101
|
Gavish-Izakson M, Velpula BB, Elkon R, Prados-Carvajal R, Barnabas GD, Ugalde AP, Agami R, Geiger T, Huertas P, Ziv Y, Shiloh Y. Nuclear poly(A)-binding protein 1 is an ATM target and essential for DNA double-strand break repair. Nucleic Acids Res 2018; 46:730-747. [PMID: 29253183 PMCID: PMC5778506 DOI: 10.1093/nar/gkx1240] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 11/28/2017] [Accepted: 12/04/2017] [Indexed: 12/13/2022] Open
Abstract
The DNA damage response (DDR) is an extensive signaling network that is robustly mobilized by DNA double-strand breaks (DSBs). The primary transducer of the DSB response is the protein kinase, ataxia-telangiectasia, mutated (ATM). Here, we establish nuclear poly(A)-binding protein 1 (PABPN1) as a novel target of ATM and a crucial player in the DSB response. PABPN1 usually functions in regulation of RNA processing and stability. We establish that PABPN1 is recruited to the DDR as a critical regulator of DSB repair. A portion of PABPN1 relocalizes to DSB sites and is phosphorylated on Ser95 in an ATM-dependent manner. PABPN1 depletion sensitizes cells to DSB-inducing agents and prolongs the DSB-induced G2/M cell-cycle arrest, and DSB repair is hampered by PABPN1 depletion or elimination of its phosphorylation site. PABPN1 is required for optimal DSB repair via both nonhomologous end-joining (NHEJ) and homologous recombination repair (HRR), and specifically is essential for efficient DNA-end resection, an initial, key step in HRR. Using mass spectrometry analysis, we capture DNA damage-induced interactions of phospho-PABPN1, including well-established DDR players as well as other RNA metabolizing proteins. Our results uncover a novel ATM-dependent axis in the rapidly growing interface between RNA metabolism and the DDR.
Collapse
Affiliation(s)
- Michal Gavish-Izakson
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Bhagya Bhavana Velpula
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Rosario Prados-Carvajal
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER) and Department of Genetics, University of Sevilla, Sevilla, Spain
| | - Georgina D Barnabas
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Alejandro Pineiro Ugalde
- Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Reuven Agami
- Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Pablo Huertas
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER) and Department of Genetics, University of Sevilla, Sevilla, Spain
| | - Yael Ziv
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yosef Shiloh
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
102
|
Tehrani SS, Karimian A, Parsian H, Majidinia M, Yousefi B. Multiple Functions of Long Non-Coding RNAs in Oxidative Stress, DNA Damage Response and Cancer Progression. J Cell Biochem 2018; 119:223-236. [PMID: 28608608 DOI: 10.1002/jcb.26217] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/12/2017] [Indexed: 12/24/2022]
Abstract
In addition to aberrant alternation of transcriptome, it is now suggested that dysregulation of the non-coding transcripts, particularly long non-coding RNAs (lncRNAs), which comprise the majority of the genome, is contributed to cancer initiation and progression. As the result of recent huge efforts, the possible roles of numerous lncRNAs in the human cancers were characterized, as well as various strategies with inhibitory effects to target these transcripts on the transformed cells. Moreover, DNA damage response (DDR) pathway is a complex regulatory network responsible for the identification of disruptions in DNA structure, integrity and stability- it is reported to be associated with the up-regulation and down-regulation of lncRNAs. This review explores the involvement of the various lncRNAs in different human cancers, afterwards discusses the association of the lncRNAs expression with the DDR and oxidative stress, which are implicated in a myriad pathophysiological and physiological intra- and extracellular damages. J. Cell. Biochem. 119: 223-236, 2018. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Sadra Samavarchi Tehrani
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
- Department of Clinical Biochemistry, Babol University of Medical Sciences, Babol, Iran
| | - Ansar Karimian
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
- Department of Clinical Biochemistry, Babol University of Medical Sciences, Babol, Iran
| | - Hadi Parsian
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
- Department of Clinical Biochemistry, Babol University of Medical Sciences, Babol, Iran
| | - Maryam Majidinia
- Solid Tumor Research Center, Urmia University of Medical Sciences, Urmia, Iran
| | - Bahman Yousefi
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Faculty of Medicine, Department of Clinical Biochemistry and Laboratory Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Faculty of Medicine, Molecular Targeting Therapy Research Group, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|
103
|
DNA Damage as a Driver for Growth Delay: Chromosome Instability Syndromes with Intrauterine Growth Retardation. BIOMED RESEARCH INTERNATIONAL 2017; 2017:8193892. [PMID: 29238724 PMCID: PMC5702399 DOI: 10.1155/2017/8193892] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 06/16/2017] [Accepted: 07/17/2017] [Indexed: 12/20/2022]
Abstract
DNA is constantly exposed to endogenous and exogenous mutagenic stimuli that are capable of producing diverse lesions. In order to protect the integrity of the genetic material, a wide array of DNA repair systems that can target each specific lesion has evolved. Despite the availability of several repair pathways, a common general program known as the DNA damage response (DDR) is stimulated to promote lesion detection, signaling, and repair in order to maintain genetic integrity. The genes that participate in these pathways are subject to mutation; a loss in their function would result in impaired DNA repair and genomic instability. When the DDR is constitutionally altered, every cell of the organism, starting from development, will show DNA damage and subsequent genomic instability. The cellular response to this is either uncontrolled proliferation and cell cycle deregulation that ensues overgrowth, or apoptosis and senescence that result in tissue hypoplasia. These diverging growth abnormalities can clinically translate as cancer or growth retardation; both features can be found in chromosome instability syndromes (CIS). The analysis of the clinical, cellular, and molecular phenotypes of CIS with intrauterine growth retardation allows inferring that replication alteration is their unifying feature.
Collapse
|
104
|
A ubiquitin-dependent signalling axis specific for ALKBH-mediated DNA dealkylation repair. Nature 2017; 551:389-393. [PMID: 29144457 PMCID: PMC6458054 DOI: 10.1038/nature24484] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 10/04/2017] [Indexed: 01/06/2023]
Abstract
DNA repair is essential to prevent the cytotoxic or mutagenic effects of various types of DNA lesions, which are sensed by distinct pathways to recruit repair factors specific to the damage type. Although biochemical mechanisms for repairing several forms of genomic insults are well understood, the upstream signalling pathways that trigger repair are established for only certain types of damage, such as double-stranded breaks and interstrand crosslinks. Understanding the upstream signalling events that mediate recognition and repair of DNA alkylation damage is particularly important, since alkylation chemotherapy is one of the most widely used systemic modalities for cancer treatment and because environmental chemicals may trigger DNA alkylation. Here we demonstrate that human cells have a previously unrecognized signalling mechanism for sensing damage induced by alkylation. We find that the alkylation repair complex ASCC (activating signal cointegrator complex) relocalizes to distinct nuclear foci specifically upon exposure of cells to alkylating agents. These foci associate with alkylated nucleotides, and coincide spatially with elongating RNA polymerase II and splicing components. Proper recruitment of the repair complex requires recognition of K63-linked polyubiquitin by the CUE (coupling of ubiquitin conjugation to ER degradation) domain of the subunit ASCC2. Loss of this subunit impedes alkylation adduct repair kinetics and increases sensitivity to alkylating agents, but not other forms of DNA damage. We identify RING finger protein 113A (RNF113A) as the E3 ligase responsible for upstream ubiquitin signalling in the ASCC pathway. Cells from patients with X-linked trichothiodystrophy, which harbour a mutation in RNF113A, are defective in ASCC foci formation and are hypersensitive to alkylating agents. Together, our work reveals a previously unrecognized ubiquitin-dependent pathway induced specifically to repair alkylation damage, shedding light on the molecular mechanism of X-linked trichothiodystrophy.
Collapse
|
105
|
Sakasai R, Isono M, Wakasugi M, Hashimoto M, Sunatani Y, Matsui T, Shibata A, Matsunaga T, Iwabuchi K. Aquarius is required for proper CtIP expression and homologous recombination repair. Sci Rep 2017; 7:13808. [PMID: 29061988 PMCID: PMC5653829 DOI: 10.1038/s41598-017-13695-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 09/26/2017] [Indexed: 01/01/2023] Open
Abstract
Accumulating evidence indicates that transcription is closely related to DNA damage formation and that the loss of RNA biogenesis factors causes genome instability. However, whether such factors are involved in DNA damage responses remains unclear. We focus here on the RNA helicase Aquarius (AQR), a known R-loop processing factor, and show that its depletion in human cells results in the accumulation of DNA damage during S phase, mediated by R-loop formation. We investigated the involvement of Aquarius in DNA damage responses and found that AQR knockdown decreased DNA damage-induced foci formation of Rad51 and replication protein A, suggesting that Aquarius contributes to homologous recombination (HR)-mediated repair of DNA double-strand breaks (DSBs). Interestingly, the protein level of CtIP, a DSB processing factor, was decreased in AQR-knockdown cells. Exogenous expression of Aquarius partially restored CtIP protein level; however, CtIP overproduction did not rescue defective HR in AQR-knockdown cells. In accordance with these data, Aquarius depletion sensitized cells to genotoxic agents. We propose that Aquarius contributes to the maintenance of genomic stability via regulation of HR by CtIP-dependent and -independent pathways.
Collapse
Affiliation(s)
- Ryo Sakasai
- Department of Biochemistry I, Kanazawa Medical University, Ishikawa, Japan
| | - Mayu Isono
- Education and Research Support Center, Gunma University, Ishikawa, Japan
| | - Mitsuo Wakasugi
- Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Ishikawa, Japan
| | | | - Yumi Sunatani
- Department of Biochemistry I, Kanazawa Medical University, Ishikawa, Japan
| | - Tadashi Matsui
- Department of Biochemistry I, Kanazawa Medical University, Ishikawa, Japan
| | - Atsushi Shibata
- Education and Research Support Center, Gunma University, Ishikawa, Japan
| | - Tsukasa Matsunaga
- Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Ishikawa, Japan
| | - Kuniyoshi Iwabuchi
- Department of Biochemistry I, Kanazawa Medical University, Ishikawa, Japan.
| |
Collapse
|
106
|
Zinger A, Cho WC, Ben-Yehuda A. Cancer and Aging - the Inflammatory Connection. Aging Dis 2017; 8:611-627. [PMID: 28966805 PMCID: PMC5614325 DOI: 10.14336/ad.2016.1230] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 12/30/2016] [Indexed: 12/13/2022] Open
Abstract
Aging and cancer are highly correlated biological phenomena. Various cellular processes such as DNA damage responses and cellular senescence that serve as tumor suppressing mechanisms throughout life result in degenerative changes and contribute to the aging phenotype. In turn, aging is considered a pro-tumorigenic state, and constitutes the single most important risk factor for cancer development. However, the causative relations between aging and cancer is not straight forward, as these processes carry contradictory hallmarks; While aging is characterized by tissue degeneration and organ loss of function, cancer is a state of sustained cellular proliferation and gain of new functions. Here, we review the molecular and cellular pathways that stand in the base of aging related cancer. Specifically, we deal with the inflammatory perspective that link these two processes, and suggest possible molecular targets that may be exploited to modify their courses.
