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Kan L, Barr JJ. A Mammalian Cell's Guide on How to Process a Bacteriophage. Annu Rev Virol 2023; 10:183-198. [PMID: 37774129 DOI: 10.1146/annurev-virology-111821-111322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
Bacteriophages are enigmatic entities that defy definition. Classically, they are specialist viruses that exclusively parasitize bacterial hosts. Yet this definition becomes limiting when we consider their ubiquity in the body coupled with their vast capacity to directly interact with the mammalian host. While phages certainly do not infect nor replicate within mammalian cells, they do interact with and gain unfettered access to the eukaryotic cell structure. With the growing appreciation for the human virome, coupled with our increased application of phages to patients within clinical settings, the potential impact of phage-mammalian interactions is progressively recognized. In this review, we provide a detailed mechanistic overview of how phages interact with the mammalian cell surface, the processes through which said phages are internalized by the cell, and the intracellular processing and fate of the phages. We then summarize the current state-of-the-field with respect to phage-mammalian interactions and their associations with health and disease states.
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Affiliation(s)
- Leo Kan
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia;
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia;
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2
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Adenoviral Vector DNA- and SARS-CoV-2 mRNA-Based Covid-19 Vaccines: Possible Integration into the Human Genome - Are Adenoviral Genes Expressed in Vector-based Vaccines? Virus Res 2021; 302:198466. [PMID: 34087261 PMCID: PMC8168329 DOI: 10.1016/j.virusres.2021.198466] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/10/2021] [Accepted: 05/25/2021] [Indexed: 11/22/2022]
Abstract
Vigorous vaccination programs against SARS-CoV-2-causing Covid-19 are the major chance to fight this dreadful pandemic. The currently administered vaccines depend on adenovirus DNA vectors or on SARS-CoV-2 mRNA that might become reverse transcribed into DNA, however infrequently. In some societies, people have become sensitized against the potential short- or long-term side effects of foreign DNA being injected into humans. In my laboratory, the fate of foreign DNA in mammalian (human) cells and organisms has been investigated for many years. In this review, a summary of the results obtained will be presented. This synopsis has been put in the evolutionary context of retrotransposon insertions into pre-human genomes millions of years ago. In addition, studies on adenovirus vector-based DNA, on the fate of food-ingested DNA as well as the long-term persistence of SARS-CoV-2 RNA/DNA will be described. Actual integration of viral DNA molecules and of adenovirus vector DNA will likely be chance events whose frequency and epigenetic consequences cannot with certainty be assessed. The review also addresses problems of remaining adenoviral gene expression in adenoviral-based vectors and their role in side effects of vaccines. Eventually, it will come down to weighing the possible risks of genomic insertions of vaccine-associated foreign DNA and unknown levels of vector-carried adenoviral gene expression versus protection against the dangers of Covid-19. A decision in favor of vaccination against life-threatening disease appears prudent. Informing the public about the complexities of biology will be a reliable guide when having to reach personal decisions about vaccinations.
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3
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Bodner K, Melkonian AL, Covert MW. The Enemy of My Enemy: New Insights Regarding Bacteriophage-Mammalian Cell Interactions. Trends Microbiol 2020; 29:528-541. [PMID: 33243546 DOI: 10.1016/j.tim.2020.10.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/19/2020] [Accepted: 10/29/2020] [Indexed: 12/22/2022]
Abstract
Bacteriophages (phages) are the most abundant biological entity in the human body, but until recently the role that phages play in human health was not well characterized. Although phages do not cause infections in human cells, phages can alter the severity of bacterial infections by the dissemination of virulence factors amongst bacterial hosts. Recent studies, made possible with advances in genome engineering and microscopy, have uncovered a novel role for phages in the human body - the ability to modulate the physiology of the mammalian cells that can harbor intracellular bacteria. In this review, we synthesize key results on how phages traverse through mammalian cells - including uptake, distribution, and interaction with intracellular receptors - highlighting how these steps in turn influence host cell killing of bacteria. We discuss the implications of the growing field of phage-mammalian cell interactions for phage therapy.
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Affiliation(s)
- Katie Bodner
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA; Allen Discovery Center for Systems Modeling of Infection, Stanford University, Stanford, CA, 94305, USA
| | - Arin L Melkonian
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA; Allen Discovery Center for Systems Modeling of Infection, Stanford University, Stanford, CA, 94305, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA; Allen Discovery Center for Systems Modeling of Infection, Stanford University, Stanford, CA, 94305, USA.
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4
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Mauch-Mücke K, Schön K, Paulus C, Nevels MM. Evidence for Tethering of Human Cytomegalovirus Genomes to Host Chromosomes. Front Cell Infect Microbiol 2020; 10:577428. [PMID: 33117732 PMCID: PMC7561393 DOI: 10.3389/fcimb.2020.577428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/17/2020] [Indexed: 11/27/2022] Open
Abstract
Tethering of viral genomes to host chromosomes has been recognized in a variety of DNA and RNA viruses. It can occur during both the productive cycle and latent infection and may impact viral genomes in manifold ways including their protection, localization, transcription, replication, integration, and segregation. Tethering is typically accomplished by dedicated viral proteins that simultaneously associate with both the viral genome and cellular chromatin via nucleic acid, histone and/or non-histone protein interactions. Some of the most prominent tethering proteins have been identified in DNA viruses establishing sustained latent infections, including members of the papillomaviruses and herpesviruses. Herpesvirus particles have linear genomes that circularize in infected cell nuclei and usually persist as extrachromosomal episomes. In several γ-herpesviruses, tethering facilitates the nuclear retention and faithful segregation of viral episomes during cell division, thus contributing to persistence of these viruses in the absence of infectious particle production. However, it has not been studied whether the genomes of human Cytomegalovirus (hCMV), the prototypical β-herpesvirus, are tethered to host chromosomes. Here we provide evidence by fluorescence in situ hybridization that hCMV genomes associate with the surface of human mitotic chromosomes following infection of both non-permissive myeloid and permissive fibroblast cells. This chromosome association occurs at lower frequency in the absence of the immediate-early 1 (IE1) proteins, which bind to histones and have been implicated in the maintenance of hCMV episomes. Our findings point to a mechanism of hCMV genome maintenance through mitosis and suggest a supporting but non-essential role of IE1 in this process.
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Affiliation(s)
- Katrin Mauch-Mücke
- Institute for Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Kathrin Schön
- Institute for Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Christina Paulus
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
| | - Michael M Nevels
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
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5
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Plasmid expression level heterogeneity monitoring via heterologous eGFP production at the single-cell level in Cupriavidus necator. Appl Microbiol Biotechnol 2020; 104:5899-5914. [PMID: 32358761 DOI: 10.1007/s00253-020-10616-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/02/2020] [Accepted: 04/06/2020] [Indexed: 10/24/2022]
Abstract
A methodology for plasmid expression level monitoring of eGFP expression suitable for dynamic processes was assessed during fermentation. This technique was based on the expression of a fluorescent biosensor (eGFP) encoded on a recombinant plasmid coupled to single-cell analysis. Fluorescence intensity at single-cell level was measured by flow cytometry. We demonstrated that promoter evaluation based on single-cell analysis versus classic global analysis brings valuable insights. Single-cell analysis pointed out the fact that intrinsic fluorescence increased with the strength of the promoter up to a threshold. Beyond that, cell permeability increases to excrete the fluorescent protein in the medium. The metabolic load due to the increase in the eGFP production in the case of strong constitutive promoters leads to slower growth kinetics compared with plasmid-free cells. With the strain Cupriavidus necator Re2133, growth rate losses were measured from 3% with the weak constitutive promoter Plac to 56% with the strong constitutive promoter Pj5. Through this work, it seems crucial to find a compromise between the fluorescence intensity in single cells and the metabolic load; in our conditions, the best compromise found was the weak promoter Plac. The plasmid expression level monitoring method was tested in the presence of a heterogeneous population induced by plasmid-curing methods. For all the identified subpopulations, the plasmid expression level heterogeneity was significantly detected at the level of fluorescence intensity in single cells. After cell sorting, growth rate and cultivability were assessed for each subpopulation. In conclusion, this eGFP biosensor makes it possible to follow the variations in the level of plasmid expression under conditions of population heterogeneity.Key Points•Development of a plasmid expression level monitoring method at the single-cell level by flow cytometry.•Promoter evaluation by single-cell analysis: cell heterogeneity and strain robustness.•Reporter system optimization for efficient subpopulation detection in pure cultures.
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6
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Doerfler W. Essential concepts are missing: Foreign DNA in food invades the organisms' cells and can lead to stochastic epigenetic alterations with a wide range of possible pathogenetic consequences. Clin Epigenetics 2020; 12:21. [PMID: 32033622 PMCID: PMC7007663 DOI: 10.1186/s13148-020-0813-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 01/14/2020] [Indexed: 11/10/2022] Open
Abstract
In this article, a new concept for general pathogenesis has been proposed. Advances in molecular genetics have led to the realization that essential concepts in the framework of molecular biology are still missing. Clinical medicine is plagued by similar shortcomings: The questioning of current paradigms could open new vistas and invite challenging approaches. This article presents an unconventional idea. Foreign DNA which is regularly ingested with the essential food supply is not completely degraded. Small quantities of fragmented DNA rather persist transiently in the gastro-intestinal tract of mice and can be traced to various organ systems, except for cells in the germ line. Foreign DNA entering and persisting in mammalian cells can stochastically lead to genome-wide alterations of transcriptional and CpG DNA methylation profiles. In the course of food-ingested DNA invading somatic cells, completely new cell types can be generated which might be involved in the causation of common ailments. Projects emanating from this perception merit critical analysis and rigorous pursuit.
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Affiliation(s)
- Walter Doerfler
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nürnberg, Schlossgarten 4, 91054, Erlangen, Germany. .,Institute of Genetics, University of Cologne, Cologne, Germany.
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7
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Lynch KL, Gooding LR, Garnett-Benson C, Ornelles DA, Avgousti DC. Epigenetics and the dynamics of chromatin during adenovirus infections. FEBS Lett 2019; 593:3551-3570. [PMID: 31769503 DOI: 10.1002/1873-3468.13697] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 11/20/2019] [Accepted: 11/23/2019] [Indexed: 12/26/2022]
Abstract
The DNA genome of eukaryotic cells is compacted by histone proteins within the nucleus to form chromatin. Nuclear-replicating viruses such as adenovirus have evolved mechanisms of chromatin manipulation to promote infection and subvert host defenses. Epigenetic factors may also regulate persistent adenovirus infection and reactivation in lymphoid tissues. In this review, we discuss the viral proteins E1A and protein VII that interact with and alter host chromatin, as well as E4orf3, which separates host chromatin from sites of viral replication. We also highlight recent advances in chromatin technologies that offer new insights into virus-directed chromatin manipulation. Beyond the role of chromatin in the viral replication cycle, we discuss the nature of persistent viral genomes in lymphoid tissue and cell lines, and the potential contribution of epigenetic signals in maintaining adenovirus in a quiescent state. By understanding the mechanisms through which adenovirus manipulates host chromatin, we will understand new aspects of this ubiquitous virus and shed light on previously unknown aspects of chromatin biology.
