1
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Wang XY, Zhang WL, Zhang X, Fu YS, Wang HM, Sun QL, Li Q, Jia YL, Zhang JH, Wang TY. Combination of MAR and intron increase transgene expression of episomal vectors in CHO cells. Biotechnol J 2023; 18:e2200643. [PMID: 37551822 DOI: 10.1002/biot.202200643] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 07/22/2023] [Accepted: 08/03/2023] [Indexed: 08/09/2023]
Abstract
Previous work has shown that the EF-1α promoter of episomal vectors maintains high-level transgene expression in stably transfected Chinese hamster ovary (CHO) cells. However, the transgene expression levels need to be further increased. Here, we first incorporated matrix attachment regions (MARs), ubiquitous chromatin opening element (UCOE), stabilizing anti repressor elements 40 (STAR 40) elements into episomal vector at different sites and orientations, and systemically assessed their effects on transgene expression in transfected CHO-K1 cells. Results showed that enhanced green fluorescent protein (eGFP) expression levels increased remarkably when MAR X-29 was inserted upstream of the promoter, followed by the insertion of MAR1 downstream of the poly A, and the orientation had no significant effect. Moreover, MAR X-29 combined with human cytomegalovirus intron (hCMVI) yielded the highest transgene expression levels (4.52-fold). Transgene expression levels were not exclusively dependent on transgene copy numbers and were not related to the mRNA expression level. In addition, vector with MAR X-29+hCMVI can induce herpes simplex virus thymidine kinase (HSV-TK) protein expression, and the HSV-TK protein showed a cell-killing effect and an obvious bystander effect on HCT116 cells. In conclusion, the combination of MAR X-29 and hCMV intron can achieve high efficiency transgene expression mediated by episomal vectors in CHO-K1 cells.
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Affiliation(s)
- Xiao-Yin Wang
- School of Basic Medical Science, Xinxiang Medical University, Xinxiang, China
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, China
| | - Wei-Li Zhang
- School of Basic Medical Science, Xinxiang Medical University, Xinxiang, China
- Center for Medical Genetics, Nanyang Second General Hospital, Nanyang, China
| | - Xi Zhang
- College of Pharmacy, Xinxiang Medical University, Xinxiang, China
| | - Yu-Shun Fu
- School of Basic Medical Science, Xinxiang Medical University, Xinxiang, China
| | - Hao-Min Wang
- School of Basic Medical Science, Xinxiang Medical University, Xinxiang, China
| | - Qiu-Li Sun
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, China
| | - Qin Li
- School of Basic Medical Science, Xinxiang Medical University, Xinxiang, China
| | - Yan-Long Jia
- College of Pharmacy, Xinxiang Medical University, Xinxiang, China
| | - Jun-He Zhang
- Institutes of Health Central Plains, Xinxiang Medical University, Xinxiang, China
| | - Tian-Yun Wang
- School of Basic Medical Science, Xinxiang Medical University, Xinxiang, China
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, China
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2
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Karami Fath M, Karimfar N, Fazlollahpour Naghibi A, Shafa S, Ghasemi Shiran M, Ataei M, Dehghanzadeh H, Nabi Afjadi M, Ghadiri T, Payandeh Z, Tarhriz V. Revisiting characteristics of oncogenic extrachromosomal DNA as mobile enhancers on neuroblastoma and glioma cancers. Cancer Cell Int 2022; 22:200. [PMID: 35614494 PMCID: PMC9131661 DOI: 10.1186/s12935-022-02617-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/18/2022] [Indexed: 12/21/2022] Open
Abstract
Cancer can be induced by a variety of possible causes, including tumor suppressor gene failure and proto-oncogene hyperactivation. Tumor-associated extrachromosomal circular DNA has been proposed to endanger human health and speed up the progression of cancer. The amplification of ecDNA has raised the oncogene copy number in numerous malignancies according to whole-genome sequencing on distinct cancer types. The unusual structure and function of ecDNA, and its potential role in understanding current cancer genome maps, make it a hotspot to study tumor pathogenesis and evolution. The discovery of the basic mechanisms of ecDNA in the emergence and growth of malignancies could lead researchers to develop new cancer therapies. Despite recent progress, different aspects of ecDNA require more investigation. We focused on the features, and analyzed the bio-genesis, and origin of ecDNA in this review, as well as its functions in neuroblastoma and glioma cancers.
