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Maclay T, Whalen J, Johnson M, Freudenreich CH. The DNA Damage Checkpoint Targets the Kinetochore for Relocation of Collapsed Forks to the Periphery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.17.599319. [PMID: 38948692 PMCID: PMC11212917 DOI: 10.1101/2024.06.17.599319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Hairpin forming expanded CAG/CTG repeats pose significant challenges to DNA replication which can lead to replication fork collapse. Long CAG/CTG repeat tracts relocate to the nuclear pore complex to maintain their integrity. Forks impeded by DNA structures are known to activate the DNA damage checkpoint, thus we asked whether checkpoint proteins play a role in relocation of collapsed forks to the nuclear periphery in S. cerevisiae . We show that relocation of a (CAG/CTG) 130 tract is dependent on activation of the Mrc1/Rad53 replication checkpoint. Further, checkpoint-mediated phosphorylation of the kinetochore protein Cep3 is required for relocation, implicating detachment of the centromere from the spindle pole body. Activation of this pathway leads to DNA damage-induced microtubule recruitment to the repeat. These data suggest a role for the DNA replication checkpoint in facilitating movement of collapsed replication forks to the nuclear periphery by centromere release and microtubule-directed motion. Highlights The DNA damage checkpoint is needed for relocation of a structure-forming CAG repeat tract to the nuclear pore complexThe importance of Mrc1 (hClaspin) implicates fork uncoupling as the initial checkpoint signalPhosphorylation of the Cep3 kinetochore protein by Dun1 kinase modulates centromere release, which is critical for collapsed fork repositioningDamage-inducible nuclear microtubules colocalize with the CAG repeat locus and are required for relocalizationEstablishes a new role for the DNA replication and DNA damage checkpoint response to trigger repositioning of collapsed forks within the nucleus.
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2
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Meschichi A, Rosa S. Plant chromatin on the move: an overview of chromatin mobility during transcription and DNA repair. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:953-962. [PMID: 36811211 DOI: 10.1111/tpj.16159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/16/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
It has become increasingly clear in recent years that chromosomes are highly dynamic entities. Chromatin mobility and re-arrangement are involved in many biological processes, including gene regulation and the maintenance of genome stability. Despite extensive studies on chromatin mobility in yeast and animal systems, up until recently, not much had been investigated at this level in plants. For plants to achieve proper growth and development, they need to respond rapidly and appropriately to environmental stimuli. Therefore, understanding how chromatin mobility can support plant responses may offer profound insights into the functioning of plant genomes. In this review, we discuss the state of the art related to chromatin mobility in plants, including the available technologies for their role in various cellular processes.
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Affiliation(s)
- Anis Meschichi
- Plant Biology Department, Swedish University of Agricultural Sciences (SLU), Almas Allé 5, Uppsala, Sweden
| | - Stefanie Rosa
- Plant Biology Department, Swedish University of Agricultural Sciences (SLU), Almas Allé 5, Uppsala, Sweden
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3
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Kolbin D, Walker BL, Hult C, Stanton JD, Adalsteinsson D, Forest MG, Bloom K. Polymer Modeling Reveals Interplay between Physical Properties of Chromosomal DNA and the Size and Distribution of Condensin-Based Chromatin Loops. Genes (Basel) 2023; 14:2193. [PMID: 38137015 PMCID: PMC10742461 DOI: 10.3390/genes14122193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/28/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Transient DNA loops occur throughout the genome due to thermal fluctuations of DNA and the function of SMC complex proteins such as condensin and cohesin. Transient crosslinking within and between chromosomes and loop extrusion by SMCs have profound effects on high-order chromatin organization and exhibit specificity in cell type, cell cycle stage, and cellular environment. SMC complexes anchor one end to DNA with the other extending some distance and retracting to form a loop. How cells regulate loop sizes and how loops distribute along chromatin are emerging questions. To understand loop size regulation, we employed bead-spring polymer chain models of chromatin and the activity of an SMC complex on chromatin. Our study shows that (1) the stiffness of the chromatin polymer chain, (2) the tensile stiffness of chromatin crosslinking complexes such as condensin, and (3) the strength of the internal or external tethering of chromatin chains cooperatively dictate the loop size distribution and compaction volume of induced chromatin domains. When strong DNA tethers are invoked, loop size distributions are tuned by condensin stiffness. When DNA tethers are released, loop size distributions are tuned by chromatin stiffness. In this three-way interaction, the presence and strength of tethering unexpectedly dictates chromatin conformation within a topological domain.
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Affiliation(s)
- Daniel Kolbin
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (D.K.); (J.D.S.)
| | - Benjamin L. Walker
- Department of Mathematics, University of California-Irvine, Irvine, CA 92697, USA;
| | - Caitlin Hult
- Department of Mathematics, Gettysburg College, Gettysburg, PA 17325, USA
| | - John Donoghue Stanton
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (D.K.); (J.D.S.)
| | - David Adalsteinsson
- Department of Mathematics and Carolina Center for Interdisciplinary Applied Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (D.A.); (M.G.F.)
| | - M. Gregory Forest
- Department of Mathematics and Carolina Center for Interdisciplinary Applied Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (D.A.); (M.G.F.)
- Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (D.K.); (J.D.S.)
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4
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Vasquez PA, Walker B, Bloom K, Kolbin D, Caughman N, Freeman R, Lysy M, Hult C, Newhall KA, Papanikolas M, Edelmaier C, Forest MG. The power of weak, transient interactions across biology: A paradigm of emergent behavior. PHYSICA D. NONLINEAR PHENOMENA 2023; 454:133866. [PMID: 38274029 PMCID: PMC10806540 DOI: 10.1016/j.physd.2023.133866] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
A growing list of diverse biological systems and their equally diverse functionalities provides realizations of a paradigm of emergent behavior. In each of these biological systems, pervasive ensembles of weak, short-lived, spatially local interactions act autonomously to convey functionalities at larger spatial and temporal scales. In this article, a range of diverse systems and functionalities are presented in a cursory manner with literature citations for further details. Then two systems and their properties are discussed in more detail: yeast chromosome biology and human respiratory mucus.
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Affiliation(s)
- Paula A. Vasquez
- Department of Mathematics, University of South Carolina, United States of America
| | - Ben Walker
- Department of Mathematics, University of California at Irvine, United States of America
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, United States of America
| | - Daniel Kolbin
- Department of Biology, University of North Carolina at Chapel Hill, United States of America
| | - Neall Caughman
- Department of Mathematics, University of North Carolina at Chapel Hill, United States of America
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, United States of America
| | - Martin Lysy
- Department of Statistics and Actuarial Science, University of Waterloo, Canada
| | - Caitlin Hult
- Department of Mathematics, Gettysburg College, United States of America
| | - Katherine A. Newhall
- Department of Mathematics, University of North Carolina at Chapel Hill, United States of America
| | - Micah Papanikolas
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, United States of America
| | - Christopher Edelmaier
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, United States of America
- Center for Computational Biology, Flatiron Institute, United States of America
| | - M. Gregory Forest
- Department of Mathematics, University of North Carolina at Chapel Hill, United States of America
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, United States of America
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5
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García Fernández F, Huet S, Miné-Hattab J. Multi-Scale Imaging of the Dynamic Organization of Chromatin. Int J Mol Sci 2023; 24:15975. [PMID: 37958958 PMCID: PMC10649806 DOI: 10.3390/ijms242115975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Chromatin is now regarded as a heterogeneous and dynamic structure occupying a non-random position within the cell nucleus, where it plays a key role in regulating various functions of the genome. This current view of chromatin has emerged thanks to high spatiotemporal resolution imaging, among other new technologies developed in the last decade. In addition to challenging early assumptions of chromatin being regular and static, high spatiotemporal resolution imaging made it possible to visualize and characterize different chromatin structures such as clutches, domains and compartments. More specifically, super-resolution microscopy facilitates the study of different cellular processes at a nucleosome scale, providing a multi-scale view of chromatin behavior within the nucleus in different environments. In this review, we describe recent imaging techniques to study the dynamic organization of chromatin at high spatiotemporal resolution. We also discuss recent findings, elucidated by these techniques, on the chromatin landscape during different cellular processes, with an emphasis on the DNA damage response.
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Affiliation(s)
- Fabiola García Fernández
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, 75005 Paris, France;
| | - Sébastien Huet
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR 6290, BIOSIT-UMS 3480, 35000 Rennes, France;
- Institut Universitaire de France, 75231 Paris, France
| | - Judith Miné-Hattab
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, 75005 Paris, France;
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Scelfo A, Fachinetti D. Centromere: A Trojan horse for genome stability. DNA Repair (Amst) 2023; 130:103569. [PMID: 37708591 DOI: 10.1016/j.dnarep.2023.103569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/22/2023] [Accepted: 09/05/2023] [Indexed: 09/16/2023]
Abstract
Centromeres play a key role in the maintenance of genome stability to prevent carcinogenesis and diseases. They are specialized chromosome loci essential to ensure faithful transmission of genomic information across cell generations by mediating the interaction with spindle microtubules. Nonetheless, while fulfilling these essential roles, their distinct repetitive composition and susceptibility to mechanical stresses during cell division render them susceptible to breakage events. In this review, we delve into the present understanding of the underlying causes of centromere fragility, from the mechanisms governing its DNA replication and repair, to the pathways acting to counteract potential challenges. We propose that the centromere represents a "Trojan horse" exerting vital functions that, at the same time, potentially threatens whole genome stability.
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Affiliation(s)
- Andrea Scelfo
- Institut Curie, CNRS, UMR 144, Sorbonne University, 26 rue d'Ulm, 75005 Paris, France.
| | - Daniele Fachinetti
- Institut Curie, CNRS, UMR 144, Sorbonne University, 26 rue d'Ulm, 75005 Paris, France.
