151
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Lottersberger F, Karssemeijer RA, Dimitrova N, de Lange T. 53BP1 and the LINC Complex Promote Microtubule-Dependent DSB Mobility and DNA Repair. Cell 2016; 163:880-93. [PMID: 26544937 DOI: 10.1016/j.cell.2015.09.057] [Citation(s) in RCA: 220] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 09/14/2015] [Accepted: 09/28/2015] [Indexed: 01/13/2023]
Abstract
Increased mobility of chromatin surrounding double-strand breaks (DSBs) has been noted in yeast and mammalian cells but the underlying mechanism and its contribution to DSB repair remain unclear. Here, we use a telomere-based system to track DNA damage foci with high resolution in living cells. We find that the greater mobility of damaged chromatin requires 53BP1, SUN1/2 in the linker of the nucleoskeleton, and cytoskeleton (LINC) complex and dynamic microtubules. The data further demonstrate that the excursions promote non-homologous end joining of dysfunctional telomeres and implicated Nesprin-4 and kinesins in telomere fusion. 53BP1/LINC/microtubule-dependent mobility is also evident at irradiation-induced DSBs and contributes to the mis-rejoining of drug-induced DSBs in BRCA1-deficient cells showing that DSB mobility can be detrimental in cells with numerous DSBs. In contrast, under physiological conditions where cells have only one or a few lesions, DSB mobility is proposed to prevent errors in DNA repair.
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Affiliation(s)
- Francisca Lottersberger
- Laboratory for Cell Biology and Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Roos Anna Karssemeijer
- Laboratory for Cell Biology and Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Nadya Dimitrova
- Laboratory for Cell Biology and Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Titia de Lange
- Laboratory for Cell Biology and Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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152
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DNA damage signalling targets the kinetochore to promote chromatin mobility. Nat Cell Biol 2016; 18:281-90. [PMID: 26829389 DOI: 10.1038/ncb3308] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 01/04/2016] [Indexed: 12/11/2022]
Abstract
In budding yeast, chromatin mobility increases after a DNA double-strand break (DSB). This increase is dependent on Mec1, the yeast ATR kinase, but the targets responsible for this phenomenon are unknown. Here we report that the Mec1-dependent phosphorylation of Cep3, a kinetochore component, is required to stimulate chromatin mobility after DNA breaks. Cep3 phosphorylation counteracts a constraint on chromosome movement imposed by the attachment of centromeres to the spindle pole body. A second constraint, imposed by the tethering of telomeres to the nuclear periphery, is also relieved after chromosome breakage. A non-phosphorylatable Cep3 mutant that impairs DSB-induced chromatin mobility is proficient in DSB repair, suggesting that break-induced chromatin mobility may be dispensable for homology search. Rather, we propose that the relief of centromeric constraint promotes cell cycle arrest and faithful chromosome segregation through the engagement of the spindle assembly checkpoint.
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153
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Hirakawa T, Matsunaga S. Chromatin Tagging Systems Contribute to Live Imaging Analyses for Chromatin Dynamics. CYTOLOGIA 2016. [DOI: 10.1508/cytologia.81.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Takeshi Hirakawa
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
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154
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Hirakawa T, Matsunaga S. Three-Dimensional, Live-Cell Imaging of Chromatin Dynamics in Plant Nuclei Using Chromatin Tagging Systems. Methods Mol Biol 2016; 1469:189-195. [PMID: 27557696 DOI: 10.1007/978-1-4939-4931-1_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In plants, chromatin dynamics spatiotemporally change in response to various environmental stimuli. However, little is known about chromatin dynamics in the nuclei of plants. Here, we introduce a three-dimensional, live-cell imaging method that can monitor chromatin dynamics in nuclei via a chromatin tagging system that can visualize specific genomic loci in living plant cells. The chromatin tagging system is based on a bacterial operator/repressor system in which the repressor is fused to fluorescent proteins. A recent refinement of promoters for the system solved the problem of gene silencing and abnormal pairing frequencies between operators. Using this system, we can detect the spatiotemporal dynamics of two homologous loci as two fluorescent signals within a nucleus and monitor the distance between homologous loci. These live-cell imaging methods will provide new insights into genome organization, development processes, and subnuclear responses to environmental stimuli in plants.
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Affiliation(s)
- Takeshi Hirakawa
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641, Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641, Yamazaki, Noda, Chiba, 278-8510, Japan.
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155
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Caron P, Choudjaye J, Clouaire T, Bugler B, Daburon V, Aguirrebengoa M, Mangeat T, Iacovoni JS, Álvarez-Quilón A, Cortés-Ledesma F, Legube G. Non-redundant Functions of ATM and DNA-PKcs in Response to DNA Double-Strand Breaks. Cell Rep 2015; 13:1598-609. [PMID: 26586426 PMCID: PMC4670905 DOI: 10.1016/j.celrep.2015.10.024] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 09/04/2015] [Accepted: 10/06/2015] [Indexed: 12/13/2022] Open
Abstract
DNA double-strand breaks (DSBs) elicit the so-called DNA damage response (DDR), largely relying on ataxia telangiectasia mutated (ATM) and DNA-dependent protein kinase (DNA-PKcs), two members of the PI3K-like kinase family, whose respective functions during the sequential steps of the DDR remains controversial. Using the DIvA system (DSB inducible via AsiSI) combined with high-resolution mapping and advanced microscopy, we uncovered that both ATM and DNA-PKcs spread in cis on a confined region surrounding DSBs, independently of the pathway used for repair. However, once recruited, these kinases exhibit non-overlapping functions on end joining and γH2AX domain establishment. More specifically, we found that ATM is required to ensure the association of multiple DSBs within "repair foci." Our results suggest that ATM acts not only on chromatin marks but also on higher-order chromatin organization to ensure repair accuracy and survival.
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Affiliation(s)
- Pierre Caron
- Université de Toulouse, UPS, LBCMCP, 118 route de Narbonne, 31062 Toulouse, France; CNRS, LBCMCP, 31062 Toulouse, France
| | - Jonathan Choudjaye
- Université de Toulouse, UPS, LBCMCP, 118 route de Narbonne, 31062 Toulouse, France; CNRS, LBCMCP, 31062 Toulouse, France
| | - Thomas Clouaire
- Université de Toulouse, UPS, LBCMCP, 118 route de Narbonne, 31062 Toulouse, France; CNRS, LBCMCP, 31062 Toulouse, France
| | - Béatrix Bugler
- Université de Toulouse, UPS, LBCMCP, 118 route de Narbonne, 31062 Toulouse, France; CNRS, LBCMCP, 31062 Toulouse, France
| | - Virginie Daburon
- Université de Toulouse, UPS, LBCMCP, 118 route de Narbonne, 31062 Toulouse, France; CNRS, LBCMCP, 31062 Toulouse, France
| | - Marion Aguirrebengoa
- Université de Toulouse, UPS, LBCMCP, 118 route de Narbonne, 31062 Toulouse, France; CNRS, LBCMCP, 31062 Toulouse, France
| | - Thomas Mangeat
- Université de Toulouse, UPS, LBCMCP, 118 route de Narbonne, 31062 Toulouse, France; CNRS, LBCMCP, 31062 Toulouse, France
| | - Jason S Iacovoni
- Bioinformatic Plateau I2MC, INSERM and University of Toulouse, 1 Avenue Jean Poulhes, BP 84225, 31432 Toulouse Cedex 4, France
| | - Alejandro Álvarez-Quilón
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), CSIC-Universidad de Sevilla, Sevilla 41092, Spain
| | - Felipe Cortés-Ledesma
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), CSIC-Universidad de Sevilla, Sevilla 41092, Spain
| | - Gaëlle Legube
- Université de Toulouse, UPS, LBCMCP, 118 route de Narbonne, 31062 Toulouse, France; CNRS, LBCMCP, 31062 Toulouse, France.
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156
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Kowalczykowski SC. An Overview of the Molecular Mechanisms of Recombinational DNA Repair. Cold Spring Harb Perspect Biol 2015; 7:a016410. [PMID: 26525148 PMCID: PMC4632670 DOI: 10.1101/cshperspect.a016410] [Citation(s) in RCA: 320] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Recombinational DNA repair is a universal aspect of DNA metabolism and is essential for genomic integrity. It is a template-directed process that uses a second chromosomal copy (sister, daughter, or homolog) to ensure proper repair of broken chromosomes. The key steps of recombination are conserved from phage through human, and an overview of those steps is provided in this review. The first step is resection by helicases and nucleases to produce single-stranded DNA (ssDNA) that defines the homologous locus. The ssDNA is a scaffold for assembly of the RecA/RAD51 filament, which promotes the homology search. On finding homology, the nucleoprotein filament catalyzes exchange of DNA strands to form a joint molecule. Recombination is controlled by regulating the fate of both RecA/RAD51 filaments and DNA pairing intermediates. Finally, intermediates that mature into Holliday structures are disjoined by either nucleolytic resolution or topological dissolution.
