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Yu Y, Wang X, Fox J, Li Q, Yu Y, Hastings PJ, Chen K, Ira G. RPA and Rad27 limit templated and inverted insertions at DNA breaks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583931. [PMID: 38496432 PMCID: PMC10942419 DOI: 10.1101/2024.03.07.583931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Formation of templated insertions at DNA double-strand breaks (DSBs) is very common in cancer cells. The mechanisms and enzymes regulating these events are largely unknown. Here, we investigated templated insertions in yeast at DSBs using amplicon sequencing across a repaired locus. We document very short (most ∼5-34 bp), templated inverted duplications at DSBs. They are generated through a foldback mechanism that utilizes microhomologies adjacent to the DSB. Enzymatic requirements suggest a hybrid mechanism wherein one end requires Polδ-mediated synthesis while the other end is captured by nonhomologous end joining (NHEJ). This process is exacerbated in mutants with low levels or mutated RPA ( rtt105 Δ; rfa1 -t33) or extensive resection mutant ( sgs1 Δ exo1 Δ). Templated insertions from various distant genomic locations also increase in these mutants as well as in rad27 Δ and originate from fragile regions of the genome. Among complex insertions, common events are insertions of two sequences, originating from the same locus and with inverted orientation. We propose that these inversions are also formed by microhomology-mediated template switching. Taken together, we propose that a shortage of RPA typical in cancer cells is one possible factor stimulating the formation of templated insertions.
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Lyu XH, Suo F, Li W, Jia GS, Yang YS, Du LL. Diverse modes of chromosome terminal deletion in spontaneous canavanine-resistant Schizosaccharomyces pombe mutants. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001132. [PMID: 38404922 PMCID: PMC10884838 DOI: 10.17912/micropub.biology.001132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 02/03/2024] [Accepted: 02/02/2024] [Indexed: 02/27/2024]
Abstract
Canavanine resistance has been used to analyze mutation rates in the fission yeast Schizosaccharomyces pombe . However, the genetic basis of canavanine resistance in this organism remains incompletely understood. Here, we performed whole genome sequencing on five spontaneously arising canavanine-resistant S. pombe mutants, including the can2-1 mutant isolated in the 1970s. This analysis revealed that three mutants, including can2-1 , experienced terminal deletions of the left arm of chromosome II, leading to the loss of multiple amino acid transporter genes. Interestingly, these three mutants underwent chromosome terminal deletion through distinct mechanisms, including homology-driven translocation, homology-independent chromosome fusion, and de novo telomere addition. Our findings shed new light on the genetic basis of canavanine resistance and mechanisms underlying chromosome terminal deletions in fission yeast.
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Affiliation(s)
- Xiao-Hui Lyu
- National Institute of Biological Sciences, Beijing, China
| | - Fang Suo
- National Institute of Biological Sciences, Beijing, China
| | - Wen Li
- National Institute of Biological Sciences, Beijing, China
| | - Guo-Song Jia
- National Institute of Biological Sciences, Beijing, China
| | - Yu-Sheng Yang
- National Institute of Biological Sciences, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
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Gan X, Zhang Y, Jiang D, Shi J, Zhao H, Xie C, Wang Y, Xu J, Zhang X, Cai G, Wang H, Huang J, Chen X. Proper RPA acetylation promotes accurate DNA replication and repair. Nucleic Acids Res 2023; 51:5565-5583. [PMID: 37140030 PMCID: PMC10287905 DOI: 10.1093/nar/gkad291] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 05/05/2023] Open
Abstract
The single-stranded DNA (ssDNA) binding protein complex RPA plays a critical role in promoting DNA replication and multiple DNA repair pathways. However, how RPA is regulated to achieve its functions precisely in these processes remains elusive. Here, we found that proper acetylation and deacetylation of RPA are required to regulate RPA function in promoting high-fidelity DNA replication and repair. We show that yeast RPA is acetylated on multiple conserved lysines by the acetyltransferase NuA4 upon DNA damage. Mimicking constitutive RPA acetylation or blocking its acetylation causes spontaneous mutations with the signature of micro-homology-mediated large deletions or insertions. In parallel, improper RPA acetylation/deacetylation impairs DNA double-strand break (DSB) repair by the accurate gene conversion or break-induced replication while increasing the error-prone repair by single-strand annealing or alternative end joining. Mechanistically, we show that proper acetylation and deacetylation of RPA ensure its normal nuclear localization and ssDNA binding ability. Importantly, mutation of the equivalent residues in human RPA1 also impairs RPA binding on ssDNA, leading to attenuated RAD51 loading and homologous recombination repair. Thus, timely RPA acetylation and deacetylation likely represent a conserved mechanism promoting high-fidelity replication and repair while discriminating the error-prone repair mechanisms in eukaryotes.
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Affiliation(s)
- Xiaoli Gan
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Yueyue Zhang
- The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Donghao Jiang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Jingyao Shi
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Han Zhao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Chengyu Xie
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Yanyan Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Jingyan Xu
- Department of Hematology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Xinghua Zhang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Gang Cai
- The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Hailong Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Jun Huang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xuefeng Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
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4
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DNA Damage and Its Role in Cancer Therapeutics. Int J Mol Sci 2023; 24:ijms24054741. [PMID: 36902170 PMCID: PMC10003233 DOI: 10.3390/ijms24054741] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/05/2023] Open
Abstract
DNA damage is a double-edged sword in cancer cells. On the one hand, DNA damage exacerbates gene mutation frequency and cancer risk. Mutations in key DNA repair genes, such as breast cancer 1 (BRCA1) and/or breast cancer 2 (BRCA2), induce genomic instability and promote tumorigenesis. On the other hand, the induction of DNA damage using chemical reagents or radiation kills cancer cells effectively. Cancer-burdening mutations in key DNA repair-related genes imply relatively high sensitivity to chemotherapy or radiotherapy because of reduced DNA repair efficiency. Therefore, designing specific inhibitors targeting key enzymes in the DNA repair pathway is an effective way to induce synthetic lethality with chemotherapy or radiotherapy in cancer therapeutics. This study reviews the general pathways involved in DNA repair in cancer cells and the potential proteins that could be targeted for cancer therapeutics.
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Kuppa S, Deveryshetty J, Chadda R, Mattice JR, Pokhrel N, Kaushik V, Patterson A, Dhingra N, Pangeni S, Sadauskas MK, Shiekh S, Balci H, Ha T, Zhao X, Bothner B, Antony E. Rtt105 regulates RPA function by configurationally stapling the flexible domains. Nat Commun 2022; 13:5152. [PMID: 36056028 PMCID: PMC9440123 DOI: 10.1038/s41467-022-32860-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 08/18/2022] [Indexed: 11/23/2022] Open
Abstract
Replication Protein A (RPA) is a heterotrimeric complex that binds to single-stranded DNA (ssDNA) and recruits over three dozen RPA-interacting proteins to coordinate multiple aspects of DNA metabolism including DNA replication, repair, and recombination. Rtt105 is a molecular chaperone that regulates nuclear localization of RPA. Here, we show that Rtt105 binds to multiple DNA binding and protein-interaction domains of RPA and configurationally staples the complex. In the absence of ssDNA, Rtt105 inhibits RPA binding to Rad52, thus preventing spurious binding to RPA-interacting proteins. When ssDNA is available, Rtt105 promotes formation of high-density RPA nucleoprotein filaments and dissociates during this process. Free Rtt105 further stabilizes the RPA-ssDNA filaments by inhibiting the facilitated exchange activity of RPA. Collectively, our data suggest that Rtt105 sequesters free RPA in the nucleus to prevent untimely binding to RPA-interacting proteins, while stabilizing RPA-ssDNA filaments at DNA lesion sites. The single stranded DNA binding protein RPA coordinates DNA metabolism using multiple protein and DNA interaction domains. Here, the authors show that the chaperone-like protein Rtt105 staples RPA domains to prevent untimely protein interactions.
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Affiliation(s)
- Sahiti Kuppa
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Jaigeeth Deveryshetty
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Rahul Chadda
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Jenna R Mattice
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Nilisha Pokhrel
- Department of Biological Sciences, Marquette University, Milwaukee, WI, 53201, USA.,Laronde Bio, Cambridge, MA, USA
| | - Vikas Kaushik
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Angela Patterson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Nalini Dhingra
- Molecular Biology Department, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Sushil Pangeni
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Marisa K Sadauskas
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Sajad Shiekh
- Department of Physics, Kent State University, Kent, OH, 44242, USA
| | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH, 44242, USA
| | - Taekjip Ha
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, 21205, USA.,Howard Hughes Medical Institute, Baltimore, MD, 21205, USA
| | - Xiaolan Zhao
- Molecular Biology Department, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Edwin Antony
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA. .,Department of Biological Sciences, Marquette University, Milwaukee, WI, 53201, USA.
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6
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Mirisola MG, Longo VD. Yeast Chronological Lifespan: Longevity Regulatory Genes and Mechanisms. Cells 2022; 11:cells11101714. [PMID: 35626750 PMCID: PMC9139625 DOI: 10.3390/cells11101714] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/14/2022] [Accepted: 05/18/2022] [Indexed: 02/04/2023] Open
Abstract
S. cerevisiae plays a pivotal role as a model system in understanding the biochemistry and molecular biology of mammals including humans. A considerable portion of our knowledge on the genes and pathways involved in cellular growth, resistance to toxic agents, and death has in fact been generated using this model organism. The yeast chronological lifespan (CLS) is a paradigm to study age-dependent damage and longevity. In combination with powerful genetic screening and high throughput technologies, the CLS has allowed the identification of longevity genes and pathways but has also introduced a unicellular “test tube” model system to identify and study macromolecular and cellular damage leading to diseases. In addition, it has played an important role in studying the nutrients and dietary regimens capable of affecting stress resistance and longevity and allowing the characterization of aging regulatory networks. The parallel description of the pro-aging roles of homologs of RAS, S6 kinase, adenylate cyclase, and Tor in yeast and in higher eukaryotes in S. cerevisiae chronological survival studies is valuable to understand human aging and disease. Here we review work on the S. cerevisiae chronological lifespan with a focus on the genes regulating age-dependent macromolecular damage and longevity extension.
