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Macromolecular Structure of Linearly Arranged Eukaryotic Chromosomes. Int J Mol Sci 2022; 23:ijms23169503. [PMID: 36012767 PMCID: PMC9409004 DOI: 10.3390/ijms23169503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/05/2022] [Accepted: 08/11/2022] [Indexed: 11/22/2022] Open
Abstract
Eukaryotic chromosomes have not been visualized during the interphase. The fact that chromosomes cannot be seen during the interphase of the cell cycle does not mean that there are no means to make them visible. This work provides visual evidence that reversible permeabilization of the cell membrane followed by the regeneration of cell membranes allows getting a glimpse behind the nuclear curtain. Reversibly permeable eukaryotic cells have been used to synthesize nascent DNA, analyze the 5′-end of RNA primers, view individual replicons and visualize interphase chromosomes. Dextran T-150 in a slightly hypotonic buffer prevented cells from disruption. Upon reversal of permeabilization, the nucleus could be opened at any time during the interphase. A broad spectrum of a flexible chromatin folding pattern was revealed through a series of transient geometric forms of chromosomes. Linear attachment of chromosomes was visualized in several mammalian and lower eukaryotic cells. The linear connection of chromosomes is maintained throughout the cell cycle showing that rather than individual chromosomes, a linear array of chromosomes is the functional giant macromolecule. This study proves that not only the prokaryotic genome but also linearly attached eukaryotic chromosomes form a giant macromolecular unit.
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Abstract
In early S phase the newly replicated DNA is folded back to increasingly compact structures. The process of chromatin condensation inside the nucleus starts with the formation of a micronucleus observed in five established cell lines (K562, CHO, Indian muntjac, murine preB and SCC). Supercoiling of chromatin generates a polarized end-plate region extruded from the nucleus. The extruded chromatin is turned around itself forming the head portion (micronucleus) visible by fluorescence microscopy until the middle of S phase when chromatin structures are succeeded by distinguishable early forms of chromosomes. The generation of micronuclei upon apoptotic treatment was achieved by the methotrexate (MTX) treatment of cells. A close correlation was found between the frequency of micronucleus and MTX concentration, with low frequency at low (0.1 µM) and increasingly higher frequency between 1 and 100 µM concentrations. Characteristic deformation and shrinkage of nuclei indicated apoptosis. High MTX concentration (100 µM) caused the enlargement and necrotic disruption of nuclei. Inhibition of DNA synthesis during replicative DNA synthesis by biotinylated nucleotide prevented the formation of metaphase chromosomes and elevated the frequency of early intermediates of chromosome condensation including micronucleus formation. Based on these observations the micronucleus is regarded as: (a) a regularly occuring element of early chromatin condensation and (b) a typical sign of nuclear membrane damage under toxic conditions. Explanation is given why the micronucleus is hidden in nuclei under normal chromatin condensation and why chromatin motifs including micronuclei become visible upon cellular damage.
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Nagy G, Tanczos B, Fidrus E, Talas L, Banfalvi G. Chemically Induced Cell Cycle Arrest in Perfusion Cell Culture. Methods Mol Biol 2017; 1524:161-176. [PMID: 27815902 DOI: 10.1007/978-1-4939-6603-5_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In contrast to most present methods, continuous imaging of live cells would require full automation in each processing step. As an integrated system that would meet all requirements does not exist, we have established a long-term scanning-perfusion platform that: (a) replaces old medium with fresh one, (b) bypasses physical contact with the cell culture during continuous cell growth, (c) provides uninterrupted photomicrography of single cells, and (d) secures near physiological conditions and sterility up to several weeks. The system was validated by synchronizing cells using serum starvation and butyrate-induced cell cycle arrest of HaCaT cells.
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Affiliation(s)
- Gabor Nagy
- Department of Biotechnology and Microbiology, University of Debrecen, 1 Egyetem Square, Debrecen, 4010, Hungary
| | - Bence Tanczos
- Department of Biotechnology and Microbiology, University of Debrecen, 1 Egyetem Square, Debrecen, 4010, Hungary
| | - Eszter Fidrus
- Department of Biotechnology and Microbiology, University of Debrecen, 1 Egyetem Square, Debrecen, 4010, Hungary
| | - Laszlo Talas
- Department of Biotechnology and Microbiology, University of Debrecen, 1 Egyetem Square, Debrecen, 4010, Hungary
| | - Gaspar Banfalvi
- Department of Biotechnology and Microbiology, University of Debrecen, 1 Egyetem Square, Debrecen, 4010, Hungary.
