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Brown DM, Glass JI. Technology used to build and transfer mammalian chromosomes. Exp Cell Res 2020; 388:111851. [PMID: 31952951 DOI: 10.1016/j.yexcr.2020.111851] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/09/2020] [Accepted: 01/14/2020] [Indexed: 01/05/2023]
Abstract
In the near twenty-year existence of the human and mammalian artificial chromosome field, the technologies for artificial chromosome construction and installation into desired cell types or organisms have evolved with the rest of modern molecular and synthetic biology. Medical, industrial, pharmaceutical, agricultural, and basic research scientists seek the as yet unrealized promise of human and mammalian artificial chromosomes. Existing technologies for both top-down and bottom-up approaches to construct these artificial chromosomes for use in higher eukaryotes are very different but aspire to achieve similar results. New capacity for production of chromosome sized synthetic DNA will likely shift the field towards more bottom-up approaches, but not completely. Similarly, new approaches to install human and mammalian artificial chromosomes in target cells will compete with the microcell mediated cell transfer methods that currently dominate the field.
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Brown DM, Chan YA, Desai PJ, Grzesik P, Oldfield LM, Vashee S, Way JC, Silver PA, Glass JI. Efficient size-independent chromosome delivery from yeast to cultured cell lines. Nucleic Acids Res 2017; 45:e50. [PMID: 27980064 PMCID: PMC5397165 DOI: 10.1093/nar/gkw1252] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 12/13/2016] [Indexed: 01/04/2023] Open
Abstract
The delivery of large DNA vectors (>100 000 bp) remains a limiting step in the engineering of mammalian cells and the development of human artificial chromosomes (HACs). Yeast is commonly used to assemble genetic constructs in the megabase size range, and has previously been used to transfer constructs directly into cultured cells. We improved this method to efficiently deliver large (1.1 Mb) synthetic yeast centromeric plasmids (YCps) to cultured cell lines at rates similar to that of 12 kb YCps. Synchronizing cells in mitosis improved the delivery efficiency by 10-fold and a statistical design of experiments approach was employed to boost the vector delivery rate by nearly 300-fold from 1/250 000 to 1/840 cells, and subsequently optimize the delivery process for multiple mammalian, avian, and insect cell lines. We adapted this method to rapidly deliver a 152 kb herpes simplex virus 1 genome cloned in yeast into mammalian cells to produce infectious virus.
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Affiliation(s)
- David M Brown
- Synthetic Biology and Bioenergy, J. Craig Venter Institute, Rockville, MD, 20850, USA.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Yujia A Chan
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.,Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA
| | - Prashant J Desai
- Johns Hopkins University, Sidney Kimmel Comprehensive Cancer Center Johns Hopkins, Viral Oncology Program, Baltimore, MD 21231, USA
| | - Peter Grzesik
- Johns Hopkins University, Sidney Kimmel Comprehensive Cancer Center Johns Hopkins, Viral Oncology Program, Baltimore, MD 21231, USA
| | - Lauren M Oldfield
- Synthetic Biology and Bioenergy, J. Craig Venter Institute, Rockville, MD, 20850, USA
| | - Sanjay Vashee
- Synthetic Biology and Bioenergy, J. Craig Venter Institute, Rockville, MD, 20850, USA
| | - Jeffrey C Way
- Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.,Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA
| | - John I Glass
- Synthetic Biology and Bioenergy, J. Craig Venter Institute, Rockville, MD, 20850, USA
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Recillas-Targa F. Multiple strategies for gene transfer, expression, knockdown, and chromatin influence in mammalian cell lines and transgenic animals. Mol Biotechnol 2007; 34:337-54. [PMID: 17284781 DOI: 10.1385/mb:34:3:337] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/1999] [Revised: 11/30/1999] [Accepted: 11/30/1999] [Indexed: 12/31/2022]
Abstract
Manipulation of the eukaryotic genome has contributed to the progress in our knowledge of multicellular organisms but has also ameliorated our experimental strategies. Biological questions can now be addressed with more efficiency and reproducibility. There are new and varied strategies for gene transfer and sequence manipulation with improved methodologies that facilitate the acquisition of results. Cellular systems and transgenic animals have demonstrated their invaluable benefits. In this review, I present an overview of the methods of gene transfer with particular attention to cultured cell lines and large-scale sequence vectors, like artificial chromosomes, with the possibility of their manipulation based on homologous recombination strategies. Alternative strategies of gene transfer, including retroviral vectors, are also described and the applications of such methods are discussed. Finally, several comments are made about the influence of chromatin structure on gene expression. Recent experimental data have shown that for convenient stable transgene expression, the influence of chromatin structure should be seriously taken into account. Novel chromatin regulatory and structural elements are proposed as an alternative for proper and sustained gene expression. These chromatin elements are facing a new era in transgenesis and we are probably beginning a new generation of gene and cancer therapy vectors.
