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Sugiyama Y, Okada S, Daigaku Y, Kusumoto E, Ito T. Strategic targeting of Cas9 nickase induces large segmental duplications. CELL GENOMICS 2024; 4:100610. [PMID: 39053455 DOI: 10.1016/j.xgen.2024.100610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 04/15/2024] [Accepted: 07/02/2024] [Indexed: 07/27/2024]
Abstract
Gene/segmental duplications play crucial roles in genome evolution and variation. Here, we introduce paired nicking-induced amplification (PNAmp) for their experimental induction. PNAmp strategically places two Cas9 nickases upstream and downstream of a replication origin on opposite strands. This configuration directs the sister replication forks initiated from the origin to break at the nicks, generating a pair of one-ended double-strand breaks. If homologous sequences flank the two break sites, then end resection converts them to single-stranded DNAs that readily anneal to drive duplication of the region bounded by the homologous sequences. PNAmp induces duplication of segments as large as ∼1 Mb with efficiencies exceeding 10% in the budding yeast Saccharomyces cerevisiae. Furthermore, appropriate splint DNAs allow PNAmp to duplicate/multiplicate even segments not bounded by homologous sequences. We also provide evidence for PNAmp in mammalian cells. Therefore, PNAmp provides a prototype method to induce structural variations by manipulating replication fork progression.
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Affiliation(s)
- Yuki Sugiyama
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Satoshi Okada
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Yasukazu Daigaku
- Cancer Genome Dynamics Project, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
| | - Emiko Kusumoto
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan.
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2
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Ferguson R, Goold R, Coupland L, Flower M, Tabrizi SJ. Therapeutic validation of MMR-associated genetic modifiers in a human ex vivo model of Huntington disease. Am J Hum Genet 2024; 111:1165-1183. [PMID: 38749429 PMCID: PMC11179424 DOI: 10.1016/j.ajhg.2024.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 06/09/2024] Open
Abstract
The pathological huntingtin (HTT) trinucleotide repeat underlying Huntington disease (HD) continues to expand throughout life. Repeat length correlates both with earlier age at onset (AaO) and faster progression, making slowing its expansion an attractive therapeutic approach. Genome-wide association studies have identified candidate variants associated with altered AaO and progression, with many found in DNA mismatch repair (MMR)-associated genes. We examine whether lowering expression of these genes affects the rate of repeat expansion in human ex vivo models using HD iPSCs and HD iPSC-derived striatal medium spiny neuron-enriched cultures. We have generated a stable CRISPR interference HD iPSC line in which we can specifically and efficiently lower gene expression from a donor carrying over 125 CAG repeats. Lowering expression of each member of the MMR complexes MutS (MSH2, MSH3, and MSH6), MutL (MLH1, PMS1, PMS2, and MLH3), and LIG1 resulted in characteristic MMR deficiencies. Reduced MSH2, MSH3, and MLH1 slowed repeat expansion to the largest degree, while lowering either PMS1, PMS2, or MLH3 slowed it to a lesser degree. These effects were recapitulated in iPSC-derived striatal cultures where MutL factor expression was lowered. CRISPRi-mediated lowering of key MMR factor expression to levels feasibly achievable by current therapeutic approaches was able to effectively slow the expansion of the HTT CAG tract. We highlight members of the MutL family as potential targets to slow pathogenic repeat expansion with the aim to delay onset and progression of HD and potentially other repeat expansion disorders exhibiting somatic instability.
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Affiliation(s)
- Ross Ferguson
- Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK; Dementia Research Institute at UCL, London WC1N 3BG, UK
| | - Robert Goold
- Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK; Dementia Research Institute at UCL, London WC1N 3BG, UK
| | - Lucy Coupland
- Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK; Dementia Research Institute at UCL, London WC1N 3BG, UK
| | - Michael Flower
- Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK; Dementia Research Institute at UCL, London WC1N 3BG, UK
| | - Sarah J Tabrizi
- Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK; Dementia Research Institute at UCL, London WC1N 3BG, UK.