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Abstract
Synchronized populations of large numbers of cells can be obtained by centrifugal elutriation on the basis of sedimentation properties of small round particles, with minimal perturbation of cellular functions. The physical characteristics of cell size and sedimentation velocity are operative in the technique of centrifugal elutriation also known as counterstreaming centrifugation. The elutriator is an advanced device for increasing the sedimentation rate to yield enhanced resolution of cell separation. A random population of cells is introduced into the elutriation chamber of an elutriator rotor running in a specially designed centrifuge. By increasing step-by-step the flow rate of the elutriation fluid, successive populations of relatively homogeneous cell size can be removed from the elutriation chamber and used as synchronized subpopulations. For cell synchronization by centrifugal elutriation, early log S phase cell populations are most suitable where most of the cells are in G1 and S phase (>80 %). Apoptotic cells can be found in the early elutriation fractions belonging to the sub-Go window. Protocols for the synchronization of nuclei of murine pre-B cells and high-resolution centrifugal elutriation of CHO cells are given. The verification of purity and cell cycle positions of cells in elutriated fractions includes the measurement of DNA synthesis by [3H]-thymidine incorporation and DNA content by propidium iodide flow cytometry.
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Affiliation(s)
- Gaspar Banfalvi
- Department of Biotechnology and Microbiology, University of Debrecen, 1 Egyetem Square, Debrecen, 4010, Hungary.
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5
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Abstract
Synchronized populations of large numbers of cells can be obtained by centrifugal elutriation on the basis of sedimentation properties of small round particles, with minimal perturbation of cellular functions. The physical characteristics of cell size and sedimentation velocity are operative in the technique of centrifugal elutriation also known as counterstreaming centrifugation. The elutriator is an advanced device for increasing the sedimentation rate to yield enhanced resolution of cell separation. A random population of cells is introduced into the elutriation chamber of an elutriator rotor running in a specially designed centrifuge. By increasing step by step the flow rate of the elutriation fluid, successive populations of relatively homogeneous cell size can be removed from the elutriation chamber and used as synchronized subpopulations. For cell synchronization by centrifugal elutriation early log S phase cell populations are most suitable where most of the cells are in G1 and S phase (>80%). Protocols for the synchronization of nuclei of murine pre-B cells and high-resolution centrifugal elutriation of CHO cells are given. The verification of purity and cell cycle positions of cells in elutriated fractions includes the measurement of DNA synthesis by [(3)H]-thymidine incorporation and DNA content by propidium iodide flow cytometry.
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Affiliation(s)
- Gaspar Banfalvi
- Department of Microbial Biotechnology and Cell Biology, University of Debrecen, Debrecen, 4010, Hungary.
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Banfalvi G. Cell cycle synchronization of animal cells and nuclei by centrifugal elutriation. Nat Protoc 2008; 3:663-73. [DOI: 10.1038/nprot.2008.34] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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7
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Banfalvi G, Klaisz M, Ujvarosi K, Trencsenyi G, Rozsa D, Nagy G. Gamma irradiation induced apoptotic changes in the chromatin structure of human erythroleukemia K562 cells. Apoptosis 2007; 12:2271-83. [DOI: 10.1007/s10495-007-0146-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Ujvarosi K, Hunyadi J, Nagy G, Pocsi I, Banfalvi G. Preapoptotic chromatin changes induced by ultraviolet B irradiation in human erythroleukemia K562 cells. Apoptosis 2007; 12:2089-99. [PMID: 17701356 DOI: 10.1007/s10495-007-0118-0] [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] [Received: 06/07/2007] [Accepted: 07/24/2007] [Indexed: 10/23/2022]
Abstract
Exponentially growing human erythroleukemia K562 cells were permeabilized and the dose dependent decrease of DNA synthesis rate was measured after ultraviolet (UV B, 290 nm) irradiation. Cells were able to overcome 2 and 5 J/m2 UV doses, partial recovery was observed at 15 J/m2, while at high (25 J/m2) UV dose replicative DNA synthesis remained suppressed. K562 cells were subjected to synchronization prior to and after UV irradiation (24 J/m2) and 18 fractions were collected by centrifugal elutriation. Cell cycle analysis by flow cytometry did not show early apoptotic cells after UV irradiation. The gradual increase in DNA content typical for non-irradiated cells was contrasted by an early S phase block between 2.2 and 2.4 C-values after UV irradiation. Cell cycle dependent chromatin changes after ultraviolet irradiation were seen as a fine fibrillary network covering the mainly fibrous chromatin structures and incompletely folded primitive chromosomes. Based on observations after UV irradiation and on earlier results with cadmium treatment and gamma irradiation, we confirm that typical chromatin changes characteristic to genotoxic agents can be recognized and classified.
