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.

• Klíčová slova
• database pattern analysis, dynamic genome organization, epigenetic interactions, fluorescence microscopy, gene activity oscillations, heterochromatin and self-organization, nucleotide k-mers, organizational and functional networks, topological genome analysis, transposon-effected regulation,
• MeSH
• buněčná diferenciace genetika   MeSH
• buněčné jádro * metabolismus   MeSH
• genom * MeSH
• Publikační typ
• kongresy MeSH
• přehledy MeSH

Methylation of histones H4 at lysine 20 position (H4K20me), which is functional in DNA repair, represents a binding site for the 53BP1 protein. Here, we show a radiation-induced increase in the level of H4K20me3 while the levels of H4K20me1 and H4K20me2 remained intact. H4K20me3 was significantly pronounced at DNA lesions in only the G1 phase of the cycle, while this histone mark was reduced in very late S and G2 phases when PCNA was recruited to locally micro-irradiated chromatin. H4K20me3 was diminished in locally irradiated Suv39h1/h2 double knockout (dn) fibroblasts, and the same phenomenon was observed for H3K9me3 and its binding partner, the HP1β protein. Immunoprecipitation showed the existence of an interaction between H3K9me3-53BP1 and H4K20me3-53BP1; however, HP1β did not interact with 53BP1. Together, H3K9me3 and H4K20me3 represent epigenetic markers that are important for the function of the 53BP1 protein in non-homologous end joining (NHEJ) repair. The very late S phase represents the cell cycle breakpoint when a DDR function of the H4K20me3-53BP1 complex is abrogated due to recruitment of the PCNA protein and other DNA repair factors of homologous recombination to DNA lesions.

• Klíčová slova
• DNA damage, H3K9me3, H4K20me1/me2/me3, Suv39h1/h2, epigenetics,
• MeSH
• 53BP1 genetika   metabolismus   MeSH
• buněčné jádro genetika   metabolismus   účinky záření   MeSH
• buněčné linie MeSH
• buněčný cyklus MeSH
• chromozomální proteiny, nehistonové metabolismus   MeSH
• epigeneze genetická * účinky záření   MeSH
• histony metabolismus   MeSH
• homolog proteinu s chromoboxem 5 MeSH
• lidé MeSH
• metylace DNA * účinky záření   MeSH
• metylace MeSH
• myši MeSH
• oprava DNA spojením konců * MeSH
• poškození DNA * MeSH
• proliferační antigen buněčného jádra metabolismus   MeSH
• restrukturace chromatinu MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• 53BP1 MeSH
• CBX1 protein, human MeSH Prohlížeč
• Cbx1 protein, mouse MeSH Prohlížeč
• chromozomální proteiny, nehistonové MeSH
• histony MeSH
• homolog proteinu s chromoboxem 5 MeSH
• PCNA protein, human MeSH Prohlížeč
• proliferační antigen buněčného jádra MeSH
• TP53BP1 protein, human MeSH Prohlížeč
• Trp53bp1 protein, mouse MeSH Prohlížeč

The nucleolus is a well-organized site of ribosomal gene transcription. Moreover, many DNA repair pathway proteins, including ATM, ATR kinases, MRE11, PARP1 and Ku70/80, localize to the nucleolus (Moore et al., 2011 ). We analyzed the consequences of DNA damage in nucleoli following ultraviolet A (UVA), C (UVC), or γ-irradiation in order to test whether and how radiation-mediated genome injury affects local motion and morphology of nucleoli. Because exposure to radiation sources can induce changes in the pattern of UBF1-positive nucleolar regions, we visualized nucleoli in living cells by GFP-UBF1 expression for subsequent morphological analyses and local motion studies. UVA radiation, but not 5 Gy of γ-rays, induced apoptosis as analyzed by an advanced computational method. In non-apoptotic cells, we observed that γ-radiation caused nucleolar re-positioning over time and changed several morphological parameters, including the size of the nucleolus and the area of individual UBF1-positive foci. Radiation-induced nucleoli re-arrangement was observed particularly in G2 phase of the cell cycle, indicating repair of ribosomal genes in G2 phase and implying that nucleoli are less stable, thus sensitive to radiation, in G2 phase.

