1
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Gambogi CW, Birchak GJ, Mer E, Brown DM, Yankson G, Kixmoeller K, Gavade JN, Espinoza JL, Kashyap P, Dupont CL, Logsdon GA, Heun P, Glass JI, Black BE. Efficient formation of single-copy human artificial chromosomes. Science 2024; 383:1344-1349. [PMID: 38513017 PMCID: PMC11059994 DOI: 10.1126/science.adj3566] [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: 06/21/2023] [Accepted: 01/23/2024] [Indexed: 03/23/2024]
Abstract
Large DNA assembly methodologies underlie milestone achievements in synthetic prokaryotic and budding yeast chromosomes. While budding yeast control chromosome inheritance through ~125-base pair DNA sequence-defined centromeres, mammals and many other eukaryotes use large, epigenetic centromeres. Harnessing centromere epigenetics permits human artificial chromosome (HAC) formation but is not sufficient to avoid rampant multimerization of the initial DNA molecule upon introduction to cells. We describe an approach that efficiently forms single-copy HACs. It employs a ~750-kilobase construct that is sufficiently large to house the distinct chromatin types present at the inner and outer centromere, obviating the need to multimerize. Delivery to mammalian cells is streamlined by employing yeast spheroplast fusion. These developments permit faithful chromosome engineering in the context of metazoan cells.
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Affiliation(s)
- Craig W. Gambogi
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute
| | - Gabriel J. Birchak
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Graduate Program in Cell and Molecular Biology Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104 USA
| | - Elie Mer
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute
| | | | - George Yankson
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Kathryn Kixmoeller
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute
| | - Janardan N. Gavade
- Department of Biochemistry and Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute
| | | | - Prakriti Kashyap
- Department of Biochemistry and Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute
| | | | - Glennis A. Logsdon
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute
| | - Patrick Heun
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | | | - Ben E. Black
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute
- Graduate Program in Cell and Molecular Biology Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104 USA
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2
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Gambogi CW, Mer E, Brown DM, Yankson G, Gavade JN, Logsdon GA, Heun P, Glass JI, Black BE. Efficient Formation of Single-copy Human Artificial Chromosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.30.547284. [PMID: 37546784 PMCID: PMC10402137 DOI: 10.1101/2023.06.30.547284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Large DNA assembly methodologies underlie milestone achievements in synthetic prokaryotic and budding yeast chromosomes. While budding yeast control chromosome inheritance through ~125 bp DNA sequence-defined centromeres, mammals and many other eukaryotes use large, epigenetic centromeres. Harnessing centromere epigenetics permits human artificial chromosome (HAC) formation but is not sufficient to avoid rampant multimerization of the initial DNA molecule upon introduction to cells. Here, we describe an approach that efficiently forms single-copy HACs. It employs a ~750 kb construct that is sufficiently large to house the distinct chromatin types present at the inner and outer centromere, obviating the need to multimerize. Delivery to mammalian cells is streamlined by employing yeast spheroplast fusion. These developments permit faithful chromosome engineering in the context of metazoan cells.
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Affiliation(s)
- Craig W. Gambogi
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104 USA
| | - Elie Mer
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104 USA
| | | | - George Yankson
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Janardan N. Gavade
- Department of Biochemistry and Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104 USA
| | - Glennis A. Logsdon
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104 USA
| | - Patrick Heun
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | | | - Ben E. Black
- Department of Biochemistry and Biophysics
- Graduate Program in Biochemistry and Molecular Biophysics
- Penn Center for Genome Integrity
- Epigenetics Institute Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104 USA
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3
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Logsdon GA, Gambogi CW, Liskovykh MA, Barrey EJ, Larionov V, Miga KH, Heun P, Black BE. Human Artificial Chromosomes that Bypass Centromeric DNA. Cell 2019; 178:624-639.e19. [PMID: 31348889 PMCID: PMC6657561 DOI: 10.1016/j.cell.2019.06.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 04/07/2019] [Accepted: 06/03/2019] [Indexed: 11/29/2022]
Abstract
Recent breakthroughs with synthetic budding yeast chromosomes expedite the creation of synthetic mammalian chromosomes and genomes. Mammals, unlike budding yeast, depend on the histone H3 variant, CENP-A, to epigenetically specify the location of the centromere-the locus essential for chromosome segregation. Prior human artificial chromosomes (HACs) required large arrays of centromeric α-satellite repeats harboring binding sites for the DNA sequence-specific binding protein, CENP-B. We report the development of a type of HAC that functions independently of these constraints. Formed by an initial CENP-A nucleosome seeding strategy, a construct lacking repetitive centromeric DNA formed several self-sufficient HACs that showed no uptake of genomic DNA. In contrast to traditional α-satellite HAC formation, the non-repetitive construct can form functional HACs without CENP-B or initial CENP-A nucleosome seeding, revealing distinct paths to centromere formation for different DNA sequence types. Our developments streamline the construction and characterization of HACs to facilitate mammalian synthetic genome efforts.
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Affiliation(s)
- Glennis A Logsdon
- Department of Biochemistry and Biophysics, Graduate Program in Biochemistry and Molecular Biophysics, and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Craig W Gambogi
- Department of Biochemistry and Biophysics, Graduate Program in Biochemistry and Molecular Biophysics, and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mikhail A Liskovykh
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Evelyne J Barrey
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Karen H Miga
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Patrick Heun
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Ben E Black
- Department of Biochemistry and Biophysics, Graduate Program in Biochemistry and Molecular Biophysics, and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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4
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The nucleosomes that mark centromere location on chromosomes old and new. Essays Biochem 2019; 63:15-27. [DOI: 10.1042/ebc20180060] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/07/2019] [Accepted: 03/13/2019] [Indexed: 01/02/2023]
Abstract
Abstract
Proper segregation of chromosomes is an essential component of cell division. The centromere is the locus at which the kinetochore—the proteinaceous complex that ties chromosomes to microtubules—forms during mitosis and meiosis. Thus, the centromere is critical for equal segregation of chromosomes. The centromere is characterized by both protein and DNA elements: the histone H3 variant CENP-A epigenetically defines the location of the centromere while centromeric DNA sequences are neither necessary nor sufficient for centromere function. Paradoxically, the DNA sequences play a critical role in new centromere formation. In this essay, we discuss the contribution of both epigenetics and genetics at the centromere. Understanding these contributions is vital to efforts to control centromere formation on synthetic/artificial chromosomes and centromere strength on natural ones.
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5
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Huang YX, Li L, Yang L, Zhang Y. Technique of laser chromosome welding for chromosome repair and artificial chromosome creation. BIOMEDICAL OPTICS EXPRESS 2018; 9:1783-1794. [PMID: 29675319 PMCID: PMC5905923 DOI: 10.1364/boe.9.001783] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/05/2018] [Accepted: 03/06/2018] [Indexed: 06/08/2023]
Abstract
Here we report a technique of laser chromosome welding that uses a violet pulse laser micro-beam for welding. The technique can integrate any size of a desired chromosome fragment into recipient chromosomes by combining with other techniques of laser chromosome manipulation such as chromosome cutting, moving, and stretching. We demonstrated that our method could perform chromosomal modifications with high precision, speed and ease of use in the absence of restriction enzymes, DNA ligases and DNA polymerases. Unlike the conventional methods such as de novo artificial chromosome synthesis, our method has no limitation on the size of the inserted chromosome fragment. The inserted DNA size can be precisely defined and the processed chromosome can retain its intrinsic structure and integrity. Therefore, our technique provides a high quality alternative approach to directed genetic recombination, and can be used for chromosomal repair, removal of defects and artificial chromosome creation. The technique may also have applicability on the manipulation and extension of large pieces of synthetic DNA.
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6
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Athanasopoulos T, Munye MM, Yáñez-Muñoz RJ. Nonintegrating Gene Therapy Vectors. Hematol Oncol Clin North Am 2017; 31:753-770. [DOI: 10.1016/j.hoc.2017.06.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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7
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LaFountaine JS, Fathe K, Smyth HDC. Delivery and therapeutic applications of gene editing technologies ZFNs, TALENs, and CRISPR/Cas9. Int J Pharm 2015; 494:180-94. [PMID: 26278489 DOI: 10.1016/j.ijpharm.2015.08.029] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/05/2015] [Accepted: 08/09/2015] [Indexed: 12/24/2022]
Abstract
In recent years, several new genome editing technologies have been developed. Of these the zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the CRISPR/Cas9 RNA-guided endonuclease system are the most widely described. Each of these technologies utilizes restriction enzymes to introduce a DNA double stranded break at a targeted location with the guide of homologous binding proteins or RNA. Such targeting is viewed as a significant advancement compared to current gene therapy methods that lack such specificity. Proof-of-concept studies have been performed to treat multiple disorders, including in vivo experiments in mammals and even early phase human trials. Careful consideration and investigation of delivery strategies will be required so that the therapeutic potential for gene editing is achieved. In this review, the mechanisms of each of these gene editing technologies and evidence of therapeutic potential will be briefly described and a comprehensive list of past studies will be provided. The pharmaceutical approaches of each of these technologies are discussed along with the current delivery obstacles. The topics and information reviewed herein provide an outline of the groundbreaking research that is being performed, but also highlights the potential for progress yet to be made using these gene editing technologies.
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Affiliation(s)
- Justin S LaFountaine
- The University of Texas at Austin, 2409 University Avenue, Austin, TX 78712, USA
| | - Kristin Fathe
- The University of Texas at Austin, 2409 University Avenue, Austin, TX 78712, USA
| | - Hugh D C Smyth
- The University of Texas at Austin, 2409 University Avenue, Austin, TX 78712, USA.
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8
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Katona RL. De novo formed satellite DNA-based mammalian artificial chromosomes and their possible applications. Chromosome Res 2015; 23:143-57. [DOI: 10.1007/s10577-014-9458-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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9
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Wong SP, Argyros O, Harbottle RP. Sustained expression from DNA vectors. ADVANCES IN GENETICS 2014; 89:113-152. [PMID: 25620010 DOI: 10.1016/bs.adgen.2014.11.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA vectors have the potential to become powerful medical tools for treatment of human disease. The human body has, however, developed a range of defensive strategies to detect and silence foreign or misplaced DNA, which is more typically encountered during infection or chromosomal damage. A clinically relevant human gene therapy vector must overcome or avoid these protections whilst delivering sustained levels of therapeutic gene product without compromising the vitality of the recipient host. Many non-viral DNA vectors trigger these defense mechanisms and are subsequently destroyed or rendered silent. Thus, without modification or considered design, the clinical utility of a typical DNA vector is fundamentally limited due to the transient nature of its transgene expression. The development of safe and persistently expressing DNA vectors is a crucial prerequisite for its successful clinical application and subsequently remains, therefore, one of the main strategic tasks of non-viral gene therapy research. In this chapter we will describe our current understanding of the mechanisms that can destroy or silence DNA vectors and discuss strategies, which have been utilized to improve their sustenance and the level and duration of their transgene expression.
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Affiliation(s)
- Suet Ping Wong
- Leukocyte Biology Section, National Heart & Lung Institute, Imperial College London, London, UK
| | - Orestis Argyros
- Division of Pharmacology-Pharmacotechnology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Richard P Harbottle
- DNA Vector Research, German Cancer Research Centre (DKFZ), Heidelberg, Germany
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10
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Birchler JA. Engineered minichromosomes in plants. CURRENT OPINION IN PLANT BIOLOGY 2014; 19:76-80. [PMID: 24906050 DOI: 10.1016/j.pbi.2014.05.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 04/23/2014] [Accepted: 05/06/2014] [Indexed: 06/03/2023]
Abstract
Platforms for the development of synthetic chromosomes in plants have been produced in several species using telomere mediated chromosomal truncation with the simultaneous inclusion of sites that facilitate further additions to the newly generated minichromosome. By utilizing truncated supernumerary or B chromosomes, the output of the genes on the minichromosome can be amplified. Proof of concept experiments have been successful illustrating that minichromosome platforms can be modified in vivo. Engineered minichromosomes can likely be combined with haploid breeding if they are incorporated into inducer lines given that the observations that basically inert chromosomes from haploid inducer lines can be recovered at workable frequencies in otherwise haploid plants. Future needs of synthetic chromosome development are discussed.
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Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, United States.
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11
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Tóth A, Fodor K, Praznovszky T, Tubak V, Udvardy A, Hadlaczky G, Katona RL. Novel method to load multiple genes onto a mammalian artificial chromosome. PLoS One 2014; 9:e85565. [PMID: 24454889 PMCID: PMC3893256 DOI: 10.1371/journal.pone.0085565] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 12/03/2013] [Indexed: 01/05/2023] Open
Abstract
Mammalian artificial chromosomes are natural chromosome-based vectors that may carry a vast amount of genetic material in terms of both size and number. They are reasonably stable and segregate well in both mitosis and meiosis. A platform artificial chromosome expression system (ACEs) was earlier described with multiple loading sites for a modified lambda-integrase enzyme. It has been shown that this ACEs is suitable for high-level industrial protein production and the treatment of a mouse model for a devastating human disorder, Krabbe's disease. ACEs-treated mutant mice carrying a therapeutic gene lived more than four times longer than untreated counterparts. This novel gene therapy method is called combined mammalian artificial chromosome-stem cell therapy. At present, this method suffers from the limitation that a new selection marker gene should be present for each therapeutic gene loaded onto the ACEs. Complex diseases require the cooperative action of several genes for treatment, but only a limited number of selection marker genes are available and there is also a risk of serious side-effects caused by the unwanted expression of these marker genes in mammalian cells, organs and organisms. We describe here a novel method to load multiple genes onto the ACEs by using only two selectable marker genes. These markers may be removed from the ACEs before therapeutic application. This novel technology could revolutionize gene therapeutic applications targeting the treatment of complex disorders and cancers. It could also speed up cell therapy by allowing researchers to engineer a chromosome with a predetermined set of genetic factors to differentiate adult stem cells, embryonic stem cells and induced pluripotent stem (iPS) cells into cell types of therapeutic value. It is also a suitable tool for the investigation of complex biochemical pathways in basic science by producing an ACEs with several genes from a signal transduction pathway of interest.
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Affiliation(s)
- Anna Tóth
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Katalin Fodor
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Tünde Praznovszky
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Vilmos Tubak
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Andor Udvardy
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Gyula Hadlaczky
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Robert L. Katona
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
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12
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Enukashvily NI, Ponomartsev NV. Mammalian satellite DNA: a speaking dumb. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013; 90:31-65. [PMID: 23582201 DOI: 10.1016/b978-0-12-410523-2.00002-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The tandemly organized highly repetitive satellite DNA is the main DNA component of centromeric/pericentromeric constitutive heterochromatin. For almost a century, it was considered as "junk DNA," only a small portion of which is used for kinetochore formation. The current review summarizes recent data about satellite DNA transcription. The possible functions of the transcripts are discussed.
