complex multifunctional circuits in eukaryotic cells, this protocol describes a platform for the assembly and functional screening of serine-integrase-based genetic switches designed to control gene expression by directional inversions of DNA sequence orientation. The system consists of two sets of plasmids, an effector module and a reporter module, both sets assembled with regulatory components (as promoter and terminator regions) appropriate for expression in mammals, including humans, and plants. The complete method involves plasmid design, DNA delivery, testing and both molecular and phenotypical assessment of results. This platform presents a suitable workflow for the identification and functional validation of new tools for the genetic regulation and reprogramming of organisms with importance in different fields, from medical applications to crop enhancement, as shown by the initial results obtained. This protocol can be completed in 4 weeks for mammalian cells or up to 8 weeks for plant cells, considering cell culture or plant growth time.
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Affiliation(s)
- Marco A. de Oliveira
- Department of Cell Biology, Institute of Biological Science, University of Brasília, Brasília, Distrito Federal, Brazil
- National Institute of Science and Technology in Synthetic Biology (INCT BioSyn), Brasília, Distrito Federal, Brazil
| | - Lilian H. Florentino
- Department of Cell Biology, Institute of Biological Science, University of Brasília, Brasília, Distrito Federal, Brazil
- National Institute of Science and Technology in Synthetic Biology (INCT BioSyn), Brasília, Distrito Federal, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
| | - Thais T. Sales
- Department of Cell Biology, Institute of Biological Science, University of Brasília, Brasília, Distrito Federal, Brazil
- National Institute of Science and Technology in Synthetic Biology (INCT BioSyn), Brasília, Distrito Federal, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
| | - Rayane N. Lima
- National Institute of Science and Technology in Synthetic Biology (INCT BioSyn), Brasília, Distrito Federal, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
| | - Luciana R. C. Barros
- Center for Translational Research in Oncology, Instituto do Câncer do Estado de São Paulo, Hospital das Clínicas da Faculdade de Medicina de Universidade de São Paulo, São Paulo, Brazil
| | - Cintia G. Limia
- Molecular Carcinogenesis Program, Research Coordination, National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Mariana S. M. Almeida
- National Institute of Science and Technology in Synthetic Biology (INCT BioSyn), Brasília, Distrito Federal, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
| | - Maria L. Robledo
- Molecular Carcinogenesis Program, Research Coordination, National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Leila M. G. Barros
- National Institute of Science and Technology in Synthetic Biology (INCT BioSyn), Brasília, Distrito Federal, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
| | - Eduardo O. Melo
- National Institute of Science and Technology in Synthetic Biology (INCT BioSyn), Brasília, Distrito Federal, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
| | - Daniela M. Bittencourt
- National Institute of Science and Technology in Synthetic Biology (INCT BioSyn), Brasília, Distrito Federal, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
| | - Stevens K. Rehen
- D’Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil
- Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Martín H. Bonamino
- Cell and Gene Therapy Program, Research Coordination, National Cancer Institute (INCA), Rio de Janeiro, Brazil
- Vice-Presidency of Research and Biological Collections (VPPCB), FIOCRUZ – Oswaldo Cruz Foundation Institute, Rio de Janeiro, Brazil
| | - Elibio Rech
- National Institute of Science and Technology in Synthetic Biology (INCT BioSyn), Brasília, Distrito Federal, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
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Contreras E, Liang C, Mahoney HL, Javier JL, Luce ML, Labastida Medina K, Bozza T, Schmidt TM. Flp-recombinase mouse line for genetic manipulation of ipRGCs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.06.592761. [PMID: 38766000 PMCID: PMC11100754 DOI: 10.1101/2024.05.06.592761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Light has myriad impacts on behavior, health, and physiology. These signals originate in the retina and are relayed to the brain by more than 40 types of retinal ganglion cells (RGCs). Despite a growing appreciation for the diversity of RGCs, how these diverse channels of light information are ultimately integrated by the ~50 retinorecipient brain targets to drive these light-evoked effects is a major open question. This gap in understanding primarily stems from a lack of genetic tools that specifically label, manipulate, or ablate specific RGC types. Here, we report the generation and characterization of a new mouse line (Opn4FlpO), in which FlpO is expressed from the Opn4 locus, to manipulate the melanopsin-expressing, intrinsically photosensitive retinal ganglion cells. We find that the Opn4FlpO line, when crossed to multiple reporters, drives expression that is confined to ipRGCs and primarily labels the M1-M3 subtypes. Labeled cells in this mouse line show the expected intrinsic, melanopsin-based light response and morphological features consistent with the M1-M3 subtypes. In alignment with the morphological and physiological findings, we see strong innervation of non-image forming brain targets by ipRGC axons, and weaker innervation of image forming targets in Opn4FlpO mice labeled using AAV-based and FlpO-reporter lines. Consistent with the FlpO insertion disrupting the endogenous Opn4 transcript, we find that Opn4FlpO/FlpO mice show deficits in the pupillary light reflex, demonstrating their utility for behavioral research in future experiments. Overall, the Opn4FlpO mouse line drives Flp-recombinase expression that is confined to ipRGCs and most effectively drives recombination in M1-M3 ipRGCs. This mouse line will be of broad use to those interested in manipulating ipRGCs through a Flp-based recombinase for intersectional studies or in combination with other, non-Opn4 Cre driver lines.
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Affiliation(s)
- E Contreras
- Department of Neurobiology, Northwestern University, Evanston, IL
- Northwestern University Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, United States
| | - C Liang
- Department of Neurobiology, Northwestern University, Evanston, IL
| | - H L Mahoney
- Department of Neurobiology, Northwestern University, Evanston, IL
| | - J L Javier
- Department of Neurobiology, Northwestern University, Evanston, IL
| | - M L Luce
- Department of Neurobiology, Northwestern University, Evanston, IL
| | | | - T Bozza
- Department of Neurobiology, Northwestern University, Evanston, IL
| | - T M Schmidt
- Department of Neurobiology, Northwestern University, Evanston, IL
- Department of Ophthalmology, Feinberg School of Medicine, Chicago, IL
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Shin S, Kim SH, Lee JS, Lee GM. Streamlined Human Cell-Based Recombinase-Mediated Cassette Exchange Platform Enables Multigene Expression for the Production of Therapeutic Proteins. ACS Synth Biol 2021; 10:1715-1727. [PMID: 34133132 DOI: 10.1021/acssynbio.1c00113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A platform, based on targeted integration of transgenes using recombinase-mediated cassette exchange (RMCE) coupled with CRISPR/Cas9, is increasingly being used for the development of mammalian cell lines that produce therapeutic proteins, because of reduced clonal variation and predictable transgene expression. However, low efficiency of the RMCE process has hampered its application in multicopy or multisite integration of transgenes. To improve RMCE efficiency, nuclear transport of RMCE components such as site-specific recombinase and donor plasmid was accelerated by incorporation of nuclear localization signal and DNA nuclear-targeting sequence, respectively. Consequently, the efficiency of RMCE in dual-landing pad human embryonic kidney 293 (HEK293) cell lines harboring identical or orthogonal pairs of recombination sites at two well-known human safe harbors (AAVS1 and ROSA26 loci), increased 6.7- and 8.1-fold, respectively. This platform with enhanced RMCE efficiency enabled simultaneous integration of transgenes at the two sites using a single transfection without performing selection and enrichment processes. The use of a homotypic dual-landing pad HEK293 cell line capable of incorporating the same transgenes at two sites resulted in a 2-fold increase in the transgene expression level compared to a single-landing pad HEK293 cell line. In addition, the use of a heterotypic dual-landing pad HEK293 cell line, which can incorporate transgenes for a recombinant protein at one site and an effector transgene for cell engineering at another site, increased recombinant protein production. Overall, a streamlined RMCE platform can be a versatile tool for mammalian cell line development by facilitating multigene expression at genomic safe harbors.
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Affiliation(s)
- Seunghyeon Shin
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
| | - Su Hyun Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
| | - Jae Seong Lee
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Gyun Min Lee
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
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Ahmed HMM, Heese F, Wimmer EA. Improvement on the genetic engineering of an invasive agricultural pest insect, the cherry vinegar fly, Drosophila suzukii. BMC Genet 2020; 21:139. [PMID: 33339511 PMCID: PMC7747376 DOI: 10.1186/s12863-020-00940-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Background The invasive fly Drosophila suzukii has become an established fruit pest in Europe, the USA, and South America with no effective and safe pest management. Genetic engineering enables the development of transgene-based novel genetic control strategies against insect pests and disease vectors. This, however, requires the establishment of reliable germline transformation techniques. Previous studies have shown that D. suzukii is amenable to transgenesis using the transposon-based vectors piggyBac and Minos, site-specific recombination (lox/Cre), and CRISPR/Cas9 genome editing. Results We experienced differences in the usability of piggyBac-based germline transformation in different strains of D. suzukii: we obtained no transgenic lines in a US strain, a single rare transgenic line in an Italian strain, but observed a reliable transformation rate of 2.5 to 11% in a strain from the French Alps. This difference in efficiency was confirmed by comparative examination of these three strains. In addition, we used an attP landing site line to successfully established φC31-integrase-mediated plasmid integration at a rate of 10% and generated landing site lines with two attP sequences to effectively perform φC31-Recombinase Mediated Cassette Exchange (φC31-RMCE) with 11% efficiency. Moreover, we isolated and used the endogenous regulatory regions of Ds nanos to express φC31 integrase maternally to generate self-docking lines for φC31-RMCE. Besides, we isolated the promoter/enhancer of Ds serendipity α to drive the heterologous tetracycline-controlled transactivator (tTA) during early embryonic development and generated a testes-specific tTA driver line using the endogenous beta-2-tubulin (β2t) promoter/enhancer. Conclusion Our results provide evidence that the D. suzukii strain AM derived from the French Alps is more suitable for piggyBac germline transformation than other strains. We demonstrated the feasibility of using φC31-RMCE in the cherry vinegar fly and generated a set of lines that can be used for highly efficient integration of larger constructs. The φC31-based integration will facilitate modification and stabilization of previously generated transgenic lines that carry at least one attP site in the transgene construction. An early embryo-specific and a spermatogenesis-specific driver line were generated for future use of the binary expression system tet-off to engineer tissue- and stage-specific effector gene expression for genetic pest control strategies. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-020-00940-5.