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Affiliation(s)
- Kinga Ujvarosi
- Department of Microbial Biotechnology and Cell Biology, University of Debrecen, 1 Egyetem Square, Debrecen 4010, Hungary
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Trencsenyi G, Ujvarosi K, Nagy G, Banfalvi G. Transition from Chromatin Bodies to Linear Chromosomes in Nuclei of Murine PreB Cells Synchronized in S Phase. DNA Cell Biol 2007; 26:549-56. [PMID: 17688406 DOI: 10.1089/dna.2007.0603] [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: 11/13/2022] Open
Abstract
Chromatin structures and individual interphase chromosomes escaping nuclei of reversibly permeabilized cells were analyzed in a cell cycle-dependent manner. Cells were synchronized by counterflow centrifugal elutriation. Individual interphase chromosomes became visible as distinct fibrous chromatin bodies from mid-S-phase, turning to elongated chromosomes by the end of S phase. Major interphase chromosomal forms include (1) mid-S-phase chromatin bodies at 3.0 C-value, (2) elongated chromatin bodies later in mid-S-phase (3.25 C-value), (3) chromatin bodies with head and leg portions later in S phase (3.5 C-value), (4) supercoiled ribbons later in S phase seen as twisted prechromosomes (3.7 C-value), and (5) end-S-phase elongated, bent prechromosomal structures (3.9 C-value). The first karyotype analysis of the earliest forms of chromosomes referred to as chromatin bodies was performed.
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Affiliation(s)
- Gyorgy Trencsenyi
- Department of Microbial Biotechnology and Cell Biology, University of Debrecen, Debrecen, Hungary
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Banfalvi G, Ujvarosi K, Trencsenyi G, Somogyi C, Nagy G, Basnakian A. Cell culture density dependent toxicity and chromatin changes upon cadmium treatment in murine pre-B-cells. Apoptosis 2007; 12:1219-28. [PMID: 17260184 DOI: 10.1007/s10495-006-0045-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Murine pre-B-cells grown in the presence of lower (1 microM) or higher (5 microM) concentration of cadmium chloride were separated into 13 fractions by centrifugal elutriation. The rate of DNA synthesis after cadmium treatment determined in permeable cells was dependent on cell culture density during cadmium treatment. Cell cycle analysis revealed a shift in the profile of DNA synthesis from replicative to repair DNA synthesis upon cadmium treatment. The study of the relationship between cell culture density and cell diameter at lower and higher cell densities in the presence of 1 microM cadmium chloride concentration showed that a. at 5 x 10(5) cell/ml or lower densities cells were shrinking indicating apoptotic changes, b. at higher cell culture densities the average cell size increased, c. the treatment of cells with low CdCl(2) concentration (1 microM) at higher cell culture density (>5 x 10(5) cell/ml) did not change significantly the average cell diameter. At 5 microM cadmium concentration and higher cell culture densities (>5 x 10(5) cell/ml) the average cell size decreased in each elutriated fraction. Most significant inhibition of cell growth took place in early S phase (2.0-2.5 C value). Apoptotic chromatin changes in chromatin structure after cadmium treatment were seen as large extensive disruptions, holes in the nuclear membrane and stickiness of incompletely folded chromosomes.
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Affiliation(s)
- Gaspar Banfalvi
- Department of Microbial Biotechnology and Cell Biology, University of Debrecen, 1 Egyetem Square, Debrecen, 4032, Hungary.
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Banfalvi G, Trencsenyi G, Ujvarosi K, Nagy G, Ombodi T, Bedei M, Somogyi C, Basnakian AG. Supranucleosomal Organization of Chromatin Fibers in Nuclei ofDrosophilaS2 Cells. DNA Cell Biol 2007; 26:55-62. [PMID: 17263597 DOI: 10.1089/dna.2006.0524] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Earlier, the interphase chromatin structures could not be visualized due to the stickiness of the nuclear material. We have reduced stickiness by the reversal of permeabilization allowing the isolation and microscopic imaging of interphase chromatin structures. By using a high resolution of synchronization, collecting 36 elutriation fractions, we show that major intermediates of chromatin condensation include: (a) decondensed veillike chromatin at the unset of the S phase (2.0-2.2 C-value), (b) polarization of veiled chromatin (2.2-2.6 C), (c) fibrous chromatin (2.6-3.0 C), chromatin bodies (3.0-3.3 C), early precondensed chromosomes (3.3-3.6). The compaction of Drosophila chromosomes did not reach that of the mammalian cells in the final stage of condensation (3.6-4.0 C). Drosophila chromosomes consist of smaller units called rodlets. Results demonstrate that nucleosomal chromatin ("beads on string") does not form a solenoid structure; rather, the topological arrangement consists of meandering and plectonemic loops.
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Affiliation(s)
- Gaspar Banfalvi
- Department of Microbial Biotechnology and Cell Biology, University of Debrecen, Debrecen, Hungary.
