1
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Kuse R, Ishii K. Flexible Attachment and Detachment of Centromeres and Telomeres to and from Chromosomes. Biomolecules 2023; 13:1016. [PMID: 37371596 DOI: 10.3390/biom13061016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/15/2023] [Accepted: 06/18/2023] [Indexed: 06/29/2023] Open
Abstract
Accurate transmission of genomic information across multiple cell divisions and generations, without any losses or errors, is fundamental to all living organisms. To achieve this goal, eukaryotes devised chromosomes. Eukaryotic genomes are represented by multiple linear chromosomes in the nucleus, each carrying a centromere in the middle, a telomere at both ends, and multiple origins of replication along the chromosome arms. Although all three of these DNA elements are indispensable for chromosome function, centromeres and telomeres possess the potential to detach from the original chromosome and attach to new chromosomal positions, as evident from the events of telomere fusion, centromere inactivation, telomere healing, and neocentromere formation. These events seem to occur spontaneously in nature but have not yet been elucidated clearly, because they are relatively infrequent and sometimes detrimental. To address this issue, experimental setups have been developed using model organisms such as yeast. In this article, we review some of the key experiments that provide clues as to the extent to which these paradoxical and elusive features of chromosomally indispensable elements may become valuable in the natural context.
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Affiliation(s)
- Riku Kuse
- Laboratory of Chromosome Function and Regulation, Graduate School of Engineering, Kochi University of Technology, Kochi 782-8502, Japan
| | - Kojiro Ishii
- Laboratory of Chromosome Function and Regulation, Graduate School of Engineering, Kochi University of Technology, Kochi 782-8502, Japan
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2
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Chakraborty S, Singh M, Pandita RK, Singh V, Lo CS, Leonard F, Horikoshi N, Moros EG, Guha D, Hunt CR, Chau E, Ahmed KM, Sethi P, Charaka V, Godin B, Makhijani K, Scherthan H, Deck J, Hausmann M, Mushtaq A, Altaf M, Ramos KS, Bhat KM, Taneja N, Das C, Pandita TK. Heat-induced SIRT1-mediated H4K16ac deacetylation impairs resection and SMARCAD1 recruitment to double strand breaks. iScience 2022; 25:104142. [PMID: 35434547 PMCID: PMC9010620 DOI: 10.1016/j.isci.2022.104142] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/16/2022] [Accepted: 03/21/2022] [Indexed: 12/17/2022] Open
Abstract
Hyperthermia inhibits DNA double-strand break (DSB) repair that utilizes homologous recombination (HR) pathway by a poorly defined mechanism(s); however, the mechanisms for this inhibition remain unclear. Here we report that hyperthermia decreases H4K16 acetylation (H4K16ac), an epigenetic modification essential for genome stability and transcription. Heat-induced reduction in H4K16ac was detected in humans, Drosophila, and yeast, indicating that this is a highly conserved response. The examination of histone deacetylase recruitment to chromatin after heat-shock identified SIRT1 as the major deacetylase subsequently enriched at gene-rich regions. Heat-induced SIRT1 recruitment was antagonized by chromatin remodeler SMARCAD1 depletion and, like hyperthermia, the depletion of the SMARCAD1 or combination of the two impaired DNA end resection and increased replication stress. Altered repair protein recruitment was associated with heat-shock-induced γ-H2AX chromatin changes and DSB repair processing. These results support a novel mechanism whereby hyperthermia impacts chromatin organization owing to H4K16ac deacetylation, negatively affecting the HR-dependent DSB repair.
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Affiliation(s)
- Sharmistha Chakraborty
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Radiation Oncology, University of Texas Southwestern Medical Centre, Dallas, TX, USA
| | - Mayank Singh
- Department of Radiation Oncology, University of Texas Southwestern Medical Centre, Dallas, TX, USA
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Raj K. Pandita
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Radiation Oncology, University of Texas Southwestern Medical Centre, Dallas, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Departments of Radiation Oncology, Washington University, St Louis, MO, USA
| | - Vipin Singh
- Biophysics & Structural Genomics Division Saha Institute of Nuclear Physics, Bidhan Nagar, Kolkata, West Bengal 700064, India
- Homi Bhaba National Institute, Mumbai, India
| | - Calvin S.C. Lo
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 Rotterdam, CA, the Netherlands
| | - Fransisca Leonard
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Nobuo Horikoshi
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Radiation Oncology, University of Texas Southwestern Medical Centre, Dallas, TX, USA
- Departments of Radiation Oncology, Washington University, St Louis, MO, USA
| | - Eduardo G. Moros
- Departments of Radiation Oncology, Washington University, St Louis, MO, USA
- Departments of Radiation Oncology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Deblina Guha
- Biophysics & Structural Genomics Division Saha Institute of Nuclear Physics, Bidhan Nagar, Kolkata, West Bengal 700064, India
| | - Clayton R. Hunt
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Radiation Oncology, University of Texas Southwestern Medical Centre, Dallas, TX, USA
- Departments of Radiation Oncology, Washington University, St Louis, MO, USA
| | - Eric Chau
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Kazi M. Ahmed
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Prayas Sethi
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Vijaya Charaka
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Biana Godin
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Kalpana Makhijani
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Harry Scherthan
- Bundeswehr Institute of Radiobiology Affiliated to the University of Ulm, Neuherbergstr. 11, 80937 Munich, Germany
| | - Jeanette Deck
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
| | - Michael Hausmann
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
| | - Arjamand Mushtaq
- Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir 190006, India
| | - Mohammad Altaf
- Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir 190006, India
| | - Kenneth S. Ramos
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, TX, USA
| | - Krishna M. Bhat
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Nitika Taneja
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 Rotterdam, CA, the Netherlands
| | - Chandrima Das
- Biophysics & Structural Genomics Division Saha Institute of Nuclear Physics, Bidhan Nagar, Kolkata, West Bengal 700064, India
- Homi Bhaba National Institute, Mumbai, India
| | - Tej K. Pandita
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Radiation Oncology, University of Texas Southwestern Medical Centre, Dallas, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Departments of Radiation Oncology, Washington University, St Louis, MO, USA
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, TX, USA
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3
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Chanou A, Hamperl S. Single-Molecule Techniques to Study Chromatin. Front Cell Dev Biol 2021; 9:699771. [PMID: 34291054 PMCID: PMC8287188 DOI: 10.3389/fcell.2021.699771] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 05/26/2021] [Indexed: 12/14/2022] Open
Abstract
Besides the basic organization in nucleosome core particles (NCPs), eukaryotic chromatin is further packed through interactions with numerous protein complexes including transcription factors, chromatin remodeling and modifying enzymes. This nucleoprotein complex provides the template for many important biological processes, such as DNA replication, transcription, and DNA repair. Thus, to understand the molecular basis of these DNA transactions, it is critical to define individual changes of the chromatin structure at precise genomic regions where these machineries assemble and drive biological reactions. Single-molecule approaches provide the only possible solution to overcome the heterogenous nature of chromatin and monitor the behavior of individual chromatin transactions in real-time. In this review, we will give an overview of currently available single-molecule methods to obtain mechanistic insights into nucleosome positioning, histone modifications and DNA replication and transcription analysis-previously unattainable with population-based assays.
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Affiliation(s)
| | - Stephan Hamperl
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
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4
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Técher H, Pasero P. The Replication Stress Response on a Narrow Path Between Genomic Instability and Inflammation. Front Cell Dev Biol 2021; 9:702584. [PMID: 34249949 PMCID: PMC8270677 DOI: 10.3389/fcell.2021.702584] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/03/2021] [Indexed: 02/06/2023] Open
Abstract
The genome of eukaryotic cells is particularly at risk during the S phase of the cell cycle, when megabases of chromosomal DNA are unwound to generate two identical copies of the genome. This daunting task is executed by thousands of micro-machines called replisomes, acting at fragile structures called replication forks. The correct execution of this replication program depends on the coordinated action of hundreds of different enzymes, from the licensing of replication origins to the termination of DNA replication. This review focuses on the mechanisms that ensure the completion of DNA replication under challenging conditions of endogenous or exogenous origin. It also covers new findings connecting the processing of stalled forks to the release of small DNA fragments into the cytoplasm, activating the cGAS-STING pathway. DNA damage and fork repair comes therefore at a price, which is the activation of an inflammatory response that has both positive and negative impacts on the fate of stressed cells. These new findings have broad implications for the etiology of interferonopathies and for cancer treatment.
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Affiliation(s)
- Hervé Técher
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, Montpellier, France
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue Contre le Cancer, Montpellier, France
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5
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Moreno E, Toussaint MJ, van Essen SC, Bongiovanni L, van Liere EA, Koster MH, Yuan R, van Deursen JM, Westendorp B, de Bruin A. E2F7 Is a Potent Inhibitor of Liver Tumor Growth in Adult Mice. Hepatology 2021; 73:303-317. [PMID: 32259305 PMCID: PMC7898887 DOI: 10.1002/hep.31259] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 03/12/2020] [Accepted: 03/19/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS Up-regulation of the E2F-dependent transcriptional network has been identified in nearly every human malignancy and is an important driver of tumorigenesis. Two members of the E2F family, E2F7 and E2F8, are potent repressors of E2F-dependent transcription. They are atypical in that they do not bind to dimerization partner proteins and are not controlled by retinoblastoma protein. The physiological relevance of E2F7 and E2F8 remains incompletely understood, largely because tools to manipulate their activity in vivo have been lacking. APPROACH AND RESULTS Here, we generated transgenic mice with doxycycline-controlled transcriptional activation of E2f7 and E2f8 and induced their expression during postnatal development, in adulthood, and in the context of cancer. Systemic induction of E2f7 and, to lesser extent, E2f8 transgenes in juvenile mice impaired cell proliferation, caused replication stress, DNA damage, and apoptosis, and inhibited animal growth. In adult mice, however, E2F7 and E2F8 induction was well tolerated, yet profoundly interfered with DNA replication, DNA integrity, and cell proliferation in diethylnitrosamine-induced liver tumors. CONCLUSION Collectively, our findings demonstrate that atypical E2Fs can override cell-cycle entry and progression governed by other E2F family members and suggest that this property can be exploited to inhibit proliferation of neoplastic hepatocytes when growth and development have subsided during adulthood.