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Affiliation(s)
- Stephen C Kowalczykowski
- Department of Microbiology & Molecular Genetics and Department of Molecular and Cellular Biology, University of California, Davis, Davis, California 95616
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157
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Heterochromatic breaks move to the nuclear periphery to continue recombinational repair. Nat Cell Biol 2015; 17:1401-11. [PMID: 26502056 PMCID: PMC4628585 DOI: 10.1038/ncb3258] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 09/21/2015] [Indexed: 12/16/2022]
Abstract
Heterochromatin mostly comprises repeated sequences prone to harmful ectopic recombination during double-strand break (DSB) repair. In Drosophila cells, ‘safe’ homologous recombination (HR) repair of heterochromatic breaks relies on a specialized pathway that relocalizes damaged sequences away from the heterochromatin domain before strand invasion. Here we show that heterochromatic DSBs move to the nuclear periphery to continue HR repair. Relocalization depends on nuclear pore and inner nuclear membrane proteins (INMPs) that anchor repair sites to the nuclear periphery via the Smc5/6-interacting proteins STUbL/RENi. Both the initial block to HR progression inside the heterochromatin domain, and the targeting of repair sites to the nuclear periphery, rely on SUMO and SUMO E3 ligases. This study reveals a critical role for SUMOylation in the spatial and temporal regulation of HR repair in heterochromatin, and identifies the nuclear periphery as a specialized site for heterochromatin repair in a multicellular eukaryote.
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158
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Géli V, Lisby M. Recombinational DNA repair is regulated by compartmentalization of DNA lesions at the nuclear pore complex. Bioessays 2015; 37:1287-92. [PMID: 26422820 DOI: 10.1002/bies.201500084] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The nuclear pore complex (NPC) is emerging as a center for recruitment of a class of "difficult to repair" lesions such as double-strand breaks without a repair template and eroded telomeres in telomerase-deficient cells. In addition to such pathological situations, a recent study by Su and colleagues shows that also physiological threats to genome integrity such as DNA secondary structure-forming triplet repeat sequences relocalize to the NPC during DNA replication. Mutants that fail to reposition the triplet repeat locus to the NPC cause repeat instability. Here, we review the types of DNA lesions that relocalize to the NPC, the putative mechanisms of relocalization, and the types of recombinational repair that are stimulated by the NPC, and present a model for NPC-facilitated repair.
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Affiliation(s)
- Vincent Géli
- Marseille Cancer Research Center (CRCM), U1068 Inserm, UMR7258 CNRS, Aix Marseille University, Institut Paoli-Calmettes, LNCC (Equipe labellisée), Marseille, France
| | - Michael Lisby
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
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159
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Abstract
Clear organizational patterns on the genome have emerged from the statistics of population studies of fixed cells. However, how these results translate into the dynamics of individual living cells remains unexplored. We use statistical mechanics models derived from polymer physics to inquire into the effects that chromosome properties and dynamics have in the temporal and spatial behavior of the genome. Overall, changes in the properties of individual chains affect the behavior of all other chains in the domain. We explore two modifications of chain behavior: single chain motion and chain-chain interactions. We show that there is not a direct relation between these effects, as increase in motion, doesn't necessarily translate into an increase on chain interaction.
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Affiliation(s)
- Paula A Vasquez
- a Department of Mathematics; University of South Carolina; Columbia, SC USA
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160
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Abstract
Recombination is a central process to stably maintain and transmit a genome through somatic cell divisions and to new generations. Hence, recombination needs to be coordinated with other events occurring on the DNA template, such as DNA replication, transcription, and the specialized chromosomal functions at centromeres and telomeres. Moreover, regulation with respect to the cell-cycle stage is required as much as spatiotemporal coordination within the nuclear volume. These regulatory mechanisms impinge on the DNA substrate through modifications of the chromatin and directly on recombination proteins through a myriad of posttranslational modifications (PTMs) and additional mechanisms. Although recombination is primarily appreciated to maintain genomic stability, the process also contributes to gross chromosomal arrangements and copy-number changes. Hence, the recombination process itself requires quality control to ensure high fidelity and avoid genomic instability. Evidently, recombination and its regulatory processes have significant impact on human disease, specifically cancer and, possibly, neurodegenerative diseases.
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Affiliation(s)
- Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616-8665 Department of Molecular and Cellular Biology, University of California, Davis, Davis, California 95616-8665
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161
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Amitai A, Toulouze M, Dubrana K, Holcman D. Analysis of Single Locus Trajectories for Extracting In Vivo Chromatin Tethering Interactions. PLoS Comput Biol 2015; 11:e1004433. [PMID: 26317360 PMCID: PMC4552938 DOI: 10.1371/journal.pcbi.1004433] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 07/06/2015] [Indexed: 12/16/2022] Open
Abstract
Is it possible to extract tethering forces applied on chromatin from the statistics of a single locus trajectories imaged in vivo? Chromatin fragments interact with many partners such as the nuclear membrane, other chromosomes or nuclear bodies, but the resulting forces cannot be directly measured in vivo. However, they impact chromatin dynamics and should be reflected in particular in the motion of a single locus. We present here a method based on polymer models and statistics of single trajectories to extract the force characteristics and in particular when they are generated by the gradient of a quadratic potential well. Using numerical simulations of a Rouse polymer and live cell imaging of the MAT-locus located on the yeast Saccharomyces cerevisiae chromosome III, we recover the amplitude and the distance between the observed and the interacting monomer. To conclude, the confined trajectories we observed in vivo reflect local interaction on chromatin.
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Affiliation(s)
- Assaf Amitai
- Institute for Medical Engineering & Science, The Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, United States of America
| | - Mathias Toulouze
- Laboratory of genetic instability and nuclear organization, CEA, Fontenay-aux-Roses, France
| | - Karine Dubrana
- Laboratory of genetic instability and nuclear organization, CEA, Fontenay-aux-Roses, France
| | - David Holcman
- IBENS, Ecole Normale Supérieure, Paris, France and Mathematical Institute, University of Oxford, Oxford, United Kingdom
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162
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Perinuclear tethers license telomeric DSBs for a broad kinesin- and NPC-dependent DNA repair process. Nat Commun 2015. [PMID: 26205667 DOI: 10.1038/ncomms8742] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
DNA double-strand breaks (DSBs) are often targeted to nuclear pore complexes (NPCs) for repair. How targeting is achieved and the DNA repair pathways involved in this process remain unclear. Here, we show that the kinesin-14 motor protein complex (Cik1-Kar3) cooperates with chromatin remodellers to mediate interactions between subtelomeric DSBs and the Nup84 nuclear pore complex to ensure cell survival via break-induced replication (BIR), an error-prone DNA repair process. Insertion of a DNA zip code near the subtelomeric DSB site artificially targets it to NPCs hyperactivating this repair mechanism. Kinesin-14 and Nup84 mediate BIR-dependent repair at non-telomeric DSBs whereas perinuclear telomere tethers are only required for telomeric BIR. Furthermore, kinesin-14 plays a critical role in telomerase-independent telomere maintenance. Thus, we uncover roles for kinesin and NPCs in DNA repair by BIR and reveal that perinuclear telomere anchors license subtelomeric DSBs for this error-prone DNA repair mechanism.
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163
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Abstract
Homology-dependent exchange of genetic information between DNA molecules has a profound impact on the maintenance of genome integrity by facilitating error-free DNA repair, replication, and chromosome segregation during cell division as well as programmed cell developmental events. This chapter will focus on homologous mitotic recombination in budding yeast Saccharomyces cerevisiae. However, there is an important link between mitotic and meiotic recombination (covered in the forthcoming chapter by Hunter et al. 2015) and many of the functions are evolutionarily conserved. Here we will discuss several models that have been proposed to explain the mechanism of mitotic recombination, the genes and proteins involved in various pathways, the genetic and physical assays used to discover and study these genes, and the roles of many of these proteins inside the cell.