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Affiliation(s)
- Kelsey L Lynch
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Linda R Gooding
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | | | - David A Ornelles
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Daphne C Avgousti
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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Doerfler W. Epigenetic consequences of genome manipulations: caveats for human germline therapy and genetically modified organisms. Epigenomics 2019; 11:247-250. [PMID: 30753116 DOI: 10.2217/epi-2018-0201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Walter Doerfler
- Institute for Clinical & Molecular Virology, Friedrich-Alexander University Erlangen-Nürnberg, D-91054 Erlangen & Institute of Genetics, University of Cologne, D-50674 Cologne, Germany
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Keilwagen J, Lehnert H, Berner T, Beier S, Scholz U, Himmelbach A, Stein N, Badaeva ED, Lang D, Kilian B, Hackauf B, Perovic D. Detecting Large Chromosomal Modifications Using Short Read Data From Genotyping-by-Sequencing. FRONTIERS IN PLANT SCIENCE 2019; 10:1133. [PMID: 31608087 PMCID: PMC6771380 DOI: 10.3389/fpls.2019.01133] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 08/16/2019] [Indexed: 05/02/2023]
Abstract
Markers linked to agronomic traits are of the prerequisite for molecular breeding. Genotyping-by-sequencing (GBS) data enables to detect small polymorphisms including single nucleotide polymorphisms (SNPs) and short insertions or deletions (InDels) that can be used, for instance, for marker-assisted selection, population genetics, and genome-wide association studies (GWAS). Here, we aim at detecting large chromosomal modifications in barley and wheat based on GBS data. These modifications could be duplications, deletions, substitutions including introgressions as well as alterations of DNA methylation. We demonstrate that GBS coverage analysis is capable to detect Hordeum vulgare/Hordeum bulbosum introgression lines. Furthermore, we identify large chromosomal modifications in barley and wheat collections. Hence, large chromosomal modifications, including introgressions and copy number variations (CNV), can be detected easily and can be used as markers in research and breeding without additional wet-lab experiments.
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Affiliation(s)
- Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology, Julius Kuehn Institute, Quedlinburg, Germany
- *Correspondence: Jens Keilwagen,
| | - Heike Lehnert
- Institute for Biosafety in Plant Biotechnology, Julius Kuehn Institute, Quedlinburg, Germany
| | - Thomas Berner
- Institute for Biosafety in Plant Biotechnology, Julius Kuehn Institute, Quedlinburg, Germany
| | - Sebastian Beier
- Research Group Bioinformatics and Information Technology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Uwe Scholz
- Research Group Bioinformatics and Information Technology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Axel Himmelbach
- Research Group Genomics of Genetic Resources, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Nils Stein
- Research Group Genomics of Genetic Resources, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Ekaterina D. Badaeva
- Laboratory of Genetic Basis of Plant Identification, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Daniel Lang
- PGSB, Helmholtz Center Munich, Neuherberg, Germany
| | | | - Bernd Hackauf
- Institute for Breeding Research on Agricultural Crops, Julius Kuehn Institute, Quedlinburg, Germany
| | - Dragan Perovic
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn Institute, Quedlinburg, Germany
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Doerfler W, Weber S, Naumann A. Inheritable epigenetic response towards foreign DNA entry by mammalian host cells: a guardian of genomic stability. Epigenetics 2018; 13:1141-1153. [PMID: 30458693 DOI: 10.1080/15592294.2018.1549463] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Apart from its well-documented role in long-term promoter silencing, the genome-wide distribution patterns of ~ 28 million methylated or unmethylated CpG dinucleotides, e. g. in the human genome, is in search of genetic functions. We have set out to study changes in the cellular CpG methylation profile upon introducing foreign DNA into mammalian cells. As stress factors served the genomic integration of foreign (viral or bacterial plasmid) DNA, virus infections or the immortalization of cells with Epstein Barr Virus (EBV). In all instances investigated, alterations in cellular CpG methylation and transcription profiles were observed to different degrees. In the case of adenovirus DNA integration in adenovirus type 12 (Ad12)-transformed hamster cells, the extensive changes in cellular CpG methylation persisted even after the complete loss of all transgenomic Ad12 DNA. Hence, stress-induced alterations in CpG methylation can be inherited independent of the continued presence of the transgenome. Upon virus infections, changes in cellular CpG methylation appear early after infection. In EBV immortalized as compared to control cells, CpG hypermethylation in the far-upstream region of the human FMR1 promoter decreased four-fold. We conclude that in the wake of cellular stress due to foreign DNA entry, preexisting CpG methylation patterns were altered, possibly at specific CpG dinucleotides. Frequently, transcription patterns were also affected. As a working concept, we view CpG methylation profiles in mammalian genomes as a guarding sensor for genomic stability under epigenetic control. As a caveat towards manipulations of cells with foreign DNA, such cells can no longer be considered identical to their un-manipulated counterparts.
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Affiliation(s)
- Walter Doerfler
- a Institute for Virology , Friedrich-Alexander University Erlangen-Nürnberg , Erlangen , Germany.,b Institute of Genetics , Cologne University , Cologne , Germany
| | - Stefanie Weber
- a Institute for Virology , Friedrich-Alexander University Erlangen-Nürnberg , Erlangen , Germany
| | - Anja Naumann
- a Institute for Virology , Friedrich-Alexander University Erlangen-Nürnberg , Erlangen , Germany
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Discoveries in Molecular Genetics with the Adenovirus 12 System: Integration of Viral DNA and Epigenetic Consequences. EPIGENETICS OF INFECTIOUS DISEASES 2017. [PMCID: PMC7120421 DOI: 10.1007/978-3-319-55021-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Starting in the 1960s, the human adenovirus type 12 (Ad12) system has been used in my laboratory to investigate basic mechanisms in molecular biology and viral oncology. Ad12 replicates in human cells but undergoes a completely abortive cycle in Syrian hamster cells. Ad12 induces neuro-ectodermal tumors in newborn hamsters (Mesocricetus auratus). Each tumor cell or Ad12-transformed hamster cell carries multiple copies of integrated Ad12 DNA. Ad12 DNA usually integrates at one chromosomal site which is not specific since Ad12 DNA can integrate at many different locations in the hamster genome. Epigenetic research occupies a prominent role in tumor biology. We have been using the human Ad12 Syrian hamster cell system for the analysis of epigenetic alterations in Ad12-infected cells and in Ad12-induced hamster tumors. Virion or free intracellular Ad12 DNA remains unmethylated at CpG sites, whereas the integrated viral genomes become de novo methylated in specific patterns. Inverse correlations between promoter methylation and activity were described for the first time in this system and initiated active research in the field of DNA methylation and epigenetics. Today, promoter methylation has been recognized as an important factor in long-term genome silencing. We have also discovered that the insertion of foreign (Ad12, bacteriophage lambda, plasmid) DNA into mammalian genomes can lead to genome-wide alterations in methylation and transcription patterns in the recipient genomes. This concept has been verified recently in a pilot study with human cells which had been rendered transgenomic for a 5.6 kbp bacterial plasmid. Currently, we study epigenetic effects on cellular methylation and transcription patterns in Ad12-infected cells and in Ad12-induced hamster tumor cells. These epigenetic alterations are considered crucial elements in (viral) oncogenesis.
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12
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Doerfler W. Beware of manipulations on the genome: epigenetic destabilization through (foreign) DNA insertions. Epigenomics 2016; 8:587-91. [PMID: 26997469 DOI: 10.2217/epi-2016-0019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Walter Doerfler
- Institute for Virology, Friedrich-Alexander-University Erlangen-Nürnberg, D-91054 Erlangen, Germany; and Institute of Genetics, University of Cologne, D-50674 Cologne, Germany
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13
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Weber S, Jung S, Doerfler W. DNA methylation and transcription in HERV (K, W, E) and LINE sequences remain unchanged upon foreign DNA insertions. Epigenomics 2016; 8:157-65. [DOI: 10.2217/epi.15.109] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Aim: DNA methylation and transcriptional profiles were determined in the regulatory sequences of the human endogenous retroviral (HERV-K, -W, -E) and LINE-1.2 elements and were compared between non-transgenomic and plasmid-transgenomic cells. Methods: DNA methylation profiles in the HERV (K, W, E) and LINE sequences were determined by bisulfite genomic sequencing. The transcription of these genome segments was assessed by quantitative real-time PCR. Results: In HERV-K, HERV-W and LINE-1.2 the levels of DNA methylation ranged between 75 and 98%, while in HERV-E they were around 60%. Nevertheless, the HERV and LINE-1.2 sequences were actively transcribed. No differences were found in comparisons of HERV and LINE-1.2 CpG methylation and transcription patterns between non-transgenomic and plasmid-transgenomic HCT116 cells. Conclusion: The insertion of a 5.6 kbp plasmid into the HCT116 genome had no effect on the HERV and LINE-1.2 methylation and transcription profiles, although other parts of the HCT116 genome had shown marked changes. These repetitive sequences are transcribed, probably because the large number of HERV and LINE-1.2 elements harbor copies with non- or hypo-methylated long terminal repeat sequences.
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Affiliation(s)
- Stefanie Weber
- Institute of Clinical & Molecular Virology, University Erlangen-Nürnberg Medical School, 91054 Erlangen, Germany
| | - Susan Jung
- Pediatric Research Center, University Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Walter Doerfler
- Institute of Clinical & Molecular Virology, University Erlangen-Nürnberg Medical School, 91054 Erlangen, Germany
- Institute of Genetics, University of Cologne, 50674 Cologne, Germany
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Abstract
DNA tumor viruses including members of the polyomavirus, adenovirus, papillomavirus, and herpes virus families are presently the subject of intense interest with respect to the role that epigenetics plays in control of the virus life cycle and the transformation of a normal cell to a cancer cell. To date, these studies have primarily focused on the role of histone modification, nucleosome location, and DNA methylation in regulating the biological consequences of infection. Using a wide variety of strategies and techniques ranging from simple ChIP to ChIP-chip and ChIP-seq to identify histone modifications, nuclease digestion to genome wide next generation sequencing to identify nucleosome location, and bisulfite treatment to MeDIP to identify DNA methylation sites, the epigenetic regulation of these viruses is slowly becoming better understood. While the viruses may differ in significant ways from each other and cellular chromatin, the role of epigenetics appears to be relatively similar. Within the viral genome nucleosomes are organized for the expression of appropriate genes with relevant histone modifications particularly histone acetylation. DNA methylation occurs as part of the typical gene silencing during latent infection by herpesviruses. In the simple tumor viruses like the polyomaviruses, adenoviruses, and papillomaviruses, transformation of the cell occurs via integration of the virus genome such that the virus's normal regulation is disrupted. This results in the unregulated expression of critical viral genes capable of redirecting cellular gene expression. The redirected cellular expression is a consequence of either indirect epigenetic regulation where cellular signaling or transcriptional dysregulation occurs or direct epigenetic regulation where epigenetic cofactors such as histone deacetylases are targeted. In the more complex herpersviruses transformation is a consequence of the expression of the viral latency proteins and RNAs which again can have either a direct or indirect effect on epigenetic regulation of cellular expression. Nevertheless, many questions still remain with respect to the specific mechanisms underlying epigenetic regulation of the viruses and transformation.