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Affiliation(s)
- Hassan M M Ahmed
- Department of Developmental Biology, Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology, Göttingen Center for Molecular Biosciences, Georg-August-University Göttingen, 37077, Göttingen, Germany.,Department of Crop Protection, Faculty of Agriculture-University of Khartoum, P.O. Box 32, 13314, Khartoum North, Khartoum, Sudan
| | - Fabienne Heese
- Department of Developmental Biology, Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology, Göttingen Center for Molecular Biosciences, Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Ernst A Wimmer
- Department of Developmental Biology, Johann-Friedrich-Blumenbach-Institute of Zoology and Anthropology, Göttingen Center for Molecular Biosciences, Georg-August-University Göttingen, 37077, Göttingen, Germany.
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CRISPR FokI Dead Cas9 System: Principles and Applications in Genome Engineering. Cells 2020; 9:cells9112518. [PMID: 33233344 PMCID: PMC7700487 DOI: 10.3390/cells9112518] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 11/05/2020] [Accepted: 11/19/2020] [Indexed: 12/18/2022] Open
Abstract
The identification of the robust clustered regularly interspersed short palindromic repeats (CRISPR) associated endonuclease (Cas9) system gene-editing tool has opened up a wide range of potential therapeutic applications that were restricted by more complex tools, including zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). Nevertheless, the high frequency of CRISPR system off-target activity still limits its applications, and, thus, advanced strategies for highly specific CRISPR/Cas9-mediated genome editing are continuously under development including CRISPR–FokI dead Cas9 (fdCas9). fdCas9 system is derived from linking a FokI endonuclease catalytic domain to an inactive Cas9 protein and requires a pair of guide sgRNAs that bind to the sense and antisense strands of the DNA in a protospacer adjacent motif (PAM)-out orientation, with a defined spacer sequence range around the target site. The dimerization of FokI domains generates DNA double-strand breaks, which activates the DNA repair machinery and results in genomic edit. So far, all the engineered fdCas9 variants have shown promising gene-editing activities in human cells when compared to other platforms. Herein, we review the advantages of all published variants of fdCas9 and their current applications in genome engineering.
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Gale GAR, Schiavon Osorio AA, Mills LA, Wang B, Lea-Smith DJ, McCormick AJ. Emerging Species and Genome Editing Tools: Future Prospects in Cyanobacterial Synthetic Biology. Microorganisms 2019; 7:E409. [PMID: 31569579 PMCID: PMC6843473 DOI: 10.3390/microorganisms7100409] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 09/22/2019] [Accepted: 09/24/2019] [Indexed: 12/19/2022] Open
Abstract
Recent advances in synthetic biology and an emerging algal biotechnology market have spurred a prolific increase in the availability of molecular tools for cyanobacterial research. Nevertheless, work to date has focused primarily on only a small subset of model species, which arguably limits fundamental discovery and applied research towards wider commercialisation. Here, we review the requirements for uptake of new strains, including several recently characterised fast-growing species and promising non-model species. Furthermore, we discuss the potential applications of new techniques available for transformation, genetic engineering and regulation, including an up-to-date appraisal of current Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein (CRISPR/Cas) and CRISPR interference (CRISPRi) research in cyanobacteria. We also provide an overview of several exciting molecular tools that could be ported to cyanobacteria for more advanced metabolic engineering approaches (e.g., genetic circuit design). Lastly, we introduce a forthcoming mutant library for the model species Synechocystis sp. PCC 6803 that promises to provide a further powerful resource for the cyanobacterial research community.
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Affiliation(s)
- Grant A R Gale
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK.
| | - Alejandra A Schiavon Osorio
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
| | - Lauren A Mills
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
| | - Baojun Wang
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK.
| | - David J Lea-Smith
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
| | - Alistair J McCormick
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
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Kalds P, Zhou S, Cai B, Liu J, Wang Y, Petersen B, Sonstegard T, Wang X, Chen Y. Sheep and Goat Genome Engineering: From Random Transgenesis to the CRISPR Era. Front Genet 2019; 10:750. [PMID: 31552084 PMCID: PMC6735269 DOI: 10.3389/fgene.2019.00750] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/17/2019] [Indexed: 12/16/2022] Open
Abstract
Sheep and goats are valuable livestock species that have been raised for their production of meat, milk, fiber, and other by-products. Due to their suitable size, short gestation period, and abundant secretion of milk, sheep and goats have become important model animals in agricultural, pharmaceutical, and biomedical research. Genome engineering has been widely applied to sheep and goat research. Pronuclear injection and somatic cell nuclear transfer represent the two primary procedures for the generation of genetically modified sheep and goats. Further assisted tools have emerged to enhance the efficiency of genetic modification and to simplify the generation of genetically modified founders. These tools include sperm-mediated gene transfer, viral vectors, RNA interference, recombinases, transposons, and endonucleases. Of these tools, the four classes of site-specific endonucleases (meganucleases, ZFNs, TALENs, and CRISPRs) have attracted wide attention due to their DNA double-strand break-inducing role, which enable desired DNA modifications based on the stimulation of native cellular DNA repair mechanisms. Currently, CRISPR systems dominate the field of genome editing. Gene-edited sheep and goats, generated using these tools, provide valuable models for investigations on gene functions, improving animal breeding, producing pharmaceuticals in milk, improving animal disease resistance, recapitulating human diseases, and providing hosts for the growth of human organs. In addition, more promising derivative tools of CRISPR systems have emerged such as base editors which enable the induction of single-base alterations without any requirements for homology-directed repair or DNA donor. These precise editors are helpful for revealing desirable phenotypes and correcting genetic diseases controlled by single bases. This review highlights the advances of genome engineering in sheep and goats over the past four decades with particular emphasis on the application of CRISPR/Cas9 systems.
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Affiliation(s)
- Peter Kalds
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- Department of Animal and Poultry Production, Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, Egypt
| | - Shiwei Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bei Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jiao Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ying Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bjoern Petersen
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt, Germany
| | | | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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Jusiak B, Jagtap K, Gaidukov L, Duportet X, Bandara K, Chu J, Zhang L, Weiss R, Lu TK. Comparison of Integrases Identifies Bxb1-GA Mutant as the Most Efficient Site-Specific Integrase System in Mammalian Cells. ACS Synth Biol 2019; 8:16-24. [PMID: 30609349 DOI: 10.1021/acssynbio.8b00089] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Phage-derived integrases can catalyze irreversible, site-specific integration of transgenic payloads into a chromosomal locus, resulting in mammalian cells that stably express transgenes or circuits of interest. Previous studies have demonstrated high-efficiency integration by the Bxb1 integrase in mammalian cells. Here, we show that a point mutation (Bxb1-GA) in Bxb1 target sites significantly increases Bxb1-mediated integration efficiency at the Rosa26 locus in Chinese hamster ovary cells, resulting in the highest integration efficiency reported with a site-specific integrase in mammalian cells. Bxb1-GA point mutant sites do not cross-react with Bxb1 wild-type sites, enabling their use in applications that require orthogonal pairs of target sites. In comparison, we test the efficiency and orthogonality of ϕC31 and Wβ integrases, and show that Wβ has an integration efficiency between those of Bxb1-GA and wild-type Bxb1. Our data present a toolbox of integrases for inserting payloads such as gene circuits or therapeutic transgenes into mammalian cell lines.
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Affiliation(s)
- Barbara Jusiak
- Research Laboratory of Electronics, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kalpana Jagtap
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Leonid Gaidukov
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Xavier Duportet
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kalpanie Bandara
- Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts 01810, United States
| | - Jianlin Chu
- Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts 01810, United States
| | - Lin Zhang
- Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts 01810, United States
| | - Ron Weiss
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Timothy K. Lu
- Research Laboratory of Electronics, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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10
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Naddafi F, Mahboudi F, Tabarzad M, Aliabadi Farahani Z, Hosein Shirazi F, Davami F. The Epigenetic Regulation of Blinatumomab Gene Expression: Tumor Cell-dependent T cell Response against Lymphoma Cells and Cytotoxic Activity. INTERNATIONAL JOURNAL OF MOLECULAR AND CELLULAR MEDICINE 2019; 8:55-66. [PMID: 32195205 PMCID: PMC7073260 DOI: 10.22088/ijmcm.bums.8.1.55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 06/03/2019] [Indexed: 11/24/2022]
Abstract
Conventional treatment for cancer such as surgical resection and chemotherapy can cause damage in cases with advanced cancers. Moreover, the identification of tumor-specific targets has great importance in T-cell therapies. For decades, T cell activity has been stimulated to improve anti-tumor activity. Bispecific antibodies have attracted strong interest from pharmaceutical companies, for their diagnostic and therapeutic use. Blinatumomab is a first-in-class bispecific T engager antibody for the treatment of relapsed or refractory precursor B- cell acute lymphoblastic leukemia. But, it can benefit several cases with CD19+ malignancies in the future. PhiC31 integrase-based vectors could selectively integrate therapeutic transgenes into pseudo-attP sites in CHO genome. In this study, production of Blinatumomab in CHO cells using this type of vectors was investigated. We evaluated the effects of histone deacetylases (HDACs) inhibitors such as sodium butyrate and valproic acid, on specific productivity and cell viability of antibody expressing cells. Although sodium butyrate increased specific productivity about 1.7-fold and valproic acid about 1.4-fold, valproic acid was found more efficient because of its less cytotoxic effect on cell growth. We examined the efficacy of expressed Blinatumomab at various effector to target (E/T) ratios. A dose-response analyses of calcein-acetoxymethyl release assay illustrated that the effective dose of expressed mAb required for antibody mediated cytotoxicity was 100 ng/ml and the expressed mAb was more effective at E/T ratios of 10:1 and 5:1. Results of this study indicated that the expressed blinatumomab can be useful for enhancing the cytotoxicity of CD3+ T-cells against CD19 + target cells in vitro.