Collapse
Affiliation(s)
- Adar Zinger
- 1Department of Medicine, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - William C Cho
- 2Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - Arie Ben-Yehuda
- 1Department of Medicine, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| |
Collapse
|
107
|
The melanocortin signaling cAMP axis accelerates repair and reduces mutagenesis of platinum-induced DNA damage. Sci Rep 2017; 7:11708. [PMID: 28916831 PMCID: PMC5601928 DOI: 10.1038/s41598-017-12056-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 09/01/2017] [Indexed: 12/22/2022] Open
Abstract
Using primary melanocytes and HEK293 cells, we found that cAMP signaling accelerates repair of bi- and mono-functional platinum-induced DNA damage. Elevating cAMP signaling either by the agonistic MC1R ligand melanocyte stimulating hormone (MSH) or by pharmacologic cAMP induction by forskolin enhanced clearance of intrastrand cisplatin-adducts in melanocytes or MC1R-transfected HEK293 cells. MC1R antagonists human beta-defensin 3 and agouti signaling protein blocked MSH- but not forskolin-mediated enhancement of platinum-induced DNA damage. cAMP-enhanced repair of cisplatin-induced DNA damage was dependent on PKA-mediated phosphorylation of ATR on S435 which promoted ATR’s interaction with the key NER factor xeroderma pigmentosum A (XPA) and facilitated recruitment of an XPA-ATR-pS435 complex to sites of cisplatin DNA damage. Moreover, we developed an oligonucleotide retrieval immunoprecipitation (ORiP) assay using a novel platinated-DNA substrate to establish kinetics of ATR-pS435 and XPA’s associations with cisplatin-damaged DNA. Expression of a non-phosphorylatable ATR-S435A construct or deletion of A kinase-anchoring protein 12 (AKAP12) impeded platinum adduct clearance and prevented cAMP-mediated enhancement of ATR and XPA’s associations with cisplatin-damaged DNA, indicating that ATR phosphorylation at S435 is necessary for cAMP-enhanced repair of platinum-induced damage and protection against cisplatin-induced mutagenesis. These data implicate cAMP signaling as a critical regulator of genomic stability against platinum-induced mutagenesis.
Collapse
|
108
|
Lane SIR, Morgan SL, Wu T, Collins JK, Merriman JA, ElInati E, Turner JM, Jones KT. DNA damage induces a kinetochore-based ATM/ATR-independent SAC arrest unique to the first meiotic division in mouse oocytes. Development 2017; 144:3475-3486. [PMID: 28851706 PMCID: PMC5665484 DOI: 10.1242/dev.153965] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 08/18/2017] [Indexed: 12/31/2022]
Abstract
Mouse oocytes carrying DNA damage arrest in meiosis I, thereby preventing creation of embryos with deleterious mutations. The arrest is dependent on activation of the spindle assembly checkpoint, which results in anaphase-promoting complex (APC) inhibition. However, little is understood about how this checkpoint is engaged following DNA damage. Here, we find that within minutes of DNA damage checkpoint proteins are assembled at the kinetochore, not at damage sites along chromosome arms, such that the APC is fully inhibited within 30 min. Despite this robust response, there is no measurable loss in k-fibres, or tension across the bivalent. Through pharmacological inhibition we observed that the response is dependent on Mps1 kinase, aurora kinase and Haspin. Using oocyte-specific knockouts we find the response does not require the DNA damage response kinases ATM or ATR. Furthermore, checkpoint activation does not occur in response to DNA damage in fully mature eggs during meiosis II, despite the divisions being separated by just a few hours. Therefore, mouse oocytes have a unique ability to sense DNA damage rapidly by activating the checkpoint at their kinetochores.
Collapse
Affiliation(s)
- Simon I R Lane
- Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Stephanie L Morgan
- Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Tianyu Wu
- Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Josie K Collins
- Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Julie A Merriman
- Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Elias ElInati
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - James M Turner
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Keith T Jones
- Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| |
Collapse
|
109
|
Saldivar JC, Cortez D, Cimprich KA. The essential kinase ATR: ensuring faithful duplication of a challenging genome. Nat Rev Mol Cell Biol 2017; 18:622-636. [PMID: 28811666 DOI: 10.1038/nrm.2017.67] [Citation(s) in RCA: 523] [Impact Index Per Article: 74.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
One way to preserve a rare book is to lock it away from all potential sources of damage. Of course, an inaccessible book is also of little use, and the paper and ink will continue to degrade with age in any case. Like a book, the information stored in our DNA needs to be read, but it is also subject to continuous assault and therefore needs to be protected. In this Review, we examine how the replication stress response that is controlled by the kinase ataxia telangiectasia and Rad3-related (ATR) senses and resolves threats to DNA integrity so that the DNA remains available to read in all of our cells. We discuss the multiple data that have revealed an elegant yet increasingly complex mechanism of ATR activation. This involves a core set of components that recruit ATR to stressed replication forks, stimulate kinase activity and amplify ATR signalling. We focus on the activities of ATR in the control of cell cycle checkpoints, origin firing and replication fork stability, and on how proper regulation of these processes is crucial to ensure faithful duplication of a challenging genome.
Collapse
Affiliation(s)
- Joshua C Saldivar
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, California 94305-5441, USA
| | - David Cortez
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, California 94305-5441, USA
| |
Collapse
|
110
|
Nickoloff JA, Jones D, Lee SH, Williamson EA, Hromas R. Drugging the Cancers Addicted to DNA Repair. J Natl Cancer Inst 2017; 109:3832892. [PMID: 28521333 PMCID: PMC5436301 DOI: 10.1093/jnci/djx059] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 03/10/2017] [Indexed: 12/29/2022] Open
Abstract
Defects in DNA repair can result in oncogenic genomic instability. Cancers occurring from DNA repair defects were once thought to be limited to rare inherited mutations (such as BRCA1 or 2). It now appears that a clinically significant fraction of cancers have acquired DNA repair defects. DNA repair pathways operate in related networks, and cancers arising from loss of one DNA repair component typically become addicted to other repair pathways to survive and proliferate. Drug inhibition of the rescue repair pathway prevents the repair-deficient cancer cell from replicating, causing apoptosis (termed synthetic lethality). However, the selective pressure of inhibiting the rescue repair pathway can generate further mutations that confer resistance to the synthetic lethal drugs. Many such drugs currently in clinical use inhibit PARP1, a repair component to which cancers arising from inherited BRCA1 or 2 mutations become addicted. It is now clear that drugs inducing synthetic lethality may also be therapeutic in cancers with acquired DNA repair defects, which would markedly broaden their applicability beyond treatment of cancers with inherited DNA repair defects. Here we review how each DNA repair pathway can be attacked therapeutically and evaluate DNA repair components as potential drug targets to induce synthetic lethality. Clinical use of drugs targeting DNA repair will markedly increase when functional and genetic loss of repair components are consistently identified. In addition, future therapies will exploit artificial synthetic lethality, where complementary DNA repair pathways are targeted simultaneously in cancers without DNA repair defects.
Collapse
Affiliation(s)
- Jac A Nickoloff
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Dennie Jones
- Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, FL, USA
| | - Suk-Hee Lee
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Elizabeth A Williamson
- Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, FL, USA
| | - Robert Hromas
- Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, FL, USA
| |
Collapse
|
111
|
Lee MYWT, Wang X, Zhang S, Zhang Z, Lee EYC. Regulation and Modulation of Human DNA Polymerase δ Activity and Function. Genes (Basel) 2017; 8:genes8070190. [PMID: 28737709 PMCID: PMC5541323 DOI: 10.3390/genes8070190] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/07/2017] [Accepted: 07/11/2017] [Indexed: 12/28/2022] Open
Abstract
This review focuses on the regulation and modulation of human DNA polymerase δ (Pol δ). The emphasis is on the mechanisms that regulate the activity and properties of Pol δ in DNA repair and replication. The areas covered are the degradation of the p12 subunit of Pol δ, which converts it from a heterotetramer (Pol δ4) to a heterotrimer (Pol δ3), in response to DNA damage and also during the cell cycle. The biochemical mechanisms that lead to degradation of p12 are reviewed, as well as the properties of Pol δ4 and Pol δ3 that provide insights into their functions in DNA replication and repair. The second focus of the review involves the functions of two Pol δ binding proteins, polymerase delta interaction protein 46 (PDIP46) and polymerase delta interaction protein 38 (PDIP38), both of which are multi-functional proteins. PDIP46 is a novel activator of Pol δ4, and the impact of this function is discussed in relation to its potential roles in DNA replication. Several new models for the roles of Pol δ3 and Pol δ4 in leading and lagging strand DNA synthesis that integrate a role for PDIP46 are presented. PDIP38 has multiple cellular localizations including the mitochondria, the spliceosomes and the nucleus. It has been implicated in a number of cellular functions, including the regulation of specialized DNA polymerases, mitosis, the DNA damage response, mouse double minute 2 homolog (Mdm2) alternative splicing and the regulation of the NADPH oxidase 4 (Nox4).
Collapse
Affiliation(s)
- Marietta Y W T Lee
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
| | - Xiaoxiao Wang
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
| | - Sufang Zhang
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
| | - Zhongtao Zhang
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
| | - Ernest Y C Lee
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
| |
Collapse
|
112
|
Zhou W, Tian D, He J, Zhang L, Tang X, Zhang L, Wang Y, Li L, Zhao J, Yuan X, Peng S. Exposure scenario: Another important factor determining the toxic effects of PM2.5 and possible mechanisms involved. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 226:412-425. [PMID: 28449967 DOI: 10.1016/j.envpol.2017.04.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 03/31/2017] [Accepted: 04/04/2017] [Indexed: 06/07/2023]
Abstract
Worsening air pollution is a serious threat to public health in many urban and heavily industrialized areas. Particle size and chemical composition are well known determinants of the pathological response to air pollution. In addition, pathological responses may depend on the exposure profile (or scenario) of air pollution. For instance, we previously demonstrated that repeated exposure to low levels of fine airborne particulate matter (PM2.5) induced distinct epigenetic changes compared to acute high-doses exposure. In the present study, we evaluated the differential pathological responses of BEAS-2B human bronchial epithelial cells to two distinct PM2.5 exposure scenarios: 24-h exposure to high-doses PM2.5 (0, 6, 12, 24, 48, 96 μg/cm2) and 10 days' repeated exposure to low levels of PM2.5 (0, 1.5, 3, 6 μg/cm2). Acute exposure to high concentrations of PM2.5 caused ROS burst, marked DNA damage, dysfunction of the endoplasmic reticulum (ER) stress response, autophagy and necrotic cell death. In contrast, repeated low levels of PM2.5 led to sustained low-grade ROS accumulation, milder DNA damage, ER stress/unfolded protein response (UPR), S-phase arrest, apoptosis, and autophagy. Notably, most cells surviving repeated low-level exposure showed a series of abnormal adaptive responses, such as inhibition of mitochondria biogenesis and epigenetic dysregulation. These results indicate that different PM2.5 exposure scenarios induce distinct forms cytotoxicity and adaptive response. In addition to particle size and chemical composition, exposure scenario may be a critical factor determining the toxic health effects of PM2.5.
Collapse
Affiliation(s)
- Wei Zhou
- Evaluation and Research Center for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 100071, PR China
| | - Dongdong Tian
- Evaluation and Research Center for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 100071, PR China
| | - Jun He
- Evaluation and Research Center for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 100071, PR China
| | - Li Zhang
- Evaluation and Research Center for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 100071, PR China
| | - Xiuli Tang
- Evaluation and Research Center for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 100071, PR China
| | - Lijun Zhang
- Evaluation and Research Center for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 100071, PR China
| | - Yimei Wang
- Evaluation and Research Center for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 100071, PR China
| | - Lizhong Li
- Evaluation and Research Center for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 100071, PR China
| | - Jun Zhao
- Evaluation and Research Center for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 100071, PR China
| | - Xiaoyan Yuan
- Evaluation and Research Center for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 100071, PR China.
| | - Shuangqing Peng
- Evaluation and Research Center for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, 100071, PR China.
| |
Collapse
|
113
|
Abstract
Ataxia Telangiectasia Mutated (ATM) has been known for decades as the main kinase mediating the DNA Double-Strand Break Response (DDR). Extensive studies have revealed its dual role in locally promoting detection and repair of DSBs as well as in activating global DNA damage checkpoints. However, recent studies pinpoint additional unanticipated functions for ATM in modifying both the local chromatin landscape and the global chromosome organization, more particularly at persistent breaks. Given the emergence of a novel and unexpected class of DSBs prevalently arising in transcriptionally active genes and intrinsically difficult to repair, a specific role of ATM at refractory DSBs could be an important and so far overlooked feature of Ataxia Telangiectasia (A-T) a severe disorder associated with ATM mutations.