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12
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Abstract
The escape of individual interphase chromosomes from nuclei of reversibly permeabilized Chinese hamster ovary (CHO) cells was utilized for the visualization of condensing interphase chromosomes in a cell cycle-dependent manner in synchronized cells. Major interphase chromosomal forms include: (a) mid-S-phase globular chromosomes at 3.0 C-value, (b) late mid-S-phase fibrous hemicircular forms (3.3 C), (c) late-S-phase supercoiled ribbons (3.7 C), and (d) end-S-phase elongated, bent prechromosomal structures (4.0 C).
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Affiliation(s)
- Gaspar Banfalvi
- Department of Microbial Biotechnology and Cell Biology, University of Debrecen, Debrecen, Hungary.
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13
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Abstract
Fluorescent images of interphase chromatin structures and chromosome structures isolated from reversibly permeable Drosophila cells were analyzed. Decondensed chromatin in early S phase (2.0-2.5 C-value) consisted of a veil-like fibrillary network. Fibrillar chromatin formed rodlets later in the early S phase (2.5-2.75 C). Drosophila chromosomes contain several smaller subunits called rodlets. Fibrillar chromatin turned to chromatin ribbon and the early mid-S-phase globular chromosomes (2.75-3.0 C), then to opened fibrous globular forms later in the mid-S-phase (3.0-3.25 C), to late-S-phase supercoiled ribbons (3.25-3.5 C), end-S-phase elongated prechromosomes (3.5-3.75 C), bent and linear chromosomes (3.75-4.0 C). Early-S phase chromatin fibrils in the nuclei of Drosophila cells are thinner than the veil-like structures in mammalian cells. The connectivity of chromosomes shows linear arrangement (3, 1, 2, 4), with larger chromosomes (1 and 2) inside and smaller chromosomes (3, 4) at the two ends in the chromosomal chain.
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Affiliation(s)
- Gaspar Banfalvi
- Department of Animal Anatomy and Physiology, University of Debrecen, Debrecen, Hungary.
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Banfalvi G. Linear Connection of Condensing Chromosomes in Nuclei of Synchronized CHO Cells. DNA Cell Biol 2006; 25:541-5. [PMID: 16989577 DOI: 10.1089/dna.2006.25.541] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Reversibly permeabilized cells allowed the analysis of intermediates of large-scale chomatin condensation in a cell cycle-dependent manner. This paper summarizes major intermediates of chromatin condensation and visualizes connectivity between different forms of chromosomes. At the early S phase the veil-like fibrillary chromatin is supercoiled to form chromatin bodies representing the earliest visible chromosomes. Supercoiling results in a chromatin fiber, which turns to rope (thick fiber) forming loops and chromatin ribbon. The elongated shape of prechromosomes indicates that they are arranged head to tail. Bent forms (loop, c-, and v-shaped structures) of interphase chromosomes open at the end of S phase. Linear arrangement of chromosomes was observed to the end of the condensation process, suggesting that connectivity of chromosomes is maintained throughout the cell cycle.
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Affiliation(s)
- Gaspar Banfalvi
- Department of Animal Anatomy and Physiology, University of Debrecen, Debrecen, Hungary.
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Banfalvi G, Nagy G, Gacsi M, Roszer T, Basnakian AG. Common Pathway of Chromosome Condensation in Mammalian Cells. DNA Cell Biol 2006; 25:295-301. [PMID: 16716119 DOI: 10.1089/dna.2006.25.295] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Chromatin folding in the interphase nucleus is not known. We compared the pattern of chromatin condensation in Indian muntjac, Chinese hamster ovary, murine pre B, and K562 human erythroleukemia cells during the cell cycle. Fluorescent microscopy showed that chromosome condensation follows a general pathway. Synchronized cells were reversibly permeabilized and used to isolate interphase chromatin structures. Based on their structures two major categories of intermediates were distinguished: (1) decondensed chromatin and (2) condensed chromosomal forms. (1) Chromatin forms were found between the G1 and mid-S phase involving veil-like, supercoiled, fibrous, ribboned structures; (2) condensing chromosomal forms appeared in the late-S, G2, and M phase, including strings, chromatin bodies, elongated pre-chromosomes, pre-condensed chromosomes, and metaphase chromosomes. Results demonstrate that interphase chromosomes are clustered in domains; condensing interphase chromosomes are linearly arranged. Our results raise questions related to telomer sequences and to the chemical nature of chromosome connectivity.
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Affiliation(s)
- Gaspar Banfalvi
- Department of Animal Anatomy and Physiology, University of Debrecen, Debrecen, Hungary.
