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Hoa NN, Shimizu T, Zhou ZW, Wang ZQ, Deshpande RA, Paull TT, Akter S, Tsuda M, Furuta R, Tsutsui K, Takeda S, Sasanuma H. Mre11 Is Essential for the Removal of Lethal Topoisomerase 2 Covalent Cleavage Complexes. Mol Cell 2016; 64:580-592. [PMID: 27814490 DOI: 10.1016/j.molcel.2016.10.011] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 07/22/2016] [Accepted: 10/05/2016] [Indexed: 12/12/2022]
Abstract
The Mre11/Rad50/Nbs1 complex initiates double-strand break repair by homologous recombination (HR). Loss of Mre11 or its nuclease activity in mouse cells is known to cause genome aberrations and cellular senescence, although the molecular basis for this phenotype is not clear. To identify the origin of these defects, we characterized Mre11-deficient (MRE11-/-) and nuclease-deficient Mre11 (MRE11-/H129N) chicken DT40 and human lymphoblast cell lines. These cells exhibit increased spontaneous chromosomal DSBs and extreme sensitivity to topoisomerase 2 poisons. The defects in Mre11 compromise the repair of etoposide-induced Top2-DNA covalent complexes, and MRE11-/- and MRE11-/H129N cells accumulate high levels of Top2 covalent conjugates even in the absence of exogenous damage. We demonstrate that both the genome instability and mortality of MRE11-/- and MRE11-/H129N cells are significantly reversed by overexpression of Tdp2, an enzyme that eliminates covalent Top2 conjugates; thus, the essential role of Mre11 nuclease activity is likely to remove these lesions.
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Affiliation(s)
- Nguyen Ngoc Hoa
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tsubasa Shimizu
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Zhong Wei Zhou
- Leibniz Institute for Age Research-Fritz Lipmann Institute, Beutenbergstrasse 11, 07745 Jena, Germany
| | - Zhao-Qi Wang
- Leibniz Institute for Age Research-Fritz Lipmann Institute, Beutenbergstrasse 11, 07745 Jena, Germany
| | - Rajashree A Deshpande
- Howard Hughes Medical Institute, Department of Molecular Biosciences, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Tanya T Paull
- Howard Hughes Medical Institute, Department of Molecular Biosciences, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Salma Akter
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masataka Tsuda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Ryohei Furuta
- Department of Neurogenomics, Graduate School of Medicine, Dentistry and Pharmaceutical Science, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan
| | - Ken Tsutsui
- Department of Neurogenomics, Graduate School of Medicine, Dentistry and Pharmaceutical Science, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroyuki Sasanuma
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan.
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Verver DE, Zheng Y, Speijer D, Hoebe R, Dekker HL, Repping S, Stap J, Hamer G. Non-SMC Element 2 (NSMCE2) of the SMC5/6 Complex Helps to Resolve Topological Stress. Int J Mol Sci 2016; 17:ijms17111782. [PMID: 27792189 PMCID: PMC5133783 DOI: 10.3390/ijms17111782] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 09/14/2016] [Accepted: 10/20/2016] [Indexed: 01/05/2023] Open
Abstract
The structural maintenance of chromosomes (SMC) protein complexes shape and regulate the structure and dynamics of chromatin, thereby controlling many chromosome-based processes such as cell cycle progression, differentiation, gene transcription and DNA repair. The SMC5/6 complex is previously described to promote DNA double-strand breaks (DSBs) repair by sister chromatid recombination, and found to be essential for resolving recombination intermediates during meiotic recombination. Moreover, in budding yeast, SMC5/6 provides structural organization and topological stress relief during replication in mitotically dividing cells. Despite the essential nature of the SMC5/6 complex, the versatile mechanisms by which SMC5/6 functions and its molecular regulation in mammalian cells remain poorly understood. By using a human osteosarcoma cell line (U2OS), we show that after the CRISPR-Cas9-mediated removal of the SMC5/6 subunit NSMCE2, treatment with the topoisomerase II inhibitor etoposide triggered an increased sensitivity in cells lacking NSMCE2. In contrast, NSMCE2 appeared not essential for a proper DNA damage response or cell survival after DSB induction by ionizing irradiation (IR). Interestingly, by way of immunoprecipitations (IPs) and mass spectrometry, we found that the SMC5/6 complex physically interacts with the DNA topoisomerase II α (TOP2A). We therefore propose that the SMC5/6 complex functions in resolving TOP2A-mediated DSB-repair intermediates generated during replication.
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Affiliation(s)
- Dideke E Verver
- Center for Reproductive Medicine, Amsterdam Research Institute Reproduction and Development, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
| | - Yi Zheng
- Center for Reproductive Medicine, Amsterdam Research Institute Reproduction and Development, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
| | - Dave Speijer
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
| | - Ron Hoebe
- Department of Cell Biology and Histology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
| | - Henk L Dekker
- Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, University of Amsterdam, 1090 GE Amsterdam, The Netherlands.
| | - Sjoerd Repping
- Center for Reproductive Medicine, Amsterdam Research Institute Reproduction and Development, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
| | - Jan Stap
- Department of Cell Biology and Histology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
| | - Geert Hamer
- Center for Reproductive Medicine, Amsterdam Research Institute Reproduction and Development, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
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53
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Colosio A, Frattini C, Pellicanò G, Villa-Hernández S, Bermejo R. Nucleolytic processing of aberrant replication intermediates by an Exo1-Dna2-Sae2 axis counteracts fork collapse-driven chromosome instability. Nucleic Acids Res 2016; 44:10676-10690. [PMID: 27672038 PMCID: PMC5159547 DOI: 10.1093/nar/gkw858] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 09/14/2016] [Accepted: 09/17/2016] [Indexed: 12/16/2022] Open
Abstract
Problems during DNA replication underlie genomic instability and drive malignant transformation. The DNA damage checkpoint stabilizes stalled replication forks thus counteracting aberrant fork transitions, DNA breaks and chromosomal rearrangements. We analyzed fork processing in checkpoint deficient cells by coupling psoralen crosslinking with replication intermediate two-dimensional gel analysis. This revealed a novel role for Exo1 nuclease in resecting reversed replication fork structures and counteracting the accumulation of aberrant intermediates resembling fork cleavage products. Genetic analyses demonstrated a functional interplay of Exo1 with Mus81, Dna2 and Sae2 nucleases in promoting cell survival following replication stress, suggestive of concerted nucleolytic processing of stalled forks. While Mus81 and other Structure Specific Endonucleases do not contribute to obvious collapsed fork transitions, Dna2 promotes reversed fork resection likely by facilitating Exo1 access to nascent strands. Instead, Sae2 cooperates with Exo1 in counteracting putative fork cleavage events linked to double strand breaks formation and increased gross chromosomal rearrangement rates. Our data indicate that in checkpoint deficient cells diverse nuclease activities interface to eliminate aberrant replication intermediates and prevent chromosome instability.
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Affiliation(s)
- Arianna Colosio
- The F.I.R.C. Institute of Molecular Oncology (IFOM) Foundation, Via Adamello 16, 20139 Milan, Italy
| | - Camilla Frattini
- Instituto de Biología Funcional y Genómica (IBFG-CSIC), Universidad de Salamanca, Calle Zacarías González 2, 37007 Salamanca, Spain
| | - Grazia Pellicanò
- Centro de Investigaciones Biológicas (CIB-CSIC), Calle Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Sara Villa-Hernández
- Instituto de Biología Funcional y Genómica (IBFG-CSIC), Universidad de Salamanca, Calle Zacarías González 2, 37007 Salamanca, Spain.,Centro de Investigaciones Biológicas (CIB-CSIC), Calle Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Rodrigo Bermejo
- Instituto de Biología Funcional y Genómica (IBFG-CSIC), Universidad de Salamanca, Calle Zacarías González 2, 37007 Salamanca, Spain .,Centro de Investigaciones Biológicas (CIB-CSIC), Calle Ramiro de Maeztu 9, 28040 Madrid, Spain
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54
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Pommier Y, Sun Y, Huang SYN, Nitiss JL. Roles of eukaryotic topoisomerases in transcription, replication and genomic stability. Nat Rev Mol Cell Biol 2016; 17:703-721. [DOI: 10.1038/nrm.2016.111] [Citation(s) in RCA: 540] [Impact Index Per Article: 67.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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55
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Vijayraghavan S, Tsai FL, Schwacha A. A Checkpoint-Related Function of the MCM Replicative Helicase Is Required to Avert Accumulation of RNA:DNA Hybrids during S-phase and Ensuing DSBs during G2/M. PLoS Genet 2016; 12:e1006277. [PMID: 27556397 PMCID: PMC4996524 DOI: 10.1371/journal.pgen.1006277] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 08/04/2016] [Indexed: 01/10/2023] Open
Abstract
The Mcm2-7 complex is the catalytic core of the eukaryotic replicative helicase. Here, we identify a new role for this complex in maintaining genome integrity. Using both genetic and cytological approaches, we find that a specific mcm allele (mcm2DENQ) causes elevated genome instability that correlates with the appearance of numerous DNA-damage associated foci of γH2AX and Rad52. We further find that the triggering events for this genome instability are elevated levels of RNA:DNA hybrids and an altered DNA topological state, as over-expression of either RNaseH (an enzyme specific for degradation of RNA in RNA:DNA hybrids) or Topoisomerase 1 (an enzyme that relieves DNA supercoiling) can suppress the mcm2DENQ DNA-damage phenotype. Moreover, the observed DNA damage has several additional unusual properties, in that DNA damage foci appear only after S-phase, in G2/M, and are dependent upon progression into metaphase. In addition, we show that the resultant DNA damage is not due to spontaneous S-phase fork collapse. In total, these unusual mcm2DENQ phenotypes are markedly similar to those of a special previously-studied allele of the checkpoint sensor kinase ATR/MEC1, suggesting a possible regulatory interplay between Mcm2-7 and ATR during unchallenged growth. As RNA:DNA hybrids primarily result from transcription perturbations, we suggest that surveillance-mediated modulation of the Mcm2-7 activity plays an important role in preventing catastrophic conflicts between replication forks and transcription complexes. Possible relationships among these effects and the recently discovered role of Mcm2-7 in the DNA replication checkpoint induced by HU treatment are discussed.
