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Sridalla K, Woodhouse MV, Hu J, Scheer J, Ferlez B, Crickard JB. The translocation activity of Rad54 reduces crossover outcomes during homologous recombination. Nucleic Acids Res 2024:gkae474. [PMID: 38828785 DOI: 10.1093/nar/gkae474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 05/16/2024] [Accepted: 05/21/2024] [Indexed: 06/05/2024] Open
Abstract
Homologous recombination (HR) is a template-based DNA double-strand break repair pathway that requires the selection of an appropriate DNA sequence to facilitate repair. Selection occurs during a homology search that must be executed rapidly and with high fidelity. Failure to efficiently perform the homology search can result in complex intermediates that generate genomic rearrangements, a hallmark of human cancers. Rad54 is an ATP dependent DNA motor protein that functions during the homology search by regulating the recombinase Rad51. How this regulation reduces genomic exchanges is currently unknown. To better understand how Rad54 can reduce these outcomes, we evaluated several amino acid mutations in Rad54 that were identified in the COSMIC database. COSMIC is a collection of amino acid mutations identified in human cancers. These substitutions led to reduced Rad54 function and the discovery of a conserved motif in Rad54. Through genetic, biochemical and single-molecule approaches, we show that disruption of this motif leads to failure in stabilizing early strand invasion intermediates, causing increased crossovers between homologous chromosomes. Our study also suggests that the translocation rate of Rad54 is a determinant in balancing genetic exchange. The latch domain's conservation implies an interaction likely fundamental to eukaryotic biology.
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Affiliation(s)
- Krishay Sridalla
- Deparment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Mitchell V Woodhouse
- Deparment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jingyi Hu
- Deparment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jessica Scheer
- Deparment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Bryan Ferlez
- Deparment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - J Brooks Crickard
- Deparment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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Kyriukha Y, Watkins MB, Redington JM, Dastvan R, Uversky VN, Hopkins JB, Pozzi N, Korolev S. The strand exchange domain of tumor suppressor PALB2 is intrinsically disordered and promotes oligomerization-dependent DNA compaction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.01.543259. [PMID: 37333393 PMCID: PMC10274692 DOI: 10.1101/2023.06.01.543259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The Partner and Localizer of BRCA2 (PALB2) is a scaffold protein that links BRCA1 with BRCA2 to initiate homologous recombination (HR). PALB2 interaction with DNA strongly enhances HR efficiency in cells. The PALB2 DNA-binding domain (PALB2-DBD) supports strand exchange, a complex multistep reaction conducted by only a few proteins such as RecA-like recombinases and Rad52. Using bioinformatics analysis, small-angle X-ray scattering, circular dichroism, and electron paramagnetic spectroscopy, we determined that PALB2-DBD is an intrinsically disordered region (IDR) forming compact molten globule-like dimer. IDRs contribute to oligomerization synergistically with the coiled-coil interaction. Using confocal single-molecule FRET we demonstrated that PALB2-DBD compacts single-stranded DNA even in the absence of DNA secondary structures. The compaction is bimodal, oligomerization-dependent, and is driven by IDRs, suggesting a novel strand exchange mechanism. Intrinsically disordered proteins (IDPs) are prevalent in the human proteome. Novel DNA binding properties of PALB2-DBD and the complexity of strand exchange mechanism significantly expands the functional repertoire of IDPs. Multivalent interactions and bioinformatics analysis suggest that PALB2 function is likely to depend on formation of protein-nucleic acids condensates. Similar intrinsically disordered DBDs may use chaperone-like mechanism to aid formation and resolution of DNA and RNA multichain intermediates during DNA replication, repair and recombination.
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Affiliation(s)
- Yevhenii Kyriukha
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | - Maxwell B Watkins
- The Biophysics Collaborative Access Team (BioCat), Departments of Biology and Physics, Illinois Institute of Technology, Chicago, IL
| | - Jennifer M Redington
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | - Reza Dastvan
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCat), Departments of Biology and Physics, Illinois Institute of Technology, Chicago, IL
| | - Nicola Pozzi
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | - Sergey Korolev
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
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3
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Fernandez R, Berro J. CRISPR-Cas9 editing efficiency in fission yeast is not limited by homology search and is improved by combining gap-repair with fluoride selection. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001191. [PMID: 38778900 PMCID: PMC11109758 DOI: 10.17912/micropub.biology.001191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 01/01/1970] [Accepted: 05/03/2024] [Indexed: 05/25/2024]
Abstract
Protocols for CRISPR-Cas9 editing have been implemented in most model organisms, including fission yeast, for which some improvements have also been later described. Here, we report an improvement to the CRISPR-Cas9 protocol in fission yeast, as we combine a cloning free gap-repair method with our previously described fluoride selection marker, which speeds up genome editing. We also report a wide variability of editing efficiencies at different loci along the genome, and we demonstrate that this variability cannot be explained by the location of the edited sequences in the genome. Lastly, our attempt at improving editing efficiency by targeting the donor DNA to the cut site using a HaloTag strategy to link the donor DNA to two proteins of the homologous recombination repair machinery ( Rad51 or Rad52 ) fell short, which shows that editing efficiency in fission yeast is likely not limited by homology search.
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Affiliation(s)
- Ronan Fernandez
- Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States
| | - Julien Berro
- Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, United States
- Cell Biology, Yale University School of Medicine
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Zhang Z, Zhang S, Wong HT, Li D, Feng B. Targeted Gene Insertion: The Cutting Edge of CRISPR Drug Development with Hemophilia as a Highlight. BioDrugs 2024; 38:369-385. [PMID: 38489061 PMCID: PMC11055778 DOI: 10.1007/s40259-024-00654-5] [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] [Accepted: 02/15/2024] [Indexed: 03/17/2024]
Abstract
The remarkable advance in gene editing technology presents unparalleled opportunities for transforming medicine and finding cures for hereditary diseases. Human trials of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein-9 nuclease (Cas9)-based therapeutics have demonstrated promising results in disrupting or deleting target sequences to treat specific diseases. However, the potential of targeted gene insertion approaches, which offer distinct advantages over disruption/deletion methods, remains largely unexplored in human trials due to intricate technical obstacles and safety concerns. This paper reviews the recent advances in preclinical studies demonstrating in vivo targeted gene insertion for therapeutic benefits, targeting somatic solid tissues through systemic delivery. With a specific emphasis on hemophilia as a prominent disease model, we highlight advancements in insertion strategies, including considerations of DNA repair pathways, targeting site selection, and donor design. Furthermore, we discuss the complex challenges and recent breakthroughs that offer valuable insights for progressing towards clinical trials.
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Affiliation(s)
- Zhenjie Zhang
- School of Biomedical Sciences, Faculty of Medicine, CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Room 105A, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, Shatin, NT, Hong Kong SAR, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Chinese Academy of Sciences, Hong Kong SAR, China
| | - Siqi Zhang
- School of Biomedical Sciences, Faculty of Medicine, CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Room 105A, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, Shatin, NT, Hong Kong SAR, China
| | - Hoi Ting Wong
- School of Biomedical Sciences, Faculty of Medicine, CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Room 105A, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, Shatin, NT, Hong Kong SAR, China
| | - Dali Li
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Bo Feng
- School of Biomedical Sciences, Faculty of Medicine, CUHK-GIBH CAS Joint Research Laboratory on Stem Cell and Regenerative Medicine, The Chinese University of Hong Kong, Room 105A, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, Shatin, NT, Hong Kong SAR, China.
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Chinese Academy of Sciences, Hong Kong SAR, China.
- Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
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Singh A, Patel G, Patel SS. Twinkle-Catalyzed Toehold-Mediated DNA Strand Displacement Reaction. J Am Chem Soc 2023:10.1021/jacs.3c04970. [PMID: 37917930 PMCID: PMC11063129 DOI: 10.1021/jacs.3c04970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
Strand exchange between homologous nucleic acid sequences is the basis for cellular DNA repair, recombination, and genome editing technologies. Specialized enzymes catalyze cellular strand exchange; however, the reaction occurs spontaneously when a single-stranded DNA toehold can dock the invader strand on the target DNA to initiate strand exchange through branch migration. Due to its precise response, the spontaneous toehold-mediated strand displacement (TMSD) reaction is widely employed in DNA nanotechnology. However, enzyme-free TMSD suffers from slow rates, resulting in slow response times. Here, we show that human mitochondrial DNA helicase Twinkle can accelerate TMSD up to 6000-fold. Mechanistic studies indicate that Twinkle accelerates TMSD by catalyzing the docking step, which typically limits spontaneous reactions. The catalysis occurs without ATP, and Twinkle-catalyzed TMSD rates remain sensitive to base-pair mismatches. The simple catalysis, tunability, and speed improvement of the catalyzed TMSD can be leveraged in nanotechnology, requiring sensitive detection and faster response times.
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Affiliation(s)
- Anupam Singh
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey, USA
| | - Gayatri Patel
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey, USA
| | - Smita S. Patel
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey, USA
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Kyriukha Y, Watkins MB, Redington JM, Dastvan R, Uversky VN, Hopkins J, Pozzi N, Korolev S. The PALB2 DNA-binding domain is an intrinsically disordered recombinase. RESEARCH SQUARE 2023:rs.3.rs-3235465. [PMID: 37790553 PMCID: PMC10543426 DOI: 10.21203/rs.3.rs-3235465/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The Partner and Localizer of BRCA2 (PALB2) tumor suppressor is a scaffold protein that links BRCA1 with BRCA2 to initiate homologous recombination (HR). PALB2 interaction with DNA strongly enhances HR efficiency. The PALB2 DNA-binding domain (PALB2-DBD) supports DNA strand exchange, a complex multistep reaction supported by only a few protein families such as RecA-like recombinases or Rad52. The mechanisms of PALB2 DNA binding and strand exchange are unknown. We performed circular dichroism, electron paramagnetic spectroscopy, and small-angle X-ray scattering analyses and determined that PALB2-DBD is intrinsically disordered, even when bound to DNA. The intrinsically disordered nature of this domain was further supported by bioinformatics analysis. Intrinsically disordered proteins (IDPs) are prevalent in the human proteome and have many important biological functions. The complexity of the strand exchange reaction significantly expands the functional repertoire of IDPs. The results of confocal single-molecule FRET indicated that PALB2-DBD binding leads to oligomerization-dependent DNA compaction. We hypothesize that PALB2-DBD uses a chaperone-like mechanism to aid formation and resolution of complex DNA and RNA multichain intermediates during DNA replication and repair. Since PALB2-DBD alone or within the full-length PALB2 is predicted to have strong liquid-liquid phase separation (LLPS) potential, protein-nucleic acids condensates are likely to play a role in complex functionality of PALB2-DBD. Similar DNA-binding intrinsically disordered regions may represent a novel class of functional domains that evolved to function in eukaryotic nucleic acid metabolism complexes.
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Affiliation(s)
- Yevhenii Kyriukha
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | | | - Jennifer M Redington
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | - Reza Dastvan
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL
| | - Jesse Hopkins
- BioCat, Advanced Photon Source, Argonne National Lab, Argonne, IL
| | - Nicola Pozzi
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | - Sergey Korolev
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
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Hernández-Suárez B, Gillespie DA, Dejnaka E, Kupczyk P, Obmińska-Mrukowicz B, Pawlak A. Studying the DNA damage response pathway in hematopoietic canine cancer cell lines, a necessary step for finding targets to generate new therapies to treat cancer in dogs. Front Vet Sci 2023; 10:1227683. [PMID: 37655260 PMCID: PMC10467447 DOI: 10.3389/fvets.2023.1227683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/31/2023] [Indexed: 09/02/2023] Open
Abstract
Background Dogs present a significant opportunity for studies in comparative oncology. However, the study of cancer biology phenomena in canine cells is currently limited by restricted availability of validated antibody reagents and techniques. Here, we provide an initial characterization of the expression and activity of key components of the DNA Damage Response (DDR) in a panel of hematopoietic canine cancer cell lines, with the use of commercially available antibody reagents. Materials and methods The techniques used for this validation analysis were western blot, qPCR, and DNA combing assay. Results Substantial variations in both the basal expression (ATR, Claspin, Chk1, and Rad51) and agonist-induced activation (p-Chk1) of DDR components were observed in canine cancer cell lines. The expression was stronger in the CLBL-1 (B-cell lymphoma) and CLB70 (B-cell chronic lymphocytic leukemia) cell lines than in the GL-1 (B-cell leukemia) cell line, but the biological significance of these differences requires further investigation. We also validated methodologies for quantifying DNA replication dynamics in hematopoietic canine cancer cell lines, and found that the GL-1 cell line presented a higher replication fork speed than the CLBL-1 cell line, but that both showed a tendency to replication fork asymmetry. Conclusion These findings will inform future studies on cancer biology, which will facilitate progress in developing novel anticancer therapies for canine patients. They can also provide new knowledge in human oncology.
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Affiliation(s)
- Beatriz Hernández-Suárez
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - David A. Gillespie
- Facultad de Medicina, Instituto de Tecnologías Biomédicas, Universidad de La Laguna, Tenerife, Spain
| | - Ewa Dejnaka
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Piotr Kupczyk
- Division of General and Experimental Pathology, Department of Clinical and Experimental Pathology, Faculty of Medicine, Wroclaw Medical University, Wroclaw, Poland
| | - Bożena Obmińska-Mrukowicz
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Aleksandra Pawlak
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
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Lyu M, Sun Y, Yan N, Chen Q, Wang X, Wei Z, Zhang Z, Xu K. Efficient CRISPR/Cas9-mediated gene editing in mammalian cells by the novel selectable traffic light reporters. Int J Biol Macromol 2023:124926. [PMID: 37217056 DOI: 10.1016/j.ijbiomac.2023.124926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 04/30/2023] [Accepted: 05/04/2023] [Indexed: 05/24/2023]
Abstract
CRISPR/Cas9 is a powerful tool for gene editing in various cell types and organisms. However, it is still challenging to screen genetically modified cells from an excess of unmodified cells. Our previous studies demonstrated that surrogate reporters can be used for efficient screening of genetically modified cells. Here, we developed two novel traffic light screening reporters, puromycin-mCherry-EGFP (PMG) based on single-strand annealing (SSA) and homology-directed repair (HDR), respectively, to measure the nuclease cleavage activity within transfected cells and to select genetically modified cells. We found that the two reporters could be self-repaired coupling the genome editing events driven by different CRISPR/Cas nucleases, resulting in a functional puromycin-resistance and EGFP selection cassette that can be afforded to screen genetically modified cells by puromycin selection or FACS enrichment. We further compared the novel reporters with different traditional reporters at several endogenous loci in different cell lines, for the enrichment efficiencies of genetically modified cells. The results indicated that the SSA-PMG reporter exhibited improvements in enriching gene knockout cells, while the HDR-PMG system was very useful in enriching knock-in cells. These results provide robust and efficient surrogate reporters for the enrichment of CRISPR/Cas9-mediated editing in mammalian cells, thereby advancing basic and applied research.
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Affiliation(s)
- Ming Lyu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yongsen Sun
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Nana Yan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qiang Chen
- Shaanxi Stem Cell Engineering and Technology Research Center, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Xin Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Zehui Wei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Zhiying Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| | - Kun Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
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Soniat MM, Nguyen G, Kuo HC, Finkelstein IJ. The MRN complex and topoisomerase IIIa-RMI1/2 synchronize DNA resection motor proteins. J Biol Chem 2023; 299:102802. [PMID: 36529288 PMCID: PMC9971906 DOI: 10.1016/j.jbc.2022.102802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 12/08/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022] Open
Abstract
DNA resection-the nucleolytic processing of broken DNA ends-is the first step of homologous recombination. Resection is catalyzed by the resectosome, a multienzyme complex that includes bloom syndrome helicase (BLM), DNA2 or exonuclease 1 nucleases, and additional DNA-binding proteins. Although the molecular players have been known for over a decade, how the individual proteins work together to regulate DNA resection remains unknown. Using single-molecule imaging, we characterized the roles of the MRE11-RAD50-NBS1 complex (MRN) and topoisomerase IIIa (TOP3A)-RMI1/2 during long-range DNA resection. BLM partners with TOP3A-RMI1/2 to form the BTRR (BLM-TOP3A-RMI1/2) complex (or BLM dissolvasome). We determined that TOP3A-RMI1/2 aids BLM in initiating DNA unwinding, and along with MRN, stimulates DNA2-mediated resection. Furthermore, we found that MRN promotes the association between BTRR and DNA and synchronizes BLM and DNA2 translocation to prevent BLM from pausing during resection. Together, this work provides direct observation of how MRN and DNA2 harness the BTRR complex to resect DNA efficiently and how TOP3A-RMI1/2 regulates the helicase activity of BLM to promote efficient DNA repair.
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Affiliation(s)
- Michael M Soniat
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, USA.
| | - Giaochau Nguyen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Hung-Che Kuo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, USA.
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Abstract
DNA polymerase θ (Pol θ) is a DNA repair enzyme widely conserved in animals and plants. Pol θ uses short DNA sequence homologies to initiate repair of double-strand breaks by theta-mediated end joining. The DNA polymerase domain of Pol θ is at the C terminus and is connected to an N-terminal DNA helicase-like domain by a central linker. Pol θ is crucial for maintenance of damaged genomes during development, protects DNA against extensive deletions, and limits loss of heterozygosity. The cost of using Pol θ for genome protection is that a few nucleotides are usually deleted or added at the repair site. Inactivation of Pol θ often enhances the sensitivity of cells to DNA strand-breaking chemicals and radiation. Since some homologous recombination-defective cancers depend on Pol θ for growth, inhibitors of Pol θ may be useful in treating such tumors.
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Affiliation(s)
- Richard D Wood
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Center, Houston, Texas, USA;
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, USA;
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Pan-cancer analysis of co-occurring mutations in RAD52 and the BRCA1-BRCA2-PALB2 axis in human cancers. PLoS One 2022; 17:e0273736. [PMID: 36107942 PMCID: PMC9477347 DOI: 10.1371/journal.pone.0273736] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/12/2022] [Indexed: 11/19/2022] Open
Abstract
In human cells homologous recombination (HR) is critical for repair of DNA double strand breaks (DSBs) and rescue of stalled or collapsed replication forks. HR is facilitated by RAD51 which is loaded onto DNA by either BRCA2-BRCA1-PALB2 or RAD52. In human culture cells, double-knockdowns of RAD52 and genes in the BRCA1-BRCA2-PALB2 axis are lethal. Mutations in BRCA2, BRCA1 or PALB2 significantly impairs error free HR as RAD51 loading relies on RAD52 which is not as proficient as BRCA2-BRCA1-PALB2. RAD52 also facilitates Single Strand Annealing (SSA) that produces intra-chromosomal deletions. Some RAD52 mutations that affect the SSA function or decrease RAD52 association with DNA can suppress certain BRCA2 associated phenotypes in breast cancers. In this report we did a pan-cancer analysis using data reported on the Catalogue of Somatic Mutations in Cancers (COSMIC) to identify double mutants between RAD52 and BRCA1, BRCA2 or PALB2 that occur in cancer cells. We find that co-occurring mutations are likely in certain cancer tissues but not others. However, all mutations occur in a heterozygous state. Further, using computational and machine learning tools we identified only a handful of pathogenic or driver mutations predicted to significantly affect the function of the proteins. This supports previous findings that co-inactivation of RAD52 with any members of the BRCA2-BRCA1-PALB2 axis is lethal. Molecular modeling also revealed that pathogenic RAD52 mutations co-occurring with mutations in BRCA2-BRCA1-PALB2 axis are either expected to attenuate its SSA function or its interaction with DNA. This study extends previous breast cancer findings to other cancer types and shows that co-occurring mutations likely destabilize HR by similar mechanisms as in breast cancers.
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Rajagopal T, Seshachalam A, Rathnam KK, Talluri S, Venkatabalasubramanian S, Dunna NR. Homologous recombination DNA repair gene RAD51, XRCC2 & XRCC3 polymorphisms and breast cancer risk in South Indian women. PLoS One 2022; 17:e0259761. [PMID: 35061678 PMCID: PMC8782413 DOI: 10.1371/journal.pone.0259761] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/26/2021] [Indexed: 01/04/2023] Open
Abstract
Background Homologous recombination repair (HRR) accurately repairs the DNA double-strand breaks (DSBs) and is crucial for genome stability. Genetic polymorphisms in crucial HRR pathway genes might affect genome stability and promote tumorigenesis. Up to our knowledge, the present study is the first to investigate the impact of HRR gene polymorphisms on BC development in South Indian women. The present population-based case-control study investigated the association of polymorphisms in three key HRR genes (XRCC2-Arg188His, XRCC3-Thr241Met and RAD51-G135C) with BC risk. Materials and methods Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was used for genotyping the HRR variants in 491 BC cases and 493 healthy women. Results We observed that the XRCC3 Met allele was significantly associated with BC risk [OR:1.27 (95% CI: 1.02–1.60); p = 0.035]. In addition, the homozygous mutant (C/C) genotype of RAD51 G135C variant conferred 2.19 fold elevated risk of BC [OR: 2.19 (95% CI: 1.06–4.54); p = 0.034]. Stratified analysis of HRR variants and BC clinicopathological features revealed that the XRCC3-Thr241Met and RAD51-G135C variants are associated with BC progression. Combined SNP analysis revealed that the individuals with RAD51-C/C, XRCC2-Arg/Arg, and XRCC3-Thr/Thr genotype combination have three-fold increased BC risk. Conclusion The present study imparts additional evidence that genetic variants in crucial HRR pathway genes might play a pivotal role in modulating BC risk in South Indian women.
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Affiliation(s)
- Taruna Rajagopal
- Cancer Genomics Laboratory, Department of Biotechnology, School of Chemical and Biotechnology, SASTRA–Deemed University, Thanjavur, India
| | - Arun Seshachalam
- Department of Medical and Paediatric Oncology, Dr.G.V.N Cancer Institute, Singarathope, Trichy, India
| | - Krishna Kumar Rathnam
- Department of Hemato Oncology–Medical Oncology and Bone Marrow Transplantation, Meenakshi Mission Hospital & Research Centre, Madurai, India
| | - Srikanth Talluri
- Dana Farber Cancer Institute, Boston, MA, United States of America
- Veterans Administration Boston Healthcare System, West Roxbury, MA, United States of America
| | | | - Nageswara Rao Dunna
- Cancer Genomics Laboratory, Department of Biotechnology, School of Chemical and Biotechnology, SASTRA–Deemed University, Thanjavur, India
- * E-mail:
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13
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Filipe A, Katopodis P, Chudasama D, Kerslake R, Jeyaneethi J, Anikin V, Silva E, Kyrou I, Randeva HS, Sisu C, Hall M, Karteris E. Differential Expression of RAD51AP1 in Ovarian Cancer: Effects of siRNA In Vitro. J Pers Med 2022; 12:jpm12020201. [PMID: 35207688 PMCID: PMC8876735 DOI: 10.3390/jpm12020201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 01/08/2022] [Accepted: 01/25/2022] [Indexed: 11/16/2022] Open
Abstract
Background: DNA double strand breaks can affect genome integrity potentially leading to cancer. RAD51-associated protein 1 (RAD51AP1), an accessory protein to RAD51, is critical for homologous recombination, a key DNA damage response pathway. Emerging studies indicate a novel role for RAD51AP1 in carcinogenesis. Here we provide additional insight into the role of RAD51AP1 in ovarian cancer (OvCa). Methods: Gene expression and patient phenotype data were obtained from TCGA and GTEX project consortia for bioinformatics analysis. Immunohistochemistry of OvCa tissue microarray was undertaken. Functional analyses were performed in a SKOV3 OvCa cell line with down-regulation of RAD51AP1 using siRNA. Results: RAD51AP1 is overexpressed at gene level in primary and recurrent OvCa compared to controls. At protein level, RAD51AP1 was up-regulated in low grade serous tumors compared to high grade OvCa. There was higher expression of RAD51AP1 in OvCa metastatic to lymph nodes compared to primary cancer samples. Gene enrichment analyses identified 12 differentially expressed genes (DEGs) related to OvCa, eight of which are also common in tissue from patients with type 2 diabetes mellitus (T2DM). Conclusions: RAD51AP1 is overexpressed in OvCa, Given the link between OvCa and T2DM, the eight-gene signature shows potential for predictive value.
