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Carvajal-Maldonado D, Li Y, Returan M, Averill AM, Doublié S, Wood RD. Dynamic stem-loop extension by Pol θ and templated insertion during DNA repair. J Biol Chem 2024; 300:107461. [PMID: 38876299 PMCID: PMC11292364 DOI: 10.1016/j.jbc.2024.107461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/26/2024] [Accepted: 05/28/2024] [Indexed: 06/16/2024] Open
Abstract
Theta-mediated end joining (TMEJ) is critical for survival of cancer cells when other DNA double-stranded break repair pathways are impaired. Human DNA polymerase theta (Pol θ) can extend ssDNA oligonucleotides, but little is known about preferred substrates and mechanism. We show that Pol θ can extend both ssDNA and RNA substrates by unimolecular stem-loop synthesis initiated by only two 3' terminal base pairs. Given sufficient time, Pol θ uses alternative pairing configurations that greatly expand the repertoire of sequence outcomes. Further primer-template adjustments yield low-fidelity outcomes when the nucleotide pool is imbalanced. Unimolecular stem-loop synthesis competes with bimolecular end joining, even when a longer terminal microhomology for end joining is available. Both reactions are partially suppressed by the ssDNA-binding protein replication protein A. Protein-primer grasp residues that are specific to Pol θ are needed for rapid stem-loop synthesis. The ability to perform stem-loop synthesis from a minimally paired primer is rare among human DNA polymerases, but we show that human DNA polymerases Pol η and Pol λ can catalyze related reactions. Using purified human Pol θ, we reconstituted in vitro TMEJ incorporating an insertion arising from a stem-loop extension. These activities may help explain TMEJ repair events that include inverted repeat sequences.
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Affiliation(s)
- Denisse Carvajal-Maldonado
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Center, Houston, Texas, USA
| | - Yuzhen Li
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Center, Houston, Texas, USA
| | - Mark Returan
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Center, Houston, Texas, USA
| | - April M Averill
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, USA
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, USA
| | - Richard D Wood
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Center, Houston, Texas, USA.
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2
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Zhang H, Jiang L, Du X, Qian Z, Wu G, Jiang Y, Mao Z. The cGAS-Ku80 complex regulates the balance between two end joining subpathways. Cell Death Differ 2024; 31:792-803. [PMID: 38664591 PMCID: PMC11164703 DOI: 10.1038/s41418-024-01296-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 06/12/2024] Open
Abstract
As the major DNA sensor that activates the STING-TBK1 signaling cascade, cGAS is mainly present in the cytosol. A number of recent reports have indicated that cGAS also plays critical roles in the nucleus. Our previous work demonstrated for the first time that cGAS is translocated to the nucleus upon the occurrence of DNA damage and inhibits homologous recombination (HR), one of the two major pathways of DNA double strand break (DSB) repair. However, whether nuclear cGAS regulates the other DSB repair pathway, nonhomologous end joining (NHEJ), which can be further divided into the less error-prone canonical NHEJ (c-NHEJ) and more mutagenic alternative NHEJ (alt-NHEJ) subpathways, has not been characterized. Here, we demonstrated that cGAS tipped the balance of the two NHEJ subpathways toward c-NHEJ. Mechanistically, the cGAS-Ku80 complex enhanced the interaction between DNA-PKcs and the deubiquitinase USP7 to improve DNA-PKcs protein stability, thereby promoting c-NHEJ. In contrast, the cGAS-Ku80 complex suppressed alt-NHEJ by directly binding to the promoter of Polθ to suppress its transcription. Together, these findings reveal a novel function of nuclear cGAS in regulating DSB repair, suggesting that the presence of cGAS in the nucleus is also important in the maintenance of genome integrity.
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Affiliation(s)
- Haiping Zhang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Lijun Jiang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xinyi Du
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhen Qian
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Guizhu Wu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China.
| | - Ying Jiang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.
| | - Zhiyong Mao
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.