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Affiliation(s)
- Sriram Vijayraghavan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Feng-Ling Tsai
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Anthony Schwacha
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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56
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García-Muse T, Aguilera A. Transcription–replication conflicts: how they occur and how they are resolved. Nat Rev Mol Cell Biol 2016; 17:553-63. [DOI: 10.1038/nrm.2016.88] [Citation(s) in RCA: 238] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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57
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Ribeyre C, Zellweger R, Chauvin M, Bec N, Larroque C, Lopes M, Constantinou A. Nascent DNA Proteomics Reveals a Chromatin Remodeler Required for Topoisomerase I Loading at Replication Forks. Cell Rep 2016; 15:300-9. [PMID: 27050524 DOI: 10.1016/j.celrep.2016.03.027] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 02/18/2016] [Accepted: 03/06/2016] [Indexed: 11/28/2022] Open
Abstract
During transcription and DNA replication, the DNA template is overwound ahead of RNA and DNA polymerases and relaxed by DNA topoisomerases. Inhibitors of topoisomerases are potent anti-cancer agents. Camptothecin traps topoisomerase I on DNA and exerts preferential cytotoxicity toward cancer cells by way of its interference with the progression of replication forks. Starting with an unbiased proteomic analysis, we find that the chromatin remodeling complex BAZ1B-SMARCA5 accumulates near replication forks in camptothecin-exposed cells. We report that BAZ1B associates with topoisomerase I and facilitates its access to replication forks. Single-molecule analyses of replication structures show that BAZ1B contributes to replication interference by camptothecin. A lack of BAZ1B confers increased cellular tolerance of camptothecin. These findings reveal BAZ1B as a key facilitator of topoisomerase I function during DNA replication that affects the response of cancer cells to topoisomerase I inhibitors.
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Affiliation(s)
- Cyril Ribeyre
- Institute of Human Genetics, Centre National de la Recherche Scientifique (CNRS) UPR 1142, University of Montpellier, 34396 Montpellier, France.
| | - Ralph Zellweger
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland
| | - Maeva Chauvin
- Institute of Human Genetics, Centre National de la Recherche Scientifique (CNRS) UPR 1142, University of Montpellier, 34396 Montpellier, France
| | - Nicole Bec
- Institut de Recherche en Cancérologie de Montpellier, INSERM, U1194, University of Montpellier, 34298 Montpellier, France
| | - Christian Larroque
- Institut de Recherche en Cancérologie de Montpellier, INSERM, U1194, University of Montpellier, 34298 Montpellier, France
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland
| | - Angelos Constantinou
- Institute of Human Genetics, Centre National de la Recherche Scientifique (CNRS) UPR 1142, University of Montpellier, 34396 Montpellier, France.
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58
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p53 Maintains Genomic Stability by Preventing Interference between Transcription and Replication. Cell Rep 2016; 15:132-146. [PMID: 27052176 DOI: 10.1016/j.celrep.2016.03.011] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 12/17/2015] [Accepted: 02/26/2016] [Indexed: 01/23/2023] Open
Abstract
p53 tumor suppressor maintains genomic stability, typically acting through cell-cycle arrest, senescence, and apoptosis. We discovered a function of p53 in preventing conflicts between transcription and replication, independent of its canonical roles. p53 deficiency sensitizes cells to Topoisomerase (Topo) II inhibitors, resulting in DNA damage arising spontaneously during replication. Topoisomerase IIα (TOP2A)-DNA complexes preferentially accumulate in isogenic p53 mutant or knockout cells, reflecting an increased recruitment of TOP2A to regulate DNA topology. We propose that p53 acts to prevent DNA topological stress originating from transcription during the S phase and, therefore, promotes normal replication fork progression. Consequently, replication fork progression is impaired in the absence of p53, which is reversed by transcription inhibition. Pharmacologic inhibition of transcription also attenuates DNA damage and decreases Topo-II-DNA complexes, restoring cell viability in p53-deficient cells. Together, our results demonstrate a function of p53 that may underlie its role in tumor suppression.
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59
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The Smc5/6 Complex Is an ATP-Dependent Intermolecular DNA Linker. Cell Rep 2015; 12:1471-82. [PMID: 26299966 DOI: 10.1016/j.celrep.2015.07.048] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 06/30/2015] [Accepted: 07/23/2015] [Indexed: 12/13/2022] Open
Abstract
The structural maintenance of chromosome (SMC) protein complexes cohesin and condensin and the Smc5/6 complex (Smc5/6) are crucial for chromosome dynamics and stability. All contain essential ATPase domains, and cohesin and condensin interact with chromosomes through topological entrapment of DNA. However, how Smc5/6 binds DNA and chromosomes has remained largely unknown. Here, we show that purified Smc5/6 binds DNA through a mechanism that requires ATP hydrolysis by the complex and circular DNA to be established. This also promotes topoisomerase 2-dependent catenation of plasmids, suggesting that Smc5/6 interconnects two DNA molecules using ATP-regulated topological entrapment of DNA, similar to cohesin. We also show that a complex containing an Smc6 mutant that is defective in ATP binding fails to interact with DNA and chromosomes and leads to cell death with concomitant accumulation of DNA damage when overexpressed. Taken together, these results indicate that Smc5/6 executes its cellular functions through ATP-regulated intermolecular DNA linking.
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60
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Schalbetter SA, Mansoubi S, Chambers AL, Downs JA, Baxter J. Fork rotation and DNA precatenation are restricted during DNA replication to prevent chromosomal instability. Proc Natl Acad Sci U S A 2015; 112:E4565-70. [PMID: 26240319 PMCID: PMC4547287 DOI: 10.1073/pnas.1505356112] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Faithful genome duplication and inheritance require the complete resolution of all intertwines within the parental DNA duplex. This is achieved by topoisomerase action ahead of the replication fork or by fork rotation and subsequent resolution of the DNA precatenation formed. Although fork rotation predominates at replication termination, in vitro studies have suggested that it also occurs frequently during elongation. However, the factors that influence fork rotation and how rotation and precatenation may influence other replication-associated processes are unknown. Here we analyze the causes and consequences of fork rotation in budding yeast. We find that fork rotation and precatenation preferentially occur in contexts that inhibit topoisomerase action ahead of the fork, including stable protein-DNA fragile sites and termination. However, generally, fork rotation and precatenation are actively inhibited by Timeless/Tof1 and Tipin/Csm3. In the absence of Tof1/Timeless, excessive fork rotation and precatenation cause extensive DNA damage following DNA replication. With Tof1, damage related to precatenation is focused on the fragile protein-DNA sites where fork rotation is induced. We conclude that although fork rotation and precatenation facilitate unwinding in hard-to-replicate contexts, they intrinsically disrupt normal chromosome duplication and are therefore restricted by Timeless/Tipin.
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Affiliation(s)
- Stephanie A Schalbetter
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, United Kingdom
| | - Sahar Mansoubi
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, United Kingdom
| | - Anna L Chambers
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, United Kingdom; School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Jessica A Downs
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, United Kingdom
| | - Jonathan Baxter
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, United Kingdom;
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61
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Xu Y, Her C. Inhibition of Topoisomerase (DNA) I (TOP1): DNA Damage Repair and Anticancer Therapy. Biomolecules 2015; 5:1652-70. [PMID: 26287259 PMCID: PMC4598769 DOI: 10.3390/biom5031652] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 07/14/2015] [Indexed: 12/31/2022] Open
Abstract
Most chemotherapy regimens contain at least one DNA-damaging agent that preferentially affects the growth of cancer cells. This strategy takes advantage of the differences in cell proliferation between normal and cancer cells. Chemotherapeutic drugs are usually designed to target rapid-dividing cells because sustained proliferation is a common feature of cancer [1,2]. Rapid DNA replication is essential for highly proliferative cells, thus blocking of DNA replication will create numerous mutations and/or chromosome rearrangements—ultimately triggering cell death [3]. Along these lines, DNA topoisomerase inhibitors are of great interest because they help to maintain strand breaks generated by topoisomerases during replication. In this article, we discuss the characteristics of topoisomerase (DNA) I (TOP1) and its inhibitors, as well as the underlying DNA repair pathways and the use of TOP1 inhibitors in cancer therapy.
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Affiliation(s)
- Yang Xu
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Mail Drop 64-7520, Pullman, WA 99164, USA.
| | - Chengtao Her
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Mail Drop 64-7520, Pullman, WA 99164, USA.
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62
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DNA Topoisomerases Are Required for Preinitiation Complex Assembly during GAL Gene Activation. PLoS One 2015; 10:e0132739. [PMID: 26173127 PMCID: PMC4501763 DOI: 10.1371/journal.pone.0132739] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 06/17/2015] [Indexed: 12/17/2022] Open
Abstract
To investigate the importance of topoisomerases for transcription of the galactose induced genes, we have studied the expression of GAL1, GAL2, GAL7 and GAL10 in Saccharomyces cerevisiae cells deficient for topoisomerases I and II. We find that topoisomerases are required for transcriptional activation of the GAL genes, but are dispensable for ongoing transcription, eliminating a role of the enzymes in transcriptional elongation. Furthermore, we demonstrate that promoter chromatin remodeling of the GAL genes is unaffected in the topoisomerase deficient strain. However, the cells fail to successfully recruit RNA polymerase II due to an inability of the TATA-binding protein (TBP) to bind to the TATA box in these promoters. We therefore argue that topoisomerases are required for accurate assembly of the preinitiation complex at the promoters of the GAL genes.
