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Liakopoulos D. Coupling DNA Replication and Spindle Function in Saccharomyces cerevisiae. Cells 2021; 10:cells10123359. [PMID: 34943867 PMCID: PMC8699587 DOI: 10.3390/cells10123359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/24/2021] [Accepted: 11/27/2021] [Indexed: 12/02/2022] Open
Abstract
In the yeast Saccharomyces cerevisiae DNA replication and spindle assembly can overlap. Therefore, signaling mechanisms modulate spindle dynamics in order to ensure correct timing of chromosome segregation relative to genome duplication, especially when replication is incomplete or the DNA becomes damaged. This review focuses on the molecular mechanisms that coordinate DNA replication and spindle dynamics, as well as on the role of spindle-dependent forces in DNA repair. Understanding the coupling between genome duplication and spindle function in yeast cells can provide important insights into similar processes operating in other eukaryotic organisms, including humans.
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Affiliation(s)
- Dimitris Liakopoulos
- CRBM, Université de Montpellier, CNRS, 1919 Route de Mende, 34293 Montpellier, France;
- Laboratory of Biology, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece
- University Research Center of loannina, University of Ioannina, 45110 Ioannina, Greece
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Ivanova T, Maier M, Missarova A, Ziegler-Birling C, Dam M, Gomar-Alba M, Carey LB, Mendoza M. Budding yeast complete DNA synthesis after chromosome segregation begins. Nat Commun 2020; 11:2267. [PMID: 32385287 PMCID: PMC7210879 DOI: 10.1038/s41467-020-16100-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 04/14/2020] [Indexed: 01/22/2023] Open
Abstract
To faithfully transmit genetic information, cells must replicate their entire genome before division. This is thought to be ensured by the temporal separation of replication and chromosome segregation. Here we show that in 20–40% of unperturbed yeast cells, DNA synthesis continues during anaphase, late in mitosis. High cyclin-Cdk activity inhibits DNA synthesis in metaphase, and the decrease in cyclin-Cdk activity during mitotic exit allows DNA synthesis to finish at subtelomeric and some difficult-to-replicate regions. DNA synthesis during late mitosis correlates with elevated mutation rates at subtelomeric regions, including copy number variation. Thus, yeast cells temporally overlap DNA synthesis and chromosome segregation during normal growth, possibly allowing cells to maximize population-level growth rate while simultaneously exploring greater genetic space. In the S phase of the cell cycle, the full genome needs to be replicated before cell division occurs. Here, authors show that in budding yeast DNA synthesis is completed after chromosome segregation begins.
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Affiliation(s)
- Tsvetomira Ivanova
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Michael Maier
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | | | | | - Monica Dam
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Mercè Gomar-Alba
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Lucas B Carey
- Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,Center for Quantitative Biology and Peking-Tsinghua Center for the Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
| | - Manuel Mendoza
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France. .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France. .,Université de Strasbourg, Strasbourg, France.
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Shi L, Oberdoerffer P. Chromatin dynamics in DNA double-strand break repair. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:811-9. [PMID: 22285574 DOI: 10.1016/j.bbagrm.2012.01.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 12/28/2011] [Accepted: 01/05/2012] [Indexed: 12/29/2022]
Abstract
DNA double-strand breaks (DSBs) occur in the context of a highly organized chromatin environment and are, thus, a significant threat to the epigenomic integrity of eukaryotic cells. Changes in break-proximal chromatin structure are thought to be a prerequisite for efficient DNA repair and may help protect the structural integrity of the nucleus. Unlike most bona fide DNA repair factors, chromatin influences the repair process at several levels: the existing chromatin context at the site of damage directly affects the access and kinetics of the repair machinery; DSB induced chromatin modifications influence the choice of repair factors, thereby modulating repair outcome; lastly, DNA damage can have a significant impact on chromatin beyond the site of damage. We will discuss recent findings that highlight both the complexity and importance of dynamic and tightly orchestrated chromatin reorganization to ensure efficient DSB repair and nuclear integrity. This article is part of a Special Issue entitled: Chromatin in time and space.
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Affiliation(s)
- Lei Shi
- Mouse Cancer Genetics Program, NCI- Frederick, NIH, Frederick, MD 21702, USA
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Goldar A, Labit H, Marheineke K, Hyrien O. A dynamic stochastic model for DNA replication initiation in early embryos. PLoS One 2008; 3:e2919. [PMID: 18682801 PMCID: PMC2488399 DOI: 10.1371/journal.pone.0002919] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2008] [Accepted: 07/16/2008] [Indexed: 12/14/2022] Open
Abstract
Background Eukaryotic cells seem unable to monitor replication completion during normal S phase, yet must ensure a reliable replication completion time. This is an acute problem in early Xenopus embryos since DNA replication origins are located and activated stochastically, leading to the random completion problem. DNA combing, kinetic modelling and other studies using Xenopus egg extracts have suggested that potential origins are much more abundant than actual initiation events and that the time-dependent rate of initiation, I(t), markedly increases through S phase to ensure the rapid completion of unreplicated gaps and a narrow distribution of completion times. However, the molecular mechanism that underlies this increase has remained obscure. Methodology/Principal Findings Using both previous and novel DNA combing data we have confirmed that I(t) increases through S phase but have also established that it progressively decreases before the end of S phase. To explore plausible biochemical scenarios that might explain these features, we have performed comparisons between numerical simulations and DNA combing data. Several simple models were tested: i) recycling of a limiting replication fork component from completed replicons; ii) time-dependent increase in origin efficiency; iii) time-dependent increase in availability of an initially limiting factor, e.g. by nuclear import. None of these potential mechanisms could on its own account for the data. We propose a model that combines time-dependent changes in availability of a replication factor and a fork-density dependent affinity of this factor for potential origins. This novel model quantitatively and robustly accounted for the observed changes in initiation rate and fork density. Conclusions/Significance This work provides a refined temporal profile of replication initiation rates and a robust, dynamic model that quantitatively explains replication origin usage during early embryonic S phase. These results have significant implications for the organisation of replication origins in higher eukaryotes.
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Affiliation(s)
- Arach Goldar
- Service de Biologie Intégrative et de Génétique Moléculaire, Commissariat à l'Énergie Atomique, Gif-sur-Yvette, France
- * E-mail: (AG); (OH)
| | - Hélène Labit
- Ecole Normale Supérieure, CNRS UMR 8541, Paris, France
| | | | - Olivier Hyrien
- Ecole Normale Supérieure, CNRS UMR 8541, Paris, France
- * E-mail: (AG); (OH)
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