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Chen Z, Wang X, Gao X, Arslanovic N, Chen K, Tyler J. Transcriptional inhibition after irradiation occurs preferentially at highly expressed genes in a manner dependent on cell cycle progression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.20.567799. [PMID: 38045243 PMCID: PMC10690177 DOI: 10.1101/2023.11.20.567799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
In response to DNA double strand damage, ongoing transcription is inhibited to facilitate accurate DNA repair while transcriptional recovery occurs after DNA repair is complete. However, the mechanisms at play and identity of the transcripts being regulated in this manner are unclear. In contrast to the situation following UV damage, we found that transcriptional recovery after ionizing radiation (IR) occurs in a manner independent of the HIRA histone chaperone. Sequencing of the nascent transcripts identified a programmed transcriptional response, where certain transcripts and pathways are rapidly downregulated after IR, while other transcripts and pathways are upregulated. Specifically, most of the loss of nascent transcripts occurring after IR is due to inhibition of transcriptional initiation of the highly transcribed histone genes and the rDNA. To identify factors responsible for transcriptional inhibition after IR in an unbiased manner, we performed a whole genome gRNA library CRISPR / Cas9 screen. Many of the top hits in our screen were factors required for protein neddylation. However, at short times after inhibition of neddylation, transcriptional inhibition still occurred after IR, even though neddylation was effectively inhibited. Persistent inhibition of neddylation blocked transcriptional inhibition after IR, and it also leads to cell cycle arrest. Indeed, we uncovered that many inhibitors and conditions that lead to cell cycle arrest in G 1 or G 2 phase also prevent transcriptional inhibition after IR. As such, it appears that transcriptional inhibition after IR occurs preferentially at highly expressed genes in cycling cells.
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2
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Boukoura S, Larsen DH. Nucleolar organization and ribosomal DNA stability in response to DNA damage. Curr Opin Cell Biol 2024; 89:102380. [PMID: 38861757 DOI: 10.1016/j.ceb.2024.102380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 06/13/2024]
Abstract
Eukaryotic nuclei are structured into sub-compartments orchestrating various cellular functions. The nucleolus is the largest nuclear organelle: a biomolecular condensate with an architecture composed of immiscible fluids facilitating ribosome biogenesis. The nucleolus forms upon the transcription of the repetitive ribosomal RNA genes (rDNA) that cluster in this compartment. rDNA is intrinsically unstable and prone to rearrangements and copy number variation. Upon DNA damage, a specialized nucleolar-DNA Damage Response (n-DDR) is activated: nucleolar transcription is inhibited, the architecture is rearranged, and rDNA is relocated to the nucleolar periphery. Recent data have highlighted how the composition of nucleoli, its structure, chemical and physical properties, contribute to rDNA stability. In this mini-review we focus on recent data that start to reveal how nucleolar composition and the n-DDR work together to ensure rDNA integrity.
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Affiliation(s)
- Stavroula Boukoura
- Nucleolar Stress and Disease Group, Danish Cancer Institute, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Dorthe Helena Larsen
- Nucleolar Stress and Disease Group, Danish Cancer Institute, Strandboulevarden 49, 2100 Copenhagen, Denmark.
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3
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Xin D, Gai X, Ma Y, Li Z, Li Q, Yu X. Pre-rRNA Facilitates TopBP1-Mediated DNA Double-Strand Break Response. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206931. [PMID: 37582658 PMCID: PMC10558638 DOI: 10.1002/advs.202206931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 06/28/2023] [Indexed: 08/17/2023]
Abstract
In response to genotoxic stress-induced DNA damage, TopBP1 mediates ATR activation for signaling transduction and DNA damage repair. However, the detailed molecular mechanism remains elusive. Here, using unbiased protein affinity purification and RNA sequencing, it is found that TopBP1 is associated with pre-ribosomal RNA (pre-rRNA). Pre-rRNA co-localized with TopBP1 at DNA double-strand breaks (DSBs). Similar to pre-rRNA, ribosomal proteins also colocalize with TopBP1 at DSBs. The recruitment of TopBP1 to DSBs is suppressed when cells are transiently treated with RNA polymerase I inhibitor (Pol I-i) to suppress pre-rRNA biogenesis but not protein translation. Moreover, the BRCT4-5 of TopBP1 recognizes pre-rRNA and forms liquid-liquid phase separation (LLPS) with pre-rRNA, which may be the molecular basis of DSB-induced foci of TopBP1. Finally, Pol I-i treatment impairs TopBP1-associated cell cycle checkpoint activation and homologous recombination repair. Collectively, this study reveals that pre-rRNA plays a key role in the TopBP1-dependent DNA damage response.
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Affiliation(s)
- Di Xin
- School of Life SciencesWestlake UniversityHangzhouZhejiang310024China
- Department of Hepatobiliary and Pancreatic Surgery and Zhejiang Provincial Key Laboratory of Pancreatic DiseaseThe First Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310003China
- Westlake Laboratory of Life Sciences and BiomedicineHangzhouZhejiang310024China
- Institute of Basic Medical SciencesWestlake Institute for Advanced StudyHangzhouZhejiang310024China
| | - Xiaochen Gai
- School of Life SciencesWestlake UniversityHangzhouZhejiang310024China
- Westlake Laboratory of Life Sciences and BiomedicineHangzhouZhejiang310024China
- Institute of Basic Medical SciencesWestlake Institute for Advanced StudyHangzhouZhejiang310024China
| | - Yidi Ma
- School of Life SciencesWestlake UniversityHangzhouZhejiang310024China
- Westlake Laboratory of Life Sciences and BiomedicineHangzhouZhejiang310024China
- Institute of Basic Medical SciencesWestlake Institute for Advanced StudyHangzhouZhejiang310024China
| | - Zexing Li
- School of Life SciencesTianjin UniversityTianjin300072China
| | - Qilin Li
- School of Life SciencesWestlake UniversityHangzhouZhejiang310024China
- Westlake Laboratory of Life Sciences and BiomedicineHangzhouZhejiang310024China
- Institute of Basic Medical SciencesWestlake Institute for Advanced StudyHangzhouZhejiang310024China
| | - Xiaochun Yu
- School of Life SciencesWestlake UniversityHangzhouZhejiang310024China
- Westlake Laboratory of Life Sciences and BiomedicineHangzhouZhejiang310024China
- Institute of Basic Medical SciencesWestlake Institute for Advanced StudyHangzhouZhejiang310024China
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4
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Li J, Yan S. Molecular mechanisms of nucleolar DNA damage checkpoint response. Trends Cell Biol 2023; 33:361-364. [PMID: 36933998 PMCID: PMC10215988 DOI: 10.1016/j.tcb.2023.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 03/18/2023]
Abstract
Ribosomal DNA (rDNA) is transcribed into RNA in the nucleolus and is often challenged by different stress conditions. However, the underlying mechanisms of nucleolar DNA damage response (DDR) pathways remain elusive. Here, we provide distinct perspectives on how nucleolar DDR checkpoint pathways are activated by different stresses or by liquid-liquid phase separation (LLPS).
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Affiliation(s)
- Jia Li
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Shan Yan
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; School of Data Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
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5
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Fukumoto Y, Ikeuchi M, Nakayama Y, Ogra Y. Rad17 Translocates to Nucleolus upon UV Irradiation through Nucleolar Localization Signal in the Central Basic Domain. Int J Mol Sci 2022; 23:ijms232012300. [PMID: 36293155 PMCID: PMC9603387 DOI: 10.3390/ijms232012300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/08/2022] [Accepted: 10/12/2022] [Indexed: 11/04/2022] Open
Abstract
The nucleolus is a non-membranous structure in the nucleus and forms around ribosomal DNA repeats. It plays a major role in ribosomal biogenesis through the transcription of ribosomal DNA and regulates mRNA translation in response to cellular stress including DNA damage. Rad17 is one of the proteins that initiate and maintain the activation of the ATR pathway, one of the major DNA damage checkpoints. We have recently reported that the central basic domain of Rad17 contains a nuclear localization signal and that the nuclear translocation of Rad17 promotes its proteasomal degradation. Here, we show that the central basic domain contains the nucleolar localization signal as well as the nuclear localization signal. The nucleolar localization signal overlaps with the nuclear localization signal and is capable of transporting an exogenous protein into the nucleolus. Phosphomimetic mutations of the central basic domain inhibit nucleolar accumulation, suggesting that the post-translational modification sites regulate the nucleolar localization. Nucleolar accumulation of Rad17 is promoted by proteasome inhibition and UV irradiation. Our data show the nucleolar localization of Rad17 and suggest a possible role of Rad17 in the nucleolus upon UV irradiation.
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Affiliation(s)
- Yasunori Fukumoto
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
- Correspondence: ; Tel./Fax: +81-43-226-2945
| | - Masayoshi Ikeuchi
- Department of Biochemistry & Molecular Biology, Kyoto Pharmaceutical University, Kyoto 607-8414, Japan
| | - Yuji Nakayama
- Department of Biochemistry & Molecular Biology, Kyoto Pharmaceutical University, Kyoto 607-8414, Japan
| | - Yasumitsu Ogra
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
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6
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Li J, Zhao H, McMahon A, Yan S. APE1 assembles biomolecular condensates to promote the ATR-Chk1 DNA damage response in nucleolus. Nucleic Acids Res 2022; 50:10503-10525. [PMID: 36200829 PMCID: PMC9561277 DOI: 10.1093/nar/gkac853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 09/14/2022] [Accepted: 10/03/2022] [Indexed: 11/13/2022] Open
Abstract
Multifunctional protein APE1/APEX1/HAP1/Ref-1 (designated as APE1) plays important roles in nuclease-mediated DNA repair and redox regulation in transcription. However, it is unclear how APE1 regulates the DNA damage response (DDR) pathways. Here we show that siRNA-mediated APE1-knockdown or APE1 inhibitor treatment attenuates the ATR–Chk1 DDR under stress conditions in multiple immortalized cell lines. Congruently, APE1 overexpression (APE1-OE) activates the ATR DDR under unperturbed conditions, which is independent of APE1 nuclease and redox functions. Structural and functional analysis reveals a direct requirement of the extreme N-terminal motif within APE1 in the assembly of distinct biomolecular condensates in vitro and DNA/RNA-independent activation of the ATR DDR. Overexpressed APE1 co-localizes with nucleolar NPM1 and assembles biomolecular condensates in nucleoli in cancer but not non-malignant cells, which recruits ATR and activator molecules TopBP1 and ETAA1. APE1 protein can directly activate ATR to phosphorylate its substrate Chk1 in in vitro kinase assays. W119R mutant of APE1 is deficient in nucleolar condensation, and is incapable of activating nucleolar ATR DDR in cells and ATR kinase in vitro. APE1-OE-induced nucleolar ATR DDR activation leads to compromised ribosomal RNA transcription and reduced cell viability. Taken together, we propose distinct mechanisms by which APE1 regulates ATR DDR pathways.
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Affiliation(s)
- Jia Li
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Haichao Zhao
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Anne McMahon
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Shan Yan
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.,School of Data Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.,Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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7
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De Marco Zompit M, Esteban MT, Mooser C, Adam S, Rossi SE, Jeanrenaud A, Leimbacher PA, Fink D, Shorrocks AMK, Blackford AN, Durocher D, Stucki M. The CIP2A-TOPBP1 complex safeguards chromosomal stability during mitosis. Nat Commun 2022; 13:4143. [PMID: 35842428 PMCID: PMC9288427 DOI: 10.1038/s41467-022-31865-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 07/06/2022] [Indexed: 12/29/2022] Open
Abstract
The accurate repair of DNA double-strand breaks (DSBs), highly toxic DNA lesions, is crucial for genome integrity and is tightly regulated during the cell cycle. In mitosis, cells inactivate DSB repair in favor of a tethering mechanism that stabilizes broken chromosomes until they are repaired in the subsequent cell cycle phases. How this is achieved mechanistically is not yet understood, but the adaptor protein TOPBP1 is critically implicated in this process. Here, we identify CIP2A as a TOPBP1-interacting protein that regulates TOPBP1 localization specifically in mitosis. Cells lacking CIP2A display increased radio-sensitivity, micronuclei formation and chromosomal instability. CIP2A is actively exported from the cell nucleus in interphase but, upon nuclear envelope breakdown at the onset of mitosis, gains access to chromatin where it forms a complex with MDC1 and TOPBP1 to promote TOPBP1 recruitment to sites of mitotic DSBs. Collectively, our data uncover CIP2A-TOPBP1 as a mitosis-specific genome maintenance complex.
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Affiliation(s)
- Mara De Marco Zompit
- Department of Gynecology, University of Zurich and University Hospital Zurich, Schlieren, Switzerland
| | - Mònica Torres Esteban
- Department of Gynecology, University of Zurich and University Hospital Zurich, Schlieren, Switzerland
| | - Clémence Mooser
- Department of Gynecology, University of Zurich and University Hospital Zurich, Schlieren, Switzerland
| | - Salomé Adam
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Silvia Emma Rossi
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Alain Jeanrenaud
- Department of Gynecology, University of Zurich and University Hospital Zurich, Schlieren, Switzerland
| | - Pia-Amata Leimbacher
- Department of Gynecology, University of Zurich and University Hospital Zurich, Schlieren, Switzerland
| | - Daniel Fink
- Department of Gynecology, University of Zurich and University Hospital Zurich, Schlieren, Switzerland
| | - Ann-Marie K Shorrocks
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Andrew N Blackford
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Manuel Stucki
- Department of Gynecology, University of Zurich and University Hospital Zurich, Schlieren, Switzerland.