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Affiliation(s)
- Mario G. Mirisola
- Department of Surgery, Oncology and Oral Sciences, University of Palermo, Via del Vespro 129, 90127 Palermo, Italy
- Correspondence: (M.G.M.); (V.D.L.)
| | - Valter D. Longo
- Department of Biological Sciences, Longevity Institute, Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- IFOM, FIRC Institute of Molecular Oncology, 20139 Milan, Italy
- Correspondence: (M.G.M.); (V.D.L.)
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Gain-of-Function Mutations in RPA1 Cause a Syndrome with Short Telomeres and Somatic Genetic Rescue. Blood 2021; 139:1039-1051. [PMID: 34767620 PMCID: PMC8854676 DOI: 10.1182/blood.2021011980] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 10/15/2021] [Indexed: 11/20/2022] Open
Abstract
Germline RPA1 gain-of-function missense mutations result in a telomere biology disorder phenotype. Somatic rescue events arise in hematopoiesis secondary to germline RPA1 mutation.
Human telomere biology disorders (TBD)/short telomere syndromes (STS) are heterogeneous disorders caused by inherited loss-of-function mutations in telomere-associated genes. Here, we identify 3 germline heterozygous missense variants in the RPA1 gene in 4 unrelated probands presenting with short telomeres and varying clinical features of TBD/STS, including bone marrow failure, myelodysplastic syndrome, T- and B-cell lymphopenia, pulmonary fibrosis, or skin manifestations. All variants cluster to DNA-binding domain A of RPA1 protein. RPA1 is a single-strand DNA-binding protein required for DNA replication and repair and involved in telomere maintenance. We showed that RPA1E240K and RPA1V227A proteins exhibit increased binding to single-strand and telomeric DNA, implying a gain in DNA-binding function, whereas RPA1T270A has binding properties similar to wild-type protein. To study the mutational effect in a cellular system, CRISPR/Cas9 was used to knock-in the RPA1E240K mutation into healthy inducible pluripotent stem cells. This resulted in severe telomere shortening and impaired hematopoietic differentiation. Furthermore, in patients with RPA1E240K, we discovered somatic genetic rescue in hematopoietic cells due to an acquired truncating cis RPA1 mutation or a uniparental isodisomy 17p with loss of mutant allele, coinciding with stabilized blood counts. Using single-cell sequencing, the 2 somatic genetic rescue events were proven to be independently acquired in hematopoietic stem cells. In summary, we describe the first human disease caused by germline RPA1 variants in individuals with TBD/STS.
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Rtt105 promotes high-fidelity DNA replication and repair by regulating the single-stranded DNA-binding factor RPA. Proc Natl Acad Sci U S A 2021; 118:2106393118. [PMID: 34140406 DOI: 10.1073/pnas.2106393118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Single-stranded DNA (ssDNA) covered with the heterotrimeric Replication Protein A (RPA) complex is a central intermediate of DNA replication and repair. How RPA is regulated to ensure the fidelity of DNA replication and repair remains poorly understood. Yeast Rtt105 is an RPA-interacting protein required for RPA nuclear import and efficient ssDNA binding. Here, we describe an important role of Rtt105 in high-fidelity DNA replication and recombination and demonstrate that these functions of Rtt105 primarily depend on its regulation of RPA. The deletion of RTT105 causes elevated spontaneous DNA mutations with large duplications or deletions mediated by microhomologies. Rtt105 is recruited to DNA double-stranded break (DSB) ends where it promotes RPA assembly and homologous recombination repair by gene conversion or break-induced replication. In contrast, Rtt105 attenuates DSB repair by the mutagenic single-strand annealing or alternative end joining pathway. Thus, Rtt105-mediated regulation of RPA promotes high-fidelity replication and recombination while suppressing repair by deleterious pathways. Finally, we show that the human RPA-interacting protein hRIP-α, a putative functional homolog of Rtt105, also stimulates RPA assembly on ssDNA, suggesting the conservation of an Rtt105-mediated mechanism.
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Giovannini S, Weller MC, Hanzlíková H, Shiota T, Takeda S, Jiricny J. ATAD5 deficiency alters DNA damage metabolism and sensitizes cells to PARP inhibition. Nucleic Acids Res 2020; 48:4928-4939. [PMID: 32297953 PMCID: PMC7229844 DOI: 10.1093/nar/gkaa255] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/31/2020] [Accepted: 04/04/2020] [Indexed: 01/05/2023] Open
Abstract
Replication factor C (RFC), a heteropentamer of RFC1-5, loads PCNA onto DNA during replication and repair. Once DNA synthesis has ceased, PCNA must be unloaded. Recent findings assign the uloader role primarily to an RFC-like (RLC) complex, in which the largest RFC subunit, RFC1, has been replaced with ATAD5 (ELG1 in Saccharomyces cerevisiae). ATAD5-RLC appears to be indispensable, given that Atad5 knock-out leads to embryonic lethality. In order to learn how the retention of PCNA on DNA might interfere with normal DNA metabolism, we studied the response of ATAD5-depleted cells to several genotoxic agents. We show that ATAD5 deficiency leads to hypersensitivity to methyl methanesulphonate (MMS), camptothecin (CPT) and mitomycin C (MMC), agents that hinder the progression of replication forks. We further show that ATAD5-depleted cells are sensitive to poly(ADP)ribose polymerase (PARP) inhibitors and that the processing of spontaneous oxidative DNA damage contributes towards this sensitivity. We posit that PCNA molecules trapped on DNA interfere with the correct metabolism of arrested replication forks, phenotype reminiscent of defective homologous recombination (HR). As Atad5 heterozygous mice are cancer-prone and as ATAD5 mutations have been identified in breast and endometrial cancers, our finding may open a path towards the therapy of these tumours.
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Affiliation(s)
- Sara Giovannini
- Institute of Molecular Life Sciences of the University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Institute of Molecular Cancer Research of the University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Institute of Biochemistry of the Swiss Federal Institute of Technology, Otto-Stern-Weg 3, 8093 Zurich, Switzerland
| | - Marie-Christine Weller
- Institute of Molecular Cancer Research of the University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Hana Hanzlíková
- Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, 142-20 Prague 4, Czech Republic
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Tetsuya Shiota
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, 606-8501 Kyoto, Japan
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, 606-8501 Kyoto, Japan
| | - Josef Jiricny
- Institute of Molecular Life Sciences of the University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Institute of Molecular Cancer Research of the University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Institute of Biochemistry of the Swiss Federal Institute of Technology, Otto-Stern-Weg 3, 8093 Zurich, Switzerland
- To whom correspondence should be addressed. Tel: +41 44 633 6260;
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Epum EA, Mohan MJ, Ruppe NP, Friedman KL. Interaction of yeast Rad51 and Rad52 relieves Rad52-mediated inhibition of de novo telomere addition. PLoS Genet 2020; 16:e1008608. [PMID: 32012161 PMCID: PMC7018233 DOI: 10.1371/journal.pgen.1008608] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 02/13/2020] [Accepted: 01/13/2020] [Indexed: 12/26/2022] Open
Abstract
DNA double-strand breaks (DSBs) are toxic forms of DNA damage that must be repaired to maintain genome integrity. Telomerase can act upon a DSB to create a de novo telomere, a process that interferes with normal repair and creates terminal deletions. We previously identified sequences in Saccharomyces cerevisiae (SiRTAs; Sites of Repair-associated Telomere Addition) that undergo unusually high frequencies of de novo telomere addition, even when the original chromosome break is several kilobases distal to the eventual site of telomerase action. Association of the single-stranded telomere binding protein Cdc13 with a SiRTA is required to stimulate de novo telomere addition. Because extensive resection must occur prior to Cdc13 binding, we utilized these sites to monitor the effect of proteins involved in homologous recombination. We find that telomere addition is significantly reduced in the absence of the Rad51 recombinase, while loss of Rad52, required for Rad51 nucleoprotein filament formation, has no effect. Deletion of RAD52 suppresses the defect of the rad51Δ strain, suggesting that Rad52 inhibits de novo telomere addition in the absence of Rad51. The ability of Rad51 to counteract this effect of Rad52 does not require DNA binding by Rad51, but does require interaction between the two proteins, while the inhibitory effect of Rad52 depends on its interaction with Replication Protein A (RPA). Intriguingly, the genetic interactions we report between RAD51 and RAD52 are similar to those previously observed in the context of checkpoint adaptation. Forced recruitment of Cdc13 fully restores telomere addition in the absence of Rad51, suggesting that Rad52, through its interaction with RPA-coated single-stranded DNA, inhibits the ability of Cdc13 to bind and stimulate telomere addition. Loss of the Rad51-Rad52 interaction also stimulates a subset of Rad52-dependent microhomology-mediated repair (MHMR) events, consistent with the known ability of Rad51 to prevent single-strand annealing. DNA double-strand breaks (DSBs) can lead to chromosome loss and rearrangement associated with cancer and genetic disease, so understanding how the cell coordinates multiple possible repair pathways is of critical importance. Telomerase is a ribonucleoprotein enzyme that uses an intrinsic RNA component as a template for the addition of highly repetitive, protective sequences (called telomeres) at normal chromosome ends. Rarely, telomerase acts upon a DSB to create a new or de novo telomere with resultant loss of sequences distal to the site of telomere addition. Here, we show that interactions between proteins with known roles during DSB repair modulate the probability of telomerase action at hotspots of de novo telomere addition in the yeast genome by influencing the association of Cdc13, a protein required for telomerase recruitment, with sites of telomere addition. Intriguingly, the same interactions that facilitate telomere addition prevent other types of rearrangements in response to chromosome breaks.