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Banfalvi G, Gacsi M, Nagy G, Kiss ZB, Basnakian AG. Cadmium induced apoptotic changes in chromatin structure and subphases of nuclear growth during the cell cycle in CHO cells. Apoptosis 2005; 10:631-42. [PMID: 15909124 DOI: 10.1007/s10495-005-1897-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
CHO cells were grown in the presence of 1 mu M CdCl(2) and subjected to ATP-dependent replicative DNA synthesis after permeabilization. By decreasing the density of the cell culture replicative DNA synthesis was diminishing. At higher than 2 x 10(6) cell/ml concentration Cd had virtually no effect on the rate of DNA replication. Growth at higher cell concentrations could be suppressed by increasing Cd concentration. After Cd treatment cells were synchronized by counterflow centrifugal elutriation. Cadmium toxicity on cell growth in early and mid S phase led to the accumulation of enlarged cells in late S phase. Flow cytometry showed increased cellular and nuclear sizes after Cd treatment. As the cells progressed through the S phase, 11 subpopulations of nuclear sizes were distinguished. Apoptotic chromatin changes were visualized by fluorescent microscopy in a cell cycle dependent manner. In the control untreated cells the main transitory forms of chromatin corresponded to those we have published earlier (veil-like, supercoiled chromatin, fibrous, ribboned structures, chromatin strings, elongated prechromosomes, precondensed chromosomes). Cadmium treatment caused: (a) the absence of decondensed veil-like structures and premature chromatin condensation in the form of apoptotic bodies in early S phase (2.2-2.4 average C-value), (b) the absence of fibrous structures, the lack of supercoiled chromatin, the appearance of uncoiled ribboned chromatin and perichromatin semicircles, in early mid S phase (2.5-2.9 C), (c) the presence of perichromatin fibrils and chromatin bodies in mid S phase (2.9-3.2 C), (d) early intra-nuclear inclusions, elongated forms of premature chromosomes, the extrusion and rupture of nuclear membrane later in mid S phase (3.3-3.4 C), (e) the exclusion of chromatin bodies and the formation of clusters of large-sized perichromatin granules in late S phase (3.5-3.8 C) and (f) large extensive disruptions and holes in the nuclear membrane and the clumping of incompletely folded chromosomes (3.8-4. C).
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Affiliation(s)
- G Banfalvi
- Department of Animal Anatomy and Physiology, University of Debrecen, Debrecen 4032, Hungary.
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Gacsi M, Nagy G, Pinter G, Basnakian AG, Banfalvi G. Condensation of interphase chromatin in nuclei of synchronized chinese hamster ovary (CHO-K1) cells. DNA Cell Biol 2005; 24:43-53. [PMID: 15684719 DOI: 10.1089/dna.2005.24.43] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Reversibly permeabilized cells have been used to visualize interphase chromatin structures in the presence and absence of biotinylated nucleotides. By reversing permeabilization, it was possible to confirm the existence of a flexible chromatin folding pattern through a series of transient geometric forms such as supercoiled, circular forms, chromatin bodies, thin and thick fibers, and elongated chromosomes. Our results show that the incorporation of biotin-11-dUTP interferes with chromatin condensation, leading to the accumulation of decondensed chromatin structures. Chromatin condensation without nucleotide incorporation was also studied in cell populations synchronized by centrifugal elutriation. After reversal of permeabilization, nuclei were isolated and chromatin structures were visualized after DAPI staining by fluorescent microscopy. Decondensed veil-like structures were observed in the early S phase (at an average C-value of 2.21), supercoiled chromatin later in the early S (2, 55 C), fibrous structures in the early mid S phase (2, 76 C), ribboned structures in the mid-S phase (2, 98 C), continuous chromatin strings later in the mid-S phase (3,28), elongated prechromosomes in the late S-phase (3, 72 C), precondensed chromosomes at the end and after the S phase (3, 99 C). Fluorescent microscopy revealed that neither interphase nor metaphase chromosomes are separate entities but form a linear array arranged in a semicircle. Linear arrangement was confirmed by computer image analysis.
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Affiliation(s)
- Mariann Gacsi
- Department of Animal Anatomy and Physiology, University of Debrecen, Debrecen, Hungary
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18
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Szepessy E, Nagy G, Jenei Z, Serfozo Z, Csuka I, James J, Banfalvi G. Multiple subphases of DNA repair and poly (ADP-ribose) synthesis in Chinese hamster ovary (CHO-K1) cells. Eur J Cell Biol 2003; 82:201-7. [PMID: 12751906 DOI: 10.1078/0171-9335-00301] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The two types of DNA synthesis as well as poly(ADP-ribose) biosynthesis were measured simultaneously in synchronized intact populations of CHO cells throughout the duration of S phase. Naturally occurring DNA fragmentation was detected by random primed oligonucleotide synthesis (ROPS assay). Fractions of synchronous cell populations were obtained by counterflow centrifugal elutriation. By gradually increasing the resolution of centrifugal elutriation multiple non-overlapping repair and replication peaks were obtained. The elutriation profile of DNA repair peaks corresponded to the DNA fragmentation pattern measured by ROPS assay. The number and position of poly(ADP-ribose) peaks during S phase resembled those seen in the DNA replication profile. Our results indicate that PAR synthesis is coupled to DNA replication serving the purpose of genomic stability.