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3
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Stroik S, Luthman AJ, Ramsden DA. Templated insertions-DNA repair gets acrobatic. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024; 65 Suppl 1:82-89. [PMID: 37438951 PMCID: PMC10962320 DOI: 10.1002/em.22564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/28/2023] [Accepted: 07/07/2023] [Indexed: 07/14/2023]
Abstract
Deletions associated with the repair of DNA double-strand breaks is a source of genetic alternation and a recognized source of disease-causing mutagenesis. Theta-mediated end joining is a DNA repair mechanism, which guarantees deletions by its employment of microhomology (MH) alignment to facilitate end joining. A lesser-characterized templated insertion ability of this pathway, on the other hand, is associated with both deletion and insertion. This mechanism is characterized by at least one round of polymerase θ-mediated synthesis, which does not result in successful repair, followed by a subsequent round of polymerase engagement and synthesis that does lead to repair. Here we focus on the mechanisms by which polymerase θ introduces these insertions-direct, inverse, and a new class which we have termed strand switching. We observe this new class of templated insertions at multiple loci and across multiple species, often at a comparable frequency to those previously characterized. Templated insertion mutations are often enriched in cancer genomes and repeat expansion disorders. This repair mechanism thus contributes to disease-associated mutagenesis, and may plausibly even promote disease. Characterization of the types of polymerase θ-dependent insertions can provide new insight into these diseases and clinical promise for treatment.
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Affiliation(s)
- Susanna Stroik
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Adam J. Luthman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill NC, USA
| | - Dale A. Ramsden
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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4
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Merker L, Feller L, Dorn A, Puchta H. Deficiency of both classical and alternative end-joining pathways leads to a synergistic defect in double-strand break repair but not to an increase in homology-dependent gene targeting in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:242-254. [PMID: 38179887 DOI: 10.1111/tpj.16604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 10/13/2023] [Accepted: 12/12/2023] [Indexed: 01/06/2024]
Abstract
In eukaryotes, double-strand breaks (DSBs) are either repaired by homologous recombination (HR) or non-homologous end-joining (NHEJ). In somatic plant cells, HR is very inefficient. Therefore, the vast majority of DSBs are repaired by two different pathways of NHEJ. The classical (cNHEJ) pathway depends on the heterodimer KU70/KU80, while polymerase theta (POLQ) is central to the alternative (aNHEJ) pathway. Surprisingly, Arabidopsis plants are viable, even when both pathways are impaired. However, they exhibit severe growth retardation and reduced fertility. Analysis of mitotic anaphases indicates that the double mutant is characterized by a dramatic increase in chromosome fragmentation due to defective DSB repair. In contrast to the single mutants, the double mutant was found to be highly sensitive to the DSB-inducing genotoxin bleomycin. Thus, both pathways can complement for each other efficiently in DSB repair. We speculated that in the absence of both NHEJ pathways, HR might be enhanced. This would be especially attractive for gene targeting (GT) in which predefined changes are introduced using a homologous template. Unexpectedly, the polq single mutant as well as the double mutant showed significantly lower GT frequencies in comparison to wildtype plants. Accordingly, we were able to show that elimination of both NHEJ pathways does not pose an attractive approach for Agrobacterium-mediated GT. However, our results clearly indicate that a loss of cNHEJ leads to an increase in GT frequency, which is especially drastic and attractive for practical applications, in which the in planta GT strategy is used.
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Affiliation(s)
- Laura Merker
- Joseph Gottlieb Kölreuter Institute for Plant Sciences, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Laura Feller
- Joseph Gottlieb Kölreuter Institute for Plant Sciences, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Annika Dorn
- Joseph Gottlieb Kölreuter Institute for Plant Sciences, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
| | - Holger Puchta
- Joseph Gottlieb Kölreuter Institute for Plant Sciences, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, Karlsruhe, 76131, Germany
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5
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Li Z, You L, Hermann A, Bier E. Developmental progression of DNA double-strand break repair deciphered by a single-allele resolution mutation classifier. Nat Commun 2024; 15:2629. [PMID: 38521791 PMCID: PMC10960810 DOI: 10.1038/s41467-024-46479-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/27/2024] [Indexed: 03/25/2024] Open
Abstract
DNA double-strand breaks (DSBs) are repaired by a hierarchically regulated network of pathways. Factors influencing the choice of particular repair pathways, however remain poorly characterized. Here we develop an Integrated Classification Pipeline (ICP) to decompose and categorize CRISPR/Cas9 generated mutations on genomic target sites in complex multicellular insects. The ICP outputs graphic rank ordered classifications of mutant alleles to visualize discriminating DSB repair fingerprints generated from different target sites and alternative inheritance patterns of CRISPR components. We uncover highly reproducible lineage-specific mutation fingerprints in individual organisms and a developmental progression wherein Microhomology-Mediated End-Joining (MMEJ) or Insertion events predominate during early rapid mitotic cell cycles, switching to distinct subsets of Non-Homologous End-Joining (NHEJ) alleles, and then to Homology-Directed Repair (HDR)-based gene conversion. These repair signatures enable marker-free tracking of specific mutations in dynamic populations, including NHEJ and HDR events within the same samples, for in-depth analysis of diverse gene editing events.