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Affiliation(s)
- Esther A. Epum
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Michael J. Mohan
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Nicholas P. Ruppe
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Katherine L. Friedman
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail:
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11
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Adaptation to DNA damage checkpoint in senescent telomerase-negative cells promotes genome instability. Genes Dev 2018; 32:1499-1513. [PMID: 30463903 PMCID: PMC6295172 DOI: 10.1101/gad.318485.118] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/03/2018] [Indexed: 01/04/2023]
Abstract
Here, Coutelier et al. used a microfluidic-based approach and live-cell imaging in yeast to capture early mutation events during replicative senescence and observed that prolonged checkpoint arrests occurred frequently in telomerase-negative lineages. Their results demonstrate that the adaptation pathway is a major contributor to the genome instability induced during replicative senescence. In cells lacking telomerase, telomeres gradually shorten during each cell division to reach a critically short length, permanently activate the DNA damage checkpoint, and trigger replicative senescence. The increase in genome instability that occurs as a consequence may contribute to the early steps of tumorigenesis. However, because of the low frequency of mutations and the heterogeneity of telomere-induced senescence, the timing and mechanisms of genome instability increase remain elusive. Here, to capture early mutation events during replicative senescence, we used a combined microfluidic-based approach and live-cell imaging in yeast. We analyzed DNA damage checkpoint activation in consecutive cell divisions of individual cell lineages in telomerase-negative yeast cells and observed that prolonged checkpoint arrests occurred frequently in telomerase-negative lineages. Cells relied on the adaptation to the DNA damage pathway to bypass the prolonged checkpoint arrests, allowing further cell divisions despite the presence of unrepaired DNA damage. We demonstrate that the adaptation pathway is a major contributor to the genome instability induced during replicative senescence. Therefore, adaptation plays a critical role in shaping the dynamics of genome instability during replicative senescence.
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12
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GC content elevates mutation and recombination rates in the yeast Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2018; 115:E7109-E7118. [PMID: 29987035 PMCID: PMC6064992 DOI: 10.1073/pnas.1807334115] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The chromosomes of many eukaryotes have regions of high GC content interspersed with regions of low GC content. In the yeast Saccharomyces cerevisiae, high-GC regions are often associated with high levels of meiotic recombination. In this study, we constructed URA3 genes that differ substantially in their base composition [URA3-AT (31% GC), URA3-WT (43% GC), and URA3-GC (63% GC)] but encode proteins with the same amino acid sequence. The strain with URA3-GC had an approximately sevenfold elevated rate of ura3 mutations compared with the strains with URA3-WT or URA3-AT About half of these mutations were single-base substitutions and were dependent on the error-prone DNA polymerase ζ. About 30% were deletions or duplications between short (5-10 base) direct repeats resulting from DNA polymerase slippage. The URA3-GC gene also had elevated rates of meiotic and mitotic recombination relative to the URA3-AT or URA3-WT genes. Thus, base composition has a substantial effect on the basic parameters of genome stability and evolution.
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13
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Stirpe M, Palermo V, Ferrari M, Mroczek S, Kufel J, Falcone C, Mazzoni C. Increased levels of RNA oxidation enhance the reversion frequency in aging pro-apoptotic yeast mutants. Apoptosis 2018; 22:200-206. [PMID: 27803986 PMCID: PMC5306349 DOI: 10.1007/s10495-016-1319-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Despite recent advances in understanding the complexity of RNA processes, regulation of the metabolism of oxidized cellular RNAs and the mechanisms through which oxidized ribonucleotides affect mRNA translation, and consequently cell viability, are not well characterized. We show here that the level of oxidized RNAs is markedly increased in a yeast decapping Kllsm4Δ1 mutant, which accumulates mRNAs, ages much faster that the wild type strain and undergoes regulated-cell-death. We also found that in Kllsm4Δ1 cells the mutation rate increases during chronological life span indicating that the capacity to handle oxidized RNAs in yeast declines with aging. Lowering intracellular ROS levels by antioxidants recovers the wild-type phenotype of mutant cells, including reduced amount of oxidized RNAs and lower mutation rate. Since mRNA oxidation was reported to occur in different neurodegenerative diseases, decapping-deficient cells may represent a useful tool for deciphering molecular mechanisms of cell response to such conditions, providing new insights into RNA modification-based pathogenesis.
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Affiliation(s)
- Mariarita Stirpe
- Department of Biology and Biotechnology "Charles Darwin", Istituto Pasteur Italia-Fondazione Cenci Bolognetti, University "Sapienza" of Rome, Piazzale Aldo Moro 5, Rome, Italy
| | - Vanessa Palermo
- Department of Biology and Biotechnology "Charles Darwin", Istituto Pasteur Italia-Fondazione Cenci Bolognetti, University "Sapienza" of Rome, Piazzale Aldo Moro 5, Rome, Italy
| | - Matteo Ferrari
- Department of Biology and Biotechnology "Charles Darwin", Istituto Pasteur Italia-Fondazione Cenci Bolognetti, University "Sapienza" of Rome, Piazzale Aldo Moro 5, Rome, Italy
| | - Seweryn Mroczek
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Joanna Kufel
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Claudio Falcone
- Department of Biology and Biotechnology "Charles Darwin", Istituto Pasteur Italia-Fondazione Cenci Bolognetti, University "Sapienza" of Rome, Piazzale Aldo Moro 5, Rome, Italy
| | - Cristina Mazzoni
- Department of Biology and Biotechnology "Charles Darwin", Istituto Pasteur Italia-Fondazione Cenci Bolognetti, University "Sapienza" of Rome, Piazzale Aldo Moro 5, Rome, Italy.
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14
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Abstract
Genome rearrangements underlie different human diseases including many cancers. Determining the rates at which genome rearrangements arise and isolating unique, independent genome rearrangements is critical to understanding the genes and pathways that prevent or promote genome rearrangements. Here, we describe quantitative S. cerevisiae genetic assays for measuring the rates of accumulating genome rearrangements including deletions, translocations, and broken chromosomes healed by de novo telomere addition that result in the deletion of two counter-selectable genes, CAN1 and URA3, placed in the nonessential regions of the S. cerevisiae genome. The assays also allow for the isolation of individual genome rearrangements for structural studies, and a method for analyzing genome rearrangements by next-generation DNA sequencing is provided.
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Affiliation(s)
- Anjana Srivatsan
- Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0669, USA
| | - Christopher D Putnam
- Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0669, USA
- Department of Medicine, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0669, USA
| | - Richard D Kolodner
- Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0669, USA.
- Department of Cellular and Molecular Medicine, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0669, USA.
- Moores-UCSD Cancer Center, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0669, USA.
- Institute of Genomic Medicine, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0669, USA.
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15
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Pathways and Mechanisms that Prevent Genome Instability in Saccharomyces cerevisiae. Genetics 2017; 206:1187-1225. [PMID: 28684602 PMCID: PMC5500125 DOI: 10.1534/genetics.112.145805] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 04/26/2017] [Indexed: 12/13/2022] Open
Abstract
Genome rearrangements result in mutations that underlie many human diseases, and ongoing genome instability likely contributes to the development of many cancers. The tools for studying genome instability in mammalian cells are limited, whereas model organisms such as Saccharomyces cerevisiae are more amenable to these studies. Here, we discuss the many genetic assays developed to measure the rate of occurrence of Gross Chromosomal Rearrangements (called GCRs) in S. cerevisiae. These genetic assays have been used to identify many types of GCRs, including translocations, interstitial deletions, and broken chromosomes healed by de novo telomere addition, and have identified genes that act in the suppression and formation of GCRs. Insights from these studies have contributed to the understanding of pathways and mechanisms that suppress genome instability and how these pathways cooperate with each other. Integrated models for the formation and suppression of GCRs are discussed.
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16
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Deshpande I, Seeber A, Shimada K, Keusch JJ, Gut H, Gasser SM. Structural Basis of Mec1-Ddc2-RPA Assembly and Activation on Single-Stranded DNA at Sites of Damage. Mol Cell 2017; 68:431-445.e5. [PMID: 29033322 DOI: 10.1016/j.molcel.2017.09.019] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/18/2017] [Accepted: 09/14/2017] [Indexed: 10/18/2022]
Abstract
Mec1-Ddc2 (ATR-ATRIP) is a key DNA-damage-sensing kinase that is recruited through the single-stranded (ss) DNA-binding replication protein A (RPA) to initiate the DNA damage checkpoint response. Activation of ATR-ATRIP in the absence of DNA damage is lethal. Therefore, it is important that damage-specific recruitment precedes kinase activation, which is achieved at least in part by Mec1-Ddc2 homodimerization. Here, we report a structural, biochemical, and functional characterization of the yeast Mec1-Ddc2-RPA assembly. High-resolution co-crystal structures of Ddc2-Rfa1 and Ddc2-Rfa1-t11 (K45E mutant) N termini and of the Ddc2 coiled-coil domain (CCD) provide insight into Mec1-Ddc2 homodimerization and damage-site targeting. Based on our structural and functional findings, we present a Mec1-Ddc2-RPA-ssDNA composite structural model. By way of validation, we show that RPA-dependent recruitment of Mec1-Ddc2 is crucial for maintaining its homodimeric state at ssDNA and that Ddc2's recruitment domain and CCD are important for Mec1-dependent survival of UV-light-induced DNA damage.
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Affiliation(s)
- Ishan Deshpande
- Friedrich Miescher Institute for Biomedical Research (FMI), Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Faculty of Natural Sciences, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Andrew Seeber
- Friedrich Miescher Institute for Biomedical Research (FMI), Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Kenji Shimada
- Friedrich Miescher Institute for Biomedical Research (FMI), Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Jeremy J Keusch
- Friedrich Miescher Institute for Biomedical Research (FMI), Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Heinz Gut
- Friedrich Miescher Institute for Biomedical Research (FMI), Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research (FMI), Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Faculty of Natural Sciences, Klingelbergstrasse 50, 4056 Basel, Switzerland.
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17
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Sorenson KS, Mahaney BL, Lees-Miller SP, Cobb JA. The non-homologous end-joining factor Nej1 inhibits resection mediated by Dna2-Sgs1 nuclease-helicase at DNA double strand breaks. J Biol Chem 2017; 292:14576-14586. [PMID: 28679532 DOI: 10.1074/jbc.m117.796011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 07/03/2017] [Indexed: 12/25/2022] Open
Abstract
Double strand breaks (DSBs) represent highly deleterious DNA damage and need to be accurately repaired. Homology-directed repair and non-homologous end joining (NHEJ) are the two major DSB repair pathways that are highly conserved from yeast to mammals. The choice between these pathways is largely based on 5' to 3' DNA resection, and NHEJ proceeds only if resection has not been initiated. In yeast, yKu70/80 rapidly localizes to the break, protecting DNA ends from nuclease accessibility, and recruits additional NHEJ factors, including Nej1 and Lif1. Cells harboring the nej1-V338A mutant exhibit NHEJ-mediated repair deficiencies and hyper-resection 0.15 kb from the DSB that was dependent on the nuclease activity of Dna2-Sgs1. The integrity of Nej1 is also important for inhibiting long-range resection, 4.8 kb from the break, and for preventing the formation of large genomic deletions at sizes >700 bp around the break. Nej1V338A localized to a DSB similarly to WT Nej1, indicating that the Nej1-Lif1 interaction becomes critical for blocking hyper-resection mainly after their recruitment to the DSB. This work highlights that Nej1 inhibits 5' DNA hyper-resection mediated by Dna2-Sgs1, a function distinct from its previously reported role in supporting Dnl4 ligase activity, and has implications for repair pathway choice and resection regulation upon DSB formation.
