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Perdyan A, Jąkalski M, Horbacz M, Beheshti A, Mieczkowski J. Chromosomal positioning and epigenetic architecture influence DNA methylation patterns triggered by galactic cosmic radiation. Sci Rep 2024; 14:1324. [PMID: 38225252 PMCID: PMC10789781 DOI: 10.1038/s41598-024-51756-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/09/2024] [Indexed: 01/17/2024] Open
Abstract
Despite surging interest in space travel in recent decades, the impacts of prolonged, elevated exposure to galactic cosmic radiation (GCR) on human health remain poorly understood. This form of ionizing radiation causes significant changes to biological systems including damage to DNA structure by altering epigenetic phenotype with emphasis on DNA methylation. Building on previous work by Kennedy et al. (Sci Rep 8(1): 6709. 10.1038/S41598-018-24755-8), we evaluated spatial DNA methylation patterns triggered by high-LET (56Fe, 28Si) and low-LET (X-ray) radiation and the influence of chromosome positioning and epigenetic architecture in distinct radial layers of cell nucleus. Next, we validated our results using gene expression data of mice irradiated with simulated GCR and JAXA astronauts. We showed that primarily 56Fe induces a persistent DNA methylation increase whereas 28Si and X-ray induce a decrease DNA methylation which is not persistent with time. Moreover, we highlighted the role of nuclear chromatin architecture in cell response to external radiation. In summary, our study provides novel insights towards epigenetic and transcriptomic response as well as chromatin multidimensional structure influence on galactic cosmic radiation damage.
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Affiliation(s)
- Adrian Perdyan
- International Research Agenda 3P - Medicine Laboratory, Medical University of Gdansk, Marii Sklodowskiej Curie 3a, 80-210, Gdansk, Poland
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Marcin Jąkalski
- International Research Agenda 3P - Medicine Laboratory, Medical University of Gdansk, Marii Sklodowskiej Curie 3a, 80-210, Gdansk, Poland
| | - Monika Horbacz
- International Research Agenda 3P - Medicine Laboratory, Medical University of Gdansk, Marii Sklodowskiej Curie 3a, 80-210, Gdansk, Poland
| | - Afshin Beheshti
- Space Biosciences Division, NASA Ames Research Center, Blue Marble Space Institute of Science, Moffett Field, CA, 94035, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jakub Mieczkowski
- International Research Agenda 3P - Medicine Laboratory, Medical University of Gdansk, Marii Sklodowskiej Curie 3a, 80-210, Gdansk, Poland.
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2
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Fischer EF, Pilarczyk G, Hausmann M. Microscopic Analysis of Heterochromatin, Euchromatin and Cohesin in Cancer Cell Models and under Anti-Cancer Treatment. Curr Issues Mol Biol 2023; 45:8152-8172. [PMID: 37886958 PMCID: PMC10605351 DOI: 10.3390/cimb45100515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/01/2023] [Accepted: 10/03/2023] [Indexed: 10/28/2023] Open
Abstract
The spatial organization of euchromatin (EC) and heterochromatin (HC) appears as a cell-type specific network, which seems to have an impact on gene regulation and cell fate. The spatial organization of cohesin should thus also be characteristic for a cell type since it is involved in a TAD (topologically associating domain) formation, and thus in gene regulation or DNA repair processes. Based on the previous hypotheses and results on the general importance of heterochromatin organization on genome functions in particular, the configurations of these organizational units (EC represented by H3K4me3-positive regions, HC represented by H3K9me3-positive regions, cohesins) are investigated in the cell nuclei of different cancer and non-cancerous cell types and under different anti-cancer treatments. Confocal microscopic images of the model cell systems