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Affiliation(s)
- Fatemeh Naddafi
- Pharmaceutical Sciences Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Maryam Tabarzad
- Protein Technology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Farshad Hosein Shirazi
- Pharmaceutical Sciences Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Davami
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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11
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Abstract
Serine integrases catalyze precise rearrangement of DNA through site-specific recombination of small sequences of DNA called attachment (att) sites. Unlike other site-specific recombinases, the recombination reaction driven by serine integrases is highly directional and can only be reversed in the presence of an accessory protein called a recombination directionality factor (RDF). The ability to control reaction directionality has led to the development of serine integrases as tools for controlled rearrangement and modification of DNA in synthetic biology, gene therapy, and biotechnology. This review discusses recent advances in serine integrase technologies focusing on their applications in genome engineering, DNA assembly, and logic and data storage devices.
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Affiliation(s)
- Christine A. Merrick
- School
of Biological Sciences, University of Edinburgh, Roger Land Building, Alexander Crum
Brown Road, Edinburgh EH9
3FF, U.K
| | - Jia Zhao
- Novo
Nordisk (China) Pharmaceuticals Co., Ltd., Lei Shing Hong Center, Guangshunnan Avenue, Beijing 100102, China
| | - Susan J. Rosser
- School
of Biological Sciences, University of Edinburgh, Roger Land Building, Alexander Crum
Brown Road, Edinburgh EH9
3FF, U.K
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12
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McLellan MA, Rosenthal NA, Pinto AR. Cre-loxP-Mediated Recombination: General Principles and Experimental Considerations. ACTA ACUST UNITED AC 2017; 7:1-12. [DOI: 10.1002/cpmo.22] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Micheal A. McLellan
- The Jackson Laboratory; Bar Harbor Maine
- Graduate Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University; Boston Massachusetts
| | - Nadia A. Rosenthal
- The Jackson Laboratory; Bar Harbor Maine
- Australian Regenerative Medicine Institute, Monash University; Melbourne Victoria Australia
- National Heart and Lung Institute, Imperial College London; London United Kingdom
| | - Alexander R. Pinto
- The Jackson Laboratory; Bar Harbor Maine
- Australian Regenerative Medicine Institute, Monash University; Melbourne Victoria Australia
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13
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Ahmadi M, Mahboudi F, Akbari Eidgahi MR, Nasr R, Nematpour F, Ahmadi S, Ebadat S, Aghaeepoor M, Davami F. Evaluating the efficiency of phiC31 integrase-mediated monoclonal antibody expression in CHO cells. Biotechnol Prog 2016; 32:1570-1576. [PMID: 27604579 DOI: 10.1002/btpr.2362] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 07/19/2016] [Indexed: 01/02/2023]
Abstract
Traditional methods to generate CHO cell lines rely on random integration(s) of the gene of interest and result in unpredictable and unstable protein expression. In comparison, site-specific recombination methods increase the recombinant protein expression by inserting transgene at a locus with specific expression features. PhiC31 serine integrase, catalyze unidirectional integration that occurs at higher frequency in comparison with the reversible integration carried out by recombinases such as Cre. In this study, using different ratios of phiC31 serine integrase, we evaluated the phiC31 mediated gene integration for expression of a humanized IgG1 antibody (mAb0014) in CHO-S cells. Light chain (LC) and heavy chain (HC) genes were expressed in one operon under EF1α promoter and linked by internal ribosome entry site (IRES) element. The clonal selection was carried out by limiting dilution. Targeted integration approach increased recombinant protein yield and stability in cell pools. The productivity of targeted cell pools was about 4 mg/L and about 40 µg/L in the control cell pool. The number of integrated transgenes was about 19 fold higher than the control cells pools. Our results confirmed that the phiC31 integrase leads to mAb expression in more than 90% of colonies. The productivity of the PhiC31 integrated cell pools was stable for three months in the absence of selection as compared with conventional transfection methods. Hence, utilizing PhiC31 integrase can increase protein titer and decrease the required time for protein expression. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1570-1576, 2016.
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Affiliation(s)
- Maryam Ahmadi
- Medical Biotechnology Dept., Semnan University of Medical Sciences, Semnan, Iran.,Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | | | | | - Reza Nasr
- Medical Biotechnology Dept., Semnan University of Medical Sciences, Semnan, Iran
| | - Fatemeh Nematpour
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Samira Ahmadi
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Saeedeh Ebadat
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mojtaba Aghaeepoor
- Medical Biotechnology Dept., Semnan University of Medical Sciences, Semnan, Iran
| | - Fatemeh Davami
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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14
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Abstract
The fields of molecular genetics, biotechnology and synthetic biology are demanding ever more sophisticated molecular tools for programmed precise modification of cell genomic DNA and other DNA sequences. This review presents the current state of knowledge and development of one important group of DNA-modifying enzymes, the site-specific recombinases (SSRs). SSRs are Nature's 'molecular machines' for cut-and-paste editing of DNA molecules by inserting, deleting or inverting precisely defined DNA segments. We survey the SSRs that have been put to use, and the types of applications for which they are suitable. We also discuss problems associated with uses of SSRs, how these problems can be minimized, and how recombinases are being re-engineered for improved performance and novel applications.
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15
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Xu Z, Brown WRA. Comparison and optimization of ten phage encoded serine integrases for genome engineering in Saccharomyces cerevisiae. BMC Biotechnol 2016; 16:13. [PMID: 26860416 PMCID: PMC4748531 DOI: 10.1186/s12896-016-0241-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 01/19/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Phage-encoded serine integrases, such as ϕC31 integrase, are widely used for genome engineering but have not been optimized for use in Saccharomyces cerevisiae although this organism is a widely used organism in biotechnology. RESULTS The activities of derivatives of fourteen serine integrases that either possess or lack a nuclear localization signal were compared using a standardized recombinase mediated cassette exchange reaction. The relative activities of these integrases in S. cerevisiae and in mammalian cells suggested that the major determinant of the activity of an integrase is the enzyme itself and not the cell in which it is working. We used an inducible promoter to show that six integrases were toxic as judged by their effects upon the proliferative ability of transformed yeast. We show that in general the active phage-encoded serine integrases were an order of magnitude more efficient in promoting genome integration reactions than a simple homologous recombination. CONCLUSIONS The results of our study allow us to identify the integrases of the phage ϕBT1, TP901 ~ nls, R4, Bxb1, MR11, A118, ϕK38, ϕC31 ~ nls, Wβ and SPBC ~ nls as active in S. cerevisiae and indicate that vertebrate cells are more restricted than yeast in terms of which integrases are active.
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Affiliation(s)
- Zhengyao Xu
- School of Life Sciences, Queens Medical Centre, Nottingham University, Nottingham, NG7 2UH, UK.
| | - William R A Brown
- School of Life Sciences, Queens Medical Centre, Nottingham University, Nottingham, NG7 2UH, UK.
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16
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Aouida M, Eid A, Ali Z, Cradick T, Lee C, Deshmukh H, Atef A, AbuSamra D, Gadhoum SZ, Merzaban J, Bao G, Mahfouz M. Efficient fdCas9 Synthetic Endonuclease with Improved Specificity for Precise Genome Engineering. PLoS One 2015; 10:e0133373. [PMID: 26225561 PMCID: PMC4520497 DOI: 10.1371/journal.pone.0133373] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 06/25/2015] [Indexed: 12/26/2022] Open
Abstract
The Cas9 endonuclease is used for genome editing applications in diverse eukaryotic species. A high frequency of off-target activity has been reported in many cell types, limiting its applications to genome engineering, especially in genomic medicine. Here, we generated a synthetic chimeric protein between the catalytic domain of the FokI endonuclease and the catalytically inactive Cas9 protein (fdCas9). A pair of guide RNAs (gRNAs) that bind to sense and antisense strands with a defined spacer sequence range can be used to form a catalytically active dimeric fdCas9 protein and generate double-strand breaks (DSBs) within the spacer sequence. Our data demonstrate an improved catalytic activity of the fdCas9 endonuclease, with a spacer range of 15-39 nucleotides, on surrogate reporters and genomic targets. Furthermore, we observed no detectable fdCas9 activity at known Cas9 off-target sites. Taken together, our data suggest that the fdCas9 endonuclease variant is a superior platform for genome editing applications in eukaryotic systems including mammalian cells.