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164
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Georgescu W, Osseiran A, Rojec M, Liu Y, Bombrun M, Tang J, Costes SV. Characterizing the DNA Damage Response by Cell Tracking Algorithms and Cell Features Classification Using High-Content Time-Lapse Analysis. PLoS One 2015; 10:e0129438. [PMID: 26107175 PMCID: PMC4479605 DOI: 10.1371/journal.pone.0129438] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 05/10/2015] [Indexed: 01/08/2023] Open
Abstract
Traditionally, the kinetics of DNA repair have been estimated using immunocytochemistry by labeling proteins involved in the DNA damage response (DDR) with fluorescent markers in a fixed cell assay. However, detailed knowledge of DDR dynamics across multiple cell generations cannot be obtained using a limited number of fixed cell time-points. Here we report on the dynamics of 53BP1 radiation induced foci (RIF) across multiple cell generations using live cell imaging of non-malignant human mammary epithelial cells (MCF10A) expressing histone H2B-GFP and the DNA repair protein 53BP1-mCherry. Using automatic extraction of RIF imaging features and linear programming techniques, we were able to characterize detailed RIF kinetics for 24 hours before and 24 hours after exposure to low and high doses of ionizing radiation. High-content-analysis at the single cell level over hundreds of cells allows us to quantify precisely the dose dependence of 53BP1 protein production, RIF nuclear localization and RIF movement after exposure to X-ray. Using elastic registration techniques based on the nuclear pattern of individual cells, we could describe the motion of individual RIF precisely within the nucleus. We show that DNA repair occurs in a limited number of large domains, within which multiple small RIFs form, merge and/or resolve with random motion following normal diffusion law. Large foci formation is shown to be mainly happening through the merging of smaller RIF rather than through growth of an individual focus. We estimate repair domain sizes of 7.5 to 11 µm2 with a maximum number of ~15 domains per MCF10A cell. This work also highlights DDR which are specific to doses larger than 1 Gy such as rapid 53BP1 protein increase in the nucleus and foci diffusion rates that are significantly faster than for spontaneous foci movement. We hypothesize that RIF merging reflects a "stressed" DNA repair process that has been taken outside physiological conditions when too many DSB occur at once. High doses of ionizing radiation lead to RIF merging into repair domains which in turn increases DSB proximity and misrepair. Such finding may therefore be critical to explain the supralinear dose dependence for chromosomal rearrangement and cell death measured after exposure to ionizing radiation.
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Affiliation(s)
- Walter Georgescu
- Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, United States of America
| | - Alma Osseiran
- Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, United States of America
| | - Maria Rojec
- Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, United States of America
| | - Yueyong Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, United States of America
| | | | - Jonathan Tang
- Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, United States of America
| | - Sylvain V. Costes
- Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, United States of America
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165
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DNA double-strand breaks alter the spatial arrangement of homologous loci in plant cells. Sci Rep 2015; 5:11058. [PMID: 26046331 PMCID: PMC4457028 DOI: 10.1038/srep11058] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/11/2015] [Indexed: 12/31/2022] Open
Abstract
Chromatin dynamics and arrangement are involved in many biological processes in nuclei of eukaryotes including plants. Plants have to respond rapidly to various environmental stimuli to achieve growth and development because they cannot move. It is assumed that the alteration of chromatin dynamics and arrangement support the response to these stimuli; however, there is little information in plants. In this study, we investigated the chromatin dynamics and arrangement with DNA damage in Arabidopsis thaliana by live-cell imaging with the lacO/LacI-EGFP system and simulation analysis. It was revealed that homologous loci kept a constant distance in nuclei of A. thaliana roots in general growth. We also found that DNA double-strand breaks (DSBs) induce the approach of the homologous loci with γ-irradiation. Furthermore, AtRAD54, which performs an important role in the homologous recombination repair pathway, was involved in the pairing of homologous loci with γ-irradiation. These results suggest that homologous loci approach each other to repair DSBs, and AtRAD54 mediates these phenomena.
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166
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Wang R, Mozziconacci J, Bancaud A, Gadal O. Principles of chromatin organization in yeast: relevance of polymer models to describe nuclear organization and dynamics. Curr Opin Cell Biol 2015; 34:54-60. [PMID: 25956973 DOI: 10.1016/j.ceb.2015.04.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 03/17/2015] [Accepted: 04/15/2015] [Indexed: 11/29/2022]
Abstract
Nuclear organization can impact on all aspects of the genome life cycle. This organization is thoroughly investigated by advanced imaging and chromosome conformation capture techniques, providing considerable amount of datasets describing the spatial organization of chromosomes. In this review, we will focus on polymer models to describe chromosome statics and dynamics in the yeast Saccharomyces cerevisiae. We suggest that the equilibrium configuration of a polymer chain tethered at both ends and placed in a confined volume is consistent with the current literature, implying that local chromatin interactions play a secondary role in yeast nuclear organization. Future challenges are to reach an integrated multi-scale description of yeast chromosome organization, which is crucially needed to improve our understanding of the regulation of genomic transaction.
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Affiliation(s)
- Renjie Wang
- LBME du CNRS, France; Laboratoire de Biologie Moleculaire Eucaryote, Université de Toulouse, 118 route de Narbonne, F-31000 Toulouse, France
| | - Julien Mozziconacci
- Laboratory for Theoretical Physics of Condensed Matter UMR7600, Sorbonne University, UPMC, 75005 Paris, France; Groupement de recherche Architecture et Dynamique Nucléaire (GDR ADN), France
| | - Aurélien Bancaud
- Groupement de recherche Architecture et Dynamique Nucléaire (GDR ADN), France; CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France; Univ de Toulouse, LAAS, F-31400 Toulouse, France
| | - Olivier Gadal
- LBME du CNRS, France; Laboratoire de Biologie Moleculaire Eucaryote, Université de Toulouse, 118 route de Narbonne, F-31000 Toulouse, France; Groupement de recherche Architecture et Dynamique Nucléaire (GDR ADN), France.
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167
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Cho NW, Dilley RL, Lampson MA, Greenberg RA. Interchromosomal homology searches drive directional ALT telomere movement and synapsis. Cell 2015; 159:108-121. [PMID: 25259924 DOI: 10.1016/j.cell.2014.08.030] [Citation(s) in RCA: 261] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Revised: 06/16/2014] [Accepted: 08/25/2014] [Indexed: 12/17/2022]
Abstract
Telomere length maintenance is a requisite feature of cellular immortalization and a hallmark of human cancer. While most human cancers express telomerase activity, ∼10%-15% employ a recombination-dependent telomere maintenance pathway known as alternative lengthening of telomeres (ALT) that is characterized by multitelomere clusters and associated promyelocytic leukemia protein bodies. Here, we show that a DNA double-strand break (DSB) response at ALT telomeres triggers long-range movement and clustering between chromosome termini, resulting in homology-directed telomere synthesis. Damaged telomeres initiate increased random surveillance of nuclear space before displaying rapid directional movement and association with recipient telomeres over micron-range distances. This phenomenon required Rad51 and the Hop2-Mnd1 heterodimer, which are essential for homologous chromosome synapsis during meiosis. These findings implicate a specialized homology searching mechanism in ALT-dependent telomere maintenance and provide a molecular basis underlying the preference for recombination between nonsister telomeres during ALT.
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Affiliation(s)
- Nam Woo Cho
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104-6160, USA
| | - Robert L Dilley
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104-6160, USA
| | - Michael A Lampson
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Roger A Greenberg
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104-6160, USA; Department of Pathology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104-6160, USA; Abramson Family Cancer Research Institute, Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA 19104-6160, USA.
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168
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Su XA, Dion V, Gasser SM, Freudenreich CH. Regulation of recombination at yeast nuclear pores controls repair and triplet repeat stability. Genes Dev 2015; 29:1006-17. [PMID: 25940904 PMCID: PMC4441049 DOI: 10.1101/gad.256404.114] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 04/10/2015] [Indexed: 12/16/2022]
Abstract
Secondary structure-forming DNA sequences such as CAG repeats interfere with replication and repair, provoking fork stalling, chromosome fragility, and recombination. In budding yeast, Su et al. find that expanded CAG repeats are more likely than unexpanded repeats to localize to the nuclear periphery and that the relocation of damage to nuclear pores plays an important role in a naturally occurring repair process. Secondary structure-forming DNA sequences such as CAG repeats interfere with replication and repair, provoking fork stalling, chromosome fragility, and recombination. In budding yeast, we found that expanded CAG repeats are more likely than unexpanded repeats to localize to the nuclear periphery. This positioning is transient, occurs in late S phase, requires replication, and is associated with decreased subnuclear mobility of the locus. In contrast to persistent double-stranded breaks, expanded CAG repeats at the nuclear envelope associate with pores but not with the inner nuclear membrane protein Mps3. Relocation requires Nup84 and the Slx5/8 SUMO-dependent ubiquitin ligase but not Rad51, Mec1, or Tel1. Importantly, the presence of the Nup84 pore subcomplex and Slx5/8 suppresses CAG repeat fragility and instability. Repeat instability in nup84, slx5, or slx8 mutant cells arises through aberrant homologous recombination and is distinct from instability arising from the loss of ligase 4-dependent end-joining. Genetic and physical analysis of Rad52 sumoylation and binding at the CAG tract suggests that Slx5/8 targets sumoylated Rad52 for degradation at the pore to facilitate recovery from acute replication stress by promoting replication fork restart. We thereby confirmed that the relocation of damage to nuclear pores plays an important role in a naturally occurring repair process.