were used and analyzed using analytical processes of quantification created in Fiji, an imaging tool box well established in different fields of science. Human fibroblasts, breast cancer and glioblastoma cells as well as murine embryonal terato-carcinoma cells were used as these cell models and compared according to the different parameters of spatial arrangements. In addition, proliferating, quiescent and from the quiescent state reactivated fibroblasts were analyzed. In some selected cases, the cells were treated with X-rays or azacitidine. Heterogeneous results were obtained by the analyses of the configurations of the three different organizational units: granulation and a loss of H3K4me3-positive regions (EC) occurred after irradiation with 4 Gy or azacitidine treatment. While fibroblasts responded to irradiation with an increase in cohesin and granulation, in breast cancer cells, it resulted in decreases in cohesin and changes in granulation. H3K9me3-positive regions (HC) in fibroblasts experienced increased granulation, whereas in breast cancer cells, the amount of such regions increased. After azacitidine treatment, murine stem cells showed losses of cohesin and granulation and an increase in the granulation of H3K9me3-positive regions. Fibroblasts that were irradiated with 2 Gy only showed irregularities in structural amounts and granulation. Quiescent fibroblasts contained less euchromatin-related H3K4me3-positive signals and cohesin levels as well as higher heterochromatin-related H3K9me3-positive signals than non-quiescent ones. In general, fibroblasts responded more intensely to X-ray irradiation than breast cancer cells. The results indicate the usefulness of model cell systems and show that, in general, characteristic differences initially existing in chromatin and cohesin organizations result in specific responses to anti-cancer treatment.
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Affiliation(s)
| | | | - Michael Hausmann
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany; (E.F.F.); (G.P.)
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3
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Sievers A, Sauer L, Bisch M, Sprengel J, Hausmann M, Hildenbrand G. Moderation of Structural DNA Properties by Coupled Dinucleotide Contents in Eukaryotes. Genes (Basel) 2023; 14:genes14030755. [PMID: 36981025 PMCID: PMC10048725 DOI: 10.3390/genes14030755] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/16/2023] [Accepted: 03/18/2023] [Indexed: 03/30/2023] Open
Abstract
Dinucleotides are known as determinants for various structural and physiochemical properties of DNA and for binding affinities of proteins to DNA. These properties (e.g., stiffness) and bound proteins (e.g., transcription factors) are known to influence important biological functions, such as transcription regulation and 3D chromatin organization. Accordingly, the question arises of how the considerable variations in dinucleotide contents of eukaryotic chromosomes could still provide consistent DNA properties resulting in similar functions and 3D conformations. In this work, we investigate the hypothesis that coupled dinucleotide contents influence DNA properties in opposite directions to moderate each other's influences. Analyzing all 2478 chromosomes of 155 eukaryotic species, considering bias from coding sequences and enhancers, we found sets of correlated and anti-correlated dinucleotide contents. Using computational models, we estimated changes of DNA properties resulting from this coupling. We found that especially pure A/T dinucleotides (AA, TT, AT, TA), known to influence histone positioning and AC/GT contents, are relevant moderators and that, e.g., the Roll property, which is known to influence histone affinity of DNA, is preferably moderated. We conclude that dinucleotide contents might indirectly influence transcription and chromatin 3D conformation, via regulation of histone occupancy and/or other mechanisms.