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Affiliation(s)
- Mohsen Karami Fath
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Nastaran Karimfar
- Faculty of Veterinary Medicine, Islamic Azad University, Tabriz Branch, Tabriz, Iran
| | | | - Shahriyar Shafa
- School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Melika Ghasemi Shiran
- Department of Biology, Faculty of Sciences, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Mehran Ataei
- Department of Biology, Faculty of Sciences, Shahid Chamran University, Ahvaz, Iran
| | | | - Mohsen Nabi Afjadi
- Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran.
| | - Tahereh Ghadiri
- Department of Neuroscience and Cognition, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran. .,Shefa Neuroscience Research Center, Khatam Alanbia Hospital, Tehran, Iran. .,Neurosiences Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Zahra Payandeh
- Department Medical Biochemistry and Biophysics, Division Medical Inflammation Research, Karolinska Institute, Stockholm, Sweden.
| | - Vahideh Tarhriz
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.
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3
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Smirnov A, Battulin N. Concatenation of Transgenic DNA: Random or Orchestrated? Genes (Basel) 2021; 12:genes12121969. [PMID: 34946918 PMCID: PMC8701086 DOI: 10.3390/genes12121969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/18/2022] Open
Abstract
Generation of transgenic organisms by pronuclear microinjection has become a routine procedure. However, while the process of DNA integration in the genome is well understood, we still do not know much about the recombination between transgene molecules that happens in the first moments after DNA injection. Most of the time, injected molecules are joined together in head-to-tail tandem repeats-the so-called concatemers. In this review, we focused on the possible concatenation mechanisms and how they could be studied with genetic reporters tracking individual copies in concatemers. We also discuss various features of concatemers, including palindromic junctions and repeat-induced gene silencing (RIGS). Finally, we speculate how cooperation of DNA repair pathways creates a multicopy concatenated insert.
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Affiliation(s)
- Alexander Smirnov
- Laboratory of Developmental Genetics, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia;
| | - Nariman Battulin
- Laboratory of Developmental Genetics, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia;
- Institute of Genetic Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
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Gene Amplification and the Extrachromosomal Circular DNA. Genes (Basel) 2021; 12:genes12101533. [PMID: 34680928 PMCID: PMC8535887 DOI: 10.3390/genes12101533] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/09/2021] [Accepted: 09/23/2021] [Indexed: 12/12/2022] Open
Abstract
Oncogene amplification is closely linked to the pathogenesis of a broad spectrum of human malignant tumors. The amplified genes localize either to the extrachromosomal circular DNA, which has been referred to as cytogenetically visible double minutes (DMs), or submicroscopic episome, or to the chromosomal homogeneously staining region (HSR). The extrachromosomal circle from a chromosome arm can initiate gene amplification, resulting in the formation of DMs or HSR, if it had a sequence element required for replication initiation (the replication initiation region/matrix attachment region; the IR/MAR), under a genetic background that permits gene amplification. In this article, the nature, intracellular behavior, generation, and contribution to cancer genome plasticity of such extrachromosomal circles are summarized and discussed by reviewing recent articles on these topics. Such studies are critical in the understanding and treating human cancer, and also for the production of recombinant proteins such as biopharmaceuticals by increasing the recombinant genes in the cells.
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SIRT1 stabilizes extrachromosomal gene amplification and contributes to repeat-induced gene silencing. J Biol Chem 2021; 296:100356. [PMID: 33539925 PMCID: PMC7949162 DOI: 10.1016/j.jbc.2021.100356] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/15/2021] [Accepted: 01/28/2021] [Indexed: 12/17/2022] Open
Abstract
Sirtuin 1 (SIRT1) is a protein deacetylase that maintains genome stability by preventing the activation of latent replication origins. Amplified genes in cancer cells localize on either extrachromosomal double minutes (DMs) or the chromosomal homogeneously staining region. Previously, we found that a plasmid with a mammalian replication initiation region and a matrix attachment region spontaneously mimics gene amplification in cultured animal cells and efficiently generates DMs and/or an homogeneously staining region. Here, we addressed the possibility that SIRT1 might be involved in initiation region/matrix attachment region–mediated gene amplification using SIRT1-knockout human COLO 320DM cells. Consequently, we found that extrachromosomal amplification was infrequent in SIRT1-deficient cells, suggesting that DNA breakage caused by latent origin activation prevented the formation of stable extrachromosomal amplicons. Moreover, we serendipitously found that reporter gene expression from the amplified repeats, which is commonly silenced by repeat-induced gene silencing (RIGS) in SIRT1-proficient cells, was strikingly higher in SIRT1-deficient cells, especially in the culture treated with the histone deacetylase inhibitor butyrate. Compared with the SIRT1-proficient cells, the gene expression per copy was up to thousand-fold higher in the sorter-isolated highest 10% cells among the SIRT1-deficient cells. These observations suggest that SIRT1 depletion alleviates RIGS. Thus, SIRT1 may stabilize extrachromosomal amplicons and facilitate RIGS. This result could have implications in cancer malignancy and protein expression.
