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Article

Dynamics of Whole-Genome Contacts of Nucleoli in Drosophila Cells Suggests a Role for rDNA Genes in Global Epigenetic Regulation

by
Nickolai A. Tchurikov
*,
Elena S. Klushevskaya
,
Daria M. Fedoseeva
,
Ildar R. Alembekov
,
Galina I. Kravatskaya
,
Vladimir R. Chechetkin
,
Yuri V. Kravatsky
and
Olga V. Kretova
Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia
*
Author to whom correspondence should be addressed.
Cells 2020, 9(12), 2587; https://doi.org/10.3390/cells9122587
Submission received: 17 November 2020 / Revised: 27 November 2020 / Accepted: 30 November 2020 / Published: 3 December 2020
(This article belongs to the Section Cell Nuclei: Function, Transport and Receptors)
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Abstract

Chromosomes are organized into 3D structures that are important for the regulation of gene expression and differentiation. Important role in formation of inter-chromosome contacts play rDNA clusters that make up nucleoli. In the course of differentiation, heterochromatization of rDNA units in mouse cells is coupled with the repression or activation of different genes. Furthermore, the nucleoli of human cells shape the direct contacts with genes that are involved in differentiation and cancer. Here, we identified and categorized the genes located in the regions where rDNA clusters make frequent contacts. Using a 4C approach, we demonstrate that in Drosophila S2 cells, rDNA clusters form contacts with genes that are involved in chromosome organization and differentiation. Heat shock treatment induces changes in the contacts between nucleoli and hundreds of genes controlling morphogenesis. We show that nucleoli form contacts with regions that are enriched with active or repressive histone marks and where small non-coding RNAs are mapped. These data indicate that rDNA contacts are involved in the repression and activation of gene expression and that rDNA clusters orchestrate large groups of Drosophila genes involved in differentiation.
Keywords: rDNA clusters; 4C; gene ontology; chromatin marks; epigenetics; development; differentiation; heat shock rDNA clusters; 4C; gene ontology; chromatin marks; epigenetics; development; differentiation; heat shock

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MDPI and ACS Style

Tchurikov, N.A.; Klushevskaya, E.S.; Fedoseeva, D.M.; Alembekov, I.R.; Kravatskaya, G.I.; Chechetkin, V.R.; Kravatsky, Y.V.; Kretova, O.V. Dynamics of Whole-Genome Contacts of Nucleoli in Drosophila Cells Suggests a Role for rDNA Genes in Global Epigenetic Regulation. Cells 2020, 9, 2587. https://doi.org/10.3390/cells9122587

AMA Style

Tchurikov NA, Klushevskaya ES, Fedoseeva DM, Alembekov IR, Kravatskaya GI, Chechetkin VR, Kravatsky YV, Kretova OV. Dynamics of Whole-Genome Contacts of Nucleoli in Drosophila Cells Suggests a Role for rDNA Genes in Global Epigenetic Regulation. Cells. 2020; 9(12):2587. https://doi.org/10.3390/cells9122587

Chicago/Turabian Style

Tchurikov, Nickolai A., Elena S. Klushevskaya, Daria M. Fedoseeva, Ildar R. Alembekov, Galina I. Kravatskaya, Vladimir R. Chechetkin, Yuri V. Kravatsky, and Olga V. Kretova. 2020. "Dynamics of Whole-Genome Contacts of Nucleoli in Drosophila Cells Suggests a Role for rDNA Genes in Global Epigenetic Regulation" Cells 9, no. 12: 2587. https://doi.org/10.3390/cells9122587

APA Style

Tchurikov, N. A., Klushevskaya, E. S., Fedoseeva, D. M., Alembekov, I. R., Kravatskaya, G. I., Chechetkin, V. R., Kravatsky, Y. V., & Kretova, O. V. (2020). Dynamics of Whole-Genome Contacts of Nucleoli in Drosophila Cells Suggests a Role for rDNA Genes in Global Epigenetic Regulation. Cells, 9(12), 2587. https://doi.org/10.3390/cells9122587

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