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13
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Kouprina N, Samoshkin A, Erliandri I, Nakano M, Lee HS, Fu H, Iida Y, Aladjem M, Oshimura M, Masumoto H, Earnshaw WC, Larionov V. Organization of synthetic alphoid DNA array in human artificial chromosome (HAC) with a conditional centromere. ACS Synth Biol 2012; 1:590-601. [PMID: 23411994 DOI: 10.1021/sb3000436] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Human artificial chromosomes (HACs) represent a novel promising episomal system for functional genomics, gene therapy, and synthetic biology. HACs are engineered from natural and synthetic alphoid DNA arrays upon transfection into human cells. The use of HACs for gene expression studies requires the knowledge of their structural organization. However, none of the de novo HACs constructed so far has been physically mapped in detail. Recently we constructed a synthetic alphoid(tetO)-HAC that was successfully used for expression of full-length genes to correct genetic deficiencies in human cells. The HAC can be easily eliminated from cell populations by inactivation of its conditional kinetochore. This unique feature provides a control for phenotypic changes attributed to expression of HAC-encoded genes. This work describes organization of a megabase-size synthetic alphoid DNA array in the alphoid(tetO)-HAC that has been formed from a ~50 kb synthetic alphoid(tetO)-construct. Our analysis showed that this array represents a 1.1 Mb continuous sequence assembled from multiple copies of input DNA, a significant part of which was rearranged before assembling. The tandem and inverted alphoid DNA repeats in the HAC range in size from 25 to 150 kb. In addition, we demonstrated that the structure and functional domains of the HAC remains unchanged after several rounds of its transfer into different host cells. The knowledge of the alphoid(tetO)-HAC structure provides a tool to control HAC integrity during different manipulations. Our results also shed light on a mechanism for de novo HAC formation in human cells.
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Affiliation(s)
- Natalay Kouprina
- Laboratories of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland 20892,
United States
| | - Alexander Samoshkin
- Laboratories of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland 20892,
United States
| | - Indri Erliandri
- Laboratories of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland 20892,
United States
| | - Megumi Nakano
- Laboratory
of Cell Engineering,
Department of Human Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818,
Japan
| | - Hee-Sheung Lee
- Laboratories of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland 20892,
United States
| | - Haiging Fu
- Laboratories of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland 20892,
United States
| | - Yuichi Iida
- Department of Biomedical
Science,
Institute of Regenerative Medicine and Biofunction, Graduate School
of Medical Sciences, Tottori University, Nishi-cho, Yonago, Tottori, Japan
| | - Mirit Aladjem
- Laboratories of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland 20892,
United States
| | - Mitsuo Oshimura
- Department of Biomedical
Science,
Institute of Regenerative Medicine and Biofunction, Graduate School
of Medical Sciences, Tottori University, Nishi-cho, Yonago, Tottori, Japan
| | - Hiroshi Masumoto
- Laboratory
of Cell Engineering,
Department of Human Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818,
Japan
| | - William C. Earnshaw
- Wellcome Trust Centre for Cell
Biology, University of Edinburgh, Edinburgh
EH9 3JR, Scotland
| | - Vladimir Larionov
- Laboratories of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland 20892,
United States
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14
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HACking the centromere chromatin code: insights from human artificial chromosomes. Chromosome Res 2012; 20:505-19. [DOI: 10.1007/s10577-012-9293-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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15
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Hsu CYM, Uludağ H. Nucleic-acid based gene therapeutics: delivery challenges and modular design of nonviral gene carriers and expression cassettes to overcome intracellular barriers for sustained targeted expression. J Drug Target 2012; 20:301-28. [PMID: 22303844 DOI: 10.3109/1061186x.2012.655247] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The delivery of nucleic acid molecules into cells to alter physiological functions at the genetic level is a powerful approach to treat a wide range of inherited and acquired disorders. Biocompatible materials such as cationic polymers, lipids, and peptides are being explored as safer alternatives to viral gene carriers. However, the comparatively low efficiency of nonviral carriers currently hampers their translation into clinical settings. Controlling the size and stability of carrier/nucleic acid complexes is one of the primary hurdles as the physicochemical properties of the complexes can define the uptake pathways, which dictate intracellular routing, endosomal processing, and nucleocytoplasmic transport. In addition to nuclear import, subnuclear trafficking, posttranscriptional events, and immune responses can further limit transfection efficiency. Chemical moieties, reactive linkers or signal peptide have been conjugated to carriers to prevent aggregation, induce membrane destabilization and localize to subcellular compartments. Genetic elements can be inserted into the expression cassette to facilitate nuclear targeting, delimit expression to targeted tissue, and modulate transgene expression. The modular option afforded by both gene carriers and expression cassettes provides a two-tier multicomponent delivery system that can be optimized for targeted gene delivery in a variety of settings.
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Affiliation(s)
- Charlie Yu Ming Hsu
- Department of Biomedical Engineering, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Cananda
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16
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Kim JH, Kononenko A, Erliandri I, Kim TA, Nakano M, Iida Y, Barrett JC, Oshimura M, Masumoto H, Earnshaw WC, Larionov V, Kouprina N. Human artificial chromosome (HAC) vector with a conditional centromere for correction of genetic deficiencies in human cells. Proc Natl Acad Sci U S A 2011; 108:20048-53. [PMID: 22123967 PMCID: PMC3250132 DOI: 10.1073/pnas.1114483108] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Human artificial chromosome (HAC)-based vectors offer a promising system for delivery and expression of full-length human genes of any size. HACs avoid the limited cloning capacity, lack of copy number control, and insertional mutagenesis caused by integration into host chromosomes that plague viral vectors. We previously described a synthetic HAC that can be easily eliminated from cell populations by inactivation of its conditional kinetochore. Here, we demonstrate the utility of this HAC, which has a unique gene acceptor site, for delivery of full-length genes and correction of genetic deficiencies in human cells. A battery of functional tests was performed to demonstrate expression of NBS1 and VHL genes from the HAC at physiological levels. We also show that phenotypes arising from stable gene expression can be reversed when cells are "cured" of the HAC by inactivating its kinetochore in proliferating cell populations, a feature that provides a control for phenotypic changes attributed to expression of HAC-encoded genes. This generation of human artificial chromosomes should be suitable for studies of gene function and therapeutic applications.
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MESH Headings
- Animals
- Autoantigens/metabolism
- CHO Cells
- Cell Cycle Proteins/genetics
- Centromere/genetics
- Centromere Protein A
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomes, Artificial, Human/genetics
- Chromosomes, Artificial, Yeast/genetics
- Cloning, Molecular
- Cricetinae
- Cricetulus
- Gene Expression
- Genetic Complementation Test
- Genetic Therapy/methods
- Genetic Vectors/genetics
- Genome, Human/genetics
- Humans
- In Situ Hybridization, Fluorescence
- Integrases/metabolism
- Mutagenesis, Insertional/genetics
- Nuclear Proteins/genetics
- Recombination, Genetic/genetics
- Von Hippel-Lindau Tumor Suppressor Protein/genetics
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Affiliation(s)
| | | | | | - Tae-Aug Kim
- Tumor and Stem Cell Biology, National Cancer Institute, Bethesda, MD 20892
| | - Megumi Nakano
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Yuichi Iida
- Institute of Regenerative Medicine and Biofunction, Tottori University, Tottori 683-8503, Japan
| | - J. Carl Barrett
- Translational Sciences for Oncology Innovative Medicine, AstraZeneca, Boston, MA 02451; and
| | - Mitsuo Oshimura
- Institute of Regenerative Medicine and Biofunction, Tottori University, Tottori 683-8503, Japan
| | | | - William C. Earnshaw
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH14 4AS, Scotland
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Gaeta RT, Masonbrink RE, Krishnaswamy L, Zhao C, Birchler JA. Synthetic chromosome platforms in plants. ANNUAL REVIEW OF PLANT BIOLOGY 2011; 63:307-330. [PMID: 22136564 DOI: 10.1146/annurev-arplant-042110-103924] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Synthetic chromosomes provide the means to stack transgenes independently of the remainder of the genome. Combining them with haploid breeding could provide the means to transfer many transgenes more easily among varieties of the same species. The epigenetic nature of centromere formation complicates the production of synthetic chromosomes. However, telomere-mediated truncation coupled with the introduction of site-specific recombination cassettes has been used to produce minichromosomes consisting of little more than a centromere. Methods that have been developed to modify genes in vivo could be applied to minichromosomes to improve their utility and to continue to increase their length and genic content. Synthetic chromosomes establish the means to add or subtract multiple transgenes, multigene complexes, or whole biochemical pathways to plants to change their properties for agricultural applications or to use plants as factories for the production of foreign proteins or metabolites.