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Affiliation(s)
- Mustapha Aouida
- Laboratory for Genome Engineering, Division of Biological Sciences & Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955–6900, Kingdom of Saudi Arabia
| | - Ayman Eid
- Laboratory for Genome Engineering, Division of Biological Sciences & Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955–6900, Kingdom of Saudi Arabia
| | - Zahir Ali
- Laboratory for Genome Engineering, Division of Biological Sciences & Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955–6900, Kingdom of Saudi Arabia
| | - Thomas Cradick
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, United States of America
| | - Ciaran Lee
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, United States of America
| | - Harshavardhan Deshmukh
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, United States of America
| | - Ahmed Atef
- Laboratory for Genome Engineering, Division of Biological Sciences & Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955–6900, Kingdom of Saudi Arabia
| | - Dina AbuSamra
- Laboratory of Cell Signaling and Migration, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Samah Zeineb Gadhoum
- Laboratory of Cell Signaling and Migration, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Jasmeen Merzaban
- Laboratory of Cell Signaling and Migration, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Gang Bao
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, United States of America
| | - Magdy Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences & Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955–6900, Kingdom of Saudi Arabia
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17
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Haghighat-Khah RE, Scaife S, Martins S, St John O, Matzen KJ, Morrison N, Alphey L. Site-specific cassette exchange systems in the Aedes aegypti mosquito and the Plutella xylostella moth. PLoS One 2015; 10:e0121097. [PMID: 25830287 PMCID: PMC4382291 DOI: 10.1371/journal.pone.0121097] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/09/2015] [Indexed: 12/02/2022] Open
Abstract
Genetically engineered insects are being evaluated as potential tools to decrease the economic and public health burden of mosquitoes and agricultural pest insects. Here we describe a new tool for the reliable and targeted genome manipulation of pest insects for research and field release using recombinase mediated cassette exchange (RMCE) mechanisms. We successfully demonstrated the established ΦC31-RMCE method in the yellow fever mosquito, Aedes aegypti, which is the first report of RMCE in mosquitoes. A new variant of this RMCE system, called iRMCE, combines the ΦC31-att integration system and Cre or FLP-mediated excision to remove extraneous sequences introduced as part of the site-specific integration process. Complete iRMCE was achieved in two important insect pests, Aedes aegypti and the diamondback moth, Plutella xylostella, demonstrating the transferability of the system across a wide phylogenetic range of insect pests.
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Affiliation(s)
- Roya Elaine Haghighat-Khah
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxitec Limited, Oxford, United Kingdom
| | | | - Sara Martins
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxitec Limited, Oxford, United Kingdom
| | - Oliver St John
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxitec Limited, Oxford, United Kingdom
| | | | | | - Luke Alphey
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Oxitec Limited, Oxford, United Kingdom
- * E-mail: (LA); (KJM)
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18
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Grandchamp N, Altémir D, Philippe S, Ursulet S, Pilet H, Serre MC, Lenain A, Serguera C, Mallet J, Sarkis C. Hybrid lentivirus-phiC31-int-NLS vector allows site-specific recombination in murine and human cells but induces DNA damage. PLoS One 2014; 9:e99649. [PMID: 24956106 PMCID: PMC4067480 DOI: 10.1371/journal.pone.0099649] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 05/17/2014] [Indexed: 12/27/2022] Open
Abstract
Gene transfer allows transient or permanent genetic modifications of cells for experimental or therapeutic purposes. Gene delivery by HIV-derived lentiviral vector (LV) is highly effective but the risk of insertional mutagenesis is important and the random/uncontrollable integration of the DNA vector can deregulate the cell transcriptional activity. Non Integrative Lentiviral Vectors (NILVs) solve this issue in non-dividing cells, but they do not allow long term expression in dividing cells. In this context, obtaining stable expression while avoiding the problems inherent to unpredictable DNA vector integration requires the ability to control the integration site. One possibility is to use the integrase of phage phiC31 (phiC31-int) which catalyzes efficient site-specific recombination between the attP site in the phage genome and the chromosomal attB site of its Streptomyces host. Previous studies showed that phiC31-int is active in many eukaryotic cells, such as murine or human cells, and directs the integration of a DNA substrate into pseudo attP sites (pattP) which are homologous to the native attP site. In this study, we combined the efficiency of NILV for gene delivery and the specificity of phiC31-int for DNA substrate integration to engineer a hybrid tool for gene transfer with the aim of allowing long term expression in dividing and non-dividing cells preventing genotoxicity. We demonstrated the feasibility to target NILV integration in human and murine pattP sites with a dual NILV vectors system: one which delivers phiC31-int, the other which constitute the substrate containing an attB site in its DNA sequence. These promising results are however alleviated by the occurrence of significant DNA damages. Further improvements are thus required to prevent chromosomal rearrangements for a therapeutic use of the system. However, its use as a tool for experimental applications such as transgenesis is already applicable.
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Affiliation(s)
- Nicolas Grandchamp
- Unit of Biotechnology and Biotherapy, Centre de recherche de l'Institut du Cerveau et de la Moelle Epinière, Pierre-and-Marie-Curie University/Institut National de la Santé et de la Recherche Médicale, Paris, France
- NewVectys, Villebon-sur-Yvette, France
- Biosource, Paris, France
| | - Dorothée Altémir
- Unit of Biotechnology and Biotherapy, Centre de recherche de l'Institut du Cerveau et de la Moelle Epinière, Pierre-and-Marie-Curie University/Institut National de la Santé et de la Recherche Médicale, Paris, France
- NewVectys, Villebon-sur-Yvette, France
| | - Stéphanie Philippe
- Unit of Biotechnology and Biotherapy, Centre de recherche de l'Institut du Cerveau et de la Moelle Epinière, Pierre-and-Marie-Curie University/Institut National de la Santé et de la Recherche Médicale, Paris, France
- NewVectys, Villebon-sur-Yvette, France
- Biosource, Paris, France
| | - Suzanna Ursulet
- Unit of Biotechnology and Biotherapy, Centre de recherche de l'Institut du Cerveau et de la Moelle Epinière, Pierre-and-Marie-Curie University/Institut National de la Santé et de la Recherche Médicale, Paris, France
- NewVectys, Villebon-sur-Yvette, France
- Biosource, Paris, France
| | - Héloïse Pilet
- Unit of Biotechnology and Biotherapy, Centre de recherche de l'Institut du Cerveau et de la Moelle Epinière, Pierre-and-Marie-Curie University/Institut National de la Santé et de la Recherche Médicale, Paris, France
- NewVectys, Villebon-sur-Yvette, France
- Biosource, Paris, France
| | - Marie-Claude Serre
- Laboratoire de Virologie Moléculaire et Structurale, Gif-sur-Yvette, France
| | - Aude Lenain
- Commissariat à l'Energie Atomique, Laboratoire de Radiobiologie et Oncologie, Fontenay-aux-Roses, France
| | - Che Serguera
- Molecular Imaging Research Center - Modélisation des biothérapies, Fontenay-aux-Roses, France
| | - Jacques Mallet
- Unit of Biotechnology and Biotherapy, Centre de recherche de l'Institut du Cerveau et de la Moelle Epinière, Pierre-and-Marie-Curie University/Institut National de la Santé et de la Recherche Médicale, Paris, France
| | - Chamsy Sarkis
- Unit of Biotechnology and Biotherapy, Centre de recherche de l'Institut du Cerveau et de la Moelle Epinière, Pierre-and-Marie-Curie University/Institut National de la Santé et de la Recherche Médicale, Paris, France
- NewVectys, Villebon-sur-Yvette, France
- * E-mail:
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19
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Fogg PCM, Colloms S, Rosser S, Stark M, Smith MCM. New applications for phage integrases. J Mol Biol 2014; 426:2703-16. [PMID: 24857859 PMCID: PMC4111918 DOI: 10.1016/j.jmb.2014.05.014] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/09/2014] [Accepted: 05/16/2014] [Indexed: 11/28/2022]
Abstract
Within the last 25 years, bacteriophage integrases have rapidly risen to prominence as genetic tools for a wide range of applications from basic cloning to genome engineering. Serine integrases such as that from ϕC31 and its relatives have found an especially wide range of applications within diverse micro-organisms right through to multi-cellular eukaryotes. Here, we review the mechanisms of the two major families of integrases, the tyrosine and serine integrases, and the advantages and disadvantages of each type as they are applied in genome engineering and synthetic biology. In particular, we focus on the new areas of metabolic pathway construction and optimization, biocomputing, heterologous expression and multiplexed assembly techniques. Integrases are versatile and efficient tools that can be used in conjunction with the various extant molecular biology tools to streamline the synthetic biology production line. Phage integrases are site-specific recombinases that mediate controlled and precise DNA integration and excision. The serine integrases, such as ϕC31 integrase, can be used for efficient recombination in heterologous hosts as they use short recombination substrates, they are directional and they do not require host factors. Both serine and tyrosine integrases, such as λ integrase, are versatile tools for DNA cloning and assembly in vivo and in vitro. Controlled expression of orthologous serine integrases and their cognate recombination directionality factors can be used to generate living biocomputers. Serine integrases are increasingly being exploited for synthetic biology applications.
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Affiliation(s)
- Paul C M Fogg
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Sean Colloms
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Bower Building, Glasgow G12 8QQ, UK
| | - Susan Rosser
- School of Biological Sciences, University of Edinburgh, King's Building, Edinburgh EH9 3JR, UK
| | - Marshall Stark
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Bower Building, Glasgow G12 8QQ, UK
| | - Margaret C M Smith
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK.
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20
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Ma H, Ma Q, Lu Y, Wang J, Hu W, Gong Z, Cai L, Huang Y, Huang SZ, Zeng F. PhiC31 integrase induces efficient site-specific recombination in the Capra hircus genome. DNA Cell Biol 2014; 33:484-91. [PMID: 24754538 DOI: 10.1089/dna.2013.2124] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Streptomyces phage φC31 integrase induces efficient site-specific recombination capable of integrating exogenous genes at pseudo attP sites in human, mouse, rat, rabbit, sheep, Drosophila, and bovine genomes. However, the φC31-mediated recombination between attB and the corresponding pseudo attP sites has not been investigated in Capra hircus. Here, we identified eight pseudo attP sites located in the intron or intergenic regions of the C. hircus genome, and demonstrated different levels of foreign gene expression after φC31 integrase-mediated integration. These pseudo attP sites share similar sequences with each other and with pseudo attP sites in other mammalian genomes, and these are associated with a neighboring consensus motif found in other genomes. The application of the φC31 integrase system in C. hircus provides a new option for genetic engineering of this economically important goat species.