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3
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Medina-Rivera M, Phelps S, Sridharan M, Becker J, Lamb N, Kumar C, Sutton M, Bielinsky A, Balakrishnan L, Surtees J. Elevated MSH2 MSH3 expression interferes with DNA metabolism in vivo. Nucleic Acids Res 2023; 51:12185-12206. [PMID: 37930834 PMCID: PMC10711559 DOI: 10.1093/nar/gkad934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/30/2023] [Accepted: 10/10/2023] [Indexed: 11/08/2023] Open
Abstract
The Msh2-Msh3 mismatch repair (MMR) complex in Saccharomyces cerevisiae recognizes and directs repair of insertion/deletion loops (IDLs) up to ∼17 nucleotides. Msh2-Msh3 also recognizes and binds distinct looped and branched DNA structures with varying affinities, thereby contributing to genome stability outside post-replicative MMR through homologous recombination, double-strand break repair (DSBR) and the DNA damage response. In contrast, Msh2-Msh3 promotes genome instability through trinucleotide repeat (TNR) expansions, presumably by binding structures that form from single-stranded (ss) TNR sequences. We previously demonstrated that Msh2-Msh3 binding to 5' ssDNA flap structures interfered with Rad27 (Fen1 in humans)-mediated Okazaki fragment maturation (OFM) in vitro. Here we demonstrate that elevated Msh2-Msh3 levels interfere with DNA replication and base excision repair in vivo. Elevated Msh2-Msh3 also induced a cell cycle arrest that was dependent on RAD9 and ELG1 and led to PCNA modification. These phenotypes also required Msh2-Msh3 ATPase activity and downstream MMR proteins, indicating an active mechanism that is not simply a result of Msh2-Msh3 DNA-binding activity. This study provides new mechanistic details regarding how excess Msh2-Msh3 can disrupt DNA replication and repair and highlights the role of Msh2-Msh3 protein abundance in Msh2-Msh3-mediated genomic instability.
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Affiliation(s)
- Melisa Medina-Rivera
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo NY, 14203, USA
| | - Samantha Phelps
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo NY, 14203, USA
| | - Madhumita Sridharan
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Jordan Becker
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Natalie A Lamb
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo NY, 14203, USA
| | - Charanya Kumar
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo NY, 14203, USA
| | - Mark D Sutton
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo NY, 14203, USA
| | - Anja Bielinsky
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Lata Balakrishnan
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Jennifer A Surtees
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo NY, 14203, USA
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4
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Giaccherini C, Gaillard P. Control of structure-specific endonucleases during homologous recombination in eukaryotes. Curr Opin Genet Dev 2021; 71:195-205. [PMID: 34624742 DOI: 10.1016/j.gde.2021.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 01/14/2023]
Abstract
Structure-Specific Endonucleases (SSE) are specialized DNA endonucleases that recognize and process DNA secondary structures without any strict dependency on the nucleotide sequence context. This enables them to act virtually anywhere in the genome and to make key contributions to the maintenance of genome stability by removing DNA structures that may stall essential cellular processes such as DNA replication, transcription, repair and chromosome segregation. During repair of double strand breaks by homologous recombination mechanisms, DNA secondary structures are formed and processed in a timely manner. Their homeostasis relies on the combined action of helicases, SSE and topoisomerases. In this review, we focus on how SSE contribute to DNA end resection, single-strand annealing and double-strand break repair, with an emphasis on how their action is fine-tuned in those processes.
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Affiliation(s)
- C Giaccherini
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Marseille, France
| | - Phl Gaillard
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Marseille, France.