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Affiliation(s)
- Eva Moreno
- Department of Biomolecular Health SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtthe Netherlands
| | - Mathilda J.M. Toussaint
- Department of Biomolecular Health SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtthe Netherlands
| | - Saskia C. van Essen
- Department of Biomolecular Health SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtthe Netherlands
| | - Laura Bongiovanni
- Department of Biomolecular Health SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtthe Netherlands
| | - Elsbeth A. van Liere
- Department of Biomolecular Health SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtthe Netherlands
| | - Mirjam H. Koster
- Division Molecular GeneticsDepartment of PediatricsUniversity Medical Center GroningenUniversity of GroningenGroningenthe Netherlands
| | - Ruixue Yuan
- Department of Biomolecular Health SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtthe Netherlands,Department of PathologyAcademic Medical CenterAmsterdamthe Netherlands
| | - Jan M. van Deursen
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMN,Department of Pediatric and Adolescent MedicineMayo ClinicRochesterMN
| | - Bart Westendorp
- Department of Biomolecular Health SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtthe Netherlands
| | - Alain de Bruin
- Department of Biomolecular Health SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtthe Netherlands,Division Molecular GeneticsDepartment of PediatricsUniversity Medical Center GroningenUniversity of GroningenGroningenthe Netherlands
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6
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van Schie JJM, Faramarz A, Balk JA, Stewart GS, Cantelli E, Oostra AB, Rooimans MA, Parish JL, de Almeida Estéves C, Dumic K, Barisic I, Diderich KEM, van Slegtenhorst MA, Mahtab M, Pisani FM, Te Riele H, Ameziane N, Wolthuis RMF, de Lange J. Warsaw Breakage Syndrome associated DDX11 helicase resolves G-quadruplex structures to support sister chromatid cohesion. Nat Commun 2020; 11:4287. [PMID: 32855419 PMCID: PMC7452896 DOI: 10.1038/s41467-020-18066-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 07/30/2020] [Indexed: 02/01/2023] Open
Abstract
Warsaw Breakage Syndrome (WABS) is a rare disorder related to cohesinopathies and Fanconi anemia, caused by bi-allelic mutations in DDX11. Here, we report multiple compound heterozygous WABS cases, each displaying destabilized DDX11 protein and residual DDX11 function at the cellular level. Patient-derived cell lines exhibit sensitivity to topoisomerase and PARP inhibitors, defective sister chromatid cohesion and reduced DNA replication fork speed. Deleting DDX11 in RPE1-TERT cells inhibits proliferation and survival in a TP53-dependent manner and causes chromosome breaks and cohesion defects, independent of the expressed pseudogene DDX12p. Importantly, G-quadruplex (G4) stabilizing compounds induce chromosome breaks and cohesion defects which are strongly aggravated by inactivation of DDX11 but not FANCJ. The DNA helicase domain of DDX11 is essential for sister chromatid cohesion and resistance to G4 stabilizers. We propose that DDX11 is a DNA helicase protecting against G4 induced double-stranded breaks and concomitant loss of cohesion, possibly at DNA replication forks.
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Affiliation(s)
- Janne J M van Schie
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
| | - Atiq Faramarz
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
| | - Jesper A Balk
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Erika Cantelli
- Netherlands Cancer Institute, Division of Tumor Biology and Immunology, Amsterdam, The Netherlands
| | - Anneke B Oostra
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
| | - Martin A Rooimans
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
| | - Joanna L Parish
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | | | - Katja Dumic
- Department of Pediatric Endocrinology and Diabetes, University Hospital Centre Zagreb, University of Zagreb Medical School, Zagreb, Croatia
| | - Ingeborg Barisic
- Children's Hospital Zagreb, Center of Excellence for Reproductive and Regenerative Medicine, Medical School University of Zagreb, Zagreb, Croatia
| | - Karin E M Diderich
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Mohammad Mahtab
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Naples, Italy
| | - Francesca M Pisani
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Naples, Italy
| | - Hein Te Riele
- Netherlands Cancer Institute, Division of Tumor Biology and Immunology, Amsterdam, The Netherlands
| | - Najim Ameziane
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
- Centogene, Am Strande 7, 18055, Rostock, Germany
| | - Rob M F Wolthuis
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands.
| | - Job de Lange
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands.
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7
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Benedict B, van Schie JJM, Oostra AB, Balk JA, Wolthuis RMF, Riele HT, de Lange J. WAPL-Dependent Repair of Damaged DNA Replication Forks Underlies Oncogene-Induced Loss of Sister Chromatid Cohesion. Dev Cell 2020; 52:683-698.e7. [PMID: 32084359 DOI: 10.1016/j.devcel.2020.01.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 11/19/2019] [Accepted: 01/22/2020] [Indexed: 12/22/2022]
Abstract
Premature loss of sister chromatid cohesion at metaphase is a diagnostic marker for different cohesinopathies. Here, we report that metaphase spreads of many cancer cell lines also show premature loss of sister chromatid cohesion. Cohesion loss occurs independently of mutations in cohesion factors including SA2, a cohesin subunit frequently inactivated in cancer. In untransformed cells, induction of DNA replication stress by activation of oncogenes or inhibition of DNA replication is sufficient to trigger sister chromatid cohesion loss. Importantly, cell growth under conditions of replication stress requires the cohesin remover WAPL. WAPL promotes rapid RAD51-dependent repair and restart of broken replication forks. We propose that active removal of cohesin allows cancer cells to overcome DNA replication stress. This leads to oncogene-induced cohesion loss from newly synthesized sister chromatids that may contribute to genomic instability and likely represents a targetable cancer cell vulnerability.
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Affiliation(s)
- Bente Benedict
- Netherlands Cancer Institute, Division of Tumor Biology and Immunology, Amsterdam, the Netherlands
| | - Janne J M van Schie
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Anneke B Oostra
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Jesper A Balk
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Rob M F Wolthuis
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands.
| | - Hein Te Riele
- Netherlands Cancer Institute, Division of Tumor Biology and Immunology, Amsterdam, the Netherlands.
| | - Job de Lange
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands.
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Yousefi R, Rowicka M. Stochasticity of replication forks' speeds plays a key role in the dynamics of DNA replication. PLoS Comput Biol 2019; 15:e1007519. [PMID: 31869320 PMCID: PMC6975548 DOI: 10.1371/journal.pcbi.1007519] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 01/22/2020] [Accepted: 10/29/2019] [Indexed: 11/26/2022] Open
Abstract
Eukaryotic DNA replication is elaborately orchestrated to duplicate the genome timely and faithfully. Replication initiates at multiple origins from which replication forks emanate and travel bi-directionally. The complex spatio-temporal regulation of DNA replication remains incompletely understood. To study it, computational models of DNA replication have been developed in S. cerevisiae. However, in spite of the experimental evidence of forks’ speed stochasticity, all models assumed that forks’ speeds are the same. Here, we present the first model of DNA replication assuming that speeds vary stochastically between forks. Utilizing data from both wild-type and hydroxyurea-treated yeast cells, we show that our model is more accurate than models assuming constant forks’ speed and reconstructs dynamics of DNA replication faithfully starting both from population-wide data and data reflecting fork movement in individual cells. Completion of replication in a timely manner is a challenge due to its stochasticity; we propose an empirically derived modification to replication speed based on the distance to the approaching fork, which promotes timely completion of replication. In summary, our work discovers a key role that stochasticity of the forks’ speed plays in the dynamics of DNA replication. We show that without including stochasticity of forks’ speed it is not possible to accurately reconstruct movement of individual replication forks, measured by DNA combing. DNA replication in eukaryotes starts from multiple sites termed replication origins. Replication timing at individual sites is stochastic, but reproducible population-wide. Complex and not yet completely understood mechanisms ensure that genome is replicated exactly once and that replication is finished in time. This complex spatio-temporal organization of DNA replication makes computational modeling a useful tool to study replication mechanisms. For simplicity, all previous models assumed constant replication forks’ speed. Here, we show that such models are incapable of accurately reconstructing distances travelled by individual replication forks. Therefore, we propose a model assuming that replication speed varies stochastically between forks. We show that such model reproduces faithfully distances travelled by individual replication forks. Moreover, our model is simpler than previous model and thus avoids over-learning (fitting noise). We also discover how replication speed may be attuned to timely complete replication. We propose that forks’ speed increases with diminishing distance to the approaching fork, which we show promotes timely completion of replication. Such speed up can be e.g. explained by a synergy effect of chromatin unwinding by both forks. Our model can be used to simulate phenomena beyond replication, e.g. DNA double-strand breaks resulting from broken replication forks.
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Affiliation(s)
- Razie Yousefi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
| | - Maga Rowicka
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
- Institute of Translational Sciences, University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
- * E-mail:
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9
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Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads. Nat Methods 2019; 16:429-436. [PMID: 31011185 DOI: 10.1038/s41592-019-0394-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 03/18/2019] [Indexed: 12/19/2022]
Abstract
Replication of eukaryotic genomes is highly stochastic, making it difficult to determine the replication dynamics of individual molecules with existing methods. We report a sequencing method for the measurement of replication fork movement on single molecules by detecting nucleotide analog signal currents on extremely long nanopore traces (D-NAscent). Using this method, we detect 5-bromodeoxyuridine (BrdU) incorporated by Saccharomyces cerevisiae to reveal, at a genomic scale and on single molecules, the DNA sequences replicated during a pulse-labeling period. Under conditions of limiting BrdU concentration, D-NAscent detects the differences in BrdU incorporation frequency across individual molecules to reveal the location of active replication origins, fork direction, termination sites, and fork pausing/stalling events. We used sequencing reads of 20-160 kilobases to generate a whole-genome single-molecule map of DNA replication dynamics and discover a class of low-frequency stochastic origins in budding yeast. The D-NAscent software is available at https://github.com/MBoemo/DNAscent.git .
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10
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Candelli T, Gros J, Libri D. Pervasive transcription fine-tunes replication origin activity. eLife 2018; 7:40802. [PMID: 30556807 PMCID: PMC6314782 DOI: 10.7554/elife.40802] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 12/17/2018] [Indexed: 12/22/2022] Open
Abstract
RNA polymerase (RNAPII) transcription occurs pervasively, raising the important question of its functional impact on other DNA-associated processes, including replication. In budding yeast, replication originates from Autonomously Replicating Sequences (ARSs), generally located in intergenic regions. The influence of transcription on ARSs function has been studied for decades, but these earlier studies have neglected the role of non-annotated transcription. We studied the relationships between pervasive transcription and replication origin activity using high-resolution transcription maps. We show that ARSs alter the pervasive transcription landscape by pausing and terminating neighboring RNAPII transcription, thus limiting the occurrence of pervasive transcription within origins. We propose that quasi-symmetrical binding of the ORC complex to ARS borders and/or pre-RC formation are responsible for pausing and termination. We show that low, physiological levels of pervasive transcription impact the function of replication origins. Overall, our results have important implications for understanding the impact of genomic location on origin function.