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Affiliation(s)
- Aaron Sievers
- Kirchhoff Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany
- Institute for Human Genetics, University Hospital Heidelberg, INF 366, 69117 Heidelberg, Germany
| | - Liane Sauer
- Kirchhoff Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany
- Institute for Human Genetics, University Hospital Heidelberg, INF 366, 69117 Heidelberg, Germany
| | - Marc Bisch
- Kirchhoff Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany
| | - Jan Sprengel
- Kirchhoff Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany
| | - Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany
| | - Georg Hildenbrand
- Kirchhoff Institute for Physics, Heidelberg University, INF 227, 69117 Heidelberg, Germany
- Faculty of Engeneering, University of Applied Science Aschaffenburg, Würzburger Str. 45, 63743 Aschaffenburg, Germany
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4
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Weidner J, Neitzel C, Gote M, Deck J, Küntzelmann K, Pilarczyk G, Falk M, Hausmann M. Advanced image-free analysis of the nano-organization of chromatin and other biomolecules by Single Molecule Localization Microscopy (SMLM). Comput Struct Biotechnol J 2023; 21:2018-2034. [PMID: 36968017 PMCID: PMC10030913 DOI: 10.1016/j.csbj.2023.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/08/2023] [Accepted: 03/08/2023] [Indexed: 03/11/2023] Open
Abstract
The cell as a system of many components, governed by the laws of physics and chemistry drives molecular functions having an impact on the spatial organization of these systems and vice versa. Since the relationship between structure and function is an almost universal rule not only in biology, appropriate methods are required to parameterize the relationship between the structure and function of biomolecules and their networks, the mechanisms of the processes in which they are involved, and the mechanisms of regulation of these processes. Single molecule localization microscopy (SMLM), which we focus on here, offers a significant advantage for the quantitative parametrization of molecular organization: it provides matrices of coordinates of fluorescently labeled biomolecules that can be directly subjected to advanced mathematical analytical procedures without the need for laborious and sometimes misleading image processing. Here, we propose mathematical tools for comprehensive quantitative computer data analysis of SMLM point patterns that include Ripley distance frequency analysis, persistent homology analysis, persistent 'imaging', principal component analysis and co-localization analysis. The application of these methods is explained using artificial datasets simulating different, potentially possible and interpretatively important situations. Illustrative analyses of real complex biological SMLM data are presented to emphasize the applicability of the proposed algorithms. This manuscript demonstrated the extraction of features and parameters quantifying the influence of chromatin (re)organization on genome function, offering a novel approach to study chromatin architecture at the nanoscale. However, the ability to adapt the proposed algorithms to analyze essentially any molecular organizations, e.g., membrane receptors or protein trafficking in the cytosol, offers broad flexibility of use.
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Mushtaq A, Mir US, Altaf M. Multifaceted functions of RNA-binding protein vigilin in gene silencing, genome stability, and autism-related disorders. J Biol Chem 2023; 299:102988. [PMID: 36758804 PMCID: PMC10011833 DOI: 10.1016/j.jbc.2023.102988] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
RNA-binding proteins (RBPs) are emerging as important players in regulating eukaryotic gene expression and genome stability. Specific RBPs have been shown to mediate various chromatin-associated processes ranging from transcription to gene silencing and DNA repair. One of the prominent classes of RBPs is the KH domain-containing proteins. Vigilin, an evolutionarily conserved KH domain-containing RBP has been shown to be associated with diverse biological processes like RNA transport and metabolism, sterol metabolism, chromosome segregation, and carcinogenesis. We have previously reported that vigilin is essential for heterochromatin-mediated gene silencing in fission yeast. More recently, we have identified that vigilin in humans plays a critical role in efficient repair of DNA double-stranded breaks and functions in homology-directed DNA repair. In this review, we highlight the multifaceted functions of vigilin and discuss the findings in the context of gene expression, genome organization, cancer, and autism-related disorders.
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Affiliation(s)
- Arjamand Mushtaq
- Centre for Interdisciplinary Research and Innovations, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Ulfat Syed Mir
- Centre for Interdisciplinary Research and Innovations, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Mohammad Altaf
- Centre for Interdisciplinary Research and Innovations, University of Kashmir, Srinagar, Jammu and Kashmir, India.