Collapse
Affiliation(s)
- Thomas Clouaire
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, France
| | - Aline Marnef
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, France
| | - Gaëlle Legube
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, France.
| |
Collapse
|
114
|
Interactive Roles of DNA Helicases and Translocases with the Single-Stranded DNA Binding Protein RPA in Nucleic Acid Metabolism. Int J Mol Sci 2017; 18:ijms18061233. [PMID: 28594346 PMCID: PMC5486056 DOI: 10.3390/ijms18061233] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 05/30/2017] [Accepted: 06/01/2017] [Indexed: 01/05/2023] Open
Abstract
Helicases and translocases use the energy of nucleoside triphosphate binding and hydrolysis to unwind/resolve structured nucleic acids or move along a single-stranded or double-stranded polynucleotide chain, respectively. These molecular motors facilitate a variety of transactions including replication, DNA repair, recombination, and transcription. A key partner of eukaryotic DNA helicases/translocases is the single-stranded DNA binding protein Replication Protein A (RPA). Biochemical, genetic, and cell biological assays have demonstrated that RPA interacts with these human molecular motors physically and functionally, and their association is enriched in cells undergoing replication stress. The roles of DNA helicases/translocases are orchestrated with RPA in pathways of nucleic acid metabolism. RPA stimulates helicase-catalyzed DNA unwinding, enlists translocases to sites of action, and modulates their activities in DNA repair, fork remodeling, checkpoint activation, and telomere maintenance. The dynamic interplay between DNA helicases/translocases and RPA is just beginning to be understood at the molecular and cellular levels, and there is still much to be learned, which may inform potential therapeutic strategies.
Collapse
|
115
|
Knight JC, Koustoulidou S, Cornelissen B. Imaging the DNA damage response with PET and SPECT. Eur J Nucl Med Mol Imaging 2017; 44:1065-1078. [PMID: 28058462 PMCID: PMC5397662 DOI: 10.1007/s00259-016-3604-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/16/2016] [Indexed: 01/05/2023]
Abstract
DNA integrity is constantly challenged by endogenous and exogenous factors that can alter the DNA sequence, leading to mutagenesis, aberrant transcriptional activity, and cytotoxicity. Left unrepaired, damaged DNA can ultimately lead to the development of cancer. To overcome this threat, a series of complex mechanisms collectively known as the DNA damage response (DDR) are able to detect the various types of DNA damage that can occur and stimulate the appropriate repair process. Each DNA damage repair pathway leads to the recruitment, upregulation, or activation of specific proteins within the nucleus, which, in some cases, can represent attractive targets for molecular imaging. Given the well-established involvement of DDR during tumorigenesis and cancer therapy, the ability to monitor these repair processes non-invasively using nuclear imaging techniques may facilitate the earlier detection of cancer and may also assist in monitoring response to DNA damaging treatment. This review article aims to provide an overview of recent efforts to develop PET and SPECT radiotracers for imaging of DNA damage repair proteins.
Collapse
Affiliation(s)
- James C Knight
- CR-UK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Off Roosevelt Drive, Oxford, OX3 7LJ, UK
| | - Sofia Koustoulidou
- CR-UK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Off Roosevelt Drive, Oxford, OX3 7LJ, UK
| | - Bart Cornelissen
- CR-UK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Off Roosevelt Drive, Oxford, OX3 7LJ, UK.
| |
Collapse
|
116
|
Morio T. Recent advances in the study of immunodeficiency and DNA damage response. Int J Hematol 2017; 106:357-365. [PMID: 28550350 DOI: 10.1007/s12185-017-2263-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 05/17/2017] [Indexed: 12/13/2022]
Abstract
DNA breaks can be induced by exogenous stimuli or by endogenous stress, but are also generated during recombination of V, D, and J genes (V(D)J recombination), immunoglobulin class switch recombination (CSR). Among various DNA breaks generated, DNA double strand break (DSB) is the most deleterious one. DNA damage response (DDR) is initiated when DSBs are detected, leading to DNA break repair by non-homologous end joining (NHEJ). The process is critically important for the generation of diversity for foreign antigens; and failure to exert DNA repair leads to immunodeficiency such as severe combined immunodeficiency and hyper-IgM syndrome. In V(D)J recombination, DSBs are induced by RAG1/2; and generated post-cleavage hairpins are resolved by Artemis/DNA-PKcs/KU70/KU80. DDR is initiated by ataxia-telangiectasia mutated as a master regulator together with MRE11/RAD50/NBS1 complex. Finally, DSBs are repaired by NHEJ. The defect of one of the molecules shows various degree of immunodeficiency and radiosensitivity. Upon CSR inducing signal, DSBs induced by activation-induced cytidine deaminase and endonucleases elicit DDR. Broken ends are repaired either by NHEJ or by mismatch repair system. Patients with radiosensitive SCID require hematopoietic cell transplantation as a curative therapy; but the procedures for eradication of recipient hematopoietic cells are often associated with severe toxicity.
Collapse
Affiliation(s)
- Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan.
| |
Collapse
|
117
|
Huang J, Gali H, Gichimu J, Bellani MA, Pokharel D, Paramasivam M, Seidman MM. Single Molecule Analysis of Laser Localized Psoralen Adducts. J Vis Exp 2017. [PMID: 28448050 DOI: 10.3791/55541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The DNA Damage Response (DDR) has been extensively characterized in studies of double strand breaks (DSBs) induced by laser micro beam irradiation in live cells. The DDR to helix distorting covalent DNA modifications, including interstrand DNA crosslinks (ICLs), is not as well defined. We have studied the DDR stimulated by ICLs, localized by laser photoactivation of immunotagged psoralens, in the nuclei of live cells. In order to address fundamental questions about adduct distribution and replication fork encounters, we combined laser localization with two other technologies. DNA fibers are often used to display the progress of replication forks by immunofluorescence of nucleoside analogues incorporated during short pulses. Immunoquantum dots have been widely employed for single molecule imaging. In the new approach, DNA fibers from cells carrying laser localized ICLs are spread onto microscope slides. The tagged ICLs are displayed with immunoquantum dots and the inter-lesion distances determined. Replication fork collisions with ICLs can be visualized and different encounter patterns identified and quantitated.
Collapse
Affiliation(s)
- Jing Huang
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health
| | - Himabindu Gali
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health
| | - Julia Gichimu
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health
| | - Marina A Bellani
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health
| | - Durga Pokharel
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health
| | - Manikandan Paramasivam
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health
| | - Michael M Seidman
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health;
| |
Collapse
|
118
|
Capozzo I, Iannelli F, Francia S, d'Adda di Fagagna F. Express or repress? The transcriptional dilemma of damaged chromatin. FEBS J 2017; 284:2133-2147. [PMID: 28231404 DOI: 10.1111/febs.14048] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/23/2017] [Accepted: 02/20/2017] [Indexed: 01/06/2023]
Abstract
The fine modulation of transcriptional activity around DNA lesions is essential to carefully regulate the crosstalk between the activation of the DNA damage response, DNA repair and transcription, particularly when the lesion occurs next to actively transcribed genes. Recently, several studies have been carried out to investigate how DNA lesions impact on local transcription, but the emerging model remains incomplete. Transcription of genes around damaged DNA is actively downregulated by the DNA damage response through different mechanisms, which appear specific to the chromatin context, the type of DNA damage or its complexity. Intriguingly, emerging evidence also indicates that transcription of noncoding RNAs (ncRNAs) is induced at sites of DNA damage, producing small ncRNAs that are, in turn, required for a full DNA damage response activation. We discuss here these recent findings, highlighting the major unresolved questions in the field, and propose ways to reconcile these apparently contradictory observations.
Collapse
Affiliation(s)
- Ilaria Capozzo
- Istituto di Genetica Molecolare, CNR - Consiglio Nazionale delle Ricerche, Pavia, Italy.,Scuola Universitaria Superiore IUSS Pavia, Italy
| | - Fabio Iannelli
- IFOM Foundation - FIRC Institute of Molecular Oncology Foundation, Milan, Italy
| | - Sofia Francia
- Istituto di Genetica Molecolare, CNR - Consiglio Nazionale delle Ricerche, Pavia, Italy.,IFOM Foundation - FIRC Institute of Molecular Oncology Foundation, Milan, Italy
| | - Fabrizio d'Adda di Fagagna
- Istituto di Genetica Molecolare, CNR - Consiglio Nazionale delle Ricerche, Pavia, Italy.,IFOM Foundation - FIRC Institute of Molecular Oncology Foundation, Milan, Italy
| |
Collapse
|
119
|
Abstract
Genomic instability is a hallmark of cancer and a common feature of human disorders, characterized by growth defects, neurodegeneration, cancer predisposition, and aging. Recent evidence has shown that DNA replication stress is a major driver of genomic instability and tumorigenesis. Cells can undergo mitosis with under-replicated DNA or unresolved DNA structures, and specific pathways are dedicated to resolving these structures during mitosis, suggesting that mitotic rescue from replication stress (MRRS) is a key process influencing genome stability and cellular homeostasis. Deregulation of MRRS following oncogene activation or loss-of-function of caretaker genes may be the cause of chromosomal aberrations that promote cancer initiation and progression. In this review, we discuss the causes and consequences of replication stress, focusing on its persistence in mitosis as well as the mechanisms and factors involved in its resolution, and the potential impact of incomplete replication or aberrant MRRS on tumorigenesis, aging and disease.
Collapse
Affiliation(s)
- Michalis Fragkos
- a CNRS UMR8200 , University Paris-Saclay , Gustave Roussy, Villejuif , France
| | - Valeria Naim
- a CNRS UMR8200 , University Paris-Saclay , Gustave Roussy, Villejuif , France
| |
Collapse
|
120
|
Fu X, Cui K, Yi Q, Yu L, Xu Y. DNA repair mechanisms in embryonic stem cells. Cell Mol Life Sci 2017; 74:487-493. [PMID: 27614628 PMCID: PMC11107665 DOI: 10.1007/s00018-016-2358-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Revised: 08/28/2016] [Accepted: 09/05/2016] [Indexed: 10/21/2022]
Abstract
Embryonic stem cells (ESCs) can undergo unlimited self-renewal and retain the pluripotency to differentiate into all cell types in the body. Therefore, as a renewable source of various functional cells in the human body, ESCs hold great promise for human cell therapy. During the rapid proliferation of ESCs in culture, DNA damage, such as DNA double-stranded breaks, will occur in ESCs. Therefore, to realize the potential of ESCs in human cell therapy, it is critical to understand the mechanisms how ESCs activate DNA damage response and DNA repair to maintain genomic stability, which is a prerequisite for their use in human therapy. In this context, it has been shown that ESCs harbor much fewer spontaneous mutations than somatic cells. Consistent with the finding that ESCs are genetically more stable than somatic cells, recent studies have indicated that ESCs can mount more robust DNA damage responses and DNA repair than somatic cells to ensure their genomic integrity.
Collapse
Affiliation(s)
- Xuemei Fu
- Shenzhen Children's Hospital, 7019 Yitian Road, Shenzhen, 518026, China.
| | - Ke Cui
- Center for Regenerative and Translational Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Qiuxiang Yi
- Center for Regenerative and Translational Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Lili Yu
- Guangdong Provincial Key Laboratory of Cancer Immunotherapy, Cancer Research Institute, Southern Medical University, Guangzhou, Guangdong, China
| | - Yang Xu
- Center for Regenerative and Translational Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.
- Guangdong Provincial Key Laboratory of Cancer Immunotherapy, Cancer Research Institute, Southern Medical University, Guangzhou, Guangdong, China.
- Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
| |
Collapse
|
121
|
The crosstalk between Wnt/β-catenin signaling pathway with DNA damage response and oxidative stress: Implications in cancer therapy. DNA Repair (Amst) 2017; 51:14-19. [PMID: 28108274 DOI: 10.1016/j.dnarep.2017.01.003] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 01/09/2017] [Indexed: 01/01/2023]
Abstract
DNA repair is essential for maintaining genomic integrity in cells. The dependence of cancer cell survival on proper DNA repair provides an opportunity to treat defective tumors by DNA damaging agents. Not only Wnt signaling has important functions in controlling gene expression, as well as cell polarity, adhesion and behavior, it also highly interacts with DNA damage response (DDR) in different levels. Furthermore, oxidative stress, which is responsible for majority of DNA lesions, affects Wnt signaling in different ways. A better understanding of the cross-talk between these pathways and events could provide strategies for treatment of cancer cells with deficient DNA repair capacity. As such, we will give a brief overview of the importance of the DNA repair machinery, signaling mechanisms of Wnt/β-catenin pathway, and DDR. We will further review the interactions between Wnt signaling and DDR, and the impact of oxidative stress on Wnt signaling. Finally, Wnt signaling is discussed as a potential treatment strategy for cancer.
Collapse
|
122
|
Paget S, Dubuissez M, Dehennaut V, Nassour J, Harmon BT, Spruyt N, Loison I, Abbadie C, Rood BR, Leprince D. HIC1 (hypermethylated in cancer 1) SUMOylation is dispensable for DNA repair but is essential for the apoptotic DNA damage response (DDR) to irreparable DNA double-strand breaks (DSBs). Oncotarget 2017; 8:2916-2935. [PMID: 27935866 PMCID: PMC5356852 DOI: 10.18632/oncotarget.13807] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 11/23/2016] [Indexed: 11/25/2022] Open
Abstract
The tumor suppressor gene HIC1 (Hypermethylated In Cancer 1) encodes a transcriptional repressor mediating the p53-dependent apoptotic response to irreparable DNA double-strand breaks (DSBs) through direct transcriptional repression of SIRT1. HIC1 is also essential for DSB repair as silencing of endogenous HIC1 in BJ-hTERT fibroblasts significantly delays DNA repair in functional Comet assays. HIC1 SUMOylation favours its interaction with MTA1, a component of NuRD complexes. In contrast with irreparable DSBs induced by 16-hours of etoposide treatment, we show that repairable DSBs induced by 1 h etoposide treatment do not increase HIC1 SUMOylation or its interaction with MTA1. Furthermore, HIC1 SUMOylation is dispensable for DNA repair since the non-SUMOylatable E316A mutant is as efficient as wt HIC1 in Comet assays. Upon induction of irreparable DSBs, the ATM-mediated increase of HIC1 SUMOylation is independent of its effector kinase Chk2. Moreover, irreparable DSBs strongly increase both the interaction of HIC1 with MTA1 and MTA3 and their binding to the SIRT1 promoter. To characterize the molecular mechanisms sustained by this increased repression potential, we established global expression profiles of BJ-hTERT fibroblasts transfected with HIC1-siRNA or control siRNA and treated or not with etoposide. We identified 475 genes potentially repressed by HIC1 with cell death and cell cycle as the main cellular functions identified by pathway analysis. Among them, CXCL12, EPHA4, TGFβR3 and TRIB2, also known as MTA1 target-genes, were validated by qRT-PCR analyses. Thus, our data demonstrate that HIC1 SUMOylation is important for the transcriptional response to non-repairable DSBs but dispensable for DNA repair.
Collapse
Affiliation(s)
- Sonia Paget
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161-M3T-Mechanisms of Tumorigenesis and Targeted Therapies, Lille, France
| | - Marion Dubuissez
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161-M3T-Mechanisms of Tumorigenesis and Targeted Therapies, Lille, France
- Present Address: Maisonneuve-Rosemont Hospital Research Center, Maisonneuve-Rosemont Hospital, Boulevard l'Assomption Montreal, Canada
| | - Vanessa Dehennaut
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161-M3T-Mechanisms of Tumorigenesis and Targeted Therapies, Lille, France
| | - Joe Nassour
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161-M3T-Mechanisms of Tumorigenesis and Targeted Therapies, Lille, France
- Present Address: The Salk Institute for Biological Studies, Molecular and Cell Biology Department, La Jolla, California, USA
| | - Brennan T. Harmon
- Genomics Core, Children's National Medical Center, Washington DC, USA
| | - Nathalie Spruyt
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161-M3T-Mechanisms of Tumorigenesis and Targeted Therapies, Lille, France
| | - Ingrid Loison
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161-M3T-Mechanisms of Tumorigenesis and Targeted Therapies, Lille, France
| | - Corinne Abbadie
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161-M3T-Mechanisms of Tumorigenesis and Targeted Therapies, Lille, France
| | - Brian R. Rood
- Center for Cancer and Immunology Research, Children's National Medical Center, Washington DC, USA
| | - Dominique Leprince
- University Lille, CNRS, Institut Pasteur de Lille, UMR 8161-M3T-Mechanisms of Tumorigenesis and Targeted Therapies, Lille, France
| |
Collapse
|
123
|
Zhang M, Skirkanich J, Lampson MA, Klein PS. Cell Cycle Remodeling and Zygotic Gene Activation at the Midblastula Transition. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 953:441-487. [DOI: 10.1007/978-3-319-46095-6_9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
124
|
Shiloh Y, Lederman HM. Ataxia-telangiectasia (A-T): An emerging dimension of premature ageing. Ageing Res Rev 2017; 33:76-88. [PMID: 27181190 DOI: 10.1016/j.arr.2016.05.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/02/2016] [Accepted: 05/10/2016] [Indexed: 12/28/2022]
Abstract
A-T is a prototype genome instability syndrome and a multifaceted disease. A-T leads to neurodegeneration - primarily cerebellar atrophy, immunodeficiency, oculocutaneous telangiectasia (dilated blood vessels), vestigial thymus and gonads, endocrine abnormalities, cancer predisposition and varying sensitivity to DNA damaging agents, particularly those that induce DNA double-strand breaks. With the recent increase in life expectancy of A-T patients, the premature ageing component of this disease is gaining greater awareness. The complex A-T phenotype reflects the ever growing number of functions assigned to the protein encoded by the responsible gene - the homeostatic protein kinase, ATM. The quest to thoroughly understand the complex A-T phenotype may reveal yet elusive ATM functions.
Collapse
|
125
|
Barzilai A, Schumacher B, Shiloh Y. Genome instability: Linking ageing and brain degeneration. Mech Ageing Dev 2017; 161:4-18. [DOI: 10.1016/j.mad.2016.03.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/23/2016] [Accepted: 03/26/2016] [Indexed: 02/06/2023]
|
126
|
Rahal ON, Fatfat M, Hankache C, Osman B, Khalife H, Machaca K, Muhtasib HG. Chk1 and DNA-PK mediate TPEN-induced DNA damage in a ROS dependent manner in human colon cancer cells. Cancer Biol Ther 2016; 17:1139-1148. [PMID: 27690730 DOI: 10.1080/15384047.2016.1235658] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Recently, we showed that the metal chelator TPEN targets colon cancer cells through redox cycling of copper. Here, we studied the DNA damage potential of TPEN and deciphered the role of Chk1, ATM and DNA-PK in TPEN-induced toxicity in 3 human colon cancer cell lines, HCT116, SW480 and HT29. We also investigated the role of reactive oxygen species (ROS) in TPEN-induced DNA damage. TPEN reduced cell viability in a dose- and time-dependent manner. Cytotoxicity was associated with significant DNA damage and higher expression of γ-H2AX protein and activation of ATM/ATR signaling pathway. Cell death by TPEN was dependent on ROS generation as evidenced by the reversal of cell viability, and DNA damage and the abrogation of γ-H2AX levels in the presence of antioxidants. Treatment with antioxidants, however, failed to reverse cytotoxicity at high TPEN concentrations (10µM). TPEN-induced cell death was also dependent on the redox cycling of copper since the copper chelator neocuproine inhibited DNA damage and reduced pChk1, γ-H2AX, and ATM protein expression. Cell death by low TPEN concentrations, involved ATM/ATR signaling in all 3 cell lines, since pre-incubation with specific inhibitors of ATM and DNA-PK led to the recovery of cells from TPEN-induced DNA damage. In addition, siRNA silencing of Chk1, DNA-PK and ATM abrogated the expression of γ-H2AX and reversed cell death, suggesting that Chk1 and DNA-PK mediate TPEN-induced cytotoxicity in colon cancer cells. This study shows for the first time the involvement of Chk1, DNA-PK and ATM in TPEN-induced DNA damage and confirms our previous findings that ROS generation and the redox cycling of copper in response to TPEN are the main mechanisms by which this compound induces cell death in human colon cancer cells. Inhibition of ATM or DNA-PK did not reverse cytotoxicity at high TPEN concentrations that cause excessive levels of ROS and irreversible cellular damage.
Collapse
Affiliation(s)
| | - Maamoun Fatfat
- a Department of Biology , American University of Beirut , Lebanon
| | - Carla Hankache
- a Department of Biology , American University of Beirut , Lebanon
| | - Bassam Osman
- a Department of Biology , American University of Beirut , Lebanon
| | - Hala Khalife
- b Department of Biology , Lebanese University , Lebanon
| | - Khaled Machaca
- c Department of Physiology and Biophysics , Weill Cornell Medical College , Qatar
| | | |
Collapse
|
127
|
p27Kip1 Is Required to Mediate a G1 Cell Cycle Arrest Downstream of ATM following Genotoxic Stress. PLoS One 2016; 11:e0162806. [PMID: 27611996 PMCID: PMC5017644 DOI: 10.1371/journal.pone.0162806] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 08/29/2016] [Indexed: 11/20/2022] Open
Abstract
The DNA damage response (DDR) is a coordinated signaling network that ensures the maintenance of genome stability under DNA damaging stress. In response to DNA lesions, activation of the DDR leads to the establishment of cell cycle checkpoints that delay cell-cycle progression and allow repair of the defects. The tumor suppressor p27Kip1 is a cyclin-CDK inhibitor that plays an important role in regulating quiescence in a variety of tissues. Several studies have suggested that p27Kip1 also plays a role in the maintenance of genomic integrity. Here we demonstrate that p27Kip1 is essential for the establishment of a G1 checkpoint arrest after DNA damage. We also uncovered that ATM phosphorylates p27Kip1 on a previously uncharacterized residue (Ser-140), which leads to its stabilization after induction of DNA double-strand breaks. Inhibition of this stabilization by replacing endogenous p27Kip1 with a Ser-140 phospho-mutant (S140A) significantly sensitized cells to IR treatments. Our findings reveal a novel role for p27Kip1 in the DNA damage response pathway and suggest that part of its tumor suppressing functions relies in its ability to mediate a G1 arrest after the induction of DNA double strand breaks.
Collapse
|
128
|
Nicotinamide Suppresses the DNA Damage Sensitivity of Saccharomyces cerevisiae Independently of Sirtuin Deacetylases. Genetics 2016; 204:569-579. [PMID: 27527516 DOI: 10.1534/genetics.116.193524] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 08/15/2016] [Indexed: 11/18/2022] Open
Abstract
Nicotinamide is both a reaction product and an inhibitor of the conserved sirtuin family of deacetylases, which have been implicated in a broad range of cellular functions in eukaryotes from yeast to humans. Phenotypes observed following treatment with nicotinamide are most often assumed to stem from inhibition of one or more of these enzymes. Here, we used this small molecule to inhibit multiple sirtuins at once during treatment with DNA damaging agents in the Saccharomyces cerevisiae model system. Since sirtuins have been previously implicated in the DNA damage response, we were surprised to observe that nicotinamide actually increased the survival of yeast cells exposed to the DNA damage agent MMS. Remarkably, we found that enhanced resistance to MMS in the presence of nicotinamide was independent of all five yeast sirtuins. Enhanced resistance was also independent of the nicotinamide salvage pathway, which uses nicotinamide as a substrate to generate NAD+, and of a DNA damage-induced increase in the salvage enzyme Pnc1 Our data suggest a novel and unexpected function for nicotinamide that has broad implications for its use in the study of sirtuin biology across model systems.
