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Nowicka A, Tokarz B, Zwyrtková J, Dvořák Tomaštíková E, Procházková K, Ercan U, Finke A, Rozhon W, Poppenberger B, Otmar M, Niezgodzki I, Krečmerová M, Schubert I, Pecinka A. Comparative analysis of epigenetic inhibitors reveals different degrees of interference with transcriptional gene silencing and induction of DNA damage. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:68-84. [PMID: 31733119 DOI: 10.1111/tpj.14612] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/25/2019] [Accepted: 10/29/2019] [Indexed: 06/10/2023]
Abstract
Repetitive DNA sequences and some genes are epigenetically repressed by transcriptional gene silencing (TGS). When genetic mutants are not available or problematic to use, TGS can be suppressed by chemical inhibitors. However, informed use of epigenetic inhibitors is partially hampered by the absence of any systematic comparison. In addition, there is emerging evidence that epigenetic inhibitors cause genomic instability, but the nature of this damage and its repair remain unclear. To bridge these gaps, we compared the effects of 5-azacytidine (AC), 2'-deoxy-5-azacytidine (DAC), zebularine and 3-deazaneplanocin A (DZNep) on TGS and DNA damage repair. The most effective inhibitor of TGS was DAC, followed by DZNep, zebularine and AC. We confirmed that all inhibitors induce DNA damage and suggest that this damage is repaired by multiple pathways with a critical role of homologous recombination and of the SMC5/6 complex. A strong positive link between the degree of cytidine analog-induced DNA demethylation and the amount of DNA damage suggests that DNA damage is an integral part of cytidine analog-induced DNA demethylation. This helps us to understand the function of DNA methylation in plants and opens the possibility of using epigenetic inhibitors in biotechnology.
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Affiliation(s)
- Anna Nowicka
- Institute of Experimental Botany (IEB), Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), CZ-779 00, Olomouc, Czech Republic
- Max Planck Institute for Plant Breeding Research (MPIPZ), DE-50829, Cologne, Germany
- The Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Niezapominajek 21, PL-30 239, Krakow, Poland
| | - Barbara Tokarz
- Institute of Experimental Botany (IEB), Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), CZ-779 00, Olomouc, Czech Republic
- Unit of Botany and Plant Physiology, Institute of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Al. 29 Listopada 54, PL-31 425, Krakow, Poland
| | - Jana Zwyrtková
- Institute of Experimental Botany (IEB), Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), CZ-779 00, Olomouc, Czech Republic
| | - Eva Dvořák Tomaštíková
- Institute of Experimental Botany (IEB), Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), CZ-779 00, Olomouc, Czech Republic
| | - Klára Procházková
- Institute of Experimental Botany (IEB), Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), CZ-779 00, Olomouc, Czech Republic
| | - Ugur Ercan
- Max Planck Institute for Plant Breeding Research (MPIPZ), DE-50829, Cologne, Germany
| | - Andreas Finke
- Max Planck Institute for Plant Breeding Research (MPIPZ), DE-50829, Cologne, Germany
| | - Wilfried Rozhon
- Biotechnology of Horticultural Crops, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Liesel-Beckmann-Straße 1, DE-85354, Freising, Germany
| | - Brigitte Poppenberger
- Biotechnology of Horticultural Crops, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Liesel-Beckmann-Straße 1, DE-85354, Freising, Germany
| | - Miroslav Otmar
- Institute of Organic Chemistry and Biochemistry, CZ-166 10, Praha 6, Czech Republic
| | - Igor Niezgodzki
- Biogeosystem Modelling Group, ING PAN - Institute of Geological Sciences Polish Academy of Sciences, Research Center in Krakow, Senacka 1, PL-31 002, Krakow, Poland
| | - Marcela Krečmerová
- Institute of Organic Chemistry and Biochemistry, CZ-166 10, Praha 6, Czech Republic
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research, Stadt Seeland, DE-06466, Gatersleben, OT, Germany
| | - Ales Pecinka
- Institute of Experimental Botany (IEB), Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), CZ-779 00, Olomouc, Czech Republic
- Max Planck Institute for Plant Breeding Research (MPIPZ), DE-50829, Cologne, Germany
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Yao Y, Kovalchuk I. Exposure to zebularine and 5-azaC triggers microsatellite instability in the exposed Arabidopsis thaliana plants and their progeny. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2018. [DOI: 10.1016/j.bcab.2017.11.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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3