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Affiliation(s)
- Tito Candelli
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Julien Gros
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Domenico Libri
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
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11
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Benedict B, van Harn T, Dekker M, Hermsen S, Kucukosmanoglu A, Pieters W, Delzenne-Goette E, Dorsman JC, Petermann E, Foijer F, te Riele H. Loss of p53 suppresses replication-stress-induced DNA breakage in G1/S checkpoint deficient cells. eLife 2018; 7:e37868. [PMID: 30322449 PMCID: PMC6221544 DOI: 10.7554/elife.37868] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/28/2018] [Indexed: 12/12/2022] Open
Abstract
In cancer cells, loss of G1/S control is often accompanied by p53 pathway inactivation, the latter usually rationalized as a necessity for suppressing cell cycle arrest and apoptosis. However, we found an unanticipated effect of p53 loss in mouse and human G1-checkpoint-deficient cells: reduction of DNA damage. We show that abrogation of the G1/S-checkpoint allowed cells to enter S-phase under growth-restricting conditions at the expense of severe replication stress manifesting as decelerated DNA replication, reduced origin firing and accumulation of DNA double-strand breaks. In this system, loss of p53 allowed mitogen-independent proliferation, not by suppressing apoptosis, but rather by restoring origin firing and reducing DNA breakage. Loss of G1/S control also caused DNA damage and activation of p53 in an in vivo retinoblastoma model. Moreover, in a teratoma model, loss of p53 reduced DNA breakage. Thus, loss of p53 may promote growth of incipient cancer cells by reducing replication-stress-induced DNA damage.
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Affiliation(s)
- Bente Benedict
- Division of Tumor Biology and ImmunologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Tanja van Harn
- Division of Tumor Biology and ImmunologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Marleen Dekker
- Division of Tumor Biology and ImmunologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Simone Hermsen
- Division of Tumor Biology and ImmunologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Asli Kucukosmanoglu
- Division of Tumor Biology and ImmunologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Wietske Pieters
- Division of Tumor Biology and ImmunologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Elly Delzenne-Goette
- Division of Tumor Biology and ImmunologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Josephine C Dorsman
- Department of Clinical GeneticsVU University Medical CenterAmsterdamThe Netherlands
| | - Eva Petermann
- School of Cancer SciencesUniversity of BirminghamBirminghamUnited Kingdom
| | - Floris Foijer
- Division of Tumor Biology and ImmunologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
- European Research Institute for the Biology of AgeingUniversity Medical Center GroningenAmsterdamThe Netherlands
| | - Hein te Riele
- Division of Tumor Biology and ImmunologyThe Netherlands Cancer InstituteAmsterdamThe Netherlands
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12
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Analysis of Fission Yeast Single DNA Molecules on the Megabase Scale Using DNA Combing. Methods Mol Biol 2018; 1721:9-24. [PMID: 29423843 DOI: 10.1007/978-1-4939-7546-4_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
DNA combing enables the quantitative analysis of DNA replication, DNA recombination, DNA-protein interaction, and DNA methylation along genomic single DNA molecules at 1 kb resolution. However, DNA combing has been restricted to short 200-500 kb long DNA fragments, which introduces significant bias in data analysis. An improved DNA combing methodology that allows to routinely image Mb-scale single DNA molecules and occasionally up to full-length fission yeast chromosomes is presented in this chapter. DNA combing of Mb-scale single DNA molecules can be applied to accurately measure the dynamic properties of DNA replication such as the rate of origin firing, replication fork velocity, fork directionality and the frequency of fork blockage. In addition, Mb-scale single DNA molecules enable the quantitative analysis of complex genomic rearrangements including gross chromosomal translocations, repetitive DNA sequences, large deletions, and duplications, which are difficult to investigate with deep sequencing strategies.
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13
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Saldivar JC, Cortez D, Cimprich KA. The essential kinase ATR: ensuring faithful duplication of a challenging genome. Nat Rev Mol Cell Biol 2017; 18:622-636. [PMID: 28811666 DOI: 10.1038/nrm.2017.67] [Citation(s) in RCA: 523] [Impact Index Per Article: 74.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
One way to preserve a rare book is to lock it away from all potential sources of damage. Of course, an inaccessible book is also of little use, and the paper and ink will continue to degrade with age in any case. Like a book, the information stored in our DNA needs to be read, but it is also subject to continuous assault and therefore needs to be protected. In this Review, we examine how the replication stress response that is controlled by the kinase ataxia telangiectasia and Rad3-related (ATR) senses and resolves threats to DNA integrity so that the DNA remains available to read in all of our cells. We discuss the multiple data that have revealed an elegant yet increasingly complex mechanism of ATR activation. This involves a core set of components that recruit ATR to stressed replication forks, stimulate kinase activity and amplify ATR signalling. We focus on the activities of ATR in the control of cell cycle checkpoints, origin firing and replication fork stability, and on how proper regulation of these processes is crucial to ensure faithful duplication of a challenging genome.
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Affiliation(s)
- Joshua C Saldivar
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, California 94305-5441, USA
| | - David Cortez
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, California 94305-5441, USA
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14
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Tourrière H, Saksouk J, Lengronne A, Pasero P. Single-molecule Analysis of DNA Replication Dynamics in Budding Yeast and Human Cells by DNA Combing. Bio Protoc 2017; 7:e2305. [PMID: 34541074 DOI: 10.21769/bioprotoc.2305] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 02/01/2017] [Accepted: 04/24/2017] [Indexed: 11/02/2022] Open
Abstract
The DNA combing method allows the analysis of DNA replication at the level of individual DNA molecules stretched along silane-coated glass coverslips. Before DNA extraction, ongoing DNA synthesis is labeled with halogenated analogues of thymidine. Replication tracks are visualized by immunofluorescence using specific antibodies. Unlike biochemical and NGS-based methods, DNA combing provides unique information on cell-to-cell variations in DNA replication profiles, including initiation and elongation. Finally, this assay can be used to monitor the effect of DNA lesions on fork progression, arrest and restart.
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Affiliation(s)
- Hélène Tourrière
- Institute of Human Genetics, CNRS UMR 9002 and University of Montpellier, Equipe labéllisée LIGUE 2017, Montpellier, France
| | - Julie Saksouk
- Institute of Human Genetics, CNRS UMR 9002 and University of Montpellier, Equipe labéllisée LIGUE 2017, Montpellier, France
| | - Armelle Lengronne
- Institute of Human Genetics, CNRS UMR 9002 and University of Montpellier, Equipe labéllisée LIGUE 2017, Montpellier, France
| | - Philippe Pasero
- Institute of Human Genetics, CNRS UMR 9002 and University of Montpellier, Equipe labéllisée LIGUE 2017, Montpellier, France
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15
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Sanders MA, Haynes B, Nangia-Makker P, Polin LA, Shekhar MP. Pharmacological targeting of RAD6 enzyme-mediated translesion synthesis overcomes resistance to platinum-based drugs. J Biol Chem 2017; 292:10347-10363. [PMID: 28490629 DOI: 10.1074/jbc.m117.792192] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 05/08/2017] [Indexed: 12/13/2022] Open
Abstract
Platinum drug-induced cross-link repair requires the concerted activities of translesion synthesis (TLS), Fanconi anemia (FA), and homologous recombination repair pathways. The E2 ubiquitin-conjugating enzyme RAD6 is essential for TLS. Here, we show that RAD6 plays a universal role in platinum-based drug tolerance. Using a novel RAD6-selective small-molecule inhibitor (SMI#9) targeting the RAD6 catalytic site, we demonstrate that SMI#9 potentiates the sensitivities of cancer cells with innate or acquired cisplatin or oxaliplatin resistance. 5-Iododeoxyuridine/5-chlorodeoxyuridine pulse-labeling experiments showed that RAD6 is necessary for overcoming cisplatin-induced replication fork stalling, as replication-restart was impaired in both SMI#9-pretreated and RAD6B-silenced cells. Consistent with the role of RAD6/TLS in late-S phase, SMI#9-induced DNA replication inhibition occurred preferentially in mid/late-S phase. The compromised DNA repair and chemosensitization induced by SMI#9 or RAD6B depletion were associated with decreased platinum drug-induced proliferating cell nuclear antigen (PCNA) and FANCD2 monoubiquitinations (surrogate markers of TLS and FA pathway activation, respectively) and with attenuated FANCD2, RAD6, γH2AX, and POL η foci formation and cisplatin-adduct removal. SMI#9 pretreatment synergistically increased cisplatin inhibition of MDA-MB-231 triple-negative breast cancer cell proliferation and tumor growth. Using an isogenic HCT116 colon cancer model of oxaliplatin resistance, we further show that γH2AX and monoubiquitinated PCNA and FANCD2 are constitutively up-regulated in oxaliplatin-resistant HCT116 (HCT116-OxR) cells and that γH2AX, PCNA, and FANCD2 monoubiquitinations are induced by oxaliplatin in parental HCT116 cells. SMI#9 pretreatment sensitized HCT116-OxR cells to oxaliplatin. These data deepen insights into the vital role of RAD6/TLS in platinum drug tolerance and reveal clinical benefits of targeting RAD6 with SMI#9 for managing chemoresistant cancers.
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Affiliation(s)
- Matthew A Sanders
- From the Karmanos Cancer Institute and.,the Departments of Oncology and
| | - Brittany Haynes
- From the Karmanos Cancer Institute and.,the Departments of Oncology and
| | - Pratima Nangia-Makker
- From the Karmanos Cancer Institute and.,Pathology, Wayne State University School of Medicine, Detroit, Michigan 48201
| | - Lisa A Polin
- From the Karmanos Cancer Institute and.,the Departments of Oncology and
| | - Malathy P Shekhar
- From the Karmanos Cancer Institute and .,the Departments of Oncology and.,Pathology, Wayne State University School of Medicine, Detroit, Michigan 48201
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16
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Abstract
Understanding the mechanisms of replication stress response following genotoxic stress induction is rapidly emerging as a central theme in cell survival and human disease. The DNA fiber assay is one of the most powerful tools to study alterations in replication fork dynamics genome-wide at single-molecule resolution. This approach relies on the ability of many organisms to incorporate thymidine analogs into replicating DNA and is widely used to study how genotoxic agents perturb DNA replication. Here, we review different approaches available to prepare DNA fibers and discuss important limitations of each approach. We also review how DNA fiber analysis can be used to shed light upon several replication parameters including fork progression, restart, termination, and new origin firing. Next, we discuss a modified DNA fiber protocol to monitor the presence of single-stranded DNA (ssDNA) gaps on ongoing replication forks. ssDNA gaps are very common intermediates of several replication stress response mechanisms, but they cannot be detected by standard DNA fiber approaches due to the resolution limits of this technique. We discuss a novel strategy that relies on the use of an ssDNA-specific endonuclease to nick the ssDNA gaps and generate shorter DNA fibers that can be used as readout for the presence of ssDNA gaps. Finally, we describe a follow-up DNA fiber approach that can be used to study how ssDNA gaps are repaired postreplicatively.
