301
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Ligasová A, Strunin D, Friedecký D, Adam T, Koberna K. A fatal combination: a thymidylate synthase inhibitor with DNA damaging activity. PLoS One 2015; 10:e0117459. [PMID: 25671308 PMCID: PMC4324964 DOI: 10.1371/journal.pone.0117459] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 12/25/2014] [Indexed: 12/28/2022] Open
Abstract
2′-deoxy-5-ethynyluridine (EdU) has been previously shown to be a cell poison whose toxicity depends on the particular cell line. The reason is not known. Our data indicates that different efficiency of EdU incorporation plays an important role. The EdU-mediated toxicity was elevated by the inhibition of 2′-deoxythymidine 5′-monophosphate synthesis. EdU incorporation resulted in abnormalities of the cell cycle including the slowdown of the S phase and a decrease in DNA synthesis. The slowdown but not the cessation of the first cell division after EdU administration was observed in all of the tested cell lines. In HeLa cells, a 10 μM EdU concentration led to the cell death in the 100% of cells probably due to the activation of an intra S phase checkpoint in the subsequent S phase. Our data also indicates that this EdU concentration induces interstrand DNA crosslinks in HeLa cells. We suppose that these crosslinks are the primary DNA damage resulting in cell death. According to our results, the EdU-mediated toxicity is further increased by the inhibition of thymidylate synthase by EdU itself at its higher concentrations.
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Affiliation(s)
- Anna Ligasová
- Institute of Molecular and Translational Medicine, Faculty of Medicine, Palacký University, Olomouc, 779 00, Czech Republic
- * E-mail:
| | - Dmytro Strunin
- Institute of Molecular and Translational Medicine, Faculty of Medicine, Palacký University, Olomouc, 779 00, Czech Republic
| | - David Friedecký
- Institute of Molecular and Translational Medicine, Faculty of Medicine, Palacký University, Olomouc, 779 00, Czech Republic
| | - Tomáš Adam
- Institute of Molecular and Translational Medicine, Faculty of Medicine, Palacký University, Olomouc, 779 00, Czech Republic
| | - Karel Koberna
- Institute of Molecular and Translational Medicine, Faculty of Medicine, Palacký University, Olomouc, 779 00, Czech Republic
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302
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Kotsantis P, Jones RM, Higgs MR, Petermann E. Cancer therapy and replication stress: forks on the road to perdition. Adv Clin Chem 2015; 69:91-138. [PMID: 25934360 DOI: 10.1016/bs.acc.2014.12.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Deregulated DNA replication occurs in cancer where it contributes to genomic instability. This process is a target of cytotoxic therapies. Chemotherapies exploit high DNA replication in cancer cells by modifying the DNA template or by inhibiting vital enzymatic activities that lead to slowing or stalling replication fork progression. Stalled replication forks can be converted into toxic DNA double-strand breaks resulting in cell death, i.e., replication stress. While likely crucial for many cancer treatments, replication stress is poorly understood due to its complexity. While we still know relatively little about the role of replication stress in cancer therapy, technical advances in recent years have shed new light on the effect that cancer therapeutics have on replication forks and the molecular mechanisms that lead from obstructed fork progression to cell death. This chapter will give an overview of our current understanding of replication stress in the context of cancer therapy.
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Affiliation(s)
- Panagiotis Kotsantis
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Rebecca M Jones
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Martin R Higgs
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Eva Petermann
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom.
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303
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Hirota K, Yoshikiyo K, Guilbaud G, Tsurimoto T, Murai J, Tsuda M, Phillips LG, Narita T, Nishihara K, Kobayashi K, Yamada K, Nakamura J, Pommier Y, Lehmann A, Sale JE, Takeda S. The POLD3 subunit of DNA polymerase δ can promote translesion synthesis independently of DNA polymerase ζ. Nucleic Acids Res 2015; 43:1671-83. [PMID: 25628356 PMCID: PMC4330384 DOI: 10.1093/nar/gkv023] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The replicative DNA polymerase Polδ consists of a catalytic subunit POLD1/p125 and three regulatory subunits POLD2/p50, POLD3/p66 and POLD4/p12. The ortholog of POLD3 in Saccharomyces cerevisiae, Pol32, is required for a significant proportion of spontaneous and UV-induced mutagenesis through its additional role in translesion synthesis (TLS) as a subunit of DNA polymerase ζ. Remarkably, chicken DT40 B lymphocytes deficient in POLD3 are viable and able to replicate undamaged genomic DNA with normal kinetics. Like its counterpart in yeast, POLD3 is required for fully effective TLS, its loss resulting in hypersensitivity to a variety of DNA damaging agents, a diminished ability to maintain replication fork progression after UV irradiation and a significant decrease in abasic site-induced mutagenesis in the immunoglobulin loci. However, these defects appear to be largely independent of Polζ, suggesting that POLD3 makes a significant contribution to TLS independently of Polζ in DT40 cells. Indeed, combining polη, polζ and pold3 mutations results in synthetic lethality. Additionally, we show in vitro that POLD3 promotes extension beyond an abasic by the Polδ holoenzyme suggesting that while POLD3 is not required for normal replication, it may help Polδ to complete abasic site bypass independently of canonical TLS polymerases.
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Affiliation(s)
- Kouji Hirota
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan Department of Chemistry, GraduateSchool of Science and Engineering, Tokyo Metropolitan University, Minami-Osawa, Hachioji- shi, Tokyo 192-0397, Japan
| | - Kazunori Yoshikiyo
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Guillaume Guilbaud
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Toshiki Tsurimoto
- Department of Biology, School of Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Junko Murai
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Masataka Tsuda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Lara G Phillips
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Takeo Narita
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kana Nishihara
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kaori Kobayashi
- Department of Chemistry, GraduateSchool of Science and Engineering, Tokyo Metropolitan University, Minami-Osawa, Hachioji- shi, Tokyo 192-0397, Japan
| | - Kouich Yamada
- Division of Genetic Biochemistry, National Institute of Health and Nutrition, Tokyo 162-8636, Japan
| | - Jun Nakamura
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Yves Pommier
- Department of Biology, School of Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Alan Lehmann
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Julian E Sale
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
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304
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Hyrien O. Peaks cloaked in the mist: the landscape of mammalian replication origins. J Cell Biol 2015; 208:147-60. [PMID: 25601401 PMCID: PMC4298691 DOI: 10.1083/jcb.201407004] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 12/16/2014] [Indexed: 12/23/2022] Open
Abstract
Replication of mammalian genomes starts at sites termed replication origins, which historically have been difficult to locate as a result of large genome sizes, limited power of genetic identification schemes, and rareness and fragility of initiation intermediates. However, origins are now mapped by the thousands using microarrays and sequencing techniques. Independent studies show modest concordance, suggesting that mammalian origins can form at any DNA sequence but are suppressed by read-through transcription or that they can overlap the 5' end or even the entire gene. These results require a critical reevaluation of whether origins form at specific DNA elements and/or epigenetic signals or require no such determinants.
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Affiliation(s)
- Olivier Hyrien
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique UMR8197 and Institut National de la Santé et de la Recherche Médicale U1024, 75005 Paris, France
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305
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FBH1 influences DNA replication fork stability and homologous recombination through ubiquitylation of RAD51. Nat Commun 2015; 6:5931. [PMID: 25585578 DOI: 10.1038/ncomms6931] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 11/19/2014] [Indexed: 11/09/2022] Open
Abstract
Unscheduled homologous recombination (HR) can lead to genomic instability, which greatly increases the threat of neoplastic transformation in humans. The F-box DNA helicase 1 (FBH1) is a 3'-5' DNA helicase with a putative function as a negative regulator of HR. It is the only known DNA helicase to contain an F-box, suggesting that one of its functions is to act as a ubiquitin ligase as part of an SCF (SKP1, CUL1 and F-box) complex. Here we report that the central player in HR, RAD51, is ubiquitylated by the SCF(FBH1) complex. Expression of an ubiquitylation-resistant form of RAD51 in human cells leads to hyperrecombination, as well as several phenotypes indicative of an altered response to DNA replication stress. These effects are likely to be mediated by the enhanced nuclear matrix association of the ubiquitylation-resistant RAD51. These data are consistent with FBH1 acting as a negative regulator of RAD51 function in human cells.
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306
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Ulianov SV, Gavrilov AA, Razin SV. Nuclear Compartments, Genome Folding, and Enhancer-Promoter Communication. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 315:183-244. [DOI: 10.1016/bs.ircmb.2014.11.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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307
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Lebeaupin T, Sellou H, Timinszky G, Huet S. Chromatin dynamics at DNA breaks: what, how and why? AIMS BIOPHYSICS 2015. [DOI: 10.3934/biophy.2015.4.458] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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308
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Interaction of Chk1 with Treslin negatively regulates the initiation of chromosomal DNA replication. Mol Cell 2014; 57:492-505. [PMID: 25557548 DOI: 10.1016/j.molcel.2014.12.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/16/2014] [Accepted: 11/24/2014] [Indexed: 01/13/2023]
Abstract
Treslin helps to trigger the initiation of DNA replication by promoting integration of Cdc45 into the replicative helicase. Treslin is a key positive-regulatory target of cell-cycle control mechanisms; activation of Treslin by cyclin-dependent kinase is essential for the initiation of replication. Here we demonstrate that Treslin is also a critical locus for negative regulatory mechanisms that suppress initiation. We found that the checkpoint-regulatory kinase Chk1 associates specifically with a C-terminal domain of Treslin (designated TRCT). Mutations in the TRCT domain abolish binding of Chk1 to Treslin and thereby eliminate Chk1-catalyzed phosphorylation of Treslin. Significantly, abolition of the Treslin-Chk1 interaction results in elevated initiation of chromosomal DNA replication during an unperturbed cell cycle, which reveals a function for Chk1 during a normal S phase. This increase is due to enhanced loading of Cdc45 onto potential replication origins. These studies provide important insights into how vertebrate cells orchestrate proper initiation of replication.