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Zagelbaum J, Gautier J. Double-strand break repair and mis-repair in 3D. DNA Repair (Amst) 2023; 121:103430. [PMID: 36436496 PMCID: PMC10799305 DOI: 10.1016/j.dnarep.2022.103430] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]
Abstract
DNA double-strand breaks (DSBs) are lesions that arise frequently from exposure to damaging agents as well as from ongoing physiological DNA transactions. Mis-repair of DSBs leads to rearrangements and structural variations in chromosomes, including insertions, deletions, and translocations implicated in disease. The DNA damage response (DDR) limits pathologic mutations and large-scale chromosome rearrangements. DSB repair initiates in 2D at DNA lesions with the stepwise recruitment of repair proteins and local chromatin remodeling which facilitates break accessibility. More complex structures are then formed via protein assembly into nanodomains and via genome folding into chromatin loops. Subsequently, 3D reorganization of DSBs is guided by clustering forces which drive the assembly of repair domains harboring multiple lesions. These domains are further stabilized and insulated into condensates via liquid-liquid phase-separation. Here, we discuss the benefits and risks associated with this 3D reorganization of the broken genome.
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Affiliation(s)
- Jennifer Zagelbaum
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jean Gautier
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Genetics and Development, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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8
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García Fernández F, Almayrac E, Carré Simon À, Batrin R, Khalil Y, Boissac M, Fabre E. Global chromatin mobility induced by a DSB is dictated by chromosomal conformation and defines the HR outcome. eLife 2022; 11:78015. [PMID: 36125964 PMCID: PMC9489209 DOI: 10.7554/elife.78015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 09/08/2022] [Indexed: 12/16/2022] Open
Abstract
Repair of DNA double-strand breaks (DSBs) is crucial for genome integrity. A conserved response to DSBs is an increase in chromatin mobility that can be local, at the site of the DSB, or global, at undamaged regions of the genome. Here, we address the function of global chromatin mobility during homologous recombination (HR) of a single, targeted, controlled DSB. We set up a system that tracks HR in vivo over time and show that two types of DSB-induced global chromatin mobility are involved in HR, depending on the position of the DSB. Close to the centromere, a DSB induces global mobility that depends solely on H2A(X) phosphorylation and accelerates repair kinetics, but is not essential. In contrast, the global mobility induced by a DSB away from the centromere becomes essential for HR repair and is triggered by homology search through a mechanism that depends on H2A(X) phosphorylation, checkpoint progression, and Rad51. Our data demonstrate that global mobility is governed by chromosomal conformation and differentially coordinates repair by HR.
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Affiliation(s)
| | - Etienne Almayrac
- Université de Paris, IRSL, INSERM, U944, CNRS, UMR7212, Paris, France
| | - Ànnia Carré Simon
- Université de Paris, IRSL, INSERM, U944, CNRS, UMR7212, Paris, France
| | - Renaud Batrin
- Université de Paris, IRSL, INSERM, U944, CNRS, UMR7212, Paris, France
| | - Yasmine Khalil
- Université de Paris, IRSL, INSERM, U944, CNRS, UMR7212, Paris, France
| | - Michel Boissac
- Université de Paris, IRSL, INSERM, U944, CNRS, UMR7212, Paris, France
| | - Emmanuelle Fabre
- Université de Paris, IRSL, INSERM, U944, CNRS, UMR7212, Paris, France
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9
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García Fernández F, Fabre E. The Dynamic Behavior of Chromatin in Response to DNA Double-Strand Breaks. Genes (Basel) 2022; 13:genes13020215. [PMID: 35205260 PMCID: PMC8872016 DOI: 10.3390/genes13020215] [Citation(s) in RCA: 4] [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] [Received: 12/03/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 02/05/2023] Open
Abstract
The primary functions of the eukaryotic nucleus as a site for the storage, retrieval, and replication of information require a highly dynamic chromatin organization, which can be affected by the presence of DNA damage. In response to double-strand breaks (DSBs), the mobility of chromatin at the break site is severely affected and, to a lesser extent, that of other chromosomes. The how and why of such movement has been widely studied over the last two decades, leading to different mechanistic models and proposed potential roles underlying both local and global mobility. Here, we review the state of the knowledge on current issues affecting chromatin mobility upon DSBs, and highlight its role as a crucial step in the DNA damage response (DDR).
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Affiliation(s)
- Fabiola García Fernández
- Institut Curie, CNRS UMR3664, Sorbonne Université, F-75005 Paris, France
- Correspondence: (F.G.F.); (E.F.)
| | - Emmanuelle Fabre
- Génomes Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Université de Paris, F-75010 Paris, France
- Correspondence: (F.G.F.); (E.F.)
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10
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3D Genome Organization: Causes and Consequences for DNA Damage and Repair. Genes (Basel) 2021; 13:genes13010007. [PMID: 35052348 PMCID: PMC8775012 DOI: 10.3390/genes13010007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/16/2021] [Accepted: 12/18/2021] [Indexed: 01/02/2023] Open
Abstract
The inability to repair damaged DNA severely compromises the integrity of any organism. In eukaryotes, the DNA damage response (DDR) operates within chromatin, a tightly organized DNA–histone complex in a non-random manner within the nucleus. Chromatin thus orchestrates various cellular processes, including repair. Here, we examine the chromatin landscape before, during, and after the DNA damage, focusing on double strand breaks (DSBs). We study how chromatin is modified during the repair process, not only around the damaged region (in cis), but also genome-wide (in trans). Recent evidence has highlighted a complex landscape in which different chromatin parameters (stiffness, compaction, loops) are transiently modified, defining “codes” for each specific stage of the DDR. We illustrate a novel aspect of DDR where chromatin modifications contribute to the movement of DSB-damaged chromatin, as well as undamaged chromatin, ensuring the mobilization of DSBs, their clustering, and their repair processes.
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11
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Liakopoulos D. Coupling DNA Replication and Spindle Function in Saccharomyces cerevisiae. Cells 2021; 10:cells10123359. [PMID: 34943867 PMCID: PMC8699587 DOI: 10.3390/cells10123359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/24/2021] [Accepted: 11/27/2021] [Indexed: 12/02/2022] Open
Abstract
In the yeast Saccharomyces cerevisiae DNA replication and spindle assembly can overlap. Therefore, signaling mechanisms modulate spindle dynamics in order to ensure correct timing of chromosome segregation relative to genome duplication, especially when replication is incomplete or the DNA becomes damaged. This review focuses on the molecular mechanisms that coordinate DNA replication and spindle dynamics, as well as on the role of spindle-dependent forces in DNA repair. Understanding the coupling between genome duplication and spindle function in yeast cells can provide important insights into similar processes operating in other eukaryotic organisms, including humans.
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Affiliation(s)
- Dimitris Liakopoulos
- CRBM, Université de Montpellier, CNRS, 1919 Route de Mende, 34293 Montpellier, France;
- Laboratory of Biology, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece
- University Research Center of loannina, University of Ioannina, 45110 Ioannina, Greece
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12
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Uncovering bleomycin-induced genomic alterations and underlying mechanisms in yeast. Appl Environ Microbiol 2021; 88:e0170321. [PMID: 34731050 DOI: 10.1128/aem.01703-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bleomycin (BLM) is a widely used chemotherapeutic drug. BLM-treated cells showed an elevated rate of mutations, but the underlying mechanisms remained unclear. In this study, the global genomic alterations in BLM-treated cells were explored in the yeast Saccharomyces cerevisiae. Using genetic assay and whole-genome sequencing, we found that the mutation rate could be greatly elevated in S. cerevisiae cells that underwent ZeocinTM (a BLM member) treatment. One-base deletion and T to G substitution at the 5'-GT-3' motif was the most striking signature of ZeocinTM-induced mutations. This was mainly the result of translesion DNA synthesis involving Rev1 and polymerase ζ. ZeocinTM treatment led to the frequent loss of heterozygosity and chromosomal rearrangements in the diploid strains. The breakpoints of recombination events were significantly associated with certain chromosomal elements. Lastly, we identified multiple genomic alterations that contributed to BLM resistance in the ZeocinTM-treated mutants. Overall, this study provides new insights into the genotoxicity and evolutional effects of BLM. Importance Bleomycin is an antitumor antibiotic that can mutate genomic DNA. Using yeast models in combination with genome sequencing, the mutational signatures of ZeocinTM (a member of the bleomycin family) are disclosed. Translesion-synthesis polymerases are crucial for the viability of ZeocinTM-treated yeast cells at the sacrifice of a higher mutation rate. We also confirmed that multiple genomic alterations were associated with the improved resistance to ZeocinTM, providing novel insights into how bleomycin resistance is developed in cells.
