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Tsegay PS, Lai Y, Liu Y. Replication Stress and Consequential Instability of the Genome and Epigenome. Molecules 2019; 24:molecules24213870. [PMID: 31717862 PMCID: PMC6864812 DOI: 10.3390/molecules24213870] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/25/2019] [Accepted: 10/25/2019] [Indexed: 12/12/2022] Open
Abstract
Cells must faithfully duplicate their DNA in the genome to pass their genetic information to the daughter cells. To maintain genomic stability and integrity, double-strand DNA has to be replicated in a strictly regulated manner, ensuring the accuracy of its copy number, integrity and epigenetic modifications. However, DNA is constantly under the attack of DNA damage, among which oxidative DNA damage is the one that most frequently occurs, and can alter the accuracy of DNA replication, integrity and epigenetic features, resulting in DNA replication stress and subsequent genome and epigenome instability. In this review, we summarize DNA damage-induced replication stress, the formation of DNA secondary structures, peculiar epigenetic modifications and cellular responses to the stress and their impact on the instability of the genome and epigenome mainly in eukaryotic cells.
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Affiliation(s)
- Pawlos S. Tsegay
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA;
| | - Yanhao Lai
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA;
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Yuan Liu
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA;
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA;
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
- Correspondence:
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Li X, Jin X, Sharma S, Liu X, Zhang J, Niu Y, Li J, Li Z, Zhang J, Cao Q, Hou W, Du LL, Liu B, Lou H. Mck1 defines a key S-phase checkpoint effector in response to various degrees of replication threats. PLoS Genet 2019; 15:e1008136. [PMID: 31381575 PMCID: PMC6695201 DOI: 10.1371/journal.pgen.1008136] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/15/2019] [Accepted: 07/19/2019] [Indexed: 01/23/2023] Open
Abstract
The S-phase checkpoint plays an essential role in regulation of the ribonucleotide reductase (RNR) activity to maintain the dNTP pools. How eukaryotic cells respond appropriately to different levels of replication threats remains elusive. Here, we have identified that a conserved GSK-3 kinase Mck1 cooperates with Dun1 in regulating this process. Deleting MCK1 sensitizes dun1Δ to hydroxyurea (HU) reminiscent of mec1Δ or rad53Δ. While Mck1 is downstream of Rad53, it does not participate in the post-translational regulation of RNR as Dun1 does. Mck1 phosphorylates and releases the Crt1 repressor from the promoters of DNA damage-inducible genes as RNR2-4 and HUG1. Hug1, an Rnr2 inhibitor normally silenced, is induced as a counterweight to excessive RNR. When cells suffer a more severe threat, Mck1 inhibits HUG1 transcription. Consistently, only a combined deletion of HUG1 and CRT1, confers a dramatic boost of dNTP levels and the survival of mck1Δdun1Δ or mec1Δ cells assaulted by a lethal dose of HU. These findings reveal the division-of-labor between Mck1 and Dun1 at the S-phase checkpoint pathway to fine-tune dNTP homeostasis.
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Affiliation(s)
- Xiaoli Li
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, P.R. China
| | - Xuejiao Jin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Hangzhou, China
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan, Gothenburg, Sweden
| | - Sushma Sharma
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Xiaojing Liu
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, P.R. China
| | - Jiaxin Zhang
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, P.R. China
| | - Yanling Niu
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, P.R. China
| | - Jiani Li
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, P.R. China
| | - Zhen Li
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, P.R. China
| | - Jingjing Zhang
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, P.R. China
| | - Qinhong Cao
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, P.R. China
| | - Wenya Hou
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, P.R. China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China
| | - Beidong Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Hangzhou, China
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan, Gothenburg, Sweden
- * E-mail: (BL); (HL)
| | - Huiqiang Lou
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, P.R. China
- * E-mail: (BL); (HL)
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Estrem C, Moore JK. Astral microtubule forces alter nuclear organization and inhibit DNA repair in budding yeast. Mol Biol Cell 2019; 30:2000-2013. [PMID: 31067146 PMCID: PMC6727761 DOI: 10.1091/mbc.e18-12-0808] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Dividing cells must balance the maintenance of genome integrity with the generation of cytoskeletal forces that control chromosome position. In this study, we investigate how forces on astral microtubules impact the genome during cell division by using live-cell imaging of the cytoskeleton, chromatin, and DNA damage repair in budding yeast. Our results demonstrate that dynein-dependent forces on astral microtubules are propagated through the spindle during nuclear migration and when in excess can increase the frequency of double-stranded breaks (DSBs). Under these conditions, we find that homology-directed repair of DSBs is delayed, indicating antagonism between nuclear migration and the mechanism of homology-directed repair. These effects are partially rescued by mutants that weaken pericentric cohesion or mutants that decrease constriction on the nucleus as it moves through the bud neck. We propose that minimizing nuclear movement aids in finding a donor strand for homologous recombination.