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Affiliation(s)
- Kyle S Sorenson
- From the Departments of Biochemistry and Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N. W., Calgary, Alberta T2N 4N1, Canada
| | - Brandi L Mahaney
- From the Departments of Biochemistry and Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N. W., Calgary, Alberta T2N 4N1, Canada
| | - Susan P Lees-Miller
- From the Departments of Biochemistry and Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N. W., Calgary, Alberta T2N 4N1, Canada
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18
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Abstract
DNA repair is essential to maintain genomic integrity and initiate genetic diversity. While gene conversion and classical nonhomologous end-joining are the most physiologically predominant forms of DNA repair mechanisms, emerging lines of evidence suggest the usage of several noncanonical homology-directed repair (HDR) pathways in both prokaryotes and eukaryotes in different contexts. Here we review how these alternative HDR pathways are executed, specifically focusing on the determinants that dictate competition between them and their relevance to cancers that display complex genomic rearrangements or maintain their telomeres by homology-directed DNA synthesis.
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19
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Dynamic control of strand excision during human DNA mismatch repair. Proc Natl Acad Sci U S A 2016; 113:3281-6. [PMID: 26951673 DOI: 10.1073/pnas.1523748113] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Mismatch repair (MMR) is activated by evolutionarily conserved MutS homologs (MSH) and MutL homologs (MLH/PMS). MSH recognizes mismatched nucleotides and form extremely stable sliding clamps that may be bound by MLH/PMS to ultimately authorize strand-specific excision starting at a distant 3'- or 5'-DNA scission. The mechanical processes associated with a complete MMR reaction remain enigmatic. The purified human (Homo sapien or Hs) 5'-MMR excision reaction requires the HsMSH2-HsMSH6 heterodimer, the 5' → 3' exonuclease HsEXOI, and the single-stranded binding heterotrimer HsRPA. The HsMLH1-HsPMS2 heterodimer substantially influences 5'-MMR excision in cell extracts but is not required in the purified system. Using real-time single-molecule imaging, we show that HsRPA or Escherichia coli EcSSB restricts HsEXOI excision activity on nicked or gapped DNA. HsMSH2-HsMSH6 activates HsEXOI by overcoming HsRPA/EcSSB inhibition and exploits multiple dynamic sliding clamps to increase tract length. Conversely, HsMLH1-HsPMS2 regulates tract length by controlling the number of excision complexes, providing a link to 5' MMR.
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20
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Sinha S, Villarreal D, Shim EY, Lee SE. Risky business: Microhomology-mediated end joining. Mutat Res 2016; 788:17-24. [PMID: 26790771 DOI: 10.1016/j.mrfmmm.2015.12.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 12/03/2015] [Accepted: 12/22/2015] [Indexed: 11/16/2022]
Abstract
Prevalence of microhomology (MH) at the breakpoint junctions in somatic and germ-line chromosomal rearrangements and in the programmed immune receptor rearrangements from cells deficient in classical end joining reveals an enigmatic process called MH-mediated end joining (MMEJ). MMEJ repairs DNA double strand breaks (DSBs) by annealing flanking MH and deleting genetic information at the repair junctions from yeast to humans. Being genetically distinct from canonical DNA DSB pathways, MMEJ is involved with the fusions of eroded/uncapped telomeres as well as with the assembly of chromosome fragments in chromothripsis. In this review article, we will discuss an up-to-date model representing the MMEJ process and the mechanism by which cells regulate MMEJ to limit repair-associated mutagenesis. We will also describe the possible therapeutic gains resulting from the inhibition of MMEJ in recombination deficient cancers. Lastly, we will embark on two contentious issues associated with MMEJ such as the significance of MH at the repair junction to be the hallmark of MMEJ and the relationship of MMEJ to other mechanistically related DSB repair pathways.
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Affiliation(s)
- Supriya Sinha
- Department of Molecular Medicine, Institute of Biotechnology, United States
| | - Diana Villarreal
- Children's Hospital of San Antonio, Baylor College of Medicine, San Antonio, TX 78207, United States
| | - Eun Yong Shim
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, TX 78229, United States
| | - Sang Eun Lee
- Department of Molecular Medicine, Institute of Biotechnology, United States; Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, TX 78229, United States.
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21
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Furgason JM, Koncar RF, Michelhaugh SK, Sarkar FH, Mittal S, Sloan AE, Barnholtz-Sloan JS, Bahassi EM. Whole genome sequence analysis links chromothripsis to EGFR, MDM2, MDM4, and CDK4 amplification in glioblastoma. Oncoscience 2015; 2:618-28. [PMID: 26328271 PMCID: PMC4549359 DOI: 10.18632/oncoscience.178] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 07/25/2015] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Findings based on recent advances in next-generation sequence analysis suggest that, in some tumors, a single catastrophic event, termed chromothripsis, results in several simultaneous tumorigenic alterations. Previous studies have suggested that glioblastoma (GBM) may exhibit chromothripsis at a higher rate (39%) than other tumors (9%). Primary glioblastoma is an aggressive form of brain cancer that typically appears suddenly in older adults. With aggressive treatment, the median survival time is only 15 months. Their acute onset and widespread genomic instability indicates that chromothripsis may play a key role in their initiation and progression. GBMs are often characterized by EGFR amplification, CDKN2A and PTEN deletion, although approximately 20% of GBMs harbor additional amplifications in MDM2 or MDM4 with CDK4. METHODS We used the chromothripsis prediction tool, Shatterproof, in conjunction with a custom whole genome sequence analysis pipeline in order to generate putative regions of chromothripsis. The data derived from this study was further expanded on using fluorescence in situ hybridization (FISH) analysis and susceptibility studies with colony formation assays. RESULTS We show that primary GBMs are associated with higher chromothripsis scores and establish a link between chromothripsis and gene amplification of receptor tyrosine kinases (RTKs), as well as modulators of the TP53 and RB1 pathways. CONCLUSIONS Utilizing a newly introduced bioinformatic tool, we provide evidence that chromothripsis is associated with the formation of amplicons containing several oncogenes involved in key pathways that are likely essential for post-chromothriptic cell survival.
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Affiliation(s)
- John M Furgason
- Department of Internal Medicine, Division of Hematology/Oncology and UC Brain Tumor Center, University of Cincinnati, Cincinnati OH, USA
| | - Robert F Koncar
- Department of Internal Medicine, Division of Hematology/Oncology and UC Brain Tumor Center, University of Cincinnati, Cincinnati OH, USA
| | - Sharon K Michelhaugh
- Department of Neurosurgery, Wayne State University and Karmanos Cancer Institute, Detroit, MI, USA
| | - Fazlul H Sarkar
- Department of Pathology, Wayne State University College of Medicine, Detroit, MI, USA
| | - Sandeep Mittal
- Department of Neurosurgery, Wayne State University and Karmanos Cancer Institute, Detroit, MI, USA
| | - Andrew E Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA ; Department of Neurological Surgery, University Hospitals Case Medical Center, Cleveland, Ohio, USA
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - El Mustapha Bahassi
- Department of Internal Medicine, Division of Hematology/Oncology and UC Brain Tumor Center, University of Cincinnati, Cincinnati OH, USA
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22
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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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23
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Guven M, Brem R, Macpherson P, Peacock M, Karran P. Oxidative Damage to RPA Limits the Nucleotide Excision Repair Capacity of Human Cells. J Invest Dermatol 2015; 135:2834-2841. [PMID: 26134950 DOI: 10.1038/jid.2015.255] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/01/2015] [Accepted: 06/18/2015] [Indexed: 12/13/2022]
Abstract
Nucleotide excision repair (NER) protects against sunlight-induced skin cancer. Defective NER is associated with photosensitivity and a high skin cancer incidence. Some clinical treatments that cause photosensitivity can also increase skin cancer risk. Among these, the immunosuppressant azathioprine and the fluoroquinolone antibiotics ciprofloxacin and ofloxacin interact with UVA radiation to generate reactive oxygen species that diminish NER capacity by causing protein damage. The replication protein A (RPA) DNA-binding protein has a pivotal role in DNA metabolism and is an essential component of NER. The relationship between protein oxidation and NER inhibition was investigated in cultured human cells expressing different levels of RPA. We show here that RPA is limiting for NER and that oxidative damage to RPA compromises NER capability. Our findings reveal that cellular RPA is surprisingly vulnerable to oxidation, and we identify oxidized forms of RPA that are associated with impaired NER. The vulnerability of NER to inhibition by oxidation provides a connection between cutaneous photosensitivity, protein damage, and increased skin cancer risk. Our findings emphasize that damage to DNA repair proteins, as well as to DNA itself, is likely to be an important contributor to skin cancer risk.
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Affiliation(s)
- Melisa Guven
- Francis Crick Institute, Clare Hall Laboratory, South Mimms, Herts, UK
| | - Reto Brem
- Francis Crick Institute, Clare Hall Laboratory, South Mimms, Herts, UK
| | - Peter Macpherson
- Francis Crick Institute, Clare Hall Laboratory, South Mimms, Herts, UK
| | - Matthew Peacock
- Francis Crick Institute, Clare Hall Laboratory, South Mimms, Herts, UK
| | - Peter Karran
- Francis Crick Institute, Clare Hall Laboratory, South Mimms, Herts, UK.