Collapse
|
129
|
Defective DNA repair and chromatin organization in patients with quiescent systemic lupus erythematosus. Arthritis Res Ther 2016; 18:182. [PMID: 27492607 PMCID: PMC4973109 DOI: 10.1186/s13075-016-1081-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 07/21/2016] [Indexed: 11/21/2022] Open
Abstract
Background Excessive autoantibody production characterizing systemic lupus erythematosus (SLE) occurs irrespective of the disease’s clinical status and is linked to increased lymphocyte apoptosis. Herein, we tested the hypothesis that defective DNA damage repair contributes to increased apoptosis in SLE. Methods We evaluated nucleotide excision repair at the N-ras locus, DNA double-strand breaks repair and apoptosis rates in peripheral blood mononuclear cells from anti-dsDNA autoantibody-positive patients (six with quiescent disease and six with proliferative nephritis) and matched healthy controls following ex vivo treatment with melphalan. Chromatin organization and expression levels of DNA repair- and apoptosis-associated genes were also studied in quiescent SLE. Results Defective nucleotide excision repair and DNA double-strand breaks repair were found in SLE, with lupus nephritis patients showing higher DNA damage levels than those with quiescent disease. Melphalan-induced apoptosis rates were higher in SLE than control cells and correlated inversely with DNA repair efficiency. Chromatin at the N-ras locus was more condensed in SLE than controls, while treatment with the histone deacetylase inhibitor vorinostat resulted in hyperacetylation of histone H4, chromatin decondensation, amelioration of DNA repair efficiency and decreased apoptosis. Accordingly, genes involved in DNA damage repair and signaling pathways, such as DDB1, ERCC2, XPA, XPC, MRE11A, RAD50, PARP1, MLH1, MLH3, and ATM were significantly underexpressed in SLE versus controls, whereas PPP1R15A, BARD1 and BBC3 genes implicated in apoptosis were significantly overexpressed. Conclusions Epigenetically regulated functional abnormalities of DNA repair machinery occur in SLE, regardless of clinical disease activity, and may promote lymphocyte apoptosis. Approaches to correct these abnormalities may be of therapeutic value in SLE. Electronic supplementary material The online version of this article (doi:10.1186/s13075-016-1081-3) contains supplementary material, which is available to authorized users.
Collapse
|
130
|
Ribezzo F, Shiloh Y, Schumacher B. Systemic DNA damage responses in aging and diseases. Semin Cancer Biol 2016; 37-38:26-35. [PMID: 26773346 PMCID: PMC4886830 DOI: 10.1016/j.semcancer.2015.12.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 12/28/2015] [Accepted: 12/31/2015] [Indexed: 01/09/2023]
Abstract
The genome is constantly attacked by a variety of genotoxic insults. The causal role for DNA damage in aging and cancer is exemplified by genetic defects in DNA repair that underlie a broad spectrum of acute and chronic human disorders that are characterized by developmental abnormalities, premature aging, and cancer predisposition. The disease symptoms are typically tissue-specific with uncertain genotype-phenotype correlation. The cellular DNA damage response (DDR) has been extensively investigated ever since yeast geneticists discovered DNA damage checkpoint mechanisms, several decades ago. In recent years, it has become apparent that not only cell-autonomous but also systemic DNA damage responses determine the outcome of genome instability in organisms. Understanding the mechanisms of non-cell-autonomous DNA damage responses will provide important new insights into the role of genome instability in human aging and a host of diseases including cancer and might better explain the complex phenotypes caused by genome instability.
Collapse
Affiliation(s)
- Flavia Ribezzo
- Institute for Genome Stability in Ageing and Disease, Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases (CECAD) Research Center, Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Yosef Shiloh
- The David and Inez Myers Laboratory for Genetic Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Björn Schumacher
- Institute for Genome Stability in Ageing and Disease, Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases (CECAD) Research Center, Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany.
| |
Collapse
|
131
|
Kaminsky N, Bihari O, Kanner S, Barzilai A. Connecting Malfunctioning Glial Cells and Brain Degenerative Disorders. GENOMICS, PROTEOMICS & BIOINFORMATICS 2016; 14:155-165. [PMID: 27245308 PMCID: PMC4936608 DOI: 10.1016/j.gpb.2016.04.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 12/19/2022]
Abstract
The DNA damage response (DDR) is a complex biological system activated by different types of DNA damage. Mutations in certain components of the DDR machinery can lead to genomic instability disorders that culminate in tissue degeneration, premature aging, and various types of cancers. Intriguingly, malfunctioning DDR plays a role in the etiology of late onset brain degenerative disorders such as Parkinson's, Alzheimer's, and Huntington's diseases. For many years, brain degenerative disorders were thought to result from aberrant neural death. Here we discuss the evidence that supports our novel hypothesis that brain degenerative diseases involve dysfunction of glial cells (astrocytes, microglia, and oligodendrocytes). Impairment in the functionality of glial cells results in pathological neuro-glial interactions that, in turn, generate a "hostile" environment that impairs the functionality of neuronal cells. These events can lead to systematic neural demise on a scale that appears to be proportional to the severity of the neurological deficit.
Collapse
Affiliation(s)
- Natalie Kaminsky
- Department of Neurobiology, George S. Wise, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ofer Bihari
- Department of Neurobiology, George S. Wise, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sivan Kanner
- Department of Neurobiology, George S. Wise, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel.
| | - Ari Barzilai
- Department of Neurobiology, George S. Wise, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel.
| |
Collapse
|
132
|
How Diet Intervention via Modulation of DNA Damage Response through MicroRNAs May Have an Effect on Cancer Prevention and Aging, an in Silico Study. Int J Mol Sci 2016; 17:ijms17050752. [PMID: 27213347 PMCID: PMC4881573 DOI: 10.3390/ijms17050752] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 04/29/2016] [Accepted: 05/09/2016] [Indexed: 12/11/2022] Open
Abstract
The DNA damage response (DDR) is a molecular mechanism that cells have evolved to sense DNA damage (DD) to promote DNA repair, or to lead to apoptosis, or cellular senescence if the damage is too extensive. Recent evidence indicates that microRNAs (miRs) play a critical role in the regulation of DDR. Dietary bioactive compounds through miRs may affect activity of numerous genes. Among the most studied bioactive compounds modulating expression of miRs are epi-gallocatechin-3-gallate, curcumin, resveratrol and n3-polyunsaturated fatty acids. To compare the impact of these dietary compounds on DD/DDR network modulation, we performed a literature search and an in silico analysis by the DIANA-mirPathv3 software. The in silico analysis allowed us to identify pathways shared by different miRs involved in DD/DDR vis-à-vis the specific compounds. The results demonstrate that certain miRs (e.g., -146, -21) play a central role in the interplay among DD/DDR and the bioactive compounds. Furthermore, some specific pathways, such as "fatty acids biosynthesis/metabolism", "extracellular matrix-receptor interaction" and "signaling regulating the pluripotency of stem cells", appear to be targeted by most miRs affected by the studied compounds. Since DD/DDR and these pathways are strongly related to aging and carcinogenesis, the present in silico results of our study suggest that monitoring the induction of specific miRs may provide the means to assess the antiaging and chemopreventive properties of particular dietary compounds.
Collapse
|
133
|
Acevedo J, Yan S, Michael WM. Direct Binding to Replication Protein A (RPA)-coated Single-stranded DNA Allows Recruitment of the ATR Activator TopBP1 to Sites of DNA Damage. J Biol Chem 2016; 291:13124-31. [PMID: 27129245 DOI: 10.1074/jbc.m116.729194] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Indexed: 12/29/2022] Open
Abstract
A critical event for the ability of cells to tolerate DNA damage and replication stress is activation of the ATR kinase. ATR activation is dependent on the BRCT (BRCA1 C terminus) repeat-containing protein TopBP1. Previous work has shown that recruitment of TopBP1 to sites of DNA damage and stalled replication forks is necessary for downstream events in ATR activation; however, the mechanism for this recruitment was not known. Here, we use protein binding assays and functional studies in Xenopus egg extracts to show that TopBP1 makes a direct interaction, via its BRCT2 domain, with RPA-coated single-stranded DNA. We identify a point mutant that abrogates this interaction and show that this mutant fails to accumulate at sites of DNA damage and that the mutant cannot activate ATR. These data thus supply a mechanism for how the critical ATR activator, TopBP1, senses DNA damage and stalled replication forks to initiate assembly of checkpoint signaling complexes.
Collapse
Affiliation(s)
- Julyana Acevedo
- From the Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089 and
| | - Shan Yan
- the Department of Biological Sciences, University of North Carolina, Charlotte, North Carolina 28223
| | - W Matthew Michael
- From the Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089 and
| |
Collapse
|
134
|
DNA damage regulation and its role in drug-related phenotypes in the malaria parasites. Sci Rep 2016; 6:23603. [PMID: 27033103 PMCID: PMC4817041 DOI: 10.1038/srep23603] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 03/10/2016] [Indexed: 11/29/2022] Open
Abstract
DNA of malaria parasites, Plasmodium falciparum, is subjected to extraordinary high levels of genotoxic insults during its complex life cycle within both the mosquito and human host. Accordingly, most of the components of DNA repair machinery are conserved in the parasite genome. Here, we investigated the genome-wide responses of P. falciparum to DNA damaging agents and provided transcriptional evidence of the existence of the double strand break and excision repair system. We also showed that acetylation at H3K9, H4K8, and H3K56 play a role in the direct and indirect response to DNA damage induced by an alkylating agent, methyl methanesulphonate (MMS). Artemisinin, the first line antimalarial chemotherapeutics elicits a similar response compared to MMS which suggests its activity as a DNA damaging agent. Moreover, in contrast to the wild-type P. falciparum, two strains (Dd2 and W2) previously shown to exhibit a mutator phenotype, fail to induce their DNA repair upon MMS-induced DNA damage. Genome sequencing of the two mutator strains identified point mutations in 18 DNA repair genes which may contribute to this phenomenon.
Collapse
|
135
|
Svetec N, Cridland JM, Zhao L, Begun DJ. The Adaptive Significance of Natural Genetic Variation in the DNA Damage Response of Drosophila melanogaster. PLoS Genet 2016; 12:e1005869. [PMID: 26950216 PMCID: PMC4780809 DOI: 10.1371/journal.pgen.1005869] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/22/2016] [Indexed: 01/15/2023] Open
Abstract
Despite decades of work, our understanding of the distribution of fitness effects of segregating genetic variants in natural populations remains largely incomplete. One form of selection that can maintain genetic variation is spatially varying selection, such as that leading to latitudinal clines. While the introduction of population genomic approaches to understanding spatially varying selection has generated much excitement, little successful effort has been devoted to moving beyond genome scans for selection to experimental analysis of the relevant biology and the development of experimentally motivated hypotheses regarding the agents of selection; it remains an interesting question as to whether the vast majority of population genomic work will lead to satisfying biological insights. Here, motivated by population genomic results, we investigate how spatially varying selection in the genetic model system, Drosophila melanogaster, has led to genetic differences between populations in several components of the DNA damage response. UVB incidence, which is negatively correlated with latitude, is an important agent of DNA damage. We show that sensitivity of early embryos to UVB exposure is strongly correlated with latitude such that low latitude populations show much lower sensitivity to UVB. We then show that lines with lower embryo UVB sensitivity also exhibit increased capacity for repair of damaged sperm DNA by the oocyte. A comparison of the early embryo transcriptome in high and low latitude embryos provides evidence that one mechanism of adaptive DNA repair differences between populations is the greater abundance of DNA repair transcripts in the eggs of low latitude females. Finally, we use population genomic comparisons of high and low latitude samples to reveal evidence that multiple components of the DNA damage response and both coding and non-coding variation likely contribute to adaptive differences in DNA repair between populations.