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Affiliation(s)
- Zhiqian Li
- Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Lang You
- Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Anita Hermann
- Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ethan Bier
- Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA.
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA.
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6
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Nishizawa‐Yokoi A, Gelvin SB. Transformation and regeneration of DNA polymerase Θ mutant rice plants. PLANT DIRECT 2023; 7:e526. [PMID: 37681196 PMCID: PMC10480422 DOI: 10.1002/pld3.526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/05/2023] [Accepted: 08/09/2023] [Indexed: 09/09/2023]
Abstract
Agrobacterium T-DNA integration into the plant genome is essential for the process of transgenesis and is widely used for genome engineering. The importance of the non-homologous end-joining (NHEJ) protein DNA polymerase Θ, encoded by the PolQ gene, for T-DNA integration is controversial, with some groups claiming it is essential whereas others claim T-DNA integration in Arabidopsis and rice polQ mutant plant tissue. Because of pleiotropic effects of PolQ loss on plant development, scientists have previously had difficulty regenerating transgenic polQ mutant plants. We describe a protocol for regenerating transgenic polQ mutant rice plants using a sequential transformation method. This protocol may be applicable to other plant species.
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Affiliation(s)
- Ayako Nishizawa‐Yokoi
- Institute of Agrobiological SciencesNational Agriculture and Food Research OrganizationTsukubaJapan
| | - Stanton B. Gelvin
- Department of Biological SciencesPurdue UniversityWest LafayetteIndianaUSA
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7
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Schimmel J, Muñoz-Subirana N, Kool H, van Schendel R, van der Vlies S, Kamp JA, de Vrij FMS, Kushner SA, Smith GCM, Boulton SJ, Tijsterman M. Modulating mutational outcomes and improving precise gene editing at CRISPR-Cas9-induced breaks by chemical inhibition of end-joining pathways. Cell Rep 2023; 42:112019. [PMID: 36701230 DOI: 10.1016/j.celrep.2023.112019] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/18/2022] [Accepted: 01/09/2023] [Indexed: 01/26/2023] Open
Abstract
Gene editing through repair of CRISPR-Cas9-induced chromosomal breaks offers a means to correct a wide range of genetic defects. Directing repair to produce desirable outcomes by modulating DNA repair pathways holds considerable promise to increase the efficiency of genome engineering. Here, we show that inhibition of non-homologous end joining (NHEJ) or polymerase theta-mediated end joining (TMEJ) can be exploited to alter the mutational outcomes of CRISPR-Cas9. We show robust inhibition of TMEJ activity at CRISPR-Cas9-induced double-strand breaks (DSBs) using ART558, a potent polymerase theta (Polϴ) inhibitor. Using targeted sequencing, we show that ART558 suppresses the formation of microhomology-driven deletions in favor of NHEJ-specific outcomes. Conversely, NHEJ deficiency triggers the formation of large kb-sized deletions, which we show are the products of mutagenic TMEJ. Finally, we show that combined chemical inhibition of TMEJ and NHEJ increases the efficiency of homology-driven repair (HDR)-mediated precise gene editing. Our work reports a robust strategy to improve the fidelity and safety of genome engineering.
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Affiliation(s)
- Joost Schimmel
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Núria Muñoz-Subirana
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Hanneke Kool
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Robin van Schendel
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Sven van der Vlies
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Juliette A Kamp
- Department of Psychiatry, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Femke M S de Vrij
- Department of Psychiatry, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Steven A Kushner
- Department of Psychiatry, Erasmus Medical Center, Rotterdam, the Netherlands; Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Graeme C M Smith
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Simon J Boulton
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK; The Francis Crick Institute, London, UK
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands; Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands.