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Affiliation(s)
- Félix Recillas-Targa
- Instituto de Fisiología Celular, Departamento de Genética Molecular, Universidad Nacional Autónoma de México Apartado Postal 70-242, México D.F. 04510.
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Abstract
Realizing the potential of stem cell biology requires the modulation of self-renewal and differentiation, both of which are incompletely understood. This chapter describes methods for the design, development, and implementation of cell-based screens of small molecules, genes and expressed proteins for modulation of stem and progenitor cell fate. These include the engineering of embryonic and other stem cells with gene promoter-reporter protein constructs and their application in automated screening. We discuss considerations of promoter reporter selection, assay development and implementation, and image acquisition, analysis, and data handling. Such black-box screens are useful for the identification of probes of developmental processes and should provide tools that will identify druggable targets for biochemical assays.
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Affiliation(s)
- Paul J Bushway
- Burnham Institute for Medical Research, La Jolla, CA, USA
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Howell GR, Munroe RJ, Schimenti JC. Transgenic rescue of the mouse t complex haplolethal locus Thl1. Mamm Genome 2005; 16:838-46. [PMID: 16284799 DOI: 10.1007/s00335-005-0045-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2005] [Accepted: 07/07/2005] [Indexed: 10/25/2022]
Abstract
Chromosomal deletions can uncover haploinsufficient or imprinted regions of the genome. Previously, the haploinsufficient locus t haplolethal 1 (Thl1) was identified and localized to a 1.3-Mb region using overlapping deletions around the Sod2 and D17Leh94 loci of the mouse t complex on Chr 17. Germline chimeric mice, produced from embryonic stem (ES) cells containing radiation-induced deletions of the Thl1 locus, never produced viable deletion-bearing progeny when mated to C57BL/6J (B6) females. However, deletion-bearing offspring could be obtained by mating to females of other strains. In this article we describe a transgenic approach to narrow the critical region for Thl1. BAC clones were introduced into a deletion-bearing ES cell line and one was shown to rescue the Thl1 phenotype, reducing the critical region to 140 kb. Analysis of the gene content of this region suggests two strong Thl1 candidates, Pdcd2 and a novel SET domain-containing gene termed Tset1. A more detailed analysis using mice carrying overlapping deletions identified subregions that influence the phenotypic characteristics of Thl1 hemizygotes.