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63
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Replication stress in Mammalian cells and its consequences for mitosis. Genes (Basel) 2015; 6:267-98. [PMID: 26010955 PMCID: PMC4488665 DOI: 10.3390/genes6020267] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 05/15/2015] [Accepted: 05/18/2015] [Indexed: 12/23/2022] Open
Abstract
The faithful transmission of genetic information to daughter cells is central to maintaining genomic stability and relies on the accurate and complete duplication of genetic material during each cell cycle. However, the genome is routinely exposed to endogenous and exogenous stresses that can impede the progression of replication. Such replication stress can be an early cause of cancer or initiate senescence. Replication stress, which primarily occurs during S phase, results in consequences during mitosis, jeopardizing chromosome segregation and, in turn, genomic stability. The traces of replication stress can be detected in the daughter cells during G1 phase. Alterations in mitosis occur in two types: 1) local alterations that correspond to breaks, rearrangements, intertwined DNA molecules or non-separated sister chromatids that are confined to the region of the replication dysfunction; 2) genome-wide chromosome segregation resulting from centrosome amplification (although centrosomes do not contain DNA), which amplifies the local replication stress to the entire genome. Here, we discuss the endogenous causes of replication perturbations, the mechanisms of replication fork restart and the consequences for mitosis, chromosome segregation and genomic stability.
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64
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Williams JS, Clausen AR, Lujan SA, Marjavaara L, Clark AB, Burgers PM, Chabes A, Kunkel TA. Evidence that processing of ribonucleotides in DNA by topoisomerase 1 is leading-strand specific. Nat Struct Mol Biol 2015; 22:291-7. [PMID: 25751426 PMCID: PMC4835660 DOI: 10.1038/nsmb.2989] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 02/11/2015] [Indexed: 01/26/2023]
Abstract
Ribonucleotides incorporated during DNA replication are removed by RNase H2-dependent ribonucleotide excision repair (RER). In RER-defective yeast, topoisomerase 1 (Top1) incises DNA at unrepaired ribonucleotides, initiating their removal, but this is accompanied by RNA-DNA-damage phenotypes. Here we show that these phenotypes are incurred by a high level of ribonucleotides incorporated by a leading strand-replicase variant, DNA polymerase (Pol) ɛ, but not by orthologous variants of the lagging-strand replicases, Pols α or δ. Moreover, loss of both RNases H1 and H2 is lethal in combination with increased ribonucleotide incorporation by Pol ɛ but not by Pols α or δ. Several explanations for this asymmetry are considered, including the idea that Top1 incision at ribonucleotides relieves torsional stress in the nascent leading strand but not in the nascent lagging strand, in which preexisting nicks prevent the accumulation of superhelical tension.
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Affiliation(s)
- Jessica S. Williams
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA
| | - Anders R. Clausen
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA
| | - Scott A. Lujan
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA
| | - Lisette Marjavaara
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden
| | - Alan B. Clark
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA
| | - Peter M. Burgers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87, Umeå, Sweden
| | - Thomas A. Kunkel
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA
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65
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Kumar A, Mazzanti M, Mistrik M, Kosar M, Beznoussenko GV, Mironov AA, Garrè M, Parazzoli D, Shivashankar GV, Scita G, Bartek J, Foiani M. ATR mediates a checkpoint at the nuclear envelope in response to mechanical stress. Cell 2015; 158:633-46. [PMID: 25083873 PMCID: PMC4121522 DOI: 10.1016/j.cell.2014.05.046] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Revised: 04/14/2014] [Accepted: 05/28/2014] [Indexed: 11/16/2022]
Abstract
ATR controls chromosome integrity and chromatin dynamics. We have previously shown that yeast Mec1/ATR promotes chromatin detachment from the nuclear envelope to counteract aberrant topological transitions during DNA replication. Here, we provide evidence that ATR activity at the nuclear envelope responds to mechanical stress. Human ATR associates with the nuclear envelope during S phase and prophase, and both osmotic stress and mechanical stretching relocalize ATR to nuclear membranes throughout the cell cycle. The ATR-mediated mechanical response occurs within the range of physiological forces, is reversible, and is independent of DNA damage signaling. ATR-defective cells exhibit aberrant chromatin condensation and nuclear envelope breakdown. We propose that mechanical forces derived from chromosome dynamics and torsional stress on nuclear membranes activate ATR to modulate nuclear envelope plasticity and chromatin association to the nuclear envelope, thus enabling cells to cope with the mechanical strain imposed by these molecular processes. ATR localizes at the nuclear envelope in S phase and prophase ATR responds to mechanical stress by relocalizing to the nuclear envelope The ATR mechanical response is fast and reversible ATR coordinates chromatin condensation and nuclear envelope breakdown
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Affiliation(s)
- Amit Kumar
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), Via Adamello 16, 20139 Milan, Italy
| | | | - Martin Mistrik
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 77115 Olomouc, Czech Republic
| | - Martin Kosar
- Danish Cancer Society Research Center, 2100 Copenhagen, Denmark; Institute of Molecular Genetics, v.v.i., Academy of Sciences of the Czech Republic, 14220 Prague, Czech Republic
| | - Galina V Beznoussenko
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Alexandre A Mironov
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Massimiliano Garrè
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Dario Parazzoli
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - G V Shivashankar
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411 Singapore, Singapore
| | - Giorgio Scita
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), Via Adamello 16, 20139 Milan, Italy; Università degli Studi di Milano, 20122 Milan, Italy
| | - Jiri Bartek
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 77115 Olomouc, Czech Republic; Danish Cancer Society Research Center, 2100 Copenhagen, Denmark; Institute of Molecular Genetics, v.v.i., Academy of Sciences of the Czech Republic, 14220 Prague, Czech Republic.
| | - Marco Foiani
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), Via Adamello 16, 20139 Milan, Italy; Università degli Studi di Milano, 20122 Milan, Italy.
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66
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Baxter J. “Breaking Up Is Hard to Do”: The Formation and Resolution of Sister Chromatid Intertwines. J Mol Biol 2015; 427:590-607. [DOI: 10.1016/j.jmb.2014.08.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 08/08/2014] [Accepted: 08/20/2014] [Indexed: 10/24/2022]
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67
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Autosomal Recessive Ataxias Due to Defects in DNA Repair. Mov Disord 2015. [DOI: 10.1016/b978-0-12-405195-9.00067-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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68
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Ostrow AZ, Viggiani CJ, Aparicio JG, Aparicio OM. ChIP-Seq to Analyze the Binding of Replication Proteins to Chromatin. Methods Mol Biol 2015; 1300:155-68. [PMID: 25916712 DOI: 10.1007/978-1-4939-2596-4_11] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chromatin immunoprecipitation (ChIP) is a widely used method to study interactions between proteins and discrete chromosomal loci in vivo. ChIP was originally developed for in vivo analysis of protein associations with candidate DNA sequences known or suspected to bind the protein of interest. The advent of DNA microarrays enabled the unbiased, genome-scale identification of all DNA sequences enriched by ChIP, providing a genomic map of a protein's chromatin binding. This method, termed ChIP-chip, is broadly applicable and has been particularly valuable in DNA replication studies to map potential replication origins in Saccharomyces cerevisiae and other organisms based on the specific association of certain replication proteins with these chromosomal elements, which are distributed throughout the genome. More recently, high-throughput sequencing (HTS) technologies have replaced microarrays as the preferred method for genomic analysis of ChIP experiments, and this combination is termed ChIP-Seq. We present a detailed ChIP-Seq protocol for S. cerevisiae that can be adapted for different HTS platforms and for different organisms. We also outline general schemes for data analysis; however, HTS data analyses usually must be tailored specifically for individual studies, depending on the experimental design, data characteristics, and the genome being analyzed.
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Affiliation(s)
- A Zachary Ostrow
- Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA
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69
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Yadav P, Harcy V, Argueso JL, Dominska M, Jinks-Robertson S, Kim N. Topoisomerase I plays a critical role in suppressing genome instability at a highly transcribed G-quadruplex-forming sequence. PLoS Genet 2014; 10:e1004839. [PMID: 25473964 PMCID: PMC4256205 DOI: 10.1371/journal.pgen.1004839] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 10/20/2014] [Indexed: 11/18/2022] Open
Abstract
G-quadruplex or G4 DNA is a non-B secondary DNA structure that comprises a stacked array of guanine-quartets. Cellular processes such as transcription and replication can be hindered by unresolved DNA secondary structures potentially endangering genome maintenance. As G4-forming sequences are highly frequent throughout eukaryotic genomes, it is important to define what factors contribute to a G4 motif becoming a hotspot of genome instability. Using a genetic assay in Saccharomyces cerevisiae, we previously demonstrated that a potential G4-forming sequence derived from a guanine-run containing immunoglobulin switch Mu (Sμ) region becomes highly unstable when actively transcribed. Here we describe assays designed to survey spontaneous genome rearrangements initiated at the Sμ sequence in the context of large genomic areas. We demonstrate that, in the absence of Top1, a G4 DNA-forming sequence becomes a strong hotspot of gross chromosomal rearrangements and loss of heterozygosity associated with mitotic recombination within the ∼20 kb or ∼100 kb regions of yeast chromosome V or III, respectively. Transcription confers a critical strand bias since genome rearrangements at the G4-forming Sμ are elevated only when the guanine-runs are located on the non-transcribed strand. The direction of replication and transcription, when in a head-on orientation, further contribute to the elevated genome instability at a potential G4 DNA-forming sequence. The implications of our identification of Top1 as a critical factor in suppression of instability associated with potential G4 DNA-forming sequences are discussed. Genome instability is not evenly distributed, but rather is highly elevated at certain genomic loci containing DNA sequences that can fold into non-canonical secondary structures. The four-stranded G-quadruplex or G4 DNA is one such DNA structure capable of instigating transcription and/or replication obstruction and subsequent genome instability. In this study, we used a reporter system to quantitatively measure the level of genome instability occurring at a G4 DNA motif integrated into the yeast genome. We showed that the disruption of Topoisomerase I function significantly elevated various types of genome instability at the highly transcribed G4 motif generating loss of heterozygosity and copy number alterations (deletions and duplications), both of which are frequently observed in cancer genomes.