• Klíčová slova
• DNA damage, UBF1, live cells, nucleolus, nuncleoli tracking,
• MeSH
• apoptóza účinky záření   MeSH
• buněčné jadérko účinky záření   MeSH
• buněčné linie MeSH
• buněčný cyklus účinky záření   MeSH
• G2 fáze účinky záření   MeSH
• genetická transkripce MeSH
• myši MeSH
• nádorové buněčné linie MeSH
• poškození DNA účinky záření   MeSH
• transkripční iniciační komplex Pol1 - proteiny genetika   metabolismus   MeSH
• ultrafialové záření MeSH
• výpočetní biologie MeSH
• záření gama škodlivé účinky   MeSH
• zvířata MeSH
• Check Tag
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• transcription factor UBF MeSH Prohlížeč
• transkripční iniciační komplex Pol1 - proteiny MeSH

BACKGROUND: Oct4 is a specific marker of embryonic stem cell (ESC) pluripotency. However, little is known regarding how Oct4 responds to DNA damage. Here, we investigated whether Oct4 recognizes damaged chromatin in mouse ESCs stably expressing GFP-Oct4. These experiments should contribute to the knowledge of how ESC genomic integrity is maintained, which is crucial for potential application of human ESCs in regenerative medicine. METHODOLOGY/PRINCIPAL FINDINGS: We used time-lapse confocal microscopy, microirradiation by UV laser (355 nm), induction of DNA lesions by specific agents, and GFP technology to study the Oct4 response to DNA damage. We found that Oct4 accumulates in UV-damaged regions immediately after irradiation in an adenosine triphosphate-dependent manner. Intriguingly, this event was not accompanied by pronounced Nanog and c-MYC recruitment to the UV-damaged sites. The accumulation of Oct4 to UV-damaged chromatin occurred simultaneously with H3K9 deacetylation and H2AX phosphorylation (γH2AX). Moreover, we observed an ESC-specific nuclear distribution of γH2AX after interference to cellular processes, including histone acetylation, transcription, and cell metabolism. Inhibition of histone deacetylases mostly prevented pronounced Oct4 accumulation at UV-irradiated chromatin. CONCLUSIONS/SIGNIFICANCE: Our studies demonstrate pluripotency-specific events that accompany DNA damage responses. Here, we discuss how ESCs might respond to DNA damage caused by genotoxic injury that might lead to unwanted genomic instability.

• MeSH
• 53BP1 MeSH
• adenosintrifosfát metabolismus   MeSH
• buněčné jádro metabolismus   MeSH
• chromatin metabolismus   MeSH
• chromozomální proteiny, nehistonové metabolismus   MeSH
• DNA vazebné proteiny metabolismus   MeSH
• embryonální kmenové buňky cytologie   MeSH
• fibroblasty metabolismus   MeSH
• fosforylace MeSH
• genetická transkripce MeSH
• histony chemie   MeSH
• kinetika MeSH
• myši MeSH
• oktamerní transkripční faktor 3 metabolismus   MeSH
• poškození DNA MeSH
• regenerativní lékařství metody   MeSH
• regulace genové exprese * MeSH
• ultrafialové záření MeSH
• zvířata MeSH
• Check Tag
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• 53BP1 MeSH
• adenosintrifosfát MeSH
• chromatin MeSH
• chromozomální proteiny, nehistonové MeSH
• DNA vazebné proteiny MeSH
• histony MeSH
• oktamerní transkripční faktor 3 MeSH
• Pou5f1 protein, mouse MeSH Prohlížeč
• Trp53bp1 protein, mouse MeSH Prohlížeč

Higher-order compartments of nuclear chromatin have been defined according to the replication timing, transcriptional activity, and information content (Ferreira et al. 1997, Sadoni et al. 1999). The results presented in this work contribute to this model of nuclear organization. Using different human blood cells, nuclear positioning of genes, centromeres, and whole chromosomes was investigated. Genes are located mostly in the interior of cell nuclei; centromeres are located near the nuclear periphery in agreement with the definition of the higher-order compartments. Genetic loci are found in specific subregions of cell nuclei which form distinct layers at defined centre-of-nucleus to locus distances. Inside these layers, the genetic loci are distributed randomly. Some chromosomes are polarized with genes located in the inner parts of the nucleus and centromere located on the nuclear periphery; polar organization was not found for some other chromosomes. The internal structure of the higher-order compartments as well as the polar and non-polar organization of chromosomes are basically conserved in different cell types and at various stages of the cell cycle. Some features of the nuclear structure are conserved even in differentiated cells and during cellular repair after irradiation, although shifted positioning of genetic loci was systematically observed during these processes.

• MeSH
• buněčné jádro genetika   účinky záření   ultrastruktura   MeSH
• buněčný cyklus MeSH
• buňky kostní dřeně účinky záření   ultrastruktura   MeSH
• centromera účinky záření   MeSH
• geny účinky záření   MeSH
• HL-60 buňky MeSH
• hybridizace in situ fluorescenční MeSH
• interfáze MeSH
• kompartmentace buňky MeSH
• leukopoéza MeSH
• lidé MeSH
• lidské chromozomy účinky záření   MeSH
• lymfocyty cytologie   účinky záření   ultrastruktura   MeSH
• U937 buňky MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH