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Morgan STB, Whelan DR, Rozario AM. Visualizing DNA damage and repair using single molecule super resolution microscopy. Methods Cell Biol 2023; 182:237-245. [PMID: 38359980 DOI: 10.1016/bs.mcb.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Single molecule super resolution microscopy overcomes the diffraction limit by separating individual fluorophore emissions over time, resulting in spatial resolutions that are far superior to epifluorescence microscopy. This allows for DNA damage response (DDR) events to be investigated in greater detail. A variety of DNA damaging drugs can be used on S-phase synchronized immortalized cell lines alongside 5-ethynyl-2'-deoxyuridine (EdU) pulse labelling to ultimately visualize DNA repair pathways at distinct time points and quantify colocalizations between nascent DNA and immunolabeled DDR proteins. This chapter will outline super resolution microscopy assays to interrogate the spatiotemporal organization of DNA repair proteins at damaged foci during DDR events within immortalized cell lines.
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Affiliation(s)
- Sophie T B Morgan
- La Trobe Institute for Molecular Science, La Trobe Rural Health School, La Trobe University, Bendigo, VIC, Australia
| | - Donna R Whelan
- La Trobe Institute for Molecular Science, La Trobe Rural Health School, La Trobe University, Bendigo, VIC, Australia
| | - Ashley M Rozario
- La Trobe Institute for Molecular Science, La Trobe Rural Health School, La Trobe University, Bendigo, VIC, Australia.
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Zhang Y, Han W, Wang L, Wang H, Jia Q, Chen T, Wang S, Li M. Correlative Escherichia coli Transcription Rate and Bubble Conformation Remodeled by NusA and NusG. J Phys Chem B 2023; 127:2909-2917. [PMID: 36977198 DOI: 10.1021/acs.jpcb.2c08771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Transcription is highly regulated by a variety of transcription factors, among which NusA and NusG act contradictorily in Escherichia coli (E. coli) that NusA stabilizes a paused RNA polymerase (RNAP) and NusG suppresses it. The mechanism of the NusA and NusG regulations on RNAP transcription has been addressed, but their effect on the conformational changes of the transcription bubble correlated with transcription kinetics remains elusive. By using single-molecule magnetic trap, we identify a reduction in the transcription rate of ∼40% events by NusA. Although the rest ∼60% of transcription events exhibit unaffected transcription rates, a NusA-enhanced standard deviation of the transcription rate is observed. NusA remodeling also increases the extent of DNA unwinding in the transcription bubble by 1-2 base pairs, which can be reduced by NusG. The NusG remodeling is more significant on the RNAP molecules with reduced transcription rates rather than those without. Our results provide a quantitative view on the mechanisms of transcriptional regulation by NusA and NusG factors.
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Affiliation(s)
- Yuqiong Zhang
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, Guangdong 510631, China
- Guangdong Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, Guangdong 510631, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Weijing Han
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Lisha Wang
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Hao Wang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Qi Jia
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Tongsheng Chen
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, Guangdong 510631, China
- Guangdong Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, Guangdong 510631, China
| | - Shuang Wang
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Ming Li
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
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Roy U, Kwon Y, Marie L, Symington L, Sung P, Lisby M, Greene EC. The Rad51 paralog complex Rad55-Rad57 acts as a molecular chaperone during homologous recombination. Mol Cell 2021; 81:1043-1057.e8. [PMID: 33421364 PMCID: PMC8262405 DOI: 10.1016/j.molcel.2020.12.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/02/2020] [Accepted: 12/10/2020] [Indexed: 12/29/2022]
Abstract
Homologous recombination (HR) is essential for maintenance of genome integrity. Rad51 paralogs fulfill a conserved but undefined role in HR, and their mutations are associated with increased cancer risk in humans. Here, we use single-molecule imaging to reveal that the Saccharomyces cerevisiae Rad51 paralog complex Rad55-Rad57 promotes assembly of Rad51 recombinase filament through transient interactions, providing evidence that it acts like a classical molecular chaperone. Srs2 is an ATP-dependent anti-recombinase that downregulates HR by actively dismantling Rad51 filaments. Contrary to the current model, we find that Rad55-Rad57 does not physically block the movement of Srs2. Instead, Rad55-Rad57 promotes rapid re-assembly of Rad51 filaments after their disruption by Srs2. Our findings support a model in which Rad51 is in flux between free and single-stranded DNA (ssDNA)-bound states, the rate of which is controlled dynamically though the opposing actions of Rad55-Rad57 and Srs2.
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Affiliation(s)
- Upasana Roy
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Youngho Kwon
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Lea Marie
- Department of Microbiology and Immunology, Columbia University, New York, NY 10032, USA
| | - Lorraine Symington
- Department of Microbiology and Immunology, Columbia University, New York, NY 10032, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Michael Lisby
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark; Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Hylton HM, Lucas BE, Petreaca RC. Schizosaccharomyces pombe Assays to Study Mitotic Recombination Outcomes. Genes (Basel) 2020; 11:E79. [PMID: 31936815 DOI: 10.3390/genes11010079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/07/2020] [Accepted: 01/07/2020] [Indexed: 01/16/2023] Open
Abstract
The fission yeast—Schizosaccharomyces pombe—has emerged as a powerful tractable system for studying DNA damage repair. Over the last few decades, several powerful in vivo genetic assays have been developed to study outcomes of mitotic recombination, the major repair mechanism of DNA double strand breaks and stalled or collapsed DNA replication forks. These assays have significantly increased our understanding of the molecular mechanisms underlying the DNA damage response pathways. Here, we review the assays that have been developed in fission yeast to study mitotic recombination.