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García Fernández F, Lemos B, Khalil Y, Batrin R, Haber JE, Fabre E. Modified chromosome structure caused by phosphomimetic H2A modulates the DNA damage response by increasing chromatin mobility in yeast. J Cell Sci 2021; 134:jcs.258500. [PMID: 33622771 DOI: 10.1242/jcs.258500] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 02/06/2021] [Indexed: 12/23/2022] Open
Abstract
In budding yeast and mammals, double-strand breaks (DSBs) trigger global chromatin mobility together with rapid phosphorylation of histone H2A over an extensive region of the chromatin. To assess the role of H2A phosphorylation in this response to DNA damage, we have constructed strains where H2A has been mutated to the phosphomimetic H2A-S129E. We show that mimicking H2A phosphorylation leads to an increase in global chromatin mobility in the absence of DNA damage. The intrinsic chromatin mobility of H2A-S129E is not due to downstream checkpoint activation, histone degradation or kinetochore anchoring. Rather, the increased intrachromosomal distances observed in the H2A-S129E mutant are consistent with chromatin structural changes. Strikingly, in this context the Rad9-dependent checkpoint becomes dispensable. Moreover, increased chromatin dynamics in the H2A-S129E mutant correlates with improved DSB repair by non-homologous end joining and a sharp decrease in interchromosomal translocation rate. We propose that changes in chromosomal conformation due to H2A phosphorylation are sufficient to modulate the DNA damage response and maintain genome integrity.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Fabiola García Fernández
- Institut de recherche Saint-Louis (IRSL), Université de Paris, INSERM U944, CNRS UMR7212, Genome and Cell Biology of Diseases Unit, F-75010 Paris, France
| | - Brenda Lemos
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454-9110, USA
| | - Yasmine Khalil
- Institut de recherche Saint-Louis (IRSL), Université de Paris, INSERM U944, CNRS UMR7212, Genome and Cell Biology of Diseases Unit, F-75010 Paris, France
| | - Renaud Batrin
- Institut de recherche Saint-Louis (IRSL), Université de Paris, INSERM U944, CNRS UMR7212, Genome and Cell Biology of Diseases Unit, F-75010 Paris, France
| | - James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454-9110, USA
| | - Emmanuelle Fabre
- Institut de recherche Saint-Louis (IRSL), Université de Paris, INSERM U944, CNRS UMR7212, Genome and Cell Biology of Diseases Unit, F-75010 Paris, France
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14
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Mackenroth B, Alani E. Collaborations between chromatin and nuclear architecture to optimize DNA repair fidelity. DNA Repair (Amst) 2021; 97:103018. [PMID: 33285474 PMCID: PMC8486310 DOI: 10.1016/j.dnarep.2020.103018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/18/2020] [Accepted: 11/05/2020] [Indexed: 01/22/2023]
Abstract
Homologous recombination (HR), considered the highest fidelity DNA double-strand break (DSB) repair pathway that a cell possesses, is capable of repairing multiple DSBs without altering genetic information. However, in "last resort" scenarios, HR can be directed to low fidelity subpathways which often use non-allelic donor templates. Such repair mechanisms are often highly mutagenic and can also yield chromosomal rearrangements and/or deletions. While the choice between HR and its less precise counterpart, non-homologous end joining (NHEJ), has received much attention, less is known about how cells manage and prioritize HR subpathways. In this review, we describe work focused on how chromatin and nuclear architecture orchestrate subpathway choice and repair template usage to maintain genome integrity without sacrificing cell survival. Understanding the relationships between nuclear architecture and recombination mechanics will be critical to understand these cellular repair decisions.
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Affiliation(s)
- Beata Mackenroth
- Department of Molecular Biology and Genetics, Cornell University, 459 Biotechnology Building, Ithaca, NY, 14853-2703, United States
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, 459 Biotechnology Building, Ithaca, NY, 14853-2703, United States.
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15
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Kakui Y, Barrington C, Barry DJ, Gerguri T, Fu X, Bates PA, Khatri BS, Uhlmann F. Fission yeast condensin contributes to interphase chromatin organization and prevents transcription-coupled DNA damage. Genome Biol 2020; 21:272. [PMID: 33153481 PMCID: PMC7643427 DOI: 10.1186/s13059-020-02183-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 10/19/2020] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Structural maintenance of chromosomes (SMC) complexes are central organizers of chromatin architecture throughout the cell cycle. The SMC family member condensin is best known for establishing long-range chromatin interactions in mitosis. These compact chromatin and create mechanically stable chromosomes. How condensin contributes to chromatin organization in interphase is less well understood. RESULTS Here, we use efficient conditional depletion of fission yeast condensin to determine its contribution to interphase chromatin organization. We deplete condensin in G2-arrested cells to preempt confounding effects from cell cycle progression without condensin. Genome-wide chromatin interaction mapping, using Hi-C, reveals condensin-mediated chromatin interactions in interphase that are qualitatively similar to those observed in mitosis, but quantitatively far less prevalent. Despite their low abundance, chromatin mobility tracking shows that condensin markedly confines interphase chromatin movements. Without condensin, chromatin behaves as an unconstrained Rouse polymer with excluded volume, while condensin constrains its mobility. Unexpectedly, we find that condensin is required during interphase to prevent ongoing transcription from eliciting a DNA damage response. CONCLUSIONS In addition to establishing mitotic chromosome architecture, condensin-mediated long-range chromatin interactions contribute to shaping chromatin organization in interphase. The resulting structure confines chromatin mobility and protects the genome from transcription-induced DNA damage. This adds to the important roles of condensin in maintaining chromosome stability.
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Affiliation(s)
- Yasutaka Kakui
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Waseda Institute for Advanced Study, Waseda University, 1-21-1, Nishiwaseda, Shinjuku-ku, Tokyo, 169-0051, Japan.
| | - Christopher Barrington
- Bioinformatics & Biostatistics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - David J Barry
- Advanced Light Microscopy Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Tereza Gerguri
- Biomolecular Modelling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Xiao Fu
- Biomolecular Modelling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Paul A Bates
- Biomolecular Modelling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Bhavin S Khatri
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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16
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Cheblal A, Challa K, Seeber A, Shimada K, Yoshida H, Ferreira HC, Amitai A, Gasser SM. DNA Damage-Induced Nucleosome Depletion Enhances Homology Search Independently of Local Break Movement. Mol Cell 2020; 80:311-326.e4. [PMID: 32970994 DOI: 10.1016/j.molcel.2020.09.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 08/31/2020] [Accepted: 08/31/2020] [Indexed: 01/02/2023]
Abstract
To determine whether double-strand break (DSB) mobility enhances the physical search for an ectopic template during homology-directed repair (HDR), we tested the effects of factors that control chromatin dynamics, including cohesin loading and kinetochore anchoring. The former but not the latter is altered in response to DSBs. Loss of the nonhistone high-mobility group protein Nhp6 reduces histone occupancy and increases chromatin movement, decompaction, and ectopic HDR. The loss of nucleosome remodeler INO80-C did the opposite. To see whether enhanced HDR depends on DSB mobility or the global chromatin response, we tested the ubiquitin ligase mutant uls1Δ, which selectively impairs local but not global movement in response to a DSB. Strand invasion occurs in uls1Δ cells with wild-type kinetics, arguing that global histone depletion rather than DSB movement is rate limiting for HDR. Impaired break movement in uls1Δ correlates with elevated MRX and cohesin loading, despite normal resection and checkpoint activation.
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Affiliation(s)
- Anaïs Cheblal
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Faculty of Natural Sciences, 4056 Basel, Switzerland
| | - Kiran Challa
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Andrew Seeber
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; Present address: Center for Advanced Imaging, Northwest Building, 52 Oxford St, Suite 147, Harvard University, Cambridge, MA 02138, USA
| | - Kenji Shimada
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Haruka Yoshida
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Helder C Ferreira
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Assaf Amitai
- Department of Chemical Engineering, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Faculty of Natural Sciences, 4056 Basel, Switzerland.
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17
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Miné-Hattab J, Chiolo I. Complex Chromatin Motions for DNA Repair. Front Genet 2020; 11:800. [PMID: 33061931 PMCID: PMC7481375 DOI: 10.3389/fgene.2020.00800] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/06/2020] [Indexed: 12/26/2022] Open
Abstract
A number of studies across different model systems revealed that chromatin undergoes significant changes in dynamics in response to DNA damage. These include local motion changes at damage sites, increased nuclear exploration of both damaged and undamaged loci, and directed motions to new nuclear locations associated with certain repair pathways. These studies also revealed the need for new analytical methods to identify directed motions in a context of mixed trajectories, and the importance of investigating nuclear dynamics over different time scales to identify diffusion regimes. Here we provide an overview of the current understanding of this field, including imaging and analytical methods developed to investigate nuclear dynamics in different contexts. These dynamics are essential for genome integrity. Identifying the molecular mechanisms responsible for these movements is key to understanding how their misregulation contributes to cancer and other genome instability disorders.
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Affiliation(s)
- Judith Miné-Hattab
- UMR 3664, CNRS, Institut Curie, PSL Research University, Paris, France
- UMR 3664, CNRS, Institut Curie, Sorbonne Université, Paris, France
| | - Irene Chiolo
- Molecular and Computational Biology Department, University of Southern California, Los Angeles, CA, United States
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18
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Shaban HA, Seeber A. Monitoring global chromatin dynamics in response to DNA damage. Mutat Res 2020; 821:111707. [PMID: 32505939 DOI: 10.1016/j.mrfmmm.2020.111707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 05/08/2020] [Accepted: 05/16/2020] [Indexed: 02/08/2023]
Abstract
DNA damage induced global chromatin motion has been observed in yeast and mammalian cells. Currently, it is unclear what mechanisms may be driving these changes in whole genome dynamics. Recent advances in live-cell microscopy now enable chromatin motion to be quantified throughout the whole nucleus. In addition, much work has improved quantification of single particle trajectories. This topic is particularly important to the field of DNA repair as there are a large number of unanswered questions that can be tackled by monitoring global chromatin movement. Foremost, is how local DNA repair mechanisms interact and change global chromatin structure and whether this impacts repair pathway choice or efficiency. In this review, we describe methodologies to monitor global chromatin movement putting them into context with the DNA repair field highlighting how these techniques can drive new discoveries.
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Affiliation(s)
- Haitham A Shaban
- Center for Advanced Imaging, Harvard University, Cambridge, MA, 02138, USA; Spectroscopy Department, Physics Division, National Research Centre, Dokki, 12622 Cairo, Egypt
| | - Andrew Seeber
- Center for Advanced Imaging, Harvard University, Cambridge, MA, 02138, USA.