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309
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Poly(ADP-ribosyl) glycohydrolase prevents the accumulation of unusual replication structures during unperturbed S phase. Mol Cell Biol 2014; 35:856-65. [PMID: 25535335 DOI: 10.1128/mcb.01077-14] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Poly(ADP-ribosyl)ation (PAR) has been implicated in various aspects of the cellular response to DNA damage and genome stability. Although 17 human poly(ADP-ribose) polymerase (PARP) genes have been identified, a single poly(ADP-ribosyl) glycohydrolase (PARG) mediates PAR degradation. Here we investigated the role of PARG in the replication of human chromosomes. We show that PARG depletion affects cell proliferation and DNA synthesis, leading to replication-coupled H2AX phosphorylation. Furthermore, PARG depletion or inhibition per se slows down individual replication forks similarly to mild chemotherapeutic treatment. Electron microscopic analysis of replication intermediates reveals marked accumulation of reversed forks and single-stranded DNA (ssDNA) gaps in unperturbed PARG-defective cells. Intriguingly, while we found no physical evidence for chromosomal breakage, PARG-defective cells displayed both ataxia-telangiectasia-mutated (ATM) and ataxia-Rad3-related (ATR) activation, as well as chromatin recruitment of standard double-strand-break-repair factors, such as 53BP1 and RAD51. Overall, these data prove PAR degradation to be essential to promote resumption of replication at endogenous and exogenous lesions, preventing idle recruitment of repair factors to remodeled replication forks. Furthermore, they suggest that fork remodeling and restarting are surprisingly frequent in unperturbed cells and provide a molecular rationale to explore PARG inhibition in cancer chemotherapy.
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310
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Moreno SP, Bailey R, Campion N, Herron S, Gambus A. Polyubiquitylation drives replisome disassembly at the termination of DNA replication. Science 2014; 346:477-81. [PMID: 25342805 DOI: 10.1126/science.1253585] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Resolution of replication forks during termination of DNA replication is essential for accurate duplication of eukaryotic genomes. Here we present evidence consistent with the idea that polyubiquitylation of a replisome component (Mcm7) leads to its disassembly at the converging terminating forks because of the action of the p97/VCP/Cdc48 protein remodeler. Using Xenopus laevis egg extract, we have shown that blocking polyubiquitylation results in the prolonged association of the active helicase with replicating chromatin. The Mcm7 subunit is the only component of the active helicase that we find polyubiquitylated during replication termination. The observed polyubiquitylation is followed by disassembly of the active helicase dependent on p97/VCP/Cdc48. Altogether, our data provide insight into the mechanism of replisome disassembly during eukaryotic DNA replication termination.
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Affiliation(s)
- Sara Priego Moreno
- School of Cancer Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK
| | - Rachael Bailey
- School of Cancer Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK
| | - Nicholas Campion
- School of Cancer Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK
| | - Suzanne Herron
- School of Cancer Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK
| | - Agnieszka Gambus
- School of Cancer Sciences, University of Birmingham, Vincent Drive, Birmingham B15 2TT, UK.
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311
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Basile G, Leuzzi G, Pichierri P, Franchitto A. Checkpoint-dependent and independent roles of the Werner syndrome protein in preserving genome integrity in response to mild replication stress. Nucleic Acids Res 2014; 42:12628-39. [PMID: 25352544 PMCID: PMC4227752 DOI: 10.1093/nar/gku1022] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Werner syndrome (WS) is a human chromosomal instability disorder associated with cancer predisposition and caused by mutations in the WRN gene. WRN helicase activity is crucial in limiting breakage at common fragile sites (CFS), which are the preferential targets of genome instability in precancerous lesions. However, the precise function of WRN in response to mild replication stress, like that commonly used to induce breaks at CFS, is still missing. Here, we establish that WRN plays a role in mediating CHK1 activation under moderate replication stress. We provide evidence that phosphorylation of CHK1 relies on the ATR-mediated phosphorylation of WRN, but not on WRN helicase activity. Analysis of replication fork dynamics shows that loss of WRN checkpoint mediator function as well as of WRN helicase activity hamper replication fork progression, and lead to new origin activation to allow recovery from replication slowing upon replication stress. Furthermore, bypass of WRN checkpoint mediator function through overexpression of a phospho-mimic form of CHK1 restores fork progression and chromosome stability to the wild-type levels. Together, these findings are the first demonstration that WRN regulates the ATR-checkpoint activation upon mild replication stress, preventing chromosome fragility.
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Affiliation(s)
- Giorgia Basile
- Section of Molecular Epidemiology, Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena, 299-00161 Rome, Italy Genome Stability Group, Istituto Superiore di Sanità, Viale Regina Elena, 299-00161 Rome, Italy
| | - Giuseppe Leuzzi
- Section of Molecular Epidemiology, Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena, 299-00161 Rome, Italy Genome Stability Group, Istituto Superiore di Sanità, Viale Regina Elena, 299-00161 Rome, Italy
| | - Pietro Pichierri
- Genome Stability Group, Istituto Superiore di Sanità, Viale Regina Elena, 299-00161 Rome, Italy Section of Experimental and Computational Carcinogenesis, Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena, 299-00161 Rome, Italy
| | - Annapaola Franchitto
- Section of Molecular Epidemiology, Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena, 299-00161 Rome, Italy Genome Stability Group, Istituto Superiore di Sanità, Viale Regina Elena, 299-00161 Rome, Italy
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312
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Smirnov E, Borkovec J, Kováčik L, Svidenská S, Schröfel A, Skalníková M, Švindrych Z, Křížek P, Ovesný M, Hagen GM, Juda P, Michalová K, Cardoso MC, Cmarko D, Raška I. Separation of replication and transcription domains in nucleoli. J Struct Biol 2014; 188:259-66. [PMID: 25450594 DOI: 10.1016/j.jsb.2014.10.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 10/02/2014] [Accepted: 10/05/2014] [Indexed: 01/07/2023]
Abstract
In mammalian cells, active ribosomal genes produce the 18S, 5.8S and 28S RNAs of ribosomal particles. Transcription levels of these genes are very high throughout interphase, and the cell needs a special strategy to avoid collision of the DNA polymerase and RNA polymerase machineries. To investigate this problem, we measured the correlation of various replication and transcription signals in the nucleoli of HeLa, HT-1080 and NIH 3T3 cells using a specially devised software for analysis of confocal images. Additionally, to follow the relationship between nucleolar replication and transcription in living cells, we produced a stable cell line expressing GFP-RPA43 (subunit of RNA polymerase I, pol I) and RFP-PCNA (the sliding clamp protein) based on human fibrosarcoma HT-1080 cells. We found that replication and transcription signals are more efficiently separated in nucleoli than in the nucleoplasm. In the course of S phase, separation of PCNA and pol I signals gradually increased. During the same period, separation of pol I and incorporated Cy5-dUTP signals decreased. Analysis of single molecule localization microscopy (SMLM) images indicated that transcriptionally active FC/DFC units (i.e. fibrillar centers with adjacent dense fibrillar components) did not incorporate DNA nucleotides. Taken together, our data show that replication of the ribosomal genes is spatially separated from their transcription, and FC/DFC units may provide a structural basis for that separation.
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Affiliation(s)
- E Smirnov
- Institute of Cell Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - J Borkovec
- Institute of Cell Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - L Kováčik
- Institute of Cell Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - S Svidenská
- Institute of Cell Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - A Schröfel
- Institute of Cell Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - M Skalníková
- Institute of Cell Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Z Švindrych
- Institute of Cell Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - P Křížek
- Institute of Cell Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - M Ovesný
- Institute of Cell Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - G M Hagen
- Institute of Cell Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - P Juda
- Institute of Cell Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - K Michalová
- Centre of Oncocytogenetics, Institute of Medical Biochemistry and Laboratory Diagnosis, General University Hospital and First Faculty of Medicine, Charles University in Prague, Czech Republic
| | - M C Cardoso
- Department of Biology, Technische Universitat Darmstadt, Darmstadt, Germany
| | - D Cmarko
- Institute of Cell Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - I Raška
- Institute of Cell Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
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313
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Parplys AC, Kratz K, Speed MC, Leung SG, Schild D, Wiese C. RAD51AP1-deficiency in vertebrate cells impairs DNA replication. DNA Repair (Amst) 2014; 24:87-97. [PMID: 25288561 DOI: 10.1016/j.dnarep.2014.09.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/06/2014] [Accepted: 09/16/2014] [Indexed: 01/03/2023]
Abstract
RAD51-associated protein 1 (RAD51AP1) is critical for homologous recombination (HR) by interacting with and stimulating the activities of the RAD51 and DMC1 recombinases. In human somatic cells, knockdown of RAD51AP1 results in increased sensitivity to DNA damaging agents and to impaired HR, but the formation of DNA damage-induced RAD51 foci is unaffected. Here, we generated a genetic model system, based on chicken DT40 cells, to assess the phenotype of fully inactivated RAD51AP1 in vertebrate cells. Targeted inactivation of both RAD51AP1 alleles has no effect on either viability or doubling-time in undamaged cells, but leads to increased levels of cytotoxicity after exposure to cisplatin or to ionizing radiation. Interestingly, ectopic expression of GgRAD51AP1, but not of HsRAD51AP1 is able to fully complement in cell survival assays. Notably, in RAD51AP1-deficient DT40 cells the resolution of DNA damage-induced RAD51 foci is greatly slowed down, while their formation is not impaired. We also identify, for the first time, an important role for RAD51AP1 in counteracting both spontaneous and DNA damage-induced replication stress. In human and in chicken cells, RAD51AP1 is required to maintain wild type speed of replication fork progression, and both RAD51AP1-depleted human cells and RAD51AP1-deficient DT40 cells respond to replication stress by a slow-down of replication fork elongation rates. However, increased firing of replication origins occurs in RAD51AP1-/- DT40 cells, likely to ensure the timely duplication of the entire genome. Taken together, our results may explain why RAD51AP1 commonly is overexpressed in tumor cells and tissues, and we speculate that the disruption of RAD51AP1 function could be a promising approach in targeted tumor therapy.
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Affiliation(s)
- Ann C Parplys
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Katja Kratz
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Michael C Speed
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Stanley G Leung
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - David Schild
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
| | - Claudia Wiese
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
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314
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Mutations in SPRTN cause early onset hepatocellular carcinoma, genomic instability and progeroid features. Nat Genet 2014; 46:1239-44. [PMID: 25261934 DOI: 10.1038/ng.3103] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 09/04/2014] [Indexed: 12/30/2022]
Abstract
Age-related degenerative and malignant diseases represent major challenges for health care systems. Elucidation of the molecular mechanisms underlying carcinogenesis and age-associated pathologies is thus of growing biomedical relevance. We identified biallelic germline mutations in SPRTN (also called C1orf124 or DVC1) in three patients from two unrelated families. All three patients are affected by a new segmental progeroid syndrome characterized by genomic instability and susceptibility toward early onset hepatocellular carcinoma. SPRTN was recently proposed to have a function in translesional DNA synthesis and the prevention of mutagenesis. Our in vivo and in vitro characterization of identified mutations has uncovered an essential role for SPRTN in the prevention of DNA replication stress during general DNA replication and in replication-related G2/M-checkpoint regulation. In addition to demonstrating the pathogenicity of identified SPRTN mutations, our findings provide a molecular explanation of how SPRTN dysfunction causes accelerated aging and susceptibility toward carcinoma.
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315
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HAN XIAORUI, BAI XIZHUANG, SUN YU, YANG YAN. Nuclear ING2 expression is reduced in osteosarcoma. Oncol Rep 2014; 32:1967-72. [DOI: 10.3892/or.2014.3458] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/05/2014] [Indexed: 11/06/2022] Open
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316
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Zaghloul L, Drillon G, Boulos RE, Argoul F, Thermes C, Arneodo A, Audit B. Large replication skew domains delimit GC-poor gene deserts in human. Comput Biol Chem 2014; 53 Pt A:153-65. [PMID: 25224847 DOI: 10.1016/j.compbiolchem.2014.08.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2014] [Indexed: 01/25/2023]
Abstract
Besides their large-scale organization in isochores, mammalian genomes display megabase-sized regions, spanning both genes and intergenes, where the strand nucleotide composition asymmetry decreases linearly, possibly due to replication activity. These so-called skew-N domains cover about a third of the human genome and are bordered by two skew upward jumps that were hypothesized to compose a subset of "master" replication origins active in the germline. Skew-N domains were shown to exhibit a particular gene organization. Genes with CpG-rich promoters likely expressed in the germline are over represented near the master replication origins, with large genes being co-oriented with replication fork progression, which suggests some coordination of replication and transcription. In this study, we describe another skew structure that covers ∼13% of the human genome and that is bordered by putative master replication origins similar to the ones flanking skew-N domains. These skew-split-N domains have a shape reminiscent of a N, but split in half, leaving in the center a region of null skew whose length increases with domain size. These central regions (median size ∼860 kb) have a homogeneous composition, i.e. both a null and constant skew and a constant and low GC content. They correspond to heterochromatin gene deserts found in low-GC isochores with an average gene density of 0.81 promoters/Mb as compared to 7.73 promoters/Mb genome wide. The analysis of epigenetic marks and replication timing data confirms that, in these late replicating heterochomatic regions, the initiation of replication is likely to be random. This contrasts with the transcriptionally active euchromatin state found around the bordering well positioned master replication origins. Altogether skew-N domains and skew-split-N domains cover about 50% of the human genome.
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Affiliation(s)
- Lamia Zaghloul
- Université de Lyon, F-69000 Lyon, France; Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France
| | - Guénola Drillon
- Université de Lyon, F-69000 Lyon, France; Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France
| | - Rasha E Boulos
- Université de Lyon, F-69000 Lyon, France; Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France
| | - Françoise Argoul
- Université de Lyon, F-69000 Lyon, France; Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France
| | - Claude Thermes
- Centre de Génétique Moléculaire, CNRS UPR 3404, Gif-sur-Yvette, France
| | - Alain Arneodo
- Université de Lyon, F-69000 Lyon, France; Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France
| | - Benjamin Audit
- Université de Lyon, F-69000 Lyon, France; Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France.
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317
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Castillo A, Paul A, Sun B, Huang TH, Wang Y, Yazinski SA, Tyler J, Li L, You MJ, Zou L, Yao J, Wang B. The BRCA1-interacting protein Abraxas is required for genomic stability and tumor suppression. Cell Rep 2014; 8:807-17. [PMID: 25066119 DOI: 10.1016/j.celrep.2014.06.050] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/18/2014] [Accepted: 06/25/2014] [Indexed: 11/16/2022] Open
Abstract
Germline mutations of BRCA1 confer hereditary susceptibility to breast and ovarian cancer. However, somatic mutation of BRCA1 is infrequent in sporadic breast cancers. The BRCA1 protein C terminus (BRCT) domains interact with multiple proteins and are required for BRCA1's tumor-suppressor function. In this study, we demonstrated that Abraxas, a BRCA1 BRCT domain-interacting protein, plays a role in tumor suppression. Abraxas exerts its function through binding to BRCA1 to regulate DNA repair and maintain genome stability. Both homozygous and heterozygous Abraxas knockout mice exhibited decreased survival and increased tumor incidence. The gene encoding Abraxas suffers from gene copy loss and somatic mutations in multiple human cancers including breast, ovarian, and endometrial cancers, suggesting that mutation and loss of function of Abraxas may contribute to tumor development in human patients.
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Affiliation(s)
- Andy Castillo
- Department of Genetics, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Atanu Paul
- Department of Genetics, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA; Genes and Development Program, The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Baohua Sun
- Department of Genetics, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Ting Hsiang Huang
- Department of Biochemistry and Molecular Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA; Genes and Development Program, The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Yucai Wang
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Stephanie A Yazinski
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jessica Tyler
- Department of Biochemistry and Molecular Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Lei Li
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - M James You
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jun Yao
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Bin Wang
- Department of Genetics, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA; Genes and Development Program, The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
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318
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Maya-Mendoza A, Merchut-Maya JM, Bartkova J, Bartek J, Streuli CH, Jackson DA. Immortalised breast epithelia survive prolonged DNA replication stress and return to cycle from a senescent-like state. Cell Death Dis 2014; 5:e1351. [PMID: 25058425 PMCID: PMC4123104 DOI: 10.1038/cddis.2014.315] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 06/09/2014] [Accepted: 06/11/2014] [Indexed: 12/20/2022]
Abstract
Mammalian cells have mechanisms to counteract the effects of metabolic and exogenous stresses, many of that would be mutagenic if ignored. Damage arising during DNA replication is a major source of mutagenesis. The extent of damage dictates whether cells undergo transient cell cycle arrest and damage repair, senescence or apoptosis. Existing dogma defines these alternative fates as distinct choices. Here we show that immortalised breast epithelial cells are able to survive prolonged S phase arrest and subsequently re-enter cycle after many days of being in an arrested, senescence-like state. Prolonged cell cycle inhibition in fibroblasts induced DNA damage response and cell death. However, in immortalised breast epithelia, efficient S phase arrest minimised chromosome damage and protected sufficient chromatin-bound replication licensing complexes to allow cell cycle re-entry. We propose that our observation could have implications for the design of drug therapies for breast cancer.
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Affiliation(s)
- A Maya-Mendoza
- 1] Faculty of Life Sciences and Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Oxford Road, Manchester M13 9PT, UK [2] Genome Integrity Unit, Danish Cancer Society Research Centre, Copenhagen, Denmark
| | - J M Merchut-Maya
- Genome Integrity Unit, Danish Cancer Society Research Centre, Copenhagen, Denmark
| | - J Bartkova
- Genome Integrity Unit, Danish Cancer Society Research Centre, Copenhagen, Denmark
| | - J Bartek
- 1] Genome Integrity Unit, Danish Cancer Society Research Centre, Copenhagen, Denmark [2] Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, CZ-779 00 Olomouc, Czech Republic
| | - C H Streuli
- Faculty of Life Sciences and Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - D A Jackson
- Faculty of Life Sciences and Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Oxford Road, Manchester M13 9PT, UK
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319
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Vassileva I, Yanakieva I, Peycheva M, Gospodinov A, Anachkova B. The mammalian INO80 chromatin remodeling complex is required for replication stress recovery. Nucleic Acids Res 2014; 42:9074-86. [PMID: 25016522 PMCID: PMC4132725 DOI: 10.1093/nar/gku605] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A number of studies have implicated the yeast INO80 chromatin remodeling complex in DNA replication, but the function of the human INO80 complex during S phase remains poorly understood. Here, we have systematically investigated the involvement of the catalytic subunit of the human INO80 complex during unchallenged replication and under replication stress by following the effects of its depletion on cell survival, S-phase checkpoint activation, the fate of individual replication forks, and the consequences of fork collapse. We report that INO80 was specifically needed for efficient replication elongation, while it was not required for initiation of replication. In the absence of the Ino80 protein, cells became hypersensitive to hydroxyurea and displayed hyperactive ATR-Chk1 signaling. Using bulk and fiber labeling of DNA, we found that cells deficient for Ino80 and Arp8 had impaired replication restart after treatment with replication inhibitors and accumulated double-strand breaks as evidenced by the formation of γ-H2AX and Rad51 foci. These data indicate that under conditions of replication stress mammalian INO80 protects stalled forks from collapsing and allows their subsequent restart.