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6
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Erenpreisa J, Giuliani A, Yoshikawa K, Falk M, Hildenbrand G, Salmina K, Freivalds T, Vainshelbaum N, Weidner J, Sievers A, Pilarczyk G, Hausmann M. Spatial-Temporal Genome Regulation in Stress-Response and Cell-Fate Change. Int J Mol Sci 2023; 24:ijms24032658. [PMID: 36769000 PMCID: PMC9917235 DOI: 10.3390/ijms24032658] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/17/2023] [Accepted: 01/22/2023] [Indexed: 02/04/2023] Open
Abstract
Complex functioning of the genome in the cell nucleus is controlled at different levels: (a) the DNA base sequence containing all relevant inherited information; (b) epigenetic pathways consisting of protein interactions and feedback loops; (c) the genome architecture and organization activating or suppressing genetic interactions between different parts of the genome. Most research so far has shed light on the puzzle pieces at these levels. This article, however, attempts an integrative approach to genome expression regulation incorporating these different layers. Under environmental stress or during cell development, differentiation towards specialized cell types, or to dysfunctional tumor, the cell nucleus seems to react as a whole through coordinated changes at all levels of control. This implies the need for a framework in which biological, chemical, and physical manifestations can serve as a basis for a coherent theory of gene self-organization. An international symposium held at the Biomedical Research and Study Center in Riga, Latvia, on 25 July 2022 addressed novel aspects of the abovementioned topic. The present article reviews the most recent results and conclusions of the state-of-the-art research in this multidisciplinary field of science, which were delivered and discussed by scholars at the Riga symposium.
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Affiliation(s)
| | - Alessandro Giuliani
- Istituto Superiore di Sanita Environment and Health Department, 00161 Roma, Italy
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
| | - Martin Falk
- Institute of Biophysics, The Czech Academy of Sciences, 612 65 Brno, Czech Republic
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Georg Hildenbrand
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
- Faculty of Engineering, University of Applied Science Aschaffenburg, 63743 Aschaffenburg, Germany
| | - Kristine Salmina
- Latvian Biomedicine Research and Study Centre, LV1067 Riga, Latvia
| | - Talivaldis Freivalds
- Institute of Cardiology and Regenerative Medicine, University of Latvia, LV1004 Riga, Latvia
| | - Ninel Vainshelbaum
- Latvian Biomedicine Research and Study Centre, LV1067 Riga, Latvia
- Doctoral Study Program, University of Latvia, LV1004 Riga, Latvia
| | - Jonas Weidner
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Aaron Sievers
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
- Institute for Human Genetics, University Hospital Heidelberg, 69117 Heidelberg, Germany
| | - Götz Pilarczyk
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
- Correspondence:
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7
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Chapman KB, Filipsky F, Peschke N, Gelléri M, Weinhardt V, Braun A, Hausmann M, Cremer C. A comprehensive method to study the DNA's association with lamin and chromatin compaction in intact cell nuclei at super resolution. NANOSCALE 2023; 15:742-756. [PMID: 36524744 PMCID: PMC9813922 DOI: 10.1039/d2nr02684h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 10/14/2022] [Indexed: 06/17/2023]
Abstract
Super-resolution fluorescence microscopy has revolutionized multicolor imaging of nuclear structures due to the combination of high labeling specificity and high resolution. Here we expanded the recently developed fBALM (DNA structure fluctuation-assisted binding activated localization microscopy) method by developing a stable methodological sequence that enables dual-color imaging of high-resolution genomic DNA together with an immunofluorescently labeled intranuclear protein. Our measurements of the nuclear periphery, imaging DNA and LaminB1 in biologically relevant samples, show that this novel dual-color imaging method is feasible for further quantitative evaluations. We were able to study the relative spatial signal organization between DNA and LaminB1 by means of highly specific colocalization measurements at nanometer resolution. Measurements were performed with and without the antifade embedding medium ProLong Gold, which proved to be essential for imaging of LaminB1, but not for imaging of SytoxOrange labeled DNA. The localization precision was used to differentiate between localizations with higher and lower amounts of emitting photons. We interpret high intensity localizations to be renatured DNA sections in which a high amount of Sytox Orange molecules were bound. This could give insight into the denaturation kinetics of DNA during fBALM. These results were further complemented by measurements of γH2AX and H3K9me3 signal organization to demonstrate differences within the chromatin landscape, which were quantified with image processing methods such as Voronoi segmentation.