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Affiliation(s)
- Alice Filipe
- Department of Life Sciences, Division of Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK; (A.F.); (P.K.); (D.C.); (R.K.); (J.J.); (E.S.); (C.S.)
| | - Periklis Katopodis
- Department of Life Sciences, Division of Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK; (A.F.); (P.K.); (D.C.); (R.K.); (J.J.); (E.S.); (C.S.)
- Division of Thoracic Surgery, The Royal Brompton & Harefield NHS Foundation Trust, Harefield Hospital, Harefield UB9 6JH, UK;
| | - Dimple Chudasama
- Department of Life Sciences, Division of Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK; (A.F.); (P.K.); (D.C.); (R.K.); (J.J.); (E.S.); (C.S.)
| | - Rachel Kerslake
- Department of Life Sciences, Division of Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK; (A.F.); (P.K.); (D.C.); (R.K.); (J.J.); (E.S.); (C.S.)
- Division of Thoracic Surgery, The Royal Brompton & Harefield NHS Foundation Trust, Harefield Hospital, Harefield UB9 6JH, UK;
| | - Jeyarooban Jeyaneethi
- Department of Life Sciences, Division of Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK; (A.F.); (P.K.); (D.C.); (R.K.); (J.J.); (E.S.); (C.S.)
- Division of Thoracic Surgery, The Royal Brompton & Harefield NHS Foundation Trust, Harefield Hospital, Harefield UB9 6JH, UK;
| | - Vladimir Anikin
- Division of Thoracic Surgery, The Royal Brompton & Harefield NHS Foundation Trust, Harefield Hospital, Harefield UB9 6JH, UK;
- Department of Oncology and Reconstructive Surgery, Sechenov First Moscow State, Medical University, 119146 Moscow, Russia
| | - Elisabete Silva
- Department of Life Sciences, Division of Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK; (A.F.); (P.K.); (D.C.); (R.K.); (J.J.); (E.S.); (C.S.)
| | - Ioannis Kyrou
- Warwickshire Institute for the Study of Diabetes, Endocrinology and Metabolism (WISDEM), University Hospitals Coventry and Warwickshire NHS Trust, Coventry CV2 2DX, UK; (I.K.); (H.S.R.)
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
- Centre for Sport, Exercise and Life Sciences, Research Institute for Health & Wellbeing, Coventry University, Coventry CV1 5FB, UK
- Aston Medical Research Institute, Aston Medical School, College of Health and Life Sciences, Aston University, Birmingham B4 7ET, UK
- Department of Food Science & Human Nutrition, School of Food and Nutritional Sciences, Agricultural University of Athens, 11855 Athens, Greece
| | - Harpal S. Randeva
- Warwickshire Institute for the Study of Diabetes, Endocrinology and Metabolism (WISDEM), University Hospitals Coventry and Warwickshire NHS Trust, Coventry CV2 2DX, UK; (I.K.); (H.S.R.)
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Cristina Sisu
- Department of Life Sciences, Division of Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK; (A.F.); (P.K.); (D.C.); (R.K.); (J.J.); (E.S.); (C.S.)
| | - Marcia Hall
- Department of Life Sciences, Division of Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK; (A.F.); (P.K.); (D.C.); (R.K.); (J.J.); (E.S.); (C.S.)
- Mount Vernon Cancer Centre, Northwood, London HA6 2RN, UK
- Correspondence: (M.H.); (E.K.)
| | - Emmanouil Karteris
- Department of Life Sciences, Division of Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK; (A.F.); (P.K.); (D.C.); (R.K.); (J.J.); (E.S.); (C.S.)
- Division of Thoracic Surgery, The Royal Brompton & Harefield NHS Foundation Trust, Harefield Hospital, Harefield UB9 6JH, UK;
- Correspondence: (M.H.); (E.K.)
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14
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Rad54 and Rdh54 prevent Srs2-mediated disruption of Rad51 presynaptic filaments. Proc Natl Acad Sci U S A 2022; 119:2113871119. [PMID: 35042797 PMCID: PMC8795549 DOI: 10.1073/pnas.2113871119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2021] [Indexed: 11/18/2022] Open
Abstract
Homologous DNA recombination is an essential pathway necessary for the repair of double-stranded DNA breaks. Defects in this pathway are associated with hereditary breast cancer, ovarian cancer, and cancer-prone syndromes. Although essential, too much recombination is also bad and can lead to genetic mutations. Thus, cells have evolved “antirecombinase” enzymes that can actively dismantle recombination intermediates to prevent excessive recombination. However, our current understanding of how antirecombinases are themselves regulated remains very limited. Here, we study the antirecombinase Srs2 and its regulation by the recombination accessory factors Rad54 and Rdh54. Our data suggest that Rad54 and Rdh54 act synergistically to function as key regulators of Srs2, thus serving as “licensing factors” that enable timely progression of DNA repair. Srs2 is a superfamily 1 (SF1) helicase that participates in several pathways necessary for the repair of damaged DNA. Srs2 regulates formation of early homologous recombination (HR) intermediates by actively removing the recombinase Rad51 from single-stranded DNA (ssDNA). It is not known whether and how Srs2 itself is down-regulated to allow for timely HR progression. Rad54 and Rdh54 are two closely related superfamily 2 (SF2) motor proteins that promote the formation of Rad51-dependent recombination intermediates. Rad54 and Rdh54 bind tightly to Rad51-ssDNA and act downstream of Srs2, suggesting that they may affect the ability of Srs2 to dismantle Rad51 filaments. Here, we used DNA curtains to determine whether Rad54 and Rdh54 alter the ability of Srs2 to disrupt Rad51 filaments. We show that Rad54 and Rdh54 act synergistically to greatly restrict the antirecombinase activity of Srs2. Our findings suggest that Srs2 may be accorded only a limited time window to act and that Rad54 and Rdh54 fulfill a role of prorecombinogenic licensing factors.
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15
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Xie C, Wang W, Tu C, Meng L, Lu G, Lin G, Lu LY, Tan YQ. OUP accepted manuscript. Hum Reprod Update 2022; 28:763-797. [PMID: 35613017 DOI: 10.1093/humupd/dmac024] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 04/18/2022] [Indexed: 11/12/2022] Open
Affiliation(s)
- Chunbo Xie
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Weili Wang
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Chaofeng Tu
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Central South University, Changsha, China
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Lanlan Meng
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Guangxiu Lu
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Central South University, Changsha, China
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Ge Lin
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Central South University, Changsha, China
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Lin-Yu Lu
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Yue-Qiu Tan
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Central South University, Changsha, China
- College of Life Sciences, Hunan Normal University, Changsha, China
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16
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Hernández-Suárez B, Gillespie DA, Pawlak A. DNA Damage Response (DDR) proteins in canine cancer as potential research targets in comparative oncology. Vet Comp Oncol 2021; 20:347-361. [PMID: 34923737 PMCID: PMC9304296 DOI: 10.1111/vco.12795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 11/22/2022]
Abstract
The DNA damage response (DDR) is a complex signal transduction network that is activated when endogenous or exogenous genotoxins damage or interfere with the replication of genomic DNA. Under such conditions, the DDR promotes DNA repair and ensures accurate replication and division of the genome. High levels of genomic instability are frequently observed in cancers and can stem from germline loss‐of‐function mutations in certain DDR genes, such as BRCA1, BRCA2, and p53, that form the basis of human cancer predisposition syndromes. In addition, mutation and/or aberrant expression of multiple DDR genes are frequently observed in sporadic human cancers. As a result, the DDR is considered to represent a viable target for cancer therapy in humans and a variety of strategies are under investigation. Cancer is also a significant cause of mortality in dogs, a species that offers certain advantages for experimental oncology. Domestic dogs present numerous inbred lines, many of which display predisposition to specific forms of cancer and the study of which may provide insight into the biological basis of this susceptibility. In addition, clinical trials are possible in dogs and may lead to therapeutic insights that could ultimately be extended to humans. Here we review what is known specifically about the DDR in dogs and discuss how this knowledge could be extended and exploited to advance experimental oncology in this species.
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Affiliation(s)
- Beatriz Hernández-Suárez
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Poland
| | - David A Gillespie
- Instituto de Tecnologías Biomédicas, Facultad de Medicina, Campus Ciencias de la Salud, Universidad de La Laguna, La Laguna 38071, Tenerife, Spain
| | - Aleksandra Pawlak
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Wroclaw University of Environmental and Life Sciences, Poland
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17
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Ray U, Raghavan SC. Understanding the DNA double-strand break repair and its therapeutic implications. DNA Repair (Amst) 2021; 106:103177. [PMID: 34325086 DOI: 10.1016/j.dnarep.2021.103177] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 06/25/2021] [Accepted: 07/07/2021] [Indexed: 10/20/2022]
Abstract
Repair of DNA double-strand breaks (DSBs) and its regulation are tightly integrated inside cells. Homologous recombination, nonhomologous end joining and microhomology mediated end joining are three major DSB repair pathways in mammalian cells. Targeting proteins associated with these repair pathways using small molecule inhibitors can prove effective in tumors, especially those with deregulated repair. Sensitization of cancer to current age therapy including radio and chemotherapy, using small molecule inhibitors is promising and warrant further development. Although several are under clinical trial, till date no repair inhibitor is approved for commercial use in cancer patients, with the exception of PARP inhibitors targeting single-strand break repair. Based on molecular profiling of repair proteins, better prognostic and therapeutic output can be achieved in patients. In the present review, we highlight the different mechanisms of DSB repair, chromatin dynamics to provide repair accessibility and modulation of inhibitors in association with molecular profiling and current gold standard treatment modalities for cancer.
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Affiliation(s)
- Ujjayinee Ray
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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18
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Abstract
The formation of crossovers between homologous chromosomes is key to sexual reproduction. In most species, crossovers are spaced further apart than would be expected if they formed independently, a phenomenon termed crossover interference. Despite more than a century of study, the molecular mechanisms implementing crossover interference remain a subject of active debate. Recent findings of how signaling proteins control the formation of crossovers and about the interchromosomal interface in which crossovers form offer new insights into this process. In this Review, we present a cell biological and biophysical perspective on crossover interference, summarizing the evidence that links interference to the spatial, dynamic, mechanical and molecular properties of meiotic chromosomes. We synthesize this physical understanding in the context of prevailing mechanistic models that aim to explain how crossover interference is implemented.
