Genes encoding ribosomal RNA (rDNA) are essential for cell survival and are particularly sensitive to factors leading to genomic instability. Their repetitive character makes them prone to inappropriate recombinational events arising from collision of transcriptional and replication machineries, resulting in unstable rDNA copy numbers. In this review, we summarize current knowledge on the structure and organization of rDNA, its role in sensing changes in the genome, and its linkage to aging. We also review recent findings on the main factors involved in chromatin assembly and DNA repair in the maintenance of rDNA stability in the model plants Arabidopsis thaliana and the moss Physcomitrella patens, providing a view across the plant evolutionary tree.

• Klíčová slova
• CAF-1, RAD51, RTEL1, genome stability, rDNA organization, rRNA genes, ribosome,
• MeSH
• Arabidopsis genetika   MeSH
• DNA rostlinná genetika   MeSH
• genetická transkripce MeSH
• genová dávka MeSH
• lidé MeSH
• mechy genetika   MeSH
• nestabilita genomu MeSH
• oprava DNA * MeSH
• replikace DNA MeSH
• restrukturace chromatinu MeSH
• ribozomální DNA genetika   MeSH
• stárnutí genetika   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• DNA rostlinná MeSH
• ribozomální DNA MeSH

Understanding how the packaging of chromatin in the nucleus is regulated and organized to guide complex cellular and developmental programmes, as well as responses to environmental cues is a major question in biology. Technological advances have allowed remarkable progress within this field over the last years. However, we still know very little about how the 3D genome organization within the cell nucleus contributes to the regulation of gene expression. The nuclear space is compartmentalized in several domains such as the nucleolus, chromocentres, telomeres, protein bodies, and the nuclear periphery without the presence of a membrane around these domains. The role of these domains and their possible impact on nuclear activities is currently under intense investigation. In this review, we discuss new data from research in plants that clarify functional links between the organization of different nuclear domains and plant genome function with an emphasis on the potential of this organization for gene regulation.

• Klíčová slova
• 3D Chromatin organization, chromocentres, gene expression, liquid–liquid phase separation (LLPS), nuclear bodies, nuclear domains, nuclear periphery, nucleolus, telomeres, topologically associated domains (TADs),
• MeSH
• buněčné jadérko MeSH
• buněčné jádro * MeSH
• chromatin * MeSH
• regulace genové exprese MeSH
• rostliny genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Názvy látek
• chromatin * MeSH

Diverse stress insults trigger interactions of PML with nucleolus, however, the function of these PML nucleolar associations (PNAs) remains unclear. Here we show that during induction of DNA damage-induced senescence in human non-cancerous cells, PML accumulates at the nucleolar periphery simultaneously with inactivation of RNA polymerase I (RNAP I) and nucleolar segregation. Using time-lapse and high-resolution microscopy, we followed the genesis, structural transitions and destiny of PNAs to show that: 1) the dynamic structural changes of the PML-nucleolar interaction are tightly associated with inactivation and reactivation of RNAP I-mediated transcription, respectively; 2) the PML-nucleolar compartment develops sequentially under stress and, upon stress termination, it culminates in either of two fates: disappearance or persistence; 3) all PNAs stages can associate with DNA damage markers; 4) the persistent, commonly long-lasting PML multi-protein nucleolar structures (PML-NDS) associate with markers of DNA damage, indicating a role of PNAs in persistent DNA damage response characteristic for senescent cells. Given the emerging evidence implicating PML in homologous recombination-directed DNA repair, we propose that PNAs contribute to sequestration and faithful repair of the highly unstable ribosomal DNA repeats, a fundamental process to maintain a precise balance between DNA repair mechanisms, with implications for genomic integrity and aging.