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8
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A PARylation-phosphorylation cascade promotes TOPBP1 loading and RPA-RAD51 exchange in homologous recombination. Mol Cell 2022; 82:2571-2587.e9. [PMID: 35597237 DOI: 10.1016/j.molcel.2022.04.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 02/14/2022] [Accepted: 04/22/2022] [Indexed: 01/30/2023]
Abstract
The efficiency of homologous recombination (HR) in the repair of DNA double-strand breaks (DSBs) is closely associated with genome stability and tumor response to chemotherapy. While many factors have been functionally characterized in HR, such as TOPBP1, their precise regulation remains unclear. Here, we report that TOPBP1 interacts with the RNA-binding protein HTATSF1 in a cell-cycle- and phosphorylation-dependent manner. Mechanistically, CK2 phosphorylates HTATSF1 to facilitate binding to TOPBP1, which promotes S-phase-specific TOPBP1 recruitment to damaged chromatin and subsequent RPA/RAD51-dependent HR, genome integrity, and cancer-cell viability. The localization of HTATSF1-TOPBP1 to DSBs is potentially independent of the transcription-coupled RNA-binding and processing capacity of HTATSF1 but rather relies on the recognition of poly(ADP-ribosyl)ated RPA by HTATSF1, which can be blunted with PARP inhibitors. Together, our study provides a mechanistic insight into TOPBP1 loading at HR-prone DSB sites via HTATSF1 and reveals how RPA-RAD51 exchange is tuned by a PARylation-phosphorylation cascade.
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9
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Gál Z, Nieto B, Boukoura S, Rasmussen AV, Larsen DH. Treacle Sticks the Nucleolar Responses to DNA Damage Together. Front Cell Dev Biol 2022; 10:892006. [PMID: 35646927 PMCID: PMC9133508 DOI: 10.3389/fcell.2022.892006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/21/2022] [Indexed: 01/05/2023] Open
Abstract
The importance of chromatin environment for DNA repair has gained increasing recognition in recent years. The nucleolus is the largest sub-compartment within the nucleus: it has distinct biophysical properties, selective protein retention, and houses the specialized ribosomal RNA genes (collectively referred to as rDNA) with a unique chromatin composition. These genes have high transcriptional activity and a repetitive nature, making them susceptible to DNA damage and resulting in the highest frequency of rearrangements across the genome. A distinct DNA damage response (DDR) secures the fidelity of this genomic region, the so-called nucleolar DDR (n-DDR). The composition of the n-DDR reflects the characteristics of nucleolar chromatin with the nucleolar protein Treacle (also referred to as TCOF1) as a central coordinator retaining several well-characterized DDR proteins in the nucleolus. In this review, we bring together data on the structure of Treacle, its known functions in ribosome biogenesis, and its involvement in multiple branches of the n-DDR to discuss their interconnection. Furthermore, we discuss how the functions of Treacle in ribosome biogenesis and in the n-DDR may contribute to Treacher Collins Syndrome, a disease caused by mutations in Treacle. Finally, we outline outstanding questions that need to be addressed for a more comprehensive understanding of Treacle, the n-DDR, and the coordination of ribosome biogenesis and DNA repair.
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10
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p53 at the crossroad of DNA replication and ribosome biogenesis stress pathways. Cell Death Differ 2022; 29:972-982. [PMID: 35444234 PMCID: PMC9090812 DOI: 10.1038/s41418-022-00999-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 01/05/2023] Open
Abstract
Despite several decades of intense research focused on understanding function(s) and disease-associated malfunction of p53, there is no sign of any “mid-life crisis” in this rapidly advancing area of biomedicine. Firmly established as the hub of cellular stress responses and tumor suppressor targeted in most malignancies, p53’s many talents continue to surprise us, providing not only fresh insights into cell and organismal biology, but also new avenues to cancer treatment. Among the most fruitful lines of p53 research in recent years have been the discoveries revealing the multifaceted roles of p53-centered pathways in the fundamental processes of DNA replication and ribosome biogenesis (RiBi), along with cellular responses to replication and RiBi stresses, two intertwined areas of cell (patho)physiology that we discuss in this review. Here, we first provide concise introductory notes on the canonical roles of p53, the key interacting proteins, downstream targets and post-translational modifications involved in p53 regulation. We then highlight the emerging involvement of p53 as a key component of the DNA replication Fork Speed Regulatory Network and the mechanistic links of p53 with cellular checkpoint responses to replication stress (RS), the driving force of cancer-associated genomic instability. Next, the tantalizing, yet still rather foggy functional crosstalk between replication and RiBi (nucleolar) stresses is considered, followed by the more defined involvement of p53-mediated monitoring of the multistep process of RiBi, including the latest updates on the RPL5/RPL11/5 S rRNA-MDM2-p53-mediated Impaired Ribosome Biogenesis Checkpoint (IRBC) pathway and its involvement in tumorigenesis. The diverse defects of RiBi and IRBC that predispose and/or contribute to severe human pathologies including developmental syndromes and cancer are then outlined, along with examples of promising small-molecule-based strategies to therapeutically target the RS- and particularly RiBi- stress-tolerance mechanisms to which cancer cells are addicted due to their aberrant DNA replication, repair, and proteo-synthesis demands. ![]()
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11
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Feng S, Manley JL. Replication protein A associates with nucleolar R loops and regulates rRNA transcription and nucleolar morphology. Genes Dev 2021; 35:1579-1594. [PMID: 34819354 PMCID: PMC8653787 DOI: 10.1101/gad.348858.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/22/2021] [Indexed: 11/24/2022]
Abstract
Here, Feng and Manley report novel functions of the DNA replication and repair factor replication protein A (RPA) in control of nucleolar homeostasis. Their findings both indicate new roles for RPA in nucleoli through pre-rRNA transcriptional control and also emphasize that RPA function in nucleolar homeostasis is linked to R-loop resolution under both physiological and pathological conditions. The nucleolus is an important cellular compartment in which ribosomal RNAs (rRNAs) are transcribed and where certain stress pathways that are crucial for cell growth are coordinated. Here we report novel functions of the DNA replication and repair factor replication protein A (RPA) in control of nucleolar homeostasis. We show that loss of the DNA:RNA helicase senataxin (SETX) promotes RPA nucleolar localization, and that this relocalization is dependent on the presence of R loops. Notably, this nucleolar RPA phenotype was also observed in the presence of camptothecin (CPT)-induced genotoxic stress, as well as in SETX-deficient AOA2 patient fibroblasts. Extending these results, we found that RPA is recruited to rDNA following CPT treatment, where RPA prevents R-loop-induced DNA double-strand breaks. Furthermore, we show that loss of RPA significantly decreased 47S pre-rRNA levels, which was accompanied by increased expression of both RNAP II-mediated “promoter and pre-rRNA antisense” RNA as well as RNAP I-transcribed intragenic spacer RNAs. Finally, and likely reflecting the above, we found that loss of RPA promoted nucleolar structural disorganization, characterized by the appearance of reduced size nucleoli. Our findings both indicate new roles for RPA in nucleoli through pre-rRNA transcriptional control and also emphasize that RPA function in nucleolar homeostasis is linked to R-loop resolution under both physiological and pathological conditions.