Collapse
Affiliation(s)
- Nicolas Svetec
- Department of Evolution and Ecology, University of California, Davis, Davis, California, United States of America
| | - Julie M. Cridland
- Department of Evolution and Ecology, University of California, Davis, Davis, California, United States of America
| | - Li Zhao
- Department of Evolution and Ecology, University of California, Davis, Davis, California, United States of America
| | - David J. Begun
- Department of Evolution and Ecology, University of California, Davis, Davis, California, United States of America
| |
Collapse
|
136
|
Tresini M, Marteijn JA, Vermeulen W. Bidirectional coupling of splicing and ATM signaling in response to transcription-blocking DNA damage. RNA Biol 2016; 13:272-8. [PMID: 26913497 PMCID: PMC4829274 DOI: 10.1080/15476286.2016.1142039] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 01/08/2016] [Accepted: 01/08/2016] [Indexed: 12/24/2022] Open
Abstract
In response to DNA damage cells activate intricate protein networks to ensure genomic fidelity and tissue homeostasis. DNA damage response signaling pathways coordinate these networks and determine cellular fates, in part, by modulating RNA metabolism. Here we discuss a replication-independent pathway activated by transcription-blocking DNA lesions, which utilizes the ATM signaling kinase to regulate spliceosome function in a reciprocal manner. We present a model according to which, displacement of co-transcriptional spliceosomes from lesion-arrested RNA polymerases, culminates in R-loop formation and non-canonical ATM activation. ATM signals in a feed-forward fashion to further impede spliceosome organization and regulates UV-induced gene expression and alternative splicing genome-wide. This reciprocal coupling between ATM and the spliceosome highlights the importance of ATM signaling in the cellular response to transcription-blocking lesions and supports a key role of the splicing machinery in this process.
Collapse
Affiliation(s)
- Maria Tresini
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jurgen A. Marteijn
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| |
Collapse
|
137
|
The Adenovirus E4orf4 Protein Provides a Novel Mechanism for Inhibition of the DNA Damage Response. PLoS Pathog 2016; 12:e1005420. [PMID: 26867009 PMCID: PMC4750969 DOI: 10.1371/journal.ppat.1005420] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 01/06/2016] [Indexed: 12/20/2022] Open
Abstract
The DNA damage response (DDR) is a conglomerate of pathways designed to detect DNA damage and signal its presence to cell cycle checkpoints and to the repair machinery, allowing the cell to pause and mend the damage, or if the damage is too severe, to trigger apoptosis or senescence. Various DDR branches are regulated by kinases of the phosphatidylinositol 3-kinase-like protein kinase family, including ataxia-telangiectasia mutated (ATM) and ATM- and Rad3-related (ATR). Replication intermediates and linear double-stranded genomes of DNA viruses are perceived by the cell as DNA damage and activate the DDR. If allowed to operate, the DDR will stimulate ligation of viral genomes and will inhibit virus replication. To prevent this outcome, many DNA viruses evolved ways to limit the DDR. As part of its attack on the DDR, adenovirus utilizes various viral proteins to cause degradation of DDR proteins and to sequester the MRN damage sensor outside virus replication centers. Here we show that adenovirus evolved yet another novel mechanism to inhibit the DDR. The E4orf4 protein, together with its cellular partner PP2A, reduces phosphorylation of ATM and ATR substrates in virus-infected cells and in cells treated with DNA damaging drugs, and causes accumulation of damaged DNA in the drug-treated cells. ATM and ATR are not mutually required for inhibition of their signaling pathways by E4orf4. ATM and ATR deficiency as well as E4orf4 expression enhance infection efficiency. Furthermore, E4orf4, previously reported to induce cancer-specific cell death when expressed alone, sensitizes cells to killing by sub-lethal concentrations of DNA damaging drugs, likely because it inhibits DNA damage repair. These findings provide one explanation for the cancer-specificity of E4orf4-induced cell death as many cancers have DDR deficiencies leading to increased reliance on the remaining intact DDR pathways and to enhanced susceptibility to DDR inhibitors such as E4orf4. Thus DDR inhibition by E4orf4 contributes both to the efficiency of adenovirus replication and to the ability of E4orf4 to kill cancer cells.
Collapse
|
138
|
An J, Guo P, Shang Y, Zhong Y, Zhang X, Yu Y, Yu Z. The "adaptive responses" of low concentrations of HBCD in L02 cells and the underlying molecular mechanisms. CHEMOSPHERE 2016; 145:68-76. [PMID: 26688241 DOI: 10.1016/j.chemosphere.2015.11.071] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 11/18/2015] [Accepted: 11/19/2015] [Indexed: 06/05/2023]
Abstract
This study aimed to investigate the "adaptive responses" of hexabromocyclododecanes (HBCD) at environmentally relevant concentrations in human hepatocytes L02. L02 cells were pre-treated with low concentrations of HBCD (10(-13)-10(-11) M), followed by treatment with high concentrations of HBCD, α-hexachlorocyclohexane (α-HCH), polychlorinated biphenyls (PCBs), or polybrominated diphenyl ether-47 (BDE47). The results showed that the pre-treatment with low concentrations of HBCD induced "adaptive responses" to high concentrations of HBCD/α-HCH exposure (but not to PCBs and BDE47), as evidenced by attenuation of survival inhibition, reactive oxygen species (ROS) over-production, and deoxyribonucleic acid (DNA) damage induction. The "adaptive responses" induced by low concentrations of HBCD, which depended on the activation of the phosphatidylinositide 3-kinase/protein kinase B (PI3K/Akt) pathway, reduced the phosphorylation of adenosine monophosphate-activated kinase (AMPK) and enhanced the phosphorylation of p38 mitogen-activated protein kinases (p38 MAPK). The observations were further confirmed by the experiments with inhibitors. Moreover, the evaluation on the changes of metabolic enzymes revealed that HBCD and α-HCH shared a similar pattern of cytochrome P450 induction (CYP2B6), which was different from those of PCBs and BDE47 (CYP1A1 and CYP2B6). These results indicated that low concentrations of HBCD could induce "adaptive responses" to the subsequent treatment with high concentrations of HBCD/α-HCH in L02 cells, which was associated with the PI3K/Akt pathway, and AMPK and p38 MAPK signaling. The "adaptive responses" seemed to be dependent on the types of chemicals in terms of the metabolic patterns and chemical structures.
Collapse
Affiliation(s)
- Jing An
- Institute of Environmental Pollution and Health, School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, PR China.
| | - Panpan Guo
- Institute of Environmental Pollution and Health, School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, PR China
| | - Yu Shang
- Institute of Environmental Pollution and Health, School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, PR China
| | - Yufang Zhong
- Institute of Environmental Pollution and Health, School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, PR China
| | - Xinyu Zhang
- Institute of Environmental Pollution and Health, School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, PR China
| | - Yingxin Yu
- Institute of Environmental Pollution and Health, School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, PR China
| | - Zhiqiang Yu
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, PR China
| |
Collapse
|
139
|
Li Z, Pearlman AH, Hsieh P. DNA mismatch repair and the DNA damage response. DNA Repair (Amst) 2016; 38:94-101. [PMID: 26704428 PMCID: PMC4740233 DOI: 10.1016/j.dnarep.2015.11.019] [Citation(s) in RCA: 199] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 09/17/2015] [Accepted: 11/30/2015] [Indexed: 12/12/2022]
Abstract
This review discusses the role of DNA mismatch repair (MMR) in the DNA damage response (DDR) that triggers cell cycle arrest and, in some cases, apoptosis. Although the focus is on findings from mammalian cells, much has been learned from studies in other organisms including bacteria and yeast [1,2]. MMR promotes a DDR mediated by a key signaling kinase, ATM and Rad3-related (ATR), in response to various types of DNA damage including some encountered in widely used chemotherapy regimes. An introduction to the DDR mediated by ATR reveals its immense complexity and highlights the many biological and mechanistic questions that remain. Recent findings and future directions are highlighted.
Collapse
Affiliation(s)
- Zhongdao Li
- Genetics & Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bldg. 5 Rm. 324, 5 Memorial Dr. MSC 0538, Bethesda, MD 20892-0538, USA
| | - Alexander H Pearlman
- Genetics & Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bldg. 5 Rm. 324, 5 Memorial Dr. MSC 0538, Bethesda, MD 20892-0538, USA
| | - Peggy Hsieh
- Genetics & Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bldg. 5 Rm. 324, 5 Memorial Dr. MSC 0538, Bethesda, MD 20892-0538, USA.
| |
Collapse
|
140
|
RFWD3-Dependent Ubiquitination of RPA Regulates Repair at Stalled Replication Forks. Mol Cell 2016; 60:280-93. [PMID: 26474068 DOI: 10.1016/j.molcel.2015.09.011] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 08/02/2015] [Accepted: 09/10/2015] [Indexed: 02/07/2023]
Abstract
We have used quantitative proteomics to profile ubiquitination in the DNA damage response (DDR). We demonstrate that RPA, which functions as a protein scaffold in the replication stress response, is multiply ubiquitinated upon replication fork stalling. Ubiquitination of RPA occurs on chromatin, involves sites outside its DNA binding channel, does not cause proteasomal degradation, and increases under conditions of fork collapse, suggesting a role in repair at stalled forks. We demonstrate that the E3 ligase RFWD3 mediates RPA ubiquitination. RFWD3 is necessary for replication fork restart, normal repair kinetics during replication stress, and homologous recombination (HR) at stalled replication forks. Mutational analysis suggests that multisite ubiquitination of the entire RPA complex is responsible for repair at stalled forks. Multisite protein group sumoylation is known to promote HR in yeast. Our findings reveal a similar requirement for multisite protein group ubiquitination during HR at stalled forks in mammalian cells.
Collapse
|
141
|
Zhou X. How do kinases contribute to tonicity-dependent regulation of the transcription factor NFAT5? World J Nephrol 2016; 5:20-32. [PMID: 26788461 PMCID: PMC4707165 DOI: 10.5527/wjn.v5.i1.20] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/12/2015] [Accepted: 12/11/2015] [Indexed: 02/06/2023] Open
Abstract
NFAT5 plays a critical role in maintaining the renal functions. Its dis-regulation in the kidney leads to or is associated with certain renal diseases or disorders, most notably the urinary concentration defect. Hypertonicity, which the kidney medulla is normally exposed to, activates NFAT5 through phosphorylation of a signaling molecule or NFAT5 itself. Hypotonicity inhibits NFAT5 through a similar mechanism. More than a dozen of protein and lipid kinases have been identified to contribute to tonicity-dependent regulation of NFAT5. Hypertonicity activates NFAT5 by increasing its nuclear localization and transactivating activity in the early phase and protein abundance in the late phase. The known mechanism for inhibition of NFAT5 by hypotonicity is a decrease of nuclear NFAT5. The present article reviews the effect of each kinase on NFAT5 nuclear localization, transactivation and protein abundance, and the relationship among these kinases, if known. Cyclosporine A and tacrolimus suppress immune reactions by inhibiting the phosphatase calcineurin-dependent activation of NFAT1. It is hoped that this review would stimulate the interest to seek explanations from the NFAT5 regulatory pathways for certain clinical presentations and to explore novel therapeutic approaches based on the pathways. On the basic science front, this review raises two interesting questions. The first one is how these kinases can specifically signal to NFAT5 in the context of hypertonicity or hypotonicity, because they also regulate other cellular activities and even opposite activities in some cases. The second one is why these many kinases, some of which might have redundant functions, are needed to regulate NFAT5 activity. This review reiterates the concept of signaling through cooperation. Cells need these kinases working in a coordinated way to provide the signaling specificity that is lacking in the individual one. Redundancy in regulation of NFAT5 is a critical strategy for cells to maintain robustness against hypertonic or hypotonic stress.