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Affiliation(s)
- Robert T Gaeta
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
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18
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Noskov VN, Lee NC, Larionov V, Kouprina N. Rapid generation of long tandem DNA repeat arrays by homologous recombination in yeast to study their function in mammalian genomes. Biol Proced Online 2011; 13:8. [PMID: 21982381 PMCID: PMC3200152 DOI: 10.1186/1480-9222-13-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Accepted: 10/07/2011] [Indexed: 12/18/2022] Open
Abstract
We describe here a method to rapidly convert any desirable DNA fragment, as small as 100 bp, into long tandem DNA arrays up to 140 kb in size that are inserted into a microbe vector. This method includes rolling-circle phi29 amplification (RCA) of the sequence in vitro and assembly of the RCA products in vivo by homologous recombination in the yeast Saccharomyces cerevisiae. The method was successfully used for a functional analysis of centromeric and pericentromeric repeats and construction of new vehicles for gene delivery to mammalian cells. The method may have general application in elucidating the role of tandem repeats in chromosome organization and dynamics. Each cycle of the protocol takes ~ two weeks to complete.
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Affiliation(s)
- Vladimir N Noskov
- Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, USA.
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Kurosaki H, Hiratsuka M, Imaoka N, Iida Y, Uno N, Kazuki Y, Ishihara C, Yakura Y, Mimuro J, Sakata Y, Takeya H, Oshimura M. Integration-free and stable expression of FVIII using a human artificial chromosome. J Hum Genet 2011; 56:727-33. [PMID: 21833006 DOI: 10.1038/jhg.2011.88] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human artificial chromosome (HAC) has several advantages as a gene therapy vector, including stable episomal maintenance that avoids insertional mutations and the ability to carry large gene inserts. To examine the copy number effect on the gene expression levels and its stability for a long-term culture for a future application in gene therapy, we constructed a HAC vector carrying the human factor VIII (FVIII) complementary DNA, FVIII-HAC in Chinese hamster ovary (CHO) cells. One and more copies of FVIII gene on the HAC were expressed in the copy-number-dependent manner in the CHO cells. The HAC with 16 copies of FVIII, FVIII (16)-HAC, was transferred from CHO hybrids into a human immortalized mesenchymal stem cell using microcell-mediated chromosome transfer. The expression levels of HAC-derived FVIII transgene products were compared with transfected FVIII plasmids. The former showed expression levels consistent with those of the original clones, even after 50 population doublings, whereas the latter showed a remarkable decrease in expression despite unvarying DNA content, indicating that the gene on the HAC is resistant to gene silencing. These results suggest that the HAC-mediated therapeutic gene-expression system may be a powerful tool for stable expression of transgenes, and possibly for industrial production of gene products.
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Affiliation(s)
- Hajime Kurosaki
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Yonago, Japan
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20
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Argyros O, Wong SP, Harbottle RP. Non-viral episomal modification of cells using S/MAR elements. Expert Opin Biol Ther 2011; 11:1177-91. [PMID: 21548848 DOI: 10.1517/14712598.2011.582035] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION The early potential of gene therapy is slowly becoming realized following the recent treatment of patients with severe combined immunodeficiency and ocular diseases. However at present the field of gene therapy is tempered by the toxicity issues, mainly that of the integrated retroviral vector used in most trials which led to oncogenesis in several of the treated patients. The development of safer, alternative vectors is therefore vital for further progress in this field, in particular vectors which remain episomal and are therefore less genotoxic. One such unique class of vectors are those based on scaffold matrix attachment regions (S/MARs) elements, which are maintained extra-chromosomally and replicate in vitro and in vivo. AREAS COVERED The overview here describes the most relevant studies utilizing the S/MAR element to episomally modify mammalian cells and tissues with a particular focus on liver tissue, as well as the brain, the muscle, the eye, cancer cells, embryonic cells and neonatal mice. For this purpose, recently published data in these areas (mainly articles published between 2000 and 2010) are reviewed. EXPERT OPINION The utilisation of vectors harbouring an S/MAR element is an efficient, safe and cost-effective way to episomally modify mammalian cells.
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Affiliation(s)
- Orestis Argyros
- Imperial College London, Gene Therapy Research Group, Sir Alexander Fleming Building, National Heart and Lung Institute, South Kensington, London SW7 2AZ, UK.
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Lin L, Koo DH, Zhang W, St Peter J, Jiang J. De novo assembly of potential linear artificial chromosome constructs capped with expansive telomeric repeats. PLANT METHODS 2011; 7:10. [PMID: 21496260 PMCID: PMC3101654 DOI: 10.1186/1746-4811-7-10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 04/15/2011] [Indexed: 05/29/2023]
Abstract
BACKGROUND Artificial chromosomes (ACs) are a promising next-generation vector for genetic engineering. The most common methods for developing AC constructs are to clone and combine centromeric DNA and telomeric DNA fragments into a single large DNA construct. The AC constructs developed from such methods will contain very short telomeric DNA fragments because telomeric repeats can not be stably maintained in Escherichia coli. RESULTS We report a novel approach to assemble AC constructs that are capped with long telomeric DNA. We designed a plasmid vector that can be combined with a bacterial artificial chromosome (BAC) clone containing centromeric DNA sequences from a target plant species. The recombined clone can be used as the centromeric DNA backbone of the AC constructs. We also developed two plasmid vectors containing short arrays of plant telomeric DNA. These vectors can be used to generate expanded arrays of telomeric DNA up to several kilobases. The centromeric DNA backbone can be ligated with the telomeric DNA fragments to generate AC constructs consisting of a large centromeric DNA fragment capped with expansive telomeric DNA at both ends. CONCLUSIONS We successfully developed a procedure that circumvents the problem of cloning and maintaining long arrays of telomeric DNA sequences that are not stable in E. coli. Our procedure allows development of AC constructs in different eukaryotic species that are capped with long and designed sizes of telomeric DNA fragments.
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Affiliation(s)
- Li Lin
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Dal-Hoe Koo
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Wenli Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joseph St Peter
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
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22
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Abstract
The advent of transgenic technologies has met many challenges, both technical and political; however, these technologies are now widely applied, particularly for crop improvement. Bioengineering has resulted in plants carrying resistance to herbicides, insects, and viruses, as well as entire biosynthetic pathways. Some of the technical challenges in generating transgenic plant or animal materials include: an inability to control the location and nature of the integration of transgenic DNA into the host genome, and linkage of transformed genes to selectable antibiotic resistance genes used in the production of the transgene cassette. Furthermore, successive transformation of multiple genes may require the use of several selection genes. The coordinated expression of multiple stacked genes would be required for complex biosynthetic pathways or combined traits. Engineered nonintegrating minichromosomes can overcome many of these problems and hold much promise as key players in the next generation of transgenic technologies for improved crop plants. In this review, we discuss the history of artificial chromosome technology with an emphasis on engineered plant minichromosomes.
