Мақаланы E-mail арқылы жіберу Spatial Model of the Organization of Chromatin in the Nucleus of a Biological Cell According to Small-Angle Scattering Data
- Авторлар: Yashina E.G.1,2, Varfolomeeva E.Y.1, Pantina R.A.1, Bayramukov V.Y.1, Kovalev R.A.1, Fedorova N.D.1, Pshenichnyy K.A.1, Gorshkova Y.E.3, Grigor'ev S.V.1,2
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Мекемелер:
- Petersburg Nuclear Physics Institute, National Research Center Kurchatov Institute
- St. Petersburg State University
- Joint Institute for Nuclear Research
- Шығарылым: Том 118, № 9-10 (11) (2023)
- Беттер: 776-781
- Бөлім: Articles
- URL: https://journal-vniispk.ru/0370-274X/article/view/247005
- DOI: https://doi.org/10.31857/S1234567823220123
- EDN: https://elibrary.ru/PFTLYR
- ID: 247005
Дәйексөз келтіру
Ашық рұқсат
Рұқсат берілді
Тек жазылушылар үшін
Аннотация
Small-angle neutron and X-ray scattering data for HeLa nuclei with the normal and suppressed transcription activities are reported. Small-angle neutron scattering data demonstrate the presence of a bifractal structure inside a nucleus. The logarithmic fractal structure is observed in the range from the size of the nucleus to several hundreds of nanometer, whereas the volume fractal structure exists at smaller scales down to a nucleosome structure. Small-angle X-ray scattering data show that the presence of the volume fractal structure correlates with the transcription activity of a cell. In view of the successful description of chromatin by the fractal globule model (Hi–C method data), a scenario for the formation of the bifractal structure inside the nucleus has been proposed. A system of transport channels (logarithmic fractal) is located inside close-packed chromatin, whereas active chromatin is localized near transport channels or inside them and forms volume fractal structures due to the transcription activity. Thus, the logarithmic fractal structure ensures the uniform distribution of voids at various scales, which is potentially necessary for the transcription and transport of substances inside the nucleus, whereas the volume fractal structure is due to the transcription activity of the cell.
Авторлар туралы
E. Yashina
Petersburg Nuclear Physics Institute, National Research Center Kurchatov Institute; St. Petersburg State University
Email: yashina_91@inbox.ru
188300, Gatchina, Leningrad region, Russia; 198504, St. Petersburg, Russia
E. Varfolomeeva
Petersburg Nuclear Physics Institute, National Research Center Kurchatov Institute
Email: yashina_91@inbox.ru
188300, Gatchina, Leningrad region, Russia
R. Pantina
Petersburg Nuclear Physics Institute, National Research Center Kurchatov Institute
Email: yashina_91@inbox.ru
188300, Gatchina, Leningrad region, Russia
V. Bayramukov
Petersburg Nuclear Physics Institute, National Research Center Kurchatov Institute
Email: yashina_91@inbox.ru
188300, Gatchina, Leningrad region, Russia
R. Kovalev
Petersburg Nuclear Physics Institute, National Research Center Kurchatov Institute
Email: yashina_91@inbox.ru
188300, Gatchina, Leningrad region, Russia
N. Fedorova
Petersburg Nuclear Physics Institute, National Research Center Kurchatov Institute
Email: yashina_91@inbox.ru
188300, Gatchina, Leningrad region, Russia
K. Pshenichnyy
Petersburg Nuclear Physics Institute, National Research Center Kurchatov Institute
Email: yashina_91@inbox.ru
188300, Gatchina, Leningrad region, Russia
Yu. Gorshkova
Joint Institute for Nuclear Research
Email: yashina_91@inbox.ru
141980, Dubna, Moscow region, Russia
S. Grigor'ev
Petersburg Nuclear Physics Institute, National Research Center Kurchatov Institute; St. Petersburg State University
Хат алмасуға жауапты Автор.
Email: yashina_91@inbox.ru
188300, Gatchina, Leningrad region, Russia; 198504, St. Petersburg, Russia
Әдебиет тізімі
- Ya. Joti, T. Hikima, Y. Nishino, F. Kamada, S. Hihara, H. Takata, T. Ishikawa, and K. Maeshima, Nucleus 3, 404 (2012).
- Y. Takizawa and H. Kurumizaka, Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1865, 194851 (2022).
- K. Maeshima, S. Ide, and M. Babokhov, Curr. Opin. Cell Biol. 58, 95 (2019).
- J.D. Halverson, J. Smrek, K. Kremer, and A.Y. Grosberg, Rep. Prog. Phys. 77(2), 022601 (2014).