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Affiliation(s)
- Ivelina Vassileva
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Academy G. Bonchev St. 21, 1113 Sofia, Bulgaria
| | - Iskra Yanakieva
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Academy G. Bonchev St. 21, 1113 Sofia, Bulgaria
| | - Michaela Peycheva
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Academy G. Bonchev St. 21, 1113 Sofia, Bulgaria
| | - Anastas Gospodinov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Academy G. Bonchev St. 21, 1113 Sofia, Bulgaria
| | - Boyka Anachkova
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Academy G. Bonchev St. 21, 1113 Sofia, Bulgaria
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320
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Heterozygous mutations in PALB2 cause DNA replication and damage response defects. Nat Commun 2014; 4:2578. [PMID: 24153426 PMCID: PMC3826652 DOI: 10.1038/ncomms3578] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 09/10/2013] [Indexed: 12/14/2022] Open
Abstract
Besides mutations in BRCA1/BRCA2, heterozygous defects in PALB2 are important in breast cancer predisposition. PALB2 heterozygosity increases the risk of malignancy about sixfold. PALB2 interacts with BRCA1 and BRCA2 to regulate homologous recombination and mediate DNA damage response. Here we show, by analysing lymphoblastoid cell lines from heterozygous female PALB2 mutation carriers, that PALB2 haploinsufficiency causes aberrant DNA replication/damage response. Mutation carrier cells show increased origin firing and shorter distance between consecutive replication forks. Carrier cell lines also show elevated ATR protein, but not phosphorylation levels, and a majority of them display aberrant Chk1-/Chk2-mediated DNA damage response. Elevated chromosome instability is observed in primary blood lymphocytes of PALB2 mutation carriers, indicating that the described mechanisms of genome destabilization operate also at the organism level. These findings provide a new mechanism for early stages of breast cancer development that may also apply to other heterozygous homologous recombination signalling pathway gene mutations in hereditary cancer predisposition.
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321
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Yata K, Bleuyard JY, Nakato R, Ralf C, Katou Y, Schwab RA, Niedzwiedz W, Shirahige K, Esashi F. BRCA2 coordinates the activities of cell-cycle kinases to promote genome stability. Cell Rep 2014; 7:1547-1559. [PMID: 24835992 PMCID: PMC4062933 DOI: 10.1016/j.celrep.2014.04.023] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 03/11/2014] [Accepted: 04/13/2014] [Indexed: 02/06/2023] Open
Abstract
Numerous human genome instability syndromes, including cancer, are closely associated with events arising from malfunction of the essential recombinase Rad51. However, little is known about how Rad51 is dynamically regulated in human cells. Here, we show that the breast cancer susceptibility protein BRCA2, a key Rad51 binding partner, coordinates the activity of the central cell-cycle drivers CDKs and Plk1 to promote Rad51-mediated genome stability control. The soluble nuclear fraction of BRCA2 binds Plk1 directly in a cell-cycle- and CDK-dependent manner and acts as a molecular platform to facilitate Plk1-mediated Rad51 phosphorylation. This phosphorylation is important for enhancing the association of Rad51 with stressed replication forks, which in turn protects the genomic integrity of proliferating human cells. This study reveals an elaborate but highly organized molecular interplay between Rad51 regulators and has significant implications for understanding tumorigenesis and therapeutic resistance in patients with BRCA2 deficiency.
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Affiliation(s)
- Keiko Yata
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Jean-Yves Bleuyard
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Ryuichiro Nakato
- Research Center for Epigenetic Disease, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 113-0032, Japan; CREST, Japan Science and Technology Agency (JST), K's Gobancho, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Christine Ralf
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Yuki Katou
- Research Center for Epigenetic Disease, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 113-0032, Japan
| | - Rebekka A Schwab
- The Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Wojciech Niedzwiedz
- The Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Katsuhiko Shirahige
- Research Center for Epigenetic Disease, Graduate School of Frontier Sciences, University of Tokyo, Tokyo 113-0032, Japan; CREST, Japan Science and Technology Agency (JST), K's Gobancho, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Fumiko Esashi
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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322
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Tai PWL, Zaidi SK, Wu H, Grandy RA, Montecino MM, van Wijnen AJ, Lian JB, Stein GS, Stein JL. The dynamic architectural and epigenetic nuclear landscape: developing the genomic almanac of biology and disease. J Cell Physiol 2014; 229:711-27. [PMID: 24242872 PMCID: PMC3996806 DOI: 10.1002/jcp.24508] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 11/11/2013] [Indexed: 12/31/2022]
Abstract
Compaction of the eukaryotic genome into the confined space of the cell nucleus must occur faithfully throughout each cell cycle to retain gene expression fidelity. For decades, experimental limitations to study the structural organization of the interphase nucleus restricted our understanding of its contributions towards gene regulation and disease. However, within the past few years, our capability to visualize chromosomes in vivo with sophisticated fluorescence microscopy, and to characterize chromosomal regulatory environments via massively parallel sequencing methodologies have drastically changed how we currently understand epigenetic gene control within the context of three-dimensional nuclear structure. The rapid rate at which information on nuclear structure is unfolding brings challenges to compare and contrast recent observations with historic findings. In this review, we discuss experimental breakthroughs that have influenced how we understand and explore the dynamic structure and function of the nucleus, and how we can incorporate historical perspectives with insights acquired from the ever-evolving advances in molecular biology and pathology.
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Affiliation(s)
- Phillip W. L. Tai
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Sayyed K. Zaidi
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Hai Wu
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Rodrigo A. Grandy
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Martin M. Montecino
- Center for Biomedical Research and FONDAP Center for Genome Regulation, Universidad Andres Bello, Santiago, Chile
| | - André J. van Wijnen
- Departments of Orthopedic Surgery and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN
| | - Jane B. Lian
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Gary S. Stein
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Janet L. Stein
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
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323
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Henninger EE, Pursell ZF. DNA polymerase ε and its roles in genome stability. IUBMB Life 2014; 66:339-51. [PMID: 24861832 DOI: 10.1002/iub.1276] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 05/02/2014] [Indexed: 12/14/2022]
Abstract
DNA Polymerase Epsilon (Pol ε) is one of three DNA Polymerases (along with Pol δ and Pol α) required for nuclear DNA replication in eukaryotes. Pol ε is comprised of four subunits, the largest of which is encoded by the POLE gene and contains the catalytic polymerase and exonuclease activities. The 3'-5' exonuclease proofreading activity is able to correct DNA synthesis errors and helps protect against genome instability. Recent cancer genome sequencing efforts have shown that 3% of colorectal and 7% of endometrial cancers contain mutations within the exonuclease domain of POLE and are associated with significantly elevated levels of single nucleotide substitutions (15-500 per Mb) and microsatellite stability. POLE mutations have also been found in other tumor types, though at lower frequency, suggesting roles in tumorigenesis more broadly in different tissue types. In addition to its proofreading activity, Pol ε contributes to genome stability through multiple mechanisms that are discussed in this review.
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Affiliation(s)
- Erin E Henninger
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
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324
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Nicodemi M, Pombo A. Models of chromosome structure. Curr Opin Cell Biol 2014; 28:90-5. [PMID: 24804566 DOI: 10.1016/j.ceb.2014.04.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 04/11/2014] [Indexed: 10/25/2022]
Abstract
Understanding the mechanisms that control chromosome folding in the nucleus of eukaryotes and their contribution to gene regulation is a key open issue in molecular biology. Microscopy and chromatin-capture techniques have shown that chromatin has a complex organization, which dynamically changes across organisms and cell types. The need to make sense of such a fascinating complexity has prompted the development of quantitative models from physics, to find the principles of chromosome folding, its origin and function. Here, we concisely review recent advances in chromosome modeling, focusing on a recently proposed framework, the Strings & Binders Switch (SBS) model, which recapitulates key features of chromosome organization in space and time.
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Affiliation(s)
- Mario Nicodemi
- Universita' di Napoli "Federico II", Dipartimento di Fisica, INFN Sezione di Napoli, CNR-SPIN, Complesso Universitario di Monte S. Angelo, Via Cintia, 80126 Napoli, Italy.
| | - Ana Pombo
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Robert Rössle Strasse 10, 13125 Berlin-Buch, Germany.
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325
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Maeshima K, Imai R, Tamura S, Nozaki T. Chromatin as dynamic 10-nm fibers. Chromosoma 2014; 123:225-37. [PMID: 24737122 PMCID: PMC4031381 DOI: 10.1007/s00412-014-0460-2] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 03/18/2014] [Accepted: 03/20/2014] [Indexed: 01/01/2023]
Abstract
Since Flemming described a nuclear substance in the nineteenth century and named it “chromatin,” this substance has fascinated biologists. What is the structure of chromatin? DNA is wrapped around core histones, forming a nucleosome fiber (10-nm fiber). This fiber has long been assumed to fold into a 30-nm chromatin fiber and subsequently into helically folded larger fibers or radial loops. However, several recent studies, including our cryo-EM and X-ray scattering analyses, demonstrated that chromatin is composed of irregularly folded 10-nm fibers, without 30-nm chromatin fibers, in interphase chromatin and mitotic chromosomes. This irregular folding implies a chromatin state that is physically less constrained, which could be more dynamic compared with classical regular helical folding structures. Consistent with this, recently, we uncovered by single nucleosome imaging large nucleosome fluctuations in living mammalian cells (∼50 nm/30 ms). Subsequent computational modeling suggested that nucleosome fluctuation increases chromatin accessibility, which is advantageous for many “target searching” biological processes such as transcriptional regulation. Therefore, this review provides a novel view on chromatin structure in which chromatin consists of dynamic and disordered 10-nm fibers.
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Affiliation(s)
- Kazuhiro Maeshima
- Biological Macromolecules Laboratory, Structural Biology Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan,
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326
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Hosono Y, Abe T, Higuchi M, Kajii K, Sakuraba S, Tada S, Enomoto T, Seki M. Tipin functions in the protection against topoisomerase I inhibitor. J Biol Chem 2014; 289:11374-11384. [PMID: 24573676 DOI: 10.1074/jbc.m113.531707] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The replication fork temporarily stalls when encountering an obstacle on the DNA, and replication resumes after the barrier is removed. Simultaneously, activation of the replication checkpoint delays the progression of S phase and inhibits late origin firing. Camptothecin (CPT), a topoisomerase I (Top1) inhibitor, acts as a DNA replication barrier by inducing the covalent retention of Top1 on DNA. The Timeless-Tipin complex, a component of the replication fork machinery, plays a role in replication checkpoint activation and stabilization of the replication fork. However, the role of the Timeless-Tipin complex in overcoming the CPT-induced replication block remains elusive. Here, we generated viable TIPIN gene knock-out (KO) DT40 cells showing delayed S phase progression and increased cell death. TIPIN KO cells were hypersensitive to CPT. However, homologous recombination and replication checkpoint were activated normally, whereas DNA synthesis activity was markedly decreased in CPT-treated TIPIN KO cells. Proteasome-dependent degradation of chromatin-bound Top1 was induced in TIPIN KO cells upon CPT treatment, and pretreatment with aphidicolin, a DNA polymerase inhibitor, suppressed both CPT sensitivity and Top1 degradation. Taken together, our data indicate that replication forks formed without Tipin may collide at a high rate with Top1 retained on DNA by CPT treatment, leading to CPT hypersensitivity and Top1 degradation in TIPIN KO cells.