• Klíčová slova
• DNA damage, nucleolar segregation, rDNA loci, super-resolution microscopy, time-lapse imaging,
• MeSH
• buněčné jadérko metabolismus   MeSH
• doxorubicin MeSH
• fyziologický stres MeSH
• kultivované buňky MeSH
• lidé MeSH
• poškození DNA * MeSH
• protein promyelocytické leukemie metabolismus   MeSH
• stárnutí buněk * MeSH
• zobrazování trojrozměrné MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• doxorubicin MeSH
• PML protein, human MeSH Prohlížeč
• protein promyelocytické leukemie MeSH

The biosynthesis of ribosomes is a complex process that requires the coordinated action of many factors and a huge energy investment from the cell. Ribosomes are essential for protein production, and thus for cellular survival, growth and proliferation. Ribosome biogenesis is initiated in the nucleolus and includes: the synthesis and processing of ribosomal RNAs, assembly of ribosomal proteins, transport to the cytoplasm and association of ribosomal subunits. The disruption of ribosome biogenesis at various steps, with either increased or decreased expression of different ribosomal components, can promote cell cycle arrest, senescence or apoptosis. Additionally, interference with ribosomal biogenesis is often associated with cancer, aging and age-related degenerative diseases. Here, we review current knowledge on impaired ribosome biogenesis, discuss the main factors involved in stress responses under such circumstances and focus on examples with clinical relevance.

• Klíčová slova
• aging, cancer, p53, ribosome biogenesis, ribosomopathy,
• MeSH
• biogeneze organel MeSH
• lidé MeSH
• nádory metabolismus   MeSH
• ribozomální proteiny metabolismus   MeSH
• ribozomy metabolismus   MeSH
• stárnutí metabolismus   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Názvy látek
• ribozomální proteiny MeSH

Repair of ribosomal DNA (rDNA) is a very important nuclear process due to the most active transcription of ribosomal genes. Proper repair of rDNA is required for physiological biogenesis of ribosomes. Here, we analyzed the epigenetics of the DNA damage response in a nucleolar compartment, thus in the ribosomal genes studied in nonirradiated and UVA-irradiated mouse embryonic fibroblasts (MEFs). We found that the promoter of ribosomal genes is not abundant on H4K20me2, but it is densely occupied by H4K20me3. Ribosomal genes, regulated via UBF1/2 proteins, were characterized by an interaction between UBF1/2 and H4K20me2/me3. This interaction was strengthened by UVA irradiation that additionally causes a focal accumulation of H4K20me3 in the nucleolus. No interaction has been found between UBF1/2 and H3K9me3. Interestingly, UVA irradiation decreases the levels of H3K9me3 and H4K20me3 at 28S rDNA. Altogether, the UVA light affects the epigenetic status of ribosomal genes at 28S rDNA and strengthens an interaction between UBF1/2 proteins and H4K20me2/me3.

• Klíčová slova
• DNA damage response, DNA repair, Nucleolus, UBF, UVA irradiation,
• MeSH
• buněčné jadérko metabolismus   MeSH
• buněčné jádro metabolismus   MeSH
• chromatinová imunoprecipitace MeSH
• DNA vazebné proteiny MeSH
• epigeneze genetická účinky záření   MeSH
• fluorescenční protilátková technika MeSH
• histony metabolismus   MeSH
• metylace MeSH
• myši MeSH
• promotorové oblasti (genetika) MeSH
• regulace genové exprese účinky záření   MeSH
• ribozomální DNA genetika   MeSH
• transkripční iniciační komplex Pol1 - proteiny metabolismus   MeSH
• ultrafialové záření * MeSH
• vazba proteinů MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• zvířata MeSH
• Check Tag
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA vazebné proteiny MeSH
• histony MeSH
• ribozomální DNA MeSH
• transcription factor UBF MeSH Prohlížeč
• transkripční iniciační komplex Pol1 - proteiny MeSH

Ribosome biogenesis is an energy consuming process which takes place mainly in the nucleolus. By producing ribosomes to fuel protein synthesis, it is tightly connected with cell growth and cell cycle control. Perturbation of ribosome biogenesis leads to the activation of p53 tumor suppressor protein promoting processes like cell cycle arrest, apoptosis or senescence. This ribosome biogenesis stress pathway activates p53 through sequestration of MDM2 by a subset of ribosomal proteins (RPs), thereby stabilizing p53. Here, we identify human HEATR1, as a nucleolar protein which positively regulates ribosomal RNA (rRNA) synthesis. Downregulation of HEATR1 resulted in cell cycle arrest in a manner dependent on p53. Moreover, depletion of HEATR1 also caused disruption of nucleolar structure and activated the ribosomal biogenesis stress pathway - RPL5 / RPL11 dependent stabilization and activation of p53. These findings reveal an important role for HEATR1 in ribosome biogenesis and further support the concept that perturbation of ribosome biosynthesis results in p53-dependent cell cycle checkpoint activation, with implications for human pathologies including cancer.