Collapse
|
142
|
Caron P, Choudjaye J, Clouaire T, Bugler B, Daburon V, Aguirrebengoa M, Mangeat T, Iacovoni JS, Álvarez-Quilón A, Cortés-Ledesma F, Legube G. Non-redundant Functions of ATM and DNA-PKcs in Response to DNA Double-Strand Breaks. Cell Rep 2015; 13:1598-609. [PMID: 26586426 PMCID: PMC4670905 DOI: 10.1016/j.celrep.2015.10.024] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 09/04/2015] [Accepted: 10/06/2015] [Indexed: 12/13/2022] Open
Abstract
DNA double-strand breaks (DSBs) elicit the so-called DNA damage response (DDR), largely relying on ataxia telangiectasia mutated (ATM) and DNA-dependent protein kinase (DNA-PKcs), two members of the PI3K-like kinase family, whose respective functions during the sequential steps of the DDR remains controversial. Using the DIvA system (DSB inducible via AsiSI) combined with high-resolution mapping and advanced microscopy, we uncovered that both ATM and DNA-PKcs spread in cis on a confined region surrounding DSBs, independently of the pathway used for repair. However, once recruited, these kinases exhibit non-overlapping functions on end joining and γH2AX domain establishment. More specifically, we found that ATM is required to ensure the association of multiple DSBs within "repair foci." Our results suggest that ATM acts not only on chromatin marks but also on higher-order chromatin organization to ensure repair accuracy and survival.
Collapse
Affiliation(s)
- Pierre Caron
- Université de Toulouse, UPS, LBCMCP, 118 route de Narbonne, 31062 Toulouse, France; CNRS, LBCMCP, 31062 Toulouse, France
| | - Jonathan Choudjaye
- Université de Toulouse, UPS, LBCMCP, 118 route de Narbonne, 31062 Toulouse, France; CNRS, LBCMCP, 31062 Toulouse, France
| | - Thomas Clouaire
- Université de Toulouse, UPS, LBCMCP, 118 route de Narbonne, 31062 Toulouse, France; CNRS, LBCMCP, 31062 Toulouse, France
| | - Béatrix Bugler
- Université de Toulouse, UPS, LBCMCP, 118 route de Narbonne, 31062 Toulouse, France; CNRS, LBCMCP, 31062 Toulouse, France
| | - Virginie Daburon
- Université de Toulouse, UPS, LBCMCP, 118 route de Narbonne, 31062 Toulouse, France; CNRS, LBCMCP, 31062 Toulouse, France
| | - Marion Aguirrebengoa
- Université de Toulouse, UPS, LBCMCP, 118 route de Narbonne, 31062 Toulouse, France; CNRS, LBCMCP, 31062 Toulouse, France
| | - Thomas Mangeat
- Université de Toulouse, UPS, LBCMCP, 118 route de Narbonne, 31062 Toulouse, France; CNRS, LBCMCP, 31062 Toulouse, France
| | - Jason S Iacovoni
- Bioinformatic Plateau I2MC, INSERM and University of Toulouse, 1 Avenue Jean Poulhes, BP 84225, 31432 Toulouse Cedex 4, France
| | - Alejandro Álvarez-Quilón
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), CSIC-Universidad de Sevilla, Sevilla 41092, Spain
| | - Felipe Cortés-Ledesma
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), CSIC-Universidad de Sevilla, Sevilla 41092, Spain
| | - Gaëlle Legube
- Université de Toulouse, UPS, LBCMCP, 118 route de Narbonne, 31062 Toulouse, France; CNRS, LBCMCP, 31062 Toulouse, France.
| |
Collapse
|
143
|
Kapoor P, Bao Y, Xiao J, Luo J, Shen J, Persinger J, Peng G, Ranish J, Bartholomew B, Shen X. Regulation of Mec1 kinase activity by the SWI/SNF chromatin remodeling complex. Genes Dev 2015; 29:591-602. [PMID: 25792597 PMCID: PMC4378192 DOI: 10.1101/gad.257626.114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Kapoor et al. found that the SWI/SNF chromatin remodeling complex is capable of regulating the activity of S. cerevisiae checkpoint kinase Mec1. SWI/SNF can activate Mec1 kinase activity in the absence of chromatin or known activators such as Dbp11. The subunit requirement of SWI/SNF-mediated Mec1 regulation differs from that of SWI/SNF-mediated chromatin remodeling. These findings suggest that ATP-dependent chromatin remodeling complexes can regulate non-chromatin substrates such as a checkpoint kinase. ATP-dependent chromatin remodeling complexes alter chromatin structure through interactions with chromatin substrates such as DNA, histones, and nucleosomes. However, whether chromatin remodeling complexes have the ability to regulate nonchromatin substrates remains unclear. Saccharomyces cerevisiae checkpoint kinase Mec1 (ATR in mammals) is an essential master regulator of genomic integrity. Here we found that the SWI/SNF chromatin remodeling complex is capable of regulating Mec1 kinase activity. In vivo, Mec1 activity is reduced by the deletion of Snf2, the core ATPase subunit of the SWI/SNF complex. SWI/SNF interacts with Mec1, and cross-linking studies revealed that the Snf2 ATPase is the main interaction partner for Mec1. In vitro, SWI/SNF can activate Mec1 kinase activity in the absence of chromatin or known activators such as Dpb11. The subunit requirement of SWI/SNF-mediated Mec1 regulation differs from that of SWI/SNF-mediated chromatin remodeling. Functionally, SWI/SNF-mediated Mec1 regulation specifically occurs in S phase of the cell cycle. Together, these findings identify a novel regulator of Mec1 kinase activity and suggest that ATP-dependent chromatin remodeling complexes can regulate nonchromatin substrates such as a checkpoint kinase.
Collapse
Affiliation(s)
- Prabodh Kapoor
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Yunhe Bao
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Jing Xiao
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Jie Luo
- Institute for Systems Biology, Seattle, Washington 98109, USA
| | - Jianfeng Shen
- Department of Clinical Cancer Prevention, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jim Persinger
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Guang Peng
- Department of Clinical Cancer Prevention, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jeff Ranish
- Institute for Systems Biology, Seattle, Washington 98109, USA
| | - Blaine Bartholomew
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Xuetong Shen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA;
| |
Collapse
|
144
|
Choi JH, Kim SY, Kim SK, Kemp MG, Sancar A. An Integrated Approach for Analysis of the DNA Damage Response in Mammalian Cells: NUCLEOTIDE EXCISION REPAIR, DNA DAMAGE CHECKPOINT, AND APOPTOSIS. J Biol Chem 2015; 290:28812-21. [PMID: 26438822 DOI: 10.1074/jbc.m115.690354] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Indexed: 11/06/2022] Open
Abstract
DNA damage by UV and UV-mimetic agents elicits a set of inter-related responses in mammalian cells, including DNA repair, DNA damage checkpoints, and apoptosis. Conventionally, these responses are analyzed separately using different methodologies. Here we describe a unified approach that is capable of quantifying all three responses in parallel using lysates from the same population of cells. We show that a highly sensitive in vivo excision repair assay is capable of detecting nucleotide excision repair of a wide spectrum of DNA lesions (UV damage, chemical carcinogens, and chemotherapeutic drugs) within minutes of damage induction. This method therefore allows for a real-time measure of nucleotide excision repair activity that can be monitored in conjunction with other components of the DNA damage response, including DNA damage checkpoint and apoptotic signaling. This approach therefore provides a convenient and reliable platform for simultaneously examining multiple aspects of the DNA damage response in a single population of cells that can be applied for a diverse array of carcinogenic and chemotherapeutic agents.
Collapse
Affiliation(s)
- Jun-Hyuk Choi
- From the Center for Bioanalysis, Department of Metrology for Quality of Life, Korea Research Institute of Standards and Science, Daejeon 305-340, South Korea, the Department of Bio-Analytical Science, University of Science & Technology, Daejeon 305-350, South Korea, and
| | - So-Young Kim
- From the Center for Bioanalysis, Department of Metrology for Quality of Life, Korea Research Institute of Standards and Science, Daejeon 305-340, South Korea
| | - Sook-Kyung Kim
- From the Center for Bioanalysis, Department of Metrology for Quality of Life, Korea Research Institute of Standards and Science, Daejeon 305-340, South Korea, the Department of Bio-Analytical Science, University of Science & Technology, Daejeon 305-350, South Korea, and
| | - Michael G Kemp
- the Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-7260
| | - Aziz Sancar
- the Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-7260
| |
Collapse
|
145
|
The Set3 Complex Antagonizes the MYST Acetyltransferase Esa1 in the DNA Damage Response. Mol Cell Biol 2015; 35:3714-25. [PMID: 26303527 DOI: 10.1128/mcb.00298-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 08/14/2015] [Indexed: 11/20/2022] Open
Abstract
Acetylation is a dynamic posttranslational modification that contributes to chromatin-regulated processes, including DNA replication, repair, recombination, and gene expression. Acetylation is controlled by complexes containing opposing lysine and histone acetyltransferase (KAT and HAT) and deacetylase (KDAC and HDAC) activities. The essential MYST family Esa1 KAT acetylates core histones and many nonhistone substrates. Phenotypes of esa1 mutants include transcriptional silencing and activation defects, impaired growth at high temperatures, and sensitivity to DNA damage. The KDAC Rpd3 was previously identified as an activity opposing Esa1, as its deletion suppresses growth and silencing defects of esa1 mutants. However, loss of Rpd3 does not suppress esa1 DNA damage sensitivity. In this work, we identified Hos2 as a KDAC counteracting ESA1 in the damage response. Deletion of HOS2 resulted in changes of esa1's transcriptional response upon damage. Further, loss of HOS2 or components of the Set3 complex (Set3C) in which it acts specifically suppressed damage sensitivity and restored esa1 histone H4 acetylation. This rescue was mediated via loss of either Set3C integrity or of its binding to dimethylated histone H3K4. Our results thus add new insight into the interactions of an essential MYST acetyltransferase with diverse deacetylases to respond specifically to environmental and physiological challenges.
Collapse
|
146
|
Kijas AW, Lim YC, Bolderson E, Cerosaletti K, Gatei M, Jakob B, Tobias F, Taucher-Scholz G, Gueven N, Oakley G, Concannon P, Wolvetang E, Khanna KK, Wiesmüller L, Lavin MF. ATM-dependent phosphorylation of MRE11 controls extent of resection during homology directed repair by signalling through Exonuclease 1. Nucleic Acids Res 2015; 43:8352-67. [PMID: 26240375 PMCID: PMC4787824 DOI: 10.1093/nar/gkv754] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 07/14/2015] [Indexed: 02/07/2023] Open
Abstract
The MRE11/RAD50/NBS1 (MRN) complex plays a central role as a sensor of DNA double strand breaks (DSB) and is responsible for the efficient activation of ataxia-telangiectasia mutated (ATM) kinase. Once activated ATM in turn phosphorylates RAD50 and NBS1, important for cell cycle control, DNA repair and cell survival. We report here that MRE11 is also phosphorylated by ATM at S676 and S678 in response to agents that induce DNA DSB, is dependent on the presence of NBS1, and does not affect the association of members of the complex or ATM activation. A phosphosite mutant (MRE11S676AS678A) cell line showed decreased cell survival and increased chromosomal aberrations after radiation exposure indicating a defect in DNA repair. Use of GFP-based DNA repair reporter substrates in MRE11S676AS678A cells revealed a defect in homology directed repair (HDR) but single strand annealing was not affected. More detailed investigation revealed that MRE11S676AS678A cells resected DNA ends to a greater extent at sites undergoing HDR. Furthermore, while ATM-dependent phosphorylation of Kap1 and SMC1 was normal in MRE11S676AS678A cells, there was no phosphorylation of Exonuclease 1 consistent with the defect in HDR. These results describe a novel role for ATM-dependent phosphorylation of MRE11 in limiting the extent of resection mediated through Exonuclease 1.