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Affiliation(s)
- Puja Yadav
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Victoria Harcy
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Margaret Dominska
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Nayun Kim
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
- * E-mail:
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70
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Murillo-Pineda M, Cabello-Lobato MJ, Clemente-Ruiz M, Monje-Casas F, Prado F. Defective histone supply causes condensin-dependent chromatin alterations, SAC activation and chromosome decatenation impairment. Nucleic Acids Res 2014; 42:12469-82. [PMID: 25300489 PMCID: PMC4227775 DOI: 10.1093/nar/gku927] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The structural organization of chromosomes is essential for their correct function and dynamics during the cell cycle. The assembly of DNA into chromatin provides the substrate for topoisomerases and condensins, which introduce the different levels of superhelical torsion required for DNA metabolism. In particular, Top2 and condensin are directly involved in both the resolution of precatenanes that form during replication and the formation of the intramolecular loop that detects tension at the centromeric chromatin during chromosome biorientation. Here we show that histone depletion activates the spindle assembly checkpoint (SAC) and impairs sister chromatid decatenation, leading to chromosome mis-segregation and lethality in the absence of the SAC. We demonstrate that histone depletion impairs chromosome biorientation and activates the Aurora-dependent pathway, which detects tension problems at the kinetochore. Interestingly, SAC activation is suppressed by the absence of Top2 and Smc2, an essential component of condensin. Indeed, smc2-8 suppresses catenanes accumulation, mitotic arrest and growth defects induced by histone depletion at semi-permissive temperature. Remarkably, SAC activation by histone depletion is associated with condensin-mediated alterations of the centromeric chromatin. Therefore, our results reveal the importance of a precise interplay between histone supply and condensin/Top2 for pericentric chromatin structure, precatenanes resolution and centromere biorientation.
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Affiliation(s)
- Marina Murillo-Pineda
- Departamento de Biología Molecular, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
| | - María J Cabello-Lobato
- Departamento de Biología Molecular, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
| | - Marta Clemente-Ruiz
- Departamento de Biología Molecular, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
| | | | - Félix Prado
- Departamento de Biología Molecular, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
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71
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Lin CY, Wu MY, Gay S, Marjavaara L, Lai MS, Hsiao WC, Hung SH, Tseng HY, Wright DE, Wang CY, Hsu GSW, Devys D, Chabes A, Kao CF. H2B mono-ubiquitylation facilitates fork stalling and recovery during replication stress by coordinating Rad53 activation and chromatin assembly. PLoS Genet 2014; 10:e1004667. [PMID: 25275495 PMCID: PMC4183429 DOI: 10.1371/journal.pgen.1004667] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 08/14/2014] [Indexed: 01/11/2023] Open
Abstract
The influence of mono-ubiquitylation of histone H2B (H2Bub) on transcription via nucleosome reassembly has been widely documented. Recently, it has also been shown that H2Bub promotes recovery from replication stress; however, the underling molecular mechanism remains unclear. Here, we show that H2B ubiquitylation coordinates activation of the intra-S replication checkpoint and chromatin re-assembly, in order to limit fork progression and DNA damage in the presence of replication stress. In particular, we show that the absence of H2Bub affects replication dynamics (enhanced fork progression and reduced origin firing), leading to γH2A accumulation and increased hydroxyurea sensitivity. Further genetic analysis indicates a role for H2Bub in transducing Rad53 phosphorylation. Concomitantly, we found that a change in replication dynamics is not due to a change in dNTP level, but is mediated by reduced Rad53 activation and destabilization of the RecQ helicase Sgs1 at the fork. Furthermore, we demonstrate that H2Bub facilitates the dissociation of the histone chaperone Asf1 from Rad53, and nucleosome reassembly behind the fork is compromised in cells lacking H2Bub. Taken together, these results indicate that the regulation of H2B ubiquitylation is a key event in the maintenance of genome stability, through coordination of intra-S checkpoint activation, chromatin assembly and replication fork progression. Eukaryotic DNA is organized into nucleosomes, which are the fundamental repeating units of chromatin. Coordination of chromatin structure is required for efficient and accurate DNA replication. Aberrant DNA replication results in mutations and chromosome rearrangements that may be associated with human disorders. Therefore, cellular surveillance mechanisms have evolved to counteract potential threats to DNA replication. These mechanisms include checkpoints and specialized enzymatic activities that prevent the replication and segregation of defective DNA molecules. We employed a genome-wide approach to investigate how chromatin structure affects DNA replication under stress. We report that coordination of chromatin assembly and checkpoint activity by a histone modification, H2B ubiquitylation (H2Bub), is critical for the cell response to HU-induced replication stress. In cells with a mutation that abolishes H2Bub, replication progression is enhanced, and the forks are more susceptible to damage by environmental insults. The replication proteins on replicating DNA are akin to a train on the tracks, and movement of this train is carefully controlled. Our data indicate that H2Bub helps organize DNA in the nuclei during DNA replication; this process plays a similar role to the brakes on a train, serving to slow down replication, and maintaining stable progression of replication under environmental stress.
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Affiliation(s)
- Chia-Yeh Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, Taiwan
- Graduate Institute of Nutrition and Food Sciences, Fu-Jen Catholic University, Xinzhuang, New Taipei City, Taiwan
| | - Meng-Ying Wu
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Sophie Gay
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), IFOM-IEO Campus, Milan, Italy
| | - Lisette Marjavaara
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Mong Sing Lai
- Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), IFOM-IEO Campus, Milan, Italy
| | - Wei-Chun Hsiao
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Shih-Hsun Hung
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Hsin-Yi Tseng
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Duncan Edward Wright
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Chen-Yi Wang
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, Taiwan
- Institut de Génétique et de Biologie Moléculaire. CNRS UMR 7104, INSERM U 596, Université Louis Pasteur de Strasbourg, Illkirch, CU de Strasbourg, France
| | - Guoo-Shyng W. Hsu
- Graduate Institute of Nutrition and Food Sciences, Fu-Jen Catholic University, Xinzhuang, New Taipei City, Taiwan
| | - Didier Devys
- Institut de Génétique et de Biologie Moléculaire. CNRS UMR 7104, INSERM U 596, Université Louis Pasteur de Strasbourg, Illkirch, CU de Strasbourg, France
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Cheng-Fu Kao
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, Taiwan
- * E-mail:
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72
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Jeppsson K, Carlborg KK, Nakato R, Berta DG, Lilienthal I, Kanno T, Lindqvist A, Brink MC, Dantuma NP, Katou Y, Shirahige K, Sjögren C. The chromosomal association of the Smc5/6 complex depends on cohesion and predicts the level of sister chromatid entanglement. PLoS Genet 2014; 10:e1004680. [PMID: 25329383 PMCID: PMC4199498 DOI: 10.1371/journal.pgen.1004680] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 08/18/2014] [Indexed: 11/24/2022] Open
Abstract
The cohesin complex, which is essential for sister chromatid cohesion and chromosome segregation, also inhibits resolution of sister chromatid intertwinings (SCIs) by the topoisomerase Top2. The cohesin-related Smc5/6 complex (Smc5/6) instead accumulates on chromosomes after Top2 inactivation, known to lead to a buildup of unresolved SCIs. This suggests that cohesin can influence the chromosomal association of Smc5/6 via its role in SCI protection. Using high-resolution ChIP-sequencing, we show that the localization of budding yeast Smc5/6 to duplicated chromosomes indeed depends on sister chromatid cohesion in wild-type and top2-4 cells. Smc5/6 is found to be enriched at cohesin binding sites in the centromere-proximal regions in both cell types, but also along chromosome arms when replication has occurred under Top2-inhibiting conditions. Reactivation of Top2 after replication causes Smc5/6 to dissociate from chromosome arms, supporting the assumption that Smc5/6 associates with a Top2 substrate. It is also demonstrated that the amount of Smc5/6 on chromosomes positively correlates with the level of missegregation in top2-4, and that Smc5/6 promotes segregation of short chromosomes in the mutant. Altogether, this shows that the chromosomal localization of Smc5/6 predicts the presence of the chromatid segregation-inhibiting entities which accumulate in top2-4 mutated cells. These are most likely SCIs, and our results thus indicate that, at least when Top2 is inhibited, Smc5/6 facilitates their resolution.