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Affiliation(s)
- Cassi Estrem
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045
| | - Jeffrey K Moore
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045
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Zhang ZX, Zhang J, Cao Q, Campbell JL, Lou H. The DNA Pol ϵ stimulatory activity of Mrc1 is modulated by phosphorylation. Cell Cycle 2017; 17:64-72. [PMID: 29157061 DOI: 10.1080/15384101.2017.1403680] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
DNA replication checkpoint (Mec1-Mrc1-Rad53 in budding yeast) is an evolutionarily conserved surveillance system to ensure proper DNA replication and genome stability in all eukaryotes. Compared to its well-known function as a mediator of replication checkpoint, the exact role of Mrc1 as a component of normal replication forks remains relatively unclear. In this study, we provide in vitro biochemical evidence to support that yeast Mrc1 is able to enhance the activity of DNA polymerase ϵ (Pol ϵ), the major leading strand replicase. Mrc1 can selectively bind avidly to primer/template DNA bearing a single-stranded region, but not to double-stranded DNA (dsDNA). Mutations of the lysine residues within basic patch 1 (BP1) compromise both DNA binding and polymerase stimulatory activities. Interestingly, Mrc1-3D, a mutant mimicking phosphorylation by the Hog1/MAPK kinase during the osmotic stress response, retains DNA binding but not polymerase stimulation. The stimulatory effect is also abrogated in Mrc1 purified from cells treated with hydroxyurea (HU), which elicits replication checkpoint activation. Taken together with previous findings, these results imply that under unperturbed condition, Mrc1 has a DNA synthesis stimulatory activity, which can be eliminated via Mrc1 phosphorylation in response to replication and/or osmotic stresses.
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Affiliation(s)
- Zhong-Xin Zhang
- a Beijing Advanced Innovation Center for Food Nutrition and Human Health , State Key Laboratory of Agrobiotechnology , MOA Key Laboratory of Soil Microbiology , College of Biological Sciences , China Agricultural University , Beijing 100193 , China
| | - Jingjing Zhang
- a Beijing Advanced Innovation Center for Food Nutrition and Human Health , State Key Laboratory of Agrobiotechnology , MOA Key Laboratory of Soil Microbiology , College of Biological Sciences , China Agricultural University , Beijing 100193 , China
| | - Qinhong Cao
- a Beijing Advanced Innovation Center for Food Nutrition and Human Health , State Key Laboratory of Agrobiotechnology , MOA Key Laboratory of Soil Microbiology , College of Biological Sciences , China Agricultural University , Beijing 100193 , China
| | - Judith L Campbell
- b Braun Laboratories , California Institute of Technology , Pasadena , CA 91125 , USA
| | - Huiqiang Lou
- a Beijing Advanced Innovation Center for Food Nutrition and Human Health , State Key Laboratory of Agrobiotechnology , MOA Key Laboratory of Soil Microbiology , College of Biological Sciences , China Agricultural University , Beijing 100193 , China
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Herlihy AE, de Bruin RAM. The Role of the Transcriptional Response to DNA Replication Stress. Genes (Basel) 2017; 8:E92. [PMID: 28257104 PMCID: PMC5368696 DOI: 10.3390/genes8030092] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 02/20/2017] [Accepted: 02/23/2017] [Indexed: 01/14/2023] Open
Abstract
During DNA replication many factors can result in DNA replication stress. The DNA replication stress checkpoint prevents the accumulation of replication stress-induced DNA damage and the potential ensuing genome instability. A critical role for post-translational modifications, such as phosphorylation, in the replication stress checkpoint response has been well established. However, recent work has revealed an important role for transcription in the cellular response to DNA replication stress. In this review, we will provide an overview of current knowledge of the cellular response to DNA replication stress with a specific focus on the DNA replication stress checkpoint transcriptional response and its role in the prevention of replication stress-induced DNA damage.
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Affiliation(s)
- Anna E Herlihy
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK.
| | - Robertus A M de Bruin
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK.
- The UCL Cancer Institute, University College London, London WC1E 6BT, UK.
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