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Affiliation(s)
- Lexy von Diezmann
- Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT 84112, USA.,School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Ofer Rog
- Center for Cell and Genome Sciences, University of Utah, Salt Lake City, UT 84112, USA.,School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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19
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Miura K, Ogura A, Kobatake K, Honda H, Kaminuma O. Progress of genome editing technology and developmental biology useful for radiation research. JOURNAL OF RADIATION RESEARCH 2021; 62:i53-i63. [PMID: 33978171 PMCID: PMC8114227 DOI: 10.1093/jrr/rraa127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/26/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
Following the development of genome editing technology, it has become more feasible to create genetically modified animals such as knockout (KO), knock-in, and point-mutated animals. The genome-edited animals are useful to investigate the roles of various functional genes in many fields of biological science including radiation research. Nevertheless, some researchers may experience difficulty in generating genome-edited animals, probably due to the requirement for equipment and techniques for embryo manipulation and handling. Furthermore, after obtaining F0 generation, genome-edited animals generally need to be expanded and maintained for analyzing the target gene function. To investigate genes essential for normal birth and growth, the generation of conditional KO (cKO) animals in which a tissue- or stage-specific gene mutation can be introduced is often required. Here, we describe the basic principle and application of genome editing technology including zinc-finger nuclease, transcription-activator-like effector nuclease, and clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR associated protein (Cas) systems. Recently advanced developmental biology methods have enabled application of the technology, especially CRISPR/Cas, to zygotes, leading to the prompt production of genome-edited animals. For pre-implantation embryos, genome editing via oviductal nucleic acid delivery has been developed as an embryo manipulation- or handling-free method. Examining the gene function at F0 generation is becoming possible by employing triple-target CRISPR technology. This technology, in combination with a blastocyst complementation method enables investigation of even birth- and growth-responsible genes without establishing cKO strains. We hope that this review is helpful for understanding and expanding genome editing-related technology and for progressing radiation research.
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Affiliation(s)
- Kento Miura
- Department of Disease Model, Research Institute of Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
- RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Atsuo Ogura
- RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
- RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Kohei Kobatake
- Department of Disease Model, Research Institute of Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
- Department of Urology, Hiroshima University, Hiroshima 734-8553, Japan
| | - Hiroaki Honda
- Field of Human Disease Models, Major in Advanced Life Sciences and Medicine, Institute of Laboratory Animals, Tokyo Women's Medical University, Tokyo 162-8666, Japan
| | - Osamu Kaminuma
- Department of Disease Model, Research Institute of Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
- RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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20
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Bloh K, Rivera-Torres N. A Consensus Model of Homology-Directed Repair Initiated by CRISPR/Cas Activity. Int J Mol Sci 2021; 22:3834. [PMID: 33917142 PMCID: PMC8067812 DOI: 10.3390/ijms22083834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/31/2021] [Accepted: 04/05/2021] [Indexed: 12/26/2022] Open
Abstract
The mechanism of action of ssODN-directed gene editing has been a topic of discussion within the field of CRISPR gene editing since its inception. Multiple comparable, but distinct, pathways have been discovered for DNA repair both with and without a repair template oligonucleotide. We have previously described the ExACT pathway for oligo-driven DNA repair, which consisted of a two-step DNA synthesis-driven repair catalyzed by the simultaneous binding of the repair oligonucleotide (ssODN) upstream and downstream of the double-strand break. In order to better elucidate the mechanism of ExACT-based repair, we have challenged the assumptions of the pathway with those outlines in other similar non-ssODN-based DNA repair mechanisms. This more comprehensive iteration of the ExACT pathway better described the many different ways where DNA repair can occur in the presence of a repair oligonucleotide after CRISPR cleavage, as well as how these previously distinct pathways can overlap and lead to even more unique repair outcomes.
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Affiliation(s)
- Kevin Bloh
- Gene Editing Institute, Helen F. Graham Cancer Center & Research Institute, ChristianaCare, 4701 Ogletown-Stanton Road, Newark, DE 19710, USA;
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19710, USA
| | - Natalia Rivera-Torres
- Gene Editing Institute, Helen F. Graham Cancer Center & Research Institute, ChristianaCare, 4701 Ogletown-Stanton Road, Newark, DE 19710, USA;
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21
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Mitochondrial genome stability in human: understanding the role of DNA repair pathways. Biochem J 2021; 478:1179-1197. [DOI: 10.1042/bcj20200920] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 11/17/2022]
Abstract
Mitochondria are semiautonomous organelles in eukaryotic cells and possess their own genome that replicates independently. Mitochondria play a major role in oxidative phosphorylation due to which its genome is frequently exposed to oxidative stress. Factors including ionizing radiation, radiomimetic drugs and replication fork stalling can also result in different types of mutations in mitochondrial DNA (mtDNA) leading to genome fragility. Mitochondria from myopathies, dystonia, cancer patient samples show frequent mtDNA mutations such as point mutations, insertions and large-scale deletions that could account for mitochondria-associated disease pathogenesis. The mechanism by which such mutations arise following exposure to various DNA-damaging agents is not well understood. One of the well-studied repair pathways in mitochondria is base excision repair. Other repair pathways such as mismatch repair, homologous recombination and microhomology-mediated end joining have also been reported. Interestingly, nucleotide excision repair and classical nonhomologous DNA end joining are not detected in mitochondria. In this review, we summarize the potential causes of mitochondrial genome fragility, their implications as well as various DNA repair pathways that operate in mitochondria.
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22
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Super-resolution mapping of cellular double-strand break resection complexes during homologous recombination. Proc Natl Acad Sci U S A 2021; 118:2021963118. [PMID: 33707212 PMCID: PMC7980414 DOI: 10.1073/pnas.2021963118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Homologous recombination (HR) is a major pathway for repair of DNA double-strand breaks (DSBs). The initial step that drives the HR process is resection of DNA at the DSB, during which a multitude of nucleases, mediators, and signaling proteins accumulates at the damage foci in a manner that remains elusive. Using single-molecule localization super-resolution (SR) imaging assays, we specifically visualize the spatiotemporal behavior of key mediator and nuclease proteins as they resect DNA at single-ended double-strand breaks (seDSBs) formed at collapsed replication forks. By characterizing these associations, we reveal the in vivo dynamics of resection complexes involved in generating the long single-stranded DNA (ssDNA) overhang prior to homology search. We show that 53BP1, a protein known to antagonize HR, is recruited to seDSB foci during early resection but is spatially separated from repair activities. Contemporaneously, CtBP-interacting protein (CtIP) and MRN (MRE11-RAD51-NBS1) associate with seDSBs, interacting with each other and BRCA1. The HR nucleases EXO1 and DNA2 are also recruited and colocalize with each other and with the repair helicase Bloom syndrome protein (BLM), demonstrating multiple simultaneous resection events. Quantification of replication protein A (RPA) accumulation and ssDNA generation shows that resection is completed 2 to 4 h after break induction. However, both BRCA1 and BLM persist later into HR, demonstrating potential roles in homology search and repair resolution. Furthermore, we show that initial recruitment of BRCA1 and removal of Ku are largely independent of MRE11 exonuclease activity but dependent on MRE11 endonuclease activity. Combined, our observations provide a detailed description of resection during HR repair.
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23
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Misova I, Pitelova A, Budis J, Gazdarica J, Sedlackova T, Jordakova A, Benko Z, Smondrkova M, Mayerova N, Pichlerova K, Strieskova L, Prevorovsky M, Gregan J, Cipak L, Szemes T, Polakova SB. Repression of a large number of genes requires interplay between homologous recombination and HIRA. Nucleic Acids Res 2021; 49:1914-1934. [PMID: 33511417 PMCID: PMC7913671 DOI: 10.1093/nar/gkab027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 01/06/2021] [Accepted: 01/09/2021] [Indexed: 12/13/2022] Open
Abstract
During homologous recombination, Dbl2 protein is required for localisation of Fbh1, an F-box helicase that efficiently dismantles Rad51-DNA filaments. RNA-seq analysis of dbl2Δ transcriptome showed that the dbl2 deletion results in upregulation of more than 500 loci in Schizosaccharomyces pombe. Compared with the loci with no change in expression, the misregulated loci in dbl2Δ are closer to long terminal and long tandem repeats. Furthermore, the misregulated loci overlap with antisense transcripts, retrotransposons, meiotic genes and genes located in subtelomeric regions. A comparison of the expression profiles revealed that Dbl2 represses the same type of genes as the HIRA histone chaperone complex. Although dbl2 deletion does not alleviate centromeric or telomeric silencing, it suppresses the silencing defect at the outer centromere caused by deletion of hip1 and slm9 genes encoding subunits of the HIRA complex. Moreover, our analyses revealed that cells lacking dbl2 show a slight increase of nucleosomes at transcription start sites and increased levels of methylated histone H3 (H3K9me2) at centromeres, subtelomeres, rDNA regions and long terminal repeats. Finally, we show that other proteins involved in homologous recombination, such as Fbh1, Rad51, Mus81 and Rad54, participate in the same gene repression pathway.
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Affiliation(s)
- Ivana Misova
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
| | - Alexandra Pitelova
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
| | - Jaroslav Budis
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Geneton Ltd., 841 04 Bratislava, Slovakia
- Slovak Centre of Scientific and Technical Information, 811 04 Bratislava, Slovakia
| | - Juraj Gazdarica
- Geneton Ltd., 841 04 Bratislava, Slovakia
- Slovak Centre of Scientific and Technical Information, 811 04 Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
| | - Tatiana Sedlackova
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Geneton Ltd., 841 04 Bratislava, Slovakia
| | - Anna Jordakova
- Department of Cell Biology, Faculty of Science, Charles University, 128 00 Praha 2, Czechia
| | - Zsigmond Benko
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
- Department of Molecular Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, H-4010 Debrecen, Hungary
| | - Maria Smondrkova
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
| | - Nina Mayerova
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
| | - Karoline Pichlerova
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
| | - Lucia Strieskova
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Geneton Ltd., 841 04 Bratislava, Slovakia
| | - Martin Prevorovsky
- Department of Cell Biology, Faculty of Science, Charles University, 128 00 Praha 2, Czechia
| | - Juraj Gregan
- Advanced Microscopy Facility, VBCF and Department of Chromosome Biology, Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Lubos Cipak
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
| | - Tomas Szemes
- Comenius University Science Park, 841 04 Bratislava, Slovakia
- Geneton Ltd., 841 04 Bratislava, Slovakia
- Slovak Centre of Scientific and Technical Information, 811 04 Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
| | - Silvia Bagelova Polakova
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, 841 04 Bratislava, Slovakia
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24
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Yasuda T, Takizawa K, Ui A, Hama M, Kagawa W, Sugasawa K, Tajima K. Human SIRT2 and SIRT3 deacetylases function in DNA homologous recombinational repair. Genes Cells 2021; 26:328-335. [PMID: 33624391 DOI: 10.1111/gtc.12842] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 02/04/2021] [Accepted: 02/19/2021] [Indexed: 12/14/2022]
Abstract
SIRT2 and SIRT3 protein deacetylases maintain genome integrity and stability. However, their mechanisms for maintaining the genome remain unclear. To examine the roles of SIRT2 and SIRT3 in DSB repair, I-SceI-based GFP reporter assays for HR, single-strand annealing (SSA) and nonhomologous end joining (NHEJ) repair were performed under SIRT2- or SIRT3-depleted conditions. SIRT2 or SIRT3 depletion inhibited HR repair equally to RAD52 depletion, but did not affect SSA and NHEJ repairs. SIRT2 or SIRT3 depletion disturbed the recruitment of RAD51 to DSB sites, an essential step for RAD51-dependent HR repair, but not directly through RAD52 deacetylation. SIRT2 or SIRT3 depletion decreased the colocalization of γH2AX foci with RPA1, and thus, they might be involved in initiating DSB end resection for the recruitment of RAD51 to DSB sites at an early step in HR repair. These results show the novel underlying mechanism of the SIRT2 and SIRT3 functions in HR for genome stability.