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Affiliation(s)
- Edit Szepessy
- Department of Animal Anatomy and Physiology, University of Debrecen, Debrecen, Hungary
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Abstract
Exponentially growing Drosophila S2 cells in suspension culture were synchronized at low- and high-resolution centrifugal elutriation, and DNA synthesis was measured by [(3)H]-thymidine incorporation throughout the S phase. At low resolution, one repair peak at the G(1)/G(0) border and two replication peaks known as early and late S subphases were observed. At high resolution, six chronologic compartments were distinguished. The distribution of these peaks indicated one repair peak at 2.05 C value, one minor replication peak at 2.43C, and four major subphases of replication corresponding to 2.64C, 2.89C, 3.32C, and 3.60C, representing 6.7%, 3.4%, 15.3%, 20.4%, 32.1%, and 22.0% of the synthetic activity, respectively. The five major peaks of cell growth with 2.32C, 2.56C, 2.85C, 3.18C, and 3.58C values consistently preceded those of replication subphases.
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Affiliation(s)
- M Rehak
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
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Banfalvi G, Mikhailova M, Poirier LA, Chou MW. Multiple subphases of DNA replication in Chinese hamster ovary (CHO-K1) cells. DNA Cell Biol 1997; 16:1493-8. [PMID: 9428798 DOI: 10.1089/dna.1997.16.1493] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Replicative DNA synthesis has been measured throughout the S phase in synchronized populations of Chinese hamster ovary cells. When exponentially growing, cells in suspension cultures were subjected to counterflow centrifugal elutriation and the resolution power was increased the biphasic replication profile has been resolved and multiple subphases were distinguished. These replication peaks, termed replication checkpoints, are distributed evenly throughout the S phase. The replication checkpoints have been characterized by their average C values corresponding to 2.05, 2.12, 2.2, 2.45, 2.6, 2.8, 2.95, 3.15, 3.3, 3.45, and 3.85.
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Affiliation(s)
- G Banfalvi
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University Medical School, Budapest, Hungary
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Banfalvi G, Poirier LA, Mikhailova M, Chou MW. Relationship of repair and replicative DNA synthesis to cell cycle in Chinese hamster ovary (CHO-K1) cells. DNA Cell Biol 1997; 16:1155-60. [PMID: 9364926 DOI: 10.1089/dna.1997.16.1155] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
To strengthen the causal association between repair and replicative DNA synthesis, we have simultaneously measured the two types of DNA synthesis in a cell cycle-dependent manner. Synchrony was obtained by counterflow centrifugal elutriation of logarithmic-phase Chinese hamster ovary (CHO) cells kept in suspension cultures. A comparison of cell cycle profiles of ATP-dependent replicative and ATP-independent repair synthesis in permeable cells shows opposite trends. The rates of repair synthesis and replication are inversely correlated.
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Affiliation(s)
- G Banfalvi
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry Semmelweis University Medical School, Budapest, Hungary
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Mori O, Hachisuka H, Maeyama Y, Sasai Y. A flow cytometric analysis of the DNA content of Paget cells in the epidermis and the tumor of extramammary Paget's disease. Acta Histochem 1995; 97:99-104. [PMID: 7771188 DOI: 10.1016/s0065-1281(11)80210-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In the present study, we have examined whether or not the Paget cells in cases with dermal invasion or metastasis exhibit a different DNA distribution pattern to that seen in the epidermis in extramammary Paget's disease. The DNA contents of Paget cells from the epidermis and the tumor were determined by flow cytometry in two cases of extramammary Paget's disease with tumor formation, dermal invasion and metastases. The DNA histogram of Paget cells from the epidermis of two cases appeared to be close to the normal ploidy, whereas the histogram from the tumors was aneuploid in both cases. Our data suggest that the behavior of Paget cells in the epidermis is different from that in the tumor.