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Weber S, Hofmann A, Herms S, Hoffmann P, Doerfler W. Destabilization of the human epigenome: consequences of foreign DNA insertions. Epigenomics 2015; 7:745-55. [PMID: 26088384 DOI: 10.2217/epi.15.40] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
AIM We previously reported changes of DNA methylation and transcription patterns in mammalian cells that carry integrated foreign DNA. Experiments were now designed to assess the epigenetic consequences of inserting a 5.6 kbp plasmid into the human genome. METHODS Differential transcription and CpG methylation patterns were compared between transgenomic and nontransgenomic cell clones by using gene chip microarray systems. RESULTS In 4.7% of the 28.869 gene segments analyzed, transcriptional activities were up- or downregulated in the transgenomic cell clones. Genome-wide profiling revealed differential methylation in 3791 of > 480,000 CpG's examined in transgenomic versus nontransgenomic clones. CONCLUSION The data document genome-wide effects of foreign DNA insertions on the epigenetic stability of human cells. Many fields in experimental biology and medicine employ transgenomic or otherwise genome-manipulated cells or organisms without considering the epigenetic consequences for the recipient genomes.
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Affiliation(s)
- Stefanie Weber
- Institute of Clinical & Molecular Virology, University of Erlangen-Nürnberg Medical School, D-91054 Erlangen, Germany
| | - Andrea Hofmann
- Institute of Human Genetics, Life & Brain Center, Bonn University, D-53127 Bonn, Germany
| | - Stefan Herms
- Institute of Human Genetics, Life & Brain Center, Bonn University, D-53127 Bonn, Germany.,Division of Medical Genetics, University Hospital Basel, CH-4055 Basel, Switzerland
| | - Per Hoffmann
- Institute of Human Genetics, Life & Brain Center, Bonn University, D-53127 Bonn, Germany.,Division of Medical Genetics, University Hospital Basel, CH-4055 Basel, Switzerland
| | - Walter Doerfler
- Institute of Clinical & Molecular Virology, University of Erlangen-Nürnberg Medical School, D-91054 Erlangen, Germany.,Institute of Genetics, University of Cologne, D-50674 Cologne, Germany
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16
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Luzzi A, Morettini F, Gazaneo S, Mundo L, Onnis A, Mannucci S, Rogena EA, Bellan C, Leoncini L, De Falco G. HIV-1 Tat induces DNMT over-expression through microRNA dysregulation in HIV-related non Hodgkin lymphomas. Infect Agent Cancer 2014; 9:41. [PMID: 25705251 PMCID: PMC4334912 DOI: 10.1186/1750-9378-9-41] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 11/14/2014] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND A close association between HIV infection and the development of cancer exists. Although the advent of highly active antiretroviral therapy has changed the epidemiology of AIDS-associated malignancies, a better understanding on how HIV can induce malignant transformation will help the development of novel therapeutic agents. METHODS HIV has been reported to induce the expression of DNMT1 in vitro, but still no information is available about the mechanisms regulating DNMT expression in HIV-related B-cell lymphomas. In this paper, we investigated the expression of DNMT family members (DNMT1, DNMT3a/b) in primary cases of aggressive B-cell lymphomas of HIV-positive subjects. RESULTS Our results confirmed the activation of DNMT1 by HIV in vivo, and reported for the first time a marked up-regulation of DNMT3a and DNMT3b in HIV-positive aggressive B-cell lymphomas. DNMT up-regulation in HIV-positive tumors correlated with down-regulation of specific microRNAs, as the miR29 family, the miR148-152 cluster, known to regulate their expression. Literature reports the activation of DNMTs by the human polyomavirus BKV large T-antigen and adenovirus E1a, through the pRb/E2F pathway. We have previously demonstrated that the HIV Tat protein is able to bind to the pocket proteins and to inactivate their oncosuppressive properties, resulting in uncontrolled cell proliferation. Therefore, we focused on the role of Tat, due to its capability to be released from infected cells and to dysregulate uninfected ones, using an in vitro model in which Tat was ectopically expressed in B-cells. CONCLUSIONS Our findings demonstrated that the ectopic expression of Tat was per se sufficient to determine DNMT up-regulation, based on microRNA down-regulation, and that this results in aberrant hypermethylation of target genes and microRNAs. These results point at a direct role for Tat in participating in uninfected B-cell lymphomagenesis, through dysregulation of the epigenetical control of gene expression.
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Affiliation(s)
- Anna Luzzi
- />Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Federica Morettini
- />Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Sara Gazaneo
- />Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Lucia Mundo
- />Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Anna Onnis
- />Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Susanna Mannucci
- />Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Emily A Rogena
- />Department of Medical Biotechnologies, University of Siena, Siena, Italy
- />Department of Pathology, University of Nairobi, Nairobi, Kenya
| | - Cristiana Bellan
- />Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Lorenzo Leoncini
- />Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Giulia De Falco
- />Department of Medical Biotechnologies, University of Siena, Siena, Italy
- />School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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Bryant D, Onions T, Raybould R, Jones S, Tristram A, Hibbitts S, Fiander A, Powell N. Increased methylation of Human Papillomavirus type 16 DNA correlates with viral integration in Vulval Intraepithelial Neoplasia. J Clin Virol 2014; 61:393-9. [PMID: 25218242 DOI: 10.1016/j.jcv.2014.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 07/25/2014] [Accepted: 08/08/2014] [Indexed: 11/29/2022]
Abstract
BACKGROUND Methylation of HPV16 DNA is a promising biomarker for triage of HPV positive cervical screening samples but the biological basis for the association between HPV-associated neoplasia and increased methylation is unclear. OBJECTIVES To determine whether HPV16 DNA methylation was associated with viral integration, and investigate the relationships between viral DNA methylation, integration and gene expression. STUDY DESIGN HPV16 DNA methylation, integration and gene expression were assessed using pyrosequencing, ligation-mediated PCR and QPCR, in biopsies from 25 patients attending a specialist vulval neoplasia clinic and in short-term clonal cell lines derived from vulval and vaginal neoplasia. RESULTS Increased methylation of the HPV16 L1/L2 and E2 regions was associated with integration of viral DNA into the host genome. This relationship was observed both in vivo and in vitro. Increased methylation of E2 binding sites did not appear to be associated with greater expression of viral early genes. Expression of HPV E6 and E7 did not correlate with either integration state or increased L1/L2 methylation. CONCLUSIONS The data suggest that increased HPV DNA methylation may be partly attributable to viral integration, and provide a biological rationale for quantification of L1/L2 methylation in triage of HPV positive cervical screening samples.
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Affiliation(s)
- Dean Bryant
- HPV Research Group, Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.
| | - Tiffany Onions
- HPV Research Group, Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.
| | - Rachel Raybould
- HPV Research Group, Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.
| | - Sadie Jones
- HPV Research Group, Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.
| | - Amanda Tristram
- HPV Research Group, Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.
| | - Samantha Hibbitts
- HPV Research Group, Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.
| | - Alison Fiander
- HPV Research Group, Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.
| | - Ned Powell
- HPV Research Group, Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.
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Naumann A, Kraus C, Hoogeveen A, Ramirez CM, Doerfler W. Stable DNA methylation boundaries and expanded trinucleotide repeats: role of DNA insertions. J Mol Biol 2014; 426:2554-66. [PMID: 24816393 DOI: 10.1016/j.jmb.2014.04.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 04/28/2014] [Accepted: 04/28/2014] [Indexed: 11/15/2022]
Abstract
The human genome segment upstream of the FMR1 (fragile X mental retardation 1) gene (Xq27.3) contains several genetic signals, among them is a DNA methylation boundary that is located 65-70 CpGs upstream of the CGG repeat. In fragile X syndrome (FXS), the boundary is lost, and the promoter is inactivated by methylation spreading. Here we document boundary stability in spite of critical expansions of the CGG trinucleotide repeat in male or female premutation carriers and in high functioning males (HFMs). HFMs carry a full CGG repeat expansion but exhibit an unmethylated promoter and lack the FXS phenotype. The boundary is also stable in Turner (45, X) females. A CTCF-binding site is located slightly upstream of the methylation boundary and carries a unique G-to-A polymorphism (single nucleotide polymorphism), which occurs 3.6 times more frequently in genomes with CGG expansions. The increased frequency of this single nucleotide polymorphism might have functional significance. In CGG expansions, the CTCF region does not harbor additional mutations. In FXS individuals and often in cells transgenomic for EBV (Epstein Barr Virus) DNA or for the telomerase gene, the large number of normally methylated CpGs in the far-upstream region of the boundary is decreased about 4-fold. A methylation boundary is also present in the human genome segment upstream of the HTT (huntingtin) promoter (4p16.3) and is stable both in normal and Huntington disease chromosomes. Hence, the vicinity of an expanded repeat does not per se compromise methylation boundaries. Methylation boundaries exert an important function as promoter safeguards.
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Affiliation(s)
- Anja Naumann
- Institute for Clinical and Molecular Virology, Erlangen University Medical School, D-91054 Erlangen, Germany
| | - Cornelia Kraus
- Institute for Human Genetics, Erlangen University Medical School, D-91054 Erlangen, Germany
| | - André Hoogeveen
- Department of Clinical Genetics, Erasmus University Medical School, 3000 DR Rotterdam, The Netherlands
| | - Christina M Ramirez
- Department of Biostatistics and Statistics, University of California, Los Angeles, CA 90095, USA
| | - Walter Doerfler
- Institute for Clinical and Molecular Virology, Erlangen University Medical School, D-91054 Erlangen, Germany; Institute of Genetics, University of Cologne, D-50674 Cologne, Germany.