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5
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Odango RJ, Camberos J, Fregoso FE, Fischhaber PL. SAW1 is increasingly required to recruit Rad10 as SSA flap-length increases from 20 to 50 bases in single-strand annealing in S. cerevisiae. Biochem Biophys Rep 2021; 28:101125. [PMID: 34622036 PMCID: PMC8481969 DOI: 10.1016/j.bbrep.2021.101125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 11/16/2022] Open
Abstract
SAW1 is required by the Rad1-Rad10 nuclease for efficient removal of 3′ non-homologous DNA ends (flaps) formed as intermediates during two modes of double-strand break repair in S. cerevisiae, single-strand annealing (SSA) and synthesis-dependent strand annealing (SDSA). Saw1 was shown in vitro to exhibit increasing affinity for flap DNAs as flap lengths varied from 0 to 40 deoxynucleotides (nt) with almost no binding observed when flaps were shorter than 10 nt. Accordingly, our prior in vivo fluorescence microscopy investigation showed that SAW1 was not required for recruitment of Rad10-YFP to DNA double-strand breaks (DSBs) when flaps were ∼10 nt, but it was required when flaps were ∼500 nt in G1 phase of the cell cycle. We were curious whether we would also observe an increased requirement of SAW1 for Rad10 recruitment in vivo as flaps varied from ∼20 to 50 nt, as was shown in vitro. In this investigation, we utilized SSA substrates that generate 20, 30, and 50 nt flaps in vivo in fluorescence microscopy assays and determined that SAW1 becomes increasingly necessary for SSA starting at about ∼20 nt and is completely required at ∼50 nt. Quantitative PCR experiments corroborate these results by demonstrating that repair product formation decreases in the absence of SAW1 as flap length increases. Experiments with strains containing fluorescently labeled Saw1 (Saw1-CFP) show that Saw1 localizes with Rad10 at SSA foci and that about half of the foci containing Rad10 at DSBs do not contain Saw1. Colocalization patterns of Saw1-CFP are consistent regardless of the flap length of the substrate and are roughly similar in all phases of the cell cycle. Together, these data show that Saw1 becomes increasingly important for Rad1-Rad10 recruitment and SSA repair in the ∼20–50 nt flap range, and Saw1 is present at repair sites even when not required and may depart the repair site ahead of Rad1-Rad10. There is an increasing dependence on Saw1 to recruit Rad1-Rad10 as DNA flaps increase The flap length range causing the increasing dependence is 20–50 deoxynucleotides Saw1 is found at single-strand annealing foci even when not required to recruit Rad1-Rad10 Saw1 is found in only about half of the single-strand annealing foci containing Rad1-Rad10
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Affiliation(s)
- Rowen Jane Odango
- Department of Chemistry and Biochemistry, California State University Northridge, 18111 Nordhoff St, Northridge, CA, 91330-8262, United States
| | - Juan Camberos
- Department of Chemistry and Biochemistry, California State University Northridge, 18111 Nordhoff St, Northridge, CA, 91330-8262, United States
| | - Fred Erick Fregoso
- Department of Chemistry and Biochemistry, California State University Northridge, 18111 Nordhoff St, Northridge, CA, 91330-8262, United States
| | - Paula L Fischhaber
- Department of Chemistry and Biochemistry, California State University Northridge, 18111 Nordhoff St, Northridge, CA, 91330-8262, United States
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Clear AD, Manthey GM, Lewis O, Lopez IY, Rico R, Owens S, Negritto MC, Wolf EW, Xu J, Kenjić N, Perry JJP, Adamson AW, Neuhausen SL, Bailis AM. Variants of the human RAD52 gene confer defects in ionizing radiation resistance and homologous recombination repair in budding yeast. ACTA ACUST UNITED AC 2020; 7:270-285. [PMID: 33015141 PMCID: PMC7517009 DOI: 10.15698/mic2020.10.732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
RAD52 is a structurally and functionally conserved component of the DNA double-strand break (DSB) repair apparatus from budding yeast to humans. We recently showed that expressing the human gene, HsRAD52 in rad52 mutant budding yeast cells can suppress both their ionizing radiation (IR) sensitivity and homologous recombination repair (HRR) defects. Intriguingly, we observed that HsRAD52 supports DSB repair by a mechanism of HRR that conserves genome structure and is independent of the canonical HR machinery. In this study we report that naturally occurring variants of HsRAD52, one of which suppresses the pathogenicity of BRCA2 mutations, were unable to suppress the IR sensitivity and HRR defects of rad52 mutant yeast cells, but fully suppressed a defect in DSB repair by single-strand annealing (SSA). This failure to suppress both IR sensitivity and the HRR defect correlated with an inability of HsRAD52 protein to associate with and drive an interaction between genomic sequences during DSB repair by HRR. These results suggest that HsRAD52 supports multiple, distinct DSB repair apparatuses in budding yeast cells and help further define its mechanism of action in HRR. They also imply that disruption of HsRAD52-dependent HRR in BRCA2-defective human cells may contribute to protection against tumorigenesis and provide a target for killing BRCA2-defective cancers.