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8
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Li C, Zhu H, Jin S, Maksoud LM, Jain N, Sun J, Gao Y. Structural basis of DNA polymerase θ mediated DNA end joining. Nucleic Acids Res 2023; 51:463-474. [PMID: 36583344 PMCID: PMC9841435 DOI: 10.1093/nar/gkac1201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 12/31/2022] Open
Abstract
DNA polymerase θ (Pol θ) plays an essential role in the microhomology-mediated end joining (MMEJ) pathway for repairing DNA double-strand breaks. However, the mechanisms by which Pol θ recognizes microhomologous DNA ends and performs low-fidelity DNA synthesis remain unclear. Here, we present cryo-electron microscope structures of the polymerase domain of Lates calcarifer Pol θ with long and short duplex DNA at up to 2.4 Å resolution. Interestingly, Pol θ binds to long and short DNA substrates similarly, with extensive interactions around the active site. Moreover, Pol θ shares a similar active site as high-fidelity A-family polymerases with its finger domain well-closed but differs in having hydrophilic residues surrounding the nascent base pair. Computational simulations and mutagenesis studies suggest that the unique insertion loops of Pol θ help to stabilize short DNA binding and assemble the active site for MMEJ repair. Taken together, our results illustrate the structural basis of Pol θ-mediated MMEJ.
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Affiliation(s)
- Chuxuan Li
- Department of Biosciences, Rice University, Houston, TX 77005, USA
| | - Hanwen Zhu
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Shikai Jin
- Department of Biosciences, Rice University, Houston, TX 77005, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Leora M Maksoud
- Department of Biosciences, Rice University, Houston, TX 77005, USA
| | - Nikhil Jain
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ji Sun
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Yang Gao
- Department of Biosciences, Rice University, Houston, TX 77005, USA
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9
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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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10
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CRISPR-Cas12a induced DNA double-strand breaks are repaired by multiple pathways with different mutation profiles in Magnaporthe oryzae. Nat Commun 2022; 13:7168. [PMID: 36418866 PMCID: PMC9684475 DOI: 10.1038/s41467-022-34736-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/01/2022] [Indexed: 11/24/2022] Open
Abstract
CRISPR-Cas mediated genome engineering has revolutionized functional genomics. However, understanding of DNA repair following Cas-mediated DNA cleavage remains incomplete. Using Cas12a ribonucleoprotein genome editing in the fungal pathogen, Magnaporthe oryzae, we detail non-canonical DNA repair outcomes from hundreds of transformants. Sanger and nanopore sequencing analysis reveals significant variation in DNA repair profiles, ranging from small INDELs to kilobase size deletions and insertions. Furthermore, we find the frequency of DNA repair outcomes varies between loci. The results are not specific to the Cas-nuclease or selection procedure. Through Ku80 deletion analysis, a key protein required for canonical non-homologous end joining, we demonstrate activity of an alternative end joining mechanism that creates larger DNA deletions, and uses longer microhomology compared to C-NHEJ. Together, our results suggest preferential DNA repair pathway activity in the genome that can create different mutation profiles following repair, which could create biased genome variation and impact genome engineering and genome evolution.
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11
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Jiang Y. Contribution of Microhomology to Genome Instability: Connection between DNA Repair and Replication Stress. Int J Mol Sci 2022; 23:12937. [PMID: 36361724 PMCID: PMC9657218 DOI: 10.3390/ijms232112937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/23/2022] [Accepted: 10/23/2022] [Indexed: 11/23/2023] Open
Abstract
Microhomology-mediated end joining (MMEJ) is a highly mutagenic pathway to repair double-strand breaks (DSBs). MMEJ was thought to be a backup pathway of homologous recombination (HR) and canonical nonhomologous end joining (C-NHEJ). However, it attracts more attention in cancer research due to its special function of microhomology in many different aspects of cancer. In particular, it is initiated with DNA end resection and upregulated in homologous recombination-deficient cancers. In this review, I summarize the following: (1) the recent findings and contributions of MMEJ to genome instability, including phenotypes relevant to MMEJ; (2) the interaction between MMEJ and other DNA repair pathways; (3) the proposed mechanistic model of MMEJ in DNA DSB repair and a new connection with microhomology-mediated break-induced replication (MMBIR); and (4) the potential clinical application by targeting MMEJ based on synthetic lethality for cancer therapy.