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19
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Barros SP, Offenbacher S. Modifiable risk factors in periodontal disease. Periodontol 2000 2013; 64:95-110. [DOI: 10.1111/prd.12000] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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20
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Dong Z, Wang H, Dong Y, Wang Y, Liu W, Miao G, Lin X, Wang D, Liu B. Extensive microsatellite variation in rice induced by introgression from wild rice (Zizania latifolia Griseb.). PLoS One 2013; 8:e62317. [PMID: 23638037 PMCID: PMC3634730 DOI: 10.1371/journal.pone.0062317] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 03/20/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND It is widely accepted that interspecific hybridization may induce genomic instability in the resultant hybrids. However, few studies have been performed on the genomic analysis of homoploid hybrids and introgression lines. We have reported previously that by introgressive hybridization, a set of introgression lines between rice (Oryza sativa L.) and wild rice (Zizania latifolia Griseb.) was successfully generated, and which have led to the release of several cultivars. METHODOLOGY Using 96 microsatellite markers located in the nuclear and organelle genomes of rice, we investigated microsatellite stability in three typical introgression lines. Expression of a set of mismatch repair (MMR) genes and microsatellite-containing genes was also analyzed. RESULTS/CONCLUSIONS Compared with the recipient rice cultivar (Matsumae), 55 of the 96 microsatellite loci revealed variation in one or more of the introgression lines, and 58.2% of the altered alleles were shared by at least two lines, indicating that most of the alterations had occurred in the early stages of introgression before their further differentiation. 73.9% of the non-shared variations were detected only in one introgression line, i.e. RZ2. Sequence alignment showed that the variations included substitutions and indels that occurred both within the repeat tracts and in the flanking regions. Interestingly, expression of a set of MMR genes altered dramatically in the introgression lines relative to their rice parent, suggesting participation of the MMR system in the generation of microsatellite variants. Some of the altered microsatellite loci are concordant with changed expression of the genes harboring them, suggesting their possible cis-regulatory roles in controlling gene expression. Because these genes bear meaningful homology to known-functional proteins, we conclude that the introgression-induced extensive variation of microsatellites may have contributed to the novel phenotypes in the introgression lines.
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Affiliation(s)
- Zhenying Dong
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
- The State Key Laboratory of Plant Cell and Chromosomal Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hongyan Wang
- Faculty of Life Science, Liaoning University, Shenyang, China
| | - Yuzhu Dong
- School of Life Sciences, Changchun Normal University, Changchun, China
| | - Yongming Wang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Wei Liu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Gaojian Miao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Xiuyun Lin
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Daqing Wang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
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21
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Gohlke J, Scholz CJ, Kneitz S, Weber D, Fuchs J, Hedrich R, Deeken R. DNA methylation mediated control of gene expression is critical for development of crown gall tumors. PLoS Genet 2013; 9:e1003267. [PMID: 23408907 PMCID: PMC3567176 DOI: 10.1371/journal.pgen.1003267] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 12/04/2012] [Indexed: 11/19/2022] Open
Abstract
Crown gall tumors develop after integration of the T-DNA of virulent Agrobacterium tumefaciens strains into the plant genome. Expression of the T-DNA-encoded oncogenes triggers proliferation and differentiation of transformed plant cells. Crown gall development is known to be accompanied by global changes in transcription, metabolite levels, and physiological processes. High levels of abscisic acid (ABA) in crown galls regulate expression of drought stress responsive genes and mediate drought stress acclimation, which is essential for wild-type-like tumor growth. An impact of epigenetic processes such as DNA methylation on crown gall development has been suggested; however, it has not yet been investigated comprehensively. In this study, the methylation pattern of Arabidopsis thaliana crown galls was analyzed on a genome-wide scale as well as at the single gene level. Bisulfite sequencing analysis revealed that the oncogenes Ipt, IaaH, and IaaM were unmethylated in crown galls. Nevertheless, the oncogenes were susceptible to siRNA-mediated methylation, which inhibited their expression and subsequently crown gall growth. Genome arrays, hybridized with methylated DNA obtained by immunoprecipitation, revealed a globally hypermethylated crown gall genome, while promoters were rather hypomethylated. Mutants with reduced non-CG methylation developed larger tumors than the wild-type controls, indicating that hypermethylation inhibits plant tumor growth. The differential methylation pattern of crown galls and the stem tissue from which they originate correlated with transcriptional changes. Genes known to be transcriptionally inhibited by ABA and methylated in crown galls became promoter methylated upon treatment of A. thaliana with ABA. This suggests that the high ABA levels in crown galls may mediate DNA methylation and regulate expression of genes involved in drought stress protection. In summary, our studies provide evidence that epigenetic processes regulate gene expression, physiological processes, and the development of crown gall tumors.
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Affiliation(s)
- Jochen Gohlke
- Julius-von-Sachs-Institute, Department of Molecular Plant Physiology and Biophysics, University of Wuerzburg, Wuerzburg, Germany
| | - Claus-Juergen Scholz
- IZKF Laboratory for Microarray Applications, University Hospital of Wuerzburg, Wuerzburg, Germany
| | - Susanne Kneitz
- Physiological Chemistry I, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Dana Weber
- Julius-von-Sachs-Institute, Department of Molecular Plant Physiology and Biophysics, University of Wuerzburg, Wuerzburg, Germany
| | - Joerg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Rainer Hedrich
- Julius-von-Sachs-Institute, Department of Molecular Plant Physiology and Biophysics, University of Wuerzburg, Wuerzburg, Germany
| | - Rosalia Deeken
- Julius-von-Sachs-Institute, Department of Molecular Plant Physiology and Biophysics, University of Wuerzburg, Wuerzburg, Germany
- * E-mail:
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22
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Doerfler W. Impact of foreign DNA integration on tumor biology and on evolution via epigenetic alterations. Epigenomics 2012; 4:41-9. [PMID: 22332657 DOI: 10.2217/epi.11.111] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The insertion of foreign DNA into mammalian genomes can alter their methylation and transcription patterns at remote sites from the locus of foreign DNA integration. The mechanisms leading to these fundamental changes and their frequencies are unknown. Sites and extent of changes in the recipient cells might depend on the location of foreign DNA integration. In the second part of this review, it will be hypothesized that the insertion event itself, for example, of tumor viral DNA via its epigenetic genome-wide consequences, plays an important role in oncogenesis. During evolution, the impact of ancient retrotransposon or retroviral genomes and the ensuing epigenetic alterations in the recipient genomes might have generated cells with completely different transcriptional profiles. Due to the continued presence of the transgenomes these alterations were genetically stable and were selected for or against by the environmental conditions prevalent at the time. These evolutionary effects are very different from those postulated for insertional mutagenesis, added genetic information or regulatory elements placed into the vicinity of cellular functions.
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Affiliation(s)
- Walter Doerfler
- Institute for Virology, Erlangen University, Erlangen, Germany.
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23
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Rizzi A, Raddadi N, Sorlini C, Nordgrd L, Nielsen KM, Daffonchio D. The Stability and Degradation of Dietary DNA in the Gastrointestinal Tract of Mammals: Implications for Horizontal Gene Transfer and the Biosafety of GMOs. Crit Rev Food Sci Nutr 2012; 52:142-61. [DOI: 10.1080/10408398.2010.499480] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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24
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Doerfler W. Epigenetic consequences of foreign DNA insertions: de novo methylation and global alterations of methylation patterns in recipient genomes. Rev Med Virol 2011; 21:336-46. [PMID: 21793096 DOI: 10.1002/rmv.698] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 05/04/2011] [Accepted: 05/19/2011] [Indexed: 11/09/2022]
Abstract
The insertion of foreign DNA into mammalian or plant genomes is a frequent event in biology. My laboratory has pursued a long-standing interest in the structure of integrated adenovirus genomes and in the mechanism of foreign DNA insertions in mammalian cells. The long-term consequences of the integration of alien DNA are only partly known, and even less well understood are the mechanisms that bring them about. Evidence from viral systems has contributed to the realization that foreign DNA insertions entail a complex of sequelae that have also become apparent in non-viral systems: (i) The de novo methylation of integrated foreign DNA sequences has frequently been observed. (ii) Alterations of DNA methylation patterns in the recipient genome at and remote from the site of foreign DNA insertion have been demonstrated but it remains to be investigated how generally this phenomenon occurs. Many viral genomes find and have found entry into the genomes of present-day organisms. A major portion of mammalian genomes represents incomplete retroviral genomes that frequently have become permanently silenced by DNA methylation. It is still unknown how and to what extent the insertion of retroviral or retrotransposon sequences into established genomes has altered and shaped the methylation and transcription profiles of present day genomes. An additional reason for concern about the effects of foreign DNA integration is the fact that in all fields of molecular biology and medicine, the generation of transgenic or transgenomic cells and organisms has become a ubiquitously applied experimental technique.
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Affiliation(s)
- Walter Doerfler
- Institute for Clinical and Molecular Virology, Erlangen University Medical School, Erlangen, Germany; Institute of Genetics, Cologne University, Cologne, Germany.
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25
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Dwivedi RS, Herman JG, McCaffrey TA, Raj DSC. Beyond genetics: epigenetic code in chronic kidney disease. Kidney Int 2010; 79:23-32. [PMID: 20881938 DOI: 10.1038/ki.2010.335] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Epigenetics refers to a heritable change in the pattern of gene expression that is mediated by a mechanism specifically not due to alterations in the primary nucleotide sequence. Well-known epigenetic mechanisms encompass DNA methylation, chromatin remodeling (histone modifications), and RNA interference. Functionally, epigenetics provides an extra layer of transcriptional control and plays a crucial role in normal physiological development, as well as in pathological conditions. Aberrant DNA methylation is implicated in immune dysfunction, inflammation, and insulin resistance. Epigenetic changes may be responsible for 'metabolic memory' and development of micro- and macrovascular complications of diabetes. MicroRNAs are critical in the maintenance of glomerular homeostasis and hence RNA interference may be important in the progression of renal disease. Recent studies have shown that epigenetic modifications orchestrate the epithelial-mesenchymal transition and eventually fibrosis of the renal tissue. Oxidative stress, inflammation, hyperhomocysteinemia, and uremic toxins could induce epimutations in chronic kidney disease. Epigenetic alterations are associated with inflammation and cardiovascular disease in patients with chronic kidney disease. Reversible nature of the epigenetic changes gives a unique opportunity to halt or even reverse the disease process through targeted therapeutic strategies.
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Affiliation(s)
- Rama S Dwivedi
- Division of Renal Diseases and Hypertension, The George Washington University, Washington, District of Columbia 20037, USA
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Niller HH, Wolf H, Minarovits J. Viral hit and run-oncogenesis: genetic and epigenetic scenarios. Cancer Lett 2010; 305:200-17. [PMID: 20813452 DOI: 10.1016/j.canlet.2010.08.007] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Revised: 07/29/2010] [Accepted: 08/09/2010] [Indexed: 12/31/2022]
Abstract
It is well documented that viral genomes either inserted into the cellular DNA or co-replicating with it in episomal form can be lost from neoplastic cells. Therefore, "hit and run"-mechanisms have been a topic of longstanding interest in tumor virology. The basic idea is that the transient acquisition of a complete or incomplete viral genome may be sufficient to induce malignant conversion of host cells in vivo, resulting in neoplastic development. After eliciting a heritable change in the gene expression pattern of the host cell (initiation), the genomes of tumor viruses may be completely lost, i.e. in a hit and run-scenario they are not necessary for the maintenance of the malignant state. The expression of viral oncoproteins and RNAs may interfere not only with regulators of cell proliferation, but also with DNA repair mechanisms. DNA recombinogenic activities induced by tumor viruses or activated by other mechanisms may contribute to the secondary loss of viral genomes from neoplastic cells. Viral oncoproteins can also cause epigenetic dysregulation, thereby reprogramming cellular gene expression in a heritable manner. Thus, we expect that epigenetic scenarios of viral hit and run-tumorigenesis may facilitate new, innovative experiments and clinical studies in spite of the fact that the regular presence of a suspected human tumor virus in an early phase of neoplastic development and its subsequent regular loss have not been demonstrated yet. We propose that virus-specific "epigenetic signatures", i.e. alterations of the host cell epigenome, especially altered DNA methylation patterns, may help to identify viral hit and run-oncogenic events, even after the complete loss of tumor viruses from neoplastic cells.