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Affiliation(s)
- Yoshifumi Hosono
- Molecular Cell Biology Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba 6-3, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Takuya Abe
- Instituto FIRC di Oncologia Molecolare (IFOM), Fondazione Italiana per la Ricerca sul Cancro (FIRC) Institute for Molecular Oncology Foundation, IFOM-Istituto Europeo di Oncologia Campus, Via Adamello 16, 20139 Milan, Italy
| | - Masato Higuchi
- Molecular Cell Biology Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba 6-3, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Kosa Kajii
- Department of Biochemistry, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi 981-8558, Japan
| | - Shuichi Sakuraba
- Molecular Cell Biology Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba 6-3, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Shusuke Tada
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, 4-21-2 Nakano, Nakano-ku, Tokyo 164-8530, Japan, and
| | - Takemi Enomoto
- Molecular Cell Biology Laboratory, Research Institute of Pharmaceutical Sciences, Faculty of Pharmacy, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi, Tokyo 202-8585, Japan
| | - Masayuki Seki
- Department of Biochemistry, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi 981-8558, Japan,.
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327
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Lin YF, Shih HY, Shang Z, Matsunaga S, Chen BP. DNA-PKcs is required to maintain stability of Chk1 and Claspin for optimal replication stress response. Nucleic Acids Res 2014; 42:4463-73. [PMID: 24500207 PMCID: PMC3985680 DOI: 10.1093/nar/gku116] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The ataxia telangiectasia mutated and Rad3-related (ATR)-checkpoint kinase 1 (Chk1) axis is the major signaling pathway activated in response to replication stress and is essential for the intra-S checkpoint. ATR phosphorylates and activates a number of molecules to coordinate cell cycle progression. Chk1 is the major effector downstream from ATR and plays a critical role in intra-S checkpoint on replication stress. Activation of Chk1 kinase also requires its association with Claspin, an adaptor protein essential for Chk1 protein stability, recruitment and ATR-dependent Chk1 phosphorylation. We have previously reported that, on replication stress, the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs) is rapidly phosphorylated by ATR at the stalled replication forks and is required for cellular resistance to replication stresses although the impact of DNA-PKcs onto the ATR signaling pathway remains elusive. Here we report that ATR-dependent Chk1 phosphorylation and Chk1 signaling are compromised in the absence of DNA-PKcs. Our investigation reveals that DNA-PKcs is required to maintain Chk1–Claspin complex stability and transcriptional regulation of Claspin expression. The impaired Chk1 activity results in a defective intra-S checkpoint response in DNA-PKcs–deficient cells. Taken together, these results suggest that DNA-PKcs, in addition to its direct role in DNA damage repair, facilitates ATR-Chk1 signaling pathway in response to replication stress.
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Affiliation(s)
- Yu-Fen Lin
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas, Southwestern Medical Center at Dallas, Dallas, TX 75390, USA and Division of Molecular Pharmacology, Department of Pathophysiological and Therapeutic Science, Tottori University, Japan
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328
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Ganai N, Sengupta S, Menon GI. Chromosome positioning from activity-based segregation. Nucleic Acids Res 2014; 42:4145-59. [PMID: 24459132 PMCID: PMC3985638 DOI: 10.1093/nar/gkt1417] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Chromosomes within eukaryotic cell nuclei at interphase are not positioned at random, since gene-rich chromosomes are predominantly found towards the interior of the cell nucleus across a number of cell types. The physical mechanisms that could drive and maintain the spatial segregation of chromosomes based on gene density are unknown. Here, we identify a mechanism for such segregation, showing that the territorial organization of chromosomes, another central feature of nuclear organization, emerges naturally from our model. Our computer simulations indicate that gene density-dependent radial segregation of chromosomes arises as a robust consequence of differences in non-equilibrium activity across chromosomes. Arguing that such differences originate in the inhomogeneous distribution of ATP-dependent chromatin remodeling and transcription machinery on each chromosome, we show that a variety of non-random positional distributions emerge through the interplay of such activity, nuclear shape and specific interactions of chromosomes with the nuclear envelope. Results from our model are in reasonable agreement with experimental data and we make a number of predictions that can be tested in experiments.
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Affiliation(s)
- Nirmalendu Ganai
- Department of Physics, Nabadwip Vidyasagar College, Nabadwip, Nadia 741302, India, TIFR Centre for Interdisciplinary Sciences, 21 Brundavan Colony, Narsingi, Hyderabad 500075, India, Centre for Advanced Materials, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India, The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600 113, India, Mechanobiology Institute, National University of Singapore, T-Lab, #10-01, 5A Engineering Drive 1, Singapore 117411, Singapore and Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
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329
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Luebben SW, Shima N, Kawabata T. Methods for the detection of genome instability derived from replication stress in primary mouse embryonic fibroblasts. Methods Mol Biol 2014; 1194:341-352. [PMID: 25064113 DOI: 10.1007/978-1-4939-1215-5_19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Replication stress, with its subsequent genome instability, is a hallmark of cancer from its earliest stages of development. Here, we describe assays that are sufficiently sensitive to detect intrinsic replicative stress and its consequences in primary mouse embryonic fibroblasts. First, we explain the non-denatured DNA fiber assay, a powerful tool to directly measure DNA replication kinetics via the dual-labeling of active replication forks. Then, we describe the cytokinesis-block micronucleus assay, which can be combined with detection of 53BP1 nuclear bodies to measure the levels of replication-associated genome instability carried over into G1 phase of the cell cycle.
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Affiliation(s)
- Spencer W Luebben
- Department of Genetics, Cell Biology and Development, University of Minnesota, 6-160 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA
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330
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Computational Models of Large-Scale Genome Architecture. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 307:275-349. [DOI: 10.1016/b978-0-12-800046-5.00009-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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331
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Neelsen KJ, Zanini IM, Mijic S, Herrador R, Zellweger R, Ray Chaudhuri A, Creavin KD, Blow JJ, Lopes M. Deregulated origin licensing leads to chromosomal breaks by rereplication of a gapped DNA template. Genes Dev 2013; 27:2537-42. [PMID: 24298053 PMCID: PMC3861667 DOI: 10.1101/gad.226373.113] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 10/30/2013] [Indexed: 01/01/2023]
Abstract
Deregulated origin licensing and rereplication promote genome instability and tumorigenesis by largely elusive mechanisms. Investigating the consequences of Early mitotic inhibitor 1 (Emi1) depletion in human cells, previously associated with rereplication, we show by DNA fiber labeling that origin reactivation occurs rapidly, well before accumulation of cells with >4N DNA, and is associated with checkpoint-blind ssDNA gaps and replication fork reversal. Massive RPA chromatin loading, formation of small chromosomal fragments, and checkpoint activation occur only later, once cells complete bulk DNA replication. We propose that deregulated origin firing leads to undetected discontinuities on newly replicated DNA, which ultimately cause breakage of rereplicating forks.
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Affiliation(s)
- Kai J. Neelsen
- Institute of Molecular Cancer Research, University of Zurich, CH-8057 Zurich, Switzerland
| | - Isabella M.Y. Zanini
- Institute of Molecular Cancer Research, University of Zurich, CH-8057 Zurich, Switzerland
| | - Sofija Mijic
- Institute of Molecular Cancer Research, University of Zurich, CH-8057 Zurich, Switzerland
| | - Raquel Herrador
- Institute of Molecular Cancer Research, University of Zurich, CH-8057 Zurich, Switzerland
| | - Ralph Zellweger
- Institute of Molecular Cancer Research, University of Zurich, CH-8057 Zurich, Switzerland
| | - Arnab Ray Chaudhuri
- Institute of Molecular Cancer Research, University of Zurich, CH-8057 Zurich, Switzerland
| | - Kevin D. Creavin
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - J. Julian Blow
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, CH-8057 Zurich, Switzerland
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332
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Mourón S, Rodriguez-Acebes S, Martínez-Jiménez MI, García-Gómez S, Chocrón S, Blanco L, Méndez J. Repriming of DNA synthesis at stalled replication forks by human PrimPol. Nat Struct Mol Biol 2013; 20:1383-9. [DOI: 10.1038/nsmb.2719] [Citation(s) in RCA: 197] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 10/22/2013] [Indexed: 12/22/2022]
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333
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Belmont AS. Large-scale chromatin organization: the good, the surprising, and the still perplexing. Curr Opin Cell Biol 2013; 26:69-78. [PMID: 24529248 DOI: 10.1016/j.ceb.2013.10.002] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 10/07/2013] [Accepted: 10/15/2013] [Indexed: 11/19/2022]
Abstract
Traditionally large-scale chromatin structure has been studied by microscopic approaches, providing direct spatial information but limited sequence context. In contrast, newer 3C (chromosome capture conformation) methods provide rich sequence context but uncertain spatial context. Recent demonstration of large, topologically linked DNA domains, hundreds to thousands of kb in size, may now link 3C data to actual chromosome physical structures, as visualized directly by microscopic methods. Yet, new data suggesting that 3C may measure cytological rather than molecular proximity prompts a renewed focus on understanding the origin of 3C interactions and dissecting the biological significance of long-range genomic interactions.