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Affiliation(s)
- Katarina B Chapman
- Kirchhoff-Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany.
- Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
| | - Filip Filipsky
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Nicolas Peschke
- Kirchhoff-Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany.
| | - Márton Gelléri
- Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
| | - Venera Weinhardt
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Andrejs Braun
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Michael Hausmann
- Kirchhoff-Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany.
| | - Christoph Cremer
- Kirchhoff-Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany.
- Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
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Polyploidy and Myc Proto-Oncogenes Promote Stress Adaptation via Epigenetic Plasticity and Gene Regulatory Network Rewiring. Int J Mol Sci 2022; 23:ijms23179691. [PMID: 36077092 PMCID: PMC9456078 DOI: 10.3390/ijms23179691] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
Polyploid cells demonstrate biological plasticity and stress adaptation in evolution; development; and pathologies, including cardiovascular diseases, neurodegeneration, and cancer. The nature of ploidy-related advantages is still not completely understood. Here, we summarize the literature on molecular mechanisms underlying ploidy-related adaptive features. Polyploidy can regulate gene expression via chromatin opening, reawakening ancient evolutionary programs of embryonality. Chromatin opening switches on genes with bivalent chromatin domains that promote adaptation via rapid induction in response to signals of stress or morphogenesis. Therefore, stress-associated polyploidy can activate Myc proto-oncogenes, which further promote chromatin opening. Moreover, Myc proto-oncogenes can trigger polyploidization de novo and accelerate genome accumulation in already polyploid cells. As a result of these cooperative effects, polyploidy can increase the ability of cells to search for adaptive states of cellular programs through gene regulatory network rewiring. This ability is manifested in epigenetic plasticity associated with traits of stemness, unicellularity, flexible energy metabolism, and a complex system of DNA damage protection, combining primitive error-prone unicellular repair pathways, advanced error-free multicellular repair pathways, and DNA damage-buffering ability. These three features can be considered important components of the increased adaptability of polyploid cells. The evidence presented here contribute to the understanding of the nature of stress resistance associated with ploidy and may be useful in the development of new methods for the prevention and treatment of cardiovascular and oncological diseases.
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Freyter BM, Abd Al-razaq MA, Isermann A, Dietz A, Azimzadeh O, Hekking L, Gomolka M, Rübe CE. Nuclear Fragility in Radiation-Induced Senescence: Blebs and Tubes Visualized by 3D Electron Microscopy. Cells 2022; 11:cells11020273. [PMID: 35053389 PMCID: PMC8774169 DOI: 10.3390/cells11020273] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/19/2021] [Accepted: 01/12/2022] [Indexed: 12/10/2022] Open
Abstract
Irreparable DNA damage following ionizing radiation (IR) triggers prolonged DNA damage response and induces premature senescence. Cellular senescence is a permanent state of cell-cycle arrest characterized by chromatin restructuring, altered nuclear morphology and acquisition of secretory phenotype, which contributes to senescence-related inflammation. However, the mechanistic connections for radiation-induced DNA damage that trigger these senescence-associated hallmarks are poorly understood. In our in vitro model of radiation-induced senescence, mass spectrometry-based proteomics was combined with high-resolution imaging techniques to investigate the interrelations between altered chromatin compaction, nuclear envelope destabilization and nucleo-cytoplasmic chromatin blebbing. Our findings confirm the general pathophysiology of the senescence-response, with disruption of nuclear lamin organization leading to extensive chromatin restructuring and destabilization of the nuclear membrane with release of chromatin fragments into the cytosol, thereby activating cGAS-STING-dependent interferon signaling. By serial block-face scanning electron microscopy (SBF-SEM) whole-cell datasets were acquired to investigate the morphological organization of senescent fibroblasts. High-resolution 3-dimensional (3D) reconstruction of the complex nuclear shape allows us to precisely visualize the segregation of nuclear blebs from the main nucleus and their fusion with lysosomes. By multi-view 3D electron microscopy, we identified nanotubular channels formed in lamin-perturbed nuclei of senescent fibroblasts; the potential role of these nucleo-cytoplasmic nanotubes for expulsion of damaged chromatin has to be examined.