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Affiliation(s)
- Kristian Jeppsson
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm, Sweden
| | - Kristian K. Carlborg
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm, Sweden
| | - Ryuichiro Nakato
- University of Tokyo, Institute of Molecular and Cellular Biosciences, Laboratory of Genome Structure and Function Center for Epigenetic Disease, Bunkyo-ku, Tokyo, Japan
| | - Davide G. Berta
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm, Sweden
| | - Ingrid Lilienthal
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm, Sweden
| | - Takaharu Kanno
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm, Sweden
| | - Arne Lindqvist
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm, Sweden
| | - Maartje C. Brink
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm, Sweden
| | - Nico P. Dantuma
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm, Sweden
| | - Yuki Katou
- University of Tokyo, Institute of Molecular and Cellular Biosciences, Laboratory of Genome Structure and Function Center for Epigenetic Disease, Bunkyo-ku, Tokyo, Japan
| | - Katsuhiko Shirahige
- University of Tokyo, Institute of Molecular and Cellular Biosciences, Laboratory of Genome Structure and Function Center for Epigenetic Disease, Bunkyo-ku, Tokyo, Japan
| | - Camilla Sjögren
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm, Sweden
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73
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Topoisomerase 2 is dispensable for the replication and segregation of small yeast artificial chromosomes (YACs). PLoS One 2014; 9:e104995. [PMID: 25115861 PMCID: PMC4130621 DOI: 10.1371/journal.pone.0104995] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 07/15/2014] [Indexed: 11/19/2022] Open
Abstract
DNA topoisomerases are thought to play a critical role in transcription, replication and recombination as well as in the condensation and segregation of sister duplexes during cell division. Here, we used high-resolution two-dimensional agarose gel electrophoresis to study the replication intermediates and final products of small circular and linear minichromosomes of Saccharomyces cerevisiae in the presence and absence of DNA topoisomerase 2. The results obtained confirmed that whereas for circular minichromosomes, catenated sister duplexes accumulated in the absence of topoisomerase 2, linear YACs were able to replicate and segregate regardless of this topoisomerase. The patterns of replication intermediates for circular and linear YACs displayed significant differences suggesting that DNA supercoiling might play a key role in the modulation of replication fork progression. Altogether, this data supports the notion that for linear chromosomes the torsional tension generated by transcription and replication dissipates freely throughout the telomeres.
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74
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Deschênes-Simard X, Lessard F, Gaumont-Leclerc MF, Bardeesy N, Ferbeyre G. Cellular senescence and protein degradation: breaking down cancer. Cell Cycle 2014; 13:1840-58. [PMID: 24866342 DOI: 10.4161/cc.29335] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Autophagy and the ubiquitin-proteasome pathway (UPP) are the major protein degradation systems in eukaryotic cells. Whereas the former mediate a bulk nonspecific degradation, the UPP allows a rapid degradation of specific proteins. Both systems have been shown to play a role in tumorigenesis, and the interest in developing therapeutic agents inhibiting protein degradation is steadily growing. However, emerging data point to a critical role for autophagy in cellular senescence, an established tumor suppressor mechanism. Recently, a selective protein degradation process mediated by the UPP was also shown to contribute to the senescence phenotype. This process is tightly regulated by E3 ubiquitin ligases, deubiquitinases, and several post-translational modifications of target proteins. Illustrating the complexity of UPP, more than 600 human genes have been shown to encode E3 ubiquitin ligases, a number which exceeds that of the protein kinases. Nevertheless, our knowledge of proteasome-dependent protein degradation as a regulated process in cellular contexts such as cancer and senescence remains very limited. Here we discuss the implications of protein degradation in senescence and attempt to relate this function to the protein degradation pattern observed in cancer cells.
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Affiliation(s)
- Xavier Deschênes-Simard
- Department of Biochemistry and Molecular Medicine; Université de Montréal; Montréal, Québec, Canada
| | - Frédéric Lessard
- Department of Biochemistry and Molecular Medicine; Université de Montréal; Montréal, Québec, Canada
| | | | - Nabeel Bardeesy
- Massachusetts General Hospital Cancer Center; Harvard Medical School; Boston, MA USA
| | - Gerardo Ferbeyre
- Department of Biochemistry and Molecular Medicine; Université de Montréal; Montréal, Québec, Canada
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75
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Fernández X, Díaz-Ingelmo O, Martínez-García B, Roca J. Chromatin regulates DNA torsional energy via topoisomerase II-mediated relaxation of positive supercoils. EMBO J 2014; 33:1492-501. [PMID: 24859967 DOI: 10.15252/embj.201488091] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Eukaryotic topoisomerases I (topo I) and II (topo II) relax the positive (+) and negative (-) DNA torsional stress (TS) generated ahead and behind the transcription machinery. It is unknown how this DNA relaxation activity is regulated and whether (+) and (-)TS are reduced at similar rates. Here, we used yeast circular minichromosomes to conduct the first comparative analysis of topo I and topo II activities in relaxing chromatin under (+) and (-)TS. We observed that, while topo I relaxed (+) and (-)TS with similar efficiency, topo II was more proficient and relaxed (+)TS more quickly than (-)TS. Accordingly, we found that the relaxation rate of (+)TS by endogenous topoisomerases largely surpassed that of (-)TS. We propose a model of how distinct conformations of chromatin under (+) and (-)TS may produce this unbalanced relaxation of DNA. We postulate that, while quick relaxation of (+)TS may facilitate the progression of RNA and DNA polymerases, slow relaxation of (-)TS may serve to favor DNA unwinding and other structural transitions at specific regions often required for genomic transactions.
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Affiliation(s)
- Xavier Fernández
- Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Ofelia Díaz-Ingelmo
- Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Belén Martínez-García
- Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Joaquim Roca
- Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
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76
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Singh J. Role of DNA replication in establishment and propagation of epigenetic states of chromatin. Semin Cell Dev Biol 2014; 30:131-43. [PMID: 24794003 DOI: 10.1016/j.semcdb.2014.04.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 04/03/2014] [Indexed: 10/25/2022]
Abstract
DNA replication is the fundamental process of duplication of the genetic information that is vital for survival of all living cells. The basic mechanistic steps of replication initiation, elongation and termination are conserved among bacteria, lower eukaryotes, like yeast and metazoans. However, the details of the mechanisms are different. Furthermore, there is a close coordination between chromatin assembly pathways and various components of replication machinery whereby DNA replication is coupled to "chromatin replication" during cell cycle. Thereby, various epigenetic modifications associated with different states of gene expression in differentiated cells and the related chromatin structures are faithfully propagated during the cell division through tight coupling with the DNA replication machinery. Several examples are found in lower eukaryotes like budding yeast and fission yeast with close parallels in metazoans.
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Affiliation(s)
- Jagmohan Singh
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India.
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77
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d'Alcontres MS, Palacios JA, Mejias D, Blasco MA. TopoIIα prevents telomere fragility and formation of ultra thin DNA bridges during mitosis through TRF1-dependent binding to telomeres. Cell Cycle 2014; 13:1463-81. [PMID: 24626180 PMCID: PMC4050144 DOI: 10.4161/cc.28419] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Telomeres are repetitive nucleoprotein structures at the ends of chromosomes. Like most genomic regions consisting of repetitive DNA, telomeres are fragile sites prone to replication fork stalling and generation of chromosomal instability. In particular, abrogation of the TRF1 telomere binding protein leads to stalled replication forks and aberrant telomere structures known as “multitelomeric signals”. Here, we report that TRF1 deficiency also leads to the formation of “ultra-fine bridges” (UFB) during mitosis, and to an increased time to complete mitosis mediated by the spindle assembly checkpoint proteins (SAC). We find that topoisomerase IIα (TopoIIα), an enzyme essential for resolution of DNA replication intermediates, binds telomeres in a TRF1-mediated manner. Indeed, similar to TRF1 abrogation, TopoIIα downregulation leads to telomere fragility and UFB, suggesting that these phenotypes are due to decreased TopoIIα at telomeres. We find that SAC proteins bind telomeres in vivo, and that this is disrupted upon TRF1 deletion. These findings suggest that TRF1 links TopoIIα and SAC proteins in a pathway that ensures correct telomere replication and mitotic segregation, unveiling how TRF1 protects from telomere fragility and mitotic defects.
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Affiliation(s)
- Martina Stagno d'Alcontres
- Telomeres and Telomerase Group; Molecular Oncology Programme; Spanish National Cancer Research Centre (CNIO); Madrid, Spain
| | - Jose Alejandro Palacios
- Telomeres and Telomerase Group; Molecular Oncology Programme; Spanish National Cancer Research Centre (CNIO); Madrid, Spain
| | - Diego Mejias
- Confocal Microscopy Unit; Biotechnology Programme; Spanish National Cancer Research Centre (CNIO); Madrid, Spain
| | - Maria A Blasco
- Telomeres and Telomerase Group; Molecular Oncology Programme; Spanish National Cancer Research Centre (CNIO); Madrid, Spain
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78
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Vos SM, Stewart NK, Oakley MG, Berger JM. Structural basis for the MukB-topoisomerase IV interaction and its functional implications in vivo. EMBO J 2013; 32:2950-62. [PMID: 24097060 PMCID: PMC3832749 DOI: 10.1038/emboj.2013.218] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 09/11/2013] [Indexed: 01/07/2023] Open
Abstract
Chromosome partitioning in Escherichia coli is assisted by two interacting proteins, topoisomerase (topo) IV and MukB. MukB stimulates the relaxation of negative supercoils by topo IV; to understand the mechanism of their action and to define this functional interplay, we determined the crystal structure of a minimal MukB-topo IV complex to 2.3 Å resolution. The structure shows that the so-called 'hinge' region of MukB forms a heterotetrameric assembly with a C-terminal DNA binding domain (CTD) on topo IV's ParC subunit. Biochemical studies show that the hinge stimulates topo IV by competing for a site on the CTD that normally represses activity on negatively supercoiled DNA, while complementation tests using mutants implicated in the interaction reveal that the cellular dependency on topo IV derives from a joint need for both strand passage and MukB binding. Interestingly, the configuration of the MukB·topo IV complex sterically disfavours intradimeric interactions, indicating that the proteins may form oligomeric arrays with one another, and suggesting a framework by which MukB and topo IV may collaborate during daughter chromosome disentanglement.