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Affiliation(s)
- Takeshi Yasuda
- National Institute of Radiological Sciences (NIRS), National Institutes for Quantum and Radiological Sciences and Technology (QST), Chiba, Japan
| | - Kazuya Takizawa
- National Institute of Radiological Sciences (NIRS), National Institutes for Quantum and Radiological Sciences and Technology (QST), Chiba, Japan
| | - Ayako Ui
- Department of Molecular Oncology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.,Division of Dynamic Proteome in Cancer and Aging, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Michio Hama
- National Institute of Radiological Sciences (NIRS), National Institutes for Quantum and Radiological Sciences and Technology (QST), Chiba, Japan
| | - Wataru Kagawa
- Program in Chemistry and Life Science, Department of Interdisciplinary Science and Engineering, School of Science and Engineering, Meisei University, Hino, Japan
| | - Kaoru Sugasawa
- Biosignal Research Center, and Graduate School of Science, Kobe University, Kobe, Japan
| | - Katsushi Tajima
- National Institute of Radiological Sciences (NIRS), National Institutes for Quantum and Radiological Sciences and Technology (QST), Chiba, Japan
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25
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Janysek DC, Kim J, Duijf PHG, Dray E. Clinical use and mechanisms of resistance for PARP inhibitors in homologous recombination-deficient cancers. Transl Oncol 2021; 14:101012. [PMID: 33516088 PMCID: PMC7847957 DOI: 10.1016/j.tranon.2021.101012] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/14/2020] [Accepted: 12/31/2020] [Indexed: 12/11/2022] Open
Abstract
Cells are continuously subjected to DNA damaging agents. DNA damages are repaired by one of the many pathways guarding genomic integrity. When one or several DNA damage pathways are rendered inefficient, cells can accumulate mutations, which modify normal cellular pathways, favoring abnormal cell growth. This supports malignant transformation, which can occur when cells acquire resistance to cell cycle checkpoints, apoptosis, or growth inhibition signals. Mutations in genes involved in the repair of DNA double strand breaks (DSBs), such as BRCA1, BRCA2, or PALB2, significantly increase the risk of developing cancer of the breast, ovaries, pancreas, or prostate. Fortunately, the inability of these tumors to repair DNA breaks makes them sensitive to genotoxic chemotherapies, allowing for the development of therapies precisely tailored to individuals' genetic backgrounds. Unfortunately, as with many anti-cancer agents, drugs used to treat patients carrying a BRCA1 or BRCA2 mutation create a selective pressure, and over time tumors can become drug resistant. Here, we detail the cellular function of tumor suppressors essential in DNA damage repair pathways, present the mechanisms of action of inhibitors used to create synthetic lethality in BRCA carriers, and review the major molecular sources of drug resistance. Finally, we present examples of the many strategies being developed to circumvent drug resistance.
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Affiliation(s)
- Dawn C Janysek
- School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Jennifer Kim
- School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Pascal H G Duijf
- Queensland University of Technology, IHBI at the Translational Research Institute, Brisbane, QLD, Australia; Centre for Data Science, Queensland University of Technology, Brisbane, QLD, Australia; University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Eloïse Dray
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States; Mays Cancer Center, UT Health San Antonio MD Anderson, San Antonio, TX, United States.
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26
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Inhibitors of DNA double-strand break repair at the crossroads of cancer therapy and genome editing. Biochem Pharmacol 2020; 182:114195. [DOI: 10.1016/j.bcp.2020.114195] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 08/03/2020] [Accepted: 08/10/2020] [Indexed: 12/17/2022]
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27
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Genome-wide profiling of BK polyomavirus integration in bladder cancer of kidney transplant recipients reveals mechanisms of the integration at the nucleotide level. Oncogene 2020; 40:46-54. [PMID: 33051598 DOI: 10.1038/s41388-020-01502-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 09/21/2020] [Accepted: 09/30/2020] [Indexed: 11/08/2022]
Abstract
Chronic BK polyomavirus (BKPyV) infection is recognized as a potential oncogenic factor of urothelial carcinoma (UC) in renal transplant recipients. Recent studies have reported a positive correlation among BKPyV integration, persistent overexpression of viral large T antigen (TAg), and malignancy, yet little is known about the specific integration mechanisms and the impacts of viral integration. Here, we performed whole-genome sequencing (WGS) and viral capture-based sequencing on high-grade immunohistochemically TAg-positive UCs in two renal transplant recipients. A total of 181 integration sites, including the three found by WGS, were identified by viral capture-based sequencing, indicating its enhanced sensitivity and ability in identifying low-read integration sites in subpopulations of the tumor cells. The microhomologies between human and BKPyV genomes were significantly enriched in the flanking regions of 84.5% the integration sites, with a median length of 7 bp. Notably, 75 human genes formed fusion sequences due to viral insertional integration. Among them, the expression of 15 genes were statistically associated with UC based on GEO2R expression analysis. Our results indicated a multisite and multifragment linear integration pattern and a potential microhomology or nonhomologous end joining integration mechanism at the single-nucleotide level. We put forward a potential selection mechanism driven by immunity and centered on viral integration in the carcinogenesis of BKPyV.
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28
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Komari CJ, Guttman AO, Carr SR, Trachtenberg TL, Orloff EA, Haas AV, Patrick AR, Chowdhary S, Waldman BC, Waldman AS. Alteration of genetic recombination and double-strand break repair in human cells by progerin expression. DNA Repair (Amst) 2020; 96:102975. [PMID: 33010688 DOI: 10.1016/j.dnarep.2020.102975] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/21/2020] [Accepted: 09/04/2020] [Indexed: 01/04/2023]
Abstract
Hutchinson-Gilford Progeria Syndrome (HGPS) is a rare autosomal, dominant genetic condition characterized by many features of accelerated aging. On average, children with HGPS live to about fourteen years of age. The syndrome is commonly caused by a point mutation in the LMNA gene which normally codes for lamin A and its splice variant lamin C, components of the nuclear lamina. The LMNA mutation alters splicing, leading to production of a truncated, farnesylated form of lamin A referred to as "progerin." Progerin is also expressed at very low levels in healthy individuals and appears to play a role in normal aging. HGPS is associated with an accumulation of genomic DNA double-strand breaks (DSBs), suggesting corruption of DNA repair. In this work, we investigated the influence of progerin expression on DSB repair in the human genome at the nucleotide level. We used a model system that involves a reporter DNA substrate inserted in the genome of cultured human cells. A DSB could be induced within the substrate through exogenous expression of endonuclease I-SceI, and DSB repair events occurring via either homologous recombination (HR) or nonhomologous end-joining (NHEJ) were recoverable. Additionally, spontaneous HR events were recoverable in the absence of artificial DSB induction. We compared DSB repair and spontaneous HR in cells overexpressing progerin versus cells expressing no progerin. We report that overexpression of progerin correlated with an increase in DSB repair via NHEJ relative to HR, as well as an increased fraction of HR events occurring via gene conversion. Progerin also engendered an apparent increase in spontaneous HR events, with a highly significant shift toward gene conversion events, and an increase in DNA amplification events. Such influences of progerin on DNA transactions may impact genome stability and contribute to aging.
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Affiliation(s)
- Celina J Komari
- Department of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Anne O Guttman
- Department of Exercise Science, University of South Carolina, Columbia, SC 29208, USA
| | - Shelby R Carr
- Department of Exercise Science, University of South Carolina, Columbia, SC 29208, USA
| | - Taylor L Trachtenberg
- Department of Exercise Science, University of South Carolina, Columbia, SC 29208, USA
| | - Elise A Orloff
- Department of Exercise Science, University of South Carolina, Columbia, SC 29208, USA
| | - Ashley V Haas
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Andrew R Patrick
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Sona Chowdhary
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Barbara C Waldman
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Alan S Waldman
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.
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29
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Mechanism and significance of chromosome damage repair by homologous recombination. Essays Biochem 2020; 64:779-790. [DOI: 10.1042/ebc20190093] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/22/2020] [Accepted: 06/29/2020] [Indexed: 12/29/2022]
Abstract
Abstract
Homologous recombination (HR) is a major, conserved pathway of chromosome damage repair. It not only fulfills key functions in the removal of deleterious lesions such as DNA double-strand breaks (DSBs) and interstrand cross-links (ICLs), but also in replication fork repair and protection. Several familial and acquired cancer predisposition syndromes stem from defects in HR. In particular, individuals with mutations in HR genes exhibit predisposition to breast, ovarian, pancreatic, and prostate cancers, and they also show signs of accelerated aging. However, aberrant and untimely HR events can lead to the loss of heterozygosity, genomic rearrangements, and cytotoxic nucleoprotein intermediates. Thus, it is critically important that HR be tightly regulated. In addition to DNA repair, HR is also involved in meiotic chromosome segregation and telomere maintenance in cells that lack telomerase. In this review, we focus on the role of HR in DSB repair (DSBR) and summarize the current state of the field.
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30
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Challenges of in vitro genome editing with CRISPR/Cas9 and possible solutions: A review. Gene 2020; 753:144813. [DOI: 10.1016/j.gene.2020.144813] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 04/26/2020] [Accepted: 05/23/2020] [Indexed: 12/20/2022]
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31
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Rommel Fuentes R, Hesselink T, Nieuwenhuis R, Bakker L, Schijlen E, van Dooijeweert W, Diaz Trivino S, de Haan JR, Sanchez Perez G, Zhang X, Fransz P, de Jong H, van Dijk ADJ, de Ridder D, Peters SA. Meiotic recombination profiling of interspecific hybrid F1 tomato pollen by linked read sequencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:480-492. [PMID: 31820490 DOI: 10.1111/tpj.14640] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/25/2019] [Accepted: 12/04/2019] [Indexed: 06/10/2023]
Abstract
Genome wide screening of pooled pollen samples from a single interspecific F1 hybrid obtained from a cross between tomato, Solanum lycopersicum and its wild relative, Solanum pimpinellifolium using linked read sequencing of the haploid nuclei, allowed profiling of the crossover (CO) and gene conversion (GC) landscape. We observed a striking overlap between cold regions of CO in the male gametes and our previously established F6 recombinant inbred lines (RILs) population. COs were overrepresented in non-coding regions in the gene promoter and 5'UTR regions of genes. Poly-A/T and AT rich motifs were found enriched in 1 kb promoter regions flanking the CO sites. Non-crossover associated allelic and ectopic GCs were detected in most chromosomes, confirming that besides CO, GC represents also a source for genetic diversity and genome plasticity in tomato. Furthermore, we identified processed break junctions pointing at the involvement of both homology directed and non-homology directed repair pathways, suggesting a recombination machinery in tomato that is more complex than currently anticipated.