- L.M. Almassalha, A. Tiwari, P.T. Ruhoff, Y. Stypula-Cyrus, L. Cherkezyan, H. Matsuda, M.A. Dela Cruz, J.E. Chandler, C. White, C. Maneval, H. Subramanian, I. Szleifer, H.K. Roy, and V. Backman, Sci. Rep. 7, 41061 (2017).
- E. Lieberman-Aiden, N. L. Van Berkum, L. Williams et al. (Collaboration), Science 326(5950), 289 (2009).
- L.A. Mirny, Chromosome research 19, 37 (2011).
- A.Y. Grosberg, S.K. Nechaev, and E. I. Shakhnovich, Journal de physique 49(12), 2095 (1988).
- A. Grosberg, Y. Rabin, S. Havlin, and A. Neer, Europhysics Letters 23(5), 373 (1993).
- J.D. Halverson, W.B. Lee, G. S. Grest, A.Y. Grosberg, and K. Kremer, J. Chem. Phys. 134(20), 204904 (2011).
- M.V. Imakaev, K.M. Tchourine, S.K. Nechaev, and L.A. Mirny, Soft matter 11(4), 665 (2015).
- Е. Г. Яшина, С. В. Григорьев, Поверхность. Рентгеновские, синхротронные и нейтронные исследования 9, 5 (2017).
- Е. Г. Яшина, С. В. Григорьев, ЖЭТФ 156(3), 540 (2019).
- D.V. Lebedev, M.V. Filatov, A. I. Kuklin, A.K. Islamov, E. Kentzinger, R. Pantina, B. P. Toperverg, and V.V. Isaev-Ivanov, FEBS Lett. 579(6), 1465 (2005).
- E.G. Iashina, E.V. Velichko, M.V. Filatov, W.G. Bouwman, C. P. Duif, A. Brulet, and S.V. Grigoriev, Phys. Rev. E 96(1), 012411 (2017).
- S.V. Grigoriev, E.G. Iashina, V.Yu. Bairamukov, V. Pipich, A. Radulescu, M.V. Filatov, R.A. Pantina, and E.Yu. Varfolomeeva, Phys. Rev. E 102, 032415 (2020).
- E.G. Iashina, M.V. Filatov, R.A. Pantina, E.Yu. Varfolomeeva, W.G. Bouwman, Ch.P. Duif, D. Honecker, V. Pipich, and S.V. Grigoriev, J. Appl. Cryst. 52, 844 (2019).
- S.V. Grigoriev, E.G. Iashina, B. Wu, V. Pipich, Ch. Lang, A. Radulescu, V.Yu. Bairamukov, M.V. Filatov, R.A. Pantina, and E.Yu. Varfolomeeva, Phys. Rev. E 104, 044404 (2021).
- E.G. Iashina, E.Yu. Varfolomeeva, R.A. Pantina, V.Yu. Bairamukov, R.A. Kovalev, N.D. Fedorova, V. Pipich, A. Radulescu, and S.V. Grigoriev, Phys. Rev. E 104, 064409 (2021).
- B. Mandelbrot, The Fractal Geometry of Nature, Freeman, N.Y. (1983).
- J. Feder, Fractals, Plenum, N.Y. (1998).
- A.V. Ilatovskiy, D.V. Lebedev, M.V. Filatov, M.G. Petukhov, and V.V. Isaev-Ivanov, J. Phys.: Conf. Ser. 351(1), 012007 (2012).
- S.V. Razin and I. I. Gromova, BioEssays 17(5), 443 (1995).
- T. Cremer, M. Cremer, B. Hubner, A. Silahtaroglu, M. Hendzel, C. Lanctˆot, and H. Strickfaden, BioEssays 42(2), 1900132 (2020).
- Y. Xing, C.V. Johnson, P.R. Dobner, and J. B. Lawrence, Science 259(5099), 1326 (1993).
- M. Mazzocca, T. Fillot, A. Loffreda, D. Gnani, and D. Mazza, Biochem. Soc. Trans. 49(3), 1121 (2021).
- M. Mazzocca, E. Colombo, A. Callegari, and D. Mazza, Current Opinion in Structural Biology 71, 239 (2021).
- P. Chatterjee, N. Goldenfeld, and S. Kim, Phys. Rev. Lett. 127(2)1, 218101 (2021).
- V.Yu. Bairamukov, M.V. Filatov, R.A. Kovalev, N.D. Fedorova, R.A. Pantina, A.V. Ankudinov, E.G. Iashina, S.V. Grigoriev, and E.Yu. Varfolomeeva, Biochim. Biophys. Acta Gen. Subj. 1866(12), 130234 (2022).
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