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Pecinka A, Liu CH. Drugs for Plant Chromosome and Chromatin Research. Cytogenet Genome Res 2014; 143:51-9. [DOI: 10.1159/000360774] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Majerová E, Fojtová M, Mozgová I, Bittová M, Fajkus J. Hypomethylating drugs efficiently decrease cytosine methylation in telomeric DNA and activate telomerase without affecting telomere lengths in tobacco cells. PLANT MOLECULAR BIOLOGY 2011; 77:371-80. [PMID: 21866390 DOI: 10.1007/s11103-011-9816-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 08/11/2011] [Indexed: 05/23/2023]
Abstract
Telomere homeostasis is regulated at multiple levels, including the local chromatin structure of telomeres and subtelomeres. Recent reports demonstrated that a decrease in repressive chromatin marks, such as levels of cytosine methylation in subtelomeric regions, results in telomere elongation in mouse cells. Here we show that a considerable fraction of cytosines is methylated not only in subtelomeric, but also in telomeric DNA of tobacco BY-2 cells. Drug-induced hypomethylation (demonstrated at subtelomeric, telomeric, and global DNA levels) results in activation of telomerase. However, in contrast to mouse cells, the decrease in 5-methylcytosine levels and upregulation of telomerase do not result in any changes of telomere lengths. These results demonstrate the involvement of epigenetic mechanisms in the multilevel process of regulation of telomerase activity in plant cells and, at the same time, they indicate that changes in telomerase activity can be overridden by other factors governing telomere length stability.
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Affiliation(s)
- Eva Majerová
- Department of Functional Genomics and Proteomics, Faculty of Science and Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, Czech Republic
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5
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Abreu PA, Dellamora-Ortiz G, Leão-Ferreira LR, Gouveia M, Braggio E, Zalcberg I, Santos DO, Bourguinhon S, Cabral LM, Rodrigues CR, Castro HC. DNA methylation: a promising target for the twenty-first century. Expert Opin Ther Targets 2008; 12:1035-47. [PMID: 18620524 DOI: 10.1517/14728222.12.8.1035] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND Over the last few years DNA methylation and its involvement in diseases such as cancer has become of great interest for applied research. Since reversal of aberrant DNA methylation may influence the behavior of tumors, the methylation of DNA CpG sites is a potential target for the development of inhibitors for use in cancer treatment. OBJECTIVE/METHODS We briefly review the structural and mechanistic features of DNA methylation, including a structural analysis of the three main human DNA methyltransferases and some (pre)clinical results. RESULTS/CONCLUSION Despite side effects, data obtained to date still support the vision that DNA-methylation, possibly associated with the use of histone deacetylases (HDACs) and/or artificial transcription factors (ATFs), is a promising target for improving anticancer therapy in the 21st century.
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Affiliation(s)
- Paula A Abreu
- Federal Fluminense University, Biology Institute, Department of Celular and Molecular Biology, CEP 24020-150 Niterói, Rio de Janeiro, Brazil
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6
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Fulnecek J, Matyasek R, Kovarik A. Plant 5S rDNA has multiple alternative nucleosome positions. Genome 2006; 49:840-50. [PMID: 16936792 DOI: 10.1139/g06-039] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In plants, 5S ribosomal DNA (5S rDNA) is typically found in hundreds of copies of tandemly arranged units. Nucleotide database searches revealed that the majority of 5S genes (>90%) have repeat lengths that are not simple multiples of a plant nucleosomal unit, ranging in plants from 175-185 bp. To get insight into the chromatin structure, we have determined positions of nucleosomes in the Nicotiana sylvestris and Nicotiana tomentosiformis 5S rDNA units with repeat lengths of about 430 and 645 bp, respectively. Mapping experiments carried out on isolated nucleo somal DNA revealed many (>50) micrococcal nuclease cleavage sites in each class of repeats. Permutation analysis and theoretical computer prediction showed multiple DNA bend sites, mostly located in the nontranscribed spacer region. The distance between bend sites, however, did not correspond to the average spacing of nucleosomes in 5S chromatin (approximately 180 bp). These data indicate that 5S rDNA does not have fixed nucleosomal positioning sites and that units can be wrapped in a number of alternative nucleosome frames. Consequently, accessibility of transcription factors to cognate motifs might vary across the tandem array, potentially influencing gene expression.