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Affiliation(s)
- Annabel Quinet
- Saint Louis University School of Medicine, St. Louis, MO, United States
| | | | - Delphine Lemacon
- Saint Louis University School of Medicine, St. Louis, MO, United States
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17
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Nikolova T, Göder A, Parplys A, Borgmann K. DNA Fiber Spreading Assay to Test HDACi Effects on DNA and Its Replication. Methods Mol Biol 2017; 1510:103-113. [PMID: 27761816 DOI: 10.1007/978-1-4939-6527-4_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
DNA fiber spreading assay is an invaluable technique to visualize and follow the spatial and temporal progress of individual DNA replication forks. It provides information on the DNA replication progress and its regulation under normal conditions as well as on replication stress induced by environmental genotoxic agents or cancer drugs. The method relies on the detection of incorporated thymidine analogues during DNA synthesis in the S phase of the cell cycle by indirect immunofluorescence. Here, we describe the procedure established in our laboratories for sequential pulse labeling of human cells with 5-chloro-2'-deoxyuridine (CldU) and 5-iodo-2'-deoxyuridine (IdU), cell lysis, and DNA fiber spreading on slides and sequential immunodetection of the incorporated thymidine analogues by primary antibodies recognizing specifically CldU or IdU alone. We describe also the laser scanning imaging, classification, and measurement of the detected DNA fiber tracks. The obtained quantitative data can be evaluated statistically to reveal the immediate or long-term effects of DNA-damaging agents, DNA repair inhibitors, and epigenetic modulators like HDAC inhibitors on DNA replication in normal and tumor cells.
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Affiliation(s)
- Teodora Nikolova
- Institute of Toxicology, University Medical Center Mainz, Mainz, Germany.
| | - Anja Göder
- Institute of Toxicology, University Medical Center Mainz, Mainz, Germany
| | - Ann Parplys
- Laboratory of Radiobiology Experimental Radiooncology, Clinic of Radiotherapy and Radiooncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kerstin Borgmann
- Laboratory of Radiobiology Experimental Radiooncology, Clinic of Radiotherapy and Radiooncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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18
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Vindigni A, Lopes M. Combining electron microscopy with single molecule DNA fiber approaches to study DNA replication dynamics. Biophys Chem 2016; 225:3-9. [PMID: 27939387 DOI: 10.1016/j.bpc.2016.11.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 11/30/2016] [Accepted: 11/30/2016] [Indexed: 10/20/2022]
Abstract
Replication stress is a crucial driver of genomic instability. Understanding the mechanisms of replication stress response is instrumental to improve diagnosis and treatment of human disease. Electron microscopy (EM) is currently the technique of choice to directly visualize a high number of replication intermediates and to monitor their remodeling upon stress. At the same time, DNA fiber analysis is useful to gain mechanistic insight on how genotoxic agents perturb replication fork dynamics genome-wide at single-molecule resolution. Combining these techniques has proven invaluable to achieve a comprehensive view of the mechanisms that ensure error-free processing of damaged replication forks. Here, we review how EM and single-molecule DNA fiber approaches can be used together to shed light into the mechanisms of replication stress response and discuss important cautions to be taken into account when comparing results obtained by EM and DNA fiber.
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Affiliation(s)
- Alessandro Vindigni
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA.
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland.
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19
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Lacroix J, Pélofy S, Blatché C, Pillaire MJ, Huet S, Chapuis C, Hoffmann JS, Bancaud A. Analysis of DNA Replication by Optical Mapping in Nanochannels. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:5963-5970. [PMID: 27624455 DOI: 10.1002/smll.201503795] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 06/21/2016] [Indexed: 06/06/2023]
Abstract
DNA replication is essential to maintain genome integrity in S phase of the cell division cycle. Accumulation of stalled replication forks is a major source of genetic instability, and likely constitutes a key driver of tumorigenesis. The mechanisms of regulation of replication fork progression have therefore been extensively investigated, in particular with DNA combing, an optical mapping technique that allows the stretching of single molecules and the mapping of active region for DNA synthesis by fluorescence microscopy. DNA linearization in nanochannels has been successfully used to probe genomic information patterns along single chromosomes, and has been proposed to be a competitive alternative to DNA combing. Yet this conjecture remains to be confirmed experimentally. Here, two complementary techniques are established to detect the genomic distribution of tracks of newly synthesized DNA in human cells by optical mapping in nanochannels. Their respective advantages and limitations are compared, and applied them to detect deregulations of the replication program induced by the antitumor drug hydroxyurea. The developments here thus broaden the field of applications accessible to nanofluidic technologies, and can be used in the future as part for molecular diagnostics in the context of high throughput cancer drug screening.
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Affiliation(s)
- Joris Lacroix
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400, Toulouse, France
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
| | - Sandrine Pélofy
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400, Toulouse, France
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
| | - Charline Blatché
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400, Toulouse, France
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
| | - Marie-Jeanne Pillaire
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
- Equipe "Labellisée LA LIGUE CONTRE LE CANCER 2013" - Laboratoire d'Excellence Toulouse Cancer LABEX TOUCAN - Cancer Research Center of Toulouse, Inserm U1037, CNRS ERL5294, 2 Avenue Hubert Curien, CS 53717, 31037, Toulouse, France
| | - Sébastien Huet
- CNRS, UMR 6061, Institut Génétique et Développement de Rennes, F-35043, Rennes, France
- Université Rennes 1, UEB, UMR 6290, Faculté de Médecine, F-35043, Rennes, France
| | - Catherine Chapuis
- CNRS, UMR 6061, Institut Génétique et Développement de Rennes, F-35043, Rennes, France
- Université Rennes 1, UEB, UMR 6290, Faculté de Médecine, F-35043, Rennes, France
| | - Jean-Sébastien Hoffmann
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
- Equipe "Labellisée LA LIGUE CONTRE LE CANCER 2013" - Laboratoire d'Excellence Toulouse Cancer LABEX TOUCAN - Cancer Research Center of Toulouse, Inserm U1037, CNRS ERL5294, 2 Avenue Hubert Curien, CS 53717, 31037, Toulouse, France
| | - Aurélien Bancaud
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400, Toulouse, France
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
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20
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The Replicative Consequences of Papillomavirus E2 Protein Binding to the Origin Replication Factor ORC2. PLoS Pathog 2016; 12:e1005934. [PMID: 27701460 PMCID: PMC5049798 DOI: 10.1371/journal.ppat.1005934] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 09/13/2016] [Indexed: 12/20/2022] Open
Abstract
The origin recognition complex (ORC) coordinates a series of events that lead to initiation of DNA strand duplication. As a nuclear double stranded DNA plasmid, the papillomavirus (PV) genome resembles a mini-chromosome in infected cells. To initiate its replication, the viral E2 protein binds to and recruits the E1 DNA helicase at the viral origin. PV genome replication program exhibits three stages: initial amplification from a single genome upon infection to a few copies per cell, a cell cycle linked maintenance phase, and a differentiation dependent late stage where the genome is amplified to thousands of copies. Involvement of ORC or other pre-replication complex (pre-RC) factors has not been described. We report that human PV (HPV) and bovine PV (BPV-1) E2 proteins bind to ORC2, however, ORC2 was not detected at the viral origin. Depletion of ORC2 enhanced PV replication in a transient replication model and in keratinocytes stably maintaining viral episomes, while there was no effect on copy number in a cell line with integrated HPV genomes. Consistent with this, occupancy of E1 and E2 at the viral origin increased following ORC2 silencing. These data imply that ORC2 is not necessary for activation of the PV origin by E1 and E2 but instead suppresses E2 replicative function. Furthermore, we observed that over-expression of HPV E2 decreased ORC2 occupation at two known mammalian origins of replication, suggesting that E2 restricts pre-ORC assembly that could otherwise compete for host replication complexes necessary for viral genome amplification. We infer that the ORC2 complex with E2 restricts viral replication in the maintenance phase of the viral replication program and that elevated levels of E2 that occur during the differentiation dependent amplification stage subvert ORC loading and hence DNA synthesis at cellular origins. Papillomavirus genome replication occurs during three distinct stages that are linked to the differentiation state of the infected epithelium. The viral proteins E1 and E2 recognize the viral origin and initiate a process that attracts host DNA replication factors. The origin recognition complex (ORC) coordinates initiation of chromosome duplication. While ORC2 binds to the E2 protein, its depletion does not impair PV genome replication. Instead, depletion of ORC2 stimulates viral replication, while over-expression of E2 protein decreases ORC2 occupancy at mammalian origins. We propose that the relative abundance of E2 and ORC2 in complex regulates viral and cellular origin licensing.
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21
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Langley AR, Gräf S, Smith JC, Krude T. Genome-wide identification and characterisation of human DNA replication origins by initiation site sequencing (ini-seq). Nucleic Acids Res 2016; 44:10230-10247. [PMID: 27587586 PMCID: PMC5137433 DOI: 10.1093/nar/gkw760] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/18/2016] [Accepted: 08/20/2016] [Indexed: 12/25/2022] Open
Abstract
Next-generation sequencing has enabled the genome-wide identification of human DNA replication origins. However, different approaches to mapping replication origins, namely (i) sequencing isolated small nascent DNA strands (SNS-seq); (ii) sequencing replication bubbles (bubble-seq) and (iii) sequencing Okazaki fragments (OK-seq), show only limited concordance. To address this controversy, we describe here an independent high-resolution origin mapping technique that we call initiation site sequencing (ini-seq). In this approach, newly replicated DNA is directly labelled with digoxigenin-dUTP near the sites of its initiation in a cell-free system. The labelled DNA is then immunoprecipitated and genomic locations are determined by DNA sequencing. Using this technique we identify >25,000 discrete origin sites at sub-kilobase resolution on the human genome, with high concordance between biological replicates. Most activated origins identified by ini-seq are found at transcriptional start sites and contain G-quadruplex (G4) motifs. They tend to cluster in early-replicating domains, providing a correlation between early replication timing and local density of activated origins. Origins identified by ini-seq show highest concordance with sites identified by SNS-seq, followed by OK-seq and bubble-seq. Furthermore, germline origins identified by positive nucleotide distribution skew jumps overlap with origins identified by ini-seq and OK-seq more frequently and more specifically than do sites identified by either SNS-seq or bubble-seq.