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Affiliation(s)
- Shuang Feng
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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12
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Velichko AK, Ovsyannikova N, Petrova NV, Luzhin AV, Vorobjeva M, Gavrikov AS, Mishin AS, Kireev II, Razin SV, Kantidze OL. Treacle and TOPBP1 control replication stress response in the nucleolus. J Cell Biol 2021; 220:212262. [PMID: 34100862 PMCID: PMC8190600 DOI: 10.1083/jcb.202008085] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 04/26/2021] [Accepted: 05/18/2021] [Indexed: 12/22/2022] Open
Abstract
Replication stress is one of the main sources of genome instability. Although the replication stress response in eukaryotic cells has been extensively studied, almost nothing is known about the replication stress response in nucleoli. Here, we demonstrate that initial replication stress-response factors, such as RPA, TOPBP1, and ATR, are recruited inside the nucleolus in response to drug-induced replication stress. The role of TOPBP1 goes beyond the typical replication stress response; it interacts with the low-complexity nucleolar protein Treacle (also referred to as TCOF1) and forms large Treacle-TOPBP1 foci inside the nucleolus. In response to replication stress, Treacle and TOPBP1 facilitate ATR signaling at stalled replication forks, reinforce ATR-mediated checkpoint activation inside the nucleolus, and promote the recruitment of downstream replication stress response proteins inside the nucleolus without forming nucleolar caps. Characterization of the Treacle-TOPBP1 interaction mode leads us to propose that these factors can form a molecular platform for efficient stress response in the nucleolus.
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Affiliation(s)
- Artem K Velichko
- Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia.,Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Natalia Ovsyannikova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Artem V Luzhin
- Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
| | - Maria Vorobjeva
- Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
| | - Alexey S Gavrikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Moscow, Russia
| | - Alexander S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences, Moscow, Russia
| | - Igor I Kireev
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,V.I. Kulakov National Medical Research Center for Obstetrics, Gynecology, and Perinatology, Moscow, Russia
| | - Sergey V Razin
- Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
| | - Omar L Kantidze
- Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
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13
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14
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Frattini C, Promonet A, Alghoul E, Vidal-Eychenie S, Lamarque M, Blanchard MP, Urbach S, Basbous J, Constantinou A. TopBP1 assembles nuclear condensates to switch on ATR signaling. Mol Cell 2021; 81:1231-1245.e8. [PMID: 33503405 DOI: 10.1016/j.molcel.2020.12.049] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/01/2020] [Accepted: 12/16/2020] [Indexed: 12/13/2022]
Abstract
ATR checkpoint signaling is crucial for cellular responses to DNA replication impediments. Using an optogenetic platform, we show that TopBP1, the main activator of ATR, self-assembles extensively to yield micrometer-sized condensates. These opto-TopBP1 condensates are functional entities organized in tightly packed clusters of spherical nano-particles. TopBP1 condensates are reversible, occasionally fuse, and co-localize with TopBP1 partner proteins. We provide evidence that TopBP1 condensation is a molecular switch that amplifies ATR activity to phosphorylate checkpoint kinase 1 (Chk1) and slow down replication forks. Single amino acid substitutions of key residues in the intrinsically disordered ATR activation domain disrupt TopBP1 condensation and consequently ATR/Chk1 signaling. In physiologic salt concentration and pH, purified TopBP1 undergoes liquid-liquid phase separation in vitro. We propose that the actuation mechanism of ATR signaling is the assembly of TopBP1 condensates driven by highly regulated multivalent and cooperative interactions.
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Affiliation(s)
- Camilla Frattini
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Alexy Promonet
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Emile Alghoul
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | | | - Marie Lamarque
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | | | - Serge Urbach
- Institut de Génomique Fonctionnelle, CNRS INSERM, Université de Montpellier, Montpellier, France
| | - Jihane Basbous
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France.
| | - Angelos Constantinou
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France.
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15
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Korsholm LM, Gál Z, Nieto B, Quevedo O, Boukoura S, Lund CC, Larsen DH. Recent advances in the nucleolar responses to DNA double-strand breaks. Nucleic Acids Res 2020; 48:9449-9461. [PMID: 32857853 PMCID: PMC7515731 DOI: 10.1093/nar/gkaa713] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/13/2020] [Accepted: 08/26/2020] [Indexed: 12/15/2022] Open
Abstract
DNA damage poses a serious threat to human health and cells therefore continuously monitor and repair DNA lesions across the genome. Ribosomal DNA is a genomic domain that represents a particular challenge due to repetitive sequences, high transcriptional activity and its localization in the nucleolus, where the accessibility of DNA repair factors is limited. Recent discoveries have significantly extended our understanding of how cells respond to DNA double-strand breaks (DSBs) in the nucleolus, and new kinases and multiple down-stream targets have been identified. Restructuring of the nucleolus can occur as a consequence of DSBs and new data point to an active regulation of this process, challenging previous views. Furthermore, new insights into coordination of cell cycle phases and ribosomal DNA repair argue against existing concepts. In addition, the importance of nucleolar-DNA damage response (n-DDR) mechanisms for maintenance of genome stability and the potential of such factors as anti-cancer targets is becoming apparent. This review will provide a detailed discussion of recent findings and their implications for our understanding of the n-DDR. The n-DDR shares features with the DNA damage response (DDR) elsewhere in the genome but is also emerging as an independent response unique to ribosomal DNA and the nucleolus.