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Affiliation(s)
- Haiyan Ma
- 1 Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University , Shanghai, People's Republic of China
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21
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Improved site-specific recombinase-based method to produce selectable marker- and vector-backbone-free transgenic cells. Sci Rep 2014; 4:4240. [PMID: 24577484 PMCID: PMC3937794 DOI: 10.1038/srep04240] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 02/06/2014] [Indexed: 12/30/2022] Open
Abstract
PhiC31 integrase-mediated gene delivery has been extensively used in gene therapy and animal transgenesis. However, random integration events are observed in phiC31-mediated integration in different types of mammalian cells; as a result, the efficiencies of pseudo attP site integration and evaluation of site-specific integration are compromised. To improve this system, we used an attB-TK fusion gene as a negative selection marker, thereby eliminating random integration during phiC31-mediated transfection. We also excised the selection system and plasmid bacterial backbone by using two other site-specific recombinases, Cre and Dre. Thus, we generated clean transgenic bovine fetal fibroblast cells free of selectable marker and plasmid bacterial backbone. These clean cells were used as donor nuclei for somatic cell nuclear transfer (SCNT), indicating a similar developmental competence of SCNT embryos to that of non-transgenic cells. Therefore, the present gene delivery system facilitated the development of gene therapy and agricultural biotechnology.
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22
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Hermann M, Stillhard P, Wildner H, Seruggia D, Kapp V, Sánchez-Iranzo H, Mercader N, Montoliu L, Zeilhofer HU, Pelczar P. Binary recombinase systems for high-resolution conditional mutagenesis. Nucleic Acids Res 2014; 42:3894-907. [PMID: 24413561 PMCID: PMC3973285 DOI: 10.1093/nar/gkt1361] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Conditional mutagenesis using Cre recombinase expressed from tissue specific promoters facilitates analyses of gene function and cell lineage tracing. Here, we describe two novel dual-promoter-driven conditional mutagenesis systems designed for greater accuracy and optimal efficiency of recombination. Co-Driver employs a recombinase cascade of Dre and Dre-respondent Cre, which processes loxP-flanked alleles only when both recombinases are expressed in a predetermined temporal sequence. This unique property makes Co-Driver ideal for sequential lineage tracing studies aimed at unraveling the relationships between cellular precursors and mature cell types. Co-InCre was designed for highly efficient intersectional conditional transgenesis. It relies on highly active trans-splicing inteins and promoters with simultaneous transcriptional activity to reconstitute Cre recombinase from two inactive precursor fragments. By generating native Cre, Co-InCre attains recombination rates that exceed all other binary SSR systems evaluated in this study. Both Co-Driver and Co-InCre significantly extend the utility of existing Cre-responsive alleles.
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Affiliation(s)
- Mario Hermann
- Institute of Laboratory Animal Science, University of Zurich, Sternwartstrasse 6, CH-8091 Zurich, Switzerland, Institute of Neuropathology, University Hospital of Zurich, Schmelzbergstrasse 12, CH-8091 Zurich, Switzerland, Institute of Pharmacology and Toxicology, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland, National Centre for Biotechnology (CNB-CSIC), Darwin 3, 28049 Madrid, Spain, CIBERER-ISCIII, Darwin 3, 28049 Madrid, Spain, Program of Cardiovascular Development, Department of Cardiovascular Development and Repair, Centro Nacional de Investigaciones Cardiovasculares Carlos III, calle Melchor Fernández Almagro 3, 28029 Madrid, Spain and Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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23
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Xu Z, Thomas L, Davies B, Chalmers R, Smith M, Brown W. Accuracy and efficiency define Bxb1 integrase as the best of fifteen candidate serine recombinases for the integration of DNA into the human genome. BMC Biotechnol 2013; 13:87. [PMID: 24139482 PMCID: PMC4015280 DOI: 10.1186/1472-6750-13-87] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 10/09/2013] [Indexed: 11/18/2022] Open
Abstract
Background Phage-encoded serine integrases, such as φC31 integrase, are widely used for genome engineering. Fifteen such integrases have been described but their utility for genome engineering has not been compared in uniform assays. Results We have compared fifteen serine integrases for their utility for DNA manipulations in mammalian cells after first demonstrating that all were functional in E. coli. Chromosomal recombination reporters were used to show that seven integrases were active on chromosomally integrated DNA in human fibroblasts and mouse embryonic stem cells. Five of the remaining eight enzymes were active on extra-chromosomal substrates thereby demonstrating that the ability to mediate extra-chromosomal recombination is no guide to ability to mediate site-specific recombination on integrated DNA. All the integrases that were active on integrated DNA also promoted DNA integration reactions that were not mediated through conservative site-specific recombination or damaged the recombination sites but the extent of these aberrant reactions varied over at least an order of magnitude. Bxb1 integrase yielded approximately two-fold more recombinants and displayed about two fold less damage to the recombination sites than the next best recombinase; φC31 integrase. Conclusions We conclude that the Bxb1 and φC31 integrases are the reagents of choice for genome engineering in vertebrate cells and that DNA damage repair is a major limitation upon the utility of this class of site-specific recombinase.
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Affiliation(s)
| | | | | | | | | | - William Brown
- Queens Medical Centre, School of Life Sciences, Nottingham University, Nottingham NG7 2UH, UK.
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Deussing JM. Targeted mutagenesis tools for modelling psychiatric disorders. Cell Tissue Res 2013; 354:9-25. [PMID: 24078022 DOI: 10.1007/s00441-013-1708-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 07/16/2013] [Indexed: 12/15/2022]
Abstract
In the 1980s, the basic principles of gene targeting were discovered and forged into sharp tools for efficient and precise engineering of the mouse genome. Since then, genetic mouse models have substantially contributed to our understanding of major neurobiological concepts and are of utmost importance for our comprehension of neuropsychiatric disorders. The "domestication" of site-specific recombinases and the continuous creative technological developments involving the implementation of previously identified biological principles such as transcriptional and posttranslational control now enable conditional mutagenesis with high spatial and temporal resolution. The initiation and successful accomplishment of large-scale efforts to annotate functionally the entire mouse genome and to build strategic resources for the research community have significantly accelerated the rapid proliferation and broad propagation of mouse genetic tools. Addressing neurobiological processes with the assistance of genetic mouse models is a routine procedure in psychiatric research and will be further extended in order to improve our understanding of disease mechanisms. In light of the highly complex nature of psychiatric disorders and the current lack of strong causal genetic variants, a major future challenge is to model of psychiatric disorders more appropriately. Humanized mice, and the recently developed toolbox of site-specific nucleases for more efficient and simplified tailoring of the genome, offer the perspective of significantly improved models. Ultimately, these tools will push the limits of gene targeting beyond the mouse to allow genome engineering in any model organism of interest.
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Affiliation(s)
- Jan M Deussing
- Max Planck Institute of Psychiatry, Molecular Neurogenetics, Kraepelinstrasse 2-10, 80804, Munich, Germany,
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Robert MA, Zeng Y, Raymond B, Desfossé L, Mairey E, Tremblay JP, Massie B, Gilbert R. Efficacy and site-specificity of adenoviral vector integration mediated by the phage φC31 integrase. Hum Gene Ther Methods 2013. [PMID: 23194172 DOI: 10.1089/hgtb.2012.122] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Adenoviral vectors deleted of all their viral genes (helper-dependent [HD]) are efficient gene-transfer vehicles. Because transgene expression is rapidly lost in actively dividing cells, we investigated the feasibility of using phage φC31 integrase (φC31-Int) to integrate an HD carrying an attB site and the puromycin resistance gene into human cells (HeLa) and murine myoblasts (C2C12) by co-infection with a second HD-expressing φC31-Int. Because the HD genome is linear, we also investigated whether its circularization, through expression of Cre using a third HD, affects integration. Efficacy and specificity were determined by scoring the number of puromycin-resistant colonies and by sequencing integration sites. Unexpectedly, circularization of HD was unnecessary and it even reduced the integration efficacy. The maximum integration efficacy achieved was 0.5% in HeLa cells and 0.1% in C2C12 myoblasts. Up to 76% of the integration events occurred at pseudo attP sites and previously characterized hotspots were found. A small (two- to three-fold) increase in the number of γ-H2AX positive foci, accompanied by no noticeable change in γ-H2AX expression, indicated the low genotoxicity of φC31-Int. In conclusion, integration of HD mediated by φC31-Int is an attractive alternative to engineer cells, because it permits site-specific integration of large DNA fragments with low genotoxicity.
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Affiliation(s)
- Marc-André Robert
- Biotechnology Research Institute, National Research Council Canada, Montréal, Canada, H4P 2R2
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Yau YY, Stewart CN. Less is more: strategies to remove marker genes from transgenic plants. BMC Biotechnol 2013; 13:36. [PMID: 23617583 PMCID: PMC3689633 DOI: 10.1186/1472-6750-13-36] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 03/05/2013] [Indexed: 02/07/2023] Open
Abstract
Selectable marker genes (SMGs) and selection agents are useful tools in the production of transgenic plants by selecting transformed cells from a matrix consisting of mostly untransformed cells. Most SMGs express protein products that confer antibiotic- or herbicide resistance traits, and typically reside in the end product of genetically-modified (GM) plants. The presence of these genes in GM plants, and subsequently in food, feed and the environment, are of concern and subject to special government regulation in many countries. The presence of SMGs in GM plants might also, in some cases, result in a metabolic burden for the host plants. Their use also prevents the re-use of the same SMG when a second transformation scheme is needed to be performed on the transgenic host. In recent years, several strategies have been developed to remove SMGs from GM products while retaining the transgenes of interest. This review describes the existing strategies for SMG removal, including the implementation of site specific recombination systems, TALENs and ZFNs. This review discusses the advantages and disadvantages of existing SMG-removal strategies and explores possible future research directions for SMG removal including emerging technologies for increased precision for genome modification.