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Ogaki Y, Fukuma M, Shimizu N. Repeat induces not only gene silencing, but also gene activation in mammalian cells. PLoS One 2020; 15:e0235127. [PMID: 32579599 PMCID: PMC7313748 DOI: 10.1371/journal.pone.0235127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 06/08/2020] [Indexed: 11/19/2022] Open
Abstract
Repeat-induced gene silencing (RIGS) establishes the centromere structure, prevents the spread of transposons and silences transgenes, thereby limiting recombinant protein production. We previously isolated a sequence (B-3-31) that alleviates RIGS from the human genome. Here, we developed an assay system for evaluating the influence of repeat sequences on gene expression, based on in vitro ligation followed by our original gene amplification technology in animal cells. Using this assay, we found that the repeat of B-3-31, three core sequences of replication initiation regions (G5, C12, and D8) and two matrix attachment regions (AR1 and 32–3), activated the co-amplified plasmid-encoded d2EGFP gene in both human and hamster cell lines. This upregulation effect persisted for up to 82 days, which was confirmed to be repeat-induced, and was thus designated as a repeat-induced gene activation (RIGA). In clear contrast, the repeat of three bacterial sequences (lambda-phage, Amp, and ColE1) and three human retroposon sequences (Alu, 5’-untranslated region, and ORF1 of a long interspersed nuclear element) suppressed gene expression, thus reflecting RIGS. RIGS was CpG-independent. We suggest that RIGA might be associated with replication initiation. The discovery of RIGS and RIGA has implications for the repeat in mammalian genome, as well as practical value in recombinant production.
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Affiliation(s)
- Yusuke Ogaki
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Miki Fukuma
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Noriaki Shimizu
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- * E-mail:
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Asoshina M, Myo G, Tada N, Tajino K, Shimizu N. Targeted amplification of a sequence of interest in artificial chromosome in mammalian cells. Nucleic Acids Res 2019; 47:5998-6006. [PMID: 31062017 PMCID: PMC6582328 DOI: 10.1093/nar/gkz343] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/08/2019] [Accepted: 05/01/2019] [Indexed: 12/14/2022] Open
Abstract
A plasmid with a replication initiation region (IR) and a matrix attachment region (MAR) initiates gene amplification in mammalian cells at a random chromosomal location. A mouse artificial chromosome (MAC) vector can stably carry a large genomic region. In this study we combined these two technologies with the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease (Cas)9 strategy to achieve targeted amplification of a sequence of interest. We previously showed that the IR/MAR plasmid was amplified up to the extrachromosomal tandem repeat; here we demonstrate that cleavage of these tandem plasmids and MAC by Cas9 facilitates homologous recombination between them. The plasmid array on the MAC could be further extended to form a ladder structure with high gene expression by a breakage–fusion–bridge cycle involving breakage at mouse major satellites. Amplification of genes on the MAC has the advantage that the MAC can be transferred between cells. We visualized the MAC in live cells by amplifying the lactose operator array on the MAC in cells expressing lactose repressor-green fluorescent protein fusion protein. This targeted amplification strategy is in theory be applicable to any sequence at any chromosomal site, and provides a novel tool for animal cell technology.
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Affiliation(s)
- Manami Asoshina
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima 739-8521, Japan
| | - Genki Myo
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima 739-8521, Japan
| | - Natsuko Tada
- Chromocenter Inc., Yonago, Tottori 683-0823, Japan
| | - Koji Tajino
- Chromocenter Inc., Yonago, Tottori 683-0823, Japan
| | - Noriaki Shimizu
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima 739-8521, Japan
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An efficient protein production system via gene amplification on a human artificial chromosome and the chromosome transfer to CHO cells. Sci Rep 2019; 9:16954. [PMID: 31740706 PMCID: PMC6861226 DOI: 10.1038/s41598-019-53116-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/28/2019] [Indexed: 11/08/2022] Open
Abstract
Gene amplification methods play a crucial role in establishment of cells that produce high levels of recombinant protein. However, the stability of such cell lines and the level of recombinant protein produced continue to be suboptimal. Here, we used a combination of a human artificial chromosome (HAC) vector and initiation region (IR)/matrix attachment region (MAR) gene amplification method to establish stable cells that produce high levels of recombinant protein. Amplification of Enhanced green fluorescent protein (EGFP) was induced on a HAC carrying EGFP gene and IR/MAR sequences (EGFP MAR-HAC) in CHO DG44 cells. The expression level of EGFP increased approximately 6-fold compared to the original HAC without IR/MAR sequences. Additionally, anti-vascular endothelial growth factor (VEGF) antibody on a HAC (VEGF MAR-HAC) was also amplified by utilization of this IR/MAR-HAC system, and anti-VEGF antibody levels were approximately 2-fold higher compared with levels in control cells without IR/MAR. Furthermore, the expression of anti-VEGF antibody with VEGF MAR-HAC in CHO-K1 cells increased 2.3-fold compared with that of CHO DG44 cells. Taken together, the IR/MAR-HAC system facilitated amplification of a gene of interest on the HAC vector, and could be used to establish a novel cell line that stably produced protein from mammalian cells.