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Affiliation(s)
- Jaroslav Fulnecek
- Institute of Biophysics, Academy of Scences of Czech Republic, Kralovopolska, Czech Republic
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Abstract
This paper examines telomeres from an evolutionary perspective. In the monocot plant order Asparagales two evolutionary switch-points in telomere sequence are known. The first occurred when the Arabidopsis-type telomere was replaced by a telomere based on a repeat motif more typical of vertebrates. The replacement is associated with telomerase activity, but the telomerase has low fidelity and this may have implications for the binding of telomeric proteins. At the second evolutionary switch-point, the telomere and its mode of synthesis are replaced by an unknown mechanism. Elsewhere in plants (Sessia, Vestia, Cestrum) and in arthropods, the telomere "typical" of the group is lost. Probably many other groups with "unusual" telomeres will be found. We question whether telomerase is indeed the original end-maintenance system and point to other candidate processes involving t-loops, t-circles, rolling circle replication and recombination. Possible evolutionary outcomes arising from the loss of telomerase activity in alternative lengthening of telomere (ALT) systems are discussed. We propose that elongation of minisatellite repeats using recombination/replication processes initially substitutes for the loss of telomerase function. Then in more established ALT groups, subtelomeric satellite repeats may replace the telomeric minisatellite repeat whilst maintaining the recombination/replication mechanisms for telomere elongation. Thereafter a retrotransposition-based end-maintenance system may become established. The influence of changing sequence motifs on the properties of the telomere cap is discussed. The DNA and protein components of telomeres should be regarded--as with any other chromosome elements--as evolving and co-evolving over time and responding to changes in the genome and to environmental stresses. We describe how telomere dysfunction, resulting in end-to-end chromosome fusions, can have a profound effect on chromosome evolution and perhaps even speciation.
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Affiliation(s)
- Jirí Fajkus
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, Masaryk University Brno, Královopolská 135, CZ-61265 Brno, Czech Republic.
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Wada Y, Miyamoto K, Kusano T, Sano H. Association between up-regulation of stress-responsive genes and hypomethylation of genomic DNA in tobacco plants. Mol Genet Genomics 2004; 271:658-66. [PMID: 15148604 DOI: 10.1007/s00438-004-1018-4] [Citation(s) in RCA: 144] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2003] [Accepted: 04/08/2004] [Indexed: 11/30/2022]
Abstract
Transcripts that specifically accumulate in transgenic tobacco plants expressing an anti-sense construct for a tobacco type I DNA methyltransferase, NtMET1, were screened by the differential display method. Of the 31 genes identified, 16 encoded proteins with known functions; ten of these were related to biotic and abiotic stress responses, and the other six to cellular functions. In order to examine whether expression of these genes is correlated with DNA methylation status under natural stress conditions, a pathogen-responsive gene (NtAlix1) was selected as representative, and assayed for transcript induction and genomic methylation in tobacco plants infected with tobacco mosaic virus (TMV). In inoculated leaves of wild-type plants, NtAlix1 transcripts began to accumulate 12 h after the onset of the hypersensitive response (HR), and levels remained high for up to 24 h. Changes in the methylation status at the locus became obvious 24 h later, as detected by digestion of genomic DNA with a methylation-sensitive restriction enzyme. The results suggest that the level of DNA methylation may change in response to external stresses, and that this is closely related to the activation of stress-responsive genes.