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Affiliation(s)
- Yuan-Yeu Yau
- Department of Natural Sciences, Northeastern State University, Broken Arrow, OK 74014, USA
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
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González-Prieto C, Agúndez L, Linden RM, Llosa M. HUH site-specific recombinases for targeted modification of the human genome. Trends Biotechnol 2013; 31:305-12. [PMID: 23545167 DOI: 10.1016/j.tibtech.2013.02.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 02/27/2013] [Accepted: 02/27/2013] [Indexed: 11/16/2022]
Abstract
Site-specific recombinases (SSRs) have been crucial in the development of mammalian transgenesis. For gene therapy purposes, this approach remains challenging, because, for example, SSR delivery is largely unresolved and SSR DNA substrates must pre-exist in target cells. In this review, we discuss the potential of His-hydrophobic-His (HUH) recombinases to overcome some of the limitations of conventional SSRs. Members of the HUH protein family cleave single-stranded (ss)DNA, but can mediate site-specific integration with the aid of the host replication machinery. Adeno-associated virus (AAV) Rep remains the only known example to support site-specific integration in human cells, and AAV is an excellent gene delivery vector that can be targeted to specific cells and organelles. Bacterial protein TrwC catalyzes integration into human sequences and can be delivered to human cells covalently linked to DNA, offering attractive new features for targeted genome modification.
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Affiliation(s)
- Coral González-Prieto
- Departamento de Biología Molecular (Universidad de Cantabria) and IBBTEC (UC, CSIC, SODERCAN), Santander, Spain
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Nafissi N, Slavcev R. Construction and characterization of an in-vivo linear covalently closed DNA vector production system. Microb Cell Fact 2012; 11:154. [PMID: 23216697 PMCID: PMC3540006 DOI: 10.1186/1475-2859-11-154] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 11/25/2012] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND While safer than their viral counterparts, conventional non-viral gene delivery DNA vectors offer a limited safety profile. They often result in the delivery of unwanted prokaryotic sequences, antibiotic resistance genes, and the bacterial origins of replication to the target, which may lead to the stimulation of unwanted immunological responses due to their chimeric DNA composition. Such vectors may also impart the potential for chromosomal integration, thus potentiating oncogenesis. We sought to engineer an in vivo system for the quick and simple production of safer DNA vector alternatives that were devoid of non-transgene bacterial sequences and would lethally disrupt the host chromosome in the event of an unwanted vector integration event. RESULTS We constructed a parent eukaryotic expression vector possessing a specialized manufactured multi-target site called "Super Sequence", and engineered E. coli cells (R-cell) that conditionally produce phage-derived recombinase Tel (PY54), TelN (N15), or Cre (P1). Passage of the parent plasmid vector through R-cells under optimized conditions, resulted in rapid, efficient, and one step in vivo generation of mini lcc--linear covalently closed (Tel/TelN-cell), or mini ccc--circular covalently closed (Cre-cell), DNA constructs, separated from the backbone plasmid DNA. Site-specific integration of lcc plasmids into the host chromosome resulted in chromosomal disruption and 10(5) fold lower viability than that seen with the ccc counterpart. CONCLUSION We offer a high efficiency mini DNA vector production system that confers simple, rapid and scalable in vivo production of mini lcc DNA vectors that possess all the benefits of "minicircle" DNA vectors and virtually eliminate the potential for undesirable vector integration events.
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Affiliation(s)
- Nafiseh Nafissi
- School of Pharmacy, Faculty of Science, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
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Farruggio AP, Chavez CL, Mikell CL, Calos MP. Efficient reversal of phiC31 integrase recombination in mammalian cells. Biotechnol J 2012; 7:1332-6. [PMID: 22933343 DOI: 10.1002/biot.201200283] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 08/15/2012] [Accepted: 08/29/2012] [Indexed: 02/02/2023]
Abstract
Over the past decade, the integrase enzyme from phage phiC31 has proven to be a useful genome engineering tool in a wide variety of species, including mammalian cells. The enzyme efficiently mediates recombination between two distinct sequences, attP and attB, producing recombinant product sites, attL and attR. The reaction proceeds exclusively in a unidirectional manner, because integrase is unable to synapse attL and attR. To date, use of phiC31 integrase has been limited to attP × attB recombination. The factor needed for the reverse reaction--the excisionase or recombination directionality factor (RDF)--was identified recently and shown to function in vitro and in bacterial cells. To determine whether the phiC31 RDF could also function in mammalian cells, we cloned and tested several vectors that permit assessment of phiC31 RDF activity in mammalian environments. In the human and mouse cell lines tested (HeLa, HEK293, and NIH3T3), we observed robust RDF activity, using plasmid and/or genomic assays. This work is the first to demonstrate attL-attR serine integrase activity in mammalian cells and validates phiC31 RDF as a new tool that will enable future studies to take advantage of phiC31 integrase recombination in the forward or reverse direction.
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Affiliation(s)
- Alfonso P Farruggio
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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Kapusi E, Kempe K, Rubtsova M, Kumlehn J, Gils M. phiC31 integrase-mediated site-specific recombination in barley. PLoS One 2012; 7:e45353. [PMID: 23024817 PMCID: PMC3443236 DOI: 10.1371/journal.pone.0045353] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2012] [Accepted: 08/17/2012] [Indexed: 12/28/2022] Open
Abstract
The Streptomyces phage phiC31 integrase was tested for its feasibility in excising transgenes from the barley genome through site-specific recombination. We produced transgenic barley plants expressing an active phiC31 integrase and crossed them with transgenic barley plants carrying a target locus for recombination. The target sequence involves a reporter gene encoding green fluorescent protein (GFP), which is flanked by the attB and attP recognition sites for the phiC31 integrase. This sequence disruptively separates a gusA coding sequence from an upstream rice actin promoter. We succeeded in producing site-specific recombination events in the hybrid progeny of 11 independent barley plants carrying the above target sequence after crossing with plants carrying a phiC31 expression cassette. Some of the hybrids displayed fully executed recombination. Excision of the GFP gene fostered activation of the gusA gene, as visualized in tissue of hybrid plants by histochemical staining. The recombinant loci were detected in progeny of selfed F(1), even in individuals lacking the phiC31 transgene, which provides evidence of stability and generative transmission of the recombination events. In several plants that displayed incomplete recombination, extrachromosomal excision circles were identified. Besides the technical advance achieved in this study, the generated phiC31 integrase-expressing barley plants provide foundational stock material for use in future approaches to barley genetic improvement, such as the production of marker-free transgenic plants or switching transgene activity.
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Affiliation(s)
- Eszter Kapusi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Gatersleben, Germany
| | - Katja Kempe
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Gatersleben, Germany
| | - Myroslava Rubtsova
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Gatersleben, Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Gatersleben, Germany
| | - Mario Gils
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Gatersleben, Germany
- * E-mail:
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Schmitt C, Schultheis C, Husson SJ, Liewald JF, Gottschalk A. Specific expression of channelrhodopsin-2 in single neurons of Caenorhabditis elegans. PLoS One 2012; 7:e43164. [PMID: 22952643 PMCID: PMC3431400 DOI: 10.1371/journal.pone.0043164] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 07/18/2012] [Indexed: 12/02/2022] Open
Abstract
Optogenetic approaches using light-activated proteins like Channelrhodopsin-2 (ChR2) enable investigating the function of populations of neurons in live Caenorhabditis elegans (and other) animals, as ChR2 expression can be targeted to these cells using specific promoters. Sub-populations of these neurons, or even single cells, can be further addressed by restricting the illumination to the cell of interest. However, this is technically demanding, particularly in free moving animals. Thus, it would be helpful if expression of ChR2 could be restricted to single neurons or neuron pairs, as even wide-field illumination would photostimulate only this particular cell. To this end we adopted the use of Cre or FLP recombinases and conditional ChR2 expression at the intersection of two promoter expression domains, i.e. in the cell of interest only. Success of this method depends on precise knowledge of the individual promoters' expression patterns and on relative expression levels of recombinase and ChR2. A bicistronic expression cassette with GFP helps to identify the correct expression pattern. Here we show specific expression in the AVA reverse command neurons and the aversive polymodal sensory ASH neurons. This approach shall enable to generate strains for optogenetic manipulation of each of the 302 C. elegans neurons. This may eventually allow to model the C. elegans nervous system in its entirety, based on functional data for each neuron.
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Affiliation(s)
- Cornelia Schmitt
- Buchmann Institute for Molecular Life Sciences, Goethe-University, Frankfurt, Germany
- Institute of Biochemistry, Goethe-University, Frankfurt, Germany
| | - Christian Schultheis
- Buchmann Institute for Molecular Life Sciences, Goethe-University, Frankfurt, Germany
- Institute of Biochemistry, Goethe-University, Frankfurt, Germany
| | - Steven J. Husson
- Buchmann Institute for Molecular Life Sciences, Goethe-University, Frankfurt, Germany
- Institute of Biochemistry, Goethe-University, Frankfurt, Germany
- Functional Genomics and Proteomics, Katholieke Universiteit, Leuven, Belgium
| | - Jana F. Liewald
- Buchmann Institute for Molecular Life Sciences, Goethe-University, Frankfurt, Germany
- Institute of Biochemistry, Goethe-University, Frankfurt, Germany
| | - Alexander Gottschalk
- Buchmann Institute for Molecular Life Sciences, Goethe-University, Frankfurt, Germany
- Institute of Biochemistry, Goethe-University, Frankfurt, Germany
- * E-mail:
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Imayoshi I, Hirano K, Kitano S, Miyachi H, Kageyama R. In vivo evaluation of ΦC31 recombinase activity in transgenic mice. Neurosci Res 2012; 73:106-14. [PMID: 22608021 DOI: 10.1016/j.neures.2012.02.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 02/17/2012] [Accepted: 02/20/2012] [Indexed: 11/16/2022]
Abstract
Genome engineering strategies employing site-specific recombinases (SSRs) such as Cre, Flp and PhiC31, have become powerful tools to analyze gene function and manipulate neural network in vertebrates. In the present study, we evaluated the ability of PhiC31 phage integrase to induce genomic recombination in transgenic mice. PhiC31 is the integrase encoded by the Streptomyces bacteriophage that promotes recombination between heterotypic attP and attB sites. We generated transgenic mice that express codon-optimized PhiC31 (PhiC31o) in neural stem/progenitor cells or tyrosine hydroxylase (TH) expressing catecholaminergic neurons. PhiC31 was functional in these cells and capable of excising a transcriptional stop cassette flanked by PhiC31-specific attP/B recognition sites. PhiC31-ER(T2), a fusion protein of PhiC31o (without the nuclear localization signal) and the mutated ligand-binding domain of the human estrogen receptor, was able to induce recombination in neural stem/progenitor cells in a tamoxifen-dependent manner, but the recombination rate was less efficient than for PhiC31. Thus, PhiC31 integrase is functional in transgenic mice and is suitable for mosaic recombination in restricted cell populations.