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Affiliation(s)
- Robert T Gaeta
- Department of Biological Sciences, University of Missouri, Columbia, MO, USA
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23
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Katona RL, Vanderbyl SL, Perez CF. Mammalian artificial chromosomes and clinical applications for genetic modification of stem cells: an overview. Methods Mol Biol 2011; 738:199-216. [PMID: 21431729 DOI: 10.1007/978-1-61779-099-7_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Modifying multipotent, self-renewing human stem cells with mammalian artificial chromosomes (MACs), present a promising clinical strategy for numerous diseases, especially ex vivo cell therapies that can benefit from constitutive or overexpression of therapeutic gene(s). MACs are nonintegrating, autonomously replicating, with the capacity to carry large cDNA or genomic sequences, which in turn enable potentially prolonged, safe, and regulated therapeutic transgene expression, and render MACs as attractive genetic vectors for "gene replacement" or for controlling differentiation pathways in progenitor cells. The status quo is that the most versatile target cell would be one that was pluripotent and self-renewing to address multiple disease target cell types, thus making multilineage stem cells, such as adult derived early progenitor cells and embryonic stem cells, as attractive universal host cells. We will describe the progress of MAC technologies, the subsequent modifications of stem cells, and discuss the establishment of MAC platform stem cell lines to facilitate proof-of-principle studies and preclinical development.
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Affiliation(s)
- Robert L Katona
- Institute of Genetics, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary.
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Telomere truncation in plants. Methods Mol Biol 2010. [PMID: 21181527 DOI: 10.1007/978-1-61737-957-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Telomeres are highly repetitive sequences at the ends of chromosomes that act as protection structure for chromosome stability. The integration of telomere sequences into the genome by genetic transformation can create chromosome instability because the integrated telomere sequences tend to form de novo telomeres at the site of integration. Thus, telomere repeats can be used to generate minichromosomes by telomere-mediated chromosome truncation in both plants and animals for chromosome studies as well as the applications in genetic engineering as engineered minichromosomes or artificial chromosomes. This protocol describes the procedure for telomere truncation of maize chromosomes by genetic transformation of telomere-containing constructs by both Agrobacterium- and biolistic-mediated transformations.
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25
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Kazuki Y, Hoshiya H, Takiguchi M, Abe S, Iida Y, Osaki M, Katoh M, Hiratsuka M, Shirayoshi Y, Hiramatsu K, Ueno E, Kajitani N, Yoshino T, Kazuki K, Ishihara C, Takehara S, Tsuji S, Ejima F, Toyoda A, Sakaki Y, Larionov V, Kouprina N, Oshimura M. Refined human artificial chromosome vectors for gene therapy and animal transgenesis. Gene Ther 2010; 18:384-93. [PMID: 21085194 PMCID: PMC3125098 DOI: 10.1038/gt.2010.147] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Human artificial chromosomes (HACs) have several advantages as gene therapy vectors, including stable episomal maintenance, and the ability to carry large gene inserts. We previously developed HAC vectors from the normal human chromosomes using a chromosome engineering technique. However, endogenous genes were remained in these HACs, limiting their therapeutic applications. In this study, we refined a HAC vector without endogenous genes from human chromosome 21 in homologous recombination-proficient chicken DT40 cells. The HAC was physically characterized using a transformation-associated recombination (TAR) cloning strategy followed by sequencing of TAR-bacterial artificial chromosome clones. No endogenous genes were remained in the HAC. We demonstrated that any desired gene can be cloned into the HAC using the Cre-loxP system in Chinese hamster ovary cells, or a homologous recombination system in DT40 cells. The HAC can be efficiently transferred to other type of cells including mouse ES cells via microcell-mediated chromosome transfer. The transferred HAC was stably maintained in vitro and in vivo. Furthermore, tumor cells containing a HAC carrying the suicide gene, herpes simplex virus thymidine kinase (HSV-TK), were selectively killed by ganciclovir in vitro and in vivo. Thus, this novel HAC vector may be useful not only for gene and cell therapy, but also for animal transgenesis.
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Affiliation(s)
- Y Kazuki
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Tottori, Japan
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26
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Abstract
Human artificial chromosome (HAC) has several advantages as a gene therapy vector, including stable episomal maintenance that avoids insertional mutations and the ability to carry large gene inserts including the regulatory elements. Induced pluripotent stem (iPS) cells have great potential for gene therapy, as such cells can be generated from the individual's own tissues, and when reintroduced can contribute to the specialized function of any tissue. As a proof of concept, we show herein the complete correction of a genetic deficiency in iPS cells derived from Duchenne muscular dystrophy (DMD) model (mdx) mice and a human DMD patient using a HAC with a complete genomic dystrophin sequence (DYS-HAC). Deletion or mutation of dystrophin in iPS cells was corrected by transferring the DYS-HAC via microcell-mediated chromosome transfer (MMCT). DMD patient- and mdx-specific iPS cells with the DYS-HAC gave rise to differentiation of three germ layers in the teratoma, and human dystrophin expression was detected in muscle-like tissues. Furthermore, chimeric mice from mdx-iPS (DYS-HAC) cells were produced and DYS-HAC was detected in all tissues examined, with tissue-specific expression of dystrophin. Therefore, the combination of patient-specific iPS cells and HAC-containing defective genes represents a powerful tool for gene and cell therapies.
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27
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Velthuis AJWT. Large virus for an even bigger task: can the mimivirus close the gene-therapy vector void? Future Virol 2009. [DOI: 10.2217/fvl.09.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Gene therapy holds exceptional biotechnological and medical potential, but it has not been able to unite efficient delivery with reliability over the years. Dependable genetic elements are often large and do not, quite simply, fit into the present line of efficient vectors or require therapy combinations to carefully regulate genetic constructs. Recently, however, a discovery in virology – the field of study that has produced the most efficient vectors to date – uncovered a virus with a threefold higher coding capacity than any previously described virus and, thus, can be envisioned to stimulate the development of a new line of vectors, which could combine the transfer of large, stable and reliable genetic elements with the efficiency associated with viruses. However, extensive further research is, required in order to probe the potential of this virus and verify the current hypothesis.
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Affiliation(s)
- Aartjan JW te Velthuis
- Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands and, Department of Molecular Biophysics, Delft University of Technology, Lorentzweg 1, 2628 CJ, Delft, The Netherlands
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28
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Kim JH, Ebersole T, Kouprina N, Noskov VN, Ohzeki JI, Masumoto H, Mravinac B, Sullivan BA, Pavlicek A, Dovat S, Pack SD, Kwon YW, Flanagan PT, Loukinov D, Lobanenkov V, Larionov V. Human gamma-satellite DNA maintains open chromatin structure and protects a transgene from epigenetic silencing. Genome Res 2009; 19:533-44. [PMID: 19141594 DOI: 10.1101/gr.086496.108] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The role of repetitive DNA sequences in pericentromeric regions with respect to kinetochore/heterochromatin structure and function is poorly understood. Here, we use a mouse erythroleukemia cell (MEL) system for studying how repetitive DNA assumes or is assembled into different chromatin structures. We show that human gamma-satellite DNA arrays allow a transcriptionally permissive chromatin conformation in an adjacent transgene and efficiently protect it from epigenetic silencing. These arrays contain CTCF and Ikaros binding sites. In MEL cells, this gamma-satellite DNA activity depends on binding of Ikaros proteins involved in differentiation along the hematopoietic pathway. Given our discovery of gamma-satellite DNA in pericentromeric regions of most human chromosomes and a dynamic chromatin state of gamma-satellite arrays in their natural location, we suggest that gamma-satellite DNA represents a unique region of the functional centromere with a possible role in preventing heterochromatin spreading beyond the pericentromeric region.