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Affiliation(s)
- Seychelle M Vos
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Martha G Oakley
- Department of Chemistry, Indiana University, Bloomington, IN, USA
| | - James M Berger
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA,Department of Molecular and Cell Biology, California Institute of Quantitative Biosciences, University of California at Berkeley, 374D Stanley Hall, Berkeley, CA 94720, USA. Tel.:+1 510 643 9483; Fax:+1 510 666 2768; E-mail:
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79
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R loops are linked to histone H3 S10 phosphorylation and chromatin condensation. Mol Cell 2013; 52:583-90. [PMID: 24211264 DOI: 10.1016/j.molcel.2013.10.006] [Citation(s) in RCA: 198] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 09/04/2013] [Accepted: 10/01/2013] [Indexed: 12/20/2022]
Abstract
R loops are transcription byproducts that constitute a threat to genome integrity. Here we show that R loops are tightly linked to histone H3 S10 phosphorylation (H3S10P), a mark of chromatin condensation. Chromatin immunoprecipitation (ChIP)-on-chip (ChIP-chip) analyses reveal H3S10P accumulation at centromeres, pericentromeric chromatin, and a large number of active open reading frames (ORFs) in R-loop-accumulating yeast cells, better observed in G1. Histone H3S10 plays a key role in maintaining genome stability, as scored by ectopic recombination and plasmid loss, Rad52 foci, and Rad53 checkpoint activation. H3S10P coincides with the presence of DNA-RNA hybrids, is suppressed by ribonuclease H overexpression, and causes reduced accessibility of restriction endonucleases, implying a tight connection between R loops, H3S10P, and chromatin compaction. Such histone modifications were also observed in R-loop-accumulating Caenorhabditis elegans and HeLa cells. We therefore provide a role of RNA in chromatin structure essential to understand how R loops modulate genome dynamics.
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80
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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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81
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Evertts AG, Coller HA. Back to the origin: reconsidering replication, transcription, epigenetics, and cell cycle control. Genes Cancer 2013; 3:678-96. [PMID: 23634256 DOI: 10.1177/1947601912474891] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In bacteria, replication is a carefully orchestrated event that unfolds the same way for each bacterium and each cell division. The process of DNA replication in bacteria optimizes cell growth and coordinates high levels of simultaneous replication and transcription. In metazoans, the organization of replication is more enigmatic. The lack of a specific sequence that defines origins of replication has, until recently, severely limited our ability to define the organizing principles of DNA replication. This question is of particular importance as emerging data suggest that replication stress is an important contributor to inherited genetic damage and the genomic instability in tumors. We consider here the replication program in several different organisms including recent genome-wide analyses of replication origins in humans. We review recent studies on the role of cytosine methylation in replication origins, the role of transcriptional looping and gene gating in DNA replication, and the role of chromatin's 3-dimensional structure in DNA replication. We use these new findings to consider several questions surrounding DNA replication in metazoans: How are origins selected? What is the relationship between replication and transcription? How do checkpoints inhibit origin firing? Why are there early and late firing origins? We then discuss whether oncogenes promote cancer through a role in DNA replication and whether errors in DNA replication are important contributors to the genomic alterations and gene fusion events observed in cancer. We conclude with some important areas for future experimentation.
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82
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St. Charles J, Petes TD. High-resolution mapping of spontaneous mitotic recombination hotspots on the 1.1 Mb arm of yeast chromosome IV. PLoS Genet 2013; 9:e1003434. [PMID: 23593029 PMCID: PMC3616911 DOI: 10.1371/journal.pgen.1003434] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 02/20/2013] [Indexed: 11/18/2022] Open
Abstract
Although homologous recombination is an important pathway for the repair of double-stranded DNA breaks in mitotically dividing eukaryotic cells, these events can also have negative consequences, such as loss of heterozygosity (LOH) of deleterious mutations. We mapped about 140 spontaneous reciprocal crossovers on the right arm of the yeast chromosome IV using single-nucleotide-polymorphism (SNP) microarrays. Our mapping and subsequent experiments demonstrate that inverted repeats of Ty retrotransposable elements are mitotic recombination hotspots. We found that the mitotic recombination maps on the two homologs were substantially different and were unrelated to meiotic recombination maps. Additionally, about 70% of the DNA lesions that result in LOH are likely generated during G1 of the cell cycle and repaired during S or G2. We also show that different genetic elements are associated with reciprocal crossover conversion tracts depending on the cell cycle timing of the initiating DSB. Double-strand breaks (DSBs) are DNA lesions that can be fatal to a cell if left unrepaired. They can be caused by exogenous sources, such as gamma radiation, or endogenous stresses, such as high levels of transcription. Yeast cells primarily repair DSBs that are initiated outside of meiosis by mitotic recombination, which can result in physical exchanges between chromosomes, known as crossovers. We created a mitotic recombination map of one chromosome arm, representing 10% of the genome. This recombination map allows us to determine which regions of the chromosome arm are more susceptible to DNA damage than other regions. We were able to determine that most DSBs that result in detectable genomic changes were initiated prior to DNA replication and that some secondary DNA structures can be recombination hotspots. Recombination can also occur during meiosis, as a method of ensuring proper chromosome segregation. However, previously reported meiotic recombination maps have no correlation with our mitotic recombination map.
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Affiliation(s)
- Jordan St. Charles
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Thomas D. Petes
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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83
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Jossen R, Bermejo R. The DNA damage checkpoint response to replication stress: A Game of Forks. Front Genet 2013; 4:26. [PMID: 23493417 PMCID: PMC3595514 DOI: 10.3389/fgene.2013.00026] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 02/18/2013] [Indexed: 12/23/2022] Open
Abstract
Conditions challenging replication fork progression, collectively referred to as replication stress, represent a major source of genomic instability and are associated to cancer onset. The replication checkpoint, a specialized branch of the DNA damage checkpoint, monitors fork problems, and triggers a cellular response aimed at preserving genome integrity. Here, we review the mechanisms by which the replication checkpoint monitors and responds to replication stress, focusing on the checkpoint-mediated pathways contributing to protect replication fork integrity. We discuss how cells achieve checkpoint signaling inactivation once replication stress is overcome and how a failure to timely revert checkpoint-mediated changes in cellular physiology might impact on replication dynamics and genome integrity. We also highlight the checkpoint function as an anti-cancer barrier preventing cells malignant transformation following oncogene-induced replication stress.
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Affiliation(s)
- Rachel Jossen
- Instituto de Biología Funcional y Genómica, CSIC/USAL Salamanca, Spain
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84
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Chen SH, Chan NL, Hsieh TS. New mechanistic and functional insights into DNA topoisomerases. Annu Rev Biochem 2013; 82:139-70. [PMID: 23495937 DOI: 10.1146/annurev-biochem-061809-100002] [Citation(s) in RCA: 257] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DNA topoisomerases are nature's tools for resolving the unique problems of DNA entanglement that occur owing to unwinding and rewinding of the DNA helix during replication, transcription, recombination, repair, and chromatin remodeling. These enzymes perform topological transformations by providing a transient DNA break, formed by a covalent adduct with the enzyme, through which strand passage can occur. The active site tyrosine is responsible for initiating two transesterifications to cleave and then religate the DNA backbone. The cleavage reaction intermediate is exploited by cytotoxic agents, which have important applications as antibiotics and anticancer drugs. The reactions mediated by these enzymes can also be regulated by their binding partners; one example is a DNA helicase capable of modulating the directionality of strand passage, enabling important functions like reannealing denatured DNA and resolving recombination intermediates. In this review, we cover recent advances in mechanistic insights into topoisomerases and their various cellular functions.
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Affiliation(s)
- Stefanie Hartman Chen
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.
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85
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Fission yeast RecQ helicase Rqh1 is required for the maintenance of circular chromosomes. Mol Cell Biol 2013; 33:1175-87. [PMID: 23297345 DOI: 10.1128/mcb.01713-12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Protection of telomeres protein 1 (Pot1) binds to single-stranded telomere overhangs and protects chromosome ends. RecQ helicases regulate homologous recombination at multiple stages, including resection, strand displacement, and resolution. Fission yeast pot1 and RecQ helicase rqh1 double mutants are synthetically lethal, but the mechanism is not fully understood. Here, we show that the synthetic lethality of pot1Δ rqh1Δ double mutants is due to inappropriate homologous recombination, as it is suppressed by the deletion of rad51(+). The expression of Rad51 in the pot1Δ rqh1Δ rad51Δ triple mutant, which has circular chromosomes, is lethal. Reduction of the expression of Rqh1 in a pot1 disruptant with circular chromosomes caused chromosome missegregation, and this defect was partially suppressed by the deletion of rad51(+). Taken together, our results suggest that Rqh1 is required for the maintenance of circular chromosomes when homologous recombination is active. Crossovers between circular monomeric chromosomes generate dimers that cannot segregate properly in Escherichia coli. We propose that Rqh1 inhibits crossovers between circular monomeric chromosomes to suppress the generation of circular dimers.