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Affiliation(s)
- Roven Rommel Fuentes
- Bioinformatics Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Thamara Hesselink
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Ronald Nieuwenhuis
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Linda Bakker
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Elio Schijlen
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Willem van Dooijeweert
- Centre for Genetic Resources, Wageningen University and Research, Wageningen, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Sara Diaz Trivino
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Jorn R de Haan
- Genetwister Technologies B.V., Nieuwe Kanaal 7b, 6709 PA, Wageningen, The Netherlands
| | - Gabino Sanchez Perez
- Genetwister Technologies B.V., Nieuwe Kanaal 7b, 6709 PA, Wageningen, The Netherlands
| | - Xinyue Zhang
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Paul Fransz
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Hans de Jong
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Aalt D J van Dijk
- Bioinformatics Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Biometris, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Sander A Peters
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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32
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Qian L, Soderquist C, Schrank‐Hacker A, Strauser H, Dupoux V, Tang CN, Smith JR, Sun A, Majumdar S, Nguyen T, Widura S, Landsburg DJ, Schuster SJ, Baxter RHG, Bogusz AM. Deletion 20q12 is associated with histological transformation of nodal marginal zone lymphoma to diffuse large B-cell lymphoma. Am J Hematol 2020; 95:238-244. [PMID: 31804739 DOI: 10.1002/ajh.25694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 11/26/2019] [Accepted: 11/29/2019] [Indexed: 11/06/2022]
Abstract
The genetic and molecular abnormalities underlying histological transformation (HT) of nodal marginal zone lymphoma (NMZL) to diffuse large B-cell lymphoma (DLBCL) are not well known. While del(20q12) is commonly deleted in myelodysplastic syndrome it has not previously been associated with DLBCL. We recently described a case of DLBCL harboring del(20q12) in a patient with a history of MZL involving lymph nodes and skin. Here we report eight matched cases of transformed MZL(tMZL): six from nodal MZL (tNMZL) and two from splenic MZL (tSMZL). We found >20% del(20q12) in 4/6 tNMZL, but not in tSMZL, nor in unmatched DLBCL, MZL with increased large cells (MZL-ILC), or MZL cases. To examine whether transformation is associated with a specific gene signature, the matched cases were analyzed for multiplexed gene expression using the Nanostring PanCancer Pathways panel. The differential gene expression signature revealed enrichment of inflammatory markers, as previously observed in MZL. Also, tMZL and de novo DLBCL were enriched for extracellular matrix proteins such as collagen and fibronectin, vascular development protein PDGFRβ, DNA repair protein RAD51, and oncogenic secrete protein Wnt11. A subset of genes is expressed differentially in del(20q12) tMZL cases vs non-del(20q12) tMZL cases. These results suggest a specific pathway is involved in the histological transformation of NMZL, which could serve as an indicator of aggressive clinical course in this otherwise indolent neoplasm.
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Affiliation(s)
- Lei Qian
- Department of Medical Genetics & Molecular Biochemistry, Lewis Katz School of MedicineTemple University Philadelphia Pennsylvania
| | - Craig Soderquist
- Department of Pathology and Cell BiologyColumbia University Medical Center New York Pennsylvania
| | - April Schrank‐Hacker
- Department of Pathology and Laboratory MedicineHospital of the University of Pennsylvania Philadelphia Pennsylvania
| | - Honore Strauser
- Department of Pathology and Laboratory MedicineHospital of the University of Pennsylvania Philadelphia Pennsylvania
| | - Vanessa Dupoux
- Department of Pathology and Laboratory MedicineHospital of the University of Pennsylvania Philadelphia Pennsylvania
| | - Chi Ngong Tang
- Department of Pathology and Laboratory MedicineHospital of the University of Pennsylvania Philadelphia Pennsylvania
| | - Jennifer R. Smith
- Department of Pathology and Laboratory MedicineHospital of the University of Pennsylvania Philadelphia Pennsylvania
| | - Ang Sun
- Department of BiologyTemple University Philadelphia Pennsylvania
| | - Sonali Majumdar
- Wistar Genomics Shared ResourceThe Wistar Institute Philadelphia Pennsylvania
| | - Tran Nguyen
- Wistar Genomics Shared ResourceThe Wistar Institute Philadelphia Pennsylvania
| | - Sandy Widura
- Wistar Genomics Shared ResourceThe Wistar Institute Philadelphia Pennsylvania
| | - Daniel J. Landsburg
- Department of Medicine, Perelman School of MedicineUniversity of Pennsylvania Philadelphia Pennsylvania
- Lymphoma Program, Abramson Cancer CenterUniversity of Pennsylvania Philadelphia Pennsylvania
| | - Stephen J. Schuster
- Department of Medicine, Perelman School of MedicineUniversity of Pennsylvania Philadelphia Pennsylvania
- Lymphoma Program, Abramson Cancer CenterUniversity of Pennsylvania Philadelphia Pennsylvania
| | - Richard H. G. Baxter
- Department of Medical Genetics & Molecular Biochemistry, Lewis Katz School of MedicineTemple University Philadelphia Pennsylvania
| | - Agata M. Bogusz
- Department of Pathology and Laboratory MedicineHospital of the University of Pennsylvania Philadelphia Pennsylvania
- Lymphoma Program, Abramson Cancer CenterUniversity of Pennsylvania Philadelphia Pennsylvania
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33
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March OP, Kocher T, Koller U. Context-Dependent Strategies for Enhanced Genome Editing of Genodermatoses. Cells 2020; 9:E112. [PMID: 31906492 PMCID: PMC7016731 DOI: 10.3390/cells9010112] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/27/2019] [Accepted: 12/31/2019] [Indexed: 12/17/2022] Open
Abstract
The skin provides direct protection to the human body from assault by the harsh external environment. The crucial function of this organ is significantly disrupted in genodermatoses patients. Genodermatoses comprise a heterogeneous group of largely monogenetic skin disorders, typically involving mutations in genes encoding structural proteins. Therapeutic options for this debilitating group of diseases, including epidermolysis bullosa, primarily consist of wound management. Genome editing approaches co-opt double-strand break repair pathways to introduce desired sequence alterations at specific loci. Rapid advances in genome editing technologies have the potential to propel novel genetic therapies into the clinic. However, the associated phenotypes of many mutations may be treated via several genome editing strategies. Therefore, for potential clinical applications, implementation of efficient approaches based upon mutation, gene and disease context is necessary. Here, we describe current genome editing approaches for the treatment of genodermatoses, along with a discussion of the optimal strategy for each genetic context, in order to achieve enhanced genome editing approaches.
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Affiliation(s)
| | | | - Ulrich Koller
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, 5020 Salzburg, Austria; (O.P.M.); (T.K.)
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34
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Watson JF, García-Nafría J. In vivo DNA assembly using common laboratory bacteria: A re-emerging tool to simplify molecular cloning. J Biol Chem 2019; 294:15271-15281. [PMID: 31522138 DOI: 10.1074/jbc.rev119.009109] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Molecular cloning is a cornerstone of biomedical, biotechnological, and synthetic biology research. As such, improved cloning methodologies can significantly advance the speed and cost of research projects. Whereas current popular cloning approaches use in vitro assembly of DNA fragments, in vivo cloning offers potential for greater simplification. It is generally assumed that bacterial in vivo cloning requires Escherichia coli strains with enhanced recombination ability; however, this is incorrect. A widely present, bacterial RecA-independent recombination pathway is re-emerging as a powerful tool for molecular cloning and DNA assembly. This poorly understood pathway offers optimal cloning properties (i.e. seamless, directional, and sequence-independent) without requiring in vitro DNA assembly or specialized bacteria, therefore vastly simplifying cloning procedures. Although the use of this pathway to perform DNA assembly was first reported over 25 years ago, it failed to gain popularity, possibly due to both technical and circumstantial reasons. Technical limitations have now been overcome, and recent reports have demonstrated its versatility for DNA manipulation. Here, we summarize the historical trajectory of this approach and collate recent reports to provide a roadmap for its optimal use. Given the simplified protocols and minimal requirements, cloning using in vivo DNA assembly in E. coli has the potential to become widely employed across the molecular biology community.
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Affiliation(s)
- Jake F Watson
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Javier García-Nafría
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, BIFI-IQFR (CSIC), 50018 Zaragoza, Spain
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35
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Uemura M, Ochiai K, Morimatsu M, Michishita M, Onozawa E, Azakami D, Uno Y, Yoshikawa Y, Sasaki T, Watanabe M, Omi T. The canine RAD51 mutation leads to the attenuation of interaction with PALB2. Vet Comp Oncol 2019; 18:247-255. [PMID: 31518051 DOI: 10.1111/vco.12542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/05/2019] [Accepted: 09/05/2019] [Indexed: 12/19/2022]
Abstract
RAD51 forms a complex with BRCA2 and plays a central role in the DNA damage response pathway that is associated with homologous recombination. The structures of RAD51 and its homologues are highly conserved from prokaryotes to higher eukaryotes. Although a large number of BRCA2 mutations have been reported, there are only a few reports on the mutations of RAD51, which have been shown in humans and dogs. However, several mutations of canine RAD51 were identified from mammary gland tumour tissues in a recent study. Some of these mutations seem to have an influence on the homo-oligomerization or interaction with "Partner and localizer of BRCA2" (PALB2). In this study, we cloned the canine PALB2 homologue and investigated the effect on its interaction with the RAD51 mutants to evaluate the alteration in the function of RAD51 mutants. The A209S and T225S mutants of RAD51 show an attenuation of the interaction between RAD51 and PALB2. These results indicate that the canine RAD51 mutations can potentially alter the homologous recombination pathways in response to DNA damage in dogs.
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Affiliation(s)
- Mitsuki Uemura
- School of Veterinary Nursing and Technology, Faculty of Veterinary Science, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Kazuhiko Ochiai
- School of Veterinary Nursing and Technology, Faculty of Veterinary Science, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Masami Morimatsu
- Laboratory of Laboratory Animal Science and Medicine, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Masaki Michishita
- Department of Veterinary Pathology, Faculty of Veterinary Science, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Eri Onozawa
- School of Veterinary Nursing and Technology, Faculty of Veterinary Science, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Daigo Azakami
- Laboratory of Veterinary Clinical Oncology, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Yumiko Uno
- School of Veterinary Nursing and Technology, Faculty of Veterinary Science, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Yasunaga Yoshikawa
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Kitasato University, Aomori, Japan
| | - Takanori Sasaki
- Department of Urology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Masami Watanabe
- Department of Urology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Toshinori Omi
- School of Veterinary Nursing and Technology, Faculty of Veterinary Science, Nippon Veterinary and Life Science University, Tokyo, Japan
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36
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Imrichova T, Hubackova S, Kucerova A, Kosla J, Bartek J, Hodny Z, Vasicova P. Dynamic PML protein nucleolar associations with persistent DNA damage lesions in response to nucleolar stress and senescence-inducing stimuli. Aging (Albany NY) 2019; 11:7206-7235. [PMID: 31493766 PMCID: PMC6756913 DOI: 10.18632/aging.102248] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 08/22/2019] [Indexed: 04/10/2023]
Abstract
Diverse stress insults trigger interactions of PML with nucleolus, however, the function of these PML nucleolar associations (PNAs) remains unclear. Here we show that during induction of DNA damage-induced senescence in human non-cancerous cells, PML accumulates at the nucleolar periphery simultaneously with inactivation of RNA polymerase I (RNAP I) and nucleolar segregation. Using time-lapse and high-resolution microscopy, we followed the genesis, structural transitions and destiny of PNAs to show that: 1) the dynamic structural changes of the PML-nucleolar interaction are tightly associated with inactivation and reactivation of RNAP I-mediated transcription, respectively; 2) the PML-nucleolar compartment develops sequentially under stress and, upon stress termination, it culminates in either of two fates: disappearance or persistence; 3) all PNAs stages can associate with DNA damage markers; 4) the persistent, commonly long-lasting PML multi-protein nucleolar structures (PML-NDS) associate with markers of DNA damage, indicating a role of PNAs in persistent DNA damage response characteristic for senescent cells. Given the emerging evidence implicating PML in homologous recombination-directed DNA repair, we propose that PNAs contribute to sequestration and faithful repair of the highly unstable ribosomal DNA repeats, a fundamental process to maintain a precise balance between DNA repair mechanisms, with implications for genomic integrity and aging.