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24
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Kar A, Kaur M, Ghosh T, Khan MM, Sharma A, Shekhar R, Varshney A, Saxena S. RPA70 depletion induces hSSB1/2-INTS3 complex to initiate ATR signaling. Nucleic Acids Res 2015; 43:4962-74. [PMID: 25916848 PMCID: PMC4446429 DOI: 10.1093/nar/gkv369] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 04/08/2015] [Indexed: 01/12/2023] Open
Abstract
The primary eukaryotic single-stranded DNA-binding protein, Replication protein A (RPA), binds to single-stranded DNA at the sites of DNA damage and recruits the apical checkpoint kinase, ATR via its partner protein, ATRIP. It has been demonstrated that absence of RPA incapacitates the ATR-mediated checkpoint response. We report that in the absence of RPA, human single-stranded DNA-binding protein 1 (hSSB1) and its partner protein INTS3 form sub-nuclear foci, associate with the ATR-ATRIP complex and recruit it to the sites of genomic stress. The ATRIP foci formed after RPA depletion are abrogated in the absence of INTS3, establishing that hSSB-INTS3 complex recruits the ATR-ATRIP checkpoint complex to the sites of genomic stress. Depletion of homologs hSSB1/2 and INTS3 in RPA-deficient cells attenuates Chk1 phosphorylation, indicating that the cells are debilitated in responding to stress. We have identified that TopBP1 and the Rad9-Rad1-Hus1 complex are essential for the alternate mode of ATR activation. In summation, we report that the single-stranded DNA-binding protein complex, hSSB1/2-INTS3 can recruit the checkpoint complex to initiate ATR signaling.
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Affiliation(s)
- Ananya Kar
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Manpreet Kaur
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Tanushree Ghosh
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Md Muntaz Khan
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Aparna Sharma
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Ritu Shekhar
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Akhil Varshney
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Sandeep Saxena
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
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25
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Rattray A, Santoyo G, Shafer B, Strathern JN. Elevated mutation rate during meiosis in Saccharomyces cerevisiae. PLoS Genet 2015; 11:e1004910. [PMID: 25569256 PMCID: PMC4287439 DOI: 10.1371/journal.pgen.1004910] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 11/21/2014] [Indexed: 02/04/2023] Open
Abstract
Mutations accumulate during all stages of growth, but only germ line mutations contribute to evolution. While meiosis contributes to evolution by reassortment of parental alleles, we show here that the process itself is inherently mutagenic. We have previously shown that the DNA synthesis associated with repair of a double-strand break is about 1000-fold less accurate than S-phase synthesis. Since the process of meiosis involves many programmed DSBs, we reasoned that this repair might also be mutagenic. Indeed, in the early 1960's Magni and Von Borstel observed elevated reversion of recessive alleles during meiosis, and found that the revertants were more likely to be associated with a crossover than non-revertants, a process that they called "the meiotic effect." Here we use a forward mutation reporter (CAN1 HIS3) placed at either a meiotic recombination coldspot or hotspot near the MAT locus on Chromosome III. We find that the increased mutation rate at CAN1 (6 to 21 -fold) correlates with the underlying recombination rate at the locus. Importantly, we show that the elevated mutation rate is fully dependent upon Spo11, the protein that introduces the meiosis specific DSBs. To examine associated recombination we selected for random spores with or without a mutation in CAN1. We find that the mutations isolated this way show an increased association with recombination (crossovers, loss of crossover interference and/or increased gene conversion tracts). Polζ appears to contribute about half of the mutations induced during meiosis, but is not the only source of mutations for the meiotic effect. We see no difference in either the spectrum or distribution of mutations between mitosis and meiosis. The correlation of hotspots with elevated mutagenesis provides a mechanism for organisms to control evolution rates in a gene specific manner.
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Affiliation(s)
- Alison Rattray
- Gene Regulation and Chromosome Biology Laboratory, NCI-Frederick, FNLCR, Frederick, Maryland, United States of America
| | - Gustavo Santoyo
- Gene Regulation and Chromosome Biology Laboratory, NCI-Frederick, FNLCR, Frederick, Maryland, United States of America
| | - Brenda Shafer
- Gene Regulation and Chromosome Biology Laboratory, NCI-Frederick, FNLCR, Frederick, Maryland, United States of America
| | - Jeffrey N. Strathern
- Gene Regulation and Chromosome Biology Laboratory, NCI-Frederick, FNLCR, Frederick, Maryland, United States of America
- * E-mail:
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26
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Deng SK, Chen H, Symington LS. Replication protein A prevents promiscuous annealing between short sequence homologies: Implications for genome integrity. Bioessays 2014; 37:305-13. [PMID: 25400143 DOI: 10.1002/bies.201400161] [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: 12/11/2022]
Abstract
Replication protein A (RPA) is the main eukaryotic single-stranded DNA (ssDNA) binding protein, having essential roles in all DNA metabolic reactions involving ssDNA. RPA binds ssDNA with high affinity, thereby preventing the formation of secondary structures and protecting ssDNA from the action of nucleases, and directly interacts with other DNA processing proteins. Here, we discuss recent results supporting the idea that one function of RPA is to prevent annealing between short repeats that can lead to chromosome rearrangements by microhomology-mediated end joining or the formation of hairpin structures that are substrates for structure-selective nucleases. We suggest that replication fork catastrophe caused by depletion of RPA could result from cleavage of secondary structures by nucleases, and that failure to cleave hairpin structures formed at DNA ends could lead to gene amplification. These studies highlight the important role RPA plays in maintaining genome integrity.
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Affiliation(s)
- Sarah K Deng
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, USA
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27
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Avoidance of ribonucleotide-induced mutations by RNase H2 and Srs2-Exo1 mechanisms. Nature 2014; 511:251-4. [PMID: 24896181 PMCID: PMC4140095 DOI: 10.1038/nature13292] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 03/28/2014] [Indexed: 11/09/2022]
Abstract
Srs2 helicase is known to dismantle nucleofilaments of Rad51 recombinase to prevent spurious recombination events and unwind trinucleotide sequences that are prone to hairpin formation. Here we document a new, unexpected genome maintenance role of Srs2 in the suppression of mutations arising from mis-insertion of ribonucleoside monophosphates during DNA replication. In cells lacking RNase H2, Srs2 unwinds DNA from the 5' side of a nick generated by DNA topoisomerase I at a ribonucleoside monophosphate residue. In addition, Srs2 interacts with and enhances the activity of the nuclease Exo1, to generate a DNA gap in preparation for repair. Srs2-Exo1 thus functions in a new pathway of nick processing-gap filling that mediates tolerance of ribonucleoside monophosphates in the genome. Our results have implications for understanding the basis of Aicardi-Goutières syndrome, which stems from inactivation of the human RNase H2 complex.
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Deng SK, Gibb B, de Almeida MJ, Greene EC, Symington LS. RPA antagonizes microhomology-mediated repair of DNA double-strand breaks. Nat Struct Mol Biol 2014; 21:405-12. [PMID: 24608368 PMCID: PMC3980576 DOI: 10.1038/nsmb.2786] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 02/12/2014] [Indexed: 01/21/2023]
Abstract
Microhomology-mediated end joining (MMEJ) is a Ku and Ligase IV independent mechanism for repair of DNA double-strand breaks, which contributes to chromosome rearrangements. Here we used a chromosomal end-joining assay to determine the genetic requirements for MMEJ in Saccharomyces cerevisiae. We found that end resection influences the ability to expose microhomologies; however, it is not rate limiting for MMEJ in wild-type cells. The frequency of MMEJ increased by up to 350-fold in rfa1 hypomorphic mutants, suggesting that replication protein A (RPA) bound to the ssDNA overhangs formed by resection prevents spontaneous annealing between microhomologies. In vitro, the mutant RPA complexes were unable to fully extend ssDNA and were compromised in their ability to prevent spontaneous annealing. We propose the helix-destabilizing activity of RPA channels ssDNA intermediates from mutagenic MMEJ to error-free homologous recombination, thus preserving genome integrity.
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Affiliation(s)
- Sarah K Deng
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, New York, USA
| | - Bryan Gibb
- Department of Biochemistry and Biophysics, Columbia University College of Physicians and Surgeons, New York, New York, USA
| | - Mariana Justino de Almeida
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, New York, USA
| | - Eric C Greene
- 1] Department of Biochemistry and Biophysics, Columbia University College of Physicians and Surgeons, New York, New York, USA. [2] Howard Hughes Medical Institute, Columbia University College of Physicians and Surgeons, New York, New York, USA
| | - Lorraine S Symington
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, New York, USA
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A saccharomyces cerevisiae RNase H2 interaction network functions to suppress genome instability. Mol Cell Biol 2014; 34:1521-34. [PMID: 24550002 DOI: 10.1128/mcb.00960-13] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Errors during DNA replication are one likely cause of gross chromosomal rearrangements (GCRs). Here, we analyze the role of RNase H2, which functions to process Okazaki fragments, degrade transcription intermediates, and repair misincorporated ribonucleotides, in preventing genome instability. The results demonstrate that rnh203 mutations result in a weak mutator phenotype and cause growth defects and synergistic increases in GCR rates when combined with mutations affecting other DNA metabolism pathways, including homologous recombination (HR), sister chromatid HR, resolution of branched HR intermediates, postreplication repair, sumoylation in response to DNA damage, and chromatin assembly. In some cases, a mutation in RAD51 or TOP1 suppressed the increased GCR rates and/or the growth defects of rnh203Δ double mutants. This analysis suggests that cells with RNase H2 defects have increased levels of DNA damage and depend on other pathways of DNA metabolism to overcome the deleterious effects of this DNA damage.