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Affiliation(s)
- Y Wada
- Research and Education Center for Genetic Information, Nara Institute of Science and Technology, 630-0192, Nara, Japan
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9
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Široký J, Janoušek B, Mouras A, Vyskot B. Replication Patterns of Sex Chromosomes in Melandrium Album Female Cells. Hereditas 2004. [DOI: 10.1111/j.1601-5223.1994.00175.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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10
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Sýkorová E, Cartagena J, Horáková M, Fukui K, Fajkus J. Characterization of telomere-subtelomere junctions in Silene latifolia. Mol Genet Genomics 2003; 269:13-20. [PMID: 12715149 DOI: 10.1007/s00438-003-0811-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2002] [Accepted: 12/30/2002] [Indexed: 11/30/2022]
Abstract
Telomere-associated regions represent boundaries between the relatively homogeneous telomeres and the subtelomeres, which show much greater heterogeneity in chromatin structure and DNA composition. Although a major fraction of subtelomeres is usually formed by a limited number of highly repeated DNA sequence families, their mutual arrangement, attachment to telomeres and the presence of interspersed unique or low-copy-number sequences make these terminal domains chromosome specific. In this study, we describe the structures of junctions between telomeres and a major subtelomeric repeat of the plant Silene latifolia, X43.1. Our results show that on individual chromosome arms, X43.1 is attached to the telomere either directly at sites corresponding to nucleosome boundaries previously mapped in this sequence, or via other spacer sequences, both previously characterized and newly described ones. Sites of telomere junctions are non-random in all the telomere-associated sequences analysed. These data obtained at the molecular level have been verified using in situ hybridization to metaphase chromosomes and extended DNA fibres.
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Affiliation(s)
- E Sýkorová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic
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11
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Sýkorová E, Fajkus J, Ito M, Fukui K. Transition between two forms of heterochromatin at plant subtelomeres. Chromosome Res 2002; 9:309-23. [PMID: 11419795 DOI: 10.1023/a:1016698713959] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The manner of packing of the terminal DNA loci into nucleosomes and higher order structures may strongly influence their functional interactions. Besides the structural flexibility of telomeric DNA sequences, conserved features of their chromatin including short nucleosome phasing (157 bp) and nucleosome sliding have been described previously. To gain a complementary knowledge of subtelomeres, we have analysed the chromatin structure of two subtelomeric tandem repeats from the plant Silene latifolia: X43.1 and 15Ssp. X43.1 shows two distinct nucleosome periodicities--157 and 188 bp. Preferred positions of its two nucleosomes have been mapped at both low and high resolution and the experimental results correspond to computer-predicted positions. 15Ssp is a newly-discovered sequence showing a telomere-associated position by PCR and a subtelomeric location by pulsed-field gel electrophoresis and fluorescence in situ hybridisation. Its 159 bp sequence unit shows a tandem arrangement and the presence of micrococcal nuclease-hypersensitive sites when either naked DNA or chromatin is digested. Use of a chemical nuclease results in a regular nucleosome ladder of 157 bp periodicity. Moreover, 15Ssp mononucleosomes show instability and absence of specific positioning, features typical for telomeric chromatin.
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Affiliation(s)
- E Sýkorová
- Institute of Biophysics, Czech Academy of Sciences and Department of Analysis of Biologically Important Molecular Complexes, Masaryk University Brno, Czech Republic
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12
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Horáková M, Fajkus J. TAS49--a dispersed repetitive sequence isolated from subtelomeric regions of Nicotiana tomentosiformis chromosomes. Genome 2000; 43:273-84. [PMID: 10791815 DOI: 10.1139/g99-126] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have isolated and characterized a new repetitive sequence, TAS49, from terminal restriction fragments of Nicotiana tomentosiformis genomic DNA by means of a modified vectorette approach. The TAS49 was found directly attached to telomeres of N. tabacum and one of its ancestors, N. tomentosiformis, and also at inner chromosome locations. No association with telomeres was detected neither in N. otophora nor in the second tobacco ancestor, N. sylvestris. PCR and Southern hybridization reveal similarities in the arrangement of TAS49 on the chromosomes of 9 species of the genus Nicotiana, implying its occurrence as a subunit of a conserved complex DNA repeat. TAS49 belongs to the family of dispersed repetitive sequences without features of transposons. The copy number of TAS49 varies widely in the genomes of 8 species analyzed being lowest in N. sylvestris, with 3300 copies per diploid genome. In N. tomentosiformis, TAS49 forms about 0.56% of the diploid genome, corresponding to 17400 copies. TAS49 units are about 460 bp long and show about 90% of mutual homology, but no significant homology to DNA sequences deposited in GenBank and EMBL. Although genomic clones of TAS49 contain an open reading frame encoding a proline-rich protein similar to plant extensins, no mRNA transcript was detected. TAS49 is extensively methylated at CpG and CpNpG sites and its chromatin forms nucleosomes phased with a 170 +/- 8 bp periodicity.