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Affiliation(s)
- Alissa D Clear
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA.,Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA.,bioStrategies Group, Chicago, IL, USA
| | - Glenn M Manthey
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA.,Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Olivia Lewis
- City of Hope - Duarte High School NIH Science Education Partnership Award Program, Duarte, CA, USA.,Barbara Bush Houston Literacy Foundation, Houston, TX, USA
| | - Isabelle Y Lopez
- City of Hope - Duarte High School NIH Science Education Partnership Award Program, Duarte, CA, USA.,California State Polytechnic University at Pomona, Pomona, CA, USA
| | - Rossana Rico
- City of Hope - Duarte High School NIH Science Education Partnership Award Program, Duarte, CA, USA.,Henry Samueli School of Engineering and Applied Sciences, University of California at Los Angeles, Los Angeles, CA, USA
| | - Shannon Owens
- Eugene and Ruth Roberts Summer Student Academy, Beckman Research Institute of City of Hope, Duarte, CA, USA.,Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California at Davis, Davis, CA, USA
| | | | - Elise W Wolf
- Molecular Biology Program, Pomona College, Claremont, CA, USA.,Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA, USA
| | - Jason Xu
- Molecular Biology Program, Pomona College, Claremont, CA, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nikola Kenjić
- Department of Biochemistry, University of California at Riverside, Riverside, CA, USA
| | - J Jefferson P Perry
- Department of Biochemistry, University of California at Riverside, Riverside, CA, USA
| | - Aaron W Adamson
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Adam M Bailis
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA.,Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA.,College of Health Professions, Thomas Jefferson University, Philadelphia, PA, USA
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Chen FM, Zhang YX, Li XF, Gao JF, Ma H, Wang XL, Li Y, Li C, Zhang YN, Zhang YT, Kan HX, Li H, Zhang SG, Hao FR, Wang MC. The Prognostic Value of Deficient Mismatch Repair in Stage II-IVa Nasopharyngeal Carcinoma in the Era of IMRT. Sci Rep 2020; 10:9690. [PMID: 32546739 PMCID: PMC7298002 DOI: 10.1038/s41598-020-66678-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/26/2020] [Indexed: 01/08/2023] Open
Abstract
In the era of intensity-modulated radiotherapy (IMRT), it is important to analyse the prognostic value of deficient mismatch repair (dMMR) in nasopharyngeal carcinoma (NPC). In this study, in pretreatment biopsies of 69 patients with stage II-IVa NPC, the expression levels of MMR proteins, including MLH1, MSH2, MSH6 and PMS2, were assessed by immunohistochemistry (IHC). The median follow-up time was 37.5 months (3.1-87.4 months). 50.7% of cases (35/69) showed preserved expression of all 4 MMR proteins, which was interpreted as proficient mismatch repair (pMMR). Only 1.5% of cases (1/69) lost expression of all 4 MMR proteins, 26.1% of cases (18/69) have PMS2 loss alone and 21.7% of cases (15/69) lost expression of both PMS2 and MLH1. Thus, 49.3% of cases (34/69) lost expression of one or more MMR proteins, which was interpreted as dMMR. There was no significant difference (P > 0.05) in terms of sex, age, clinical stage, T category, N category or therapy regimens between the dMMR and pMMR groups. The multivariate Cox regression analysis revealed that dMMR was an independent significant prognostic factor for distant metastasis-free survival (DMFS) (dMMR vs pMMR: P = 0.01, HR = 0.25, 95% CI: 0.09~0.75). Therefore, NPC patients with dMMR had significantly superior DMFS compared with patients with pMMR. It can be expected that dMMR will become a new independent prognostic factor for NPC.