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19
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Lawrimore CJ, Lawrimore J, He Y, Chavez S, Bloom K. Polymer perspective of genome mobilization. Mutat Res 2020; 821:111706. [PMID: 32516654 DOI: 10.1016/j.mrfmmm.2020.111706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/30/2020] [Accepted: 05/06/2020] [Indexed: 02/07/2023]
Abstract
Chromosome motion is an intrinsic feature of all DNA-based metabolic processes and is a particularly well-documented response to both DNA damage and repair. By using both biological and polymer physics approaches, many of the contributing factors of chromatin motility have been elucidated. These include the intrinsic properties of chromatin, such as stiffness, as well as the loop modulators condensin and cohesin. Various biological factors such as external tethering to nuclear domains, ATP-dependent processes, and nucleofilaments further impact chromatin motion. DNA damaging agents that induce double-stranded breaks also cause increased chromatin motion that is modulated by recruitment of repair and checkpoint proteins. Approaches that integrate biological experimentation in conjunction with models from polymer physics provide mechanistic insights into the role of chromatin dynamics in biological function. In this review we discuss the polymer models and the effects of both DNA damage and repair on chromatin motion as well as mechanisms that may underlie these effects.
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Affiliation(s)
- Colleen J Lawrimore
- Department of Biology, 623 Fordham Hall CB#3280, University of North Carolina, Chapel Hill, NC 27599-3280, United States
| | - Josh Lawrimore
- Department of Biology, 623 Fordham Hall CB#3280, University of North Carolina, Chapel Hill, NC 27599-3280, United States
| | - Yunyan He
- Department of Biology, 623 Fordham Hall CB#3280, University of North Carolina, Chapel Hill, NC 27599-3280, United States
| | - Sergio Chavez
- Department of Biology, 623 Fordham Hall CB#3280, University of North Carolina, Chapel Hill, NC 27599-3280, United States
| | - Kerry Bloom
- Department of Biology, 623 Fordham Hall CB#3280, University of North Carolina, Chapel Hill, NC 27599-3280, United States.
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20
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Oshidari R, Mekhail K, Seeber A. Mobility and Repair of Damaged DNA: Random or Directed? Trends Cell Biol 2020; 30:144-156. [DOI: 10.1016/j.tcb.2019.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 12/24/2022]
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21
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Khosraviani N, Ostrowski LA, Mekhail K. Roles for Non-coding RNAs in Spatial Genome Organization. Front Cell Dev Biol 2019; 7:336. [PMID: 31921848 PMCID: PMC6930868 DOI: 10.3389/fcell.2019.00336] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 11/29/2019] [Indexed: 12/15/2022] Open
Abstract
Genetic loci are non-randomly arranged in the nucleus of the cell. This order, which is important to overall genome expression and stability, is maintained by a growing number of factors including the nuclear envelope, various genetic elements and dedicated protein complexes. Here, we review evidence supporting roles for non-coding RNAs (ncRNAs) in the regulation of spatial genome organization and its impact on gene expression and cell survival. Specifically, we discuss how ncRNAs from single-copy and repetitive DNA loci contribute to spatial genome organization by impacting perinuclear chromosome tethering, major nuclear compartments, chromatin looping, and various chromosomal structures. Overall, our analysis of the literature highlights central functions for ncRNAs and their transcription in the modulation of spatial genome organization with connections to human health and disease.
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Affiliation(s)
- Negin Khosraviani
- Department of Laboratory Medicine and Pathobiology, MaRS Centre, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Lauren A. Ostrowski
- Department of Laboratory Medicine and Pathobiology, MaRS Centre, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Karim Mekhail
- Department of Laboratory Medicine and Pathobiology, MaRS Centre, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Canada Research Chairs Program, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
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22
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Smith MJ, Bryant EE, Joseph FJ, Rothstein R. DNA damage triggers increased mobility of chromosomes in G1-phase cells. Mol Biol Cell 2019; 30:2620-2625. [PMID: 31483739 PMCID: PMC6761769 DOI: 10.1091/mbc.e19-08-0469] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 08/30/2019] [Indexed: 01/19/2023] Open
Abstract
During S phase in Saccharomyces cerevisiae, chromosomal loci become mobile in response to DNA double-strand breaks both at the break site (local mobility) and throughout the nucleus (global mobility). Increased nuclear exploration is regulated by the recombination machinery and the DNA damage checkpoint and is likely an important aspect of homology search. While mobility in response to DNA damage has been studied extensively in S phase, the response in interphase has not, and the question of whether homologous recombination proceeds to completion in G1 phase remains controversial. Here, we find that global mobility is triggered in G1 phase. As in S phase, global mobility in G1 phase is controlled by the DNA damage checkpoint and the Rad51 recombinase. Interestingly, despite the restriction of Rad52 mediator foci to S phase, Rad51 foci form at high levels in G1 phase. Together, these observations indicate that the recombination and checkpoint machineries promote global mobility in G1 phase, supporting the notion that recombination can occur in interphase diploids.
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Affiliation(s)
- Michael J. Smith
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032
| | - Eric E. Bryant
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Fraulin J. Joseph
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032
| | - Rodney Rothstein
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032
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23
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Abstract
Maintaining the integrity of the genome in the face of DNA damage is crucial to ensure the survival of the cell and normal development. DNA lesions and repair occur in the context of the chromatin fiber, whose 3D organization and movements in the restricted volume of the nucleus are under intense scrutiny. Here, we highlight work from our and other labs that addresses how the dynamic organization of the chromatin fiber affects the repair of damaged DNA and how, conversely, DNA damage and repair affect the structure and dynamics of chromatin in the budding yeast nucleus.
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Affiliation(s)
- Emmanuelle Fabre
- a Equipe Biologie et Dynamique des Chromosomes , Institut Universitaire d'Hématologie, Hôpital St. Louis , Paris , France.,b CNRS, UMR 7212 INSERM U944, IUH, Université Paris Diderot Sorbonne Paris Cité , Paris , France
| | - Christophe Zimmer
- c Institut Pasteur, Unité Imagerie et Modélisation , 25 rue du Docteur Roux, 75015 , Paris , France.,d UMR 3691, CNRS; C3BI, USR 3756, IP CNRS , Paris , France
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24
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Estrem C, Moore JK. Help or hindrance: how do microtubule-based forces contribute to genome damage and repair? Curr Genet 2019; 66:303-311. [PMID: 31501990 DOI: 10.1007/s00294-019-01033-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/27/2019] [Accepted: 08/27/2019] [Indexed: 10/26/2022]
Abstract
Forces generated by molecular motors and the cytoskeleton move the nucleus and genome during many cellular processes, including cell migration and division. How these forces impact the genome, and whether cells regulate cytoskeletal forces to preserve genome integrity is unclear. We recently demonstrated that, in budding yeast, mutants that stabilize the microtubule cytoskeleton cause excessive movement of the mitotic spindle and nucleus. We found that increased nuclear movement results in DNA damage and increased time to repair the damage through homology-directed repair. Our results indicate that nuclear movement impairs DNA repair through increased tension on chromosomes and nuclear deformation. However, the previous studies have shown genome mobility, driven by cytoskeleton-based forces, aids in homology-directed DNA repair. This sets up an apparent paradox, where genome mobility may prevent or promote DNA repair. Hence, this review explores how the genome is affected by nuclear movement and how genome mobility could aid or hinder homology-directed repair.
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Affiliation(s)
- Cassi Estrem
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jeffrey K Moore
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO, USA.
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25
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Shukron O, Seeber A, Amitai A, Holcman D. Advances Using Single-Particle Trajectories to Reconstruct Chromatin Organization and Dynamics. Trends Genet 2019; 35:685-705. [PMID: 31371030 DOI: 10.1016/j.tig.2019.06.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 06/12/2019] [Accepted: 06/26/2019] [Indexed: 12/16/2022]
Abstract
Chromatin organization remains complex and far from understood. In this article, we review recent statistical methods of extracting biophysical parameters from in vivo single-particle trajectories of loci to reconstruct chromatin reorganization in response to cellular stress such as DNA damage. We look at methods for analyzing both single locus and multiple loci tracked simultaneously and explain how to quantify and describe chromatin motion using a combination of extractable parameters. These parameters can be converted into information about chromatin dynamics and function. Furthermore, we discuss how the timescale of recurrent encounter between loci can be extracted and interpreted. We also discuss the effect of sampling rate on the estimated parameters. Finally, we review a polymer method to reconstruct chromatin structure using crosslinkers between chromatin sites. We list and refer to some software packages that are now publicly available to simulate polymer motion. To conclude, chromatin organization and dynamics can be reconstructed from locus trajectories and predicted based on polymer models.
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Affiliation(s)
- O Shukron
- Group of Data Modeling, Computational Biology and Predictive Medicine, Institut de Biologie, CNRS/INSERM/PSL Ecole Normale Supérieure, Paris, 75005, France
| | - A Seeber
- Center for Advanced Imaging, Northwest Building, 52 Oxford St, Suite 147, Harvard University, Cambridge, MA, 02138, USA
| | - A Amitai
- Department of Chemical Engineering, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
| | - D Holcman
- Group of Data Modeling, Computational Biology and Predictive Medicine, Institut de Biologie, CNRS/INSERM/PSL Ecole Normale Supérieure, Paris, 75005, France.