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Affiliation(s)
- Andrew S Belmont
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, B107 CLSL, 601 South Goodwin Avenue, Urbana, IL 61801, United States.
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334
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Xie M, Yen Y, Owonikoko TK, Ramalingam SS, Khuri FR, Curran WJ, Doetsch PW, Deng X. Bcl2 induces DNA replication stress by inhibiting ribonucleotide reductase. Cancer Res 2013; 74:212-23. [PMID: 24197132 DOI: 10.1158/0008-5472.can-13-1536-t] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
DNA replication stress is an inefficient DNA synthesis process that leads replication forks to progress slowly or stall. Two main factors that cause replication stress are alterations in pools of deoxyribonucleotide (dNTP) precursors required for DNA synthesis and changes in the activity of proteins required for synthesis of dNTPs. Ribonucleotide reductase (RNR), containing regulatory hRRM1 and catalytic hRRM2 subunits, is the enzyme that catalyzes the conversion of ribonucleoside diphosphates (NDP) to deoxyribonucleoside diphosphates (dNDP) and thereby provides dNTP precursors needed for the synthesis of DNA. Here, we demonstrate that either endogenous or exogenous expression of Bcl2 results in decreases in RNR activity and intracellular dNTP, retardation of DNA replication fork progression, and increased rate of fork asymmetry leading to DNA replication stress. Bcl2 colocalizes with hRRM1 and hRRM2 in the cytoplasm and directly interacts via its BH4 domain with hRRM2 but not hRRM1. Removal of the BH4 domain of Bcl2 abrogates its inhibitory effects on RNR activity, dNTP pool level, and DNA replication. Intriguingly, Bcl2 directly inhibits RNR activity by disrupting the functional hRRM1/hRRM2 complex via its BH4 domain. Our findings argue that Bcl2 reduces intracellular dNTPs by inhibiting ribonucleotide reductase activity, thereby providing insight into how Bcl2 triggers DNA replication stress.
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Affiliation(s)
- Maohua Xie
- Authors' Affiliations: Departments of Radiation Oncology, Hematology and Medical Oncology, and Biochemistry, Emory University School of Medicine and Winship Cancer Institute of Emory University, Atlanta, Georgia; and Department of Clinical and Molecular Pharmacology, City of Hope National Medical Center, Duarte, California
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335
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Julienne H, Zoufir A, Audit B, Arneodo A. Human genome replication proceeds through four chromatin states. PLoS Comput Biol 2013; 9:e1003233. [PMID: 24130466 PMCID: PMC3794905 DOI: 10.1371/journal.pcbi.1003233] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 08/06/2013] [Indexed: 12/26/2022] Open
Abstract
Advances in genomic studies have led to significant progress in understanding the epigenetically controlled interplay between chromatin structure and nuclear functions. Epigenetic modifications were shown to play a key role in transcription regulation and genome activity during development and differentiation or in response to the environment. Paradoxically, the molecular mechanisms that regulate the initiation and the maintenance of the spatio-temporal replication program in higher eukaryotes, and in particular their links to epigenetic modifications, still remain elusive. By integrative analysis of the genome-wide distributions of thirteen epigenetic marks in the human cell line K562, at the 100 kb resolution of corresponding mean replication timing (MRT) data, we identify four major groups of chromatin marks with shared features. These states have different MRT, namely from early to late replicating, replication proceeds though a transcriptionally active euchromatin state (C1), a repressive type of chromatin (C2) associated with polycomb complexes, a silent state (C3) not enriched in any available marks, and a gene poor HP1-associated heterochromatin state (C4). When mapping these chromatin states inside the megabase-sized U-domains (U-shaped MRT profile) covering about 50% of the human genome, we reveal that the associated replication fork polarity gradient corresponds to a directional path across the four chromatin states, from C1 at U-domains borders followed by C2, C3 and C4 at centers. Analysis of the other genome half is consistent with early and late replication loci occurring in separate compartments, the former correspond to gene-rich, high-GC domains of intermingled chromatin states C1 and C2, whereas the latter correspond to gene-poor, low-GC domains of alternating chromatin states C3 and C4 or long C4 domains. This new segmentation sheds a new light on the epigenetic regulation of the spatio-temporal replication program in human and provides a framework for further studies in different cell types, in both health and disease. Previous studies revealed spatially coherent and biological-meaningful chromatin mark combinations in human cells. Here, we analyze thirteen epigenetic mark maps in the human cell line K562 at 100 kb resolution of MRT data. The complexity of epigenetic data is reduced to four chromatin states that display remarkable similarities with those reported in fly, worm and plants. These states have different MRT: (C1) is transcriptionally active, early replicating, enriched in CTCF; (C2) is Polycomb repressed, mid-S replicating; (C3) lacks of marks and replicates late and (C4) is a late-replicating gene-poor HP1 repressed heterochromatin state. When mapping these states inside the 876 replication U-domains of K562, the replication fork polarity gradient observed in these U-domains comes along with a remarkable epigenetic organization from C1 at U-domain borders to C2, C3 and ultimately C4 at centers. The remaining genome half displays early replicating, gene rich and high GC domains of intermingled C1 and C2 states segregating from late replicating, gene poor and low GC domains of concatenated C3 and/or C4 states. This constitutes the first evidence of epigenetic compartmentalization of the human genome into replication domains likely corresponding to autonomous units in the 3D chromatin architecture.
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Affiliation(s)
- Hanna Julienne
- Université de Lyon, Lyon, France
- Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Azedine Zoufir
- Université de Lyon, Lyon, France
- Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Benjamin Audit
- Université de Lyon, Lyon, France
- Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, Lyon, France
- * E-mail:
| | - Alain Arneodo
- Université de Lyon, Lyon, France
- Laboratoire de Physique, CNRS UMR 5672, Ecole Normale Supérieure de Lyon, Lyon, France
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336
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Takata H, Hanafusa T, Mori T, Shimura M, Iida Y, Ishikawa K, Yoshikawa K, Yoshikawa Y, Maeshima K. Chromatin compaction protects genomic DNA from radiation damage. PLoS One 2013; 8:e75622. [PMID: 24130727 PMCID: PMC3794047 DOI: 10.1371/journal.pone.0075622] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Accepted: 08/20/2013] [Indexed: 12/02/2022] Open
Abstract
Genomic DNA is organized three-dimensionally in the nucleus, and is thought to form compact chromatin domains. Although chromatin compaction is known to be essential for mitosis, whether it confers other advantages, particularly in interphase cells, remains unknown. Here, we report that chromatin compaction protects genomic DNA from radiation damage. Using a newly developed solid-phase system, we found that the frequency of double-strand breaks (DSBs) in compact chromatin after ionizing irradiation was 5–50-fold lower than in decondensed chromatin. Since radical scavengers inhibited DSB induction in decondensed chromatin, condensed chromatin had a lower level of reactive radical generation after ionizing irradiation. We also found that chromatin compaction protects DNA from attack by chemical agents. Our findings suggest that genomic DNA compaction plays an important role in maintaining genomic integrity.
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Affiliation(s)
- Hideaki Takata
- Structural Biology Center, National Institute of Genetics, Mishima, Shizuoka, Japan
- Frontier Research Base for Global Young Researchers, Graduate School of Engineering Osaka University, Suita, Osaka, Japan
- * E-mail: (HT); (KM)
| | - Tomo Hanafusa
- Structural Biology Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Toshiaki Mori
- Radiation Research Center, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Mari Shimura
- Department of Intractable Diseases, Research Institute, National Center for Global Health and Medicine, Shinjuku, Tokyo, Japan
| | - Yutaka Iida
- Inorganic Analysis Laboratories, Toray Research Center, Inc., Otsu, Shiga, Japan
| | - Kenichi Ishikawa
- Advanced Radiation Biology Research Program, Research Center for Charged Particle Therapy, National Institute of Radiological Sciences, Inage, Chiba, Japan
| | - Kenichi Yoshikawa
- Department of Physics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Yuko Yoshikawa
- Research Organization of Science and Engineering, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Kazuhiro Maeshima
- Structural Biology Center, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka, Japan
- * E-mail: (HT); (KM)
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337
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Hyrien O, Rappailles A, Guilbaud G, Baker A, Chen CL, Goldar A, Petryk N, Kahli M, Ma E, d'Aubenton-Carafa Y, Audit B, Thermes C, Arneodo A. From simple bacterial and archaeal replicons to replication N/U-domains. J Mol Biol 2013; 425:4673-89. [PMID: 24095859 DOI: 10.1016/j.jmb.2013.09.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 09/15/2013] [Accepted: 09/19/2013] [Indexed: 10/26/2022]
Abstract
The Replicon Theory proposed 50 years ago has proven to apply for replicons of the three domains of life. Here, we review our knowledge of genome organization into single and multiple replicons in bacteria, archaea and eukarya. Bacterial and archaeal replicator/initiator systems are quite specific and efficient, whereas eukaryotic replicons show degenerate specificity and efficiency, allowing for complex regulation of origin firing time. We expand on recent evidence that ~50% of the human genome is organized as ~1,500 megabase-sized replication domains with a characteristic parabolic (U-shaped) replication timing profile and linear (N-shaped) gradient of replication fork polarity. These N/U-domains correspond to self-interacting segments of the chromatin fiber bordered by open chromatin zones and replicate by cascades of origin firing initiating at their borders and propagating to their center, possibly by fork-stimulated initiation. The conserved occurrence of this replication pattern in the germline of mammals has resulted over evolutionary times in the formation of megabase-sized domains with an N-shaped nucleotide compositional skew profile due to replication-associated mutational asymmetries. Overall, these results reveal an evolutionarily conserved but developmentally plastic organization of replication that is driving mammalian genome evolution.
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Affiliation(s)
- Olivier Hyrien
- Ecole Normale Supérieure, IBENS UMR8197 U1024, Paris 75005, France.