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86
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Pedersen JM, Fredsoe J, Roedgaard M, Andreasen L, Mundbjerg K, Kruhøffer M, Brinch M, Schierup MH, Bjergbaek L, Andersen AH. DNA Topoisomerases maintain promoters in a state competent for transcriptional activation in Saccharomyces cerevisiae. PLoS Genet 2012; 8:e1003128. [PMID: 23284296 PMCID: PMC3527272 DOI: 10.1371/journal.pgen.1003128] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 10/15/2012] [Indexed: 11/19/2022] Open
Abstract
To investigate the role of DNA topoisomerases in transcription, we have studied global gene expression in Saccharomyces cerevisiae cells deficient for topoisomerases I and II and performed single-gene analyses to support our findings. The genome-wide studies show a general transcriptional down-regulation upon lack of the enzymes, which correlates with gene activity but not gene length. Furthermore, our data reveal a distinct subclass of genes with a strong requirement for topoisomerases. These genes are characterized by high transcriptional plasticity, chromatin regulation, TATA box presence, and enrichment of a nucleosome at a critical position in the promoter region, in line with a repressible/inducible mode of regulation. Single-gene studies with a range of genes belonging to this group demonstrate that topoisomerases play an important role during activation of these genes. Subsequent in-depth analysis of the inducible PHO5 gene reveals that topoisomerases are essential for binding of the Pho4p transcription factor to the PHO5 promoter, which is required for promoter nucleosome removal during activation. In contrast, topoisomerases are dispensable for constitutive transcription initiation and elongation of PHO5, as well as the nuclear entrance of Pho4p. Finally, we provide evidence that topoisomerases are required to maintain the PHO5 promoter in a superhelical state, which is competent for proper activation. In conclusion, our results reveal a hitherto unknown function of topoisomerases during transcriptional activation of genes with a repressible/inducible mode of regulation. Gene expression is controlled at many different levels to assure appropriate responses to internal and environmental changes. The effect of topological changes in the DNA double helix on gene transcription in vivo is a poorly understood factor in the regulation of eukaryotic gene expression. Topological changes are constantly generated by DNA tracking processes and may influence gene expression if not constantly removed by DNA topoisomerases. For decades it has been generally accepted that these enzymes regulate transcription by removing excess topological strain generated during tracking of the RNA polymerase, but we still lack a more holistic view of how these enzymes influence gene transcription in their native environment. Here, we examine both global and gene-specific changes in transcription following lack of DNA topoisomerases in budding yeast. Taken together, our findings show that topoisomerases play a profound role during transcriptional activation of genes with a repressible/inducible mode of regulation. For the PHO5 gene, which is investigated in more detail, we demonstrate that topoisomerases are required for binding of a transcription factor, which is crucial for promoter opening during PHO5 activation. Our data thus suggest that inducible gene promoters are highly sensitive to changes in DNA superhelicity.
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Affiliation(s)
- Jakob Madsen Pedersen
- Laboratory of Genome Research, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Jacob Fredsoe
- Laboratory of Genome Research, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Morten Roedgaard
- Laboratory of Genome Research, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Lotte Andreasen
- Laboratory of Genome Research, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | | | - Marie Brinch
- Laboratory of Genome Research, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Mikkel Heide Schierup
- Bioinformatics Research Center, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Lotte Bjergbaek
- Laboratory of Genome Research, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Anni Hangaard Andersen
- Laboratory of Genome Research, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- * E-mail:
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87
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Yang H, Liu C, Jamsen J, Wu Z, Wang Y, Chen J, Zheng L, Shen B. The DNase domain-containing protein TATDN1 plays an important role in chromosomal segregation and cell cycle progression during zebrafish eye development. Cell Cycle 2012. [PMID: 23187801 DOI: 10.4161/cc.22886] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The DNase domain-containing protein TATDN1 is a conserved nuclease in both prokaryotes and eukaryotes. It was previously implicated to play a role in apoptotic DNA fragmentation in yeast and C. elegans. However, its biological function in higher organisms, such as vertebrates, is unknown. Here, we report that zebrafish TATDN1 (zTATDN1) possesses a novel endonuclease activity, which first makes a nick at the DNA duplex and subsequently converts the nick into a DNA double-strand break in vitro. This biochemical property allows zTATDN1 to catalyze decatenation of catenated kinetoplast DNA to produce separated linear DNA in vitro. We further determine that zTATDN1 is predominantly expressed in eye cells during embryonic development. Knockdown of TATDN1 in zebrafish embryos results in an abnormal cell cycle progression, formation of polyploidy and aberrant chromatin structures. Consequently, the TATDN1-deficient morphants have disordered eye cell layers and significantly smaller eyes compared with the WT control. Altogether, our current studies suggest that zTATDN1 plays an important role in chromosome segregation and eye development in zebrafish.
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Affiliation(s)
- Hui Yang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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88
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Tittel-Elmer M, Lengronne A, Davidson MB, Bacal J, François P, Hohl M, Petrini JHJ, Pasero P, Cobb JA. Cohesin association to replication sites depends on rad50 and promotes fork restart. Mol Cell 2012; 48:98-108. [PMID: 22885006 PMCID: PMC3904740 DOI: 10.1016/j.molcel.2012.07.004] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 05/21/2012] [Accepted: 07/05/2012] [Indexed: 01/19/2023]
Abstract
The cohesin complex holds together newly replicated chromatids and is involved in diverse pathways that preserve genome integrity. We show that in budding yeast, cohesin is transiently recruited to active replication origins, and it spreads along DNA as forks progress. When DNA synthesis is impeded, cohesin accumulates at replication sites and is critical for the recovery of stalled forks. Cohesin enrichment at replication forks does not depend on γH2A(X) formation, which differs from its loading requirements at DNA double-strand breaks (DSBs). However, cohesin localization is largely reduced in rad50Δ mutants and in cells lacking both Mec1 and Tel1 checkpoint kinases. Interestingly, cohesin loading at replication sites depends on the structural features of Rad50 that are important for bridging sister chromatids, including the CXXC hook domain and the length of the coiled-coil extensions. Together, these data reveal a function for cohesin in the maintenance of genome integrity during S phase.
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Affiliation(s)
- Mireille Tittel-Elmer
- Department of Biochemistry and Molecular Biology, Southern Alberta Cancer Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB Canada T2N 4N1
- Institute of Human Genetics, Centre National de la Recherche Scientifique, Unité Propre de Recherche 1142, Montpellier, France
| | - Armelle Lengronne
- Institute of Human Genetics, Centre National de la Recherche Scientifique, Unité Propre de Recherche 1142, Montpellier, France
| | - Marta B Davidson
- Department of Biochemistry and Molecular Biology, Southern Alberta Cancer Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB Canada T2N 4N1
| | - Julien Bacal
- Institute of Human Genetics, Centre National de la Recherche Scientifique, Unité Propre de Recherche 1142, Montpellier, France
| | - Philippe François
- Institute of Human Genetics, Centre National de la Recherche Scientifique, Unité Propre de Recherche 1142, Montpellier, France
| | - Marcel Hohl
- Laboratory of Chromosome Biology, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA
| | - John H J Petrini
- Laboratory of Chromosome Biology, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA
| | - Philippe Pasero
- Institute of Human Genetics, Centre National de la Recherche Scientifique, Unité Propre de Recherche 1142, Montpellier, France
| | - Jennifer A Cobb
- Department of Biochemistry and Molecular Biology, Southern Alberta Cancer Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB Canada T2N 4N1
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89
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Preserving the genome by regulating chromatin association with the nuclear envelope. Trends Cell Biol 2012; 22:465-73. [PMID: 22771046 DOI: 10.1016/j.tcb.2012.05.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 05/28/2012] [Accepted: 05/29/2012] [Indexed: 11/24/2022]
Abstract
The nuclear envelope compartmentalizes chromatin within eukaryotic cells and influences diverse cellular functions by controlling nucleocytoplasmic trafficking. Recent evidence has revealed the importance of interactions between chromatin and nuclear envelope components in the maintenance of genome integrity. Nuclear pore complexes (NPCs), traditionally regarded as transport gateways, have emerged as specialized hubs involved in organizing genome architecture, influencing DNA topology, and modulating DNA repair. Here, we review the interplay between the nuclear envelope, chromatin and DNA damage checkpoint pathways, and discuss the physiological and pathological implications of these associations.
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90
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Kubota T, Stead DA, Hiraga SI, ten Have S, Donaldson AD. Quantitative proteomic analysis of yeast DNA replication proteins. Methods 2012; 57:196-202. [DOI: 10.1016/j.ymeth.2012.03.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 03/09/2012] [Accepted: 03/10/2012] [Indexed: 01/15/2023] Open
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91
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Preventing replication stress to maintain genome stability: resolving conflicts between replication and transcription. Mol Cell 2012; 45:710-8. [PMID: 22464441 DOI: 10.1016/j.molcel.2012.03.001] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 02/15/2012] [Accepted: 03/07/2012] [Indexed: 11/22/2022]
Abstract
DNA and RNA polymerases clash along the genome as they compete for the same DNA template. Cells have evolved specialized strategies to prevent and resolve replication and transcription interference. Here, we review the topology and architecture at sites of replication fork clashes with transcription bubbles as well as the regulatory circuits that control replication fork passage across transcribed genes. In the case of RNA polymerase II-transcribed genes, cotranscriptional processes such as mRNA maturation, splicing, and export influence the integrity of replication forks and transcribed loci. Fork passage likely contributes to reset the epigenetic landscape, influencing gene expression and transcriptional memory. When any of these processes are not properly coordinated, aberrant outcomes such as fork reversal and R-loop formation arise and trigger unscheduled recombinogenic events and genome rearrangements. The evolutionary implications of such conflicts on genome dynamics and their potential impact on oncogenic stress are discussed.
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92
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Topoisomerase I poisoning results in PARP-mediated replication fork reversal. Nat Struct Mol Biol 2012; 19:417-23. [DOI: 10.1038/nsmb.2258] [Citation(s) in RCA: 351] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 02/07/2012] [Indexed: 12/30/2022]
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93
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94
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[Molecular determinants of response to topoisomerase II inhibitors]. Bull Cancer 2012; 98:1299-310. [PMID: 22023806 DOI: 10.1684/bdc.2011.1475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Human nuclear topoisomerases II (Top2) are involved in the relaxation of DNA supercoiling during transcription and replication but also play a pivotal role in the segregation of newly replicated chromosomes and in chromatin remodelling. Top2 have been used as targets for the development of anticancer drugs. These inhibitors include anthracyclines (doxorubcin, daunorubicin, epirubicin) and epipodophyllotoxins (etoposide), which are widely used in the clinic. These drugs poison Top2 by trapping the enzyme on its DNA cleavage sites, which results in irreversible double-strand breaks that are responsible for cell death. They also include Top2 catalytic inhibitors such as bisdioxopiperazines (ICRF-187 and merbarone), which inhibit Top2 binding to its substrate. Efficacy of Top2 inhibitors is still limited by the problem of resistance, which involves various mechanisms from drug transport and/or metabolism to the signalling and/or repair of Top2-mediated DNA lesions. Secondary malignancies induced by the poisoning of Top2β are also a major clinical issue. A better understanding of these mechanisms is critical for the future development of new Top2 inhibitors and the identification of biomarkers that could be used to predict tumour response to these drugs in the clinic and to adapt the treatment to each patient.