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Affiliation(s)
- M Horáková
- Masaryk University, Department of Analysis of Biologically Important Molecular Complexes, Brno, Czech Republic
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13
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Abstract
Melandrium album (syn. Silene latifolia) belongs to dioecious plant species possessing heteromorphic sex chromosomes, X and Y. Our previous experiments using in situ nick translation and replication kinetics analysis indicated structural and functional differences between the two X chromosomes in homogametic female cells. Here we show DNA methylation patterns of M. album root tip chromosomes using the indirect immunofluorescence approach with a monoclonal antibody raised against 5-methylcytosine (5-mC). In male cells, a more intensive 5-mC labelling on the shorter arm of the only X chromosome was observed in comparison with the longer X arm. A global hypermethylation of the male Y chromosome was not found, which indicates its prevalent euchromatic character. In female cells, the specific 5-mC pattern of the X chromosome was found on a single X chromosome, whereas the other X displayed an overall higher level of 5-mC labelling. Application of a hypomethylating drug, 5-azacytidine (5-azaC), during seed germination led to a deletion of any specific differences in the 5-mC distribution between the two X chromosomes. Confocal laser scanning microscopy analysis of DNA methylation in interphase nuclei showed hypermethylated domains that were efficiently decondensed and hypomethylated by 5-azaC treatment. The presented data show reproducible differences in the DNA methylation patterns between the two X chromosomes in M. album female somatic cells, which indicate their distinct transcriptional activities as a possible consequence of the negative dosage compensation of X-linked genes.
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Affiliation(s)
- J Siroky
- Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic.
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14
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Matyásek R, Fulnecek J, Fajkus J, Bezdĕk M. Evidence for a sequence-directed conformation periodicity in the genomic highly repetitive DNA detectable with single-strand-specific chemical probe potassium permanganate. Chromosome Res 1996; 4:340-9. [PMID: 8871822 DOI: 10.1007/bf02257269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A single-strand-specific chemical probe, potassium permanganate (KMnO4), was used to study the sequence-dependent conformation periodicity of tandem multicopy repetitive DNA sequences HRS60 and GRS (Nicotiana Species) at the level of single base pair and dinucleotide step. Local DNA structures, sensitive to KMnO4, revealed periodicity of 182 +/- 2 bp, equal to the length of repeat units. Permanganate-sensitive local structures were mapped to both DNA strands of genomic HRS60 sequences and were found to be linked to d(A)n tracts. These adenine tracts are located in the proximity of the intrinsically curved domains. Distamycin A increased reactivity of the DNA but decreased the specificity of DNA cleavage. Similar conformation periodicity has been detected also in the 'canrep' family of repeats (Brassica species). All studied repetitive sequences are predominantly located in the constitutive heterochromatin. We discuss the role of conformation periodicities in relation to a structural code for nucleosome phasing at tandem arrays of DNA repeats.
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Affiliation(s)
- R Matyásek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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15
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Kato M. Methylation status of Sillago japonica satellite DNA examined by bisulfite modification. Mol Biol Rep 1996; 23:123-7. [PMID: 8983026 DOI: 10.1007/bf00424438] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A member of Sillago japonica satellite DNA contained internal subrepeats in its 174 bp unit. S. Japonica genomic DNA isolated from liver tissue was subjected to bisulfite modification, and the DNA sequences of about 40 bp flanked by both subrepeats were amplified by polymerase chain reaction (PCR). This protocol, combination of bisulfite reaction and PCR, converts cytosines in the genomic DNA to thymines in the amplified DNA, whereas 5-methylcytosines in the genomic DNA remain as cytosines. Sequence analysis of the amplified DNA fragments revealed that most of the cytosine residues at CpG were methylated in this region.