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Shimizu N, Kapoor R, Naniwa S, Sakamaru N, Yamada T, Yamamura YK, Utani KI. Generation and maintenance of acentric stable double minutes from chromosome arms in inter-species hybrid cells. BMC Mol Cell Biol 2019; 20:2. [PMID: 31041889 PMCID: PMC6446505 DOI: 10.1186/s12860-019-0186-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 03/17/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Extrachromosomal acentric double minutes (DMs) contribute to human malignancy by carrying amplified oncogenes. Recent cancer genomics revealed that the pulverization of defined chromosome arms (chromothripsis) may generate DMs, however, nobody had actually generated DMs from chromosome arm in culture. Human chromosomes are lost in human-rodent hybrid cells. RESULTS We found that human acentric DMs with amplified c-myc were stable in human-rodent hybrid cells, although the degree of stability depended on the specific rodent cell type. Based on this finding, stable human-rodent hybrids were efficiently generated by tagging human DMs with a plasmid with drug-resistance gene. After cell fusion, human chromosomes were specifically pulverised and lost. Consistent with chromothripsis, pulverization of human chromosome arms was accompanied by the incorporation into micronuclei. Such micronucleus showed different replication timing from the main nucleus. Surprisingly, we found that the hybrid cells retained not only the original DMs, but also new DMs without plasmid-tag and c-myc, but with human Alu. These DMs were devoid of telomeres and centromeres, and were stable in culture for more than 3 months. Microarray analysis showed that the new DMs were generated from several human chromosomal regions containing genes advantageous for cellular growth. Such regions were completely different from the original DMs. CONCLUSIONS The inter-species hybrid mimics the chromothripsis in culture. This is the first report that experimentally demonstrates the generation of multiple stable acentric DMs from the chromosome arm.
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Affiliation(s)
- Noriaki Shimizu
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, 739-8521, Japan.
| | - Rita Kapoor
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, 739-8521, Japan
| | - Shuhei Naniwa
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, 739-8521, Japan
| | - Naoto Sakamaru
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, 739-8521, Japan
| | - Taku Yamada
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, 739-8521, Japan
| | - You-Ki Yamamura
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, 739-8521, Japan
| | - Koh-Ichi Utani
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, 739-8521, Japan.,Present address; Kanazawa Medical University, Uchinada, Japan
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11
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Brown AJ, Kalsi D, Fernandez-Martell A, Cartwright J, Barber NOW, Patel YD, Turner R, Bryant CL, Johari YB, James DC. Expression Systems for Recombinant Biopharmaceutical Production by Mammalian Cells in Culture. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1002/9783527699124.ch13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Adam J. Brown
- University of Sheffield; Department of Chemical and Biological Engineering; Mappin St. Sheffield S1 3JD UK
| | - Devika Kalsi
- University of Sheffield; Department of Chemical and Biological Engineering; Mappin St. Sheffield S1 3JD UK
| | | | - Joe Cartwright
- University of Sheffield; Department of Chemical and Biological Engineering; Mappin St. Sheffield S1 3JD UK
| | - Nicholas O. W. Barber
- University of Sheffield; Department of Chemical and Biological Engineering; Mappin St. Sheffield S1 3JD UK
| | - Yash D. Patel
- University of Sheffield; Department of Chemical and Biological Engineering; Mappin St. Sheffield S1 3JD UK
| | | | - Claire L. Bryant
- University of Sheffield; Department of Chemical and Biological Engineering; Mappin St. Sheffield S1 3JD UK
| | - Yusuf B. Johari
- University of Sheffield; Department of Chemical and Biological Engineering; Mappin St. Sheffield S1 3JD UK
| | - David C. James
- University of Sheffield; Department of Chemical and Biological Engineering; Mappin St. Sheffield S1 3JD UK
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12
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Mitsuda SH, Shimizu N. Epigenetic Repeat-Induced Gene Silencing in the Chromosomal and Extrachromosomal Contexts in Human Cells. PLoS One 2016; 11:e0161288. [PMID: 27525955 PMCID: PMC4985131 DOI: 10.1371/journal.pone.0161288] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 08/02/2016] [Indexed: 02/06/2023] Open
Abstract