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95
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Topoisomerase II binds nucleosome-free DNA and acts redundantly with topoisomerase I to enhance recruitment of RNA Pol II in budding yeast. Proc Natl Acad Sci U S A 2011; 108:12693-8. [PMID: 21771901 DOI: 10.1073/pnas.1106834108] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA topoisomerases are believed to promote transcription by removing excessive DNA supercoils produced during elongation. However, it is unclear how topoisomerases in eukaryotes are recruited and function in the transcription pathway in the context of nucleosomes. To address this problem we present high-resolution genome-wide maps of one of the major eukaryotic topoisomerases, Topoisomerase II (Top2) and nucleosomes in the budding yeast, Saccharomyces cerevisiae. Our data indicate that at promoters Top2 binds primarily to DNA that is nucleosome-free. However, although nucleosome loss enables Top2 occupancy, the opposite is not the case and the loss of Top2 has little effect on nucleosome density. We also find that Top2 is involved in transcription. Not only is Top2 enriched at highly transcribed genes, but Top2 is required redundantly with Top1 for optimal recruitment of RNA polymerase II at their promoters. These findings and the examination of candidate-activated genes suggest that nucleosome loss induced by nucleosome remodeling factors during gene activation enables Top2 binding, which in turn acts redundantly with Top1 to enhance recruitment of RNA polymerase II.
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96
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DNA topoisomerase 2 mutant allele mildly delays the mitotic progression and activates the checkpoint protein kinase Chk1 in fission yeast Schizosaccharomyces pombe. Genet Res (Camb) 2011; 93:275-83. [PMID: 21767457 DOI: 10.1017/s0016672311000188] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
DNA topoisomerases are specialized nuclear enzymes that perform topological modifications on double-stranded DNA (dsDNA) and hence are essential for DNA metabolism such as replication, transcription, recombination, condensation and segregation. In a genetic screen, we identified a temperature-sensitive mutant allele of topoisomerase 2 that exhibits conditional synthetic lethality with a chk1 knockout strain. The mutant allele of topoisomerase 2 is defective in chromosome segregation at a non-permissive temperature and there was increase in chromosome segregation defects in the double mutant of top2-10 and chk1 delete at a non-permissive temperature. More importantly, topoisomearse 2 mutant cells mildly delay the mitotic progression at non-permissive temperature that is mediated by checkpoint protein kinase Chk1. Additionally, top2-10 mutant cells also activate the Chk1 at a non-permissive temperature and this activation of Chk1 takes place at the time of mitosis. Interestingly, top2-10 mutant cells retain their viability at a non-permissive temperature if the cells are not allowed to enter into mitosis. Taking together our results, we speculate that in the top2-10 mutant, the segregation of entangled chromatids during mitosis could result in delaying the mitotic progression through the activation of Chk1 kinase.
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Gómez-González B, García-Rubio M, Bermejo R, Gaillard H, Shirahige K, Marín A, Foiani M, Aguilera A. Genome-wide function of THO/TREX in active genes prevents R-loop-dependent replication obstacles. EMBO J 2011; 30:3106-19. [PMID: 21701562 DOI: 10.1038/emboj.2011.206] [Citation(s) in RCA: 174] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 05/25/2011] [Indexed: 11/09/2022] Open
Abstract
THO/TREX is a conserved nuclear complex that functions in mRNP biogenesis and prevents transcription-associated recombination. Whether or not it has a ubiquitous role in the genome is unknown. Chromatin immunoprecipitation (ChIP)-chip studies reveal that the Hpr1 component of THO and the Sub2 RNA-dependent ATPase have genome-wide distributions at active ORFs in yeast. In contrast to RNA polymerase II, evenly distributed from promoter to termination regions, THO and Sub2 are absent at promoters and distributed in a gradual 5' → 3' gradient. This is accompanied by a genome-wide impact of THO-Sub2 deletions on expression of highly expressed, long and high G+C-content genes. Importantly, ChIP-chips reveal an over-recruitment of Rrm3 in active genes in THO mutants that is reduced by RNaseH1 overexpression. Our work establishes a genome-wide function for THO-Sub2 in transcription elongation and mRNP biogenesis that function to prevent the accumulation of transcription-mediated replication obstacles, including R-loops.
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Affiliation(s)
- Belén Gómez-González
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC, Sevilla, Spain
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98
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Kegel A, Betts-Lindroos H, Kanno T, Jeppsson K, Ström L, Katou Y, Itoh T, Shirahige K, Sjögren C. Chromosome length influences replication-induced topological stress. Nature 2011; 471:392-6. [PMID: 21368764 DOI: 10.1038/nature09791] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Accepted: 01/05/2011] [Indexed: 11/09/2022]
Abstract
During chromosome duplication the parental DNA molecule becomes overwound, or positively supercoiled, in the region ahead of the advancing replication fork. To allow fork progression, this superhelical tension has to be removed by topoisomerases, which operate by introducing transient DNA breaks. Positive supercoiling can also be diminished if the advancing fork rotates along the DNA helix, but then sister chromatid intertwinings form in its wake. Despite these insights it remains largely unknown how replication-induced superhelical stress is dealt with on linear, eukaryotic chromosomes. Here we show that this stress increases with the length of Saccharomyces cerevisiae chromosomes. This highlights the possibility that superhelical tension is handled on a chromosome scale and not only within topologically closed chromosomal domains as the current view predicts. We found that inhibition of type I topoisomerases leads to a late replication delay of longer, but not shorter, chromosomes. This phenotype is also displayed by cells expressing mutated versions of the cohesin- and condensin-related Smc5/6 complex. The frequency of chromosomal association sites of the Smc5/6 complex increases in response to chromosome lengthening, chromosome circularization, or inactivation of topoisomerase 2, all having the potential to increase the number of sister chromatid intertwinings. Furthermore, non-functional Smc6 reduces the accumulation of intertwined sister plasmids after one round of replication in the absence of topoisomerase 2 function. Our results demonstrate that the length of a chromosome influences the need of superhelical tension release in Saccharomyces cerevisiae, and allow us to propose a model where the Smc5/6 complex facilitates fork rotation by sequestering nascent chromatid intertwinings that form behind the replication machinery.
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Affiliation(s)
- Andreas Kegel
- Department of Cell and Molecular Biology, Karolinska Institutet, von Eulers väg 3, 171 77 Stockholm, Sweden
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Fachinetti D, Bermejo R, Cocito A, Minardi S, Katou Y, Kanoh Y, Shirahige K, Azvolinsky A, Zakian VA, Foiani M. Replication termination at eukaryotic chromosomes is mediated by Top2 and occurs at genomic loci containing pausing elements. Mol Cell 2010; 39:595-605. [PMID: 20797631 DOI: 10.1016/j.molcel.2010.07.024] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 05/05/2010] [Accepted: 06/08/2010] [Indexed: 01/19/2023]
Abstract
Chromosome replication initiates at multiple replicons and terminates when forks converge. In E. coli, the Tus-TER complex mediates polar fork converging at the terminator region, and aberrant termination events challenge chromosome integrity and segregation. Since in eukaryotes, termination is less characterized, we used budding yeast to identify the factors assisting fork fusion at replicating chromosomes. Using genomic and mechanistic studies, we have identified and characterized 71 chromosomal termination regions (TERs). TERs contain fork pausing elements that influence fork progression and merging. The Rrm3 DNA helicase assists fork progression across TERs, counteracting the accumulation of X-shaped structures. The Top2 DNA topoisomerase associates at TERs in S phase, and G2/M facilitates fork fusion and prevents DNA breaks and genome rearrangements at TERs. We propose that in eukaryotes, replication fork barriers, Rrm3, and Top2 coordinate replication fork progression and fusion at TERs, thus counteracting abnormal genomic transitions.
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Affiliation(s)
- Daniele Fachinetti
- Fondazione IFOM, Istituto FIRC di Oncologia Molecolare (IFOM-IEO Campus), Via Adamello 16, 20139 Milan, Italy
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100
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Bermúdez I, García-Martínez J, Pérez-Ortín JE, Roca J. A method for genome-wide analysis of DNA helical tension by means of psoralen-DNA photobinding. Nucleic Acids Res 2010; 38:e182. [PMID: 20685815 PMCID: PMC2965259 DOI: 10.1093/nar/gkq687] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The helical tension of chromosomal DNA is one of the epigenetic landmarks most difficult to examine experimentally. The occurrence of DNA crosslinks mediated by psoralen photobinding (PB) stands as the only suitable probe for assessing this problem. PB is affected by chromatin structure when is done to saturation; but it is mainly determined by DNA helical tension when it is done to very low hit conditions. Hence, we developed a method for genome-wide analysis of DNA helical tension based on PB. We adjusted in vitro PB conditions that discern DNA helical tension and applied them to Saccharomyces cerevisiae cells. We selected the in vivo cross-linked DNA sequences and identified them on DNA arrays. The entire procedure was robust. Comparison of PB obtained in vivo with that obtained in vitro with naked DNA revealed that numerous chromosomal regions had deviated PB values. Similar analyses in yeast topoisomerase mutants uncovered further PB alterations across specific chromosomal domains. These results suggest that distinct chromosome compartments might confine different levels of DNA helical tension in yeast. Genome-wide analysis of psoralen–DNA PB can be, therefore, a useful approach to uncover a trait of the chromosome architecture not amenable to other techniques.
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Affiliation(s)
- Ignacio Bermúdez
- Instituto de Biología Molecular de Barcelona-CSIC, Barcelona, Laboratorio de Chips de DNA-SCSIE Universitat de València, Burjassot, Spain
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