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Affiliation(s)
- Itaru Imayoshi
- Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan.
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Abstract
On the strengths of forward genetics and embryology, the zebrafish Danio rerio has become an ideal system for the study of early vertebrate development. However, additional tools will be needed to perform more sophisticated analyses and to successfully carry this model into new areas of study such as adult physiology, cancer, and aging. As improved tools make transgenesis more and more efficient, the stage has been set for precise modification of the zebrafish genome such as are done in other model organisms. Genome engineering strategies employing site-specific recombinase (SSR) systems such as Cre/lox and Flp/FRT have become invaluable to the study of gene function in the mouse and Drosophila and are now being exploited in zebrafish as well. My laboratory has begun to use another such SSR, the integrase encoded by the Streptomyces bacteriophage PhiC31, for manipulation of the zebrafish genome. The PhiC31 integrase promotes recombination between an attachment site in the phage (attP) and another on the bacterial chromosome (attB). Here I describe strategies using the PhiC31 integrase to mediate recombination of transgenes containing attP and attB sites in cis to excise elements with spatial and temporal specificity. The feasibility of the intramolecular recombination approach having been established, I discuss prospects for employing PhiC31 integrase for intermolecular recombination, i.e., transgene integration at defined sites in the genome.
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Affiliation(s)
- James A Lister
- Department of Human and Molecular Genetics and Massey Cancer Center, Virginia Commonwealth University School of Medicine, Box 980033, Richmond, Virginia, USA
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Waldner C, Rempel O, Schütte F, Yanik M, Solomentsew N, Ryffel GU. Double conditional human embryonic kidney cell line based on FLP and ΦC31 mediated transgene integration. BMC Res Notes 2011; 4:420. [PMID: 22008483 PMCID: PMC3208510 DOI: 10.1186/1756-0500-4-420] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 10/18/2011] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND FLP recombinase mediated integration into a pre-integrated FRT site is routinely used to generate highly reproducible stable transgenic cell lines. In this study, we broaden the system of site specific integration by introducing ΦC31 integrase mediated integration into attP sites. RESULTS We generated a HEK293 host cell line with a single copy FRT as well as an attP site allowing site specific integration of two distinct transgenes. To achieve conditional control, we used the tetracycline and Shld1 inducible systems. By introducing fluorescent reporters we show that integration and induction of two transgenes are completely independent. We applied this new technique to investigate the effect of HNF4α on proliferation of HEK293 cells by introducing HNF4α into each integration site. We obtained in two independent cell lines highly reproducible results that prove the usefulness of this novel HEK-attP/FRT cell line. CONCLUSIONS In this study we have established and applied a HEK-attP/FRT cell line that allows site specific integration of two conditional transgenes using the FLP recombinase as well as the ΦC31 integrase.
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Affiliation(s)
- Christoph Waldner
- Institut für Zellbiologie (Tumorforschung), Universität Duisburg-Essen, Hufelandstr, 55, D-45122 Essen, Germany.
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Preliminary study on the DNA-binding properties of phage ΦC31 integrase. Gene 2011; 484:47-51. [DOI: 10.1016/j.gene.2011.05.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 05/23/2011] [Indexed: 11/22/2022]
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Iri-Sofla FJ, Rahbarizadeh F, Ahmadvand D, Rasaee MJ. Nanobody-based chimeric receptor gene integration in Jurkat cells mediated by φC31 integrase. Exp Cell Res 2011; 317:2630-41. [PMID: 21906589 DOI: 10.1016/j.yexcr.2011.08.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 08/10/2011] [Accepted: 08/22/2011] [Indexed: 11/27/2022]
Abstract
The crucial role of T lymphocytes in anti-tumor immunity has led to the development of novel strategies that can target and activate T cells against tumor cells. Recombinant DNA technology has been used to generate non-MHC-restricted chimeric antigen receptors (CARs). Here, we constructed a panel of recombinant CAR that harbors the anti-MUC1 nanobody and the signaling and co-signaling moieties (CD3ζ/CD28) with different spacer regions derived from human IgG3 with one or two repeats of the hinge sequence or the hinge region of FcγRII. The PhiC31 integrase system was employed to investigate if the recombination efficiency could be recruited for high and stable expression of T cell chimeric receptor genes. The effect of nuclear localization signal (NLS) and two different promoters (CMV and CAG) on efficacy of PhiC31 integrase in human T cell lines was evaluated. The presence of integrase in combination with NLS, mediated up to 7.6 and 8.5 fold increases in CAR expression in ZCHN-attB and ZCHHN-attB cassette integrated T cells, respectively. Our results showed that highly efficient and stable transduction of the Jurkat cell line by PhiC31 integrase is a feasible modality for generating anti-cancer chimeric T cells for use in cancer immunotherapy.
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Affiliation(s)
- Farnoush Jafari Iri-Sofla
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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Streamlined platform for short hairpin RNA interference and transgenesis in cultured mammalian cells. Proc Natl Acad Sci U S A 2011; 108:12799-804. [PMID: 21768390 DOI: 10.1073/pnas.1103532108] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Sequence-specific gene silencing by short hairpin (sh) RNAs has recently emerged as an indispensable tool for understanding gene function and a promising avenue for drug discovery. However, a wider biomedical use of this approach is hindered by the lack of straightforward methods for achieving uniform expression of shRNAs in mammalian cell cultures. Here we report a high-efficiency and low-background (HILO) recombination-mediated cassette exchange (RMCE) technology that yields virtually homogeneous cell pools containing doxycycline-inducible shRNA elements in a matter of days and with minimal efforts. To ensure immediate utility of this approach for a wider research community, we modified 11 commonly used human (A549, HT1080, HEK293T, HeLa, HeLa-S3, and U2OS) and mouse (CAD, L929, N2a, NIH 3T3, and P19) cell lines to be compatible with the HILO-RMCE process. Because of its technical simplicity and cost efficiency, the technology will be advantageous for both low- and high-throughput shRNA experiments. We also provide evidence that HILO-RMCE will facilitate a wider range of molecular and cell biology applications by allowing one to rapidly engineer cell populations expressing essentially any transgene of interest.
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Takata Y, Kondo S, Goda N, Kanegae Y, Saito I. Comparison of efficiency between FLPe and Cre for recombinase-mediated cassette exchange in vitro and in adenovirus vector production. Genes Cells 2011; 16:765-77. [DOI: 10.1111/j.1365-2443.2011.01526.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Ma QW. [Progress of φC31 integrase system in site-specific integration]. YI CHUAN = HEREDITAS 2011; 33:567-75. [PMID: 21684861 DOI: 10.3724/sp.j.1005.2011.00567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Integrase of phage fC31 catalyses the homologous recombination between Streptomyces attachment site attB and the phage attachment site attP. Meanwhile, this integrase can mediate integration of attB-containing donor plasmids into the pseudo attP sites in eukaryotic genomes by a site-specific manner and resulting long-term and robust expression of integrated genes. Nowadays, fC31 integrase system is becoming a potential tool for genome modification, gene therapy and transgenic research. Recent progress of fC31 integrase system in integration mode in mammalian genomes, efficiency improvement and researches concerned on transgenic safety were summarized in this review.
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Affiliation(s)
- Qing-Wen Ma
- Children's Hospital of Shanghai, Institute of Medical Genetics, Shanghai JiaoTong University, Shanghai 200040, China.
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Monetti C, Nishino K, Biechele S, Zhang P, Baba T, Woltjen K, Nagy A. PhiC31 integrase facilitates genetic approaches combining multiple recombinases. Methods 2011; 53:380-5. [DOI: 10.1016/j.ymeth.2010.12.023] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 12/01/2010] [Accepted: 12/17/2010] [Indexed: 01/04/2023] Open
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Brown WR, Lee NC, Xu Z, Smith MC. Serine recombinases as tools for genome engineering. Methods 2011; 53:372-9. [DOI: 10.1016/j.ymeth.2010.12.031] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 12/17/2010] [Accepted: 12/20/2010] [Indexed: 01/14/2023] Open
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Carpinteyro-Espín P, Jacinto-Ruíz S, Caballero-Vazquez P, Alvarado-Caudillo Y, Lund G, Rodríguez-Rios D, Martínez-García JA, Wrobel K, Wrobel K, Zaina S. Organomegaly and tumors in transgenic mice with targeted expression of HpaII methyltransferase in smooth muscle cells. Epigenetics 2011; 6:333-43. [PMID: 21107019 DOI: 10.4161/epi.6.3.14089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Current data suggest that angiogenesis, smooth muscle cell migration, differentiation and proliferation may be epigenetically regulated. Prokaryotic DNA methyltransferases have been proposed as tools to modify mammalian DNA methylation. In order to assess the impact of DNA hypermethylation on smooth muscle pathophysiology, we expressed an HpaII site-specific methyltransferase transgene in smooth muscle cells in mice. The enzyme is expected to target only a subset (CCGG) of unmethylated CpG dinucleotides, thus avoiding possible deleterious effects of widespread hypermethylation. Transgenics of two independent lines were born at expected frequencies, showed no obvious abnormalities and were fertile. Nevertheless, ~30% of > 1 year-old transgenics developed organomegaly and ~20% showed a range of tumors. Global DNA methylation was unchanged in transgenic tissue whether hyperplastic or normal, but tumor DNA showed a pronounced global hypermethylation. DNA hypermethylation was not indiscriminate, as five tested tumor suppressor genes showed promoter CpG and non-CpG hypermethylation and transcriptional down-regulation, whereas the methylation status of one intergenic CpG islands, repeated elements (n=2) and non-tumor suppressor gene promoters (n=3) was unchanged. Our work is the first report on the effects of HpaII methyltransferase on endogenous chromatin and in a whole animal. Furthermore, our data expand previous findings that imply that global DNA hypomethylation is not an obligate oncogenic pathway at least in the tumor types examined here.