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Affiliation(s)
- Gareth R Howell
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04660, USA
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Liu H, Kawabe A, Matsunaga S, Kim YH, Higashi T, Uchiyama S, Harashima S, Kobayashi A, Fukui K. An Arabidopsis thaliana Gene on the Yeast Artificial Chromosome Can Be Transcribed in Tobacco Cells. CYTOLOGIA 2004. [DOI: 10.1508/cytologia.69.235] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Haibo Liu
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| | - Akira Kawabe
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| | - Sachihiro Matsunaga
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| | - Yeon Hee Kim
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| | - Tsunehito Higashi
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| | - Susumu Uchiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| | - Satoshi Harashima
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| | - Akio Kobayashi
- Department of Biotechnology, Graduate School of Engineering, Osaka University
| | - Kiichi Fukui
- Department of Biotechnology, Graduate School of Engineering, Osaka University
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Bihl F, Salez L, Beaubier M, Torres D, Larivière L, Laroche L, Benedetto A, Martel D, Lapointe JM, Ryffel B, Malo D. Overexpression of Toll-like receptor 4 amplifies the host response to lipopolysaccharide and provides a survival advantage in transgenic mice. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2003; 170:6141-50. [PMID: 12794144 DOI: 10.4049/jimmunol.170.12.6141] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Toll-like receptors are transmembrane proteins that are involved in the innate immune recognition of microbial constituents. Among them, Toll-like receptor 4 (Tlr4) is a crucial signal transducer for LPS, the major component of Gram-negative bacteria outer cell membrane. The contribution of Tlr4 to the host response to LPS and to infection with virulent Salmonella typhimurium was studied in four transgenic (Tg) strains including three overexpressing Tlr4. There was a good correlation between the level of Tlr4 mRNA expression and the sensitivity to LPS both in vitro and in vivo: Tg mice possessing the highest number of Tlr4 copies respond the most to LPS. Overexpression of Tlr4 by itself appears to have a survival advantage in Tg mice early during infection: animals possessing more than two copies of the gene survived longer and in a greater percentage to Salmonella infection. The beneficial effect of Tlr4 overexpression is greatly enhanced when the mice present a wild-type allele at natural resistance-associated macrophage protein 1, another critical innate immune gene involved in resistance to infection with Salmonella. Tlr4 and natural resistance-associated macrophage protein 1 exhibit functional epistatic interaction to improve the capacity of the host to control bacterial replication. However, this early improvement in disease resistance is not conducted later during infection, because mice overexpressing Tlr4 developed an excessive inflammatory response detrimental to the host.
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MESH Headings
- Adjuvants, Immunologic/biosynthesis
- Adjuvants, Immunologic/genetics
- Adjuvants, Immunologic/physiology
- Animals
- Cell Membrane/genetics
- Cell Membrane/immunology
- Cell Membrane/metabolism
- Cells, Cultured
- Crosses, Genetic
- Flow Cytometry
- Gene Dosage
- Gene Expression Regulation/immunology
- Injections, Intraperitoneal
- Lipopolysaccharides/administration & dosage
- Lipopolysaccharides/pharmacology
- Lymphocyte Activation/immunology
- Membrane Glycoproteins/biosynthesis
- Membrane Glycoproteins/genetics
- Membrane Glycoproteins/physiology
- Mice
- Mice, Inbred C3H
- Mice, Inbred C57BL
- Mice, Transgenic
- Receptors, Cell Surface/biosynthesis
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/physiology
- Reverse Transcriptase Polymerase Chain Reaction
- Salmonella Infections, Animal/genetics
- Salmonella Infections, Animal/immunology
- Salmonella Infections, Animal/mortality
- Salmonella Infections, Animal/pathology
- Shock, Septic/genetics
- Shock, Septic/immunology
- Shock, Septic/mortality
- Survival Rate
- Toll-Like Receptor 4
- Toll-Like Receptors
- Transgenes/immunology
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Affiliation(s)
- Franck Bihl
- Department of Human Genetics, McGill University, and Center for the Study of Host Resistance, Montreal General Hospital, Montréal, Québec, Canada
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Abstract
In 1993, several groups, working independently, reported the successful generation of transgenic mice with yeast artificial chromosomes (YACs) using standard techniques. The transfer of these large fragments of cloned genomic DNA correlated with optimal expression levels of the transgenes, irrespective of their location in the host genome. Thereafter, other groups confirmed the advantages of YAC transgenesis and position-independent and copy number-dependent transgene expression were demonstrated in most cases. The transfer of YACs to the germ line of mice has become popular in many transgenic facilities to guarantee faithful expression of transgenes. This technique was rapidly exported to livestock and soon transgenic rabbits, pigs and other mammals were produced with YACs. Transgenic animals were also produced with bacterial or P1-derived artificial chromosomes (BACs/PACs) with similar success. The use of YACs, BACs and PACs in transgenesis has allowed the discovery of new genes by complementation of mutations, the identification of key regulatory sequences within genomic loci that are crucial for the proper expression of genes and the design of improved animal models of human genetic diseases. Transgenesis with artificial chromosomes has proven useful in a variety of biological, medical and biotechnological applications and is considered a major breakthrough in the generation of transgenic animals. In this report, we will review the recent history of YAC/BAC/PAC-transgenic animals indicating their benefits and the potential problems associated with them. In this new era of genomics, the generation and analysis of transgenic animals carrying artificial chromosome-type transgenes will be fundamental to functionally identify and understand the role of new genes, included within large pieces of genomes, by direct complementation of mutations or by observation of their phenotypic consequences.