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Affiliation(s)
- Xiaofeng A Su
- Department of Biology, Tufts University, Medford, Massachusetts 02155, USA
| | - Vincent Dion
- Friedrich Miescher Institute for Biomedical Research, CH-4058 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
| | - Catherine H Freudenreich
- Department of Biology, Tufts University, Medford, Massachusetts 02155, USA; Program in Genetics, Tufts University, Medford, Massachusetts 02155, USA;
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169
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Qiu GH. Protection of the genome and central protein-coding sequences by non-coding DNA against DNA damage from radiation. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2015; 764:108-17. [DOI: 10.1016/j.mrrev.2015.04.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 03/11/2015] [Accepted: 04/22/2015] [Indexed: 01/08/2023]
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170
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Abstract
Homologous recombination provides high-fidelity DNA repair throughout all domains of life. Live cell fluorescence microscopy offers the opportunity to image individual recombination events in real time providing insight into the in vivo biochemistry of the involved proteins and DNA molecules as well as the cellular organization of the process of homologous recombination. Herein we review the cell biological aspects of mitotic homologous recombination with a focus on Saccharomyces cerevisiae and mammalian cells, but will also draw on findings from other experimental systems. Key topics of this review include the stoichiometry and dynamics of recombination complexes in vivo, the choreography of assembly and disassembly of recombination proteins at sites of DNA damage, the mobilization of damaged DNA during homology search, and the functional compartmentalization of the nucleus with respect to capacity of homologous recombination.
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Affiliation(s)
- Michael Lisby
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Rodney Rothstein
- Department of Genetics and Development, Columbia University Medical Center, New York, New York 10032
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171
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Gerhold CB, Hauer MH, Gasser SM. INO80-C and SWR-C: Guardians of the Genome. J Mol Biol 2015; 427:637-51. [DOI: 10.1016/j.jmb.2014.10.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 10/13/2014] [Accepted: 10/17/2014] [Indexed: 01/01/2023]
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172
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Bianchi A, Lanzuolo C. Into the chromatin world: Role of nuclear architecture in epigenome regulation. AIMS BIOPHYSICS 2015. [DOI: 10.3934/biophy.2015.4.585] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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173
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Horigome C, Dion V, Seeber A, Gehlen LR, Gasser SM. Visualizing the spatiotemporal dynamics of DNA damage in budding yeast. Methods Mol Biol 2015; 1292:77-96. [PMID: 25804749 DOI: 10.1007/978-1-4939-2522-3_6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Fluorescence microscopy has enabled the analysis of both the spatial distribution of DNA damage and its dynamics during the DNA damage response (DDR). Three microscopic techniques can be used to study the spatiotemporal dynamics of DNA damage. In the first part we describe how we determine the position of DNA double-strand breaks (DSBs) relative to the nuclear envelope. The second part describes how to quantify the co-localization of DNA DSBs with nuclear pore clusters, or other nuclear subcompartments. The final protocols describe methods for the quantification of locus mobility over time.
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Affiliation(s)
- Chihiro Horigome
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
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174
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Lebeaupin T, Sellou H, Timinszky G, Huet S. Chromatin dynamics at DNA breaks: what, how and why? AIMS BIOPHYSICS 2015. [DOI: 10.3934/biophy.2015.4.458] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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175
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Liu J, Vidi PA, Lelièvre SA, Irudayaraj JMK. Nanoscale histone localization in live cells reveals reduced chromatin mobility in response to DNA damage. J Cell Sci 2014; 128:599-604. [PMID: 25501817 DOI: 10.1242/jcs.161885] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Nuclear functions including gene expression, DNA replication and genome maintenance intimately rely on dynamic changes in chromatin organization. The movements of chromatin fibers might play important roles in the regulation of these fundamental processes, yet the mechanisms controlling chromatin mobility are poorly understood owing to methodological limitations for the assessment of chromatin movements. Here, we present a facile and quantitative technique that relies on photoactivation of GFP-tagged histones and paired-particle tracking to measure chromatin mobility in live cells. We validate the method by comparing live cells to ATP-depleted cells and show that chromatin movements in mammalian cells are predominantly energy dependent. We also find that chromatin diffusion decreases in response to DNA breaks induced by a genotoxic drug or by the ISceI meganuclease. Timecourse analysis after cell exposure to ionizing radiation indicates that the decrease in chromatin mobility is transient and precedes subsequent increased mobility. Future applications of the method in the DNA repair field and beyond are discussed.
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Affiliation(s)
- Jing Liu
- Department of Agricultural and Biological Engineering, Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA
| | - Pierre-Alexandre Vidi
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Sophie A Lelièvre
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907, USA Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Joseph M K Irudayaraj
- Department of Agricultural and Biological Engineering, Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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176
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Lemaître C, Soutoglou E. DSB (Im)mobility and DNA repair compartmentalization in mammalian cells. J Mol Biol 2014; 427:652-8. [PMID: 25463437 DOI: 10.1016/j.jmb.2014.11.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Chromosomal translocations are considered as causal in approximately 20% of cancers. Therefore, understanding their mechanisms of formation is crucial in the prevention of carcinogenesis. The first step of translocation formation is the concomitant occurrence of double-strand DNA breaks (DSBs) in two different chromosomes. DSBs can be repaired by different repair mechanisms, including error-free homologous recombination (HR), potentially error-prone non-homologous end joining (NHEJ) and the highly mutagenic alternative end joining (alt-EJ) pathways. Regulation of DNA repair pathway choice is crucial to avoid genomic instability. In yeast, DSBs are mobile and can scan the entire nucleus to be repaired in specialized DNA repair centers or if they are persistent, in order to associate with the nuclear pores or the nuclear envelope where they can be repaired by specialized repair pathways. DSB mobility is limited in mammals; therefore, raising the question of whether the position at which a DSB occurs influences its repair. Here, we review the recent literature addressing this question. We first present the reports describing the extent of DSB mobility in mammalian cells. In a second part, we discuss the consequences of non-random gene positioning on chromosomal translocations formation. In the third part, we discuss the mobility of heterochromatic DSBs in light of our recent data on DSB repair at the nuclear lamina, and finally, we show that DSB repair compartmentalization at the nuclear periphery is conserved from yeast to mammals, further pointing to a role for gene positioning in the outcome of DSB repair. When regarded as a whole, the different studies reviewed here demonstrate the importance of nuclear architecture on DSB repair and reveal gene positioning as an important parameter in the study of tumorigenesis.
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Affiliation(s)
- Charlène Lemaître
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, CEDEX, France; Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France; Centre National de Recherche Scientifique, UMR7104, Illkirch, France; Université de Strasbourg, 67404, Illkirch, CEDEX, France
| | - Evi Soutoglou
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, CEDEX, France; Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France; Centre National de Recherche Scientifique, UMR7104, Illkirch, France; Université de Strasbourg, 67404, Illkirch, CEDEX, France.
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177
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Guarino E, Cojoc G, García-Ulloa A, Tolić IM, Kearsey SE. Real-time imaging of DNA damage in yeast cells using ultra-short near-infrared pulsed laser irradiation. PLoS One 2014; 9:e113325. [PMID: 25409521 PMCID: PMC4237433 DOI: 10.1371/journal.pone.0113325] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 10/22/2014] [Indexed: 01/12/2023] Open
Abstract
Analysis of accumulation of repair and checkpoint proteins at repair sites in yeast nuclei has conventionally used chemical agents, ionizing radiation or induction of endonucleases to inflict localized damage. In addition to these methods, similar studies in mammalian cells have used laser irradiation, which has the advantage that damage is inflicted at a specific nuclear region and at a precise time, and this allows accurate kinetic analysis of protein accumulation at DNA damage sites. We show here that it is feasible to use short pulses of near-infrared laser irradiation to inflict DNA damage in subnuclear regions of yeast nuclei by multiphoton absorption. In conjunction with use of fluorescently-tagged proteins, this allows quantitative analysis of protein accumulation at damage sites within seconds of damage induction. PCNA accumulated at damage sites rapidly, such that maximum accumulation was seen approximately 50 s after damage, then levels declined linearly over 200-1000 s after irradiation. RPA accumulated with slower kinetics such that hardly any accumulation was detected within 60 s of irradiation, and levels subsequently increased linearly over the next 900 s, after which levels were approximately constant (up to ca. 2700 s) at the damage site. This approach complements existing methodologies to allow analysis of key damage sensors and chromatin modification changes occurring within seconds of damage inception.
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Affiliation(s)
- Estrella Guarino
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Gheorghe Cojoc
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Iva M. Tolić
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Stephen E. Kearsey
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- * E-mail:
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178
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Iarovaia OV, Rubtsov M, Ioudinkova E, Tsfasman T, Razin SV, Vassetzky YS. Dynamics of double strand breaks and chromosomal translocations. Mol Cancer 2014; 13:249. [PMID: 25404525 PMCID: PMC4289179 DOI: 10.1186/1476-4598-13-249] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 10/30/2014] [Indexed: 12/27/2022] Open
Abstract
Chromosomal translocations are a major cause of cancer. At the same time, the mechanisms that lead to specific chromosomal translocations that associate different gene regions remain largely unknown. Translocations are induced by double strand breaks (DSBs) in DNA. Here we review recent data on the mechanisms of generation, mobility and repair of DSBs and stress the importance of the nuclear organization in this process.
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Affiliation(s)
| | | | | | | | | | - Yegor S Vassetzky
- UMR8126, Université Paris-Sud, CNRS, Institut de cancérologie Gustave Roussy, Villejuif 94805, France.
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179
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Lemaître C, Grabarz A, Tsouroula K, Andronov L, Furst A, Pankotai T, Heyer V, Rogier M, Attwood KM, Kessler P, Dellaire G, Klaholz B, Reina-San-Martin B, Soutoglou E. Nuclear position dictates DNA repair pathway choice. Genes Dev 2014; 28:2450-63. [PMID: 25366693 PMCID: PMC4233239 DOI: 10.1101/gad.248369.114] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Faithful DNA repair is essential to avoid chromosomal rearrangements and promote genome integrity. Lemaitre et al. demonstrate that double-strand breaks (DSBs) induced at the nuclear membrane fail to rapidly activate the DNA damage response and repair by homologous recombination (HR). DNA DSBs within lamina-associated domains do not migrate to more permissive environments for HR, like the nuclear pores or the nuclear interior, but instead are repaired in situ by alternative end-joining. Faithful DNA repair is essential to avoid chromosomal rearrangements and promote genome integrity. Nuclear organization has emerged as a key parameter in the formation of chromosomal translocations, yet little is known as to whether DNA repair can efficiently occur throughout the nucleus and whether it is affected by the location of the lesion. Here, we induce DNA double-strand breaks (DSBs) at different nuclear compartments and follow their fate. We demonstrate that DSBs induced at the nuclear membrane (but not at nuclear pores or nuclear interior) fail to rapidly activate the DNA damage response (DDR) and repair by homologous recombination (HR). Real-time and superresolution imaging reveal that DNA DSBs within lamina-associated domains do not migrate to more permissive environments for HR, like the nuclear pores or the nuclear interior, but instead are repaired in situ by alternative end-joining. Our results are consistent with a model in which nuclear position dictates the choice of DNA repair pathway, thus revealing a new level of regulation in DSB repair controlled by spatial organization of DNA within the nucleus.
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Affiliation(s)
- Charlène Lemaître
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch CEDEX, France; U964, Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch CEDEX, France; UMR7104, Centre National de Recherche Scientifique (CNRS), 67404 Illkirch CEDEX, France; Université de Strasbourg (UDS), 67404 Illkirch CEDEX, France
| | - Anastazja Grabarz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch CEDEX, France; U964, Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch CEDEX, France; UMR7104, Centre National de Recherche Scientifique (CNRS), 67404 Illkirch CEDEX, France; Université de Strasbourg (UDS), 67404 Illkirch CEDEX, France
| | - Katerina Tsouroula
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch CEDEX, France; U964, Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch CEDEX, France; UMR7104, Centre National de Recherche Scientifique (CNRS), 67404 Illkirch CEDEX, France; Université de Strasbourg (UDS), 67404 Illkirch CEDEX, France
| | - Leonid Andronov
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch CEDEX, France; U964, Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch CEDEX, France; UMR7104, Centre National de Recherche Scientifique (CNRS), 67404 Illkirch CEDEX, France; Université de Strasbourg (UDS), 67404 Illkirch CEDEX, France
| | - Audrey Furst
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch CEDEX, France; U964, Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch CEDEX, France; UMR7104, Centre National de Recherche Scientifique (CNRS), 67404 Illkirch CEDEX, France; Université de Strasbourg (UDS), 67404 Illkirch CEDEX, France
| | - Tibor Pankotai
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch CEDEX, France; U964, Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch CEDEX, France; UMR7104, Centre National de Recherche Scientifique (CNRS), 67404 Illkirch CEDEX, France; Université de Strasbourg (UDS), 67404 Illkirch CEDEX, France
| | - Vincent Heyer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch CEDEX, France; U964, Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch CEDEX, France; UMR7104, Centre National de Recherche Scientifique (CNRS), 67404 Illkirch CEDEX, France; Université de Strasbourg (UDS), 67404 Illkirch CEDEX, France
| | - Mélanie Rogier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch CEDEX, France; U964, Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch CEDEX, France; UMR7104, Centre National de Recherche Scientifique (CNRS), 67404 Illkirch CEDEX, France; Université de Strasbourg (UDS), 67404 Illkirch CEDEX, France
| | - Kathleen M Attwood
- Department of Pathology, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Pascal Kessler
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch CEDEX, France; U964, Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch CEDEX, France; UMR7104, Centre National de Recherche Scientifique (CNRS), 67404 Illkirch CEDEX, France; Université de Strasbourg (UDS), 67404 Illkirch CEDEX, France
| | - Graham Dellaire
- Department of Pathology, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Bruno Klaholz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch CEDEX, France; U964, Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch CEDEX, France; UMR7104, Centre National de Recherche Scientifique (CNRS), 67404 Illkirch CEDEX, France; Université de Strasbourg (UDS), 67404 Illkirch CEDEX, France
| | - Bernardo Reina-San-Martin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch CEDEX, France; U964, Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch CEDEX, France; UMR7104, Centre National de Recherche Scientifique (CNRS), 67404 Illkirch CEDEX, France; Université de Strasbourg (UDS), 67404 Illkirch CEDEX, France
| | - Evi Soutoglou
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch CEDEX, France; U964, Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch CEDEX, France; UMR7104, Centre National de Recherche Scientifique (CNRS), 67404 Illkirch CEDEX, France; Université de Strasbourg (UDS), 67404 Illkirch CEDEX, France
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180
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Andreadis C, Nikolaou C, Fragiadakis GS, Tsiliki G, Alexandraki D. Rad9 interacts with Aft1 to facilitate genome surveillance in fragile genomic sites under non-DNA damage-inducing conditions in S. cerevisiae. Nucleic Acids Res 2014; 42:12650-67. [PMID: 25300486 PMCID: PMC4227768 DOI: 10.1093/nar/gku915] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
DNA damage response and repair proteins are centrally involved in genome maintenance pathways. Yet, little is known about their functional role under non-DNA damage-inducing conditions. Here we show that Rad9 checkpoint protein, known to mediate the damage signal from upstream to downstream essential kinases, interacts with Aft1 transcription factor in the budding yeast. Aft1 regulates iron homeostasis and is also involved in genome integrity having additional iron-independent functions. Using genome-wide expression and chromatin immunoprecipitation approaches, we found Rad9 to be recruited to 16% of the yeast genes, often related to cellular growth and metabolism, while affecting the transcription of ∼2% of the coding genome in the absence of exogenously induced DNA damage. Importantly, Rad9 is recruited to fragile genomic regions (transcriptionally active, GC rich, centromeres, meiotic recombination hotspots and retrotransposons) non-randomly and in an Aft1-dependent manner. Further analyses revealed substantial genome-wide parallels between Rad9 binding patterns to the genome and major activating histone marks, such as H3K36me, H3K79me and H3K4me. Thus, our findings suggest that Rad9 functions together with Aft1 on DNA damage-prone chromatin to facilitate genome surveillance, thereby ensuring rapid and effective response to possible DNA damage events.
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Affiliation(s)
- Christos Andreadis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-HELLAS, Crete 70013, Greece Department of Biology, University of Crete, Crete 70013, Greece
| | | | - George S Fragiadakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-HELLAS, Crete 70013, Greece
| | - Georgia Tsiliki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-HELLAS, Crete 70013, Greece
| | - Despina Alexandraki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-HELLAS, Crete 70013, Greece Department of Biology, University of Crete, Crete 70013, Greece
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181
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Liu T, Huang J. Quality control of homologous recombination. Cell Mol Life Sci 2014; 71:3779-97. [PMID: 24858417 PMCID: PMC11114062 DOI: 10.1007/s00018-014-1649-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 05/09/2014] [Indexed: 12/21/2022]
Abstract
Exogenous and endogenous genotoxic agents, such as ionizing radiation and numerous chemical agents, cause DNA double-strand breaks (DSBs), which are highly toxic and lead to genomic instability or tumorigenesis if not repaired accurately and efficiently. Cells have over evolutionary time developed certain repair mechanisms in response to DSBs to maintain genomic integrity. Major DSB repair mechanisms include non-homologous end joining and homologous recombination (HR). Using sister homologues as templates, HR is a high-fidelity repair pathway that can rejoin DSBs without introducing mutations. However, HR execution without appropriate guarding may lead to more severe gross genome rearrangements. Here we review current knowledge regarding the factors and mechanisms required for accomplishment of accurate HR.
