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Bairamukov VY, Kovalev RA, Ankudinov AV, Pantina RA, Fedorova ND, Bukatin AS, Grigoriev SV, Varfolomeeva EY. Alterations in the chromatin packaging, driven by transcriptional activity, revealed by AFM. Biochim Biophys Acta Gen Subj 2024; 1868:130568. [PMID: 38242181 DOI: 10.1016/j.bbagen.2024.130568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
BACKGROUND The gene expression differs in the nuclei of normal and malignant mammalian cells, and transcription is a critical initial step, which defines the difference. The mechanical properties of transcriptionally active chromatin are still poorly understood. Recently we have probed transcriptionally active chromatin of the nuclei subjected to mechanical stress, by Atomic Force Microscopy (AFM) [1]. Nonetheless, a systematic study of the phenomenon is needed. METHODS Nuclei were deformed and studied by AFM. Non-deformed nuclei were studied by fluorescence confocal microscopy. Their transcriptional activity was studied by RNA electrophoresis. RESULTS The malignant nuclei under the study were stable to deformation and assembled of 100-300 nm beads-like units, while normal cell nuclei were prone to deformation. The difference in stability to deformation of the nuclei correlated with DNA supercoiling, and transcription-depended units were responsive to supercoils breakage. The inhibitors of the topoisomerases I and II disrupted supercoiling and made the malignant nucleus prone to deformation. Cell nuclei treatment with histone deacetylase inhibitors (HDACIs) preserved the mechanical stability of deformed malignant nuclei and, at the same time, made it possible to observe chromatin decondensation up to 20-60 nm units. The AFM results were supplemented with confocal microscopy and RNA electrophoresis data. CONCLUSIONS Self-assembly of transcriptionally active chromatin and its decondensation, driven by DNA supercoiling-dependent rigidity, was visualized by AFM in the mechanically deformed nuclei. GENERAL SIGNIFICANCE We demonstrated that supercoiled DNA defines the transcription mechanics, and hypothesized the nuclear mechanics in vivo should depend on the chromatin architecture.
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Affiliation(s)
- V Yu Bairamukov
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of NRC "Kurchatov Institute", 1, Orlova Roshcha, 188300 Gatchina, Russia.
| | - R A Kovalev
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of NRC "Kurchatov Institute", 1, Orlova Roshcha, 188300 Gatchina, Russia
| | - A V Ankudinov
- The Ioffe Physical-Technical Institute of the Russian Academy of Sciences, 26, Politekhnicheskaya, 194021 Saint Petersburg, Russia
| | - R A Pantina
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of NRC "Kurchatov Institute", 1, Orlova Roshcha, 188300 Gatchina, Russia
| | - N D Fedorova
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of NRC "Kurchatov Institute", 1, Orlova Roshcha, 188300 Gatchina, Russia
| | - A S Bukatin
- Alferov Saint Petersburg National Research Academic University of the Russian Academy of Sciences, 8/3, Khlopina St., 194021 Saint Petersburg, Russia
| | - S V Grigoriev
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of NRC "Kurchatov Institute", 1, Orlova Roshcha, 188300 Gatchina, Russia
| | - E Yu Varfolomeeva
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of NRC "Kurchatov Institute", 1, Orlova Roshcha, 188300 Gatchina, Russia
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Iashina EG, Varfolomeeva EY, Pantina RA, Bairamukov VY, Kovalev RA, Fedorova ND, Pipich V, Radulescu A, Grigoriev SV. Bifractal structure of chromatin in rat lymphocyte nuclei. Phys Rev E 2021; 104:064409. [PMID: 35030913 DOI: 10.1103/physreve.104.064409] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/29/2021] [Indexed: 11/07/2022]
Abstract
The small-angle neutron scattering (SANS) on the rat lymphocyte nuclei demonstrates the bifractal nature of the chromatin structural organization. The scattering intensity from rat lymphocyte nuclei is described by power law Q^{-D} with fractal dimension approximately 2.3 on smaller scales and 3 on larger scales. The crossover between two fractal structures is detected at momentum transfer near 10^{-1}nm^{-1}. The use of contrast variation (D_{2}O-H_{2}O) in SANS measurements reveals clear similarity in the structural organizations of nucleic acids (NA) and proteins. Both chromatin components show bifractal behavior with logarithmic fractal structure on the large scale and volume fractal with slightly smaller than 2.5 structure on the small scale. Scattering intensities from chromatin, protein component, and NA component demonstrate an extremely extensive range of logarithmic fractal behavior (from 10^{-3} to approximately 10^{-1}nm^{-1}). We compare the fractal arrangement of rat lymphocyte nuclei with that of chicken erythrocytes and the immortal HeLa cell line. We conclude that the bifractal nature of the chromatin arrangement is inherent in the nuclei of all these cells. The details of the fractal arrangement-its range and correlation/interaction between nuclear acids and proteins are specific for different cells and is related to their functionality.