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A method for producing transgenic cells using a multi-integrase system on a human artificial chromosome vector. PLoS One 2011; 6:e17267. [PMID: 21390305 PMCID: PMC3044732 DOI: 10.1371/journal.pone.0017267] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 01/24/2011] [Indexed: 11/19/2022] Open
Abstract
The production of cells capable of expressing gene(s) of interest is important for a variety of applications in biomedicine and biotechnology, including gene therapy and animal transgenesis. The ability to insert transgenes at a precise location in the genome, using site-specific recombinases such as Cre, FLP, and ΦC31, has major benefits for the efficiency of transgenesis. Recent work on integrases from ΦC31, R4, TP901-1 and Bxb1 phages demonstrated that these recombinases catalyze site-specific recombination in mammalian cells. In the present study, we examined the activities of integrases on site-specific recombination and gene expression in mammalian cells. We designed a human artificial chromosome (HAC) vector containing five recombination sites (ΦC31 attP, R4 attP, TP901-1 attP, Bxb1 attP and FRT; multi-integrase HAC vector) and de novo mammalian codon-optimized integrases. The multi-integrase HAC vector has several functions, including gene integration in a precise locus and avoiding genomic position effects; therefore, it was used as a platform to investigate integrase activities. Integrases carried out site-specific recombination at frequencies ranging from 39.3-96.8%. Additionally, we observed homogenous gene expression in 77.3-87.5% of colonies obtained using the multi-integrase HAC vector. This vector is also transferable to another cell line, and is capable of accepting genes of interest in this environment. These data suggest that integrases have high DNA recombination efficiencies in mammalian cells. The multi-integrase HAC vector enables us to produce transgene-expressing cells efficiently and create platform cell lines for gene expression.
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Liesner R, Zhang W, Noske N, Ehrhardt A. Critical amino acid residues within the φC31 integrase DNA-binding domain affect recombination activities in mammalian cells. Hum Gene Ther 2010; 21:1104-18. [PMID: 20415519 DOI: 10.1089/hum.2010.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The bacteriophage-derived ϕC31 integrase system represents an attractive tool for site-directed recombination in mammalian cells. Its integration reaction is based on recombination between the attachment site attB within an episomal substrate plasmid and either the bacteriophage-derived wild-type attachment site attP or pseudo-attP attachment sites (attP') present in the mammalian genome. In the present study we aimed at increasing the safety and efficiency of ϕC31 integrase-mediated recombination by mutating the DNA-binding domain located at the C terminus. Using an alanine mutagenesis approach, we generated 22 ϕC31 point mutants that were screened for activities in mammalian cells. Intramolecular excision assays based on recombination between attB and attP revealed five mutants with 2-fold enhanced excision activity. Importantly, we also identified mutants showing enhanced recombination activities between attB and three previously described attP' sites detected in the mammalian genome, indicating that there may be enhanced specificity for these hot spots. Several mutants showed, in mammalian cells, integration activities that increased in a cell line-dependent manner. The combination of beneficial mutations in addition to optimization of the integrase plasmid dose enhanced integration efficiencies up to 5.5-fold. We also identified three ϕC31 integrase mutants that were recombination defective in all applied assays, suggesting that these amino acid residues are essential for the functionality of ϕC31 integrase in mammalian cells. In summary, we identified critical amino acid residues within the ϕC31 DNA-binding domain. With respect to site-directed recombination and genome engineering these findings have important implications for improved ϕC31 protein design.
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Affiliation(s)
- Raphael Liesner
- Department of Virology, Max von Pettenkofer Institute, Ludwig Maximilians University Munich, Germany
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Sorrell DA, Robinson CJ, Smith JA, Kolb AF. Recombinase mediated cassette exchange into genomic targets using an adenovirus vector. Nucleic Acids Res 2010; 38:e123. [PMID: 20371519 PMCID: PMC2887974 DOI: 10.1093/nar/gkq192] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Recombinase mediated cassette exchange (RMCE) is a process in which site-specific recombinases exchange one gene cassette flanked by a pair of incompatible target sites for another cassette flanked by an identical pair of sites. Typically one cassette is present in the host genome, whereas the other gene cassette is introduced into the host cell by chemical or biological means. We show here that the frequency of cassette exchange is dependent on the relative and absolute quantities of the transgene cassette and the recombinase. We were able to successfully modify genomic targets not only by electroporation or chemically mediated gene transfer but also by using an adenovirus vector carrying both the transgene cassette to be inserted and the recombinase coding region. RMCE proceeds efficiently in cells in which the adenovirus vector is able to replicate. In contrast, insufficient quantities of the transgene cassette are produced in cells in which the virus cannot replicate. Additional transfection of the transgene cassette significantly enhances the RMCE frequency. This demonstrates that an RMCE system in the context of a viral vector allows the site directed insertion of a transgene into a defined genomic site.
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Affiliation(s)
- David A Sorrell
- Molecular Recognition Group, Hannah Research Institute, Ayr, KA6 5HL, UK
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Kempe K, Rubtsova M, Berger C, Kumlehn J, Schollmeier C, Gils M. Transgene excision from wheat chromosomes by phage phiC31 integrase. PLANT MOLECULAR BIOLOGY 2010; 72:673-687. [PMID: 20127141 DOI: 10.1007/s11103-010-9606-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Accepted: 01/17/2010] [Indexed: 05/28/2023]
Abstract
The Streptomyces phage phiC31 integrase was tested for its ability to excise transgenic DNA from the wheat genome by site-specific recombination. Plants that stably express phiC31 integrase were crossed to plants carrying a target construct bearing the phiC31 recognition sites, attP and attB. In the progeny, phiC31 recombinase mediates recombination between the att sites of the target locus, which results in excision of the intervening DNA. Recombination events could be identified in 34 independent wheat lines by PCR and Southern blot analysis and by sequencing of the excision footprints. Recombinant loci were inherited to the subsequent generation. The results presented here establish the integrase-att system as a tool for catalysing the precise elimination of DNA sequences from wheat chromosomes.
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Affiliation(s)
- Katja Kempe
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben, Corrensstr. 3, 06466, Gatersleben, Germany
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Aneja MK, Geiger J, Imker R, Uzgun S, Kormann M, Hasenpusch G, Maucksch C, Rudolph C. Optimization of Streptomyces bacteriophage phi C31 integrase system to prevent post integrative gene silencing in pulmonary type II cells. Exp Mol Med 2010; 41:919-34. [PMID: 19745601 DOI: 10.3858/emm.2009.41.12.098] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
phi C31 integrase has emerged as a potent tool for achieving long-term gene expression in different tissues. The present study aimed at optimizing elements of phi C31 integrase system for alveolar type II cells. Luciferase and beta-galactosidase activities were measured at different time points post transfection. 5-Aza-2'deoxycytidine (AZA) and trichostatin A (TSA) were used to inhibit DNA methyltransferase and histone deacetylase complex (HDAC) respectively. In A549 cells, expression of the integrase using a CMV promoter resulted in highest integrase activity, whereas in MLE12 cells, both CAG and CMV promoter were equally effective. Effect of polyA site was observed only in A549 cells, where replacement of SV40 polyA by bovine growth hormone (BGH) polyA site resulted in an enhancement of integrase activity. Addition of a C-terminal SV40 nuclear localization signal (NLS) did not result in any significant increase in integrase activity. Long-term expression studies with AZA and TSA, provided evidence for post-integrative gene silencing. In MLE12 cells, both DNA methylases and HDACs played a significant role in silencing, whereas in A549 cells, it could be attributed majorly to HDAC activity. Donor plasmids comprising cellular promoters ubiquitin B (UBB), ubiquitin C (UCC) and elongation factor 1 alpha (EF1 alpha) in an improved backbone prevented post-integrative gene silencing. In contrast to A549 and MLE12 cells, no silencing could be observed in human bronchial epithelial cells, BEAS-2B. Donor plasmid coding for murine erythropoietin under the EF1 alpha promoter when combined with phi C31 integrase resulted in higher long-term erythropoietin expression and subsequently higher hematocrit levels in mice after intravenous delivery to the lungs. These results provide evidence for cell specific post integrative gene silencing with C31 integrase and demonstrate the pivotal role of donor plasmid in long-term expression attained with this system.
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Affiliation(s)
- Manish Kumar Aneja
- Division of Molecular Pulmonology, Department of Pediatrics, Ludwig-Maximilians University, Lindwurmstrasse 2A, 80337 Munich, Germany
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Genetically modified mice-successes and failures of a widely used technology. Pflugers Arch 2010; 459:557-67. [PMID: 20140450 DOI: 10.1007/s00424-009-0770-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 11/28/2009] [Accepted: 11/30/2009] [Indexed: 12/31/2022]
Abstract
Genetically modified mice, created by random integration of a transgene into the genome or by targeted mutation of a specific gene, have proven to be extremely powerful tools for studying gene function in vivo. In this article, we give (1) a short overview of the traditional methods in mouse transgenesis and (2) a discussion of the problems with these methods, (3) more recent methods that were developed to overcome these problems, and (4) an outlook on future directions in gene targeting.
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