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Affiliation(s)
- Alexander R Langley
- Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK
| | - Stefan Gräf
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
- Department of Haematology, University of Cambridge, Cambridge CB2 0PT, UK
| | - James C Smith
- Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK
| | - Torsten Krude
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
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22
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Gallo D, Wang G, Yip CM, Brown GW. Analysis of Replicating Yeast Chromosomes by DNA Combing. Cold Spring Harb Protoc 2016; 2016:pdb.prot085118. [PMID: 26832684 DOI: 10.1101/pdb.prot085118] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Molecular combing of DNA fibers is a powerful technique to monitor origin usage and DNA replication fork progression in the budding yeast Saccharomyces cerevisiae. In contrast to traditional flow cytometry, microarray, or sequencing techniques, which provide population-level data, DNA combing provides DNA replication profiles of individual molecules. DNA combing uses yeast strains that express human thymidine kinase, which facilitates the incorporation of thymidine analogs into nascent DNA. First, DNA is isolated and stretched uniformly onto silanized glass coverslips. Following immunodetection with antibodies that recognize the thymidine analog and the DNA, the DNA fibers are imaged using a fluorescence microscope. Finally, the lengths of newly replicated DNA tracks are measured and converted to base pairs, allowing calculations of the speed of the replication fork and of interorigin distances. DNA combing can be applied to monitor replication defects caused by gene mutations or by chemical agents that induce replication stress. Here, we present a methodology for studying replicating yeast chromosomes by molecular DNA combing. We begin with procedures for the preparation of silanized coverslips and for assembly of a DNA combing machine (DCM) and conclude by presenting a detailed protocol for molecular DNA combing in yeast.
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Affiliation(s)
- David Gallo
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Gang Wang
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Christopher M Yip
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada; Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Grant W Brown
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
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23
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Irene C, Theis JF, Gresham D, Soteropoulos P, Newlon CS. Hst3p, a histone deacetylase, promotes maintenance of Saccharomyces cerevisiae chromosome III lacking efficient replication origins. Mol Genet Genomics 2015; 291:271-83. [PMID: 26319649 PMCID: PMC4729790 DOI: 10.1007/s00438-015-1105-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 08/12/2015] [Indexed: 01/15/2023]
Abstract
Long gaps between active replication origins probably occur frequently during chromosome replication, but little is known about how cells cope with them. To address this issue, we deleted replication origins from S. cerevisiae chromosome III to create chromosomes with long interorigin gaps and identified mutations that destabilize them [originless fragment maintenance (Ofm) mutations]. ofm6-1 is an allele of HST3, a sirtuin that deacetylates histone H3K56Ac. Hst3p and Hst4p are closely related, but hst4Δ does not cause an Ofm phenotype. Expressing HST4 under the control of the HST3 promoter suppressed the Ofm phenotype of hst3Δ, indicating Hst4p, when expressed at the appropriate levels and/or at the correct time, can fully substitute for Hst3p in maintenance of ORIΔ chromosomes. H3K56Ac is the Hst3p substrate critical for chromosome maintenance. H3K56Ac-containing nucleosomes are preferentially assembled into chromatin behind replication forks. Deletion of the H3K56 acetylase and downstream chromatin assembly factors suppressed the Ofm phenotype of hst3, indicating that persistence of H3K56Ac-containing chromatin is deleterious for the maintenance of ORIΔ chromosomes, and experiments with synchronous cultures showed that it is replication of H3K56Ac-containing chromatin that causes chromosome loss. This work shows that while normal chromosomes can tolerate hyperacetylation of H3K56Ac, deacetylation of histone H3K56Ac by Hst3p is required for stable maintenance of a chromosome with a long interorigin gap. The Ofm phenotype is the first report of a chromosome instability phenotype of an hst3 single mutant.
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Affiliation(s)
- Carmela Irene
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, ICPH, 225 Warren St., Newark, NJ, 07101-1701, USA
| | - James F Theis
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, ICPH, 225 Warren St., Newark, NJ, 07101-1701, USA
| | - David Gresham
- Department of Biology, Center for Genomics and System Biology, New York University, 100 Washington Square East, New York, NY, 10003, USA
| | - Patricia Soteropoulos
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, ICPH, 225 Warren St., Newark, NJ, 07101-1701, USA
| | - Carol S Newlon
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, ICPH, 225 Warren St., Newark, NJ, 07101-1701, USA.
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24
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Abstract
The intra-S phase checkpoint kinase of metazoa and yeast, ATR/MEC1, protects chromosomes from DNA damage and replication stress by phosphorylating subunits of the replicative helicase, MCM2-7. Here we describe an unprecedented ATR-dependent pathway in Tetrahymena thermophila in which the essential pre-replicative complex proteins, Orc1p, Orc2p and Mcm6p are degraded in hydroxyurea-treated S phase cells. Chromosomes undergo global changes during HU-arrest, including phosphorylation of histone H2A.X, deacetylation of histone H3, and an apparent diminution in DNA content that can be blocked by the deacetylase inhibitor sodium butyrate. Most remarkably, the cell cycle rapidly resumes upon hydroxyurea removal, and the entire genome is replicated prior to replenishment of ORC and MCMs. While stalled replication forks are elongated under these conditions, DNA fiber imaging revealed that most replicating molecules are produced by new initiation events. Furthermore, the sole origin in the ribosomal DNA minichromosome is inactive and replication appears to initiate near the rRNA promoter. The collective data raise the possibility that replication initiation occurs by an ORC-independent mechanism during the recovery from HU-induced replication stress. DNA damage and replication stress activate cell cycle checkpoint responses that protect the integrity of eukaryotic chromosomes. A well-conserved response involves the reversible phosphorylation of the replicative helicase, MCM2-7, which together with the origin recognition complex (ORC) dictates when and where replication initiates in chromosomes. The central role of ORC and MCMs in DNA replication is illustrated by the fact that small changes in abundance of these pre-replicative complex (pre-RC) components are poorly tolerated from yeast to humans. Here we describe an unprecedented replication stress checkpoint response in the early branching eukaryote, Tetrahymena thermophila, that is triggered by the depletion of dNTP pools with hydroxyurea (HU). Instead of transiently phosphorylating MCM subunits, ORC and MCM proteins are physically degraded in HU-treated Tetrahymena. Unexpectedly, upon HU removal the genome is completely and effortlessly replicated prior to replenishment of ORC and MCM components. Using DNA fiber imaging and 2D gel electrophoresis, we show that ORC-dependent mechanisms are bypassed during the recovery phase to produce bidirectional replication forks throughout the genome. Our findings suggest that Tetrahymena enlists an alternative mechanism for replication initiation, and that the underlying process can operate on a genome-wide scale.
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Affiliation(s)
- Pamela Y. Sandoval
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas, United States of America
| | - Po-Hsuen Lee
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, Texas, United States of America
| | - Xiangzhou Meng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Geoffrey M. Kapler
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas, United States of America
- Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, College Station, Texas, United States of America
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
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25
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Dobbelstein M, Sørensen CS. Exploiting replicative stress to treat cancer. Nat Rev Drug Discov 2015; 14:405-23. [PMID: 25953507 DOI: 10.1038/nrd4553] [Citation(s) in RCA: 215] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA replication in cancer cells is accompanied by stalling and collapse of the replication fork and signalling in response to DNA damage and/or premature mitosis; these processes are collectively known as 'replicative stress'. Progress is being made to increase our understanding of the mechanisms that govern replicative stress, thus providing ample opportunities to enhance replicative stress for therapeutic purposes. Rather than trying to halt cell cycle progression, cancer therapeutics could aim to increase replicative stress by further loosening the checkpoints that remain available to cancer cells and ultimately inducing the catastrophic failure of proliferative machineries. In this Review, we outline current and future approaches to achieve this, emphasizing the combination of conventional chemotherapy with targeted approaches.
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Affiliation(s)
- Matthias Dobbelstein
- Institute of Molecular Oncology, Göttingen Center of Molecular Biosciences, Ernst Caspari Haus, University of Göttingen, 37077 Göttingen, Germany
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26
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Kaykov A, Nurse P. The spatial and temporal organization of origin firing during the S-phase of fission yeast. Genome Res 2015; 25:391-401. [PMID: 25650245 PMCID: PMC4352884 DOI: 10.1101/gr.180372.114] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 12/29/2014] [Indexed: 11/25/2022]
Abstract
Eukaryotes duplicate their genomes using multiple replication origins, but the organization of origin firing along chromosomes and during S-phase is not well understood. Using fission yeast, we report the first genome-wide analysis of the spatial and temporal organization of replication origin firing, analyzed using single DNA molecules that can approach the full length of chromosomes. At S-phase onset, origins fire randomly and sparsely throughout the chromosomes. Later in S-phase, clusters of fired origins appear embedded in the sparser regions, which form the basis of nuclear replication foci. The formation of clusters requires proper histone methylation and acetylation, and their locations are not inherited between cell cycles. The rate of origin firing increases gradually, peaking just before mid S-phase. Toward the end of S-phase, nearly all the available origins within the unreplicated regions are fired, contributing to the timely completion of genome replication. We propose that the majority of origins do not fire as a part of a deterministic program. Instead, origin firing, both individually and as clusters, should be viewed as being mostly stochastic.
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Affiliation(s)
- Atanas Kaykov
- The Rockefeller University, New York, New York 10065, USA;
| | - Paul Nurse
- The Rockefeller University, New York, New York 10065, USA; The Francis Crick Institute, Lincoln's Inn Fields Laboratories, London WC2A 3LY, United Kingdom
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27
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Peng C, Luo H, Zhang X, Gao F. Recent advances in the genome-wide study of DNA replication origins in yeast. Front Microbiol 2015; 6:117. [PMID: 25745419 PMCID: PMC4333867 DOI: 10.3389/fmicb.2015.00117] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 01/29/2015] [Indexed: 11/13/2022] Open
Abstract
DNA replication, one of the central events in the cell cycle, is the basis of biological inheritance. In order to be duplicated, a DNA double helix must be opened at defined sites, which are called DNA replication origins (ORIs). Unlike in bacteria, where replication initiates from a single replication origin, multiple origins are utilized in the eukaryotic genomes. Among them, the ORIs in budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe have been best characterized. In recent years, advances in DNA microarray and next-generation sequencing technologies have increased the number of yeast species involved in ORIs research dramatically. The ORIs in some non-conventional yeast species such as Kluyveromyces lactis and Pichia pastoris have also been genome-widely identified. Relevant databases of replication origins in yeast were constructed, then the comparative genomic analysis can be carried out. Here, we review several experimental approaches that have been used to map replication origins in yeast and some of the available web resources related to yeast ORIs. We also discuss the sequence characteristics and chromosome structures of ORIs in the four yeast species, which can be utilized to improve yeast replication origins prediction.