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Affiliation(s)
- Ting Liu
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang China
| | - Jun Huang
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang China
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182
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Generation of cell-based systems to visualize chromosome damage and translocations in living cells. Nat Protoc 2014; 9:2476-92. [PMID: 25255091 DOI: 10.1038/nprot.2014.167] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Traditional methods for the generation of DNA damage are not well suited for the observation of spatiotemporal aspects of damaged chromosomal loci. We describe a protocol for the derivation of a cellular system to induce and to visualize chromosome damage at specific sites of the mammalian genome in living cells. The system is based on the stable integration of endonuclease I-SceI recognition sites flanked by bacterial LacO/TetO operator arrays, coupled with retroviral-mediated integration of their fluorescent repressors (LacR/TetR) to visualize the LacO/TetO sites. Expression of the I-SceI endonuclease induces double-strand breaks (DSBs) specifically at the sites of integration, and it permits the dynamics of damaged chromatin to be followed by time-lapse microscopy. Sequential LacO-I-SceI/TetO-I-SceI integrations in multiple chromosomes permit the generation of a system to visualize the formation of chromosome translocations in living cells. This protocol requires intermediate cell culture and molecular biology skills, and it is adaptable to the efficient derivation of any integrated clonal reporter system of interest in ≈ 3-5 months.
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183
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Khurana S, Kruhlak MJ, Kim J, Tran AD, Liu J, Nyswaner K, Shi L, Jailwala P, Sung MH, Hakim O, Oberdoerffer P. A macrohistone variant links dynamic chromatin compaction to BRCA1-dependent genome maintenance. Cell Rep 2014; 8:1049-62. [PMID: 25131201 PMCID: PMC4154351 DOI: 10.1016/j.celrep.2014.07.024] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 04/28/2014] [Accepted: 07/16/2014] [Indexed: 02/07/2023] Open
Abstract
Appropriate DNA double-strand break (DSB) repair factor choice is essential for ensuring accurate repair outcome and genomic integrity. The factors that regulate this process remain poorly understood. Here, we identify two repressive chromatin components, the macrohistone variant macroH2A1 and the H3K9 methyltransferase and tumor suppressor PRDM2, which together direct the choice between the antagonistic DSB repair mediators BRCA1 and 53BP1. The macroH2A1/PRDM2 module mediates an unexpected shift from accessible to condensed chromatin that requires the ataxia telangiectasia mutated (ATM)-dependent accumulation of both proteins at DSBs in order to promote DSB-flanking H3K9 dimethylation. Remarkably, loss of macroH2A1 or PRDM2, as well as experimentally induced chromatin decondensation, impairs the retention of BRCA1, but not 53BP1, at DSBs. As a result, mac-roH2A1 and/or PRDM2 depletion causes epistatic defects in DSB end resection, homology-directed repair, and the resistance to poly(ADP-ribose) polymerase (PARP) inhibition—all hallmarks of BRCA1-deficient tumors. Together, these findings identify dynamic, DSB-associated chromatin reorganization as a critical modulator of BRCA1-dependent genome maintenance.
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Affiliation(s)
- Simran Khurana
- Laboratory of Receptor Biology and Gene Expression, NCI/NIH, Bethesda, MD 20892, USA
| | | | - Jeongkyu Kim
- Laboratory of Receptor Biology and Gene Expression, NCI/NIH, Bethesda, MD 20892, USA
| | - Andy D Tran
- Laboratory of Receptor Biology and Gene Expression, NCI/NIH, Bethesda, MD 20892, USA
| | - Jinping Liu
- Laboratory of Receptor Biology and Gene Expression, NCI/NIH, Bethesda, MD 20892, USA
| | | | - Lei Shi
- Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Parthav Jailwala
- Advanced Biomedical Computing Center, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Myong-Hee Sung
- Laboratory of Receptor Biology and Gene Expression, NCI/NIH, Bethesda, MD 20892, USA
| | - Ofir Hakim
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Philipp Oberdoerffer
- Laboratory of Receptor Biology and Gene Expression, NCI/NIH, Bethesda, MD 20892, USA.
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184
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Gerhold CB, Gasser SM. INO80 and SWR complexes: relating structure to function in chromatin remodeling. Trends Cell Biol 2014; 24:619-31. [PMID: 25088669 DOI: 10.1016/j.tcb.2014.06.004] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 06/23/2014] [Accepted: 06/24/2014] [Indexed: 02/04/2023]
Abstract
Virtually all DNA-dependent processes require selective and controlled access to the DNA sequence. Governing this access are sophisticated molecular machines, nucleosome remodelers, which regulate the composition and structure of chromatin, allowing conversion from open to closed states. In most cases these multisubunit remodelers operate in concert to organize chromatin structure by depositing, moving, evicting, or selectively altering nucleosomes in an ATP-dependent manner. Despite sharing a conserved domain architecture, chromatin remodelers differ significantly in how they bind to their nucleosomal substrates. Recent structural studies link specific interactions between nucleosomes and remodelers to the diverse tasks they carry out. We review here insights into the modular organization of the INO80 family of nucleosome remodelers. Understanding their structural diversity will help to shed light on how these related ATPases modify their nucleosomal substrates.
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Affiliation(s)
- Christian B Gerhold
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Basel, Switzerland.
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185
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SWR1 and INO80 chromatin remodelers contribute to DNA double-strand break perinuclear anchorage site choice. Mol Cell 2014; 55:626-39. [PMID: 25066231 DOI: 10.1016/j.molcel.2014.06.027] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 05/05/2014] [Accepted: 06/17/2014] [Indexed: 11/23/2022]
Abstract
Persistent DNA double-strand breaks (DSBs) are recruited to the nuclear periphery in budding yeast. Both the Nup84 pore subcomplex and Mps3, an inner nuclear membrane (INM) SUN domain protein, have been implicated in DSB binding. It was unclear what, if anything, distinguishes the two potential sites of repair. Here, we characterize and distinguish the two binding sites. First, DSB-pore interaction occurs independently of cell-cycle phase and requires neither the chromatin remodeler INO80 nor recombinase Rad51 activity. In contrast, Mps3 binding is S and G2 phase specific and requires both factors. SWR1-dependent incorporation of Htz1 (H2A.Z) is necessary for break relocation to either site in both G1- and S-phase cells. Importantly, functional assays indicate that mutations in the two sites have additive repair defects, arguing that the two perinuclear anchorage sites define distinct survival pathways.
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186
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Abstract
Chromosome translocations are catastrophic genomic events and often play key roles in tumorigenesis. Yet the biogenesis of chromosome translocations is remarkably poorly understood. Recent work has delineated several distinct mechanistic steps in the formation of translocations, and it has become apparent that non-random spatial genome organization, DNA repair pathways and chromatin features, including histone marks and the dynamic motion of broken chromatin, are critical for determining translocation frequency and partner selection.
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Affiliation(s)
| | - Tom Misteli
- National Cancer Institute, Bethesda, Maryland 20892, USA
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187
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Renkawitz J, Lademann CA, Jentsch S. Mechanisms and principles of homology search during recombination. Nat Rev Mol Cell Biol 2014; 15:369-83. [PMID: 24824069 DOI: 10.1038/nrm3805] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Homologous recombination is crucial for genome stability and for genetic exchange. Although our knowledge of the principle steps in recombination and its machinery is well advanced, homology search, the critical step of exploring the genome for homologous sequences to enable recombination, has remained mostly enigmatic. However, recent methodological advances have provided considerable new insights into this fundamental step in recombination that can be integrated into a mechanistic model. These advances emphasize the importance of genomic proximity and nuclear organization for homology search and the critical role of homology search mediators in this process. They also aid our understanding of how homology search might lead to unwanted and potentially disease-promoting recombination events.
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Affiliation(s)
- Jörg Renkawitz
- 1] Department of Molecular Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany. [2] Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria. [3]
| | - Claudio A Lademann
- 1] Department of Molecular Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany. [2]
| | - Stefan Jentsch
- Department of Molecular Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
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188
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Becker A, Durante M, Taucher-Scholz G, Jakob B. ATM alters the otherwise robust chromatin mobility at sites of DNA double-strand breaks (DSBs) in human cells. PLoS One 2014; 9:e92640. [PMID: 24651490 PMCID: PMC3961414 DOI: 10.1371/journal.pone.0092640] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 02/23/2014] [Indexed: 11/18/2022] Open
Abstract
Ionizing radiation induces DNA double strand breaks (DSBs) which can lead to the formation of chromosome rearrangements through error prone repair. In mammalian cells the positional stability of chromatin contributes to the maintenance of genome integrity. DSBs exhibit only a small, submicron scale diffusive mobility, but a slight increase in the mobility of chromatin domains by the induction of DSBs might influence repair fidelity and the formation of translocations. The radiation-induced local DNA decondensation in the vicinity of DSBs is one factor potentially enhancing the mobility of DSB-containing chromatin domains. Therefore in this study we focus on the influence of different chromatin modifying proteins, known to be activated by the DNA damage response, on the mobility of DSBs. IRIF (ionizing radiation induced foci) in U2OS cells stably expressing 53BP1-GFP were used as a surrogate marker of DSBs. Low angle charged particle irradiation, known to trigger a pronounced DNA decondensation, was used for the defined induction of linear tracks of IRIF. Our results show that movement of IRIF is independent of the investigated chromatin modifying proteins like ACF1 or PARP1 and PARG. Also depletion of proteins that tether DNA strands like MRE11 and cohesin did not alter IRIF dynamics significantly. Inhibition of ATM, a key component of DNA damage response signaling, resulted in a pronounced confinement of DSB mobility, which might be attributed to a diminished radiation induced decondensation. This confinement following ATM inhibition was confirmed using X-rays, proving that this effect is not restricted to densely ionizing radiation. In conclusion, repair sites of DSBs exhibit a limited mobility on a small spatial scale that is mainly unaffected by depletion of single remodeling or DNA tethering proteins. However, it relies on functional ATM kinase which is considered to influence the chromatin structure after irradiation.