• Klíčová slova
• HEATR1, cancer, p53, ribosome biogenesis, ribosome biogenesis stress,
• MeSH
• biogeneze organel * MeSH
• fyziologický stres MeSH
• genetická transkripce * MeSH
• jaderné proteiny metabolismus   MeSH
• kontrolní body buněčného cyklu MeSH
• lidé MeSH
• nádorové buněčné linie MeSH
• nádorový supresorový protein p53 metabolismus   MeSH
• proliferace buněk MeSH
• proteiny vázající RNA metabolismus   MeSH
• protoonkogenní proteiny c-mdm2 metabolismus   MeSH
• ribozomální proteiny metabolismus   MeSH
• ribozomy metabolismus   MeSH
• RNA ribozomální biosyntéza   MeSH
• RNA-polymerasa I genetika   MeSH
• signální transdukce MeSH
• vedlejší histokompatibilní antigeny metabolismus   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• HEATR1 protein, human MeSH Prohlížeč
• jaderné proteiny MeSH
• MDM2 protein, human MeSH Prohlížeč
• nádorový supresorový protein p53 MeSH
• proteiny vázající RNA MeSH
• protoonkogenní proteiny c-mdm2 MeSH
• ribozomální proteiny MeSH
• RNA ribozomální MeSH
• RNA-polymerasa I MeSH
• vedlejší histokompatibilní antigeny MeSH

Cajal bodies (CBs) are important compartments containing accumulated proteins that preferentially regulate RNA-related nuclear events, including splicing. Here, we studied the nuclear distribution pattern of CBs in neurogenesis. In adult brains, coilin was present at a high density, but CB formation was absent in the nuclei of the choroid plexus of the lateral ventricles. Cells of the adult hippocampus were characterized by a crescent-like morphology of coilin protein. We additionally observed a 70 kDa splice variant of coilin in adult mouse brains, which was different to embryonic brains and mouse pluripotent embryonic stem cells (mESCs), characterized by the 80 kDa standard variant of coilin. Here, we also showed that depletion of coilin is induced during neural differentiation and HDAC1 deficiency in mESCs caused coilin accumulation inside the fibrillarin-positive region of the nucleoli. A similar distribution pattern was observed in adult brain hippocampi, characterized by lower levels of both coilin and HDAC1. In summary, we observed that neural differentiation and HDAC1 deficiency lead to coilin depletion and coilin accumulation in body-like structures inside the nucleoli.

• Publikační typ
• časopisecké články MeSH

DNA damage response (DDR) in ribosomal genes and mechanisms of DNA repair in embryonic stem cells (ESCs) are less explored nuclear events. DDR in ESCs should be unique due to their high proliferation rate, expression of pluripotency factors, and specific chromatin signature. Given short population doubling time and fast progress through G1 phase, ESCs require a sustained production of rRNA, which leads to the formation of large and prominent nucleoli. Although transcription of rRNA in the nucleolus is relatively well understood, little is known about DDR in this nuclear compartment. Here, we directed formation of double-strand breaks in rRNA genes with I- PpoI endonuclease, and we studied nucleolar morphology, DDR, and chromatin modifications. We observed a pronounced formation of I- PpoI-induced nucleolar caps, positive on BRCA1, NBS1, MDC1, γH2AX, and UBF1 proteins. We showed interaction of nucleolar protein TCOF1 with HDAC1 and TCOF1 with CARM1 after DNA injury. Moreover, H3R17me2a modification mediated by CARM1 was found in I- PpoI-induced nucleolar caps. Finally, we report that heterochromatin protein 1 is not involved in DNA repair of nucleolar caps.