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Affiliation(s)
- E G Iashina
- Petersburg Nuclear Physics Institute (PNPI), NRC Kurchatov Institute, Orlova roshcha 1, 188300, Gatchina, Russia.,Saint-Petersburg State University (SPSU), Ulyanovskaya str. 1, 198504, Saint-Petersburg, Russia
| | - E Yu Varfolomeeva
- Petersburg Nuclear Physics Institute (PNPI), NRC Kurchatov Institute, Orlova roshcha 1, 188300, Gatchina, Russia
| | - R A Pantina
- Petersburg Nuclear Physics Institute (PNPI), NRC Kurchatov Institute, Orlova roshcha 1, 188300, Gatchina, Russia
| | - V Yu Bairamukov
- Petersburg Nuclear Physics Institute (PNPI), NRC Kurchatov Institute, Orlova roshcha 1, 188300, Gatchina, Russia
| | - R A Kovalev
- Petersburg Nuclear Physics Institute (PNPI), NRC Kurchatov Institute, Orlova roshcha 1, 188300, Gatchina, Russia
| | - N D Fedorova
- Petersburg Nuclear Physics Institute (PNPI), NRC Kurchatov Institute, Orlova roshcha 1, 188300, Gatchina, Russia
| | - V Pipich
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ) Forschungszentrum Jülich GmbH, Lichtenbergstr. 1, D-85748 Garching, Germany
| | - A Radulescu
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ) Forschungszentrum Jülich GmbH, Lichtenbergstr. 1, D-85748 Garching, Germany
| | - S V Grigoriev
- Petersburg Nuclear Physics Institute (PNPI), NRC Kurchatov Institute, Orlova roshcha 1, 188300, Gatchina, Russia.,Saint-Petersburg State University (SPSU), Ulyanovskaya str. 1, 198504, Saint-Petersburg, Russia
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3
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Grigoriev SV, Iashina EG, Wu B, Pipich V, Lang C, Radulescu A, Bairamukov VY, Filatov MV, Pantina RA, Varfolomeeva EY. Observation of nucleic acid and protein correlation in chromatin of HeLa nuclei using small-angle neutron scattering with D_{2}O-H_{2}O contrast variation. Phys Rev E 2021; 104:044404. [PMID: 34781557 DOI: 10.1103/physreve.104.044404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 08/30/2021] [Indexed: 01/06/2023]
Abstract
The small-angle neutron scattering (SANS) on HeLa nuclei demonstrates the bifractal nature of the chromatin structural organization. The border line between two fractal structures is detected as a crossover point at Q_{c}≈4×10^{-2}nm^{-1} in the momentum transfer dependence Q^{-D}. The use of contrast variation (D_{2}O-H_{2}O) in SANS measurements reveals clear similarity in the large scale structural organizations of nucleic acids (NA) and proteins. Both NA and protein structures have a mass fractal arrangement with the fractal dimension of D≈2.5 at scales smaller than 150 nm down to 20 nm. Both NA and proteins show a logarithmic fractal behavior with D≈3 at scales larger than 150 nm up to 6000 nm. The combined analysis of the SANS and atomic force microscopy data allows one to conclude that chromatin and its constitutes (DNA and proteins) are characterized as soft, densely packed, logarithmic fractals on the large scale and as rigid, loosely packed, mass fractals on the smaller scale. The comparison of the partial cross sections from NA and proteins with one from chromatin as a whole demonstrates spatial correlation of two chromatin's components in the range up to 900 nm. Thus chromatin in HeLa nuclei is built as the unified structure of the NA and proteins entwined through each other. Correlation between two components is lost upon scale increases toward 6000 nm. The structural features at the large scale, probably, provide nuclei with the flexibility and chromatin-free space to build supercorrelations on the distance of 10^{3} nm resembling cycle cell activity, such as an appearance of nucleoli and a DNA replication.
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Affiliation(s)
- S V Grigoriev
- Petersburg Nuclear Physics Institute named by B.P.Konstantinov of NRC Kurchatov Institute, Gatchina, St-Petersburg 188300, Russia.,Saint-Petersburg State University, Ulyanovskaya 1, Saint-Petersburg 198504, Russia
| | - E G Iashina
- Petersburg Nuclear Physics Institute named by B.P.Konstantinov of NRC Kurchatov Institute, Gatchina, St-Petersburg 188300, Russia.,Saint-Petersburg State University, Ulyanovskaya 1, Saint-Petersburg 198504, Russia
| | - B Wu
- Forschungszentrum Juelich, JCNS-4 at MLZ, Lichtenbergstr. 1, 85748 Garching, Germany
| | - V Pipich
- Forschungszentrum Juelich, JCNS-4 at MLZ, Lichtenbergstr. 1, 85748 Garching, Germany
| | - Ch Lang
- Forschungszentrum Juelich, JCNS-4 at MLZ, Lichtenbergstr. 1, 85748 Garching, Germany
| | - A Radulescu
- Forschungszentrum Juelich, JCNS-4 at MLZ, Lichtenbergstr. 1, 85748 Garching, Germany
| | - V Yu Bairamukov
- Petersburg Nuclear Physics Institute named by B.P.Konstantinov of NRC Kurchatov Institute, Gatchina, St-Petersburg 188300, Russia
| | - M V Filatov
- Petersburg Nuclear Physics Institute named by B.P.Konstantinov of NRC Kurchatov Institute, Gatchina, St-Petersburg 188300, Russia
| | - R A Pantina
- Petersburg Nuclear Physics Institute named by B.P.Konstantinov of NRC Kurchatov Institute, Gatchina, St-Petersburg 188300, Russia
| | - E Yu Varfolomeeva
- Petersburg Nuclear Physics Institute named by B.P.Konstantinov of NRC Kurchatov Institute, Gatchina, St-Petersburg 188300, Russia
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Grigoriev SV, Iashina EG, Bairamukov VY, Pipich V, Radulescu A, Filatov MV, Pantina RA, Varfolomeeva EY. Switch of fractal properties of DNA in chicken erythrocytes nuclei by mechanical stress. Phys Rev E 2020; 102:032415. [PMID: 33075965 DOI: 10.1103/physreve.102.032415] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/13/2020] [Indexed: 11/07/2022]
Abstract
The small-angle neutron scattering (SANS) on the chicken erythrocyte nuclei demonstrates the bifractal nature of the chromatin structural organization. Use of the contrast variation (D_{2}O-H_{2}O) in SANS measurements reveals the differences in the DNA and protein arrangements inside the chromatin substance. It is the DNA that serves as a framework that constitutes the bifractal behavior showing the mass fractal properties with D=2.22 at a smaller scale and the logarithmic fractal behavior with D≈3 at a larger scale. The protein spatial organization shows the mass fractal properties with D≈2.34 throughout the whole nucleus. The borderline between two fractal levels can be significantly shifted toward smaller scales by centrifugation of the nuclei disposed on the dry substrate, since nuclei suffer from mechanical stress transforming them to a disklike shape. The height of this disk measured by atomic force microscopy (AFM) coincides closely with the fractal borderline, thus characterizing two types of the chromatin with the soft (at larger scale) and rigid (at smaller scale) properties. The combined SANS and AFM measurements demonstrate the stress induced switch of the DNA fractal properties from the rigid, but loosely packed, mass fractal to the soft, but densely packed, logarithmic fractal.
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Affiliation(s)
- S V Grigoriev
- Petersburg Nuclear Physics Institute, Gatchina, St-Petersburg, 188300, Russia.,Saint-Petersburg State University, Ulyanovskaya 1, Saint-Petersburg, 198504, Russia
| | - E G Iashina
- Petersburg Nuclear Physics Institute, Gatchina, St-Petersburg, 188300, Russia
| | - V Yu Bairamukov
- Petersburg Nuclear Physics Institute, Gatchina, St-Petersburg, 188300, Russia
| | - V Pipich
- Heinz Maier-Leibnitz Zentrum, Lichtenbergstraße 1, 85748 Garching bei München, Germany
| | - A Radulescu
- Heinz Maier-Leibnitz Zentrum, Lichtenbergstraße 1, 85748 Garching bei München, Germany
| | - M V Filatov
- Petersburg Nuclear Physics Institute, Gatchina, St-Petersburg, 188300, Russia
| | - R A Pantina
- Petersburg Nuclear Physics Institute, Gatchina, St-Petersburg, 188300, Russia
| | - E Yu Varfolomeeva
- Petersburg Nuclear Physics Institute, Gatchina, St-Petersburg, 188300, Russia
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Shtam TA, Burdakov VS, Landa SB, Naryzhny SN, Bairamukov VY, Malek AV, Orlov YN, Filatov MV. AGGREGATION BY LECTIN-METHODICAL APPROACH FOR EFFECTIVE ISOLATION OF EXOSOMES FROM CELL CULTURE SUPERNATANT FOR PROTEOME PROFILING. Tsitologiia 2017; 59:5-12. [PMID: 30188097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Exosomes are small membrane vesicles secreted by most cell types in vivo and in vitro. Exosomes are found in cell culture media, blood, urine, amniotic fluid, malignant ascite fluids and contain distinct subsets of microRNAs and proteins depending upon the tissue from which they are secreted. Thus exosomes constitute potential biomarkers of human diseases, such as cancer. A major bottleneck in the development of exosome-based diagnostic assays is the challenging purification of these vesicles; this requires time-consuming and instrument-based procedures. Isolation of exosomes can be a tedious, non-specific, and difficult process. Here, we provide a preparative technique for isolation of exosomes based on their ability to aggregate in the presence of lectins. The new method for lectin-based isolation of exosomes from cell culture media was developed as a sample preparation step for exosome-based protein biomarker research.
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