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338
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Abstract
The onset of genomic DNA synthesis requires precise interactions of specialized initiator proteins with DNA at sites where the replication machinery can be loaded. These sites, defined as replication origins, are found at a few unique locations in all of the prokaryotic chromosomes examined so far. However, replication origins are dispersed among tens of thousands of loci in metazoan chromosomes, thereby raising questions regarding the role of specific nucleotide sequences and chromatin environment in origin selection and the mechanisms used by initiators to recognize replication origins. Close examination of bacterial and archaeal replication origins reveals an array of DNA sequence motifs that position individual initiator protein molecules and promote initiator oligomerization on origin DNA. Conversely, the need for specific recognition sequences in eukaryotic replication origins is relaxed. In fact, the primary rule for origin selection appears to be flexibility, a feature that is modulated either by structural elements or by epigenetic mechanisms at least partly linked to the organization of the genome for gene expression.
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Affiliation(s)
- Alan C Leonard
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, Florida 32901
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339
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Damage-induced DNA replication stalling relies on MAPK-activated protein kinase 2 activity. Proc Natl Acad Sci U S A 2013; 110:16856-61. [PMID: 24082115 DOI: 10.1073/pnas.1304355110] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA damage can obstruct replication forks, resulting in replicative stress. By siRNA screening, we identified kinases involved in the accumulation of phosphohistone 2AX (γH2AX) upon UV irradiation-induced replication stress. Surprisingly, the strongest reduction of phosphohistone 2AX followed knockdown of the MAP kinase-activated protein kinase 2 (MK2), a kinase currently implicated in p38 stress signaling and G2 arrest. Depletion or inhibition of MK2 also protected cells from DNA damage-induced cell death, and mice deficient for MK2 displayed decreased apoptosis in the skin upon UV irradiation. Moreover, MK2 activity was required for damage response, accumulation of ssDNA, and decreased survival when cells were treated with the nucleoside analogue gemcitabine or when the checkpoint kinase Chk1 was antagonized. By using DNA fiber assays, we found that MK2 inhibition or knockdown rescued DNA replication impaired by gemcitabine or by Chk1 inhibition. This rescue strictly depended on translesion DNA polymerases. In conclusion, instead of being an unavoidable consequence of DNA damage, alterations of replication speed and origin firing depend on MK2-mediated signaling.
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340
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Saner N, Karschau J, Natsume T, Gierliński M, Retkute R, Hawkins M, Nieduszynski CA, Blow JJ, de Moura AP, Tanaka TU. Stochastic association of neighboring replicons creates replication factories in budding yeast. J Cell Biol 2013; 202:1001-12. [PMID: 24062338 PMCID: PMC3787376 DOI: 10.1083/jcb.201306143] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 08/26/2013] [Indexed: 01/03/2023] Open
Abstract
Inside the nucleus, DNA replication is organized at discrete sites called replication factories, consisting of DNA polymerases and other replication proteins. Replication factories play important roles in coordinating replication and in responding to replication stress. However, it remains unknown how replicons are organized for processing at each replication factory. Here we address this question using budding yeast. We analyze how individual replicons dynamically organized a replication factory using live-cell imaging and investigate how replication factories were structured using super-resolution microscopy. Surprisingly, we show that the grouping of replicons within factories is highly variable from cell to cell. Once associated, however, replicons stay together relatively stably to maintain replication factories. We derive a coherent genome-wide mathematical model showing how neighboring replicons became associated stochastically to form replication factories, which was validated by independent microscopy-based analyses. This study not only reveals the fundamental principles promoting replication factory organization in budding yeast, but also provides insight into general mechanisms by which chromosomes organize sub-nuclear structures.
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Affiliation(s)
- Nazan Saner
- Centre for Gene Regulation and Expression, and Data Analysis Group, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Jens Karschau
- Institute for Complex Systems and Mathematical Biology, SUPA, School of Natural and Computing Sciences, University of Aberdeen, Aberdeen AB24 3UE, Scotland, UK
| | - Toyoaki Natsume
- Centre for Gene Regulation and Expression, and Data Analysis Group, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Marek Gierliński
- Centre for Gene Regulation and Expression, and Data Analysis Group, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Renata Retkute
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, Nottingham NG7 2UH, England, UK
| | - Michelle Hawkins
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, Nottingham NG7 2UH, England, UK
| | - Conrad A. Nieduszynski
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, Nottingham NG7 2UH, England, UK
| | - J. Julian Blow
- Centre for Gene Regulation and Expression, and Data Analysis Group, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Alessandro P.S. de Moura
- Institute for Complex Systems and Mathematical Biology, SUPA, School of Natural and Computing Sciences, University of Aberdeen, Aberdeen AB24 3UE, Scotland, UK
| | - Tomoyuki U. Tanaka
- Centre for Gene Regulation and Expression, and Data Analysis Group, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
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341
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HMGA2 inhibits apoptosis through interaction with ATR-CHK1 signaling complex in human cancer cells. Neoplasia 2013; 15:263-80. [PMID: 23479505 DOI: 10.1593/neo.121988] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 01/15/2013] [Accepted: 01/18/2013] [Indexed: 02/08/2023] Open
Abstract
The non-histone chromatin binding protein high mobility group AT-hook 2 (HMGA2) is expressed in stem cells and many cancer cells, including tumor initiating cells, but not translated in normal human somatic cells. The presence of HMGA2 is correlated with advanced neoplastic disease and poor prognosis for patients. We had previously demonstrated a role of HMGA2 in DNA repair pathways. In the present study, we employed different human tumor cell models with endogenous and exogenous expression of HMGA2 and show that upon DNA damage, the presence of HMGA2 caused an increased and sustained phosphorylation of the ataxia telangiectasia and Rad3-related kinase (ATR) and its downstream target checkpoint kinase 1 (CHK1). The presence of activated pCHK1(Ser296) coincided with prolonged G2/M block and increased tumor cell survival, which was enhanced further in the presence of HMGA2. Our study, thus, identifies a novel relationship between the ATR-CHK1 DNA damage response pathway and HMGA2, which may support the DNA repair function of HMGA2 in cancer cells. Furthermore, our data provide a rationale for the use of inhibitors to ATR or CHK1 and HMGA2 in the treatment of HMGA2-positive human cancer cells.
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342
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Lossaint G, Larroque M, Ribeyre C, Bec N, Larroque C, Décaillet C, Gari K, Constantinou A. FANCD2 binds MCM proteins and controls replisome function upon activation of s phase checkpoint signaling. Mol Cell 2013; 51:678-90. [PMID: 23993743 DOI: 10.1016/j.molcel.2013.07.023] [Citation(s) in RCA: 180] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 06/20/2013] [Accepted: 07/25/2013] [Indexed: 10/26/2022]
Abstract
Proteins disabled in Fanconi anemia (FA) are necessary for the maintenance of genome stability during cell proliferation. Upon replication stress signaling by ATR, the FA core complex monoubiquitinates FANCD2 and FANCI in order to activate DNA repair. Here, we identified FANCD2 and FANCI in a proteomic screen of replisome-associated factors bound to nascent DNA in response to replication arrest. We found that FANCD2 can interact directly with minichromosome maintenance (MCM) proteins. ATR signaling promoted the transient association of endogenous FANCD2 with the MCM2-MCM7 replicative helicase independently of FANCD2 monoubiquitination. FANCD2 was necessary for human primary cells to restrain DNA synthesis in the presence of a reduced pool of nucleotides and prevented the accumulation of single-stranded DNA, the induction of p21, and the entry of cells into senescence. These data reveal that FANCD2 is an effector of ATR signaling implicated in a general replisome surveillance mechanism that is necessary for sustaining cell proliferation and attenuating carcinogenesis.
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Affiliation(s)
- Gérald Lossaint
- Institute of Human Genetics, UPR 1142, CNRS, 141, rue de la Cardonille, 34396 Montpellier, France
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343
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Zhang Y, Park E, Kim CS, Paik JH. ZNF365 promotes stalled replication forks recovery to maintain genome stability. Cell Cycle 2013; 12:2817-28. [PMID: 23966166 DOI: 10.4161/cc.25882] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The ZNF365 locus is associated with breast cancer risk in carriers of mutated BRCA1 and BRCA2, which are important molecules required for DNA damage response. Previously, we demonstrated that ZNF365 is necessary for timely resolution of replication intermediates of genomic fragile sites and, thus, for suppression of genomic instability; however, the mechanism underlying the function of ZNF365 on damaged DNA and stalled replication forks remains unknown. Here, we demonstrate that ZNF365 is induced by DNA double-strand break (DSB) signals, is involved in the homologous recombination (HR) repair pathway, and maintains genome integrity during DNA replication. On the mechanistic level, ZNF365 interacts with poly(ADP-ribose) polymerase (PARP) 1 to tether MRE11 to the DNA end resection site. Loss of ZNF365 results in delayed mitotic progression and exit due to increased replication stress, ultimately leading to cytokinesis failure, re-duplication of centrosomes, and increased aneuploidy. Collectively, these results suggest an HR repair-dependent function of ZNF365 in preventing genomic instability.
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Affiliation(s)
- Yuqing Zhang
- Department of Pathology and Laboratory Medicine; Weill Cornell Medical College; New York, NY USA
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344
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Mórocz M, Gali H, Raskó I, Downes CS, Haracska L. Single cell analysis of human RAD18-dependent DNA post-replication repair by alkaline bromodeoxyuridine comet assay. PLoS One 2013; 8:e70391. [PMID: 23936422 PMCID: PMC3735594 DOI: 10.1371/journal.pone.0070391] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 06/19/2013] [Indexed: 01/02/2023] Open
Abstract
Damage to DNA can block replication progression resulting in gaps in the newly synthesized DNA. Cells utilize a number of post-replication repair (PRR) mechanisms such as the RAD18 controlled translesion synthesis or template switching to overcome the discontinuities formed opposite the DNA lesions and to complete DNA replication. Gaining more insights into the role of PRR genes promotes better understanding of DNA damage tolerance and of how their malfunction can lead to increased genome instability and cancer. However, a simple and efficient method to characterise gene specific PRR deficiencies at a single cell level has not been developed. Here we describe the so named BrdU comet PRR assay to test the contribution of human RAD18 to PRR at a single cell level, by which we kinetically characterized the consequences of the deletion of human RAD18 on the replication of UV-damaged DNA. Moreover, we demonstrate the capability of our method to evaluate PRR at a single cell level in unsynchronized cell population.