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Affiliation(s)
- M Kato
- Laboratory of Molecular Biology, College of Integrated Arts and Sciences, Osaka Prefecture University, Sakai, Japan
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16
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Vyskot B, Koukalová B, Kovařík A, Sachambula L, Reynolds D, Bezděk M. Meiotic transmission of a hypomethylated repetitive DNA family in tobacco. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1995; 91:659-664. [PMID: 24169895 DOI: 10.1007/bf00223294] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/1994] [Accepted: 01/27/1995] [Indexed: 06/02/2023]
Abstract
We have recently shown that hypomethylation of cytosine residues in the HRS60 family of repetitive DNA sequences can be induced with 5-azacytidine (5-azaC) in tobacco tissue cultures. We have also proven that such a DNA methylation status is maintained during the recovery of protoplasts, plant regeneration, and vegetative development. In the present paper we follow meiotic transmission of hypomethylated HRS60 DNA. Plants obtained from seeds treated with 5-azaC were either self pollinated or crossed with a non-treated control in a reciprocal way. Analysis of the methylation status of the HRS60 DNA revealed that these sequences were hypomethylated in the progenies up to the extent found in the parental 5-azaC-treated plant. Since no parent-of-origin effect was observed, we presume that both male and female gametes transmit an artificial methylation imprint to a similar extent. This result is supported by methylcytosine evaluation in the total genomic DNA samples. A temporal analysis of 5-azaC effects on germinating seeds and a phenotypic evaluation of 5-azaC-treated tobacco plants are also presented.
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Affiliation(s)
- B Vyskot
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, The Czech Republic
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17
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Fajkus J, Kovarík A, Královics R, Bezdĕk M. Organization of telomeric and subtelomeric chromatin in the higher plant Nicotiana tabacum. MOLECULAR & GENERAL GENETICS : MGG 1995; 247:633-8. [PMID: 7603443 DOI: 10.1007/bf00290355] [Citation(s) in RCA: 105] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We have examined the structure and chromatin organization of telomeres in Nicotiana tabacum. In tobacco the blocks of simple telomeric repeats (TT-TAGGG)n are many times larger than in other plants, e.g., Arabidopsis thaliana or tomato. They are resolved as multiple fragments 60-160 kb in size (in most cases 90-130 kb) on pulsed-field gel electrophoresis (PFGE) of restriction endonuclease-digested DNA. The major subtelomeric repeat of the HRS60 family forms large homogeneous blocks of a basic 180 bp motif having comparable lengths. Micrococcal nuclease (MNase) cleaves tobacco telomeric chromatin into subunits with a short repeat length of 157 +/- 5 bp; the subtelomeric heterochromatin characterized by tandemly repeated sequences of the HRS60 family is cut by MNase with a 180 bp periodicity. The monomeric and dimeric particles of telomeric and subtelomeric chromatin differ in sensitivity to MNase treatment: the telomeric particles are readily digested, producing ladders with a periodicity of 7 bp, while the subtelomeric particles appear to be rather resistant to intranucleosomal cleavage. The results presented show apparent similarities in the organization of telomeric chromatin in higher plants and mammals.
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Affiliation(s)
- J Fajkus
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno
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18
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Gazdová B, Siroký J, Fajkus J, Brzobohatý B, Kenton A, Parokonny A, Heslop-Harrison JS, Palme K, Bezdĕk M. Characterization of a new family of tobacco highly repetitive DNA, GRS, specific for the Nicotiana tomentosiformis genomic component. Chromosome Res 1995; 3:245-54. [PMID: 7606363 DOI: 10.1007/bf00713050] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Members of a new family of highly repetitive DNA sequences called GRS were isolated from Nicotiana tabacum L. genomic DNA and characterized. Cloned, sequenced monomeric units (180-182 bp) of GRS exhibit properties characteristic of molecules that possess a stable curvature. The GRS family represents about 0.15% of total genomic DNA (10(4) copies per haploid genome) and could be derived from either Nicotiana tomentosiformis or Nicotiana otophora, two possible ancestors of the T genome of the amphidiploid N. tabacum. Sequence homology between the HRS60 (Koukalová et al. 1989) and the GRS family has been estimated to be 57%. In situ hybridization was used to localize GRS on mitotic chromosomes. Hybridization signals were obtained on five pairs of chromosomes at intercalary sites of the longer chromosome arms. The majority of GRS sequences appeared to be organized in tandem arrays and a minority were found to be dispersed through the genome in short clusters, interspersed with other types of DNA repeats, including 25S rDNA sequences. Several loci containing both GRS and HRS60 were also found. Such hybrid loci may indicate intergenomic transfer of the DNA in the amphidiploid N. tabacum. GRS sequences, like HRS60 (Fajkus et al. 1992), were found to specify the location of nucleosomes. The position of the nucleosome core has been mapped with respect to a conserved Mbol site in the GRS sequence and an oligo A/T tract is a major centre of the DNA curvature.