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Affiliation(s)
| | | | - Blanca Nieto
- Danish Cancer Society Research Center, Nucleolar Stress and Disease Group, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Oliver Quevedo
- Danish Cancer Society Research Center, Nucleolar Stress and Disease Group, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Stavroula Boukoura
- Danish Cancer Society Research Center, Nucleolar Stress and Disease Group, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Casper Carstens Lund
- Danish Cancer Society Research Center, Nucleolar Stress and Disease Group, Strandboulevarden 49, 2100 Copenhagen, Denmark
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16
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Blokhina YP, Buchwalter A. Moving fast and breaking things: Incidence and repair of DNA damage within ribosomal DNA repeats. Mutat Res 2020; 821:111715. [PMID: 32717383 DOI: 10.1016/j.mrfmmm.2020.111715] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/25/2020] [Accepted: 07/13/2020] [Indexed: 12/31/2022]
Abstract
The genes that code for ribosomal RNA are present in hundreds of tandemly arrayed copies in the human genome. Ribosomal DNA repeats transcribe vast amounts of ribosomal RNA in order to meet the cell's relentless demand for ribosome production. Intrinsic features of ribosomal DNA repeats render them uniquely vulnerable to DNA damage. Sensing and repairing damage to ribosomal DNA involves dramatic spatial reorganization of the nucleolus, the phase-separated nuclear subdomain where ribosomes are made. We highlight recent advances in detecting the incidence of DNA damage and defining the mechanisms of DNA repair on these essential genes.
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Affiliation(s)
- Yana P Blokhina
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, United States
| | - Abigail Buchwalter
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, United States; Department of Physiology, University of California, San Francisco, San Francisco, CA, United States; Chan Zuckerberg Biohub, San Francisco, CA, United States.
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17
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Zheng T, Zhou H, Li X, Peng D, Yang Y, Zeng Y, Liu H, Ren J, Zhao Y. RBMX is required for activation of ATR on repetitive DNAs to maintain genome stability. Cell Death Differ 2020; 27:3162-3176. [PMID: 32494026 DOI: 10.1038/s41418-020-0570-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 05/15/2020] [Accepted: 05/20/2020] [Indexed: 01/11/2023] Open
Abstract
ATR is a master regulator of cell response to replication stress. Adequate activation of ATR is essential for preventing genome aberrance induced by replication defect. However, the mechanism underlying ATR activation is not fully understood. Here, we identify that RBMX is an ssDNA binding protein that orchestrates a novel pathway to activate ATR. Using super-resolution STORM, we observe that RBMX and RPA bind to adjacent but nonoverlapping sites on ssDNA in response to replication stress. RBMX then binds to and facilitates positioning of TopBP1, which activates nearby ATR associated with RPA. In addition, ATR activation by ssDNA-RBMX-TopBP1 is independent of ssDNA-dsDNA junction and 9-1-1 complex. ChIP-seq analysis reveals that RBMX/RPA are highly enriched on repetitive DNAs, which are considered as fragile sites with high replication stress. RBMX depletion leads to defective localization of TopBP1 to replication stressed sites and inadequate activation of ATR. Furthermore, cells with deficient RBMX demonstrate replication defect, leading to formation of micronuclei and a high rate of sister-chromatin exchange, indicative of genome instability. Together, the results identify a new ssDNA-RBMX-TopBP1 pathway that is specifically required for activation of ATR on repetitive DNAs. Therefore, RBMX is a key factor to ensure genome stability during replication.
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Affiliation(s)
- Tian Zheng
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Haoxian Zhou
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xiaocui Li
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Di Peng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510006, China
| | - Yiding Yang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yanru Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510006, China
| | - Haiying Liu
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Jian Ren
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510006, China
| | - Yong Zhao
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China. .,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510006, China.
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18
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Oxaliplatin-Induced DHX9 Phosphorylation Promotes Oncogenic Circular RNA CCDC66 Expression and Development of Chemoresistance. Cancers (Basel) 2020; 12:cancers12030697. [PMID: 32187976 PMCID: PMC7140115 DOI: 10.3390/cancers12030697] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/11/2020] [Accepted: 03/12/2020] [Indexed: 01/04/2023] Open
Abstract
Circular RNA (circRNA), generated through backsplicing in which the downstream splice donor joins the upstream splice acceptor, is a novel class of RNA molecules. Our previous study found that a novel oncogenic circRNA—consisting exon 8–10 of CCDC66—is aberrantly expressed in colorectal cancer (CRC) tissues and cells. The failure of treatment for colorectal cancer is typically associated with recurrent and chemoresistant cancerous tissues. In this study, we aimed to investigate the role(s) of circCCDC66 during the development of chemoresistance. We discovered that the expression level of circCCDC66 is elevated in colorectal cancer cells with resistance to oxaliplatin. Knockdown of circCCDC66 caused the downregulation of a subset of genes which are regulated by circCCDC66-associated miRNAs and related to the modulation of apoptosis and the cell cycle, suppressing cell survival, promoting oxaliplatin-induced apoptosis and, thus, hindering the development of oxaliplatin-resistance (OxR). The induction of circCCDC66 was dependent on the time-course and dose of oxaliplatin treatment. Our analyses revealed that DHX9 harbors two phosphorylation sites of phosphatidylinositol 3-kinase-related kinases (PI3KKs) close to substrate-binding domains. Blockage of phosphorylation by either PI3KK inhibitors or nonphosphorable mutants of DHX9 decreased the oxaliplatin-induced circCCDC66 expression and the ability to develop chemoresistant cells. Taken together, we demonstrated and linked the functional role of DHX9 phosphorylation to oncogenic circCCDC66 expression during the development of resistance to oxaliplatin, providing a mechanistic insight for the development of therapeutic strategies to recurring/chemoresistant colorectal cancer.
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19
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Mooser C, Symeonidou IE, Leimbacher PA, Ribeiro A, Shorrocks AMK, Jungmichel S, Larsen SC, Knechtle K, Jasrotia A, Zurbriggen D, Jeanrenaud A, Leikauf C, Fink D, Nielsen ML, Blackford AN, Stucki M. Treacle controls the nucleolar response to rDNA breaks via TOPBP1 recruitment and ATR activation. Nat Commun 2020; 11:123. [PMID: 31913317 PMCID: PMC6949271 DOI: 10.1038/s41467-019-13981-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 12/10/2019] [Indexed: 01/10/2023] Open
Abstract
Induction of DNA double-strand breaks (DSBs) in ribosomal DNA (rDNA) repeats is associated with ATM-dependent repression of ribosomal RNA synthesis and large-scale reorganization of nucleolar architecture, but the signaling events that regulate these responses are largely elusive. Here we show that the nucleolar response to rDNA breaks is dependent on both ATM and ATR activity. We further demonstrate that ATM- and NBS1-dependent recruitment of TOPBP1 in the nucleoli is required for inhibition of ribosomal RNA synthesis and nucleolar segregation in response to rDNA breaks. Mechanistically, TOPBP1 recruitment is mediated by phosphorylation-dependent interactions between three of its BRCT domains and conserved phosphorylated Ser/Thr residues at the C-terminus of the nucleolar phosphoprotein Treacle. Our data thus reveal an important cooperation between TOPBP1 and Treacle in the signaling cascade that triggers transcriptional inhibition and nucleolar segregation in response to rDNA breaks.