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Affiliation(s)
- O Mori
- Department of Dermatology, Kurume University School of Medicine, Japan
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23
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24
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Neri LM, Mazzotti G, Capitani S, Maraldi NM, Cinti C, Baldini N, Rana R, Martelli AM. Nuclear matrix-bound replicational sites detected in situ by 5-bromodeoxyuridine. HISTOCHEMISTRY 1992; 98:19-32. [PMID: 1429014 DOI: 10.1007/bf00716934] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The nuclear matrix was prepared in situ from Swiss 3T3 cells, which were synchronized by contact inhibition and serum starvation and pulse-labelled for very short periods of time with 5-bromodeoxyuridine (5-BrdU). For the first time 5-BrdU has been employed to demonstrate the association of newly synthesized DNA with a nucleoskeleton. Immunofluorescence analysis using a monoclonal antibody to 5-BrdU revealed five different intranuclear staining patterns at different stages of the S phase. These patterns were observed also in intact cells and did not change during the matrix preparation steps which involve extraction with 2 M NaCl and DNase I digestion. Such an observation was also confirmed by spatial confocal microscopy studies. The intensity of fluorescence, which was evaluated by cytofluorometry, increased to reach a maximum during mid-S phase and then decreased. Because no significant difference was found in the time to label residual DNA of different 5-BrdU staining patterns, this strongly suggests that a different number of replicons is activated at different stages of the S phase. These results strengthen the hypothesis that eukaryotic DNA replication occurs in close association with an insoluble protein nuclear skeleton, which determines the three-dimensional spatial organization of chromosome duplication.
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Affiliation(s)
- L M Neri
- Istituto di Anatomia Umana Normale, Universitá di Ferrara, Italy
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25
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Yang CL, Zhang SJ, Toomey NL, Palmer TN, Lee MY. Induction of DNA polymerase activities in the regenerating rat liver. Biochemistry 1991; 30:7534-41. [PMID: 1677271 DOI: 10.1021/bi00244a024] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The levels of DNA polymerase alpha, DNA polymerase delta, and its accessory protein, proliferating cell nuclear antigen (PCNA) were examined in the regenerating rat liver. The levels of DNA polymerase alpha and delta activities in regenerating liver extracts were determined by the use of the DNA polymerase alpha specific inhibitor, BuAdATP [2-(p-n-butylanilino)-9-(2-deoxy-beta-D-ribofuranosyl) adenine 5'-triphosphate], and monoclonal antibodies. These reagents showed that the total DNA polymerase activities increased ca. 4-fold during regeneration and that the fraction of DNA polymerase delta activity at the peak was 40% of the total DNA polymerase activity. Immunoblots and inhibition studies using specific antibodies showed that DNA polymerase delta and epsilon and PCNA were concomitantly induced after partial hepatectomy. The levels of both DNA polymerase delta and epsilon and PCNA reached their maxima at 24-36 h post hepatectomy, i.e., at the same time that in vivo DNA synthesis reached its peak. Partial purification and characterization of DNA polymerases delta and epsilon from the regenerating rat liver were also performed. These observations suggest that the variation of DNA polymerase delta and epsilon and PCNA during liver regeneration is closely related to DNA synthesis and is consistent with their involvement in DNA replication.
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Affiliation(s)
- C L Yang
- Department of Medicine, University of Miami School of Medicine, Florida 33101
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26
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Schweighoffer T, Schweighoffer E, Apati A, Antoni F, Molnar G, Lapis K, Banfalvi G. Cytometric analysis of DNA replication inhibited by emetine and cyclosporin A. HISTOCHEMISTRY 1991; 96:93-7. [PMID: 1938485 DOI: 10.1007/bf00266767] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
DNA staining methods based on aspecific interactions with dye molecules have been replaced by an immunofluorescent approach to measure DNA replication. Biotin-11-dUTP was incorporated into permeable thymocytes isolated after emetine or cyclosporin A treatment of mice. Active sites of DNA replication were amplified based on biotin-avidin interaction and verified under fluorescent microscope. Cytometry of fluorescent images allow the direct measurement of replicating DNA without aspecific detection of total cellular DNA. Cytometric analysis of replication revealed that emetine acts at the early S phase, while cyclosporin A blocks in vivo DNA synthesis at mid S phase.
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Affiliation(s)
- T Schweighoffer
- Institute of Biochemistry Department I, Semmelweis Medical University, Budapest, Hungary
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27
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Nethanel T, Kaufmann G. Two DNA polymerases may be required for synthesis of the lagging DNA strand of simian virus 40. J Virol 1990; 64:5912-8. [PMID: 2173773 PMCID: PMC248760 DOI: 10.1128/jvi.64.12.5912-5918.1990] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Agents discriminating between DNA polymerase alpha and DNA polymerases of class delta (polymerase delta or epsilon) were used to characterize steps in the synthesis of the lagging DNA strand of simian virus 40 during DNA replication in isolated nuclei. The synthesis of lagging-strand intermediates below 40 nucleotides, termed DNA primers (T. Nethanel, S. Reisfeld, G. Dinter-Gottlieb, and G. Kaufmann, J. Virol. 62:2867-2873, 1988), was selectively inhibited by butylphenyl dGTP or by neutralizing DNA polymerase alpha monoclonal antibodies. The synthesis of longer lagging chains of up to 250 nucleotides (Okazaki pieces) was affected to a lesser extent, possibly indirectly, by these agents. Aphidicolin, which inhibits both alpha- and delta-class enzymes, elicited the opposite pattern: DNA primers accumulated in its presence and were not converted into Okazaki pieces. These and previous data suggest that DNA polymerase alpha primase synthesizes DNA primers, whereas another DNA polymerase, presumably DNA polymerase delta or epsilon, mediates the conversion of DNA primers into Okazaki pieces.