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Mirisola MG, Braun RJ, Petranovic D. Approaches to study yeast cell aging and death. FEMS Yeast Res 2013; 14:109-18. [DOI: 10.1111/1567-1364.12112] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 10/08/2013] [Accepted: 10/08/2013] [Indexed: 11/26/2022] Open
Affiliation(s)
| | - Ralf J. Braun
- Institut für Zellbiologie; Universität Bayreuth; Bayreuth Germany
| | - Dina Petranovic
- Department of Chemical and Biological Engineering, Systems and Synthetic Biology; Chalmers University of Technology; Göteborg Sweden
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Li C, Liu Y, Hu Z, Zhou Y. Genetic polymorphisms ofRAD51andXRCC3and acute myeloid leukemia risk: a meta-analysis. Leuk Lymphoma 2013; 55:1309-19. [DOI: 10.3109/10428194.2013.835404] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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A reversible histone H3 acetylation cooperates with mismatch repair and replicative polymerases in maintaining genome stability. PLoS Genet 2013; 9:e1003899. [PMID: 24204308 PMCID: PMC3812082 DOI: 10.1371/journal.pgen.1003899] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 09/06/2013] [Indexed: 01/06/2023] Open
Abstract
Mutations are a major driving force of evolution and genetic disease. In eukaryotes, mutations are produced in the chromatin environment, but the impact of chromatin on mutagenesis is poorly understood. Previous studies have determined that in yeast Saccharomyces cerevisiae, Rtt109-dependent acetylation of histone H3 on K56 is an abundant modification that is introduced in chromatin in S phase and removed by Hst3 and Hst4 in G2/M. We show here that the chromatin deacetylation on histone H3 K56 by Hst3 and Hst4 is required for the suppression of spontaneous gross chromosomal rearrangements, base substitutions, 1-bp insertions/deletions, and complex mutations. The rate of base substitutions in hst3Δ hst4Δ is similar to that in isogenic mismatch repair-deficient msh2Δ mutant. We also provide evidence that H3 K56 acetylation by Rtt109 is important for safeguarding DNA from small insertions/deletions and complex mutations. Furthermore, we reveal that both the deacetylation and acetylation on histone H3 K56 are involved in mutation avoidance mechanisms that cooperate with mismatch repair and the proofreading activities of replicative DNA polymerases in suppressing spontaneous mutagenesis. Our results suggest that cyclic acetylation and deacetylation of chromatin contribute to replication fidelity and play important roles in the protection of nuclear DNA from diverse spontaneous mutations. Mutations strongly predispose humans to cancer and many other diseases. Despite significant progress, we still do not fully understand the molecular mechanisms that protect us from mutations. Human DNA is part of a highly organized complex called chromatin. Chromatin regulates our development, metabolism, and behavior. Special enzymes modify chromatin by the addition and removal of chemical groups. Acetylation and deacetylation of chromatin have been conserved during evolution. The involvement of chromatin and its modifications in the protection of DNA from mutations is poorly understood. The yeast Saccharomyces cerevisiae is an excellent model for studying the connection between chromatin modifications and mutations. Using this model, we found that the deacetylation and acetylation of chromatin on histone H3 lysine 56 are required for preventing a wide range of spontaneous mutations. Future studies will determine whether acetylation and deacetylation of chromatin are involved in protecting DNA from mutations in human cells.
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Abstract
Genomes are transmitted faithfully from dividing cells to their offspring. Changes that occur during DNA repair, chromosome duplication, and transmission or via recombination provide a natural source of genetic variation. They occur at low frequency because of the intrinsic variable nature of genomes, which we refer to as genome instability. However, genome instability can be enhanced by exposure to external genotoxic agents or as the result of cellular pathologies. We review the causes of genome instability as well as how it results in hyper-recombination, genome rearrangements, and chromosome fragmentation and loss, which are mainly mediated by double-strand breaks or single-strand gaps. Such events are primarily associated with defects in DNA replication and the DNA damage response, and show high incidence at repetitive DNA, non-B DNA structures, DNA-protein barriers, and highly transcribed regions. Identifying the causes of genome instability is crucial to understanding genome dynamics during cell proliferation and its role in cancer, aging, and a number of rare genetic diseases.
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Affiliation(s)
- Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla, 41092 Seville, Spain;
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Kroll E, Coyle S, Dunn B, Koniges G, Aragon A, Edwards J, Rosenzweig F. Starvation-associated genome restructuring can lead to reproductive isolation in yeast. PLoS One 2013; 8:e66414. [PMID: 23894280 PMCID: PMC3722211 DOI: 10.1371/journal.pone.0066414] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 05/04/2013] [Indexed: 12/03/2022] Open
Abstract
Knowledge of the mechanisms that lead to reproductive isolation is essential for understanding population structure and speciation. While several models have been advanced to explain post-mating reproductive isolation, experimental data supporting most are indirect. Laboratory investigations of this phenomenon are typically carried out under benign conditions, which result in low rates of genetic change unlikely to initiate reproductive isolation. Previously, we described an experimental system using the yeast Saccharomyces cerevisiae where starvation served as a proxy to any stress that decreases reproduction and/or survivorship. We showed that novel lineages with restructured genomes quickly emerged in starved populations, and that these survivors were more fit than their ancestors when re-starved. Here we show that certain yeast lineages that survive starvation have become reproductively isolated from their ancestor. We further demonstrate that reproductive isolation arises from genomic rearrangements, whose frequency in starving yeast is several orders of magnitude greater than an unstarved control. By contrast, the frequency of point mutations is less than 2-fold greater. In a particular case, we observe that a starved lineage becomes reproductively isolated as a direct result of the stress-related accumulation of a single chromosome. We recapitulate this result by demonstrating that introducing an extra copy of one or several chromosomes into naïve, i.e. unstarved, yeast significantly diminishes their fertility. This type of reproductive barrier, whether arising spontaneously or via genetic manipulation, can be removed by making a lineage euploid for the altered chromosomes. Our model provides direct genetic evidence that reproductive isolation can arise frequently in stressed populations via genome restructuring without the precondition of geographic isolation.
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Affiliation(s)
- Evgueny Kroll
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America.
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35
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Grandin N, Charbonneau M. RPA provides checkpoint-independent cell cycle arrest and prevents recombination at uncapped telomeres of Saccharomyces cerevisiae. DNA Repair (Amst) 2013; 12:212-26. [DOI: 10.1016/j.dnarep.2012.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 11/13/2012] [Accepted: 12/08/2012] [Indexed: 12/23/2022]
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Abstract
During oncogenesis, cells acquire multiple genetic alterations that confer essential tumor-specific traits, including immortalization, escape from antimitogenic signaling, neovascularization, invasiveness, and metastatic potential. In most instances, these alterations are thought to arise incrementally over years, if not decades. However, recent progress in sequencing cancer genomes has begun to challenge this paradigm, because a radically different phenomenon, termed chromothripsis, has been suggested to cause complex intra- and interchromosomal rearrangements on short timescales. In this Review, we review established pathways crucial for genome integrity and discuss how their dysfunction could precipitate widespread chromosome breakage and rearrangement in the course of malignancy.
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Affiliation(s)
- Mathew J K Jones
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
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37
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Microhomology directs diverse DNA break repair pathways and chromosomal translocations. PLoS Genet 2012; 8:e1003026. [PMID: 23144625 PMCID: PMC3493447 DOI: 10.1371/journal.pgen.1003026] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 08/24/2012] [Indexed: 11/23/2022] Open
Abstract
Chromosomal structural change triggers carcinogenesis and the formation of other genetic diseases. The breakpoint junctions of these rearrangements often contain small overlapping sequences called “microhomology,” yet the genetic pathway(s) responsible have yet to be defined. We report a simple genetic system to detect microhomology-mediated repair (MHMR) events after a DNA double-strand break (DSB) in budding yeast cells. MHMR using >15 bp operates as a single-strand annealing variant, requiring the non-essential DNA polymerase subunit Pol32. MHMR is inhibited by sequence mismatches, but independent of extensive DNA synthesis like break-induced replication. However, MHMR using less than 14 bp is genetically distinct from that using longer microhomology and far less efficient for the repair of distant DSBs. MHMR catalyzes chromosomal translocation almost as efficiently as intra-chromosomal repair. The results suggest that the intrinsic annealing propensity between microhomology sequences efficiently leads to chromosomal rearrangements. Cancer results from an accumulation of mutations that transform a normal cell into one that proliferates uncontrollably. DNA double-strand breaks (DSBs) can lead to genetic mutations and chromosome rearrangements, underscoring the importance of functional DNA DSB repair pathways in the maintenance of chromosome integrity and tumor suppression. Ample evidence suggests that cells possess multiple DSB repair mechanisms with distinct mutational potentials, and one or more of these pathways is likely responsible for the formation of chromosomal translocations. Importantly, at the junctions of many rearrangements, small (2–20 bp in length) overlapping sequences from each of the original sequences, termed “microhomology,” are found, and they may provide a clue as to how these rearrangements form. Here, we describe our genetic investigation into how flanking microhomology influences the type and frequency of DSB repair. We also show that microhomology-mediated repair (MHMR) efficiently induces chromosomal translocations. This research provides a basic understanding of the mechanisms that utilize microhomology for mutagenic repair.
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38
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Bioinformatic identification of genes suppressing genome instability. Proc Natl Acad Sci U S A 2012; 109:E3251-9. [PMID: 23129647 DOI: 10.1073/pnas.1216733109] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Unbiased forward genetic screens for mutations causing increased gross chromosomal rearrangement (GCR) rates in Saccharomyces cerevisiae are hampered by the difficulty in reliably using qualitative GCR assays to detect mutants with small but significantly increased GCR rates. We therefore developed a bioinformatic procedure using genome-wide functional genomics screens to identify and prioritize candidate GCR-suppressing genes on the basis of the shared drug sensitivity suppression and similar genetic interactions as known GCR suppressors. The number of known suppressors was increased from 75 to 110 by testing 87 predicted genes, which identified unanticipated pathways in this process. This analysis explicitly dealt with the lack of concordance among high-throughput datasets to increase the reliability of phenotypic predictions. Additionally, shared phenotypes in one assay were imperfect predictors for shared phenotypes in other assays, indicating that although genome-wide datasets can be useful in aggregate, caution and validation methods are required when deciphering biological functions via surrogate measures, including growth-based genetic interactions.
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Abstract
Telomere maintenance in cycling cells relies on both DNA replication and capping by the protein complex shelterin. Two single-stranded DNA (ssDNA)-binding proteins, replication protein A (RPA) and protection of telomere 1 (POT1) play critical roles in DNA replication and telomere capping, respectively. While RPA binds to ssDNA in a non-sequence-specific manner, POT1 specifically recognizes singlestranded TTAGGG telomeric repeats. Loss of POT1 leads to aberrant accumulation of RPA at telomeres and activation of the ataxia telangiectasia and Rad3-related kinase (ATR)-mediated checkpoint response, suggesting that POT1 antagonizes RPA binding to telomeric ssDNA. The requirement for both POT1 and RPA in telomere maintenance and the antagonism between the two proteins raises the important question of how they function in concert on telomeric ssDNA. Two interesting models were proposed by recent studies to explain the regulation of POT1 and RPA at telomeres. Here, we discuss how these models help unravel the coordination, and also the antagonism, between POT1 and RPA during the cell cycle.