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Affiliation(s)
- Clémence Mooser
- Department of Gynecology, University of Zurich, Wagistrasse 14, CH-8952, Schlieren, Switzerland
| | - Ioanna-Eleni Symeonidou
- Department of Gynecology, University of Zurich, Wagistrasse 14, CH-8952, Schlieren, Switzerland
| | - Pia-Amata Leimbacher
- Department of Gynecology, University of Zurich, Wagistrasse 14, CH-8952, Schlieren, Switzerland
| | - Alison Ribeiro
- Department of Gynecology, University of Zurich, Wagistrasse 14, CH-8952, Schlieren, Switzerland
| | - Ann-Marie K Shorrocks
- Department of Oncology, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- Cancer Research UK/Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Stephanie Jungmichel
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Bledgamsvej 3B DK-2200, Copenhagen, Denmark
| | - Sara C Larsen
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Bledgamsvej 3B DK-2200, Copenhagen, Denmark
| | - Katja Knechtle
- Department of Gynecology, University of Zurich, Wagistrasse 14, CH-8952, Schlieren, Switzerland
| | - Arti Jasrotia
- Department of Gynecology, University of Zurich, Wagistrasse 14, CH-8952, Schlieren, Switzerland
| | - Diana Zurbriggen
- Department of Gynecology, University of Zurich, Wagistrasse 14, CH-8952, Schlieren, Switzerland
| | - Alain Jeanrenaud
- Department of Gynecology, University of Zurich, Wagistrasse 14, CH-8952, Schlieren, Switzerland
| | - Colin Leikauf
- Department of Gynecology, University of Zurich, Wagistrasse 14, CH-8952, Schlieren, Switzerland
| | - Daniel Fink
- Department of Gynecology, University of Zurich, Wagistrasse 14, CH-8952, Schlieren, Switzerland
| | - Michael L Nielsen
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Bledgamsvej 3B DK-2200, Copenhagen, Denmark
| | - Andrew N Blackford
- Department of Oncology, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- Cancer Research UK/Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Manuel Stucki
- Department of Gynecology, University of Zurich, Wagistrasse 14, CH-8952, Schlieren, Switzerland.
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20
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Velichko AK, Petrova NV, Luzhin AV, Strelkova OS, Ovsyannikova N, Kireev II, Petrova NV, Razin SV, Kantidze OL. Hypoosmotic stress induces R loop formation in nucleoli and ATR/ATM-dependent silencing of nucleolar transcription. Nucleic Acids Res 2020; 47:6811-6825. [PMID: 31114877 PMCID: PMC6648358 DOI: 10.1093/nar/gkz436] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/03/2019] [Accepted: 05/08/2019] [Indexed: 12/16/2022] Open
Abstract
The contribution of nucleoli to the cellular stress response has been discussed for over a decade. Stress-induced inhibition of RNA polymerase I-dependent transcription is hypothesized as a possible effector program in such a response. In this study, we report a new mechanism by which ribosomal DNA transcription can be inhibited in response to cellular stress. Specifically, we demonstrate that mild hypoosmotic stress induces stabilization of R loops in ribosomal genes and thus provokes the nucleoli-specific DNA damage response, which is governed by the ATM- and Rad3-related (ATR) kinase. Activation of ATR in nucleoli strongly depends on Treacle, which is needed for efficient recruitment/retention of TopBP1 in nucleoli. Subsequent ATR-mediated activation of ATM results in repression of nucleolar transcription.
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Affiliation(s)
- Artem K Velichko
- Laboratory of Genome Stability, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia.,Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Nadezhda V Petrova
- Laboratory of Genome Stability, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Artem V Luzhin
- Laboratory of Genome Stability, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Olga S Strelkova
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia
| | - Natalia Ovsyannikova
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia
| | - Igor I Kireev
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia.,V.I. Kulakov National Medical Research Center for Obstetrics, Gynecology, and Perinatology, 117997 Moscow, Russia
| | - Natalia V Petrova
- Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Sergey V Razin
- Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia.,Department of Molecular Biology, Moscow State University, 119234 Moscow, Russia.,LFR2O, Institute Gustave Roussy, F-94805 Villejuif, France
| | - Omar L Kantidze
- Laboratory of Genome Stability, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia.,LFR2O, Institute Gustave Roussy, F-94805 Villejuif, France
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21
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Siebenwirth C, Greubel C, Drexler GA, Reindl J, Walsh DWM, Schwarz B, Sammer M, Baur I, Pospiech H, Schmid TE, Dollinger G, Friedl AA. Local inhibition of rRNA transcription without nucleolar segregation after targeted ion irradiation of the nucleolus. J Cell Sci 2019; 132:jcs.232181. [PMID: 31492757 PMCID: PMC6803363 DOI: 10.1242/jcs.232181] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 08/29/2019] [Indexed: 12/18/2022] Open
Abstract
Nucleoli have attracted interest for their role as cellular stress sensors and as potential targets for cancer treatment. The effect of DNA double-strand breaks (DSBs) in nucleoli on rRNA transcription and nucleolar organisation appears to depend on the agent used to introduce DSBs, DSB frequency and the presence (or not) of DSBs outside the nucleoli. To address the controversy, we targeted nucleoli with carbon ions at the ion microbeam SNAKE. Localized ion irradiation with 1-100 carbon ions per point (about 0.3-30 Gy per nucleus) did not lead to overall reduced ribonucleotide incorporation in the targeted nucleolus or other nucleoli of the same cell. However, both 5-ethynyluridine incorporation and Parp1 protein levels were locally decreased at the damaged nucleolar chromatin regions marked by γH2AX, suggesting localized inhibition of rRNA transcription. This locally restricted transcriptional inhibition was not accompanied by nucleolar segregation, a structural reorganisation observed after inhibition of rRNA transcription by treatment with actinomycin D or UV irradiation. The presented data indicate that even multiple complex DSBs do not lead to a pan-nucleolar response if they affect only a subnucleolar region.