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Affiliation(s)
- Hans Helmut Niller
- Institute for Medical Microbiology and Hygiene of the University of Regensburg, Franz-Josef-Strauss-Allee 11, Regensburg, Germany.
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Wu R, Guo WL, Wang XR, Wang XL, Zhuang TT, Clarke JL, Liu B. Unintended consequence of plant transformation: biolistic transformation caused transpositional activation of an endogenous retrotransposon Tos17 in rice ssp. japonica cv. Matsumae. PLANT CELL REPORTS 2009; 28:1043-1051. [PMID: 19415284 DOI: 10.1007/s00299-009-0704-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Revised: 04/03/2009] [Accepted: 04/15/2009] [Indexed: 05/27/2023]
Abstract
Genetic instability could be provoked as an unintended consequence of genetic engineering in plants. Here, we report that the rice endogenous long terminal repeat (LTR) retrotransposon Tos17 was transpositionally activated only in transgenic calli and their regenerated plants produced by biolistic transformation in rice (Oryza sativa L.) ssp. japonica cv. Matsumae. Moreover, the transpositional activity of Tos17 was sustained after plant regeneration in the T0 generation, and produced new germinal insertions. In contrast, the element remained totally quiescent in calli and regenerated plants from tissue culture of this genotype. Nonetheless, transcriptional induction and cytosine demethylation of Tos17 were found to have occurred with no significant difference in both kinds of calli, tissue culture alone and transgenic. This suggests that callus culture is likely to have played an important role in destabilizing Tos17 in the direction towards transpositional activation, but that biolistic transformation is the direct causal factor.
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Affiliation(s)
- R Wu
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, 130024, Changchun, China
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28
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Wang H, Chai Y, Chu X, Zhao Y, Wu Y, Zhao J, Ngezahayo F, Xu C, Liu B. Molecular characterization of a rice mutator-phenotype derived from an incompatible cross-pollination reveals transgenerational mobilization of multiple transposable elements and extensive epigenetic instability. BMC PLANT BIOLOGY 2009; 9:63. [PMID: 19476655 PMCID: PMC2696445 DOI: 10.1186/1471-2229-9-63] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Accepted: 05/29/2009] [Indexed: 05/18/2023]
Abstract
BACKGROUND Inter-specific hybridization occurs frequently in plants, which may induce genetic and epigenetic instabilities in the resultant hybrids, allopolyploids and introgressants. It remains unclear however whether pollination by alien pollens of an incompatible species may impose a "biological stress" even in the absence of genome-merger or genetic introgression, whereby genetic and/or epigenetic instability of the maternal recipient genome might be provoked. RESULTS We report here the identification of a rice mutator-phenotype from a set of rice plants derived from a crossing experiment involving two remote and apparently incompatible species, Oryza sativa L. and Oenothera biennis L. The mutator-phenotype (named Tong211-LP) showed distinct alteration in several traits, with the most striking being substantially enlarged panicles. Expectably, gel-blotting by total genomic DNA of the pollen-donor showed no evidence for introgression. Characterization of Tong211-LP (S0) and its selfed progenies (S1) ruled out contamination (via seed or pollen) or polyploidy as a cause for its dramatic phenotypic changes, but revealed transgenerational mobilization of several previously characterized transposable elements (TEs), including a MITE (mPing), and three LTR retrotransposons (Osr7, Osr23 and Tos17). AFLP and MSAP fingerprinting revealed extensive, transgenerational alterations in cytosine methylation and to a less extent also genetic variation in Tong211-LP and its immediate progenies. mPing mobility was found to correlate with cytosine methylation alteration detected by MSAP but not with genetic variation detected by AFLP. Assay by q-RT-PCR of the steady-state transcript abundance of a set of genes encoding for the various putative DNA methyltransferases, 5-methylcytosine DNA glycosylases, and small interference RNA (siRNA) pathway-related proteins showed that, relative to the rice parental line, heritable perturbation in expression of 12 out of the 13 genes occurred in the mutator-phenotype and its sefled progenies. CONCLUSION Transgenerational epigenetic instability in the form of altered cytosine methylation and its associated TE activity occurred in a rice mutator-phenotype produced by pollinating the rice stigma with pollens of O. biennis. Heritably perturbed homeostatic expression-state of genes involved in maintenance of chromatin structure is likely an underlying cause for the alien pollination-induced transgenerational epigenetic/genetic instability, and which occurred apparently without entailing genome merger or genetic introgression.
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Affiliation(s)
- Hongyan Wang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, PR China
| | - Yang Chai
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, PR China
| | - Xiucheng Chu
- Tonghua Academy of Agricultural Sciences, Hailong 135007, Jilin Province, PR China
| | - Yunyang Zhao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, PR China
| | - Ying Wu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, PR China
| | - Jihong Zhao
- Tonghua Academy of Agricultural Sciences, Hailong 135007, Jilin Province, PR China
| | - Frédéric Ngezahayo
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, PR China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, PR China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, PR China
- Key Laboratory of Applied Statistics of MOE, Northeast Normal University, Changchun 130024, PR China
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Doerfler W. Epigenetic mechanisms in human adenovirus type 12 oncogenesis. Semin Cancer Biol 2009; 19:136-43. [PMID: 19429476 PMCID: PMC7129905 DOI: 10.1016/j.semcancer.2009.02.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2008] [Accepted: 02/11/2009] [Indexed: 11/28/2022]
Abstract
For the past 30 years, my laboratory has concentrated its work on demonstrating that the epigenetic consequences of foreign DNA insertion into established mammalian genomes – de novo DNA methylation of the integrate and alterations of methylation patterns across the recipient genome – are essential elements in setting the stage towards oncogenic transformation. We have primarily studied human adenovirus type 12 (Ad12) which induces undifferentiated tumors in Syrian hamsters (Mesocricetus auratus) either at the site of subcutaneous Ad12 injection or intraperitoneally upon intramuscular injection. Up to 90% of the hamsters injected with Ad12 develop tumors within 3–6 weeks. Integration of foreign DNA, its de novo methylation, and the consequences of insertion on the cellular methylation and transcription profiles have been studied in detail. While viral infections are a frequent source of foreign genomes entering mammalian and other hosts and often their genomes, we have also pursued the fate of food-ingested foreign DNA in the mouse organism. The persistence of this DNA in the animals is transient and there is no evidence for the expression or germ line fixation of foreign DNA. Nevertheless, the occasional cell that carries integrated genomes from that foreign source deserves the oncologist's sustained interest.
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Affiliation(s)
- Walter Doerfler
- University of Cologne, Institute of Genetics, Zülpicherstrasse 47, D-50674 Köln, Germany.
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Zhang C, Guo X, Zhang L, Lu Z, Ma N, Cheng Y, Shen F, Zhang B, Wu M, Wei L. Methylation-Related silencing of p14ARF gene correlates with telomerase activity and mRNA expression of human telomerase reverse transcriptase in hepatocellular carcinoma. J Surg Oncol 2008; 98:462-8. [DOI: 10.1002/jso.21131] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Zhu R, Li BZ, Li H, Ling YQ, Hu XQ, Zhai WR, Zhu HG. Association of p16INK4A hypermethylation with hepatitis B virus X protein expression in the early stage of HBV-associated hepatocarcinogenesis. Pathol Int 2007; 57:328-36. [PMID: 17539963 DOI: 10.1111/j.1440-1827.2007.02104.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The aim of the present study was to explore the relationship between methylation status of the p16(INK4A) promoter and some HBV-related factors, and the role of these factors in p16(INK4A) hypermethylation and hepatocellular carcinoma (HCC) progression. Twenty-three cases of surgically resected HBV-associated HCC and 25 fine-needle aspiration biopsy cases of chronic hepatitis B (CHB) were studied. The methylation status of the p16(INK4A) promoter was determined by methylation-specific polymerase chain reaction (PCR). Two-step immunohistochemical staining showed the expression of viral antigens in situ. Tissue HBV-DNA levels were determined by fluorescence quantitative real-time PCR. PCR and the direct sequencing method were used for mutation analysis. In peritumoral tissues (P = 0.025) and CHB samples (P = 0.029), the expression of hepatitis B virus X protein (HBx) was higher in methylated groups of p16(INK4A) promoter than in unmethylated groups. Other HBV factors including hepatitis B surface antigen and hepatitis B core antigen, tissue HBV-DNA levels and HBV x gene mutations had no relation to the methylation status of p16(INK4A) promoter. The data indicate that p16(INK4A) promoter hypermethylation correlated closely with higher HBx expression in the precancerous lesions, suggesting that HBx may play an important role in the early stage of HBV-associated hepatocarcinogenesis via induction of hypermethylation of p16(INK4A) promoter.
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Affiliation(s)
- Rong Zhu
- Department of Pathology, Shanghai Medical College, Fudan University, Shanghai, China
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32
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Zhu J, Kren BT, Park CW, Bilgim R, Wong PYP, Steer CJ. Erythroid-specific expression of beta-globin by the sleeping beauty transposon for Sickle cell disease. Biochemistry 2007; 46:6844-58. [PMID: 17508724 PMCID: PMC3893920 DOI: 10.1021/bi6024484] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Sickle cell disease (SCD) results predominately from a single monogenic mutation that affects thousands of individuals worldwide. Gene therapy approaches have focused on using viral vectors to transfer wild-type beta- or gamma-globin transgenes into hematopoietic stem cells for long-term expression of the recombinant globins. In this study, we investigated the use of a novel nonviral vector system, the Sleeping Beauty (SB) transposon (Tn) to insert a wild-type beta-globin expression cassette into the human genome for sustained expression of beta-globin. We initially constructed a beta-globin expression vector composed of the hybrid cytomegalovirus (CMV) enhancer chicken beta-actin promoter (CAGGS) and full-length beta-globin cDNA, as well as truncated forms lacking either the 3' or 3' and 5' untranslated regions (UTRs), to optimize expression of beta-globin. Beta-globin with its 5' UTR was efficiently expressed from its cDNA in K-562 cells induced with hemin. However, expression was constitutive and not erythroid-specific. We then constructed cis SB-Tn-beta-globin plasmids using a minimal beta-globin gene driven by hybrid promoter IHK (human ALAS2 intron 8 erythroid-specific enhancer, HS40 core element from human alphaLCR, ankyrin-1 promoter), IHbetap (human ALAS2 intron 8 erythroid-specific enhancer, HS40 core element from human alphaLCR, beta-globin promoter), or HS3betap (HS3 core element from human betaLCR, beta-globin promoter) to establish erythroid-specific expression of beta-globin. Stable genomic insertion of the minimal gene and expression of the beta-globin transgene for >5 months at a level comparable to that of the endogenous gamma-globin gene were achieved using a SB-Tn beta-globin cis construct. Interestingly, erythroid-specific expression of beta-globin driven by IHK was regulated primarily at the translational level, in contrast to post-transcriptional regulation in non-erythroid cells. The SB-Tn system is a promising nonviral vector for efficient genomic insertion conferring stable, persistent erythroid-specific expression of beta-globin.