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Affiliation(s)
- Rachel Litman Flynn
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
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40
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Genome rearrangements caused by depletion of essential DNA replication proteins in Saccharomyces cerevisiae. Genetics 2012; 192:147-60. [PMID: 22673806 DOI: 10.1534/genetics.112.141051] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Genetic screens of the collection of ~4500 deletion mutants in Saccharomyces cerevisiae have identified the cohort of nonessential genes that promote maintenance of genome integrity. Here we probe the role of essential genes needed for genome stability. To this end, we screened 217 tetracycline-regulated promoter alleles of essential genes and identified 47 genes whose depletion results in spontaneous DNA damage. We further showed that 92 of these 217 essential genes have a role in suppressing chromosome rearrangements. We identified a core set of 15 genes involved in DNA replication that are critical in preventing both spontaneous DNA damage and genome rearrangements. Mapping, classification, and analysis of rearrangement breakpoints indicated that yeast fragile sites, Ty retrotransposons, tRNA genes, early origins of replication, and replication termination sites are common features at breakpoints when essential replication genes that suppress chromosome rearrangements are downregulated. We propose mechanisms by which depletion of essential replication proteins can lead to double-stranded DNA breaks near these features, which are subsequently repaired by homologous recombination at repeated elements.
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A protein array screen for Kaposi's sarcoma-associated herpesvirus LANA interactors links LANA to TIP60, PP2A activity, and telomere shortening. J Virol 2012; 86:5179-91. [PMID: 22379092 DOI: 10.1128/jvi.00169-12] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The Kaposi's sarcoma-associated herpesvirus (KSHV) LANA protein functions in latently infected cells as an essential participant in KSHV genome replication and as a driver of dysregulated cell growth. To identify novel LANA protein-cell protein interactions that could contribute to these activities, we performed a proteomic screen in which purified, adenovirus-expressed Flag-LANA protein was incubated with an array displaying 4,192 nonredundant human proteins. Sixty-one interacting cell proteins were consistently detected. LANA interactions with high-mobility group AT-hook 1 (HMGA1), HMGB1, telomeric repeat binding factor 1 (TRF1), xeroderma pigmentosum complementation group A (XPA), pygopus homolog 2 (PYGO2), protein phosphatase 2A (PP2A)B subunit, Tat-interactive protein 60 (TIP60), replication protein A1 (RPA1), and RPA2 proteins were confirmed in coimmunoprecipitation assays. LANA-associated TIP60 retained acetyltransferase activity and, unlike human papillomavirus E6 and HIV-1 TAT proteins, LANA did not reduce TIP60 stability. The LANA-bound PP2A B subunit was associated with the PP2A A subunit but not the catalytic C subunit, suggesting a disruption of PP2A phosphatase activity. This is reminiscent of the role of simian virus 40 (SV40) small t antigen. Chromatin immunoprecipitation (ChIP) assays showed binding of RPA1 and RPA2 to the KSHV terminal repeats. Interestingly, LANA expression ablated RPA1 and RPA2 binding to the cell telomeric repeats. In U2OS cells that rely on the alternative mechanism for telomere maintenance, LANA expression had minimal effect on telomere length. However, LANA expression in telomerase immortalized endothelial cells resulted in telomere shortening. In KSHV-infected cells, telomere shortening may be one more mechanism by which LANA contributes to the development of malignancy.
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Hombauer H, Srivatsan A, Putnam CD, Kolodner RD. Mismatch repair, but not heteroduplex rejection, is temporally coupled to DNA replication. Science 2012; 334:1713-6. [PMID: 22194578 DOI: 10.1126/science.1210770] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In eukaryotes, it is unknown whether mismatch repair (MMR) is temporally coupled to DNA replication and how strand-specific MMR is directed. We fused Saccharomyces cerevisiae MSH6 with cyclins to restrict the availability of the Msh2-Msh6 mismatch recognition complex to either S phase or G2/M phase of the cell cycle. The Msh6-S cyclin fusion was proficient for suppressing mutations at three loci that replicate at mid-S phase, whereas the Msh6-G2/M cyclin fusion was defective. However, the Msh6-G2/M cyclin fusion was functional for MMR at a very late-replicating region of the genome. In contrast, the heteroduplex rejection function of MMR during recombination was partially functional during both S phase and G2/M phase. These results indicate a temporal coupling of MMR, but not heteroduplex rejection, to DNA replication.
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Affiliation(s)
- Hans Hombauer
- Ludwig Institute for Cancer Research, Departments of Medicine and Cellular and Molecular Medicine and Cancer Center, Moores-UCSD Cancer Center, University of California School of Medicine-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0669, USA
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43
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Doerfler L, Harris L, Viebranz E, Schmidt KH. Differential genetic interactions between Sgs1, DNA-damage checkpoint components and DNA repair factors in the maintenance of chromosome stability. Genome Integr 2011; 2:8. [PMID: 22040455 PMCID: PMC3231943 DOI: 10.1186/2041-9414-2-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 10/31/2011] [Indexed: 11/21/2022] Open
Abstract
Background Genome instability is associated with human cancers and chromosome breakage syndromes, including Bloom's syndrome, caused by inactivation of BLM helicase. Numerous mutations that lead to genome instability are known, yet how they interact genetically is poorly understood. Results We show that spontaneous translocations that arise by nonallelic homologous recombination in DNA-damage-checkpoint-defective yeast lacking the BLM-related Sgs1 helicase (sgs1Δ mec3Δ) are inhibited if cells lack Mec1/ATR kinase. Tel1/ATM, in contrast, acts as a suppressor independently of Mec3 and Sgs1. Translocations are also inhibited in cells lacking Dun1 kinase, but not in cells defective in a parallel checkpoint branch defined by Chk1 kinase. While we had previously shown that RAD51 deletion did not inhibit translocation formation, RAD59 deletion led to inhibition comparable to the rad52Δ mutation. A candidate screen of other DNA metabolic factors identified Exo1 as a strong suppressor of chromosomal rearrangements in the sgs1Δ mutant, becoming even more important for chromosomal stability upon MEC3 deletion. We determined that the C-terminal third of Exo1, harboring mismatch repair protein binding sites and phosphorylation sites, is dispensable for Exo1's roles in chromosomal rearrangement suppression, mutation avoidance and resistance to DNA-damaging agents. Conclusions Our findings suggest that translocations between related genes can form by Rad59-dependent, Rad51-independent homologous recombination, which is independently suppressed by Sgs1, Tel1, Mec3 and Exo1 but promoted by Dun1 and the telomerase-inhibitor Mec1. We propose a model for the functional interaction between mitotic recombination and the DNA-damage checkpoint in the suppression of chromosomal rearrangements in sgs1Δ cells.
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Affiliation(s)
- Lillian Doerfler
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Avenue, Tampa, FL 33620, USA
| | - Lorena Harris
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Avenue, Tampa, FL 33620, USA
| | - Emilie Viebranz
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Avenue, Tampa, FL 33620, USA
| | - Kristina H Schmidt
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Avenue, Tampa, FL 33620, USA
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Trapp O, Seeliger K, Puchta H. Homologs of breast cancer genes in plants. FRONTIERS IN PLANT SCIENCE 2011; 2:19. [PMID: 22629260 PMCID: PMC3355568 DOI: 10.3389/fpls.2011.00019] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 06/02/2011] [Indexed: 05/22/2023]
Abstract
Since the initial discovery of genes involved in hereditary breast cancer in humans, a vast wealth of information has been published. Breast cancer proteins were shown to work as tumor suppressors primarily through their involvement in DNA-damage repair. Surprisingly, homologs of these genes can be found in plant genomes, as well. Here, we want to give an overview of the identification and characterization of the biological roles of these proteins, in plants. In addition to the conservation of their function in DNA repair, new plant-specific characteristics have been revealed. BRCA1 is required for the efficient repair of double strand breaks (DSB) by homologous recombination in somatic cells of the model plant Arabidopsis thaliana. Bioinformatic analysis indicates that, whereas most homologs of key components of the different mammalian BRCA1 complexes are present in plant genomes, homologs of most factors involved in the recruitment of BRCA1 to the DSB cannot be identified. Thus, it is not clear at the moment whether differences exist between plants and animals at this important step. The most conserved region of BRCA1 and BARD1 homologs in plants is a PHD domain which is absent in mammals and which, in AtBARD1, might be involved in the transcriptional regulation of plant development. The presence of a plant-specific domain prompted us to reevaluate the current model for the evolution of BRCA1 homologs and to suggest a new hypothesis, in which we postulate that plant BRCA1 and BARD1 have one common predecessor that gained a PHD domain before duplication. Furthermore, work in Arabidopsis demonstrates that - as in animals - BRCA2 homologs are important for meiotic DNA recombination. Surprisingly, recent research has revealed that AtBRCA2 also has an important role in systemic acquired resistance. In Arabidopsis, BRCA2 is involved in the transcriptional regulation of pathogenesis-related (PR) genes via its interaction with the strand exchange protein RAD51.