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Affiliation(s)
- Yuning Jiang
- Department of Radiation Oncology, University of Virginia, Charlottesville, VA 22903, USA
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12
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DNA Polymerase Theta Plays a Critical Role in Pancreatic Cancer Development and Metastasis. Cancers (Basel) 2022; 14:cancers14174077. [PMID: 36077614 PMCID: PMC9454495 DOI: 10.3390/cancers14174077] [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: 07/15/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC), due to its genomic heterogeneity and lack of effective treatment, despite decades of intensive research, will become the second leading cause of cancer-related deaths by 2030. Step-wise acquisition of mutations, due to genomic instability, is considered to drive the development of PDAC; the KRAS mutation occurs in 95 to 100% of human PDAC, and is already detectable in early premalignant lesions designated as pancreatic intraepithelial neoplasia (PanIN). This mutation is possibly the key event leading to genomic instability and PDAC development. Our study aimed to investigate the role of the error-prone DNA double-strand breaks (DSBs) repair pathway, alt-EJ, in the presence of the KRAS G12D mutation in pancreatic cancer development. Our findings show that oncogenic KRAS contributes to increasing the expression of Polθ, Lig3, and Mre11, key components of alt-EJ in both mouse and human PDAC models. We further confirm increased catalytic activity of alt-EJ in a mouse and human model of PDAC bearing the KRAS G12D mutation. Subsequently, we focused on estimating the impact of alt-EJ inactivation by polymerase theta (Polθ) deletion on pancreatic cancer development, and survival in genetically engineered mouse models (GEMMs) and cancer patients. Here, we show that even though Polθ deficiency does not fully prevent the development of pancreatic cancer, it significantly delays the onset of PanIN formation, prolongs the overall survival of experimental mice, and correlates with the overall survival of pancreatic cancer patients in the TCGA database. Our study clearly demonstrates the role of alt-EJ in the development of PDAC, and alt-EJ may be an attractive therapeutic target for pancreatic cancer patients.
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13
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Ramsden DA, Carvajal-Garcia J, Gupta GP. Mechanism, cellular functions and cancer roles of polymerase-theta-mediated DNA end joining. Nat Rev Mol Cell Biol 2022; 23:125-140. [PMID: 34522048 DOI: 10.1038/s41580-021-00405-2] [Citation(s) in RCA: 87] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2021] [Indexed: 02/08/2023]
Abstract
Cellular pathways that repair chromosomal double-strand breaks (DSBs) have pivotal roles in cell growth, development and cancer. These DSB repair pathways have been the target of intensive investigation, but one pathway - alternative end joining (a-EJ) - has long resisted elucidation. In this Review, we highlight recent progress in our understanding of a-EJ, especially the assignment of DNA polymerase theta (Polθ) as the predominant mediator of a-EJ in most eukaryotes, and discuss a potential molecular mechanism by which Polθ-mediated end joining (TMEJ) occurs. We address possible cellular functions of TMEJ in resolving DSBs that are refractory to repair by non-homologous end joining (NHEJ), DSBs generated following replication fork collapse and DSBs present owing to stalling of repair by homologous recombination. We also discuss how these context-dependent cellular roles explain how TMEJ can both protect against and cause genome instability, and the emerging potential of Polθ as a therapeutic target in cancer.
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Affiliation(s)
- Dale A Ramsden
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Juan Carvajal-Garcia
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gaorav P Gupta
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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14
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Clay DE, Bretscher HS, Jezuit EA, Bush KB, Fox DT. Persistent DNA damage signaling and DNA polymerase theta promote broken chromosome segregation. J Cell Biol 2021; 220:e202106116. [PMID: 34613334 PMCID: PMC8500225 DOI: 10.1083/jcb.202106116] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/24/2021] [Accepted: 09/14/2021] [Indexed: 01/16/2023] Open
Abstract
Cycling cells must respond to DNA double-strand breaks (DSBs) to avoid genome instability. Missegregation of chromosomes with DSBs during mitosis results in micronuclei, aberrant structures linked to disease. How cells respond to DSBs during mitosis is incompletely understood. We previously showed that Drosophilamelanogaster papillar cells lack DSB checkpoints (as observed in many cancer cells). Here, we show that papillar cells still recruit early acting repair machinery (Mre11 and RPA3) and the Fanconi anemia (FA) protein Fancd2 to DSBs. These proteins persist as foci on DSBs as cells enter mitosis. Repair foci are resolved in a stepwise manner during mitosis. DSB repair kinetics depends on both monoubiquitination of Fancd2 and the alternative end-joining protein DNA polymerase θ. Disruption of either or both of these factors causes micronuclei after DNA damage, which disrupts intestinal organogenesis. This study reveals a mechanism for how cells with inactive DSB checkpoints can respond to DNA damage that persists into mitosis.