• Klíčová slova
• CARM1, DNA repair, HDAC1, NBS1, PpoI, chromatin, nucleolus,
• MeSH
• acetylace MeSH
• arginin metabolismus   MeSH
• buněčné jadérko genetika   ultrastruktura   MeSH
• buněčné linie MeSH
• dvouřetězcové zlomy DNA * MeSH
• embryonální kmenové buňky metabolismus   ultrastruktura   MeSH
• fosfoproteiny metabolismus   MeSH
• geny rRNA MeSH
• histondeacetylasa 1 metabolismus   MeSH
• histony metabolismus   MeSH
• intracelulární signální peptidy a proteiny MeSH
• jaderné proteiny metabolismus   MeSH
• metylace MeSH
• myši MeSH
• oprava DNA MeSH
• proteinarginin-N-methyltransferasy metabolismus   MeSH
• RNA ribozomální genetika   metabolismus   MeSH
• zvířata MeSH
• Check Tag
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• arginin MeSH
• coactivator-associated arginine methyltransferase 1 MeSH Prohlížeč
• fosfoproteiny MeSH
• Hdac1 protein, mouse MeSH Prohlížeč
• histondeacetylasa 1 MeSH
• histony MeSH
• intracelulární signální peptidy a proteiny MeSH
• jaderné proteiny MeSH
• proteinarginin-N-methyltransferasy MeSH
• RNA ribozomální MeSH
• Tcof1 protein, mouse MeSH Prohlížeč

The nucleolus is the site of rRNA gene transcription, rRNA processing, and ribosome biogenesis. However, the nucleolus also plays additional roles in the cell. We isolated nucleoli using fluorescence-activated cell sorting (FACS) and identified nucleolus-associated chromatin domains (NADs) by deep sequencing, comparing wild-type plants and null mutants for the nucleolar protein NUCLEOLIN 1 (NUC1). NADs are primarily genomic regions with heterochromatic signatures and include transposable elements (TEs), sub-telomeric regions, and mostly inactive protein-coding genes. However, NADs also include active rRNA genes and the entire short arm of chromosome 4 adjacent to them. In nuc1 null mutants, which alter rRNA gene expression and overall nucleolar structure, NADs are altered, telomere association with the nucleolus is decreased, and telomeres become shorter. Collectively, our studies reveal roles for NUC1 and the nucleolus in the spatial organization of chromosomes as well as telomere maintenance.

• Klíčová slova
• heterochromatin, nuclear architecture, nucleolus, nucleolus-associated chromatin domains, telomere,
• MeSH
• Arabidopsis MeSH
• buněčné jadérko metabolismus   MeSH
• exprese genu * MeSH
• fosfoproteiny metabolismus   MeSH
• genetická transkripce genetika   MeSH
• genom rostlinný * MeSH
• heterochromatin genetika   metabolismus   MeSH
• nukleolin MeSH
• proteiny vázající RNA metabolismus   MeSH
• ribozomální DNA genetika   MeSH
• RNA ribozomální metabolismus   MeSH
• telomery metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• fosfoproteiny MeSH
• heterochromatin MeSH
• proteiny vázající RNA MeSH
• ribozomální DNA MeSH
• RNA ribozomální MeSH

The actin family members, consisting of actin and actin-related proteins (ARPs), are essential components of chromatin remodeling complexes. ARP6, one of the nuclear ARPs, is part of the Snf-2-related CREB-binding protein activator protein (SRCAP) chromatin remodeling complex, which promotes the deposition of the histone variant H2A.Z into the chromatin. In this study, we showed that ARP6 influences the structure and the function of the nucleolus. ARP6 is localized in the central region of the nucleolus, and its knockdown induced a morphological change in the nucleolus. We also found that in the presence of high concentrations of glucose ARP6 contributed to the maintenance of active ribosomal DNA (rDNA) transcription by placing H2A.Z into the chromatin. In contrast, under starvation, ARP6 was required for cell survival through the repression of rDNA transcription independently of H2A.Z. These findings reveal novel pleiotropic roles for the actin family in nuclear organization and metabolic homeostasis.

• Klíčová slova
• ARP6, Actin-related protein, Histone H2A.Z, Nucleolus, Wndchrm,
• MeSH
• adenosintrifosfatasy metabolismus   MeSH
• aktiny metabolismus   fyziologie   MeSH
• buněčné jadérko metabolismus   fyziologie   MeSH
• chromozomální proteiny, nehistonové metabolismus   fyziologie   MeSH
• genetická transkripce fyziologie   MeSH
• glukosa metabolismus   MeSH
• HeLa buňky MeSH
• lidé MeSH
• ribozomální DNA genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Intramural MeSH
• Názvy látek
• ACTR6 protein, human MeSH Prohlížeč
• adenosintrifosfatasy MeSH
• aktiny MeSH
• chromozomální proteiny, nehistonové MeSH
• glukosa MeSH
• ribozomální DNA MeSH
• SRCAP protein, human MeSH Prohlížeč