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Biochemistry (Moscow)

, Volume 83, Issue 4, pp 299–301 | Cite as

Structural-Functional Organization of the Eukaryotic Cell Nucleus and Transcription Regulation: Introduction to This Special Issue of Biochemistry (Moscow)

  • S. V. Razin
Article

Abstract

This issue of Biochemistry (Moscow) is devoted to the cell nucleus and mechanisms of transcription regulation. Over the years, biochemical processes in the cell nucleus have been studied in isolation, outside the context of their spatial organization. Now it is clear that segregation of functional processes within a compartmentalized cell nucleus is very important for the implementation of basic genetic processes. The functional compartmentalization of the cell nucleus is closely related to the spatial organization of the genome, which in turn plays a key role in the operation of epigenetic mechanisms. In this issue of Biochemistry (Moscow), we present a selection of review articles covering the functional architecture of the eukaryotic cell nucleus, the mechanisms of genome folding, the role of stochastic processes in establishing 3D architecture of the genome, and the impact of genome spatial organization on transcription regulation.

Keywords

chromatin cell nucleus spatial organization of the genome macromolecular crowding functional compartmentalization of the cell nucleus 3D genomics regulation of transcription 

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References

  1. 1.
    Razin, S. V., Gavrilov, A. A., Ioudinkova, E. S., and Iarovaia, O. V. (2013) Communication of genome regulatory elements in a folded chromosome, FEBS Lett., 587, 1840–1847.CrossRefPubMedGoogle Scholar
  2. 2.
    Cremer, T., Kurz, A., Zirbel, R., Dietzel, S., Rinke, B., Schrock, E., Speicher, M. R., Mathieu, U., Jauch, A., Emmerich, P., Scherthan, H., Ried, T., Cremer, C., and Lichter, P. (1993) Role of chromosome territories in the functional compartmentalization of the cell nucleus, Cold Spring Harb. Symp. Quant. Biol., 58, 777–792.CrossRefPubMedGoogle Scholar
  3. 3.
    Cremer, T., Cremer, M., and Cremer, C. (2018) 4D nucleome: genome compartmentalization in evolutionary context, Biochemistry (Moscow), 83, 313–325.CrossRefGoogle Scholar
  4. 4.
    Misteli, T. (2001) Protein dynamics: implications for nuclear architecture and gene expression, Science, 291, 843–847.CrossRefPubMedGoogle Scholar
  5. 5.
    Sleeman, J. E., and Trinkle-Mulcahy, L. (2014) Nuclear bodies: new insights into assembly/dynamics and disease relevance, Curr. Opin. Cell Biol., 28, 76–83.CrossRefPubMedGoogle Scholar
  6. 6.
    Hancock, R. (2004) A role for macromolecular crowdingeffects in the assembly and function of compartments in the nucleus, J. Struct. Biol., 146, 281–290.CrossRefPubMedGoogle Scholar
  7. 7.
    Hancock, R. (2018) Crowding, entropic forces, and confinement: crucial factors for structures and functions in the cell nucleus, Biochemistry (Moscow), 83, 326–337.Google Scholar
  8. 8.
    Shevelyov, Y. Y., and Ulianov, S. V. (2018) Role of nuclear lamina in gene repression and in maintenance of chromosome architecture in the nucleus, Biochemistry (Moscow), 83, 359–369.CrossRefGoogle Scholar
  9. 9.
    Sharakhov, I. V., Bondarenko, S. M., Artemov, G. N., and Onufriev, A. V. (2018) Role of chromosome–nuclear envelope attachments in 3D genome, Biochemistry (Moscow), 83, 350–358.CrossRefGoogle Scholar
  10. 10.
    De Wit, E., and De Laat, W. (2012) A decade of 3C technologies: insights into nuclear organization, Genes Dev., 26, 11–24.CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    De Laat, W., and Grosveld, F. (2003) Spatial organization of gene expression: the active chromatin hub, Chromosome Res., 11, 447–459.CrossRefPubMedGoogle Scholar
  12. 12.
    Razin, S. V., and Vassetzky, Y. S. (2017) 3D genomics imposes evolution of the domain model of eukaryotic genome organization, Chromosoma, 126, 59–69.CrossRefPubMedGoogle Scholar
  13. 13.
    Razin, S. V., and Gavrilov, A. A. (2018) Structural–functional domains of the eukaryotic genome, Biochemistry (Moscow), 83, 302–312.CrossRefGoogle Scholar
  14. 14.
    Kolesnikova, T. D. (2018) Banding pattern of polytene chromosomes as a reflection of the universal principles of chromatin organization into topological domains, Biochemistry (Moscow), 83, 338–349.CrossRefGoogle Scholar
  15. 15.
    Tchurikov, N. A., Kravatsky, Y. V., and Kretova, O. V. (2018) Link between hot spots of DSBs and mechanisms of transcriptional regulation: forum domains–50–250-kb chromosomal regions possessing coordinately expressed genes, Biochemistry (Moscow), 83, 437–449.CrossRefGoogle Scholar
  16. 16.
    Fishman, V. S., Salnikov, P. A., and Battulin, N. R. (2018) Interpreting chromosomal rearrangements in the context of 3-dimensional genome organization: a practical guide for medical genetics, Biochemistry (Moscow), 83, 393–401.CrossRefGoogle Scholar
  17. 17.
    Podgornaya, O. I., Ostromyshenskii, D. I., and Enukashvily, N. I. (2018) Who needs this garbage, or the dark matter of the genome, Biochemistry (Moscow), 83, 450–466.CrossRefGoogle Scholar
  18. 18.
    Iarovaia, O. V., Kovina, A. P., Petrova, N. V., Razin, S. V., Yudinkova, T. S., Vassetzky, Y. S., and Ulianov, S. V. (2018) Genetic and epigenetic mechanisms of β-globin gene switching, Biochemistry (Moscow), 83, 381–392.CrossRefGoogle Scholar
  19. 19.
    Sall, F. B., Germini, D., Kovina, A. P., Ribrag, V., Wiels, J., Toure, A. O., Iarovaia, O. V., Lipinski, M., and Vassetzky, Y. S. (2018) Effect of environmental factors on nuclear organization and transformation of human B lymphocytes, Biochemistry (Moscow), 83, 402–410.CrossRefGoogle Scholar
  20. 20.
    Moor, N. A., and Lavrik, O. I. (2018) Protein–protein interactions in DNA base excision repair, Biochemistry (Moscow), 83, 411–422.CrossRefGoogle Scholar
  21. 21.
    Putlyaev, E. V., Ibragimov, A. N., Lebedeva, L. A., Georgiev, P. G., and Shidlovskii, Y. V. (2018) Structure and functions of mediator complex, Biochemistry (Moscow), 83, 423–436.CrossRefGoogle Scholar
  22. 22.
    Sverdlov, E. D. (2018) Unsolvable problems of biology: it is impossible to create two identical organisms, to defeat cancer, and to map organisms onto their genomes, Biochemistry (Moscow), 83, 370–380.Google Scholar

Copyright information

© Pleiades Publishing, Ltd. 2018

Authors and Affiliations

  1. 1.Institute of Gene BiologyRussian Academy of SciencesMoscowRussia
  2. 2.Lomonosov Moscow State UniversityBiological FacultyMoscowRussia

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