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Affiliation(s)
- Terezie Imrichova
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Sona Hubackova
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Present address: Institute of Biotechnology, Czech Academy of Sciences, Prague-West, Czech Republic
| | - Alena Kucerova
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Kosla
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiri Bartek
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Genome Integrity Unit, Danish Cancer Society Research Center, Copenhagen, Denmark
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Zdenek Hodny
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Pavla Vasicova
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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37
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Steinfeld JB, Beláň O, Kwon Y, Terakawa T, Al-Zain A, Smith MJ, Crickard JB, Qi Z, Zhao W, Rothstein R, Symington LS, Sung P, Boulton SJ, Greene EC. Defining the influence of Rad51 and Dmc1 lineage-specific amino acids on genetic recombination. Genes Dev 2019; 33:1191-1207. [PMID: 31371435 PMCID: PMC6719624 DOI: 10.1101/gad.328062.119] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/01/2019] [Indexed: 02/06/2023]
Abstract
The vast majority of eukaryotes possess two DNA recombinases: Rad51, which is ubiquitously expressed, and Dmc1, which is meiosis-specific. The evolutionary origins of this two-recombinase system remain poorly understood. Interestingly, Dmc1 can stabilize mismatch-containing base triplets, whereas Rad51 cannot. Here, we demonstrate that this difference can be attributed to three amino acids conserved only within the Dmc1 lineage of the Rad51/RecA family. Chimeric Rad51 mutants harboring Dmc1-specific amino acids gain the ability to stabilize heteroduplex DNA joints with mismatch-containing base triplets, whereas Dmc1 mutants with Rad51-specific amino acids lose this ability. Remarkably, RAD-51 from Caenorhabditis elegans, an organism without Dmc1, has acquired "Dmc1-like" amino acids. Chimeric C. elegans RAD-51 harboring "canonical" Rad51 amino acids gives rise to toxic recombination intermediates, which must be actively dismantled to permit normal meiotic progression. We propose that Dmc1 lineage-specific amino acids involved in the stabilization of heteroduplex DNA joints with mismatch-containing base triplets may contribute to normal meiotic recombination.
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Affiliation(s)
- Justin B Steinfeld
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Ondrej Beláň
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Youngho Kwon
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Tsuyoshi Terakawa
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Amr Al-Zain
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Michael J Smith
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - J Brooks Crickard
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Zhi Qi
- Center for Quantitative Biology, Peking University-Tsinghua University Joint Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Weixing Zhao
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Rodney Rothstein
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Lorraine S Symington
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Simon J Boulton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, New York 10032, USA
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38
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Maizels N, Davis L. Initiation of homologous recombination at DNA nicks. Nucleic Acids Res 2019; 46:6962-6973. [PMID: 29986051 PMCID: PMC6101574 DOI: 10.1093/nar/gky588] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/04/2018] [Indexed: 12/14/2022] Open
Abstract
Discontinuities in only a single strand of the DNA duplex occur frequently, as a result of DNA damage or as intermediates in essential nuclear processes and DNA repair. Nicks are the simplest of these lesions: they carry clean ends bearing 3′-hydroxyl groups that can undergo ligation or prime new DNA synthesis. In contrast, single-strand breaks also interrupt only one DNA strand, but they carry damaged ends that require clean-up before subsequent steps in repair. Despite their apparent simplicity, nicks can have significant consequences for genome stability. The availability of enzymes that can introduce a nick almost anywhere in a large genome now makes it possible to systematically analyze repair of nicks. Recent experiments demonstrate that nicks can initiate recombination via pathways distinct from those active at double-strand breaks (DSBs). Recombination at targeted DNA nicks can be very efficient, and because nicks are intrinsically less mutagenic than DSBs, nick-initiated gene correction is useful for genome engineering and gene therapy. This review revisits some physiological examples of recombination at nicks, and outlines experiments that have demonstrated that nicks initiate homology-directed repair by distinctive pathways, emphasizing research that has contributed to our current mechanistic understanding of recombination at nicks in mammalian cells.
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Affiliation(s)
- Nancy Maizels
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98195, USA.,Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Luther Davis
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98195, USA
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39
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Olson HC, Davis L, Kiianitsa K, Khoo KJ, Liu Y, Knijnenburg TA, Maizels N. Increased levels of RECQ5 shift DNA repair from canonical to alternative pathways. Nucleic Acids Res 2019; 46:9496-9509. [PMID: 30107528 PMCID: PMC6182128 DOI: 10.1093/nar/gky727] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 08/02/2018] [Indexed: 12/11/2022] Open
Abstract
RECQ5 (RECQL5) is one of several human helicases that dissociates RAD51-DNA filaments. The gene that encodes RECQ5 is frequently amplified in human tumors, but it is not known whether amplification correlates with increased gene expression, or how increased RECQ5 levels affect DNA repair at nicks and double-strand breaks. Here, we address these questions. We show that RECQ5 gene amplification correlates with increased gene expression in human tumors, by in silico analysis of over 9000 individual tumors representing 32 tumor types in the TCGA dataset. We demonstrate that, at double-strand breaks, increased RECQ5 levels inhibited canonical homology-directed repair (HDR) by double-stranded DNA donors, phenocopying the effect of BRCA deficiency. Conversely, at nicks, increased RECQ5 levels stimulated 'alternative' HDR by single-stranded DNA donors, which is normally suppressed by RAD51; this was accompanied by stimulation of mutagenic end-joining. Even modest changes (2-fold) in RECQ5 levels caused significant dysregulation of repair, especially HDR. These results suggest that in some tumors, RECQ5 gene amplification may have profound consequences for genomic instability.
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Affiliation(s)
- Henry C Olson
- Department of Biochemistry, University of Washington, 1959 NE Pacific St., Seattle, WA 98195, USA
| | - Luther Davis
- Department of Immunology, University of Washington, 1959 NE Pacific St., Seattle, WA 98195, USA
| | - Kostantin Kiianitsa
- Department of Immunology, University of Washington, 1959 NE Pacific St., Seattle, WA 98195, USA
| | - Kevin J Khoo
- Department of Biochemistry, University of Washington, 1959 NE Pacific St., Seattle, WA 98195, USA.,Department of Immunology, University of Washington, 1959 NE Pacific St., Seattle, WA 98195, USA
| | - Yilun Liu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Theo A Knijnenburg
- Institute for Systems Biology, 401 Terry Ave. N., Seattle, WA 98109, USA
| | - Nancy Maizels
- Department of Biochemistry, University of Washington, 1959 NE Pacific St., Seattle, WA 98195, USA.,Department of Immunology, University of Washington, 1959 NE Pacific St., Seattle, WA 98195, USA
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40
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Crickard J, Xue C, Wang W, Kwon Y, Sung P, Greene E. The RecQ helicase Sgs1 drives ATP-dependent disruption of Rad51 filaments. Nucleic Acids Res 2019; 47:4694-4706. [PMID: 30916344 PMCID: PMC6511845 DOI: 10.1093/nar/gkz186] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/06/2019] [Accepted: 03/20/2019] [Indexed: 12/21/2022] Open
Abstract
DNA helicases of the RecQ family are conserved among the three domains of life and play essential roles in genome maintenance. Mutations in several human RecQ helicases lead to diseases that are marked by cancer predisposition. The Saccharomyces cerevisiae RecQ helicase Sgs1 is orthologous to human BLM, defects in which cause the cancer-prone Bloom's Syndrome. Here, we use single-molecule imaging to provide a quantitative mechanistic understanding of Sgs1 activities on single stranded DNA (ssDNA), which is a central intermediate in all aspects of DNA metabolism. We show that Sgs1 acts upon ssDNA bound by either replication protein A (RPA) or the recombinase Rad51. Surprisingly, we find that Sgs1 utilizes a novel motor mechanism for disrupting ssDNA intermediates bound by the recombinase protein Rad51. The ability of Sgs1 to disrupt Rad51-ssDNA filaments may explain some of the defects engendered by RECQ helicase deficiencies in human cells.
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Affiliation(s)
- J Brooks Crickard
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Chaoyou Xue
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Weibin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, TX 78229, USA
| | - Youngho Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, TX 78229, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, TX 78229, USA
| | - Eric C Greene
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
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41
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Hunt LJ, Ahmed EA, Kaur H, Ahuja JS, Hulme L, Chou TC, Lichten M, Goldman ASH. S. cerevisiae Srs2 helicase ensures normal recombination intermediate metabolism during meiosis and prevents accumulation of Rad51 aggregates. Chromosoma 2019; 128:249-265. [PMID: 31069484 PMCID: PMC6823294 DOI: 10.1007/s00412-019-00705-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/04/2019] [Accepted: 04/24/2019] [Indexed: 01/06/2023]
Abstract
We investigated the meiotic role of Srs2, a multi-functional DNA helicase/translocase that destabilises Rad51-DNA filaments and is thought to regulate strand invasion and prevent hyper-recombination during the mitotic cell cycle. We find that Srs2 activity is required for normal meiotic progression and spore viability. A significant fraction of srs2 mutant cells progress through both meiotic divisions without separating the bulk of their chromatin, although in such cells sister centromeres often separate. Undivided nuclei contain aggregates of Rad51 colocalised with the ssDNA-binding protein RPA, suggesting the presence of persistent single-strand DNA. Rad51 aggregate formation requires Spo11-induced DSBs, Rad51 strand-invasion activity and progression past the pachytene stage of meiosis, but not the DSB end-resection or the bias towards interhomologue strand invasion characteristic of normal meiosis. srs2 mutants also display altered meiotic recombination intermediate metabolism, revealed by defects in the formation of stable joint molecules. We suggest that Srs2, by limiting Rad51 accumulation on DNA, prevents the formation of aberrant recombination intermediates that otherwise would persist and interfere with normal chromosome segregation and nuclear division.
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Affiliation(s)
- Laura J Hunt
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, S10 2TN, UK.,Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK
| | - Emad A Ahmed
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, S10 2TN, UK.,Immunology and Molecular Physiology Lab., Zoology Department, Faculty of Science, Assiut University, Markaz El-Fath, 71515, Egypt
| | - Hardeep Kaur
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA.,Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, 78229, USA
| | - Jasvinder S Ahuja
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Lydia Hulme
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Ta-Chung Chou
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, S10 2TN, UK.,All First Tech Co., Ltd, 32467, No 146-2. Hung Chun Road, Ping Zhen Dist, Taoyuan City, Taiwan
| | - Michael Lichten
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Alastair S H Goldman
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, S10 2TN, UK. .,Faculty of Life Sciences, The University of Bradford, Bradford, BD7 1AZ, UK.