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Affiliation(s)
- Annabelle Becker
- GSI, Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt, Germany
| | - Marco Durante
- GSI, Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt, Germany
- Technical University of Darmstadt, Darmstadt, Germany
| | - Gisela Taucher-Scholz
- GSI, Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt, Germany
- Technical University of Darmstadt, Darmstadt, Germany
| | - Burkhard Jakob
- GSI, Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt, Germany
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189
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Saad H, Gallardo F, Dalvai M, Tanguy-le-Gac N, Lane D, Bystricky K. DNA dynamics during early double-strand break processing revealed by non-intrusive imaging of living cells. PLoS Genet 2014; 10:e1004187. [PMID: 24625580 PMCID: PMC3952824 DOI: 10.1371/journal.pgen.1004187] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 01/06/2014] [Indexed: 11/18/2022] Open
Abstract
Chromosome breakage is a major threat to genome integrity. The most accurate way to repair DNA double strand breaks (DSB) is homologous recombination (HR) with an intact copy of the broken locus. Mobility of the broken DNA has been seen to increase during the search for a donor copy. Observing chromosome dynamics during the earlier steps of HR, mainly the resection from DSB ends that generates recombinogenic single strands, requires a visualization system that does not interfere with the process, and is small relative to the few kilobases of DNA that undergo processing. Current visualization tools, based on binding of fluorescent repressor proteins to arrays of specific binding sites, have the major drawback that highly-repeated DNA and lengthy stretches of strongly bound protein can obstruct chromatin function. We have developed a new, non-intrusive method which uses protein oligomerization rather than operator multiplicity to form visible foci. By applying it to HO cleavage of the MAT locus on Saccharomyces cerevisiae chromosome III, we provide the first real-time analysis of resection in single living cells. Monitoring the dynamics of a chromatin locus next to a DSB revealed transient confinement of the damaged chromatin region during the very early steps of resection, consistent with the need to keep DNA ends in contact. Resection in a yku70 mutant began ∼ 10 min earlier than in wild type, defining this as the period of commitment to homology-dependent repair. Beyond the insights into the dynamics and mechanism of resection, our new DNA-labelling and -targeting method will be widely applicable to fine-scale analysis of genome organization, dynamics and function in normal and pathological contexts.
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Affiliation(s)
- Hicham Saad
- University of Toulouse, UPS, Toulouse, France
- Laboratoire de Biologie Moléculaire Eucaryote, CNRS, UMR5099, Toulouse, France
| | - Franck Gallardo
- University of Toulouse, UPS, Toulouse, France
- Laboratoire de Biologie Moléculaire Eucaryote, CNRS, UMR5099, Toulouse, France
- Institut des Technologies Avancées en sciences du Vivant, ITAV, Toulouse, France
| | - Mathieu Dalvai
- University of Toulouse, UPS, Toulouse, France
- Laboratoire de Biologie Moléculaire Eucaryote, CNRS, UMR5099, Toulouse, France
| | - Nicolas Tanguy-le-Gac
- University of Toulouse, UPS, Toulouse, France
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Toulouse, France
| | - David Lane
- University of Toulouse, UPS, Toulouse, France
- Laboratoire de Microbiologie et Génétique Moléculaires, CNRS, UMR5100, Toulouse, France
| | - Kerstin Bystricky
- University of Toulouse, UPS, Toulouse, France
- Laboratoire de Biologie Moléculaire Eucaryote, CNRS, UMR5099, Toulouse, France
- Institut des Technologies Avancées en sciences du Vivant, ITAV, Toulouse, France
- * E-mail:
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190
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Loïodice I, Dubarry M, Taddei A. Scoring and manipulating gene position and dynamics using FROS in budding yeast. CURRENT PROTOCOLS IN CELL BIOLOGY 2014; 62:22.17.1-22.17.14. [PMID: 24610125 DOI: 10.1002/0471143030.cb2217s62] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The spatial organization of the genome within the nucleus is now seen as a key contributor to genome function. Studying chromatin dynamics in living cells has been rendered possible by the development of fast microscopy coupled with fluorescent repressor operator systems (FROS). In these systems, arrays of protein-binding sites integrated at specific loci by homologous recombination are monitored through the fluorescence of tagged DNA-binding proteins. In the budding yeast, where homologous recombination is efficient, this technique, combined with targeting assay and genetic analysis, has been extremely powerful for studying the determinants and function of chromatin dynamics in living cells. However, issues have been recurrently raised in different species regarding the use of these systems. Here we discuss the different uses of gene tagging with FROS and their limitations, focusing in budding yeast as a model organism.
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Affiliation(s)
- Isabelle Loïodice
- Institut Curie, Centre de Recherche, Paris, France.,Centre National de la Recherche Scientifique (CNRS), UMR 3364, Paris, France.,Université Pierre-et-Marie-Curie (UPMC), UMR 3664, Paris, France
| | - Marion Dubarry
- Université Pierre-et-Marie-Curie (UPMC), UMR 3664, Paris, France.,Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Angela Taddei
- Institut Curie, Centre de Recherche, Paris, France.,Centre National de la Recherche Scientifique (CNRS), UMR 3364, Paris, France.,Université Pierre-et-Marie-Curie (UPMC), UMR 3664, Paris, France
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191
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Wood AM, Garza-Gongora AG, Kosak ST. A Crowdsourced nucleus: understanding nuclear organization in terms of dynamically networked protein function. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1839:178-90. [PMID: 24412853 PMCID: PMC3954575 DOI: 10.1016/j.bbagrm.2014.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 12/30/2013] [Accepted: 01/02/2014] [Indexed: 01/14/2023]
Abstract
The spatial organization of the nucleus results in a compartmentalized structure that affects all aspects of nuclear function. This compartmentalization involves genome organization as well as the formation of nuclear bodies and plays a role in many functions, including gene regulation, genome stability, replication, and RNA processing. Here we review the recent findings associated with the spatial organization of the nucleus and reveal that a common theme for nuclear proteins is their ability to participate in a variety of functions and pathways. We consider this multiplicity of function in terms of Crowdsourcing, a recent phenomenon in the world of information technology, and suggest that this model provides a novel way to synthesize the many intersections between nuclear organization and function. This article is part of a Special Issue entitled: Chromatin and epigenetic regulation of animal development.
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Affiliation(s)
- Ashley M Wood
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Arturo G Garza-Gongora
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Steven T Kosak
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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192
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Krawczyk C, Dion V, Schär P, Fritsch O. Reversible Top1 cleavage complexes are stabilized strand-specifically at the ribosomal replication fork barrier and contribute to ribosomal DNA stability. Nucleic Acids Res 2014; 42:4985-95. [PMID: 24574527 PMCID: PMC4005688 DOI: 10.1093/nar/gku148] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Various topological constraints at the ribosomal DNA (rDNA) locus impose an extra challenge for transcription and DNA replication, generating constant torsional DNA stress. The topoisomerase Top1 is known to release such torsion by single-strand nicking and re-ligation in a process involving transient covalent Top1 cleavage complexes (Top1cc) with the nicked DNA. Here we show that Top1ccs, despite their usually transient nature, are specifically targeted to and stabilized at the ribosomal replication fork barrier (rRFB) of budding yeast, establishing a link with previously reported Top1 controlled nicks. Using ectopically engineered rRFBs, we establish that the rRFB sequence itself is sufficient for induction of DNA strand-specific and replication-independent Top1ccs. These Top1ccs accumulate only in the presence of Fob1 and Tof2, they are reversible as they are not subject to repair by Tdp1- or Mus81-dependent processes, and their presence correlates with Top1 provided rDNA stability. Notably, the targeted formation of these Top1ccs accounts for the previously reported broken replication forks at the rRFB. These findings implicate a novel and physiologically regulated mode of Top1 action, suggesting a mechanism by which Top1 is recruited to the rRFB and stabilized in a reversible Top1cc configuration to preserve the integrity of the rDNA.