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Affiliation(s)
- Benjamin M. Freyter
- Department of Radiation Oncology, Saarland University Medical Center, Kirrbergerstrasse Building 6.5, 66421 Homburg, Germany; (B.M.F.); (M.A.A.A.-r.); (A.I.)
| | - Mutaz A. Abd Al-razaq
- Department of Radiation Oncology, Saarland University Medical Center, Kirrbergerstrasse Building 6.5, 66421 Homburg, Germany; (B.M.F.); (M.A.A.A.-r.); (A.I.)
| | - Anna Isermann
- Department of Radiation Oncology, Saarland University Medical Center, Kirrbergerstrasse Building 6.5, 66421 Homburg, Germany; (B.M.F.); (M.A.A.A.-r.); (A.I.)
| | - Anne Dietz
- Department of Effects and Risks of Ionising & Non-Ionising Radiation, Federal Office for Radiation Protection, 85764 Oberschleißheim, Germany; (A.D.); (O.A.); (M.G.)
| | - Omid Azimzadeh
- Department of Effects and Risks of Ionising & Non-Ionising Radiation, Federal Office for Radiation Protection, 85764 Oberschleißheim, Germany; (A.D.); (O.A.); (M.G.)
| | | | - Maria Gomolka
- Department of Effects and Risks of Ionising & Non-Ionising Radiation, Federal Office for Radiation Protection, 85764 Oberschleißheim, Germany; (A.D.); (O.A.); (M.G.)
| | - Claudia E. Rübe
- Department of Radiation Oncology, Saarland University Medical Center, Kirrbergerstrasse Building 6.5, 66421 Homburg, Germany; (B.M.F.); (M.A.A.A.-r.); (A.I.)
- Correspondence: ; Tel.: +49-6841-1634614; Fax: +49-6841-1624699
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Hausmann M, Hildenbrand G, Pilarczyk G. Networks and Islands of Genome Nano-architecture and Their Potential Relevance for Radiation Biology : (A Hypothesis and Experimental Verification Hints). Results Probl Cell Differ 2022; 70:3-34. [PMID: 36348103 DOI: 10.1007/978-3-031-06573-6_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The cell nucleus is a complex biological system in which simultaneous reactions and functions take place to keep the cell as an individualized, specialized system running well. The cell nucleus contains chromatin packed in various degrees of density and separated in volumes of chromosome territories and subchromosomal domains. Between the chromatin, however, there is enough "free" space for floating RNA, proteins, enzymes, ATPs, ions, water molecules, etc. which are trafficking by super- and supra-diffusion to the interaction points where they are required. It seems that this trafficking works somehow automatically and drives the system perfectly. After exposure to ionizing radiation causing DNA damage from single base damage up to chromatin double-strand breaks, the whole system "cell nucleus" responds, and repair processes are starting to recover the fully functional and intact system. In molecular biology, many individual epigenetic pathways of DNA damage response or repair of single and double-strand breaks are described. How these responses are embedded into the response of the system as a whole is often out of the focus of consideration. In this article, we want to follow the hypothesis of chromatin architecture's impact on epigenetic pathways and vice versa. Based on the assumption that chromatin acts like an "aperiodic solid state within a limited volume," functionally determined networks and local topologies ("islands") can be defined that drive the appropriate repair process at a given damage site. Experimental results of investigations of the chromatin nano-architecture and DNA repair clusters obtained by means of single-molecule localization microscopy offer hints and perspectives that may contribute to verifying the hypothesis.