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Affiliation(s)
- Chong Peng
- Department of Physics, Tianjin University , Tianjin, China
| | - Hao Luo
- Department of Physics, Tianjin University , Tianjin, China
| | - Xi Zhang
- Department of Physics, Tianjin University , Tianjin, China
| | - Feng Gao
- Department of Physics, Tianjin University , Tianjin, China ; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University , Tianjin, China ; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering , Tianjin, China
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28
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Dellino GI, Pelicci PG. Next-generation sequencing and DNA replication in human cells: the future has arrived. Future Oncol 2015; 10:683-93. [PMID: 24754597 DOI: 10.2217/fon.13.182] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Accurate regulation of DNA replication ensures faithful transmission of eukaryotic genomes and maintenance of genomic stability and chromatin organization. However, by itself the replication process is a threat for both DNA and chromatin integrity. This becomes particularly relevant in cancer cells, where activated oncogenes induce replication-stress, including unscheduled initiation, fork stalling and collapse and, ultimately, genomic instability. Studies addressing the relationship between (epi)genome integrity and disease have been hampered by our poor knowledge of the mechanisms regulating where and when eukaryotic replication initiates. Recently developed genome-scale methods for the analysis of DNA replication in mammals will contribute to the identification of missing links between replication, chromatin regulation and genome stability in normal and cancer cells.
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Affiliation(s)
- Gaetano Ivan Dellino
- Department of Experimental Oncology, European Institute of Oncology, 20141 Milan, Italy
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29
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End of the beginning: elongation and termination features of alternative modes of chromosomal replication initiation in bacteria. PLoS Genet 2015; 11:e1004909. [PMID: 25569209 PMCID: PMC4287441 DOI: 10.1371/journal.pgen.1004909] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In bacterial cells, bidirectional replication of the circular chromosome is initiated from a single origin (oriC) and terminates in an antipodal terminus region such that movement of the pair of replication forks is largely codirectional with transcription. The terminus region is flanked by discrete Ter sequences that act as polar, or direction-dependent, arrest sites for fork progression. Alternative oriC-independent modes of replication initiation are possible, one of which is constitutive stable DNA replication (cSDR) from transcription-associated RNA–DNA hybrids or R-loops. Here, I discuss the distinctive attributes of fork progression and termination associated with different modes of bacterial replication initiation. Two hypothetical models are proposed: that head-on collisions between pairs of replication forks, which are a feature of replication termination in all kingdoms of life, provoke bilateral fork reversal reactions; and that cSDR is characterized by existence of distinct subpopulations in bacterial cultures and a widespread distribution of origins in the genome, each with a small firing potential. Since R-loops are known to exist in eukaryotic cells and to inflict genome damage in G1 phase, it is possible that cSDR-like events promote aberrant replication initiation even in eukaryotes.
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30
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Deyle DR, Hansen RS, Cornea AM, Li LB, Burt AA, Alexander IE, Sandstrom RS, Stamatoyannopoulos JA, Wei CL, Russell DW. A genome-wide map of adeno-associated virus-mediated human gene targeting. Nat Struct Mol Biol 2014; 21:969-75. [PMID: 25282150 PMCID: PMC4405182 DOI: 10.1038/nsmb.2895] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 08/27/2014] [Indexed: 02/03/2023]
Abstract
To determine which genomic features promote homologous recombination, we created a genome-wide map of gene targeting sites. We used an adeno-associated virus vector to target identical loci introduced as transcriptionally active retroviral vectors. A comparison of ~2,000 targeted and untargeted sites showed that targeting occurred throughout the human genome and was not influenced by the presence of nearby CpG islands, sequence repeats or DNase I-hypersensitive sites. Targeted sites were preferentially located within transcription units, especially when the target loci were transcribed in the opposite orientation to their surrounding chromosomal genes. We determined the impact of DNA replication by mapping replication forks, which revealed a preference for recombination at target loci transcribed toward an incoming fork. Our results constitute the first genome-wide screen of gene targeting in mammalian cells and demonstrate a strong recombinogenic effect of colliding polymerases.
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Affiliation(s)
- David R Deyle
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - R Scott Hansen
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Anda M Cornea
- Department of Molecular and Cellular Biology, University of Washington, Seattle, Washington, USA
| | - Li B Li
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Amber A Burt
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute, Westmead, New South Wales, Australia
| | - Richard S Sandstrom
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | | | - Chia-Lin Wei
- Genomic Technologies Department, Joint Genome Institute, Walnut Creek, California, USA
| | - David W Russell
- 1] Department of Medicine, University of Washington, Seattle, Washington, USA. [2] Department of Biochemistry, University of Washington, Seattle, Washington, USA
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31
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Abstract
Analysis of the formation of extended chromatin fibers (ECFs) in response to the action of gravity following lysis by hypertonic and detergent solutions is a useful technical procedure relevant for studies of the positioning of particular DNA signals on chromatin filaments. Additionally, if toluidine blue molecules are allowed to bind electrostatically to available DNA phosphates on ECFs, the birefringence brightness generated in these filaments, as observed by polarization microscopy, facilitates the description of the frequency of ECF formation and extension of the chromatin filaments generated. Thus, different patterns of DNA-nuclear matrix protein associations related to varying transcriptional activities and chromatin organization in isolated cells can be assessed. A technique for producing ECFs in different isolated cell types under variable physiological and/or pathological conditions is detailed in this chapter.
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Affiliation(s)
- Maria Luiza S Mello
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil
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32
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Tiengwe C, Marques CA, McCulloch R. Nuclear DNA replication initiation in kinetoplastid parasites: new insights into an ancient process. Trends Parasitol 2013; 30:27-36. [PMID: 24287149 DOI: 10.1016/j.pt.2013.10.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 10/28/2013] [Accepted: 10/30/2013] [Indexed: 12/23/2022]
Abstract
Nuclear DNA replication is, arguably, the central cellular process in eukaryotes, because it drives propagation of life and intersects with many other genome reactions. Perhaps surprisingly, our understanding of nuclear DNA replication in kinetoplastids was limited until a clutch of studies emerged recently, revealing new insight into both the machinery and genome-wide coordination of the reaction. Here, we discuss how these studies suggest that the earliest acting components of the kinetoplastid nuclear DNA replication machinery - the factors that demarcate sites of the replication initiation, termed origins - are diverged from model eukaryotes. In addition, we discuss how origin usage and replication dynamics relate to the highly unusual organisation of transcription in the genome of Trypanosoma brucei.
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Affiliation(s)
- Calvin Tiengwe
- The University of Glasgow, Wellcome Trust Centre for Molecular Parasitology and Institute of Infection, Immunity and Inflammation, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK; The Johns Hopkins University School of Medicine, Department of Cell Biology, Baltimore, MD, USA
| | - Catarina A Marques
- The University of Glasgow, Wellcome Trust Centre for Molecular Parasitology and Institute of Infection, Immunity and Inflammation, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK
| | - Richard McCulloch
- The University of Glasgow, Wellcome Trust Centre for Molecular Parasitology and Institute of Infection, Immunity and Inflammation, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, UK.
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33
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Hawkins M, Retkute R, Müller CA, Saner N, Tanaka TU, de Moura APS, Nieduszynski CA. High-resolution replication profiles define the stochastic nature of genome replication initiation and termination. Cell Rep 2013; 5:1132-41. [PMID: 24210825 PMCID: PMC3898788 DOI: 10.1016/j.celrep.2013.10.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 09/18/2013] [Accepted: 10/07/2013] [Indexed: 12/23/2022] Open
Abstract
Eukaryotic genome replication is stochastic, and each cell uses a different cohort of replication origins. We demonstrate that interpreting high-resolution Saccharomyces cerevisiae genome replication data with a mathematical model allows quantification of the stochastic nature of genome replication, including the efficiency of each origin and the distribution of termination events. Single-cell measurements support the inferred values for stochastic origin activation time. A strain, in which three origins were inactivated, confirmed that the distribution of termination events is primarily dictated by the stochastic activation time of origins. Cell-to-cell variability in origin activity ensures that termination events are widely distributed across virtually the whole genome. We propose that the heterogeneity in origin usage contributes to genome stability by limiting potentially deleterious events from accumulating at particular loci. Deep sequencing reveals a high-resolution view of genome replication dynamics Genome-wide modeling and single-cell imaging reveal stochastic origin activity Origin activity determines the location of replication termination events Termination events are widely distributed across the whole genome
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Affiliation(s)
- Michelle Hawkins
- Centre for Genetics and Genomics, School of Life Sciences, Queen's Medical Centre, The University of Nottingham, Nottingham NG7 2UH, UK
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34
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Abstract
The minichromosome maintenance (MCM) complex, which plays multiple important roles in DNA replication, is loaded onto chromatin following mitosis, remains on chromatin until the completion of DNA synthesis, and then is unloaded by a poorly defined mechanism that involves the MCM binding protein (MCM-BP). Here we show that MCM-BP directly interacts with the ubiquitin-specific protease USP7, that this interaction occurs predominantly on chromatin, and that MCM-BP can tether USP7 to MCM proteins. Detailed biochemical and structure analyses of the USP7-MCM-BP interaction showed that the (155)PSTS(158) MCM-BP sequence mediates critical interactions with the TRAF domain binding pocket of USP7. Analysis of the effects of USP7 knockout on DNA replication revealed that lack of USP7 results in slowed progression through late S phase without globally affecting the fork rate or origin usage. Lack of USP7 also resulted in increased levels of MCM proteins on chromatin, and investigation of the cause of this increase revealed a defect in the dissociation of MCM proteins from chromatin in mid- to late S phase. This role of USP7 mirrors the previously described role for MCM-BP in MCM complex unloading and suggests that USP7 works with MCM-BP to unload MCM complexes from chromatin at the end of S phase.
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35
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Saner N, Karschau J, Natsume T, Gierliński M, Retkute R, Hawkins M, Nieduszynski CA, Blow JJ, de Moura AP, Tanaka TU. Stochastic association of neighboring replicons creates replication factories in budding yeast. J Cell Biol 2013; 202:1001-12. [PMID: 24062338 PMCID: PMC3787376 DOI: 10.1083/jcb.201306143] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 08/26/2013] [Indexed: 01/03/2023] Open
Abstract
Inside the nucleus, DNA replication is organized at discrete sites called replication factories, consisting of DNA polymerases and other replication proteins. Replication factories play important roles in coordinating replication and in responding to replication stress. However, it remains unknown how replicons are organized for processing at each replication factory. Here we address this question using budding yeast. We analyze how individual replicons dynamically organized a replication factory using live-cell imaging and investigate how replication factories were structured using super-resolution microscopy. Surprisingly, we show that the grouping of replicons within factories is highly variable from cell to cell. Once associated, however, replicons stay together relatively stably to maintain replication factories. We derive a coherent genome-wide mathematical model showing how neighboring replicons became associated stochastically to form replication factories, which was validated by independent microscopy-based analyses. This study not only reveals the fundamental principles promoting replication factory organization in budding yeast, but also provides insight into general mechanisms by which chromosomes organize sub-nuclear structures.