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26
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Ayra-Plasencia J, Machín F. DNA double-strand breaks in telophase lead to coalescence between segregated sister chromatid loci. Nat Commun 2019; 10:2862. [PMID: 31253793 PMCID: PMC6598993 DOI: 10.1038/s41467-019-10742-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 05/30/2019] [Indexed: 12/24/2022] Open
Abstract
DNA double strand breaks (DSBs) pose a high risk for genome integrity. Cells repair DSBs through homologous recombination (HR) when a sister chromatid is available. HR is upregulated by the cycling dependent kinase (CDK) despite the paradox of telophase, where CDK is high but a sister chromatid is not nearby. Here we study in the budding yeast the response to DSBs in telophase, and find they activate the DNA damage checkpoint (DDC), leading to a telophase-to-G1 delay. Outstandingly, we observe a partial reversion of sister chromatid segregation, which includes approximation of segregated material, de novo formation of anaphase bridges, and coalescence between sister loci. We finally show that DSBs promote a massive change in the dynamics of telophase microtubules (MTs), together with dephosphorylation and relocalization of kinesin-5 Cin8. We propose that chromosome segregation is not irreversible and that DSB repair using the sister chromatid is possible in telophase.
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Affiliation(s)
- Jessel Ayra-Plasencia
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- Escuela de Doctorado y Estudios de Posgrado, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Félix Machín
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain.
- Instituto de Tecnologías Biomédicas, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.
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27
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Estrem C, Moore JK. Astral microtubule forces alter nuclear organization and inhibit DNA repair in budding yeast. Mol Biol Cell 2019; 30:2000-2013. [PMID: 31067146 PMCID: PMC6727761 DOI: 10.1091/mbc.e18-12-0808] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Dividing cells must balance the maintenance of genome integrity with the generation of cytoskeletal forces that control chromosome position. In this study, we investigate how forces on astral microtubules impact the genome during cell division by using live-cell imaging of the cytoskeleton, chromatin, and DNA damage repair in budding yeast. Our results demonstrate that dynein-dependent forces on astral microtubules are propagated through the spindle during nuclear migration and when in excess can increase the frequency of double-stranded breaks (DSBs). Under these conditions, we find that homology-directed repair of DSBs is delayed, indicating antagonism between nuclear migration and the mechanism of homology-directed repair. These effects are partially rescued by mutants that weaken pericentric cohesion or mutants that decrease constriction on the nucleus as it moves through the bud neck. We propose that minimizing nuclear movement aids in finding a donor strand for homologous recombination.
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Affiliation(s)
- Cassi Estrem
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045
| | - Jeffrey K Moore
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045
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28
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The Rabl configuration limits topological entanglement of chromosomes in budding yeast. Sci Rep 2019; 9:6795. [PMID: 31043625 PMCID: PMC6494875 DOI: 10.1038/s41598-019-42967-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 03/27/2019] [Indexed: 11/25/2022] Open
Abstract
The three dimensional organization of genomes remains mostly unknown due to their high degree of condensation. Biophysical studies predict that condensation promotes the topological entanglement of chromatin fibers and the inhibition of function. How organisms balance between functionally active genomes and a high degree of condensation remains to be determined. Here we hypothesize that the Rabl configuration, characterized by the attachment of centromeres and telomeres to the nuclear envelope, helps to reduce the topological entanglement of chromosomes. To test this hypothesis we developed a novel method to quantify chromosome entanglement complexity in 3D reconstructions obtained from Chromosome Conformation Capture (CCC) data. Applying this method to published data of the yeast genome, we show that computational models implementing the attachment of telomeres or centromeres alone are not sufficient to obtain the reduced entanglement complexity observed in 3D reconstructions. It is only when the centromeres and telomeres are attached to the nuclear envelope (i.e. the Rabl configuration) that the complexity of entanglement of the genome is comparable to that of the 3D reconstructions. We therefore suggest that the Rabl configuration is an essential player in the simplification of the entanglement of chromatin fibers.
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29
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Laflamme G, Sim S, Leary A, Pascariu M, Vogel J, D’Amours D. Interphase Microtubules Safeguard Mitotic Progression by Suppressing an Aurora B-Dependent Arrest Induced by DNA Replication Stress. Cell Rep 2019; 26:2875-2889.e3. [DOI: 10.1016/j.celrep.2019.02.051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 12/21/2018] [Accepted: 02/13/2019] [Indexed: 10/27/2022] Open
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30
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Waterman DP, Zhou F, Li K, Lee CS, Tsabar M, Eapen VV, Mazzella A, Haber JE. Live cell monitoring of double strand breaks in S. cerevisiae. PLoS Genet 2019; 15:e1008001. [PMID: 30822309 PMCID: PMC6415866 DOI: 10.1371/journal.pgen.1008001] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 03/13/2019] [Accepted: 02/01/2019] [Indexed: 11/19/2022] Open
Abstract
We have used two different live-cell fluorescent protein markers to monitor the formation and localization of double-strand breaks (DSBs) in budding yeast. Using GFP derivatives of the Rad51 recombination protein or the Ddc2 checkpoint protein, we find that cells with three site-specific DSBs, on different chromosomes, usually display 2 or 3 foci that may coalesce and dissociate. This motion is independent of Rad52 and microtubules. Rad51-GFP, by itself, is unable to repair DSBs by homologous recombination in mitotic cells, but is able to form foci and allow repair when heterozygous with a wild type Rad51 protein. The kinetics of formation and disappearance of a Rad51-GFP focus parallels the completion of site-specific DSB repair. However, Rad51-GFP is proficient during meiosis when homozygous, similar to rad51 “site II” mutants that can bind single-stranded DNA but not complete strand exchange. Rad52-RFP and Rad51-GFP co-localize to the same DSB, but a significant minority of foci have Rad51-GFP without visible Rad52-RFP. We conclude that co-localization of foci in cells with 3 DSBs does not represent formation of a homologous recombination “repair center,” as the same distribution of Ddc2-GFP foci was found in the absence of the Rad52 protein. Double strand breaks (DSBs) pose the greatest threat to the fidelity of an organism’s genome. While much work has been done on the mechanisms of DSB repair, the arrangement and interaction of multiple DSBs within a single cell remain unclear. Using two live-cell fluorescent DSB markers, we show that cells with 3 site-specific DSBs usually form 2 or 3 foci that can may coalesce into fewer foci but also dissociate. The aggregation and mobility of DSBs into a single focus does not depend on the Rad52 recombination protein that is required for various mechanisms of homologous recombination, suggesting that merging of DSBs does not reflect formation of a homologous recombination repair center.
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Affiliation(s)
- David P. Waterman
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Felix Zhou
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Kevin Li
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Cheng-Sheng Lee
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Michael Tsabar
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Vinay V. Eapen
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Allison Mazzella
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - James E. Haber
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, United States of America
- * E-mail:
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31
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Bordelet H, Dubrana K. Keep moving and stay in a good shape to find your homologous recombination partner. Curr Genet 2019; 65:29-39. [PMID: 30097675 PMCID: PMC6342867 DOI: 10.1007/s00294-018-0873-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 07/31/2018] [Accepted: 08/02/2018] [Indexed: 01/02/2023]
Abstract
Genomic DNA is constantly exposed to damage. Among the lesion in DNA, double-strand breaks (DSB), because they disrupt the two strands of the DNA double helix, are the more dangerous. DSB are repaired through two evolutionary conserved mechanisms: Non-Homologous End Joining (NHEJ) and Homologous Recombination (HR). Whereas NHEJ simply reseals the double helix with no or minimal processing, HR necessitates the formation of a 3'ssDNA through the processing of DSB ends by the resection machinery and relies on the recognition and pairing of this 3'ssDNA tails with an intact homologous sequence. Despite years of active research on HR, the manner by which the two homologous sequences find each other in the crowded nucleus, and how this modulates HR efficiency, only recently emerges. Here, we review recent advances in our understanding of the factors limiting the search of a homologous sequence during HR.
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Affiliation(s)
- Hélène Bordelet
- Laboratoire Instabilité et Organisation Nucléaire, iRCM, IBFJ, DRF, CEA. 2 INSERM, U967. 3 Université Paris Diderot et Paris Saclay, UMR967, Fontenay-aux-roses, 92265, France
| | - Karine Dubrana
- Laboratoire Instabilité et Organisation Nucléaire, iRCM, IBFJ, DRF, CEA. 2 INSERM, U967. 3 Université Paris Diderot et Paris Saclay, UMR967, Fontenay-aux-roses, 92265, France.
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32
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Abstract
Recent advances in both the technologies used to measure chromatin movement and the biophysical analysis used to model them have yielded a fuller understanding of chromatin dynamics and the polymer structure that underlies it. Changes in nucleosome packing, checkpoint kinase activation, the cell cycle, chromosomal tethers, and external forces acting on nuclei in response to external and internal stimuli can alter the basal mobility of DNA in interphase nuclei of yeast or mammalian cells. Although chromatin movement is assumed to be necessary for many DNA-based processes, including gene activation by distal enhancer–promoter interaction or sequence-based homology searches during double-strand break repair, experimental evidence supporting an essential role in these activities is sparse. Nonetheless, high-resolution tracking of chromatin dynamics has led to instructive models of the higher-order folding and flexibility of the chromatin polymer. Key regulators of chromatin motion in physiological conditions or after damage induction are reviewed here.