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Affiliation(s)
- Michael Hausmann
- Kirchhoff-Institute for Physics, Heidelberg University, Heidelberg, Germany.
| | - Georg Hildenbrand
- Kirchhoff-Institute for Physics, Heidelberg University, Heidelberg, Germany
| | - Götz Pilarczyk
- Kirchhoff-Institute for Physics, Heidelberg University, Heidelberg, Germany
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11
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Tsuchiya M, Giuliani A, Zimatore G, Erenpreisa J, Yoshikawa K. A Unified Genomic Mechanism of Cell-Fate Change. Results Probl Cell Differ 2022; 70:35-69. [PMID: 36348104 DOI: 10.1007/978-3-031-06573-6_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The purpose of our studies is to elucidate the nature of massive control of the whole genome expression with a particular emphasis on cell-fate change. The whole genome expression is coordinated by the emergence of a critical point (CP: a peculiar set of biphasic genes) with the genome acting as an integrated dynamical system. In response to stimuli, the genome expression self-organizes into local sub-, near-, and super-critical states, each exhibiting distinct collective behaviors with its center of mass acting as a local attractor, coexisting with the whole genome attractor (GA). The CP serves as the organizing center of cell-fate change, and its activation makes local perturbation to spread over the genome affecting GA. The activation of CP is in turn elicited by genes with elevated temporal variance (oscillating-mode genes), normally in charge to keep genome expression at pace with microenvironment fluctuations. When oscillation exceeds a given threshold, the CP synchronizes with the GA driving genome expression state transition. The expression synchronization wave invading the entire genome is fostered by the fusion-splitting dynamics of silencing pericentromere-associated heterochromatin domains and the consequent folding-unfolding transitions of transcribing euchromatin domains. The proposed mechanism is a unified step toward a time-evolutional transition theory of biological regulation.
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Affiliation(s)
- Masa Tsuchiya
- SEIKO Life Science Laboratory, SEIKO Research Institute for Education, Osaka, Japan.
| | - Alessandro Giuliani
- Environment and Health Department, Istituto Superiore di Sanitá, Rome, Italy.
| | | | | | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
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12
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Higher-order structure of DNA determines its positioning in cell-size droplets under crowded conditions. PLoS One 2021; 16:e0261736. [PMID: 34937071 PMCID: PMC8694483 DOI: 10.1371/journal.pone.0261736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/08/2021] [Indexed: 11/19/2022] Open
Abstract
Background It is becoming clearer that living cells use water/water (w/w) phase separation to form membraneless organelles that exhibit various important biological functions. Currently, it is believed that the specific localization of biomacromolecules, including DNA, RNA and proteins in w/w microdroplets is closely related to their bio-activity. Despite the importance of this possible role of micro segregation, our understanding of the underlying physico-chemical mechanism is still unrefined. Further research to unveil the underlying mechanism of the localization of macromolecules in relation to their steric conformation in w/w microdroplets is needed. Principal findings Single-DNA observation of genome-size DNA (T4 GT7 bacteriophage DNA; 166kbp) by fluorescence microscopy revealed that DNAs are spontaneously incorporated into w/w microdroplets generated in a binary aqueous polymer solution with polyethylene glycol (PEG) and dextran (DEX). Interestingly, DNAs with elongated coil and shrunken conformations exhibit Brownian fluctuation inside the droplet. On the other hand, tightly packed compact globules, as well as assemblies of multiple condensed DNAs, tend to be located near the interface in the droplet. Conclusion and significance The specific localization of DNA molecules depending on their higher-order structure occurs in w/w microdroplet phase-separation solution under a binary aqueous polymer solution. Such an aqueous solution with polymers mimics the crowded conditions in living cells, where aqueous macromolecules exist at a level of 30–40 weight %. The specific positioning of DNA depending on its higher-order structure in w/w microdroplets is expected to provide novel insights into the mechanism and function of membraneless organelles and micro-segregated particles in living cells.
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