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Affiliation(s)
- Nazan Saner
- Centre for Gene Regulation and Expression, and Data Analysis Group, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Jens Karschau
- Institute for Complex Systems and Mathematical Biology, SUPA, School of Natural and Computing Sciences, University of Aberdeen, Aberdeen AB24 3UE, Scotland, UK
| | - Toyoaki Natsume
- Centre for Gene Regulation and Expression, and Data Analysis Group, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Marek Gierliński
- Centre for Gene Regulation and Expression, and Data Analysis Group, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Renata Retkute
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, Nottingham NG7 2UH, England, UK
| | - Michelle Hawkins
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, Nottingham NG7 2UH, England, UK
| | - Conrad A. Nieduszynski
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, Nottingham NG7 2UH, England, UK
| | - J. Julian Blow
- Centre for Gene Regulation and Expression, and Data Analysis Group, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Alessandro P.S. de Moura
- Institute for Complex Systems and Mathematical Biology, SUPA, School of Natural and Computing Sciences, University of Aberdeen, Aberdeen AB24 3UE, Scotland, UK
| | - Tomoyuki U. Tanaka
- Centre for Gene Regulation and Expression, and Data Analysis Group, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
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36
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Yoshida K, Poveda A, Pasero P. Time to be versatile: regulation of the replication timing program in budding yeast. J Mol Biol 2013; 425:4696-705. [PMID: 24076190 DOI: 10.1016/j.jmb.2013.09.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/17/2013] [Accepted: 09/18/2013] [Indexed: 01/24/2023]
Abstract
Eukaryotic replication origins are activated at different times during the S phase of the cell cycle, following a temporal program that is stably transmitted to daughter cells. Although the mechanisms that control initiation at the level of individual origins are now well understood, much less is known on how cells coordinate replication at hundreds of origins distributed on the chromosomes. In this review, we discuss recent advances shedding new light on how this complex process is regulated in the budding yeast Saccharomyces cerevisiae. The picture that emerges from these studies is that replication timing is regulated in cis by mechanisms modulating the chromatin structure and the subnuclear organization of origins. These mechanisms do not affect the licensing of replication origins but determine their ability to compete for limiting initiation factors, which are recycled from early to late origins throughout the length of the S phase.
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Affiliation(s)
- Kazumasa Yoshida
- Institute of Human Genetics, CNRS UPR 1142, 141 rue de la Cardonille, Equipe Labellisée Ligue Contre le Cancer, 34396 Montpellier cedex 5, France; Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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37
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Técher H, Koundrioukoff S, Azar D, Wilhelm T, Carignon S, Brison O, Debatisse M, Le Tallec B. Replication dynamics: biases and robustness of DNA fiber analysis. J Mol Biol 2013; 425:4845-55. [PMID: 23557832 DOI: 10.1016/j.jmb.2013.03.040] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 03/22/2013] [Accepted: 03/25/2013] [Indexed: 12/11/2022]
Abstract
The factors that govern replication programs are still poorly identified in metazoans, especially in mammalian cells. Thanks to molecular combing, the dynamics of DNA replication can be assessed at the genome-scale level from the cumulative analysis of single DNA fibers. This technique notably enables measurement of replication fork speed and fork asymmetry and that of distances separating either initiation or termination events. The results presented here aim to evaluate requirements critical to accurate measurement of replication parameters by molecular combing. We show that sample size, fiber length and DNA counterstaining are crucial to gain robust information concerning replication dynamics. Our results thus provide a methodological frame to investigate the DNA replication program through molecular combing analyses.
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Affiliation(s)
- Hervé Técher
- Institut Curie, Centre de Recherche, 26 rue d'Ulm, 75248 Paris Cedex 05, France; Université Pierre et Marie Curie Paris 06, 4 Place Jussieu, 75005 Paris, France; Centre National de la Recherche Scientifique, Unité Mixte de Recherche 3244, 75248 Paris Cedex 05, France
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38
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Manthei KA, Keck JL. The BLM dissolvasome in DNA replication and repair. Cell Mol Life Sci 2013; 70:4067-84. [PMID: 23543275 DOI: 10.1007/s00018-013-1325-1] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 02/21/2013] [Accepted: 03/14/2013] [Indexed: 02/07/2023]
Abstract
RecQ DNA helicases are critical for proper maintenance of genomic stability, and mutations in multiple human RecQ genes are linked with genetic disorders characterized by a predisposition to cancer. RecQ proteins are conserved from prokaryotes to humans and in all cases form higher-order complexes with other proteins to efficiently execute their cellular functions. The focus of this review is a conserved complex that is formed between RecQ helicases and type-I topoisomerases. In humans, this complex is referred to as the BLM dissolvasome or BTR complex, and is comprised of the RecQ helicase BLM, topoisomerase IIIα, and the RMI proteins. The BLM dissolvasome functions to resolve linked DNA intermediates without exchange of genetic material, which is critical in somatic cells. We will review the history of this complex and highlight its roles in DNA replication, recombination, and repair. Additionally, we will review recently established interactions between BLM dissolvasome and a second set of genome maintenance factors (the Fanconi anemia proteins) that appear to allow coordinated genome maintenance efforts between the two systems.
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Affiliation(s)
- Kelly A Manthei
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706, USA
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39
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Van der Aa N, Cheng J, Mateiu L, Zamani Esteki M, Kumar P, Dimitriadou E, Vanneste E, Moreau Y, Vermeesch JR, Voet T. Genome-wide copy number profiling of single cells in S-phase reveals DNA-replication domains. Nucleic Acids Res 2013; 41:e66. [PMID: 23295674 PMCID: PMC3616740 DOI: 10.1093/nar/gks1352] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Single-cell genomics is revolutionizing basic genome research and clinical genetic diagnosis. However, none of the current research or clinical methods for single-cell analysis distinguishes between the analysis of a cell in G1-, S- or G2/M-phase of the cell cycle. Here, we demonstrate by means of array comparative genomic hybridization that charting the DNA copy number landscape of a cell in S-phase requires conceptually different approaches to that of a cell in G1- or G2/M-phase. Remarkably, despite single-cell whole-genome amplification artifacts, the log2 intensity ratios of single S-phase cells oscillate according to early and late replication domains, which in turn leads to the detection of significantly more DNA imbalances when compared with a cell in G1- or G2/M-phase. Although these DNA imbalances may, on the one hand, be falsely interpreted as genuine structural aberrations in the S-phase cell’s copy number profile and hence lead to misdiagnosis, on the other hand, the ability to detect replication domains genome wide in one cell has important applications in DNA-replication research. Genome-wide cell-type-specific early and late replicating domains have been identified by analyses of DNA from populations of cells, but cell-to-cell differences in DNA replication may be important in genome stability, disease aetiology and various other cellular processes.
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Affiliation(s)
- Niels Van der Aa
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
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40
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Agier N, Romano OM, Touzain F, Cosentino Lagomarsino M, Fischer G. The spatiotemporal program of replication in the genome of Lachancea kluyveri. Genome Biol Evol 2013; 5:370-88. [PMID: 23355306 PMCID: PMC3590768 DOI: 10.1093/gbe/evt014] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2013] [Indexed: 12/11/2022] Open
Abstract
We generated a genome-wide replication profile in the genome of Lachancea kluyveri and assessed the relationship between replication and base composition. This species diverged from Saccharomyces cerevisiae before the ancestral whole genome duplication. The genome comprises eight chromosomes among which a chromosomal arm of 1 Mb has a G + C-content much higher than the rest of the genome. We identified 252 active replication origins in L. kluyveri and found considerable divergence in origin location with S. cerevisiae and with Lachancea waltii. Although some global features of S. cerevisiae replication are conserved: Centromeres replicate early, whereas telomeres replicate late, we found that replication origins both in L. kluyveri and L. waltii do not behave as evolutionary fragile sites. In L. kluyveri, replication timing along chromosomes alternates between regions of early and late activating origins, except for the 1 Mb GC-rich chromosomal arm. This chromosomal arm contains an origin consensus motif different from other chromosomes and is replicated early during S-phase. We showed that precocious replication results from the specific absence of late firing origins in this chromosomal arm. In addition, we found a correlation between GC-content and distance from replication origins as well as a lack of replication-associated compositional skew between leading and lagging strands specifically in this GC-rich chromosomal arm. These findings suggest that the unusual base composition in the genome of L. kluyveri could be linked to replication.
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Affiliation(s)
- Nicolas Agier
- UPMC, UMR7238, Génomique des Microorganismes, Paris, France
- CNRS, UMR7238, Génomique des Microorganismes, Paris, France
| | | | - Fabrice Touzain
- UPMC, UMR7238, Génomique des Microorganismes, Paris, France
- CNRS, UMR7238, Génomique des Microorganismes, Paris, France
- Present address: ANSES, Ploufragan/Plouzané Laboratory Viral Genomics and Biosecurity Unit (GVB), Ploufragan, France
| | - Marco Cosentino Lagomarsino
- UPMC, UMR7238, Génomique des Microorganismes, Paris, France
- CNRS, UMR7238, Génomique des Microorganismes, Paris, France
| | - Gilles Fischer
- UPMC, UMR7238, Génomique des Microorganismes, Paris, France
- CNRS, UMR7238, Génomique des Microorganismes, Paris, France
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Dellino GI, Cittaro D, Piccioni R, Luzi L, Banfi S, Segalla S, Cesaroni M, Mendoza-Maldonado R, Giacca M, Pelicci PG. Genome-wide mapping of human DNA-replication origins: levels of transcription at ORC1 sites regulate origin selection and replication timing. Genome Res 2012. [PMID: 23187890 PMCID: PMC3530669 DOI: 10.1101/gr.142331.112] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We report the genome-wide mapping of ORC1 binding sites in mammals, by chromatin immunoprecipitation and parallel sequencing (ChIP-seq). ORC1 binding sites in HeLa cells were validated as active DNA replication origins (ORIs) using Repli-seq, a method that allows identification of ORI-containing regions by parallel sequencing of temporally ordered replicating DNA. ORC1 sites were universally associated with transcription start sites (TSSs) of coding or noncoding RNAs (ncRNAs). Transcription levels at the ORC1 sites directly correlated with replication timing, suggesting the existence of two classes of ORIs: those associated with moderate/high transcription levels (≥1 RNA copy/cell), firing in early S and mapping to the TSSs of coding RNAs; and those associated with low transcription levels (<1 RNA copy/cell), firing throughout the entire S and mapping to TSSs of ncRNAs. These findings are compatible with a scenario whereby TSS expression levels influence the efficiency of ORC1 recruitment at G1 and the probability of firing during S.