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Affiliation(s)
- Jung-Hyun Kim
- Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland 20892, USA
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29
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Gagos S, Chiourea M, Christodoulidou A, Apostolou E, Raftopoulou C, Deustch S, Jefford CE, Irminger-Finger I, Shay JW, Antonarakis SE. Pericentromeric instability and spontaneous emergence of human neoacrocentric and minute chromosomes in the alternative pathway of telomere lengthening. Cancer Res 2008; 68:8146-55. [PMID: 18829574 DOI: 10.1158/0008-5472.can-08-0945] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In the alternative pathway of telomere lengthening (ALT), neoplastic cell growth is prolonged by telomere recombination. We show that ALT is unexpectedly characterized by high rates of ongoing pericentromeric chromosomal instability. Combined with telomeric recombination, ALT pericentromeric instability generates neoacrocentric chromosomes. In the present studies, we describe a subgroup of ALT neoacrocentric minute chromosomes, composed of DNA entities two to five times smaller in size than human chromosome 21. The frequencies of ALT minute chromosomes were increased by gamma-irradiation and suppressed by telomerase. Continuous growth after telomerase inhibition/depletion was followed by increased rates of telomeric sister chromatid recombination and the emergence of minute chromosomes. We show that ALT minute chromosomes were derived from true centromeric fissions and/or chromosomal breakage/fusion/bridge cycles. They exhibit a two-chromatid structure, carry genomic DNA, centromeric and telomeric repeats, and display regular mitotic functionality. These observations are important in understanding the global genomic instability that characterizes most human advanced malignancies.
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Affiliation(s)
- Sarantis Gagos
- Laboratory of Genetics, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
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30
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Artificial chromosome formation in maize (Zea mays L.). Chromosoma 2008; 118:157-77. [DOI: 10.1007/s00412-008-0191-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Revised: 10/22/2008] [Accepted: 10/23/2008] [Indexed: 12/11/2022]
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Oshimura M, Katoh M. Transfer of human artificial chromosome vectors into stem cells. Reprod Biomed Online 2008; 16:57-69. [PMID: 18252049 DOI: 10.1016/s1472-6483(10)60557-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Human chromosome fragments and human artificial chromosomes (HAC) represent feasible gene delivery vectors via microcell-mediated chromosome transfer. Strategies to construct HAC involve either 'build up' or 'top-down' approaches. For each approach, techniques for manipulating HAC in donor cells in order to deliver HAC to recipient cells are required. The combination of chromosome fragments or HAC with microcell-mediated chromosome transfer has facilitated human gene mapping and various genetic studies. The recent emergence of stem cell-based tissue engineering has opened up new avenues for gene and cell therapies. The task now is to develop safe and effective vectors that can deliver therapeutic genes into specific stem cells and maintain long-term regulated expression of these genes. Although the transfer-efficiency needs to be improved, HAC possess several characteristics that are required for gene therapy vectors, including stable episomal maintenance and the capacity for large gene insets. HAC can also carry genomic loci with regulatory elements, which allow for the expression of transgenes in a genetic environment similar to the natural chromosome. This review describes the lessons and prospects learned, mainly from recent studies in developing HAC and HAC-mediated gene expression in embryonic and adult stem cells, and in transgenic animals.
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Affiliation(s)
- Mitsuo Oshimura
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, 86 Nishicho, Yonago, Tottori 683-8503, Japan.
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32
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Kazuki Y, Hoshiya H, Kai Y, Abe S, Takiguchi M, Osaki M, Kawazoe S, Katoh M, Kanatsu-Shinohara M, Inoue K, Kajitani N, Yoshino T, Shirayoshi Y, Ogura A, Shinohara T, Barrett JC, Oshimura M. Correction of a genetic defect in multipotent germline stem cells using a human artificial chromosome. Gene Ther 2008; 15:617-24. [PMID: 18305578 DOI: 10.1038/sj.gt.3303091] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Human artificial chromosomes (HACs) have several advantages as gene therapy vectors, including stable episomal maintenance that avoids insertional mutations and the ability to carry large gene inserts including regulatory elements. Multipotent germline stem (mGS) cells have a great potential for gene therapy because they can be generated from an individual's testes, and when reintroduced can contribute to the specialized function of any tissue. As a proof of concept, we herein report the functional restoration of a genetic deficiency in mouse p53-/- mGS cells, using a HAC with a genomic human p53 gene introduced via microcell-mediated chromosome transfer. The p53 phenotypes of gene regulation and radiation sensitivity were complemented by introducing the p53-HAC and the cells differentiated into several different tissue types in vivo and in vitro. Therefore, the combination of using mGS cells with HACs provides a new tool for gene and cell therapies. The next step is to demonstrate functional restoration using animal models for future gene therapy.
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Affiliation(s)
- Y Kazuki
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Yonago, Tottori, Japan
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33
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Moreno C, Lazar J, Jacob HJ, Kwitek AE. Comparative genomics for detecting human disease genes. ADVANCES IN GENETICS 2008; 60:655-97. [PMID: 18358336 DOI: 10.1016/s0065-2660(07)00423-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Originally, comparative genomics was geared toward defining the synteny of genes between species. As the human genome project accelerated, there was an increase in the number of tools and means to make comparisons culminating in having the genomic sequence for a large number of organisms spanning the evolutionary tree. With this level of resolution and a long history of comparative biology and comparative genetics, it is now possible to use comparative genomics to build or select better animal models and to facilitate gene discovery. Comparative genomics takes advantage of the functional genetic information from other organisms, (vertebrates and invertebrates), to apply it to the study of human physiology and disease. It allows for the identification of genes and regulatory regions, and for acquiring knowledge about gene function. In this chapter, the current state of comparative genomics and the available tools are discussed in the context of developing animal model systems that reflect the clinical picture.
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Affiliation(s)
- Carol Moreno
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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34
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Yu W, Han F, Birchler JA. Engineered minichromosomes in plants. Curr Opin Biotechnol 2007; 18:425-31. [DOI: 10.1016/j.copbio.2007.09.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Revised: 09/18/2007] [Accepted: 09/18/2007] [Indexed: 02/02/2023]
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Establishment and mitotic stability of an extra-chromosomal mammalian replicon. BMC Cell Biol 2007; 8:33. [PMID: 17683605 PMCID: PMC1959191 DOI: 10.1186/1471-2121-8-33] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2007] [Accepted: 08/06/2007] [Indexed: 11/15/2022] Open
Abstract
Background Basic functions of the eukaryotic nucleus, like transcription and replication, are regulated in a hierarchic fashion. It is assumed that epigenetic factors influence the efficiency and precision of these processes. In order to uncouple local and long-range epigenetic features we used an extra-chromosomal replicon to study the requirements for replication and segregation and compared its behavior to that of its integrated counterpart. Results The autonomous replicon replicates in all eukaryotic cells and is stably maintained in the absence of selection but, as other extra-chromosomal replicons, its establishment is very inefficient. We now show that following establishment the vector is stably associated with nuclear compartments involved in gene expression and chromosomal domains that replicate at the onset of S-phase. While the vector stays autonomous, its association with these compartments ensures the efficiency of replication and mitotic segregation in proliferating cells. Conclusion Using this novel minimal model system we demonstrate that relevant functions of the eukaryotic nucleus are strongly influenced by higher nuclear architecture. Furthermore our findings have relevance for the rational design of episomal vectors to be used for genetic modification of cells: in order to improve such constructs with respect to efficiency elements have to be identified which ensure that such constructs reach regions of the nucleus favorable for replication and transcription.