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Affiliation(s)
- Claudia Krawczyk
- Department of Biomedicine, University of Basel, 4058 Basel, Switzerland and Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
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193
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Rolloos M, Dohmen MHC, Hooykaas PJJ, van der Zaal BJ. Involvement of Rad52 in T-DNA circle formation duringAgrobacterium tumefaciens-mediated transformation ofSaccharomyces cerevisiae. Mol Microbiol 2014; 91:1240-51. [DOI: 10.1111/mmi.12531] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Martijn Rolloos
- Department of Molecular and Developmental Genetics; nstitute of Biology Leiden; Leiden Sylviusweg 72, 2333 BE The Netherlands
| | - Marius H. C. Dohmen
- Department of Molecular and Developmental Genetics; nstitute of Biology Leiden; Leiden Sylviusweg 72, 2333 BE The Netherlands
| | - Paul J. J. Hooykaas
- Department of Molecular and Developmental Genetics; nstitute of Biology Leiden; Leiden Sylviusweg 72, 2333 BE The Netherlands
| | - Bert J. van der Zaal
- Department of Molecular and Developmental Genetics; nstitute of Biology Leiden; Leiden Sylviusweg 72, 2333 BE The Netherlands
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194
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Affiliation(s)
- Andrew Seeber
- Friedrich Miescher Institute for Biomedical Research; Basel, Switzerland; University of Basel; Faculty of Natural Sciences; Basel, Switzerland
| | - Vincent Dion
- University of Lausanne; Center for Integrative Genomics; Lausanne, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research; Basel, Switzerland; University of Basel; Faculty of Natural Sciences; Basel, Switzerland
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195
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Bétermier M, Bertrand P, Lopez BS. Is non-homologous end-joining really an inherently error-prone process? PLoS Genet 2014; 10:e1004086. [PMID: 24453986 PMCID: PMC3894167 DOI: 10.1371/journal.pgen.1004086] [Citation(s) in RCA: 283] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
DNA double-strand breaks (DSBs) are harmful lesions leading to genomic instability or diversity. Non-homologous end-joining (NHEJ) is a prominent DSB repair pathway, which has long been considered to be error-prone. However, recent data have pointed to the intrinsic precision of NHEJ. Three reasons can account for the apparent fallibility of NHEJ: 1) the existence of a highly error-prone alternative end-joining process; 2) the adaptability of canonical C-NHEJ (Ku- and Xrcc4/ligase IV-dependent) to imperfect complementary ends; and 3) the requirement to first process chemically incompatible DNA ends that cannot be ligated directly. Thus, C-NHEJ is conservative but adaptable, and the accuracy of the repair is dictated by the structure of the DNA ends rather than by the C-NHEJ machinery. We present data from different organisms that describe the conservative/versatile properties of C-NHEJ. The advantages of the adaptability/versatility of C-NHEJ are discussed for the development of the immune repertoire and the resistance to ionizing radiation, especially at low doses, and for targeted genome manipulation.
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Affiliation(s)
- Mireille Bétermier
- CNRS, Centre de Génétique Moléculaire, UPR3404, Gif-sur-Yvette, France
- CNRS, Centre de Recherches de Gif-sur-Yvette, FRC3115, Gif-sur-Yvette, France
- Université Paris-Sud, Département de Biologie, Orsay, France
| | - Pascale Bertrand
- CEA, DSV, Institut de Radiobiologie Moléculaire et Cellulaire, Laboratoire Réparation et Vieillissement, Fontenay-aux-Roses, France
- UMR 8200 CNRS, Villejuif, France
| | - Bernard S. Lopez
- Université Paris-Sud, Département de Biologie, Orsay, France
- UMR 8200 CNRS, Villejuif, France
- Institut de Cancérologie, Gustave Roussy, Villejuif, France
- * E-mail:
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196
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Bennett G, Papamichos-Chronakis M, Peterson CL. DNA repair choice defines a common pathway for recruitment of chromatin regulators. Nat Commun 2013; 4:2084. [PMID: 23811932 PMCID: PMC3731036 DOI: 10.1038/ncomms3084] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 05/30/2013] [Indexed: 12/31/2022] Open
Abstract
DNA double-strand break (DSB) repair is essential for maintenance of genome stability. Recent work has implicated a host of chromatin regulators in the DNA damage response, and although several functional roles have been defined, the mechanisms that control their recruitment to DNA lesions remain unclear. Here, we find that efficient DSB recruitment of the INO80, SWR-C, NuA4, SWI/SNF, and RSC enzymes is inhibited by the non-homologous end joining machinery, and that their recruitment is controlled by early steps of homologous recombination. Strikingly, we find no significant role for H2A.X phosphorylation (γH2AX) in the recruitment of chromatin regulators, but rather their recruitment coincides with reduced levels of γH2AX. Our work indicates that cell cycle position plays a key role in DNA repair pathway choice and that recruitment of chromatin regulators is tightly coupled to homologous recombination.
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Affiliation(s)
- Gwendolyn Bennett
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01606, USA
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197
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Mehta IS, Kulashreshtha M, Chakraborty S, Kolthur-Seetharam U, Rao BJ. Chromosome territories reposition during DNA damage-repair response. Genome Biol 2013; 14:R135. [PMID: 24330859 PMCID: PMC4062845 DOI: 10.1186/gb-2013-14-12-r135] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 12/13/2013] [Indexed: 01/02/2023] Open
Abstract
Background Local higher-order chromatin structure, dynamics and composition of the DNA are known to determine double-strand break frequencies and the efficiency of repair. However, how DNA damage response affects the spatial organization of chromosome territories is still unexplored. Results Our report investigates the effect of DNA damage on the spatial organization of chromosome territories within interphase nuclei of human cells. We show that DNA damage induces a large-scale spatial repositioning of chromosome territories that are relatively gene dense. This response is dose dependent, and involves territories moving from the nuclear interior to the periphery and vice versa. Furthermore, we have found that chromosome territory repositioning is contingent upon double-strand break recognition and damage sensing. Importantly, our results suggest that this is a reversible process where, following repair, chromosome territories re-occupy positions similar to those in undamaged control cells. Conclusions Thus, our report for the first time highlights DNA damage-dependent spatial reorganization of whole chromosomes, which might be an integral aspect of cellular damage response.
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198
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Centromere tethering confines chromosome domains. Mol Cell 2013; 52:819-31. [PMID: 24268574 DOI: 10.1016/j.molcel.2013.10.021] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 09/10/2013] [Accepted: 10/14/2013] [Indexed: 12/20/2022]
Abstract
The organization of chromosomes into territories plays an important role in a wide range of cellular processes, including gene expression, transcription, and DNA repair. Current understanding has largely excluded the spatiotemporal dynamic fluctuations of the chromatin polymer. We combine in vivo chromatin motion analysis with mathematical modeling to elucidate the physical properties that underlie the formation and fluctuations of territories. Chromosome motion varies in predicted ways along the length of the chromosome, dependent on tethering at the centromere. Detachment of a tether upon inactivation of the centromere results in increased spatial mobility. A confined bead-spring chain tethered at both ends provides a mechanism to generate observed variations in local mobility as a function of distance from the tether. These predictions are realized in experimentally determined higher effective spring constants closer to the centromere. The dynamic fluctuations and territorial organization of chromosomes are, in part, dictated by tethering at the centromere.
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199
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Abstract
In this review, we discuss the repair of DNA double-strand breaks (DSBs) using a homologous DNA sequence (i.e., homologous recombination [HR]), focusing mainly on yeast and mammals. We provide a historical context for the current view of HR and describe how DSBs are processed during HR as well as interactions with other DSB repair pathways. We discuss the enzymology of the process, followed by studies on DSB repair in living cells. Whenever possible, we cite both original articles and reviews to aid the reader for further studies.
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Affiliation(s)
- Maria Jasin
- Developmental Biology Program, Memorial Sloan-Kettering Cancer Center New York, New York 10065
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200
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Dion V, Kalck V, Seeber A, Schleker T, Gasser SM. Cohesin and the nucleolus constrain the mobility of spontaneous repair foci. EMBO Rep 2013; 14:984-91. [PMID: 24018421 PMCID: PMC3818071 DOI: 10.1038/embor.2013.142] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 08/13/2013] [Accepted: 08/13/2013] [Indexed: 12/24/2022] Open
Abstract
The regulation of chromatin mobility in response to DNA damage is important for homologous recombination in yeast. Anchorage reduces rates of recombination, whereas increased chromatin mobility correlates with more efficient homology search. Here we tracked the mobility and localization of spontaneous S-phase lesions bound by Rad52, and find that these foci have reduced movement, unlike enzymatically induced double-strand breaks. Moreover, spontaneous repair foci are positioned in the nuclear core, abutting the nucleolus. We show that cohesin and nucleolar integrity constrain the mobility of these foci, consistent with the notion that spontaneous, S-phase damage is preferentially repaired from the sister chromatid.
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Affiliation(s)
- Vincent Dion
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel, Switzerland
| | - Véronique Kalck
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel, Switzerland
| | - Andrew Seeber
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel, Switzerland
- Faculty of Natural Sciences, University of Basel, CH-4056 Basel, Switzerland
| | - Thomas Schleker
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel, Switzerland
- Faculty of Natural Sciences, University of Basel, CH-4056 Basel, Switzerland
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