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Affiliation(s)
- Fang-Ming Chen
- Department of Radiation Oncology, Rongcheng People's Hospital, Weihai, China
| | - Yun-Xiang Zhang
- Department of Pathology, Weifang People's Hospital, Weifang, China
| | - Xiu-Feng Li
- Department of Pathology, Weifang People's Hospital, Weifang, China
| | - Jian-Fang Gao
- Department of Pathology, Weifang People's Hospital, Weifang, China
| | - Hao Ma
- Department of Pathology, Weifang People's Hospital, Weifang, China
| | - Xiao-Li Wang
- Department of Radiation Oncology, Weifang People's Hospital, Weifang, China
| | - Yang Li
- Department of Radiation Oncology, Weifang People's Hospital, Weifang, China
| | - Cheng Li
- Clinical School, Weifang Medical University, Weifang, China
| | - Ya-Nan Zhang
- Clinical School, Weifang Medical University, Weifang, China
| | - Ya-Ting Zhang
- Clinical School, Weifang Medical University, Weifang, China
| | - Hong-Xing Kan
- Department of Radiation Oncology, Yantai Yuhuangding Hospital, Yantai, China
| | - Han Li
- Department of Oncology, The Fourth People's Hospital of Zibo City, Zibo, China
| | - Shi-Geng Zhang
- Department of Radiation Oncology, Taian Tumour Prevention and Treatment Hospital, Taian, China
| | - Fu-Rong Hao
- Department of Radiation Oncology, Weifang People's Hospital, Weifang, China.
- Weifang Key Laboratory of Radiophysics and Oncological Radiobiology, Weifang, China.
| | - Ming-Chen Wang
- Department of Radiation Oncology, Weifang People's Hospital, Weifang, China.
- Weifang Key Laboratory of Radiophysics and Oncological Radiobiology, Weifang, China.
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Distinct DNA repair pathways cause genomic instability at alternative DNA structures. Nat Commun 2020; 11:236. [PMID: 31932649 PMCID: PMC6957503 DOI: 10.1038/s41467-019-13878-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 11/05/2019] [Indexed: 01/01/2023] Open
Abstract
Alternative DNA structure-forming sequences can stimulate mutagenesis and are enriched at mutation hotspots in human cancer genomes, implicating them in disease etiology. However, the mechanisms involved are not well characterized. Here, we discover that Z-DNA is mutagenic in yeast as well as human cells, and that the nucleotide excision repair complex, Rad10-Rad1(ERCC1-XPF), and the mismatch repair complex, Msh2-Msh3, are required for Z-DNA-induced genetic instability in yeast and human cells. Both ERCC1-XPF and MSH2-MSH3 bind to Z-DNA-forming sequences, though ERCC1-XPF recruitment to Z-DNA is dependent on MSH2-MSH3. Moreover, ERCC1-XPF-dependent DNA strand-breaks occur near the Z-DNA-forming region in human cell extracts, and we model these interactions at the sub-molecular level. We propose a relationship in which these complexes recognize and process Z-DNA in eukaryotes, representing a mechanism of Z-DNA-induced genomic instability.
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Distinct roles of XPF-ERCC1 and Rad1-Rad10-Saw1 in replication-coupled and uncoupled inter-strand crosslink repair. Nat Commun 2018; 9:2025. [PMID: 29795289 PMCID: PMC5966407 DOI: 10.1038/s41467-018-04327-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 04/20/2018] [Indexed: 01/17/2023] Open
Abstract
Yeast Rad1-Rad10 (XPF-ERCC1 in mammals) incises UV, oxidation, and cross-linking agent-induced DNA lesions, and contributes to multiple DNA repair pathways. To determine how Rad1-Rad10 catalyzes inter-strand crosslink repair (ICLR), we examined sensitivity to ICLs from yeast deleted for SAW1 and SLX4, which encode proteins that interact physically with Rad1-Rad10 and bind stalled replication forks. Saw1, Slx1, and Slx4 are critical for replication-coupled ICLR in mus81 deficient cells. Two rad1 mutations that disrupt interactions between Rpa1 and Rad1-Rad10 selectively disable non-nucleotide excision repair (NER) function, but retain UV lesion repair. Mutations in the analogous region of XPF also compromised XPF interactions with Rpa1 and Slx4, and are proficient in NER but deficient in ICLR and direct repeat recombination. We propose that Rad1-Rad10 makes distinct contributions to ICLR depending on cell cycle phase: in G1, Rad1-Rad10 removes ICL via NER, whereas in S/G2, Rad1-Rad10 facilitates NER-independent replication-coupled ICLR.
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