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Affiliation(s)
- T Nethanel
- Department of Biochemistry, Tel Aviv University, Ramat Aviv, Israel
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28
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Banfalvi G, Tanke H, Raap AK, Slats J, van der Ploeg M. Early replication signals in nuclei of Chinese hamster ovary cells. HISTOCHEMISTRY 1990; 94:435-40. [PMID: 2228739 DOI: 10.1007/bf00266452] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
DNA replication sites generally known as replicon domains were resolved as individual replication signals in interphase nuclei of permeabilized Chinese hamster ovary cells by immunofluorescent microscopy. Biotin-11-dUTP was utilized as a tool to label newly replicated DNA in permeable cells and to study the distribution of nascent DNA in pulselabel and in pulsechase experiments. Active sites of DNA replication were visualized in exponentially growing cells and in synchronized cultures throughout the S phase. Fluorescent images of replication sites were analyzed by standard fluorescence microscopy and in three dimensions by confocal laser scanning microscopy. The rapid increase in number of discrete foci of newly replicated DNA is an indication that DNA synthesis starts at limited number of sites in mammalian nuclei rather than at thousands of foci at the same time.
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Affiliation(s)
- G Banfalvi
- Institute of Biochemistry Department I, Semmelweis University Medical School, Budapest, Hungary
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29
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Jackson DA. Does butylphenyl-deoxyguanosine triphosphate differentially inhibit DNA polymerase alpha and delta activities in permeabilized HeLa cells? Nucleic Acids Res 1990; 18:753-8. [PMID: 2315038 PMCID: PMC330323 DOI: 10.1093/nar/18.4.753] [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: 12/31/2022] Open
Abstract
In eukaryotic cells, two enzymes, DNA polymerases alpha and delta, are thought to play major roles in DNA synthesis. I have used butylphenyl dGTP (BuPdGTP), a potent inhibitor of purified DNA polymerase alpha, to assess the relative activities of these enzymes in two permeabilized cell systems. In both instances BuPdGTP eliminated all of the activity which was sensitive to aphidicolin. However, no conditions were found where BuPdGTP preferentially inhibited the synthesis of Okazaki fragments--the presumed products of DNA polymerase alpha activity. This implies that DNA polymerase activities on the two sides of the replication fork are unable to operate independently, being just two elements of the integrated replication machinery that undertakes DNA synthesis in permeabilized cells.
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Affiliation(s)
- D A Jackson
- Sir William Dunn School of Pathology, University of Oxford, UK
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30
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Abstract
The identities and precise roles of the DNA polymerase(s) involved in mammalian cell DNA replication are uncertain. Circumstantial evidence suggests that DNA polymerase alpha and at least one form of DNA polymerase delta, that which is stimulated by Proliferating Cell Nuclear Antigen, catalyze mammalian cell replicative DNA synthesis. Further, the in vitro properties of polymerases alpha and delta suggest a model for their coordinate action at the replication fork. The present paper summarizes the current status of DNA polymerases alpha and delta in DNA replication, and describes newly available approaches to the study of those enzymes.
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Affiliation(s)
- R V Talanian
- Department of Pharmacology, University of Massachusetts Medical School, Worcester 01655
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31
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Banfalvi G, Wiegant J, Sarkar N, van Duijn P. Immunofluorescent visualization of DNA replication sites within nuclei of Chinese hamster ovary cells. HISTOCHEMISTRY 1989; 93:81-6. [PMID: 2613551 DOI: 10.1007/bf00266851] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The spatial distribution of replication sites was studied by a sensitive method in cells cultured in vitro. Exponentially growing Chinese hamster ovary cells were permeabilized and pulse labeled in the presence of deoxyribonucleoside triphosphates, dTTP being replaced by biotin-11-dUTP as a substrate for DNA replication. The distribution of replication sites was visualized in isolated nuclei by fluorescent microscopy of samples taken periodically after short-term (2 min) in vitro labeling and pulse-chase experiments. Propidium iodide and 4,6-diamino-2-phenylindole served as fluorescent probes for total cellular DNA. Avidin-fluorescein isothiocyanate and biotinylated goat antiavidin antibody were used in an amplification procedure to fluorescently label the incorporated biotin-11-dUTP. Similar experiments using synchronized cells showed the distribution of replicons at different stages of S phase.
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Affiliation(s)
- G Banfalvi
- Institute of Biochemistry Department I, Semmelweis University Medical School, Budapest, Hungary
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