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42
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Zhao XC, Fu H, Song L, Yang YJ, Zhou EC, Liu GX, Chen XF, Li Z, Wu WQ, Zhang XH. S-DNA and RecA/RAD51-Mediated Strand Exchange in Vitro. Biochemistry 2019; 58:2009-2016. [PMID: 30900876 DOI: 10.1021/acs.biochem.8b01125] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
S-DNA (stretched DNA) is an elongated base-paired DNA conformation under high tension. Because the RecA/Rad51 family DNA recombinases form helical filaments on DNA and mediate the formation of the DNA triplex (D-loop), in which the DNA is stretched, and because the extension of these nucleoprotein filaments is similar to the extension of S-DNA, S-DNA has long been hypothesized as a possible state of DNA that participants in RecA/Rad51-mediated DNA strand exchange in homologous recombination. Such a hypothesis, however, is still lacking direct experimental studies. In this work, we have studied the polymerization and strand exchange on S-DNA mediated by Escherichia coli RecA, human Rad51, and Saccharomyces cerevisiae Rad51 by single-molecule magnetic tweezers. We report that RecA/Rad51 polymerizes faster on S-DNA than on B-DNA with the same buffer conditions. Furthermore, the RecA/Rad51-mediated DNA triplex forms faster from S-DNA than from B-DNA together with the homologous single-stranded DNA. These results provide evidence that S-DNA can interact with RecA and Rad51 and shed light on the possible functions of S-DNA.
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Affiliation(s)
- Xiao-Cong Zhao
- College of Life Sciences, The Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis , Wuhan University , Wuhan 430072 , China
| | - Hang Fu
- College of Life Sciences, The Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis , Wuhan University , Wuhan 430072 , China
| | - Lun Song
- College of Life Sciences, The Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis , Wuhan University , Wuhan 430072 , China
| | - Ya-Jun Yang
- College of Life Sciences, The Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis , Wuhan University , Wuhan 430072 , China
| | - Er-Chi Zhou
- College of Life Sciences, The Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis , Wuhan University , Wuhan 430072 , China
| | - Guang-Xue Liu
- College of Life Sciences, The Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis , Wuhan University , Wuhan 430072 , China
| | - Xue-Feng Chen
- College of Life Sciences, The Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis , Wuhan University , Wuhan 430072 , China
| | - Zhuo Li
- Third Institute of Oceanography , State Oceanic Administration , Xiamen 361005 , China
| | - Wen-Qiang Wu
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology , Henan University , Kaifeng 475001 , China
| | - Xing-Hua Zhang
- College of Life Sciences, The Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis , Wuhan University , Wuhan 430072 , China
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43
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Crickard JB, Greene EC. Helicase Mechanisms During Homologous Recombination in Saccharomyces cerevisiae. Annu Rev Biophys 2019; 48:255-273. [PMID: 30857400 DOI: 10.1146/annurev-biophys-052118-115418] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Helicases are enzymes that move, manage, and manipulate nucleic acids. They can be subdivided into six super families and are required for all aspects of nucleic acid metabolism. In general, all helicases function by converting the chemical energy stored in the bond between the gamma and beta phosphates of adenosine triphosphate into mechanical work, which results in the unidirectional movement of the helicase protein along one strand of a nucleic acid. The results of this translocation activity can range from separation of strands within duplex nucleic acids to the physical remodeling or removal of nucleoprotein complexes. In this review, we focus on describing key helicases from the model organism Saccharomyces cerevisiae that contribute to the regulation of homologous recombination, which is an essential DNA repair pathway for fixing damaged chromosomes.
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Affiliation(s)
- J Brooks Crickard
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; ,
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; ,
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44
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Crickard JB, Kwon Y, Sung P, Greene EC. Dynamic interactions of the homologous pairing 2 (Hop2)-meiotic nuclear divisions 1 (Mnd1) protein complex with meiotic presynaptic filaments in budding yeast. J Biol Chem 2019; 294:490-501. [PMID: 30420424 PMCID: PMC6333877 DOI: 10.1074/jbc.ra118.006146] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/02/2018] [Indexed: 12/19/2022] Open
Abstract
Homologous recombination (HR) is a universally conserved DNA repair pathway that can result in the exchange of genetic material. In eukaryotes, HR has evolved into an essential step in meiosis. During meiosis many eukaryotes utilize a two-recombinase pathway. This system consists of Rad51 and the meiosis-specific recombinase Dmc1. Both recombinases have distinct activities during meiotic HR, despite being highly similar in sequence and having closely related biochemical activities, raising the question of how these two proteins can perform separate functions. A likely explanation for their differential regulation involves the meiosis-specific recombination proteins Hop2 and Mnd1, which are part of a highly conserved eukaryotic protein complex that participates in HR, albeit through poorly understood mechanisms. To better understand how Hop2-Mnd1 functions during HR, here we used DNA curtains in conjunction with single-molecule imaging to measure and quantify the binding of the Hop2-Mnd1 complex from Saccharomyces cerevisiae to recombination intermediates comprising Rad51- and Dmc1-ssDNA in real time. We found that yeast Hop2-Mnd1 bound rapidly to Dmc1-ssDNA filaments with high affinity and remained bound for ∼1.3 min before dissociating. We also observed that this binding interaction was highly specific for Dmc1 and found no evidence for an association of Hop2-Mnd1 with Rad51-ssDNA or RPA-ssDNA. Our findings provide new quantitative insights into the binding dynamics of Hop2-Mnd1 with the meiotic presynaptic complex. On the basis of these findings, we propose a model in which recombinase specificities for meiotic accessory proteins enhance separation of the recombinases' functions during meiotic HR.
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Affiliation(s)
- J Brooks Crickard
- From the Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032
| | - Youngho Kwon
- the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, and
- the Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas 78229
| | - Patrick Sung
- the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, and
- the Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas 78229
| | - Eric C Greene
- From the Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032,
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45
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Andres SN, Li ZM, Erie DA, Williams RS. Ctp1 protein-DNA filaments promote DNA bridging and DNA double-strand break repair. J Biol Chem 2019; 294:3312-3320. [PMID: 30626735 DOI: 10.1074/jbc.ra118.006759] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/26/2018] [Indexed: 12/13/2022] Open
Abstract
The Ctp1 protein in Schizosaccharomyces pombe is essential for DNA double-strand break (DSB) repair by homologous recombination. Fission yeast Ctp1 and its budding yeast (Sae2) and human (CtIP) homologs control Mre11-Rad50-Nbs1 nuclease complex activity and harbor DNA-binding and -bridging activities. However, the molecular basis for Ctp1-DNA transactions remains undefined. Here, we report atomic force microscopy (AFM) imaging of S. pombe Ctp1-DNA complexes revealing that Ctp1 polymerizes on dsDNA molecules and forms synaptic filaments that bridge two dsDNA strands. We observed that Ctp1 DNA filaments are typified by an average filament length of ∼180 bp of dsDNA and a Ctp1 tetramer footprint of ∼15 bp. Biochemical results characterizing Ctp1 variants with impaired DNA-binding or -bridging properties were consistent with Ctp1-mediated DNA bridging requiring the intact and correctly folded Ctp1 tetramer. Furthermore, mutations altering Ctp1 oligomerization and DNA bridging in vitro conferred cell sensitivity to DSB-producing agents. Together, these results support an important role for Ctp1-regulated DNA strand coordination required for DNA DSB repair in S. pombe.
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Affiliation(s)
- Sara N Andres
- From the Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709
| | - Zimeng M Li
- the Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27695, and
| | - Dorothy A Erie
- the Department of Chemistry, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - R Scott Williams
- From the Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709,
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46
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Liu M, Rehman S, Tang X, Gu K, Fan Q, Chen D, Ma W. Methodologies for Improving HDR Efficiency. Front Genet 2019; 9:691. [PMID: 30687381 PMCID: PMC6338032 DOI: 10.3389/fgene.2018.00691] [Citation(s) in RCA: 170] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 12/11/2018] [Indexed: 12/26/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) is a precise genome manipulating technology that can be programmed to induce double-strand break (DSB) in the genome wherever needed. After nuclease cleavage, DSBs can be repaired by non-homologous end joining (NHEJ) or homology-directed repair (HDR) pathway. For producing targeted gene knock-in or other specific mutations, DSBs should be repaired by the HDR pathway. While NHEJ can cause various length insertions/deletion mutations (indels), which can lead the targeted gene to lose its function by shifting the open reading frame (ORF). Furthermore, HDR has low efficiency compared with the NHEJ pathway. In order to modify the gene precisely, numerous methods arose by inhibiting NHEJ or enhancing HDR, such as chemical modulation, synchronized expression, and overlapping homology arm. Here we focus on the efficiency and other considerations of these methodologies.
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Affiliation(s)
- Mingjie Liu
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Saad Rehman
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Xidian Tang
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Kui Gu
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Qinlei Fan
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Dekun Chen
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Wentao Ma
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
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47
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Jimeno S, Mejías-Navarro F, Prados-Carvajal R, Huertas P. Controlling the balance between chromosome break repair pathways. DNA Repair (Amst) 2019; 115:95-134. [DOI: 10.1016/bs.apcsb.2018.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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White MF, Allers T. DNA repair in the archaea-an emerging picture. FEMS Microbiol Rev 2018; 42:514-526. [PMID: 29741625 DOI: 10.1093/femsre/fuy020] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/02/2018] [Indexed: 12/12/2022] Open
Abstract
There has long been a fascination in the DNA repair pathways of archaea, for two main reasons. Firstly, many archaea inhabit extreme environments where the rate of physical damage to DNA is accelerated. These archaea might reasonably be expected to have particularly robust or novel DNA repair pathways to cope with this. Secondly, the archaea have long been understood to be a lineage distinct from the bacteria, and to share a close relationship with the eukarya, particularly in their information processing systems. Recent discoveries suggest the eukarya arose from within the archaeal domain, and in particular from lineages related to the TACK superphylum and Lokiarchaea. Thus, archaeal DNA repair proteins and pathways can represent a useful model system. This review focuses on recent advances in our understanding of archaeal DNA repair processes including base excision repair, nucleotide excision repair, mismatch repair and double-strand break repair. These advances are discussed in the context of the emerging picture of the evolution and relationship of the three domains of life.
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Affiliation(s)
- Malcolm F White
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, Fife KY16 9ST, UK
| | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
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Abstract
Meiosis is the basis for sexual reproduction and is marked by the sequential reduction of chromosome number during successive cell cycles, resulting in four haploid gametes. A central component of the meiotic program is the formation and repair of programmed double strand breaks. Recombination-driven repair of these meiotic breaks differs from recombination during mitosis in that meiotic breaks are preferentially repaired using the homologous chromosomes in a process known as homolog bias. Homolog bias allows for physical interactions between homologous chromosomes that are required for proper chromosome segregation, and the formation of crossover products ensuring genetic diversity in progeny. An important aspect of meiosis in the differential regulation of the two eukaryotic RecA homologs, Rad51 and Dmc1. In this review we will discuss the relationship between biological programs designed to regulate recombinase function.
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Affiliation(s)
- J Brooks Crickard
- a Department of Biochemistry & Molecular Biophysics , Columbia University , New York , NY , USA
| | - Eric C Greene
- a Department of Biochemistry & Molecular Biophysics , Columbia University , New York , NY , USA
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Beggs R, Yang ES. Targeting DNA repair in precision medicine. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 115:135-155. [PMID: 30798930 DOI: 10.1016/bs.apcsb.2018.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
Precision medicine is an emerging treatment paradigm that aims to find the right therapy at the right time based on an individual's unique genetic background, environment, and lifestyle. One area of precision medicine that has had success is targeting DNA repair in cancer. DNA is exposed to constant stress and there are repair mechanisms in place to maintain genetic integrity. These repair mechanisms can be targeted as a treatment strategy. In this chapter, we will focus on current efforts to target DNA repair pathways as part of precision oncology-based treatments.
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Affiliation(s)
- Reena Beggs
- Department of Radiation Oncology, University of Alabama-Birmingham School of Medicine, Birmingham, AL, United States
| | - Eddy S Yang
- Department of Radiation Oncology, University of Alabama-Birmingham School of Medicine, Birmingham, AL, United States; Hugh Kaul Precision Medicine Institute, University of Alabama-Birmingham School of Medicine, Birmingham, AL, United States.
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