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Bellido A, Ciudad T, Hermosa B, Andaluz E, Forche A, Larriba G. Partner Choice in Spontaneous Mitotic Recombination in Wild Type and Homologous Recombination Mutants of Candida albicans. G3 (Bethesda) 2019; 9:3631-44. [PMID: 31690596 DOI: 10.1534/g3.119.400516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Candida albicans, the most common fungal pathogen, is a diploid with a genome that is rich in repeats and has high levels of heterozygosity. To study the role of different recombination pathways on direct-repeat recombination, we replaced either allele of the RAD52 gene (Chr6) with the URA-blaster cassette (hisG-URA3-hisG), measured rates of URA3 loss as resistance to 5-fluoroorotic acid (5FOAR) and used CHEF Southern hybridization and SNP-RFLP analysis to identify recombination mechanisms and their frequency in wildtype and recombination mutants. FOAR rates varied little across different strain backgrounds. In contrast, the type and frequency of mechanisms underlying direct repeat recombination varied greatly. For example, wildtype, rad59 and lig4 strains all displayed a bias for URA3 loss via pop-out/deletion vs. inter-homolog recombination and this bias was reduced in rad51 mutants. In addition, in rad51-derived 5FOAR strains direct repeat recombination was associated with ectopic translocation (5%), chromosome loss/truncation (14%) and inter-homolog recombination (6%). In the absence of RAD52, URA3 loss was mostly due to chromosome loss and truncation (80–90%), and the bias of retained allele frequency points to the presence of a recessive lethal allele on Chr6B. However, a few single-strand annealing (SSA)-like events were identified and these were independent of either Rad59 or Lig4. Finally, the specific sizes of Chr6 truncations suggest that the inserted URA-blaster could represent a fragile site.
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Lai J, Yang H, Zhu Y, Ruan M, Huang Y, Zhang Q. MiR-7-5p-mediated downregulation of PARP1 impacts DNA homologous recombination repair and resistance to doxorubicin in small cell lung cancer. BMC Cancer 2019; 19:602. [PMID: 31215481 PMCID: PMC6582543 DOI: 10.1186/s12885-019-5798-7] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/05/2019] [Indexed: 12/13/2022] Open
Abstract
Background Chemo-resistance is one of the major challenges in the therapy of small cell lung cancer (SCLC). Multiple mechanisms are thought to be involved in chemo-resistance during SCLC treatment, but unfortunately, these mechanisms have not been well elucidated. Herein, we investigated the role of miRNA in the resistance of SCLC cells to doxorubicin (Dox). Methods MiRNA microarray analysis revealed that several miRNAs, including miR-7-5p, were specifically decreased in Dox-resistant SCLC cells (H69AR) compared to parental cells (H69). The expression level of miR-7-5p was confirmed by qRT-PCR in Dox-resistant cells (H69AR and H446AR cells) and their parental cells. Bioinformatic analysis indicated that poly ADP-ribose polymerase 1 (PARP1) is a direct target of miR-7-5p. The binding sites of miR-7-5p in the PARP1 3′ UTR were verified by luciferase reporter and Western blot assays. To investigate the role of miR-7-5p in the chemo-resistance of SCLC cells to doxorubicin, mimic or inhibitor of miR-7-5p was transfected into SCLC cells, and the effect of miR-7-5p on homologous recombination (HR) repair was analyzed by HR reporter assays. Furthermore, the expression of HR repair factors (Rad51 and BRCA1) induced by doxorubicin was detected by Western blot and immunofluorescent staining in H446AR cells transfected with miR-7-5p mimic. Results The expression level of miR-7-5p was remarkably reduced (4-fold) in Dox-resistant SCLC cells (H69AR and H446AR cells) compared with that in parental cells (H69 and H446 cells). Poly ADP-ribose polymerase 1 (PARP1) is a direct target of miR-7-5p, and PARP1 expression was downregulated by miR-7-5p. MiR-7-5p impeded Dox-induced HR repair by inhibiting the expression of HR repair factors (Rad51 and BRCA1) that resulted in resensitizing SCLC cells to doxorubicin. Conclusions Our findings provide evidence that miR-7-5p targets PARP1 to exert its suppressive effects on HR repair, indicating that the alteration of the expression of miR-7-5p may be a promising strategy for overcoming chemo-resistance in SCLC therapy. Electronic supplementary material The online version of this article (10.1186/s12885-019-5798-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jinzhi Lai
- Department of Oncology, The Second Affiliated Hospital, Fujian Medical University, Quanzhou, China.,Institute of Immunotherapy, Fujian Medical University, Fuzhou, 350108, Fujian, China
| | - Hainan Yang
- Department of Ultrasound, The Second Affiliated Hospital, Fujian Medical University, Quanzhou, China
| | - Yanyang Zhu
- Institute of Immunotherapy, Fujian Medical University, Fuzhou, 350108, Fujian, China
| | - Mei Ruan
- Institute of Immunotherapy, Fujian Medical University, Fuzhou, 350108, Fujian, China
| | - Yayu Huang
- Department of Oncology, The Second Affiliated Hospital, Fujian Medical University, Quanzhou, China
| | - Qiuyu Zhang
- Institute of Immunotherapy, Fujian Medical University, Fuzhou, 350108, Fujian, China.
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