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Affiliation(s)
- Oliver Trapp
- Botanical Institute II, Karlsruhe Institute of TechnologyKarlsruhe, Germany
| | - Katharina Seeliger
- Botanical Institute II, Karlsruhe Institute of TechnologyKarlsruhe, Germany
| | - Holger Puchta
- Botanical Institute II, Karlsruhe Institute of TechnologyKarlsruhe, Germany
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Aksenova A, Volkov K, Maceluch J, Pursell ZF, Rogozin IB, Kunkel TA, Pavlov YI, Johansson E. Mismatch repair-independent increase in spontaneous mutagenesis in yeast lacking non-essential subunits of DNA polymerase ε. PLoS Genet 2010; 6:e1001209. [PMID: 21124948 PMCID: PMC2987839 DOI: 10.1371/journal.pgen.1001209] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 10/15/2010] [Indexed: 01/31/2023] Open
Abstract
Yeast DNA polymerase ε (Pol ε) is a highly accurate and processive enzyme that participates in nuclear DNA replication of the leading strand template. In addition to a large subunit (Pol2) harboring the polymerase and proofreading exonuclease active sites, Pol ε also has one essential subunit (Dpb2) and two smaller, non-essential subunits (Dpb3 and Dpb4) whose functions are not fully understood. To probe the functions of Dpb3 and Dpb4, here we investigate the consequences of their absence on the biochemical properties of Pol ε in vitro and on genome stability in vivo. The fidelity of DNA synthesis in vitro by purified Pol2/Dpb2, i.e. lacking Dpb3 and Dpb4, is comparable to the four-subunit Pol ε holoenzyme. Nonetheless, deletion of DPB3 and DPB4 elevates spontaneous frameshift and base substitution rates in vivo, to the same extent as the loss of Pol ε proofreading activity in a pol2-4 strain. In contrast to pol2-4, however, the dpb3Δdpb4Δ does not lead to a synergistic increase of mutation rates with defects in DNA mismatch repair. The increased mutation rate in dpb3Δdpb4Δ strains is partly dependent on REV3, as well as the proofreading capacity of Pol δ. Finally, biochemical studies demonstrate that the absence of Dpb3 and Dpb4 destabilizes the interaction between Pol ε and the template DNA during processive DNA synthesis and during processive 3′ to 5′exonucleolytic degradation of DNA. Collectively, these data suggest a model wherein Dpb3 and Dpb4 do not directly influence replication fidelity per se, but rather contribute to normal replication fork progression. In their absence, a defective replisome may more frequently leave gaps on the leading strand that are eventually filled by Pol ζ or Pol δ, in a post-replication process that generates errors not corrected by the DNA mismatch repair system. The high fidelity of DNA replication is safeguarded by the accuracy of nucleotide selection by DNA polymerases, proofreading activity of the replicative polymerases, and the DNA mismatch repair system. Errors made by replicative polymerases are corrected by mismatch repair, and inactivation of the mismatch repair system results in a multiplicative increase in error rates when combined with a proofreading deficient allele of a replicative polymerase. In this study, we demonstrate that the deletion of two non-essential genes encoding for two subunits of Pol ε give an increased mutation rate due to increased synthesis by the error-prone DNA polymerase ζ. Surprisingly, there was no multiplicative increase in error rates when the mismatch repair system was inactivated. We propose that the deletion of DPB3 and DPB4 gives a defective replisome, which in turn gives increased synthesis, in part, by Pol ζ during an error-prone post-replication process that is not efficiently repaired by the mismatch repair system.
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Affiliation(s)
- Anna Aksenova
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
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46
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Schmidt KH, Viebranz E, Doerfler L, Lester C, Rubenstein A. Formation of complex and unstable chromosomal translocations in yeast. PLoS One 2010; 5:e12007. [PMID: 20711256 PMCID: PMC2918500 DOI: 10.1371/journal.pone.0012007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Accepted: 07/13/2010] [Indexed: 11/19/2022] Open
Abstract
Genome instability, associated with chromosome breakage syndromes and most human cancers, is still poorly understood. In the yeast Saccharomyces cerevisiae, numerous genes with roles in the preservation of genome integrity have been identified. DNA-damage-checkpoint-deficient yeast cells that lack Sgs1, a RecQ-like DNA helicase related to the human Bloom's-syndrome-associated helicase BLM, show an increased rate of genome instability, and we have previously shown that they accumulate recurring chromosomal translocations between three similar genes, CAN1, LYP1 and ALP1. Here, the chromosomal location, copy number and sequence similarity of the translocation targets ALP1 and LYP1 were altered to gain insight into the formation of complex translocations. Among 844 clones with chromosomal rearrangements, 93 with various types of simple and complex translocations involving CAN1, LYP1 and ALP1 were identified. Breakpoint sequencing and mapping showed that the formation of complex translocation types is strictly dependent on the location of the initiating DNA break and revealed that complex translocations arise via a combination of interchromosomal translocation and template-switching, as well as from unstable dicentric intermediates. Template-switching occurred between sequences on the same chromosome, but was inhibited if the genes were transferred to different chromosomes. Unstable dicentric translocations continuously gave rise to clones with multiple translocations in various combinations, reminiscent of intratumor heterogeneity in human cancers. Base substitutions and evidence of DNA slippage near rearrangement breakpoints revealed that translocation formation can be accompanied by point mutations, and their presence in different translocation types within the same clone provides evidence that some of the different translocation types are derived from each other rather than being formed de novo. These findings provide insight into eukaryotic genome instability, especially the formation of translocations and the sources of intraclonal heterogeneity, both of which are often associated with human cancers.
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Affiliation(s)
- Kristina H Schmidt
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida, United States of America.
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Hass CS, Gakhar L, Wold MS. Functional characterization of a cancer causing mutation in human replication protein A. Mol Cancer Res 2010; 8:1017-26. [PMID: 20587534 DOI: 10.1158/1541-7786.mcr-10-0161] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Replication protein A (RPA) is the primary ssDNA-binding protein in eukaryotes. RPA is essential for DNA replication, repair, and recombination. Mutation of a conserved leucine residue to proline in the high-affinity DNA binding site of RPA (residue L221 in human RPA) has been shown to have defects in DNA repair and a high rate of chromosomal rearrangements in yeast. The homologous mutation in mice was found to be lethal when homozygous and to cause high rates of cancer when heterozygous. To understand the molecular defect causing these phenotypes, we created the homologous mutation in the human RPA1 gene (L221P) and analyzed its properties in cells and in vitro. RPA1(L221P) does not support cell cycle progression when it is the only form of RPA1 in HeLa cells. This phenotype is caused by defects in DNA replication and repair. No phenotype is observed when cells contain both wild-type and L221P forms of RPA1, indicating that L221P is not dominant. Recombinant L221P polypeptide forms a stable complex with the other subunits of RPA, indicating that the mutation does not destabilize the protein; however, the resulting complex has dramatically reduced ssDNA binding activity and cannot support SV40 DNA replication in vitro. These findings indicate that in mammals, the L221P mutation causes a defect in ssDNA binding and a nonfunctional protein complex. This suggests that haploinsufficiency of RPA causes an increase in the levels of DNA damage and in the incidence of cancer.
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Affiliation(s)
- Cathy S Hass
- Department of Biochemistry, Carver College of Medicine, University of Iowa, USA
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Defects in DNA lesion bypass lead to spontaneous chromosomal rearrangements and increased cell death. EUKARYOTIC CELL 2009; 9:315-24. [PMID: 20008080 DOI: 10.1128/ec.00260-09] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Rev3 polymerase and Mph1 DNA helicase participate in error-prone and error-free pathways, respectively, for the bypassing of template lesions during DNA replication. Here we have investigated the role of these pathways and their genetic interaction with recombination factors, other nonreplicative DNA helicases, and DNA damage checkpoint components in the maintenance of genome stability, viability, and sensitivity to the DNA-damaging agent methyl methanesulfonate (MMS). We find that cells lacking Rev3 and Mph1 exhibit a synergistic, Srs2-dependent increase in the rate of accumulating spontaneous, gross chromosomal rearrangements, suggesting that the suppression of point mutations by deletion of REV3 may lead to chromosomal rearrangements. While mph1Delta is epistatic to homologous recombination (HR) genes, both Rad51 and Rad52, but not Rad59, are required for normal growth of the rev3Delta mutant and are essential for survival of rev3Delta cells during exposure to MMS, indicating that Mph1 acts in a Rad51-dependent, Rad59-independent subpathway of HR-mediated lesion bypass. Deletion of MPH1 helicase leads to synergistic DNA damage sensitivity increases in cells with chl1Delta or rrm3Delta helicase mutations, whereas mph1Delta is hypostatic to sgs1Delta. Previously reported slow growth of mph1Delta srs2Delta cells is accompanied by G(2)/M arrest and fully suppressed by disruption of the Mec3-dependent DNA damage checkpoint. We propose a model for replication fork rescue mediated by translesion DNA synthesis and homologous recombination that integrates the role of Mph1 in unwinding D loops and its genetic interaction with Rev3 and Srs2-regulated pathways in the suppression of spontaneous genome rearrangements and in mutation avoidance.
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Stabilization of dicentric translocations through secondary rearrangements mediated by multiple mechanisms in S. cerevisiae. PLoS One 2009; 4:e6389. [PMID: 19636429 PMCID: PMC2712687 DOI: 10.1371/journal.pone.0006389] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Accepted: 06/25/2009] [Indexed: 02/05/2023] Open
Abstract
Background The gross chromosomal rearrangements (GCRs) observed in S. cerevisiae mutants with increased rates of accumulating GCRs include predicted dicentric GCRs such as translocations, chromosome fusions and isoduplications. These GCRs resemble the genome rearrangements found as mutations underlying inherited diseases as well as in the karyotypes of many cancers exhibiting ongoing genome instability Methodology/Principal Findings The structures of predicted dicentric GCRs were analyzed using multiple strategies including array-comparative genomic hybridization, pulse field gel electrophoresis, PCR amplification of predicted breakpoints and sequencing. The dicentric GCRs were found to be unstable and to have undergone secondary rearrangements to produce stable monocentric GCRs. The types of secondary rearrangements observed included: non-homologous end joining (NHEJ)-dependent intramolecular deletion of centromeres; chromosome breakage followed by NHEJ-mediated circularization or broken-end fusion to another chromosome telomere; and homologous recombination (HR)-dependent non-reciprocal translocations apparently mediated by break-induced replication. A number of these GCRs appeared to have undergone multiple bridge-fusion-breakage cycles. We also observed examples of chromosomes with extensive ongoing end decay in mec1 tlc1 mutants, suggesting that Mec1 protects chromosome ends from degradation and contributes to telomere maintenance by HR. Conclusions/Significance HR between repeated sequences resulting in secondary rearrangements was the most prevalent pathway for resolution of dicentric GCRs regardless of the structure of the initial dicentric GCR, although at least three other resolution mechanisms were observed. The resolution of dicentric GCRs to stable rearranged chromosomes could in part account for the complex karyotypes seen in some cancers.
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Faithful after break-up: suppression of chromosomal translocations. Cell Mol Life Sci 2009; 66:3149-60. [PMID: 19547915 DOI: 10.1007/s00018-009-0068-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Revised: 05/31/2009] [Accepted: 06/08/2009] [Indexed: 10/20/2022]
Abstract
Chromosome integrity in response to chemically or radiation-induced chromosome breaks and the perturbation of ongoing replication forks relies on multiple DNA repair mechanisms. However, repair of these lesions may lead to unwanted chromosome rearrangement if not properly executed or regulated. As these types of chromosomal alterations threaten the cell's and the organism's very own survival, multiple systems are developed to avoid or at least limit break-induced chromosomal rearrangements. In this review, we highlight cellular strategies for repressing DNA break-induced chromosomal translocations in multiple model systems including yeast, mouse, and human. These pathways select proper homologous templates or broken DNA ends for the faithful repair of DNA breaks to avoid undesirable chromosomal translocations.
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