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Affiliation(s)
- Jianhui Zhu
- Department of Medicine, Cell Biology, and Development, University of Minnesota Medical School, Minneapolis, Minnesota 55455
| | - Betsy T. Kren
- Department of Medicine, Cell Biology, and Development, University of Minnesota Medical School, Minneapolis, Minnesota 55455
| | - Chang Won Park
- Department of Medicine, Cell Biology, and Development, University of Minnesota Medical School, Minneapolis, Minnesota 55455
| | - Rasim Bilgim
- Department of Medicine, Cell Biology, and Development, University of Minnesota Medical School, Minneapolis, Minnesota 55455
| | - Phillip Y-P. Wong
- Department of Medicine, Cell Biology, and Development, University of Minnesota Medical School, Minneapolis, Minnesota 55455
| | - Clifford J. Steer
- Department of Medicine, Cell Biology, and Development, University of Minnesota Medical School, Minneapolis, Minnesota 55455
- Department of Genetics, Cell Biology, and Development, University of Minnesota Medical School, Minneapolis, Minnesota 55455
- To whom correspondence should be addressed: Department of Medicine, University of Minnesota Medical School, Mayo Mail Code 36, Mayo Building, Room A539, 420 Delaware Street S.E., Minneapolis, MN 55455. Telephone: (612) 624-6648. Fax: (612) 625-5620,
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Hochstein N, Muiznieks I, Mangel L, Brondke H, Doerfler W. Epigenetic status of an adenovirus type 12 transgenome upon long-term cultivation in hamster cells. J Virol 2007; 81:5349-61. [PMID: 17344292 PMCID: PMC1900229 DOI: 10.1128/jvi.02624-06] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The epigenetic status of integrated adenovirus type 12 (Ad12) DNA in hamster cells cultivated for about 4 decades has been investigated. Cell line TR12, a fibroblastic revertant of the Ad12-transformed epitheloid hamster cell line T637 with 15 copies of integrated Ad12 DNA, carries one Ad12 DNA copy plus a 3.9-kbp fragment from a second copy. The cellular insertion site for the Ad12 integrate, identical in both cell lines, is a >5.2-kbp inverted DNA repeat. The Ad12 transgenome is packaged around nucleosomes. The cellular junction is more sensitive to micrococcal nuclease at Ad12-occupied sites than at unoccupied sites. Bisulfite sequencing reveals complete de novo methylation in most of the 1,634 CpGs of the integrated viral DNA, except for its termini. Isolated unmethylated CpGs extend over the entire Ad12 integrate. The fully methylated transgenome segments are characterized by promoter silencing and histone H3 and H4 hypoacetylation. Nevertheless, there is minimal transcriptional activity of the late viral genes controlled by the fully methylated major late promoter of Ad12 DNA.
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Affiliation(s)
- Norbert Hochstein
- Institute for Clinical and Molecular Virology, Erlangen University Medical School, Schlossgarten 4, D-91054 Erlangen, Germany
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Doerfler W. Human Adenovirus Type 12. METHODS IN MOLECULAR MEDICINE™ 2007. [PMCID: PMC7120018 DOI: 10.1007/978-1-59745-277-9_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
When viruses cross species barriers, they often change their biological and pathogenetic properties. In the author's laboratory the nonproductive interaction of Syrian hamster cells with human adenovirus type 12 (Ad12) has been studied. Ad12 induces undifferentiated tumors in newborn hamsters (Mesocricetus auratus) at high frequency. Ad12 inefficiently enters hamster (BHK21) cells, and only small amounts of viral DNA reach the nucleus. Viral DNA replication and late transcription are blocked. In Ad12-induced tumor cells, multiple copies of viral DNA are chromosomally integrated. The integrated viral DNA becomes de novo methylated. Cellular DNA methylation and transcription patterns in Ad12-transformed cells and in Ad12- induced tumor cells are altered. These changes may be related to the oncogenic potential of Ad12 in hamsters. In this chapter, concepts and techniques for the study of the Ad12-hamster cell system are summarized.
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Jicai Z, Zongtao Y, Zongtao Y, Jun L, Jun L, Haiping L, Jianmin W, Lihua H. Persistent infection of hepatitis B virus is involved in high rate of p16 methylation in hepatocellular carcinoma. Mol Carcinog 2006; 45:530-6. [PMID: 16649250 DOI: 10.1002/mc.20188] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
High rate of chronic hepatitis B virus (HBV) infection and p16 promoter methylation were found in the majority of hepatocellular carcinoma (HCC). To investigate the potential linkage between high rate of p16 methylation and HBV infection, p16 methylation was detected with methylation-specific polymerase chain reaction (PCR), and HBV markers were examined with real-time PCR and immunologic method. p16 methylation was detected in 5.5% of patients with hepatitis B, 9.1% of noncancerous liver, 36.6% of cirrhotic liver tissue, and 70.5% of cancerous tissue of HCC, primarily in cirrhotic (46.7%) and cancerous tissue (90.6%) with HBV infection. In noncancerous tissue, p16 methylation could only be detected in samples with HBV infection, although no significant difference, the frequency of p16 methylation in noncancerous tissue with HBV infection was higher than those without it. The results showed that, in cancerous, cirrhotic, or noncancerous tissues, the frequency of p16 methylation in samples with HBV infection was higher than those without it, suggesting possible association between HBV infection and p16 methylation. The result of HBV-DNA analysis showed that 96.1% (49/51) samples with p16 methylation also showed detectable HBV-DNA; it signifies that replication and/or integration of HBV may contribute to high rate of p16 methylation in hepatocarcinogenesis. Generally, these results indicate that persistent HBV infection may be associated with high rate of p16 methylation, and involved in development of HCC through this way.
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Affiliation(s)
- Zhang Jicai
- Department of Laboratory Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Chen Y, Long L, Lin X, Guo W, Liu B. Isolation and characterization of a set of disease resistance-gene analogs (RGAs) from wild rice, Zizania latifolia Griseb. I. Introgression, copy number lability, sequence change, and DNA methylation alteration in several rice-Zizania introgression lines. Genome 2006; 49:150-8. [PMID: 16498465 DOI: 10.1139/g05-097] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Eight resistance-gene analogs (RGAs) were isolated from wild rice, Zizania latifolia Griseb., by degenerate primers designed according to conserved motifs at or around the nucleotide-binding site (NBS) of known NBS-containing plant resistance genes. The 8 RGAs were classified into 6 distinct groups based on their deduced amino acid sequence similarity of 60% or greater. Gel-blot hybridization of each of the RGAs to 4 rice - Z. latifolia intro gression lines indicated an array of changes at either introgressed Zizania RGAs or, more likely, their rice homologs. The changes included dramatic increase in copy number, modification at the primary DNA sequence, and alteration in DNA methylation patterns.
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Affiliation(s)
- Yu Chen
- Laboratory of Plant Epigenetics, Institute of Genetics and Cytology, Northeast Normal University , Chngchun 130024, China
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37
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Dong ZY, Wang YM, Zhang ZJ, Shen Y, Lin XY, Ou XF, Han FP, Liu B. Extent and pattern of DNA methylation alteration in rice lines derived from introgressive hybridization of rice and Zizania latifolia Griseb. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:196-205. [PMID: 16791687 DOI: 10.1007/s00122-006-0286-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2005] [Accepted: 03/31/2006] [Indexed: 05/04/2023]
Abstract
We have reported previously that introgression by Zizania latifolia resulted in extensive DNA methylation changes in the recipient rice genome, as detected by a set of pre-selected DNA segments. In this study, using the methylation-sensitive amplified polymorphism (MSAP) method, we globally assessed the extent and pattern of cytosine methylation alterations in three typical introgression lines relative to their rice parent at approximately 2,700 unbiased genomic loci each representing a recognition site cleaved by one or both of the isoschizomers, HpaII/MspI. Based on differential digestion by the isoschizomers, it is estimated that 15.9% of CCGG sites are either fully methylated at the internal Cs and/or hemi-methylated at the external Cs in the rice parental cultivar Matsumae. In comparison, a statistically significant increase in the overall level of both methylation types was detected in all three studied introgression lines (19.2, 18.6, 19.6%, respectively). Based on comparisons of MSAP profiles between the isoschizomers within the rice parent and between parent and the introgression lines, four major groups of MSAP banding patterns are recognized, which can be further divided into various subgroups as a result of inheritance of, or variation in, parental methylation patterns. The altered methylation patterns include hyper- and hypomethylation changes, as well as inter-conversion of hemi- to full-methylation, or vice versa, at the relevant CCGG site(s). Most alterations revealed by MSAP in low-copy loci can be validated by DNA gel blot analysis. The changed methylation patterns are uniform among randomly selected individuals for a given introgression line within or among selfed generations. Sequencing on 31 isolated fragments that showed different changing patterns in the introgression line(s) allowed their mapping onto variable regions on one or more of the 12 rice chromosomes. These segments include protein-coding genes, transposon/retrotransposons and sequences with no homology. Possible causes for the introgression-induced methylation changes and their implications for genome evolution and crop breeding are discussed.
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Affiliation(s)
- Z Y Dong
- Laboratory of Plant Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
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Han FP, Liu ZL, Tan M, Hao S, Fedak G, Liu B. Mobilized retrotransposon Tos17 of rice by alien DNA introgression transposes into genes and causes structural and methylation alterations of a flanking genomic region. Hereditas 2006; 141:243-51. [PMID: 15703040 DOI: 10.1111/j.1601-5223.2004.01808.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Tos17 is a copia-like endogenous retrotransposon of rice, which can be activated by various stresses such as tissue culture and alien DNA introgression. To confirm element mobilization by introgression and to study possible structural and epigenetic effects of Tos17 insertion on its target sequences, we isolated all flanking regions of Tos17 in an introgressed rice line (Tong35) that contains minute amount of genomic DNA from wild rice (Zizania latifolia). It was found that there has been apparent but limited mobilization of Tos17 in this introgression line, as being reflected by increased but stable copy number of the element in progeny of the line. Three of the five activated copies of the element have transposed into genes. Based on sequence analysis and Southern blot hybridization with several double-enzyme digests, no structural change in Tos17 could be inferred in the introgression line. Cytosine methylation status at all seven CCGG sites within Tos17 was also identical between the introgression line and its rice parent (Matsumae)-all sites being heavily methylated. In contrast, changes in structure and cytosine methylation patterns were detected in one of the three low-copy genomic regions that flank newly transposed Tos17, and all changes are stably inherited through selfed generations.