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Affiliation(s)
- Andrew Seeber
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- Faculty of Natural Sciences, University of Basel, 4056 Basel, Switzerland
- Current affiliation: Harvard Center for Advanced Imaging, Cambridge, MA 02138, USA
| | - Michael H. Hauer
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- Faculty of Natural Sciences, University of Basel, 4056 Basel, Switzerland
| | - Susan M. Gasser
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- Faculty of Natural Sciences, University of Basel, 4056 Basel, Switzerland
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33
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Smith MJ, Bryant EE, Rothstein R. Increased chromosomal mobility after DNA damage is controlled by interactions between the recombination machinery and the checkpoint. Genes Dev 2018; 32:1242-1251. [PMID: 30181361 PMCID: PMC6120718 DOI: 10.1101/gad.317966.118] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 07/02/2018] [Indexed: 12/20/2022]
Abstract
In this study, Smith et al. investigated how cells modulate chromosome mobility in response to DNA damage. They show that global chromosome mobility is regulated by the Rad51 recombinase and its mediator, Rad52, and their findings indicate that interplay between recombination factors and the checkpoint restricts increased mobility until recombination proteins are assembled at damaged sites. During homologous recombination, cells must coordinate repair, DNA damage checkpoint signaling, and movement of chromosomal loci to facilitate homology search. In Saccharomyces cerevisiae, increased movement of damaged loci (local mobility) and undamaged loci (global mobility) precedes homolog pairing in mitotic cells. How cells modulate chromosome mobility in response to DNA damage remains unclear. Here, we demonstrate that global chromosome mobility is regulated by the Rad51 recombinase and its mediator, Rad52. Surprisingly, rad51Δ rad52Δ cells display checkpoint-dependent constitutively increased mobility, indicating that a regulatory circuit exists between recombination and checkpoint machineries to govern chromosomal mobility. We found that the requirement for Rad51 in this circuit is distinct from its role in recombination and that interaction with Rad52 is necessary to alleviate inhibition imposed by mediator recruitment to ssDNA. Thus, interplay between recombination factors and the checkpoint restricts increased mobility until recombination proteins are assembled at damaged sites.
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Affiliation(s)
- Michael J Smith
- Department of Genetics and Development, Columbia University Medical Center, New York, New York 10032, USA
| | - Eric E Bryant
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Rodney Rothstein
- Department of Genetics and Development, Columbia University Medical Center, New York, New York 10032, USA
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34
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35
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Oshidari R, Strecker J, Chung DKC, Abraham KJ, Chan JNY, Damaren CJ, Mekhail K. Nuclear microtubule filaments mediate non-linear directional motion of chromatin and promote DNA repair. Nat Commun 2018; 9:2567. [PMID: 29967403 PMCID: PMC6028458 DOI: 10.1038/s41467-018-05009-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 06/07/2018] [Indexed: 12/19/2022] Open
Abstract
Damaged DNA shows increased mobility, which can promote interactions with repair-conducive nuclear pore complexes (NPCs). This apparently random mobility is paradoxically abrogated upon disruption of microtubules or kinesins, factors that typically cooperate to mediate the directional movement of macromolecules. Here, we resolve this paradox by uncovering DNA damage-inducible intranuclear microtubule filaments (DIMs) that mobilize damaged DNA and promote repair. Upon DNA damage, relief of centromeric constraint induces DIMs that cooperate with the Rad9 DNA damage response mediator and Kar3 kinesin motor to capture DNA lesions, which then linearly move along dynamic DIMs. Decreasing and hyper-inducing DIMs respectively abrogates and hyper-activates repair. Accounting for DIM dynamics across cell populations by measuring directional changes of damaged DNA reveals that it exhibits increased non-linear directional behavior in nuclear space. Abrogation of DIM-dependent processes or repair-promoting factors decreases directional behavior. Thus, inducible and dynamic nuclear microtubule filaments directionally mobilize damaged DNA and promote repair. Following DNA damage, different processes come to action to aid repair. The authors here find that microtubule filaments within the cell nucleus capture and non-randomly mobilize damaged chromatin to mediate DNA repair.
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Affiliation(s)
- Roxanne Oshidari
- Department of Laboratory Medicine and Pathobiology, MaRS Centre, University of Toronto, West Tower, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Jonathan Strecker
- Department of Molecular Genetics, MaRS Centre, University of Toronto, West Tower, 661 University Avenue, Toronto, ON, M5G 1M1, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, M5G 1X5, Canada.,Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, MA, 02142, USA
| | - Daniel K C Chung
- Department of Laboratory Medicine and Pathobiology, MaRS Centre, University of Toronto, West Tower, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Karan J Abraham
- Department of Laboratory Medicine and Pathobiology, MaRS Centre, University of Toronto, West Tower, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Janet N Y Chan
- Department of Laboratory Medicine and Pathobiology, MaRS Centre, University of Toronto, West Tower, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Christopher J Damaren
- Institute for Aerospace Studies, University of Toronto, 4925 Dufferin Street, Toronto, ON, M3H 5T6, Canada
| | - Karim Mekhail
- Department of Laboratory Medicine and Pathobiology, MaRS Centre, University of Toronto, West Tower, 661 University Avenue, Toronto, ON, M5G 1M1, Canada. .,Canada Research Chairs Program, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.
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36
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Zimmer C, Fabre E. Chromatin mobility upon DNA damage: state of the art and remaining questions. Curr Genet 2018; 65:1-9. [DOI: 10.1007/s00294-018-0852-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/30/2018] [Accepted: 06/04/2018] [Indexed: 12/14/2022]
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37
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Abstract
The health of an organism is intimately linked to its ability to repair damaged DNA. Importantly, DNA repair processes are highly dynamic. This highlights the necessity of characterizing DNA repair in live cells. Advanced genome editing and imaging approaches allow us to visualize damaged DNA and its associated factors in real time. Here, we summarize both established and recent methods that are used to induce DNA damage and visualize damaged DNA and its repair in live cells.
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Affiliation(s)
- Roxanne Oshidari
- Department of Laboratory Medicine and Pathobiology, University of Toronto, MaRS Centre, West Tower, 661 University Avenue, Toronto, Ontario M5G 1M1, Canada
| | - Karim Mekhail
- Department of Laboratory Medicine and Pathobiology, University of Toronto, MaRS Centre, West Tower, 661 University Avenue, Toronto, Ontario M5G 1M1, Canada; Canada Research Chairs Program, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.
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38
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Abstract
The repair of chromosomal double-strand breaks (DSBs) by homologous recombination is essential to maintain genome integrity. The key step in DSB repair is the RecA/Rad51-mediated process to match sequences at the broken end to homologous donor sequences that can be used as a template to repair the lesion. Here, in reviewing research about DSB repair, I consider the many factors that appear to play important roles in the successful search for homology by several homologous recombination mechanisms. See also the video abstract here: https://youtu.be/vm7-X5uIzS8.
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Affiliation(s)
- James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454-9110, USA
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39
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Caridi PC, Delabaere L, Zapotoczny G, Chiolo I. And yet, it moves: nuclear and chromatin dynamics of a heterochromatic double-strand break. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0291. [PMID: 28847828 PMCID: PMC5577469 DOI: 10.1098/rstb.2016.0291] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2017] [Indexed: 12/15/2022] Open
Abstract
Heterochromatin is mostly composed of repeated DNA sequences prone to aberrant recombination. How cells maintain the stability of these sequences during double-strand break (DSB) repair has been a long-standing mystery. Studies in Drosophila cells revealed that faithful homologous recombination repair of heterochromatic DSBs relies on the striking relocalization of repair sites to the nuclear periphery before Rad51 recruitment and repair progression. Here, we summarize our current understanding of this response, including the molecular mechanisms involved, and conserved pathways in mammalian cells. We will highlight important similarities with pathways identified in budding yeast for repair of other types of repeated sequences, including rDNA and short telomeres. We will also discuss the emerging role of chromatin composition and regulation in heterochromatin repair progression. Together, these discoveries challenged previous assumptions that repair sites are substantially static in multicellular eukaryotes, that heterochromatin is largely inert in the presence of DSBs, and that silencing and compaction in this domain are obstacles to repair. This article is part of the themed issue ‘Chromatin modifiers and remodellers in DNA repair and signalling’.
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Affiliation(s)
- P Christopher Caridi
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Laetitia Delabaere
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Grzegorz Zapotoczny
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Irene Chiolo
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
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40
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Poli J, Gasser SM, Papamichos-Chronakis M. The INO80 remodeller in transcription, replication and repair. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0290. [PMID: 28847827 DOI: 10.1098/rstb.2016.0290] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2017] [Indexed: 02/06/2023] Open
Abstract
The accessibility of eukaryotic genomes to the action of enzymes involved in transcription, replication and repair is maintained despite the organization of DNA into nucleosomes. This access is often regulated by the action of ATP-dependent nucleosome remodellers. The INO80 class of nucleosome remodellers has unique structural features and it is implicated in a diverse array of functions, including transcriptional regulation, DNA replication and DNA repair. Underlying these diverse functions is the catalytic activity of the main ATPase subunit, which in the context of a multisubunit complex can shift nucleosomes and carry out histone dimer exchange. In vitro studies showed that INO80 promotes replication fork progression on a chromatin template, while in vivo it was shown to facilitate replication fork restart after stalling and to help evict RNA polymerase II at transcribed genes following the collision of a replication fork with transcription. More recent work in yeast implicates INO80 in the general eviction and degradation of nucleosomes following high doses of oxidative DNA damage. Beyond these replication and repair functions, INO80 was shown to repress inappropriate transcription at promoters in the opposite direction to the coding sequence. Here we discuss the ways in which INO80's diverse functions help maintain genome integrity.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- Jérôme Poli
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.,University of Montpellier and Centre de Recherche en Biologie Cellulaire (CRBM), UMR5237, CNRS, Montpellier 34095, Cedex 5, France
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland .,Faculty of Natural Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Manolis Papamichos-Chronakis
- Institute for Cell and Molecular Biosciences, Newcastle University Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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41
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Mekhail K. Defining the Damaged DNA Mobility Paradox as Revealed by the Study of Telomeres, DSBs, Microtubules and Motors. Front Genet 2018; 9:95. [PMID: 29616083 PMCID: PMC5869915 DOI: 10.3389/fgene.2018.00095] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 03/07/2018] [Indexed: 11/13/2022] Open
Abstract
Eukaryotic genomes are non-randomly arranged inside the nucleus. Despite this ordered spatial genome organization, damaged DNA exhibits increased random mobility within nuclear space. This increased random movement is thought to promote DNA repair by facilitating homology search, allowing targeting to repair-conducive nuclear domains, or releasing damage from repair-repressive locations. Recent studies focusing on the relationship between telomeres, DNA repair processes, and nuclear organization have revealed that the disruption of motor proteins or microtubules, which typically mediate the directed motion of cargo, disrupts the random mobility of damaged DNA. These findings define a new biological paradox. Here, I define this as the damaged DNA mobility paradox, describe how it uncovers key gaps in knowledge, and highlight key questions to help guide us toward paradox resolution.