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36
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Basu J, Willard HF, Stromberg G. Human Artificial Chromosome Assembly by Transposon‐Based Retrofitting of Genomic BACs with Synthetic Alpha‐Satellite Arrays. ACTA ACUST UNITED AC 2007; Chapter 5:Unit 5.18. [DOI: 10.1002/0471142905.hg0518s52] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Joydeep Basu
- Duke Institute for Genome Sciences and Policy Durham North Carolina
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Manzini S, Vargiolu A, Stehle IM, Bacci ML, Cerrito MG, Giovannoni R, Zannoni A, Bianco MR, Forni M, Donini P, Papa M, Lipps HJ, Lavitrano M. Genetically modified pigs produced with a nonviral episomal vector. Proc Natl Acad Sci U S A 2006; 103:17672-7. [PMID: 17101993 PMCID: PMC1635978 DOI: 10.1073/pnas.0604938103] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Genetic modification of cells and animals is an invaluable tool for biotechnology and biomedicine. Currently, integrating vectors are used for this purpose. These vectors, however, may lead to insertional mutagenesis and variable transgene expression and can undergo silencing. Scaffold/matrix attachment region-based vectors are nonviral expression systems that replicate autonomously in mammalian cells, thereby making possible safe and reliable genetic modification of higher eukaryotic cells and organisms. In this study, genetically modified pig fetuses were produced with the scaffold/matrix attachment region-based vector pEPI, delivered to embryos by the sperm-mediated gene transfer method. The pEPI vector was detected in 12 of 18 fetuses in the different tissues analyzed and was shown to be retained as an episome. The reporter gene encoded by the pEPI vector was expressed in 9 of 12 genetically modified fetuses. In positive animals, all tissues analyzed expressed the reporter gene; moreover in these tissues, the positive cells were on the average 79%. The high percentage of EGFP-expressing cells and the absence of mosaicism have important implications for biotechnological and biomedical applications. These results are an important step forward in animal transgenesis and can provide the basis for the future development of germ-line gene therapy.
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Affiliation(s)
- Stefano Manzini
- *Department of Surgical Sciences, University of Milano-Bicocca, 20052 Milan,Italy
| | - Alessia Vargiolu
- *Department of Surgical Sciences, University of Milano-Bicocca, 20052 Milan,Italy
| | - Isa M Stehle
- Institute of Cell Biology, Witten/Herdecke University, 58448 Witten, Germany
| | - Maria Laura Bacci
- Department of Veterinary Morphophysiology and Animal Production, University of Bologna, 40064 Bologna, Italy
| | - Maria Grazia Cerrito
- *Department of Surgical Sciences, University of Milano-Bicocca, 20052 Milan,Italy
| | - Roberto Giovannoni
- *Department of Surgical Sciences, University of Milano-Bicocca, 20052 Milan,Italy
| | - Augusta Zannoni
- Department of Veterinary Morphophysiology and Animal Production, University of Bologna, 40064 Bologna, Italy
| | - Maria Rosaria Bianco
- Centro Regionale di Competenza Applicazioni Tecnologico-Industriali di Biomolecole e Biosistemi-BioTekNet-Seconda Università di Napoli, 80138 Naples, Italy; and
| | - Monica Forni
- Department of Veterinary Morphophysiology and Animal Production, University of Bologna, 40064 Bologna, Italy
| | - Pierluigi Donini
- Department of Cellular and Developmental Biology, La Sapienza University, 00185 Rome, Italy
| | - Michele Papa
- Centro Regionale di Competenza Applicazioni Tecnologico-Industriali di Biomolecole e Biosistemi-BioTekNet-Seconda Università di Napoli, 80138 Naples, Italy; and
| | - Hans J Lipps
- Institute of Cell Biology, Witten/Herdecke University, 58448 Witten, Germany
| | - Marialuisa Lavitrano
- *Department of Surgical Sciences, University of Milano-Bicocca, 20052 Milan,Italy
- To whom correspondence should be addressed. E-mail:
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Kouprina N, Larionov V. TAR cloning: insights into gene function, long-range haplotypes and genome structure and evolution. Nat Rev Genet 2006; 7:805-12. [PMID: 16983376 DOI: 10.1038/nrg1943] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The structural and functional analysis of mammalian genomes would benefit from the ability to isolate from multiple DNA samples any targeted chromosomal segment that is the size of an average human gene. A cloning technique that is based on transformation-associated recombination (TAR) in the yeast Saccharomyces cerevisiae satisfies this need. It is a unique tool to selectively recover chromosome segments that are up to 250 kb in length from complex genomes. In addition, TAR cloning can be used to characterize gene function and genome variation, including polymorphic structural rearrangements, mutations and the evolution of gene families, and for long-range haplotyping.
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Affiliation(s)
- Natalay Kouprina
- Laboratory of Biosystems and Cancer, National Cancer Institute, National Institute of Health, Building 37, Room 5032, 9000 Rockville Pike, Bethesda, Maryland 20892, USA.
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Basu J, Willard HF. Human artificial chromosomes: potential applications and clinical considerations. Pediatr Clin North Am 2006; 53:843-53, viii. [PMID: 17027613 DOI: 10.1016/j.pcl.2006.08.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Human artificial chromosomes demonstrate promise as a novel class of nonintegrative gene therapy vectors. The authors outline current developments in human artificial chromosome technology and examine their potential for clinical application.
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Affiliation(s)
- Joydeep Basu
- Institute for Genome Sciences & Policy, Duke University, 101 Science Drive, Durham, NC 27708, USA.
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Abstract
Centromeres are the elements of chromosomes that assemble the proteinaceous kinetochore, maintain sister chromatid cohesion, regulate chromosome attachment to the spindle, and direct chromosome movement during cell division. Although the functions of centromeres and the proteins that contribute to their complex structure and function are conserved in eukaryotes, centromeric DNA diverges rapidly. Human centromeres are particularly complicated. Here, we review studies on the organization of homogeneous arrays of chromosome-specific alpha-satellite repeats and evolutionary links among eukaryotic centromeric sequences. We also discuss epigenetic mechanisms of centromere identity that confer structural and functional features of the centromere through DNA-protein interactions and post-translational modifications, producing centromere-specific chromatin signatures. The assembly and organization of human centromeres, the contributions of satellite DNA to centromere identity and diversity, and the mechanism whereby centromeres are distinguished from the rest of the genome reflect ongoing puzzles in chromosome biology.
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Affiliation(s)
- Mary G Schueler
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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41
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Moralli D, Simpson KM, Wade-Martins R, Monaco ZL. A novel human artificial chromosome gene expression system using herpes simplex virus type 1 vectors. EMBO Rep 2006; 7:911-8. [PMID: 16906131 PMCID: PMC1559671 DOI: 10.1038/sj.embor.7400768] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2005] [Revised: 05/10/2006] [Accepted: 06/26/2006] [Indexed: 02/04/2023] Open
Abstract
Human artificial chromosome (HAC) vectors are an important gene transfer system for expression and complementation studies. We describe a significant advance in HAC technology using infectious herpes simplex virus type 1 (HSV-1) amplicon vectors for delivery. This highly efficient method has allowed gene-expressing HACs to be established in glioma-, kidney- and lung-derived cells. We also developed an HSV-1 hypoxanthine phosphoribosyltransferase (HPRT) HAC vector, which generated functional HPRT-expressing HACs that complemented the genetic deficiency in human cells. The transduction efficiency of the HSV-1 HAC amplicons is several orders of magnitude higher than lipofection-mediated delivery. Studies on HAC stability between cell types showed important differences that have implications for HAC development and gene expression in human cells. This is the first report of establishing gene-expressing HACs in human cells by using an efficient, high-capacity viral vector and by identifying factors that are involved in cell-type-specific HAC instability. The work is a significant advance for HAC technology and the development of HAC gene expression systems in human cells.