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Affiliation(s)
- Mónika Mórocz
- Institute of Genetics, Biological Research Centre of Hungarian Academy of Sciences, Szeged, Hungary
| | - Himabindu Gali
- Institute of Genetics, Biological Research Centre of Hungarian Academy of Sciences, Szeged, Hungary
| | - István Raskó
- Institute of Genetics, Biological Research Centre of Hungarian Academy of Sciences, Szeged, Hungary
| | - C. Stephen Downes
- Biomedical Sciences Research Institute, School of Biomedical Sciences, University of Ulster, Coleraine, Londonderry, Northern Ireland
| | - Lajos Haracska
- Institute of Genetics, Biological Research Centre of Hungarian Academy of Sciences, Szeged, Hungary
- * E-mail:
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345
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Prereplicative repair of oxidized bases in the human genome is mediated by NEIL1 DNA glycosylase together with replication proteins. Proc Natl Acad Sci U S A 2013; 110:E3090-9. [PMID: 23898192 DOI: 10.1073/pnas.1304231110] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Base oxidation by endogenous and environmentally induced reactive oxygen species preferentially occurs in replicating single-stranded templates in mammalian genomes, warranting prereplicative repair of the mutagenic base lesions. It is not clear how such lesions (which, unlike bulky adducts, do not block replication) are recognized for repair. Furthermore, strand breaks caused by base excision from ssDNA by DNA glycosylases, including Nei-like (NEIL) 1, would generate double-strand breaks during replication, which are not experimentally observed. NEIL1, whose deficiency causes a mutator phenotype and is activated during the S phase, is present in the DNA replication complex isolated from human cells, with enhanced association with DNA in S-phase cells and colocalization with replication foci containing DNA replication proteins. Furthermore, NEIL1 binds to 5-hydroxyuracil, the oxidative deamination product of C, in replication protein A-coated ssDNA template and inhibits DNA synthesis by DNA polymerase δ. We postulate that, upon encountering an oxidized base during replication, NEIL1 initiates prereplicative repair by acting as a "cowcatcher" and preventing nascent chain growth. Regression of the stalled replication fork, possibly mediated by annealing helicases, then allows lesion repair in the reannealed duplex. This model is supported by our observations that NEIL1, whose deficiency slows nascent chain growth in oxidatively stressed cells, is stimulated by replication proteins in vitro. Furthermore, deficiency of the closely related NEIL2 alone does not affect chain elongation, but combined NEIL1/2 deficiency further inhibits DNA replication. These results support a mechanism of NEIL1-mediated prereplicative repair of oxidized bases in the replicating strand, with NEIL2 providing a backup function.
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346
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Abstract
Although distinct chromatin types have been long known to replicate at different timepoints of S phase, fine replication control has only recently become considered as an epigenetic phenomenon. It is now clear that in course of differentiation significant changes in genome replication timing occur, and these changes are intimately linked with the changes in transcriptional activity and nuclear architecture. Temporally coordinate replication is organized spatially into discrete units having specific chromosomal organization and function. Even though the functional aspects of such tight control of replication timing remain to be explored, one can confidently consider the replication program as yet another fundamental feature characteristic of the given differentiation state. The present review touches upon the molecular mechanisms of spatial and temporal control of replication timing, involving individual replication origins as well as large chromatin domains.
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347
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Wójcik K, Zarębski M, Cossarizza A, Dobrucki JW. Daunomycin, an antitumor DNA intercalator, influences histone-DNA interactions. Cancer Biol Ther 2013; 14:823-32. [PMID: 23792590 DOI: 10.4161/cbt.25328] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Although daunomycin and adriamycin are considered effective antitumor drugs and have been used in the clinic for over 40 years, their mechanism of action is still a matter of debate. We investigated the influence of daunomycin on interaction between linker or core histones and DNA in live HeLa cells in vitro, using image and flow cytometry. Exposure to daunomycin at clinically relevant concentrations (25-250 nM) caused dissociation of wild-type H1.1 as well as 4 H1 point mutants from DNA, followed by their accumulation in nucleoli and aggregation of chromatin. A detectable dissociation of H2B core histones occurred only at much higher concentrations of the drug (500 nM). Replication of DNA and synthesis of RNA were not halted by daunomycin (up to 2500 nM); however the characteristic subnuclear distribution of sites of transcription and replication was lost. Dissociation of the H1.1 linker histones and subsequent loss of higher order chromatin structures may constitute an important component of the mechanism of cytotoxicity of daunomycin.
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Affiliation(s)
- Krzysztof Wójcik
- Division of Cell Biophysics; Faculty of Biochemistry, Biophysics and Biotechnology; Jagiellonian University; Kraków, Poland
| | - Mirosław Zarębski
- Division of Cell Biophysics; Faculty of Biochemistry, Biophysics and Biotechnology; Jagiellonian University; Kraków, Poland
| | - Andrea Cossarizza
- University of Modena and Reggio Emilia; School of Medicine; Department of Biomedical Sciences; Modena, Italy
| | - Jurek W Dobrucki
- Division of Cell Biophysics; Faculty of Biochemistry, Biophysics and Biotechnology; Jagiellonian University; Kraków, Poland
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348
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Gaggioli V, Le Viet B, Germe T, Hyrien O. DNA topoisomerase IIα controls replication origin cluster licensing and firing time in Xenopus egg extracts. Nucleic Acids Res 2013; 41:7313-31. [PMID: 23757188 PMCID: PMC3753627 DOI: 10.1093/nar/gkt494] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Sperm chromatin incubated in Xenopus egg extracts undergoes origin licensing and nuclear assembly before DNA replication. We found that depletion of DNA topoisomerase IIα (topo IIα), the sole topo II isozyme of eggs and its inhibition by ICRF-193, which clamps topo IIα around DNA have opposite effects on these processes. ICRF-193 slowed down replication origin cluster activation and fork progression in a checkpoint-independent manner, without altering replicon size. In contrast, topo IIα depletion accelerated origin cluster activation, and topo IIα add-back negated overinitiation. Therefore, topo IIα is not required for DNA replication, but topo IIα clamps slow replication, probably by forming roadblocks. ICRF-193 had no effect on DNA synthesis when added after nuclear assembly, confirming that topo IIα activity is dispensable for replication and revealing that topo IIα clamps formed on replicating DNA do not block replication, presumably because topo IIα acts behind and not in front of forks. Topo IIα depletion increased, and topo IIα addition reduced, chromatin loading of MCM2-7 replicative helicase, whereas ICRF-193 did not affect MCM2-7 loading. Therefore, topo IIα restrains MCM2-7 loading in an ICRF-193-resistant manner during origin licensing, suggesting a model for establishing the sequential firing of origin clusters.
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Affiliation(s)
- Vincent Gaggioli
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), S2-Génomique Fonctionnelle, CNRS UMR8197, Inserm U1024, 46 rue d'Ulm, 75005 Paris, France
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349
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Mansilla SF, Soria G, Vallerga MB, Habif M, Martínez-López W, Prives C, Gottifredi V. UV-triggered p21 degradation facilitates damaged-DNA replication and preserves genomic stability. Nucleic Acids Res 2013; 41:6942-51. [PMID: 23723248 PMCID: PMC3737556 DOI: 10.1093/nar/gkt475] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Although many genotoxic treatments upregulate the cyclin kinase inhibitor p21, agents such as UV irradiation trigger p21 degradation. This suggests that p21 blocks a process relevant for the cellular response to UV. Here, we show that forced p21 stabilization after UV strongly impairs damaged-DNA replication, which is associated with permanent deficiencies in the recruitment of DNA polymerases from the Y family involved in translesion DNA synthesis), with the accumulation of DNA damage markers and increased genomic instability. Remarkably, such noxious effects disappear when disrupting the proliferating cell nuclear antigen (PCNA) interacting motif of stable p21, thus suggesting that the release of PCNA from p21 interaction is sufficient to allow the recruitment to PCNA of partners (such as Y polymerases) relevant for the UV response. Expression of degradable p21 only transiently delays early replication events and Y polymerase recruitment after UV irradiation. These temporary defects disappear in a manner that correlates with p21 degradation with no detectable consequences on later replication events or genomic stability. Together, our findings suggest that the biological role of UV-triggered p21 degradation is to prevent replication defects by facilitating the tolerance of UV-induced DNA lesions.
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Affiliation(s)
- Sabrina F Mansilla
- Cell Cycle and Genomic Stability Laboratory, Fundación Instituto Leloir-CONICET, Buenos Aires C1405BWE, Argentina
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350
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Boos D, Yekezare M, Diffley JFX. Identification of a heteromeric complex that promotes DNA replication origin firing in human cells. Science 2013; 340:981-4. [PMID: 23704573 DOI: 10.1126/science.1237448] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Treslin/TICRR (TopBP1-interacting, replication stimulating protein/TopBP1-interacting, checkpoint, and replication regulator), the human ortholog of the yeast Sld3 protein, is an essential DNA replication factor that is regulated by cyclin-dependent kinases and the DNA damage checkpoint. We identified MDM two binding protein (MTBP) as a factor that interacts with Treslin/TICRR throughout the cell cycle. We show that MTBP depletion by means of small interfering RNA inhibits DNA replication by preventing assembly of the CMG (Cdc45-MCM-GINS) holohelicase during origin firing. Although MTBP has been implicated in the function of the p53 tumor suppressor, we found MTBP is required for DNA replication irrespective of a cell's p53 status. We propose that MTBP acts with Treslin/TICRR to integrate signals from cell cycle and DNA damage response pathways to control the initiation of DNA replication in human cells.
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Affiliation(s)
- Dominik Boos
- Cancer Research UK London Research Institute (LRI), Clare Hall Laboratories, South Mimms, Herts., UK
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