A plasmid bearing both a replication initiation region and a matrix attachment region is spontaneously amplified in transfected mammalian cells and generates plasmid repeats in the extrachromosomal double minutes (DMs) or the chromosomal homogeneously staining region (HSR). Generally, the repeat sequences are subject to repeat-induced gene silencing, the mechanism of which remains to be elucidated. Previous research showed that gene expression from the same plasmid repeat was higher from repeats located at DMs than at the HSR, which may reflect the extrachromosomal environment of the DMs. In the current study, plasmid repeats in both DMs and HSR were associated with repressive histone modifications (H3K9me3, H3K9me2), and the levels of repressive chromatin markers were higher in HSR than in DMs. Inactive chromatin is known to spread to neighboring regions in chromosome arm. Here, we found that such spreading also occurs in extrachromosomal DMs. Higher levels of active histone modifications (H3K9Ac, H3K4me3, and H3K79me2) were detected at plasmid repeats in DMs than in HSR. The level of DNA CpG methylation was generally low in both DMs and HSR; however, there were some hypermethylated copies within the population of repeated sequences, and the frequency of such copies was higher in DMs than in HSR. Together, these data suggest a “DNA methylation-core and chromatin-spread” model for repeat-induced gene silencing. The unique histone modifications at the extrachromosomal context are discussed with regard to the model.
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Affiliation(s)
- Sho-Hei Mitsuda
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, 739-8521, Japan
| | - Noriaki Shimizu
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, 739-8521, Japan
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13
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Fukuma M, Ganmyo Y, Miura O, Ohyama T, Shimizu N. Cloning and Characterization of a Human Genomic Sequence that Alleviates Repeat-Induced Gene Silencing. PLoS One 2016; 11:e0153338. [PMID: 27078685 PMCID: PMC4831671 DOI: 10.1371/journal.pone.0153338] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/28/2016] [Indexed: 01/06/2023] Open
Abstract
Plasmids bearing a mammalian replication initiation region (IR) and a nuclear matrix attachment region (MAR) are spontaneously amplified in transfected mammalian cells, and such amplification generates chromosomal homogeneously staining regions (HSRs) or extrachromosomal double minutes (DMs). This method provides a novel, efficient, and rapid way to establish cells that stably produce high levels of recombinant proteins. However, because IR/MAR plasmids are amplified as repeats, they are frequently targeted by repeat-induced gene silencing (RIGS), which silences a variety of repeated sequences in transgenes and the genome. To address this problem, we developed a novel screening system using the IR/MAR plasmid to isolate human genome sequences that alleviate RIGS. The screen identified a 3,271 bp sequence (B-3-31) that elevated transgene expression without affecting the amplification process. Neither non-B structure (i.e., the inverted repeats or bending) nor known epigenetic modifier elements such as MARs, insulators, UCOEs, or STARs could explain the anti-silencing activity of B-3-31. Instead, the activity was distributed throughout the entire B-3-31 sequence, which was extremely A/T-rich and CpG-poor. Because B-3-31 effectively and reproducibly alleviated RIGS of repeated genes, it could be used to increase recombinant protein production.
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Affiliation(s)
- Miki Fukuma
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, Japan
| | - Yuto Ganmyo
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, Japan
| | - Osamu Miura
- Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Takashi Ohyama
- Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Noriaki Shimizu
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima, Japan
- * E-mail:
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Zhang M, Zheng Y, Chen W, Zhang Y, Guo Z, Zhang Y, Liu J. Identifying an optimal promoter sequence of goat β-lactoglobulin gene for constructing high-expression vectors in mammary epithelial cells. Small Rumin Res 2015. [DOI: 10.1016/j.smallrumres.2015.08.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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Harraghy N, Calabrese D, Fisch I, Girod PA, LeFourn V, Regamey A, Mermod N. Epigenetic regulatory elements: Recent advances in understanding their mode of action and use for recombinant protein production in mammalian cells. Biotechnol J 2015; 10:967-78. [DOI: 10.1002/biot.201400649] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 04/20/2015] [Accepted: 05/20/2015] [Indexed: 12/18/2022]
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