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Affiliation(s)
- Daniela Moralli
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS, UK
| | - Kirsty M Simpson
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS, UK
| | - Richard Wade-Martins
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Zoia Larin Monaco
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS, UK
- Tel: +44 (0) 1865 222678/388; Fax: +44 (0) 1865 222500; E-mail:
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Jackson DA, Juranek S, Lipps HJ. Designing nonviral vectors for efficient gene transfer and long-term gene expression. Mol Ther 2006; 14:613-26. [PMID: 16784894 DOI: 10.1016/j.ymthe.2006.03.026] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2005] [Revised: 03/20/2006] [Accepted: 03/20/2006] [Indexed: 01/20/2023] Open
Abstract
Although the genetic therapy of human diseases has been conceptually possible for many years we still lack a vector system that allows safe and reproducible genetic modification of eukaryotic cells and ensures faithful long-term expression of transgenes. There is increasing agreement that vectors that are based exclusively on chromosomal elements, which replicate autonomously in human cells, could fulfill these criteria. The rational construction of such vectors is still hindered by our limited knowledge of the factors that regulate chromatin function in eukaryotic cells. This review sets out to summarize how our current knowledge of nuclear organization can be applied to the design of extrachromosomal gene expression vectors that can be used for human gene therapy. Within the past years a number of episomal nonviral constructs have been designed and their replication strategies, expression of transgenes, mitotic stability, and delivery strategies and the mechanisms required for their stable establishment will be discussed. To date, these nonviral vectors have not been used in clinical trials. Even so, many compelling arguments can be developed to support the view that nonviral vector systems will play a major role in future gene therapy protocols.
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Affiliation(s)
- Dean A Jackson
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PL, UK
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Moritz F, Distler O, Ospelt C, Gay RE, Gay S. Technology Insight: gene transfer and the design of novel treatments for rheumatoid arthritis. ACTA ACUST UNITED AC 2006; 2:153-62. [PMID: 16932675 DOI: 10.1038/ncprheum0117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2005] [Accepted: 11/08/2005] [Indexed: 12/19/2022]
Abstract
Rheumatoid arthritis (RA) is a chronic inflammatory disease characterized by systemic inflammation and joint destruction. Novel therapies have emerged during the past decade, marking a new era in the treatment of RA. Meanwhile, in vivo and in vitro gene-transfer studies have provided valuable insights into mechanisms of disease pathogenesis. Advanced gene-delivery techniques and animal models promise further progress in RA research and the development of novel therapeutic strategies for this disease. In this article we provide an overview of the wide spectrum of potential targets that have been identified so far, discuss currently available gene-transfer methods, and outline the barriers that need to be overcome for these approaches to be successfully applied in daily practice.
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Affiliation(s)
- Falk Moritz
- Center of Experimental Rheumatology, Department of Rheumatology, University of Zurich, Switzerland
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Spence JM, Mills W, Mann K, Huxley C, Farr CJ. Increased missegregation and chromosome loss with decreasing chromosome size in vertebrate cells. Chromosoma 2005; 115:60-74. [PMID: 16267674 DOI: 10.1007/s00412-005-0032-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Revised: 09/01/2005] [Accepted: 09/19/2005] [Indexed: 11/24/2022]
Abstract
Chromosome engineering has allowed the generation of an extensive and well-defined series of linear human X centromere-based minichromosomes, which has been used to investigate the influence of size and structure on chromosome segregation in vertebrate cells. A clear relationship between overall chromosome size and mitotic stability was detected, with decreasing size associated with increasing loss rates. In chicken DT40, the lower size limit for prolonged mitotic stability is approximately 550 kb: at 450 kb, there was a dramatic increase in chromosome loss, while structures of approximately 200 kb could not be recovered. In human HT1080 cells, the size threshold for mitotic stability is approximately 1.6 Mb. Minichromosomes of 0.55-1.0 Mb can be recovered, but display high loss rates. However, all minichromosomes examined exhibited more segregation errors than normal chromosomes in HT1080 cells. This error rate increases with decreased size and correlates with reduced levels of CENP-A and Aurora B. In mouse LA-9 and Indian muntjac FM7 cells, the size requirements for mitotic stability are much greater. In mouse, a human 2.7-Mb minichromosome is rarely able to propagate a kinetochore and behaves acentrically. In Indian muntjac, CENP-C associates with the human minichromosome, but the mitotic apparatus appears unable to handle its segregation.
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45
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Basu J, Compitello G, Stromberg G, Willard HF, Van Bokkelen G. Efficient assembly of de novo human artificial chromosomes from large genomic loci. BMC Biotechnol 2005; 5:21. [PMID: 15998466 PMCID: PMC1182356 DOI: 10.1186/1472-6750-5-21] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2005] [Accepted: 07/05/2005] [Indexed: 01/20/2023] Open
Abstract
Background Human Artificial Chromosomes (HACs) are potentially useful vectors for gene transfer studies and for functional annotation of the genome because of their suitability for cloning, manipulating and transferring large segments of the genome. However, development of HACs for the transfer of large genomic loci into mammalian cells has been limited by difficulties in manipulating high-molecular weight DNA, as well as by the low overall frequencies of de novo HAC formation. Indeed, to date, only a small number of large (>100 kb) genomic loci have been reported to be successfully packaged into de novo HACs. Results We have developed novel methodologies to enable efficient assembly of HAC vectors containing any genomic locus of interest. We report here the creation of a novel, bimolecular system based on bacterial artificial chromosomes (BACs) for the construction of HACs incorporating any defined genomic region. We have utilized this vector system to rapidly design, construct and validate multiple de novo HACs containing large (100–200 kb) genomic loci including therapeutically significant genes for human growth hormone (HGH), polycystic kidney disease (PKD1) and ß-globin. We report significant differences in the ability of different genomic loci to support de novo HAC formation, suggesting possible effects of cis-acting genomic elements. Finally, as a proof of principle, we have observed sustained ß-globin gene expression from HACs incorporating the entire 200 kb ß-globin genomic locus for over 90 days in the absence of selection. Conclusion Taken together, these results are significant for the development of HAC vector technology, as they enable high-throughput assembly and functional validation of HACs containing any large genomic locus. We have evaluated the impact of different genomic loci on the frequency of HAC formation and identified segments of genomic DNA that appear to facilitate de novo HAC formation. These genomic loci may be useful for identifying discrete functional elements that may be incorporated into future generations of HAC vectors.
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MESH Headings
- Biotechnology/methods
- Cell Line
- Chromosomes, Artificial, Bacterial/genetics
- Chromosomes, Artificial, Human/genetics
- Cloning, Molecular
- DNA
- DNA, Satellite
- Fibroblasts/cytology
- Gene Transfer Techniques
- Genetic Techniques
- Genetic Vectors
- Genome
- Globins/genetics
- Human Growth Hormone/genetics
- Humans
- In Situ Hybridization, Fluorescence
- Microscopy, Fluorescence
- Models, Genetic
- Polycystic Kidney Diseases/genetics
- RNA, Messenger/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Transfection
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Affiliation(s)
- Joydeep Basu
- Institute for Genome Sciences & Policy, Duke University, Durham, NC 27708, USA
- Athersys Inc., 3201 Carnegie Avenue, Cleveland, OH 44115, USA
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