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Affiliation(s)
- F P Han
- Laboratory of Molecular Epigenetics, Institute of Genetics & Cytology, Northeast Normal University, Changchun, PR China
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Doerfler W. De novo methylation, long-term promoter silencing, methylation patterns in the human genome, and consequences of foreign DNA insertion. Curr Top Microbiol Immunol 2006; 301:125-75. [PMID: 16570847 DOI: 10.1007/3-540-31390-7_5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
This chapter presents a personal account of the work on DNA methylation in viral and mammalian systems performed in the author's laboratory in the course of the past 30 years. The text does not attempt to give a complete and meticulous account of the work accomplished in many other laboratories; in that sense it is not a review of the field in a conventional sense. Since the author is also one of the editors of this series of Current Topics in Immunology and Microbiology on DNA methylation, to which contributions by many of our colleagues in this field have been invited, the author's conscience is alleviated that he has not cited many of the relevant and excellent reports by others. The choice of viral model systems in molecular biology is well founded. Over many decades, viruses have proved their invaluable and pioneering role as tools in molecular genetics. When our interest turned to the demonstration of genome-wide patterns of DNA methylation, we focused mainly on the human genome. The following topics in DNA methylation will be treated in detail: (1) The de novo methylation of integrated foreign genomes; (2) the long-term gene silencing effect of sequence-specific promoter methylation and its reversal; (3) the properties and specificity of patterns of DNA methylation in the human genome and their possible relations to pathogenesis; (4) the long-range global effects on cellular DNA methylation and transcriptional profiles as a consequence of foreign DNA insertion into an established genome; (5) the patterns of DNA methylation can be considered part of a cellular defense mechanism against foreign or repetitive DNA; which role has food-ingested DNA played in the elaboration of this mechanism? The interest in problems related to DNA methylation has spread-like the mechanism itself-into many neighboring fields. The nature of the transcriptional programs orchestrating embryonal and fetal development, chromatin structure, genetic imprinting, genetic disease, X chromosome inactivation, and tumor biology are but a few of the areas of research that have incorporated studies on the importance of the hitherto somewhat neglected fifth nucleotide in many genomes. Even the fly researchers now have to cope with the presence of this nucleotide, in however small quantities it exists in the genome of their model organism, at least during embryonal development. The bulk of the experimental work accomplished in the author's laboratory has been shouldered by many very motivated undergraduate and graduate students and by a number of talented postdoctoral researchers. Their contributions are reflected in the list of references in this chapter. We have also had the good luck to receive funding through a number or organizations as acknowledged.
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Affiliation(s)
- W Doerfler
- Institut für Genetik, Universität zu Köln, Germany.
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McCabe MT, Low JA, Imperiale MJ, Day ML. Human polyomavirus BKV transcriptionally activates DNA methyltransferase 1 through the pRb/E2F pathway. Oncogene 2006; 25:2727-35. [PMID: 16547506 DOI: 10.1038/sj.onc.1209266] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Many DNA tumor virus oncogenes are capable of activating and highjacking the host cell's DNA replication machinery for its own reproduction purposes through targeting and inactivation of the retinoblastoma pocket protein family. Pocket proteins function to regulate cell cycle progression and DNA synthesis through inhibitory interactions with the E2F transcription factors. The interaction of viral oncogenes with the pocket proteins is crucial for their transforming activity. We recently demonstrated that the DNA methyltransferase 1 (DNMT1) gene is an E2F target gene that is transcriptionally activated in cells lacking the retinoblastoma gene (Rb-/-). Overexpression of DNMT1 is implicated in tumor suppressor gene hypermethylation which is associated with tumorigenesis. Given that viral oncogenes potently stimulate E2F activity, we hypothesized that viral infection might activate DNMT1 and thereby promote transformation. Herein, we demonstrate that DNMT1 is strongly activated by the human polyomavirus BKV large T antigen (TAg) and adenovirus E1a. Viral oncogene mutants incapable of binding the pocket proteins are ineffective at activating DNMT1 compared to their wild-type counterparts. Additionally, mutation of the E2F sites within the DNMT1 promoters dramatically abrogates transcriptional activation. These data suggest that viral induction of DNMT1 through modulation of the pRB/E2F pathway may be involved in viral transformation.
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MESH Headings
- Adenocarcinoma/genetics
- Adenocarcinoma/metabolism
- Adenocarcinoma/virology
- Adenovirus E1A Proteins/metabolism
- Animals
- Antigens, Polyomavirus Transforming/genetics
- Antigens, Polyomavirus Transforming/metabolism
- BK Virus/physiology
- Cell Transformation, Viral
- Cells, Cultured
- DNA (Cytosine-5-)-Methyltransferase 1
- DNA (Cytosine-5-)-Methyltransferases/genetics
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- E2F Transcription Factors/genetics
- E2F Transcription Factors/metabolism
- Embryo, Mammalian/cytology
- Embryo, Mammalian/metabolism
- Enzyme Activation
- Fibroblasts/cytology
- Fibroblasts/metabolism
- Humans
- Luciferases
- Male
- Mice
- Mice, Knockout
- Mutation
- NIH 3T3 Cells/metabolism
- NIH 3T3 Cells/virology
- Polyomavirus Infections/immunology
- Polyomavirus Infections/virology
- Promoter Regions, Genetic/genetics
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/metabolism
- Prostatic Neoplasms/virology
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Retinoblastoma Protein/genetics
- Retinoblastoma Protein/physiology
- Reverse Transcriptase Polymerase Chain Reaction
- Signal Transduction
- Transcription, Genetic
- Transcriptional Activation
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Affiliation(s)
- M T McCabe
- Program in Cellular and Molecular Biology, Department of Urology, University of Michigan, Ann Arbor, MI 48109-0944, USA
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41
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Park HJ, Yu E, Shim YH. DNA methyltransferase expression and DNA hypermethylation in human hepatocellular carcinoma. Cancer Lett 2006; 233:271-8. [PMID: 15885882 DOI: 10.1016/j.canlet.2005.03.017] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2004] [Revised: 03/08/2005] [Accepted: 03/11/2005] [Indexed: 12/31/2022]
Abstract
Aberrant DNA methylation and increased expression of DNA methyltransferases (DNMTs) are features of tumor cells. To investigate roles for DNMTs during hepatocarcinogenesis, we examined DNMT expression at both the mRNA and protein level in hepatocellular carcinomas (HCCs) and paired non-neoplastic liver tissues, along with measuring the DNA methylation status of five tumor suppressor genes. Expression of DNMT1, DNMT3a and DNMT3b mRNA was detected in 33.3, 59.3, and 55.6% of HCCs and 40.7, 22.2, and 0% of non-neoplastic liver tissues, respectively. DNMT1 and DNMT3a were immunoreactive in 100 and 48% of HCCs and 52 and 0% of non-neoplastic liver tissues. The DNMT3a mRNA expression profile showed significant correlation with its immunoreactivity (P=0.022). DNA methylation status of five tumor suppressor genes, HIC-1, p16, RASSF1A, p53, and RB1 was detected in 85.2, 48.1, 44.4, 22.2, and 0% of HCCs, respectively. There was no significant correlation between DNMT mRNA expression and DNA methylation (P>0.05). DNMT immunoreactivity was also not associated with DNA methylation except HIC-1 (P=0.036) and p53 methylation (P=0.009). Despite the lack of correlation between DNA methylation status and DNMT expression, the frequency of hypermethylation of tumor suppressor genes remained relatively high in HCCs, suggesting that regional DNA hypermethylation is involved in hepatocarcinogenesis and that there may be other mechanisms for increasing DNA methylation.
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Affiliation(s)
- Hye-Jung Park
- Department of Biological Sciences and Bio/Molecular Informatics Center, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul 143-701, South Korea
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42
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Affiliation(s)
- W Doerfler
- Institut für Klinische und Molekulare Virologie, Universität Erlangen, Germany.
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43
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Doerfler W. On the biological significance of DNA methylation. BIOCHEMISTRY (MOSCOW) 2005; 70:505-24. [PMID: 15948705 DOI: 10.1007/s10541-005-0145-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
This chapter presents a personal account of the work on DNA methylation in viral and mammalian systems performed in the author's laboratory in the course of the past thirty years. The text does not attempt to give a complete and meticulous account of the many relevant and excellent reports published by many other laboratories, so it is not a review of the field in a conventional sense. The choice of viral model systems in molecular biology is well founded. Over many decades, viruses have proven their invaluable and pioneering role as tools in molecular genetics. When our interest turned to the demonstration of genome-wide patterns of DNA methylation, we focused mainly on the human genome. The following topics in DNA methylation will be treated in detail: (i) the de novo methylation of integrated foreign genomes; (ii) the long-term gene silencing effect of sequence-specific promoter methylation and its reversal; (iii) the properties and specificity of patterns of DNA methylation in the human genome and their possible relations to pathogenesis; (iv) the long-range global effects on cellular DNA methylation and transcriptional profiles as a consequence of foreign DNA insertion into an established genome; (v) the patterns of DNA methylation can be considered part of a cellular defense mechanism against foreign or repetitive DNA; what role has food-ingested DNA played in the elaboration of this mechanism?
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Affiliation(s)
- W Doerfler
- Institut für Genetik, Universität zu Köln, 50674 Köln, Germany.
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44
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Dorn A, Zhao H, Granberg F, Hösel M, Webb D, Svensson C, Pettersson U, Doerfler W. Identification of specific cellular genes up-regulated late in adenovirus type 12 infection. J Virol 2005; 79:2404-12. [PMID: 15681441 PMCID: PMC546593 DOI: 10.1128/jvi.79.4.2404-2412.2005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The infection of human cells by adenoviruses leads to a gradual reduction in the activity of host cell functions while viral gene expression progresses in a regulated way. We used the DNA microarray technique to determine the transcriptional activity profiles of cellular genes upon infection with adenovirus type 12 (Ad12). The microarray data were validated by quantitative real-time PCR for genes which showed significant alterations after Ad12 infection. At 12 h postinfection, there is a striking up-regulation between 10- and 30-fold in the expression of the G1P2, IFIT1, and IFIT2 cellular immune response genes compared to mock-infected cells. At later stages of infection, when the majority of regulated cellular genes has been turned down, a limited number of cellular genes exhibit increased activities by factors of 3 or less. These genes belong to the signal transduction or transcriptional regulator classes or are active in protein degradation, like ANPEP, an aminopeptidase. The SCD and CYP2S1 genes function in lipid metabolism. The eucaryotic translation initiation factor 4 is up-regulated, and one of the major histocompatibility complex genes is diminished in activity. For two of the genes, one up-regulated (CTSF gene) and one down-regulated (CYR61 gene), alterations in gene activity were confirmed at the protein level by Western blotting experiments. Increased genetic activity of cellular genes late in adenovirus infection has not been reported previously and demonstrates that Ad12 has a sustained control of host cell gene expression well into the late phase of infection.