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Affiliation(s)
- P Giraldo
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Madrid, Spain
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Wang Z, Engler P, Longacre A, Storb U. An efficient method for high-fidelity BAC/PAC retrofitting with a selectable marker for mammalian cell transfection. Genome Res 2001; 11:137-42. [PMID: 11156622 PMCID: PMC311050 DOI: 10.1101/gr.159001] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Large-scale genomic sequencing projects have provided DNA sequence information for many genes, but the biological functions for most of them will only be known through functional studies. Bacterial artificial chromosomes (BACs) and P1-derived artificial chromosomes (PACs) are large genomic clones stably maintained in bacteria and are very important in functional studies through transfection because of their large size and stability. Because most BAC or PAC vectors do not have a mammalian selection marker, transfecting mammalian cells with genes cloned in BACs or PACs requires the insertion into the BAC/PAC of a mammalian selectable marker. However, currently available procedures are not satisfactory in efficiency and fidelity. We describe a very simple and efficient procedure that allows one to retrofit dozens of BACs in a day with no detectable deletions or unwanted recombination. We use a BAC/PAC retrofitting vector that, on transformation into competent BAC or PAC strains, will catalyze the specific insertion of itself into BAC/PAC vectors through in vivo cre/loxP site-specific recombination.
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Affiliation(s)
- Z Wang
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois 60637, USA
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Marschall P, Malik N, Larin Z. Transfer of YACs up to 2.3 Mb intact into human cells with polyethylenimine. Gene Ther 1999; 6:1634-7. [PMID: 10490774 DOI: 10.1038/sj.gt.3300975] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The transfer of large YAC DNA into human cells is a laborious procedure. High quality pulsed field gel purified DNA is required, which is easily sheared during manipulation before transfection or degraded in the endosome of the cell following transfection. NaCl and polyamines compact and prevent DNA from shearing, but may not consistently protect DNA after transfection. We investigated if other polycations such as poly-L-lysine (PLL) and polyethylenimine (PEI) could condense and protect large YAC DNA (up to 2.3 Mb) from being degraded after lipofection. DNA condensation was monitored by a gel retardation assay, and atomic force microscopy (AFM). DNA was retarded in the gel when complexed with high concentrations of PLL and PEI, indicating that DNA had condensed. However, AFM images of PLL-DNA complexes showed aggregates of DNA molecules resulting from incomplete condensation, whereas PEI-DNA complexes produced condensed particles approximately 30-60 nm. Exogenous PLL-DNA remained intact in 36% of positive clones after lipofection, whereas PEI-DNA was intact in 100% of positive clones. PEI is a better condensing reagent than PLL, protecting DNA from shearing and endosomal degradation, and assists in delivering YACs up to 2.3 Mb intact into human cells.
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Affiliation(s)
- P Marschall
- Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS, UK
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