Collapse
Affiliation(s)
- Amanda W Kijas
- The University of Queensland, UQ Centre for Clinical Research, University of Queensland, Brisbane, Queensland 4029, Australia
| | - Yi Chieh Lim
- Brain Cancer Research Unit, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Emma Bolderson
- Genome Stability Laboratory, Translational Research Institute, Queensland University of Technology, Queensland 4102, Australia
| | - Karen Cerosaletti
- Translational Research Program, Benaroya Research Institute, Seattle, WA 981010, USA
| | - Magtouf Gatei
- The University of Queensland, UQ Centre for Clinical Research, University of Queensland, Brisbane, Queensland 4029, Australia
| | - Burkhard Jakob
- GSI Helmholtzzentrum für Schwerionenforschung, Darmstadt 64291, Germany
| | - Frank Tobias
- GSI Helmholtzzentrum für Schwerionenforschung, Darmstadt 64291, Germany
| | | | - Nuri Gueven
- School of Medicine, Faculty of Health, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Greg Oakley
- University of Nebraska College of Dentistry, Lincoln, NE 68583-0740, USA
| | - Patrick Concannon
- Genetics Institute, University of Florida, Gainesville, Florida, FL 3261, USA
| | - Ernst Wolvetang
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane 4072, Australia
| | - Kum Kum Khanna
- Signal transduction, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynaecology, University of Ulm, Ulm 89075, Germany
| | - Martin F Lavin
- The University of Queensland, UQ Centre for Clinical Research, University of Queensland, Brisbane, Queensland 4029, Australia
| |
Collapse
|
147
|
Defining the Contribution of MC1R Physiological Ligands to ATR Phosphorylation at Ser435, a Predictor of DNA Repair in Melanocytes. J Invest Dermatol 2015; 135:3086-3095. [PMID: 26168232 PMCID: PMC4648643 DOI: 10.1038/jid.2015.280] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 06/17/2015] [Accepted: 06/26/2015] [Indexed: 01/18/2023]
Abstract
The melanocortin 1 receptor (MC1R), a GS-coupled receptor that signals through cAMP and PKA, regulates pigmentation, adaptive tanning, and melanoma resistance. MC1R-cAMP signaling promotes PKA-mediated phosphorylation of ataxia telangiectasia and rad3-related (ATR) at Ser435 (ATR-pS435), a modification that enhances nucleotide excision repair (NER) by facilitating recruitment of the XPA protein to sites of UV-induced DNA damage. High-throughput methods were developed to quantify ATR-pS435, measure XPA-photodamage interactions and assess NER function. We report that melanocyte stimulating hormone (α-MSH) or adrenocorticotropic hormone (ACTH) induce ATR-pS435, enhance XPA’s association with UV-damaged DNA and optimize melanocytic NER. In contrast, MC1R antagonists agouti signaling protein (ASIP) or human β-defensin 3 (HBD3) interfere with ATR-pS435 generation, impair the XPA-DNA interaction and reduce DNA repair. Although ASIP and HBD3 each blocked α-MSH-mediated induction of the signaling pathway, only ASIP depleted basal ATR-pS435. Our findings confirm that ASIP diminishes agonist-independent MC1R basal signaling whereas HBD3 is a neutral MC1R antagonist that blocks activation by melanocortins. Furthermore, our data suggest that ATR-pS435 may be a useful biomarker for the DNA repair-deficient MC1R phenotype.
Collapse
|
148
|
Tresini M, Warmerdam DO, Kolovos P, Snijder L, Vrouwe MG, Demmers JA, van IJcken WF, Grosveld FG, Medema RH, Hoeijmakers JH, Mullenders LH, Vermeulen W, Marteijn JA. The core spliceosome as target and effector of non-canonical ATM signalling. Nature 2015; 523:53-8. [PMID: 26106861 PMCID: PMC4501432 DOI: 10.1038/nature14512] [Citation(s) in RCA: 188] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 05/11/2015] [Indexed: 01/19/2023]
Abstract
In response to DNA damage, tissue homoeostasis is ensured by protein networks promoting DNA repair, cell cycle arrest or apoptosis. DNA damage response signalling pathways coordinate these processes, partly by propagating gene-expression-modulating signals. DNA damage influences not only the abundance of messenger RNAs, but also their coding information through alternative splicing. Here we show that transcription-blocking DNA lesions promote chromatin displacement of late-stage spliceosomes and initiate a positive feedback loop centred on the signalling kinase ATM. We propose that initial spliceosome displacement and subsequent R-loop formation is triggered by pausing of RNA polymerase at DNA lesions. In turn, R-loops activate ATM, which signals to impede spliceosome organization further and augment ultraviolet-irradiation-triggered alternative splicing at the genome-wide level. Our findings define R-loop-dependent ATM activation by transcription-blocking lesions as an important event in the DNA damage response of non-replicating cells, and highlight a key role for spliceosome displacement in this process.
Collapse
Affiliation(s)
- Maria Tresini
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Daniël O. Warmerdam
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Petros Kolovos
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Loes Snijder
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mischa G. Vrouwe
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeroen A.A. Demmers
- Center for Biomics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Frank G. Grosveld
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - René H. Medema
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jan H.J. Hoeijmakers
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Leon H.F. Mullenders
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Wim Vermeulen
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jurgen A. Marteijn
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| |
Collapse
|
149
|
Meir M, Galanty Y, Kashani L, Blank M, Khosravi R, Fernández-Ávila MJ, Cruz-García A, Star A, Shochot L, Thomas Y, Garrett LJ, Chamovitz DA, Bodine DM, Kurz T, Huertas P, Ziv Y, Shiloh Y. The COP9 signalosome is vital for timely repair of DNA double-strand breaks. Nucleic Acids Res 2015; 43:4517-30. [PMID: 25855810 PMCID: PMC4482063 DOI: 10.1093/nar/gkv270] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 03/16/2015] [Accepted: 03/17/2015] [Indexed: 01/07/2023] Open
Abstract
The DNA damage response is vigorously activated by DNA double-strand breaks (DSBs). The chief mobilizer of the DSB response is the ATM protein kinase. We discovered that the COP9 signalosome (CSN) is a crucial player in the DSB response and an ATM target. CSN is a protein complex that regulates the activity of cullin ring ubiquitin ligase (CRL) complexes by removing the ubiquitin-like protein, NEDD8, from their cullin scaffold. We find that the CSN is physically recruited to DSB sites in a neddylation-dependent manner, and is required for timely repair of DSBs, affecting the balance between the two major DSB repair pathways-nonhomologous end-joining and homologous recombination repair (HRR). The CSN is essential for the processivity of deep end-resection-the initial step in HRR. Cullin 4a (CUL4A) is recruited to DSB sites in a CSN- and neddylation-dependent manner, suggesting that CSN partners with CRL4 in this pathway. Furthermore, we found that ATM-mediated phosphorylation of CSN subunit 3 on S410 is critical for proper DSB repair, and that loss of this phosphorylation site alone is sufficient to cause a DDR deficiency phenotype in the mouse. This novel branch of the DSB response thus significantly affects genome stability.
Collapse
Affiliation(s)
- Michal Meir
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, George S. Wise Faculty of Life sciences, Tel Aviv University, Tel Aviv, 69978 Israel
| | - Yaron Galanty
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, George S. Wise Faculty of Life sciences, Tel Aviv University, Tel Aviv, 69978 Israel
| | - Lior Kashani
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, George S. Wise Faculty of Life sciences, Tel Aviv University, Tel Aviv, 69978 Israel
| | - Michael Blank
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, George S. Wise Faculty of Life sciences, Tel Aviv University, Tel Aviv, 69978 Israel
| | - Rami Khosravi
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, George S. Wise Faculty of Life sciences, Tel Aviv University, Tel Aviv, 69978 Israel
| | - María Jesús Fernández-Ávila
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER) and Department of Genetics, University of Sevilla, Sevilla, 41092, Spain
| | - Andrés Cruz-García
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER) and Department of Genetics, University of Sevilla, Sevilla, 41092, Spain
| | - Ayelet Star
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, George S. Wise Faculty of Life sciences, Tel Aviv University, Tel Aviv, 69978 Israel
| | - Lea Shochot
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, George S. Wise Faculty of Life sciences, Tel Aviv University, Tel Aviv, 69978 Israel
| | - Yann Thomas
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, UK
| | - Lisa J Garrett
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Daniel A Chamovitz
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - David M Bodine
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Thimo Kurz
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, UK
| | - Pablo Huertas
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER) and Department of Genetics, University of Sevilla, Sevilla, 41092, Spain
| | - Yael Ziv
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, George S. Wise Faculty of Life sciences, Tel Aviv University, Tel Aviv, 69978 Israel
| | - Yosef Shiloh
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, George S. Wise Faculty of Life sciences, Tel Aviv University, Tel Aviv, 69978 Israel
| |
Collapse
|
150
|
Ekumi KM, Paculova H, Lenasi T, Pospichalova V, Bösken CA, Rybarikova J, Bryja V, Geyer M, Blazek D, Barboric M. Ovarian carcinoma CDK12 mutations misregulate expression of DNA repair genes via deficient formation and function of the Cdk12/CycK complex. Nucleic Acids Res 2015; 43:2575-89. [PMID: 25712099 PMCID: PMC4357706 DOI: 10.1093/nar/gkv101] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 01/05/2015] [Accepted: 01/30/2015] [Indexed: 12/11/2022] Open
Abstract
The Cdk12/CycK complex promotes expression of a subset of RNA polymerase II genes, including those of the DNA damage response. CDK12 is among only nine genes with recurrent somatic mutations in high-grade serous ovarian carcinoma. However, the influence of these mutations on the Cdk12/CycK complex and their link to cancerogenesis remain ill-defined. Here, we show that most mutations prevent formation of the Cdk12/CycK complex, rendering the kinase inactive. By examining the mutations within the Cdk12/CycK structure, we find that they likely provoke structural rearrangements detrimental to Cdk12 activation. Our mRNA expression analysis of the patient samples containing the CDK12 mutations reveals coordinated downregulation of genes critical to the homologous recombination DNA repair pathway. Moreover, we establish that the Cdk12/CycK complex occupies these genes and promotes phosphorylation of RNA polymerase II at Ser2. Accordingly, we demonstrate that the mutant Cdk12 proteins fail to stimulate the faithful DNA double strand break repair via homologous recombination. Together, we provide the molecular basis of how mutated CDK12 ceases to function in ovarian carcinoma. We propose that CDK12 is a tumor suppressor of which the loss-of-function mutations may elicit defects in multiple DNA repair pathways, leading to genomic instability underlying the genesis of the cancer.
Collapse
Affiliation(s)
- Kingsley M Ekumi
- Institute of Biomedicine, Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
| | - Hana Paculova
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
| | - Tina Lenasi
- Institute of Biomedicine, Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
| | - Vendula Pospichalova
- Institute of Experimental Biology, Faculty of Science, Masaryk University, 61137 Brno, Czech Republic
| | - Christian A Bösken
- Center of Advanced European Studies and Research, Group Physical Biochemistry, 53175 Bonn, Germany
| | - Jana Rybarikova
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
| | - Vitezslav Bryja
- Institute of Experimental Biology, Faculty of Science, Masaryk University, 61137 Brno, Czech Republic Institute of Biophysics, Academy of Sciences of the Czech Republic, 61265 Brno, Czech Republic
| | - Matthias Geyer
- Center of Advanced European Studies and Research, Group Physical Biochemistry, 53175 Bonn, Germany
| | - Dalibor Blazek
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
| | - Matjaz Barboric
- Institute of Biomedicine, Biochemistry and Developmental Biology, University of Helsinki, Helsinki FIN-00014, Finland
| |
Collapse
|