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Affiliation(s)
- Christian Siebenwirth
- Bundeswehr Institute of Radiobiology, 80937 Munich, Germany .,Institute for Applied Physics and Metrology, Universität der Bundeswehr München, 85577 Neubiberg, Germany.,Department of Radiation Therapy and Radiooncology, Technical University of Munich, 81675 Munich, Germany
| | - Christoph Greubel
- Institute for Applied Physics and Metrology, Universität der Bundeswehr München, 85577 Neubiberg, Germany
| | - Guido A Drexler
- Department of Radiation Oncology, University Hospital, Ludwig Maximilians University of Munich, 81377 Munich, Germany
| | - Judith Reindl
- Institute for Applied Physics and Metrology, Universität der Bundeswehr München, 85577 Neubiberg, Germany
| | - Dietrich W M Walsh
- Institute for Applied Physics and Metrology, Universität der Bundeswehr München, 85577 Neubiberg, Germany
| | - Benjamin Schwarz
- Institute for Applied Physics and Metrology, Universität der Bundeswehr München, 85577 Neubiberg, Germany
| | - Matthias Sammer
- Institute for Applied Physics and Metrology, Universität der Bundeswehr München, 85577 Neubiberg, Germany
| | - Iris Baur
- Department of Radiation Oncology, University Hospital, Ludwig Maximilians University of Munich, 81377 Munich, Germany
| | - Helmut Pospiech
- Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Thomas E Schmid
- Department of Radiation Therapy and Radiooncology, Technical University of Munich, 81675 Munich, Germany
| | - Günther Dollinger
- Institute for Applied Physics and Metrology, Universität der Bundeswehr München, 85577 Neubiberg, Germany
| | - Anna A Friedl
- Department of Radiation Oncology, University Hospital, Ludwig Maximilians University of Munich, 81377 Munich, Germany
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22
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Korsholm LM, Gál Z, Lin L, Quevedo O, Ahmad DA, Dulina E, Luo Y, Bartek J, Larsen DH. Double-strand breaks in ribosomal RNA genes activate a distinct signaling and chromatin response to facilitate nucleolar restructuring and repair. Nucleic Acids Res 2019; 47:8019-8035. [PMID: 31184714 PMCID: PMC6735822 DOI: 10.1093/nar/gkz518] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 12/21/2022] Open
Abstract
The nucleolus is a nuclear sub-domain containing the most highly transcribed genes in the genome. Hundreds of human ribosomal RNA (rRNA) genes, located in the nucleolus, rely on constant maintenance. DNA double-strand breaks (DSBs) in rRNA genes activate the ATM kinase, repress rRNA transcription and induce nucleolar cap formation. Yet how ribosomal-DNA (rDNA) lesions are detected and processed remains elusive. Here, we use CRISPR/Cas9-mediated induction of DSBs and report a chromatin response unique to rDNA depending on ATM-phosphorylation of the nucleolar protein TCOF1 and recruitment of the MRE11-RAD50-NBS1 (MRN) complex via the NBS1-subunit. NBS1- and MRE11-depleted cells fail to suppress rRNA transcription and to translocate rDNA into nucleolar caps. Furthermore, the DNA damage response (DDR) kinase ATR operates downstream of the ATM-TCOF1-MRN interplay and is required to fully suppress rRNA transcription and complete DSB-induced nucleolar restructuring. Unexpectedly, we find that DSBs in rDNA neither activate checkpoint kinases CHK1/CHK2 nor halt cell-cycle progression, yet the nucleolar-DDR protects against genomic aberrations and cell death. Our data highlight the concept of a specialized nucleolar DNA damage response (n-DDR) with a distinct protein composition, spatial organization and checkpoint communication. The n-DDR maintains integrity of ribosomal RNA genes, with implications for cell physiology and disease.
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Affiliation(s)
- Lea M Korsholm
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Zita Gál
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Lin Lin
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
- China National GeneBank, BGI-Shenzhen, 518083 Shenzhen, China
| | - Oliver Quevedo
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Diana A Ahmad
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Ekaterina Dulina
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
- China National GeneBank, BGI-Shenzhen, 518083 Shenzhen, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, 266555 Qingdao, China
| | - Jiri Bartek
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Genome Biology, Karolinska Institutet, SE-171 65 Solna, Sweden
| | - Dorthe H Larsen
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
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23
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Sokka M, Koalick D, Hemmerich P, Syväoja JE, Pospiech H. The ATR-Activation Domain of TopBP1 Is Required for the Suppression of Origin Firing during the S Phase. Int J Mol Sci 2018; 19:ijms19082376. [PMID: 30104465 PMCID: PMC6121618 DOI: 10.3390/ijms19082376] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 08/04/2018] [Accepted: 08/06/2018] [Indexed: 11/23/2022] Open
Abstract
The mammalian DNA replication program is controlled at two phases, the licensing of potential origins of DNA replication in early gap 1 (G1), and the selective firing of a subset of licenced origins in the synthesis (S) phase. Upon entry into the S phase, serine/threonine-protein kinase ATR (ATR) is required for successful completion of the DNA replication program by limiting unnecessary dormant origin activation. Equally important is its activator, DNA topoisomerase 2-binding protein 1 (TopBP1), which is also required for the initiation of DNA replication after a rise in S-phase kinase levels. However, it is unknown how the ATR activation domain of TopBP1 affects DNA replication dynamics. Using human cells conditionally expressing a TopBP1 mutant deficient for ATR activation, we show that functional TopBP1 is required in suppressing local dormant origin activation. Our results demonstrate a regulatory role for TopBP1 in the local balancing of replication fork firing within the S phase.
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Affiliation(s)
- Miiko Sokka
- Department of Biology, University of Eastern Finland, FI-80101 Joensuu, Finland.
- Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland.
| | - Dennis Koalick
- Leibniz Institute on Aging-Fritz Lipmann Institute, DE-07745 Jena, Germany.
| | - Peter Hemmerich
- Leibniz Institute on Aging-Fritz Lipmann Institute, DE-07745 Jena, Germany.
| | - Juhani E Syväoja
- Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland.
| | - Helmut Pospiech
- Leibniz Institute on Aging-Fritz Lipmann Institute, DE-07745 Jena, Germany.
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90014 Oulu, Finland.
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24
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Abstract
The nucleolus is a prominent subnuclear compartment, where ribosome biosynthesis takes place. Recently, the nucleolus has gained attention for its novel role in the regulation of cellular stress. Nucleolar stress is emerging as a new concept, which is characterized by diverse cellular insult-induced abnormalities in nucleolar structure and function, ultimately leading to activation of p53 or other stress signaling pathways and alterations in cell behavior. Despite a number of comprehensive reviews on this concept, straightforward and clear-cut way criteria for a nucleolar stress state, regarding the factors that elicit this state, the morphological and functional alterations as well as the rationale for p53 activation are still missing. Based on literature of the past two decades, we herein summarize the evolution of the concept and provide hallmarks of nucleolar stress. Along with updated information and thorough discussion of existing confusions in the field, we pay particular attention to the current understanding of the sensing mechanisms, i.e., how stress is integrated by p53. In addition, we propose our own emphasis regarding the role of nucleolar protein NPM1 in the hallmarks of nucleolar stress and sensing mechanisms. Finally, the links of nucleolar stress to human diseases are briefly and selectively introduced.