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Affiliation(s)
- Karim Mekhail
- Department of Laboratory Medicine and Pathobiology, University of Toronto, MaRS Centre, Toronto, ON, Canada.,Canada Research Chairs Program, University of Toronto, Toronto, ON, Canada
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42
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Caridi CP, Delabaere L, Tjong H, Hopp H, Das D, Alber F, Chiolo I. Quantitative Methods to Investigate the 4D Dynamics of Heterochromatic Repair Sites in Drosophila Cells. Methods Enzymol 2018. [PMID: 29523239 DOI: 10.1016/bs.mie.2017.11.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Heterochromatin is mostly composed of long stretches of repeated DNA sequences prone to ectopic recombination during double-strand break (DSB) repair. In Drosophila, "safe" homologous recombination (HR) repair of heterochromatic DSBs relies on a striking relocalization of repair sites to the nuclear periphery. Central to understanding heterochromatin repair is the ability to investigate the 4D dynamics (movement in space and time) of repair sites. A specific challenge of these studies is preventing phototoxicity and photobleaching effects while imaging the sample over long periods of time, and with sufficient time points and Z-stacks to track repair foci over time. Here we describe an optimized approach for high-resolution live imaging of heterochromatic DSBs in Drosophila cells, with a specific emphasis on the fluorescent markers and imaging setup used to capture the motion of repair foci over long-time periods. We detail approaches that minimize photobleaching and phototoxicity with a DeltaVision widefield deconvolution microscope, and image processing techniques for signal recovery postimaging using SoftWorX and Imaris software. We present a method to derive mean square displacement curves revealing some of the biophysical properties of the motion. Finally, we describe a method in R to identify tracts of directed motions (DMs) in mixed trajectories. These approaches enable a deeper understanding of the mechanisms of heterochromatin dynamics and genome stability in the three-dimensional context of the nucleus and have broad applicability in the field of nuclear dynamics.
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Affiliation(s)
| | | | - Harianto Tjong
- University of Southern California, Los Angeles, CA, United States
| | - Hannah Hopp
- University of Southern California, Los Angeles, CA, United States
| | - Devika Das
- University of Southern California, Los Angeles, CA, United States
| | - Frank Alber
- University of Southern California, Los Angeles, CA, United States
| | - Irene Chiolo
- University of Southern California, Los Angeles, CA, United States.
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43
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Abstract
Chromatin is organized into higher-order structures that form subcompartments in interphase nuclei. Different categories of specialized enzymes act on chromatin and regulate its compaction and biophysical characteristics in response to physiological conditions. We present an overview of the function of chromatin structure and its dynamic changes in response to genotoxic stress, focusing on both subnuclear organization and the physical mobility of DNA. We review the requirements and mechanisms that cause chromatin relocation, enhanced mobility, and chromatin unfolding as a consequence of genotoxic lesions. An intriguing link has been established recently between enhanced chromatin dynamics and histone loss.
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Affiliation(s)
- Michael H Hauer
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland.,Faculty of Natural Sciences, University of Basel, CH-4056 Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland.,Faculty of Natural Sciences, University of Basel, CH-4056 Basel, Switzerland
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44
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Hou H, Cooper JP. Stretching, scrambling, piercing and entangling: Challenges for telomeres in mitotic and meiotic chromosome segregation. Differentiation 2018; 100:12-20. [PMID: 29413748 DOI: 10.1016/j.diff.2018.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/21/2018] [Accepted: 01/23/2018] [Indexed: 12/24/2022]
Abstract
The consequences of telomere loss or dysfunction become most prominent when cells enter the nuclear division stage of the cell cycle. At this climactic stage when chromosome segregation occurs, telomere fusions or entanglements can lead to chromosome breakage, wreaking havoc on genome stability. Here we review recent progress in understanding the mechanisms of detangling and breaking telomere associations at mitosis, as well as the unique ways in which telomeres are processed to allow regulated sister telomere separation. Moreover, we discuss unexpected roles for telomeres in orchestrating nuclear envelope breakdown and spindle formation, crucial processes for nuclear division. Finally, we discuss the discovery that telomeres create microdomains in the nucleus that are conducive to centromere assembly, cementing the unexpectedly influential role of telomeres in mitosis.
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Affiliation(s)
- Haitong Hou
- Telomere Biology Section, LBMB, NCI, NIH, Building 37, Room 6050, Bethesda MD 20892, USA
| | - Julia Promisel Cooper
- Telomere Biology Section, LBMB, NCI, NIH, Building 37, Room 6050, Bethesda MD 20892, USA.
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45
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Gothe HJ, Minneker V, Roukos V. Dynamics of Double-Strand Breaks: Implications for the Formation of Chromosome Translocations. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1044:27-38. [PMID: 29956289 DOI: 10.1007/978-981-13-0593-1_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Illegitimate joining of chromosome breaks can lead to the formation of chromosome translocations, a catastrophic type of genome rearrangements that often plays key roles in tumorigenesis. Emerging evidence suggests that the mobility of broken DNA loci can be an important determinant in partner search and clustering of individual breaks, events that can influence translocation frequency. We summarize here the recent literature on the mechanisms that regulate chromatin movement, focusing on studies exploring the motion properties of double-strand breaks in the context of chromatin, the functional consequences for DNA repair, and the formation of chromosome fusions.
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46
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Amitai A, Seeber A, Gasser SM, Holcman D. Visualization of Chromatin Decompaction and Break Site Extrusion as Predicted by Statistical Polymer Modeling of Single-Locus Trajectories. Cell Rep 2017; 18:1200-1214. [PMID: 28147275 DOI: 10.1016/j.celrep.2017.01.018] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 12/02/2016] [Accepted: 01/10/2017] [Indexed: 12/15/2022] Open
Abstract
Chromatin moves with subdiffusive and spatially constrained dynamics within the cell nucleus. Here, we use single-locus tracking by time-lapse fluorescence microscopy to uncover information regarding the forces that influence chromatin movement following the induction of a persistent DNA double-strand break (DSB). Using improved time-lapse imaging regimens, we monitor trajectories of tagged DNA loci at a high temporal resolution, which allows us to extract biophysical parameters through robust statistical analysis. Polymer modeling based on these parameters predicts chromatin domain expansion near a DSB and damage extrusion from the domain. Both phenomena are confirmed by live imaging in budding yeast. Calculation of the anomalous exponent of locus movement allows us to differentiate forces imposed on the nucleus through the actin cytoskeleton from those that arise from INO80 remodeler-dependent changes in nucleosome organization. Our analytical approach can be applied to high-density single-locus trajectories obtained in any cell type.
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Affiliation(s)
- Assaf Amitai
- Institut de Biologie de l'École Normale Supérieure, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Andrew Seeber
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; Faculty of Natural Sciences, University of Basel, 4056 Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; Faculty of Natural Sciences, University of Basel, 4056 Basel, Switzerland.
| | - David Holcman
- Institut de Biologie de l'École Normale Supérieure, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 Paris, France; Department of Applied Mathematics and Theoretical Physics, University of Cambridge and Churchill College, Cambridge CB30DS, UK.
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47
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Rad52 phosphorylation by Ipl1 and Mps1 contributes to Mps1 kinetochore localization and spindle assembly checkpoint regulation. Proc Natl Acad Sci U S A 2017; 114:E9261-E9270. [PMID: 29078282 DOI: 10.1073/pnas.1705261114] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rad52 is well known as a key factor in homologous recombination. Here, we report that Rad52 has functions unrelated to homologous recombination in Saccharomyces cerevisiae; it plays a role in the recruitment of Mps1 to the kinetochores and the maintenance of spindle assembly checkpoint (SAC) activity. Deletion of RAD52 causes various phenotypes related to the dysregulation of chromosome biorientation. Rad52 directly affects efficient operation of the SAC and accurate chromosome segregation. Remarkably, by using an in vitro kinase assay, we found that Rad52 is a substrate of Ipl1/Aurora and Mps1 in yeast and humans. Ipl1-dependent phosphorylation of Rad52 facilitates the kinetochore accumulation of Mps1, and Mps1-dependent phosphorylation of Rad52 is important for the accurate regulation of the SAC under spindle damage conditions. Taken together, our data provide detailed insights into the regulatory mechanism of chromosome biorientation by mitotic kinases.