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Affiliation(s)
- Gaetano Ivan Dellino
- Department of Experimental Oncology, European Institute of Oncology, 20141 Milan, Italy.
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42
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Lin YL, Pasero P. Interference between DNA replication and transcription as a cause of genomic instability. Curr Genomics 2012; 13:65-73. [PMID: 22942676 PMCID: PMC3269018 DOI: 10.2174/138920212799034767] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 10/03/2011] [Accepted: 10/06/2011] [Indexed: 11/22/2022] Open
Abstract
Replication and transcription are key aspects of DNA metabolism that take place on the same template and potentially interfere with each other. Conflicts between these two activities include head-on or co-directional collisions between DNA and RNA polymerases, which can lead to the formation of DNA breaks and chromosome rearrangements. To avoid these deleterious consequences and prevent genomic instability, cells have evolved multiple mechanisms preventing replication forks from colliding with the transcription machinery. Yet, recent reports indicate that interference between replication and transcription is not limited to physical interactions between polymerases and that other cotranscriptional processes can interfere with DNA replication. These include DNA-RNA hybrids that assemble behind elongating RNA polymerases, impede fork progression and promote homologous recombination. Here, we discuss recent evidence indicating that R-loops represent a major source of genomic instability in all organisms, from bacteria to human, and are potentially implicated in cancer development.
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Affiliation(s)
- Yea-Lih Lin
- Institute of Human Genetics, CNRS-UPR1142, Montpellier, France
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43
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Retkute R, Nieduszynski CA, de Moura A. Mathematical modeling of genome replication. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:031916. [PMID: 23030953 PMCID: PMC3671344 DOI: 10.1103/physreve.86.031916] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 08/15/2012] [Indexed: 06/01/2023]
Abstract
Eukaryotic DNA replication is initiated from multiple sites on the chromosome, but little is known about the global and local regulation of replication. We present a mathematical model for the spatial dynamics of DNA replication, which offers insight into the kinetics of replication in different types of organisms. Most biological experiments involve average quantities over large cell populations (typically >10(7) cells) and therefore can mask the cell-to-cell variability present in the system. Although the model is formulated in terms of a population of cells, using mathematical analysis we show that one can obtain signatures of stochasticity in individual cells from averaged quantities. This work generalizes the result by Retkute et al. [Phys. Rev. Lett. 107, 068103 (2011)] to a broader set of parameter regimes.
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Affiliation(s)
- Renata Retkute
- Centre for Genetics and Genomics, University of Nottingham, Nottingham NG7 2UH, United Kingdom
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44
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Bianco JN, Poli J, Saksouk J, Bacal J, Silva MJ, Yoshida K, Lin YL, Tourrière H, Lengronne A, Pasero P. Analysis of DNA replication profiles in budding yeast and mammalian cells using DNA combing. Methods 2012; 57:149-57. [PMID: 22579803 DOI: 10.1016/j.ymeth.2012.04.007] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Revised: 04/11/2012] [Accepted: 04/14/2012] [Indexed: 11/17/2022] Open
Abstract
DNA combing is a powerful method developed by Bensimon and colleagues to stretch DNA molecules on silanized glass coverslips. This technique provides a unique way to monitor the activation of replication origins and the progression of replication forks at the level of single DNA molecules, after incorporation of thymidine analogs, such as 5-bromo-2'-deoxyuridine (BrdU), 5-iodo-2'-deoxyuridine (IdU) and 5-chloro-2'-deoxyuridine (CldU) in newly-synthesized DNA. Unlike microarray-based approaches, this assay gives access to the variability of replication profiles in individual cells. It can also be used to monitor the effect of DNA lesions on fork progression, arrest and restart. In this review, we propose standard DNA combing methods to analyze DNA replication in budding yeast and in human cells. We also show that 5-ethynyl-2'-deoxyuridine (EdU) can be used as a good alternative to BrdU for DNA combing analysis, as unlike halogenated nucleotides, it can be detected without prior denaturation of DNA.
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Affiliation(s)
- Julien N Bianco
- Institute of Human Genetics, CNRS UPR 1142, Montpellier F-34396, France
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45
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Retkute R, Nieduszynski CA, de Moura A. Dynamics of DNA replication in yeast. PHYSICAL REVIEW LETTERS 2011; 107:068103. [PMID: 21902372 PMCID: PMC3671325 DOI: 10.1103/physrevlett.107.068103] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Indexed: 05/05/2023]
Abstract
We present a mathematical model for the spatial dynamics of DNA replication. Using this model we determine the probability distribution for the time at which each chromosomal position is replicated. From this we show, contrary to previous reports, that mean replication time curves cannot be used to directly determine origin parameters. We demonstrate that the stochastic nature of replication dynamics leaves a clear signature in experimentally measured population average data, and we show that the width of the activation time probability distribution can be inferred from this data. Our results compare favorably with experimental measurements in Saccharomyces cerevisae.
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Affiliation(s)
- Renata Retkute
- Centre for Genetics and Genomics, University of Nottingham, United Kingdom
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46
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Ge XQ, Blow JJ. Chk1 inhibits replication factory activation but allows dormant origin firing in existing factories. ACTA ACUST UNITED AC 2010; 191:1285-97. [PMID: 21173116 PMCID: PMC3010067 DOI: 10.1083/jcb.201007074] [Citation(s) in RCA: 162] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
At low levels of replication stress, Chk1 favors resolving problems at stalled replication forks over initiating origin firing in unreplicated areas of the genome. Replication origins are licensed by loading MCM2-7 hexamers before entry into S phase. However, only ∼10% of licensed origins are normally used in S phase, with the others remaining dormant. When fork progression is inhibited, dormant origins initiate nearby to ensure that all of the DNA is eventually replicated. In apparent contrast, replicative stress activates ataxia telangiectasia and rad-3–related (ATR) and Chk1 checkpoint kinases that inhibit origin firing. In this study, we show that at low levels of replication stress, ATR/Chk1 predominantly suppresses origin initiation by inhibiting the activation of new replication factories, thereby reducing the number of active factories. At the same time, inhibition of replication fork progression allows dormant origins to initiate within existing replication factories. The inhibition of new factory activation by ATR/Chk1 therefore redirects replication toward active factories where forks are inhibited and away from regions that have yet to start replication. This minimizes the deleterious consequences of fork stalling and prevents similar problems from arising in unreplicated regions of the genome.
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Affiliation(s)
- Xin Quan Ge
- Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, Scotland, UK
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47
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Abstract
Single-molecule analyses of DNA replication have greatly advanced our understanding of mammalian replication restart. Several proteins that are not part of the core replication machinery promote the efficient restart of replication forks that have been stalled by replication inhibitors, suggesting that bona fide fork restart pathways exist in mammalian cells. Different models of replication fork restart can be envisaged, based on the involvement of DNA helicases, nucleases, homologous recombination factors and the importance of DNA double-strand break formation.
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48
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Abstract
Mechanisms regulating where and when eukaryotic DNA replication initiates remain a mystery. Recently, genome-scale methods have been brought to bear on this problem. The identification of replication origins and their associated proteins in yeasts is a well-integrated investigative tool, but corresponding data sets from multicellular organisms are scarce. By contrast, standardized protocols for evaluating replication timing have generated informative data sets for most eukaryotic systems. Here, I summarize the genome-scale methods that are most frequently used to analyse replication in eukaryotes, the kinds of questions each method can address and the technical hurdles that must be overcome to gain a complete understanding of the nature of eukaryotic replication origins.
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49
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S-phase progression in mammalian cells: modelling the influence of nuclear organization. Chromosome Res 2010; 18:163-78. [PMID: 20155315 DOI: 10.1007/s10577-010-9114-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The control of DNA replication is of fundamental importance as cell proliferation demands that identical copies of the genetic material are passed to the two daughter cells that form during mitosis. These genetic copies are generated in the preceding S phase, where the entire DNA complement of the mother cell must be copied exactly once. As part of this process, it is known that different regions of mammalian genomes are replicated at specific times of a temporally defined replication programme. The key feature of this programme is that active genes in euchromatin are replicated before inactive ones in heterochromatin. This separation of S phase into periods where different classes of chromatin are duplicated is important in maintaining changes in gene expression that define individual cell types. Recent attempts to understand the structure of the S-phase timing programme have focused on the use of genome-wide strategies that inevitably use DNA isolated from large cell populations for analysis. However, this approach provides a composite view of events that occur within a population without knowledge of the cell-to-cell variability across the population. In this review, we attempt to combine information generated using genome-wide and single cell strategies in order to develop a coherent molecular understanding of S-phase progression. During this integration, we have explored how available information can be introduced into a modelling environment that best describes S-phase progression in mammalian cells.
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50
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Liachko I, Bhaskar A, Lee C, Chung SCC, Tye BK, Keich U. A comprehensive genome-wide map of autonomously replicating sequences in a naive genome. PLoS Genet 2010; 6:e1000946. [PMID: 20485513 PMCID: PMC2869322 DOI: 10.1371/journal.pgen.1000946] [Citation(s) in RCA: 48] [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: 10/06/2009] [Accepted: 04/09/2010] [Indexed: 11/19/2022] Open
Abstract
Eukaryotic chromosomes initiate DNA synthesis from multiple replication origins. The machinery that initiates DNA synthesis is highly conserved, but the sites where the replication initiation proteins bind have diverged significantly. Functional comparative genomics is an obvious approach to study the evolution of replication origins. However, to date, the Saccharomyces cerevisiae replication origin map is the only genome map available. Using an iterative approach that combines computational prediction and functional validation, we have generated a high-resolution genome-wide map of DNA replication origins in Kluyveromyces lactis. Unlike other yeasts or metazoans, K. lactis autonomously replicating sequences (KlARSs) contain a 50 bp consensus motif suggestive of a dimeric structure. This motif is necessary and largely sufficient for initiation and was used to dependably identify 145 of the up to 156 non-repetitive intergenic ARSs projected for the K. lactis genome. Though similar in genome sizes, K. lactis has half as many ARSs as its distant relative S. cerevisiae. Comparative genomic analysis shows that ARSs in K. lactis and S. cerevisiae preferentially localize to non-syntenic intergenic regions, linking ARSs with loci of accelerated evolutionary change.
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Affiliation(s)
- Ivan Liachko
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Anand Bhaskar
- Department of Computer Science, Cornell University, Ithaca, New York, United States of America
| | - Chanmi Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Shau Chee Claire Chung
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Bik-Kwoon Tye
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- * E-mail:
| | - Uri Keich
- School of Mathematics and Statistics F07, University of Sydney, Sydney, Australia
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