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Affiliation(s)
- Kai Yang
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China.,Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases with Integrated Chinese-Western Medicine, Shanghai Institute of Traumatology and Orthopedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai, 200025, China
| | - Jie Yang
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Jing Yi
- Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
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Lindström MS, Jurada D, Bursac S, Orsolic I, Bartek J, Volarevic S. Nucleolus as an emerging hub in maintenance of genome stability and cancer pathogenesis. Oncogene 2018; 37:2351-2366. [PMID: 29429989 PMCID: PMC5931986 DOI: 10.1038/s41388-017-0121-z] [Citation(s) in RCA: 146] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/15/2017] [Accepted: 11/15/2017] [Indexed: 12/13/2022]
Abstract
The nucleolus is the major site for synthesis of ribosomes, complex molecular machines that are responsible for protein synthesis. A wealth of research over the past 20 years has clearly indicated that both quantitative and qualitative alterations in ribosome biogenesis can drive the malignant phenotype via dysregulation of protein synthesis. However, numerous recent proteomic, genomic, and functional studies have implicated the nucleolus in the regulation of processes that are unrelated to ribosome biogenesis, including DNA-damage response, maintenance of genome stability and its spatial organization, epigenetic regulation, cell-cycle control, stress responses, senescence, global gene expression, as well as assembly or maturation of various ribonucleoprotein particles. In this review, the focus will be on features of rDNA genes, which make them highly vulnerable to DNA damage and intra- and interchromosomal recombination as well as built-in mechanisms that prevent and repair rDNA damage, and how dysregulation of this interplay affects genome-wide DNA stability, gene expression and the balance between euchromatin and heterochromatin. We will also present the most recent insights into how malfunction of these cellular processes may be a central driving force of human malignancies, and propose a promising new therapeutic approach for the treatment of cancer.
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Affiliation(s)
- Mikael S Lindström
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Deana Jurada
- Department of Molecular Medicine and Biotechnology, School of Medicine, University of Rijeka, Rijeka, Croatia
- Scientific Center of Excellence for Reproductive and Regenerative Medicine, University of Rijeka, Rijeka, Croatia
| | - Sladana Bursac
- Department of Molecular Medicine and Biotechnology, School of Medicine, University of Rijeka, Rijeka, Croatia
- Scientific Center of Excellence for Reproductive and Regenerative Medicine, University of Rijeka, Rijeka, Croatia
| | - Ines Orsolic
- Department of Molecular Medicine and Biotechnology, School of Medicine, University of Rijeka, Rijeka, Croatia
- Scientific Center of Excellence for Reproductive and Regenerative Medicine, University of Rijeka, Rijeka, Croatia
| | - Jiri Bartek
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- The Danish Cancer Society Research Centre, Copenhagen, Denmark.
| | - Sinisa Volarevic
- Department of Molecular Medicine and Biotechnology, School of Medicine, University of Rijeka, Rijeka, Croatia.
- Scientific Center of Excellence for Reproductive and Regenerative Medicine, University of Rijeka, Rijeka, Croatia.
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Ozdian T, Holub D, Maceckova Z, Varanasi L, Rylova G, Rehulka J, Vaclavkova J, Slavik H, Moudry P, Znojek P, Stankova J, de Sanctis JB, Hajduch M, Dzubak P. Proteomic profiling reveals DNA damage, nucleolar and ribosomal stress are the main responses to oxaliplatin treatment in cancer cells. J Proteomics 2017; 162:73-85. [DOI: 10.1016/j.jprot.2017.05.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 04/26/2017] [Accepted: 05/02/2017] [Indexed: 12/18/2022]
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Abstract
ATR (Ataxia Telangiectasia and Rad3-related) is a member of the Phosphatidylinositol 3-kinase-related kinases (PIKKs) family, amongst six other vertebrate proteins known so far. ATR is indispensable for cell survival and its essential role is in sensing DNA damage and initiating appropriate repair responses. In this review we highlight emerging and recent observations connecting ATR to alternative roles in controlling the nuclear envelope, nucleolus, centrosome and other organelles in response to both internal and external stress conditions. We propose that ATR functions control cell plasticity by sensing structural deformations of different cellular components, including DNA and initiating appropriate repair responses, most of which are yet to be understood completely.
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Affiliation(s)
- Gururaj Rao Kidiyoor
- Istituto FIRC di Oncologia Molecolare, Milan, Italy; University of Milan, Milan, Italy
| | - Amit Kumar
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research, M.G. Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), India
| | - Marco Foiani
- Istituto FIRC di Oncologia Molecolare, Milan, Italy; University of Milan, Milan, Italy.
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Larsen DH, Stucki M. Nucleolar responses to DNA double-strand breaks. Nucleic Acids Res 2015; 44:538-44. [PMID: 26615196 PMCID: PMC4737151 DOI: 10.1093/nar/gkv1312] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/09/2015] [Indexed: 11/25/2022] Open
Abstract
Maintenance of cellular homeostasis is key to prevent transformation and disease. The cellular response to DNA double-strand breaks, primarily orchestrated by the ATM/ATR kinases is one of many mechanisms that serve to uphold genome stability and homeostasis. Upon detection of double-strand breaks (DSBs), several signaling cascades are activated to halt cell cycle progression and initiate repair. Furthermore, the DNA damage response (DDR) controls cellular processes such as transcription, splicing and metabolism. Recent studies have uncovered aspects of how the DDR operates within nucleoli. It appears that the DDR controls transcription in the nucleoli, not only when DNA breaks occur in the rDNA repeats, but also when a nuclear DDR is activated. In addition, we have gained first insights into how repair of DSBs is organized in the nucleolus. Collectively, these recent studies provide a more comprehensive picture of how the DDR regulates basic cellular functions to maintain cellular homeostasis. In this review we will summarize recent findings and discuss their implications for our understanding of how the DDR regulates transcription and repair in the nucleolus.
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Affiliation(s)
- Dorthe Helena Larsen
- Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Manuel Stucki
- Department of Gynecology, University of Zurich, Wagistrasse 14, CH-8952 Schlieren, Switzerland
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29
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The c.*229C > T gene polymorphism in 3′UTR region of the topoisomerase IIβ binding protein 1 gene and LOH in BRCA1/2 regions and their effect on the risk and progression of human laryngeal carcinoma. Tumour Biol 2015; 37:4541-57. [DOI: 10.1007/s13277-015-4276-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 10/19/2015] [Indexed: 02/07/2023] Open
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