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48
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Herbert S, Brion A, Arbona JM, Lelek M, Veillet A, Lelandais B, Parmar J, Fernández FG, Almayrac E, Khalil Y, Birgy E, Fabre E, Zimmer C. Chromatin stiffening underlies enhanced locus mobility after DNA damage in budding yeast. EMBO J 2017; 36:2595-2608. [PMID: 28694242 PMCID: PMC5579376 DOI: 10.15252/embj.201695842] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 05/15/2017] [Accepted: 05/18/2017] [Indexed: 12/31/2022] Open
Abstract
DNA double-strand breaks (DSBs) induce a cellular response that involves histone modifications and chromatin remodeling at the damaged site and increases chromosome dynamics both locally at the damaged site and globally in the nucleus. In parallel, it has become clear that the spatial organization and dynamics of chromosomes can be largely explained by the statistical properties of tethered, but randomly moving, polymer chains, characterized mainly by their rigidity and compaction. How these properties of chromatin are affected during DNA damage remains, however, unclear. Here, we use live cell microscopy to track chromatin loci and measure distances between loci on yeast chromosome IV in thousands of cells, in the presence or absence of genotoxic stress. We confirm that DSBs result in enhanced chromatin subdiffusion and show that intrachromosomal distances increase with DNA damage all along the chromosome. Our data can be explained by an increase in chromatin rigidity, but not by chromatin decondensation or centromeric untethering only. We provide evidence that chromatin stiffening is mediated in part by histone H2A phosphorylation. Our results support a genome-wide stiffening of the chromatin fiber as a consequence of DNA damage and as a novel mechanism underlying increased chromatin mobility.
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Affiliation(s)
- Sébastien Herbert
- Unité Imagerie et Modélisation, Institut Pasteur, Paris, France
- CNRS UMR 3691, C3BI, USR 3756 IP CNRS, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Alice Brion
- Equipe Biologie et Dynamique des Chromosomes, Institut Universitaire d'Hématologie, Hôpital St. Louis, Paris, France
- CNRS UMR 7212, INSERM U944, IUH, Université Paris Diderot Sorbonne Paris Cité, Paris, France
| | - Jean-Michel Arbona
- Unité Imagerie et Modélisation, Institut Pasteur, Paris, France
- CNRS UMR 3691, C3BI, USR 3756 IP CNRS, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Mickaël Lelek
- Unité Imagerie et Modélisation, Institut Pasteur, Paris, France
- CNRS UMR 3691, C3BI, USR 3756 IP CNRS, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Adeline Veillet
- Equipe Biologie et Dynamique des Chromosomes, Institut Universitaire d'Hématologie, Hôpital St. Louis, Paris, France
- CNRS UMR 7212, INSERM U944, IUH, Université Paris Diderot Sorbonne Paris Cité, Paris, France
| | - Benoît Lelandais
- Unité Imagerie et Modélisation, Institut Pasteur, Paris, France
- CNRS UMR 3691, C3BI, USR 3756 IP CNRS, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Jyotsana Parmar
- Unité Imagerie et Modélisation, Institut Pasteur, Paris, France
- CNRS UMR 3691, C3BI, USR 3756 IP CNRS, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Fabiola García Fernández
- Equipe Biologie et Dynamique des Chromosomes, Institut Universitaire d'Hématologie, Hôpital St. Louis, Paris, France
- CNRS UMR 7212, INSERM U944, IUH, Université Paris Diderot Sorbonne Paris Cité, Paris, France
| | - Etienne Almayrac
- Equipe Biologie et Dynamique des Chromosomes, Institut Universitaire d'Hématologie, Hôpital St. Louis, Paris, France
- CNRS UMR 7212, INSERM U944, IUH, Université Paris Diderot Sorbonne Paris Cité, Paris, France
| | - Yasmine Khalil
- Equipe Biologie et Dynamique des Chromosomes, Institut Universitaire d'Hématologie, Hôpital St. Louis, Paris, France
- CNRS UMR 7212, INSERM U944, IUH, Université Paris Diderot Sorbonne Paris Cité, Paris, France
| | - Eleonore Birgy
- Equipe Biologie et Dynamique des Chromosomes, Institut Universitaire d'Hématologie, Hôpital St. Louis, Paris, France
- CNRS UMR 7212, INSERM U944, IUH, Université Paris Diderot Sorbonne Paris Cité, Paris, France
| | - Emmanuelle Fabre
- Equipe Biologie et Dynamique des Chromosomes, Institut Universitaire d'Hématologie, Hôpital St. Louis, Paris, France
- CNRS UMR 7212, INSERM U944, IUH, Université Paris Diderot Sorbonne Paris Cité, Paris, France
| | - Christophe Zimmer
- Unité Imagerie et Modélisation, Institut Pasteur, Paris, France
- CNRS UMR 3691, C3BI, USR 3756 IP CNRS, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
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49
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Miné-Hattab J, Recamier V, Izeddin I, Rothstein R, Darzacq X. Multi-scale tracking reveals scale-dependent chromatin dynamics after DNA damage. Mol Biol Cell 2017; 28:mbc.E17-05-0317. [PMID: 28794266 PMCID: PMC5687033 DOI: 10.1091/mbc.e17-05-0317] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/21/2017] [Accepted: 08/02/2017] [Indexed: 12/19/2022] Open
Abstract
The dynamic organization of genes inside the nucleus is an important determinant for their function. Using fast DNA tracking microscopy in S. cerevisiae cells and improved analysis of mean square displacements, we quantified DNA motion at time scales ranging from 10 milliseconds to minute and found that following DNA damage, DNA exhibits distinct sub-diffusive regimes. In response to double-strand breaks, chromatin is more mobile at large time scales but, surprisingly, its mobility is reduced at short time scales. This effect is even more pronounced at the site of damage. Such a pattern of dynamics is consistent with a global increase in chromatin persistence length in response to DNA damage. Scale-dependent nuclear exploration is regulated by the Rad51 repair protein, both at the break and throughout the genome. We propose a model in which stiffening of the damaged ends by the repair complex, combined with global increased stiffness, act like a "needle in a ball of yarn", enhancing the ability of the break to traverse the chromatin meshwork.
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Affiliation(s)
- Judith Miné-Hattab
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Paris 75005, France
- Department of Genetics & Development, Columbia University Medical Center, New York, NY 10032, USA
- Nuclear Dynamics, CNRS UMR 3664, Institut Curie, Paris 75005, France
| | - Vincent Recamier
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Paris 75005, France
| | - Ignacio Izeddin
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Paris 75005, France
- Institut Langevin, CNRS, ESPCI Paris, PSL Research University, 75005 Paris, France
| | - Rodney Rothstein
- Department of Genetics & Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Xavier Darzacq
- Division of Genetics, Genomics & Development, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Paris 75005, France
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50
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Batté A, Brocas C, Bordelet H, Hocher A, Ruault M, Adjiri A, Taddei A, Dubrana K. Recombination at subtelomeres is regulated by physical distance, double-strand break resection and chromatin status. EMBO J 2017; 36:2609-2625. [PMID: 28754657 DOI: 10.15252/embj.201796631] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 06/23/2017] [Accepted: 06/26/2017] [Indexed: 11/09/2022] Open
Abstract
Homologous recombination (HR) is a conserved mechanism that repairs broken chromosomes via intact homologous sequences. How different genomic, chromatin and subnuclear contexts influence HR efficiency and outcome is poorly understood. We developed an assay to assess HR outcome by gene conversion (GC) and break-induced replication (BIR), and discovered that subtelomeric double-stranded breaks (DSBs) are preferentially repaired by BIR despite the presence of flanking homologous sequences. Overexpression of a silencing-deficient SIR3 mutant led to active grouping of telomeres and specifically increased the GC efficiency between subtelomeres. Thus, physical distance limits GC at subtelomeres. However, the repair efficiency between reciprocal intrachromosomal and subtelomeric sequences varies up to 15-fold, depending on the location of the DSB, indicating that spatial proximity is not the only limiting factor for HR EXO1 deletion limited the resection at subtelomeric DSBs and improved GC efficiency. The presence of repressive chromatin at subtelomeric DSBs also favoured recombination, by counteracting EXO1-mediated resection. Thus, repressive chromatin promotes HR at subtelomeric DSBs by limiting DSB resection and protecting against genetic information loss.
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Affiliation(s)
- Amandine Batté
- Institute of Molecular and Cellular Radiobiology, CEA/DRF, Fontenay-aux-Roses cedex, France.,Inserm U967, Fontenay-aux-Roses cedex, France.,Université Paris-Diderot et Université Paris-Sud, UMR967, Fontenay-aux-Roses cedex, France
| | - Clémentine Brocas
- Institute of Molecular and Cellular Radiobiology, CEA/DRF, Fontenay-aux-Roses cedex, France.,Inserm U967, Fontenay-aux-Roses cedex, France.,Université Paris-Diderot et Université Paris-Sud, UMR967, Fontenay-aux-Roses cedex, France
| | - Hélène Bordelet
- Institute of Molecular and Cellular Radiobiology, CEA/DRF, Fontenay-aux-Roses cedex, France.,Inserm U967, Fontenay-aux-Roses cedex, France.,Université Paris-Diderot et Université Paris-Sud, UMR967, Fontenay-aux-Roses cedex, France
| | - Antoine Hocher
- Institut Curie, PSL Research University, CNRS, UMR3664, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, Paris, France
| | - Myriam Ruault
- Institut Curie, PSL Research University, CNRS, UMR3664, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, Paris, France
| | - Adouda Adjiri
- Institut Curie, PSL Research University, CNRS, UMR3664, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, Paris, France
| | - Angela Taddei
- Institut Curie, PSL Research University, CNRS, UMR3664, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, Paris, France
| | - Karine Dubrana
- Institute of Molecular and Cellular Radiobiology, CEA/DRF, Fontenay-aux-Roses cedex, France .,Inserm U967, Fontenay-aux-Roses cedex, France.,Université Paris-Diderot et Université Paris-Sud, UMR967, Fontenay-aux-Roses cedex, France
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