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Affiliation(s)
- B Gazdová
- Institute of Biophysics of the Academy of Sciences of the Czech Republic, Brno
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19
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Fajkus J, Královics R, Kovarík A, Fajkusová L. The telomeric sequence is directly attached to the HRS60 subtelomeric tandem repeat in tobacco chromosomes. FEBS Lett 1995; 364:33-5. [PMID: 7750538 DOI: 10.1016/0014-5793(95)00347-c] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
PCR and primers derived from the telomeric repeat (CCCTAAA)n and from the tobacco subtelomeric tandemly repetitive sequence HRS60 (EMBL X12489) were used to amplify the region linking the two loci. A 131 bp PCR product was obtained both from total tobacco DNA and from the DNA fraction enriched for telomeres. Its sequence only consists of the telomeric primer and the attached region of the HRS60 repetitive unit up to the end of the sequence complementary to the HRS60 primer. The site of direct continuity between the two sequences is formed by a (dA)7 tract.
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Affiliation(s)
- J Fajkus
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno
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20
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Tulchinsky E, Grigorian M, Tkatch T, Georgiev G, Lukanidin E. Transcriptional regulation of the mts1 gene in human lymphoma cells: the role of DNA-methylation. BIOCHIMICA ET BIOPHYSICA ACTA 1995; 1261:243-8. [PMID: 7536040 DOI: 10.1016/0167-4781(95)00013-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The transcription of the mts1 gene putatively involved in the control of tumor metastasis was studied in three human lymphoma cell lines: MOLT-4, CEM and Jurkat. The level of the mts1 gene transcription is high in MOLT-4 cells, lower in CEM cells and hardly detectable in Jurkat cells. This correlates with the hypomethylation of DNA in the first exon and the first intron of the mts1 gene in the analyzed culture cells. This area was also found to be undermethylated in human peripheral blood cells--macrophages, neutrophils and lymphocytes where the mts 1 gene is highly expressed. 5-Azadeoxycytidine (AzadC)--an inhibitor of the eukaryotic DNA-methylase--significantly induces the expression of the mts1 gene in CEM and Jurkat cells and has little effect on mts1 gene transcription in MOLT-4 cells. The drug does not influence mts1 transcription in cultivated peripheral blood lymphocytes. These data indicate the possible involvement of the methylation of the first exon/first intron sequences in the transcriptional repression of the mts1 gene. The finding of two DNAaseI hypersensitivity sites (DHSs) mapped in the first intron of the mts1 gene supports this suggestion.
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Affiliation(s)
- E Tulchinsky
- Danish Cancer Society, Department of Molecular Cancer Biology, Copenhagen
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21
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Kralovics R, Fajkus J, Kovarík A, Bezdĕk M. DNA curvature of the tobacco GRS repetitive sequence family and its relation to nucleosome positioning. J Biomol Struct Dyn 1995; 12:1103-19. [PMID: 7626243 DOI: 10.1080/07391102.1995.10508800] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Recently, a highly repetitive DNA sequence family (GRS) from tobacco was described in our laboratory. These sequences were found to be localized predominantly in the pericentromeric heterochromatin of tobacco chromosomes. To test the hypothesis that these sequences play an important role in the formation of heterochromatin, we investigated the DNA curvature of the GRS sequences and its possible impact to the chromatin structure at these loci. Application of the nearest-neighbour wedge model of intrinsic DNA curvature for the GRS1 family member predicted two loci of curvature: a major bend at the 5' end of the sequence and a minor bend of opposite direction at the centre of the GRS1. The presence of the major and the minor loci of DNA curvature was studied experimentally using permutation analysis and site-directed mutagenesis. The experimental results were consistent with the computer predictions. We gave evidence that the described DNA curvature is also present in the entire GRS family. Genomic statistical sequencing showed the conservation of the major bend sequence determinants in the members of the GRS family. To investigate the chromatin structure at the GRS sequences, we determined the nucleosome positioning in vivo at these sequences using thermal cycle primer extension. A relation between the curvature pattern and the histone octamer position was observed: the major bend is excluded from the nucleosome surface to the linker region, while the minor bend is distributed along the core DNA. The suggestion is made that the sequences in the minor locus of curvature define the rotational setting of the nucleosome, and a possible role of the major bend as a factor, which defines the translational setting, is discussed.
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Affiliation(s)
- R Kralovics
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno
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