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Affiliation(s)
- Andreas Dorn
- Institute for Clinical and Molecular Virology, Erlangen University, Schlossgarten 4, D-91054 Erlangen, Germany
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Wang YM, Dong ZY, Zhang ZJ, Lin XY, Shen Y, Zhou D, Liu B. Extensive de Novo genomic variation in rice induced by introgression from wild rice (Zizania latifolia Griseb.). Genetics 2005; 170:1945-56. [PMID: 15937131 PMCID: PMC1449789 DOI: 10.1534/genetics.105.040964] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
To study the possible impact of alien introgression on a recipient plant genome, we examined >6000 unbiased genomic loci of three stable rice recombinant inbred lines (RILs) derived from intergeneric hybridization between rice (cv. Matsumae) and a wild relative (Zizania latifolia Griseb.) followed by successive selfing. Results from amplified fragment length polymorphism (AFLP) analysis showed that, whereas the introgressed Zizania DNA comprised <0.1% of the genome content in the RILs, extensive and genome-wide de novo variations occurred in up to 30% of the analyzed loci for all three lines studied. The AFLP-detected changes were validated by DNA gel-blot hybridization and/or sequence analysis of genomic loci corresponding to a subset of the differentiating AFLP fragments. A BLAST analysis revealed that the genomic variations occurred in diverse sequences, including protein-coding genes, transposable elements, and sequences of unknown functions. Pairwise sequence comparison of selected loci between a RIL and its rice parent showed that the variations represented either base substitutions or small insertion/deletions. Genome variations were detected in all 12 rice chromosomes, although their distribution was uneven both among and within chromosomes. Taken together, our results imply that even cryptic alien introgression can be highly mutagenic to a recipient plant genome.
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Affiliation(s)
- Yong-Ming Wang
- Laboratory of Molecular Epigenetics and The State Key Laboratory of Grassland and Ecology, Northeast Normal University, Changchun 130024, China
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Shan X, Liu Z, Dong Z, Wang Y, Chen Y, Lin X, Long L, Han F, Dong Y, Liu B. Mobilization of the active MITE transposons mPing and Pong in rice by introgression from wild rice (Zizania latifolia Griseb.). Mol Biol Evol 2005; 22:976-90. [PMID: 15647520 DOI: 10.1093/molbev/msi082] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Hybridization between different species plays an important role in plant genome evolution, as well as is a widely used approach for crop improvement. McClintock has predicted that plant wide hybridization constitutes a "genomic shock" whereby cryptic transposable elements may be activated. However, direct experimental evidence showing a causal relationship between plant wide hybridization and transposon mobilization has not yet been reported. The miniature-Ping (mPing) is a recently isolated active miniature inverted-repeat transposable element transposon from rice, which is mobilized by tissue culture and gamma-ray irradiation. We show herein that mPing, together with its putative transposase-encoding partner, Pong, is mobilized in three homologous recombinant inbred lines (RILs), derived from hybridization between rice (cultivar Matsumae) and wild rice (Zizania latifolia Griseb.), harboring introgressed genomic DNA from wild rice. In contrast, both elements remain immobile in two lines sharing the same parentage to the RILs but possessing no introgressed DNA. Thus, we have presented direct evidence that is consistent with McClintock's insight by demonstrating a causal link between wide hybridization and transposon mobilization in rice. In addition, we report an atypical behavior of mPing/Pong mobilization in these lines, i.e., the exclusive absence of footprints after excision.
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Affiliation(s)
- Xiaohui Shan
- Laboratory of Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
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Li X, Hui AM, Sun L, Hasegawa K, Torzilli G, Minagawa M, Takayama T, Makuuchi M. p16INK4A Hypermethylation Is Associated with Hepatitis Virus Infection, Age, and Gender in Hepatocellular Carcinoma. Clin Cancer Res 2004; 10:7484-9. [PMID: 15569978 DOI: 10.1158/1078-0432.ccr-04-1715] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Purpose: The tumor suppressor gene p16INK4A is mainly inactivated by an epigenetic change involving promoter hypermethylation in hepatocarcinogenesis. The possible clinical impact of p16INK4A methylation and the potential risk factors for this epigenetic alteration have not been thoroughly investigated.
Experimental Design: We studied the methylation status and mRNA and protein expression of p16INK4A in 50 hepatocellular carcinomas and corresponding nonneoplastic liver lesions using methylation-specific PCR, reverse transcription-PCR, and immunohistochemical techniques.
Results: p16INK4A hypermethylation was observed in 58% (29 of 50) of the hepatocellular carcinomas and 16% (6 of 38) of the corresponding chronic hepatitis and cirrhosis tissue samples. p16INK4A methylation was significantly associated with mRNA and protein expression (P < 0.001 and P = 0.003, respectively). All of the p16INK4A-methylated tumors were positive for hepatitis B virus or hepatitis C virus markers, but none of the virus-negative tumors exhibited p16INK4A methylation (P = 0.006). The frequency of p16INK4A hypermethylation tended to be higher in hepatitis C virus-related tumors (23 of 32, 72%) than in hepatitis B virus-related tumors (6 of 13, 46%; P = 0.1). Aberrant methylation of p16INK4A was also related significantly to increasing age, female gender, and normal levels of serum PIVKA-II (P = 0.02, 0.04, and 0.04, respectively). No statistically significant difference in survival was observed between patients with p16INK4A hypermethylation and those without.
Conclusions: Our observations suggest that p16INK4A hypermethylation may contribute to hepatocarcinogenesis from an early stage and that multiple risk factors, such as viral infections, age, and gender, may be associated with p16INK4A hypermethylation in hepatocarcinogenesis.
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Affiliation(s)
- Xin Li
- Hepato-Biliary-Pancreatic Surgery Division, Department of Surgery, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
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Mende Y, Schneider PM, Baldus SE, Doerfler W. PCR-screening of human esophageal and bronchial cancers reveals absence of adenoviral DNA sequences. Virus Res 2004; 104:81-5. [PMID: 15177895 DOI: 10.1016/j.virusres.2004.02.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2003] [Revised: 02/25/2004] [Accepted: 02/25/2004] [Indexed: 11/29/2022]
Abstract
A number of human esophageal (3) and bronchial (10) cancers have been characterized clinically and by their histopathology. These tumors have been investigated for the persistence of human adenoviral DNA sequences. The polymerase chain reaction (PCR) and Southern transfer hybridization (SBH) techniques have been applied. All analyses have consistently yielded negative results. These findings are discussed in the light of comparisons to the Ad12 hamster tumor system in which tumor cell or transformed cell revertants can lose the integrated Ad12 DNA sequences, but retain the oncogenic phenotype, when reinjected into hamsters. Ad12-transformed cells and Ad12-induced tumor cells have previously been shown to exhibit altered cellular methylation and transcription patterns. In one of the revertants, which has lost all Ad12 DNA sequences, changes in cellular DNA methylation patterns are also maintained. Since in the hamster tumor system the loss of Ad12 DNA sequences is still compatible with the oncogenic phenotype, the possibility exists that human tumors, though themselves devoid of viral DNA sequences, could have had cells as precursors which originally carried integrated adenoviral DNA sequences.
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Affiliation(s)
- Ylva Mende
- Institute of Genetics, University of Cologne, Weyertal 121, D-50931 Köln, Germany
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Abstract
BACKGROUND Transcriptional silencing of tumour suppressor genes by DNA hypermethylation plays a crucial role in the progression of gastric cancer. Many genes involved in the regulation of cell cycle, tissue invasion, DNA repair and apoptosis have been shown to be inactivated by this type of epigenetic mechanism. RESULTS Recent studies have demonstrated that DNA hypermethylation begins early in cancer progression, and in some cases, may precede the neoplastic process. Ageing is associated with DNA hypermethylation, and may provide a mechanistic link between ageing and cancer. Several reports have indicated that Epstein-Barr virus-related gastric cancer is associated with a high frequency of DNA hypermethylation, suggesting that viral oncogenesis might involve DNA hypermethylation with inactivation of tumour suppressor genes. Hypermethylation of hMLH1 with the resulting loss of its expression is known to cause microsatellite instability, which reflects genomic instability associated with defective DNA mismatch repair genes in the tumour. CONCLUSIONS In conclusion, recent studies demonstrate that DNA hypermethylation is a crucial mechanism of inactivation of tumour suppressor genes in gastric cancer. A better understanding of DNA hypermethylation will provide us with new opportunities in the diagnosis and therapy of gastric cancer.
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Affiliation(s)
- T Y Kim
- National Research Laboratory for Cancer Epigenetics, Cancer Research Institute, Seoul, Korea
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Piersanti S, Cherubini G, Martina Y, Salone B, Avitabile D, Grosso F, Cundari E, Di Zenzo G, Saggio I. Mammalian cell transduction and internalization properties of lambda phages displaying the full-length adenoviral penton base or its central domain. J Mol Med (Berl) 2004; 82:467-76. [PMID: 15150649 DOI: 10.1007/s00109-004-0543-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2003] [Accepted: 03/08/2004] [Indexed: 02/01/2023]
Abstract
In recent years a strong effort has been devoted to the search for new, safe and efficient gene therapy vectors. Phage lambda is a promising backbone for the development of new vectors: its genome can host large inserts, DNA is protected from degradation by the capsid and the ligand-exposed D and V proteins can be extensively modified. Current phage-based vectors are inefficient and/or receptor-independent transducers. To produce new, receptor-selective and transduction-efficient vectors for mammalian cells we engineered lambda by inserting into its genome a GFP expression cassette, and by displaying the penton base (Pb) of adenovirus or its central region (amino acids 286-393). The Pb mediates attachment, entry and endosomal escape of adenovirus in mammalian cells, and its central region (amino acids 286-393) includes the principal receptor-binding motif ((340)RGD(342)). Both the phage chimerae lambda Pb and lambda Pb (286-393) were able to transduce cell lines and primary cultures of human fibroblasts. Competition experiments showed that the transduction pathway was receptor-dependent. We also describe the different trafficking properties of lambda Pb and lambda Pb (286-393). Bafilomycin, which blocks endosome maturation, influenced the intracellular distribution of lambda Pb (286-393), but not that of lambda Pb. The proteasome inhibitor MG-132 improved the efficiency of lambda Pb (286-393)-mediated transduction, but not that of lambda Pb. In summary, this work shows the feasibility of using lambda phage as an efficient vector for gene transfer into mammalian cells. We show that lambda Pb and lambda Pb (286-393) can both mediate receptor-dependent transduction; while only lambda Pb is able to promote endosomal escape and proteasome resistance of phage particles.
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Affiliation(s)
- Stefania Piersanti
- Department of Genetics and Molecular Biology, University La Sapienza and Parco Scientifico Biomedico di Roma, S. Raffaele, Rome, Italy
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