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Affiliation(s)
- Delisa E. Clay
- Department of Cell Biology, Duke University School of Medicine, Durham, NC
| | - Heidi S. Bretscher
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC
| | - Erin A. Jezuit
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC
| | - Korie B. Bush
- University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC
| | - Donald T. Fox
- Department of Cell Biology, Duke University School of Medicine, Durham, NC
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC
- University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC
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15
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Clay DE, Fox DT. DNA Damage Responses during the Cell Cycle: Insights from Model Organisms and Beyond. Genes (Basel) 2021; 12:1882. [PMID: 34946831 PMCID: PMC8701014 DOI: 10.3390/genes12121882] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/25/2022] Open
Abstract
Genome damage is a threat to all organisms. To respond to such damage, DNA damage responses (DDRs) lead to cell cycle arrest, DNA repair, and cell death. Many DDR components are highly conserved, whereas others have adapted to specific organismal needs. Immense progress in this field has been driven by model genetic organism research. This review has two main purposes. First, we provide a survey of model organism-based efforts to study DDRs. Second, we highlight how model organism study has contributed to understanding how specific DDRs are influenced by cell cycle stage. We also look forward, with a discussion of how future study can be expanded beyond typical model genetic organisms to further illuminate how the genome is protected.
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Affiliation(s)
- Delisa E. Clay
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA;
| | - Donald T. Fox
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA;
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA
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16
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Prodhomme MK, Péricart S, Pommier RM, Morel AP, Brunac AC, Franchet C, Moyret-Lalle C, Brousset P, Puisieux A, Hoffmann JS, Tissier A. Opposite Roles for ZEB1 and TMEJ in the Regulation of Breast Cancer Genome Stability. Front Cell Dev Biol 2021; 9:727429. [PMID: 34458275 PMCID: PMC8388841 DOI: 10.3389/fcell.2021.727429] [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: 06/18/2021] [Accepted: 07/23/2021] [Indexed: 12/22/2022] Open
Abstract
Breast cancer cells frequently acquire mutations in faithful DNA repair genes, as exemplified by BRCA-deficiency. Moreover, overexpression of an inaccurate DNA repair pathway may also be at the origin of the genetic instability arising during the course of cancer progression. The specific gain in expression of POLQ, encoding the error-prone DNA polymerase Theta (POLθ) involved in theta-mediated end joining (TMEJ), is associated with a characteristic mutational signature. To gain insight into the mechanistic regulation of POLQ expression, this review briefly presents recent findings on the regulation of POLQ in the claudin-low breast tumor subtype, specifically expressing transcription factors involved in epithelial-to-mesenchymal transition (EMT) such as ZEB1 and displaying a paucity in genomic abnormality.
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Affiliation(s)
- Mélanie K Prodhomme
- INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Centre of Lyon, Équipe Labellisée Ligue Contre le Cancer, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France.,LabEx DEVweCAN, Université de Lyon, Lyon, France
| | - Sarah Péricart
- Laboratoire d'Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Toulouse, France
| | - Roxane M Pommier
- Gilles Thomas Bioinformatics Platform, Centre Léon Bérard, Cancer Research Centre of Lyon, Lyon, France
| | - Anne-Pierre Morel
- INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Centre of Lyon, Équipe Labellisée Ligue Contre le Cancer, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France.,LabEx DEVweCAN, Université de Lyon, Lyon, France
| | - Anne-Cécile Brunac
- Laboratoire d'Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Toulouse, France
| | - Camille Franchet
- Laboratoire d'Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Toulouse, France
| | - Caroline Moyret-Lalle
- INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Centre of Lyon, Équipe Labellisée Ligue Contre le Cancer, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France.,LabEx DEVweCAN, Université de Lyon, Lyon, France
| | - Pierre Brousset
- Laboratoire d'Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Toulouse, France
| | - Alain Puisieux
- INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Centre of Lyon, Équipe Labellisée Ligue Contre le Cancer, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France.,Institut Curie, Versailles Saint-Quentin-en-Yvelines University, PSL Research University, Paris, France
| | - Jean-Sébastien Hoffmann
- Laboratoire d'Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Toulouse, France
| | - Agnès Tissier
- INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Centre of Lyon, Équipe Labellisée Ligue Contre le Cancer, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France.,LabEx DEVweCAN, Université de Lyon, Lyon, France
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17
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Sizova I, Kelterborn S, Verbenko V, Kateriya S, Hegemann P. Chlamydomonas POLQ is necessary for CRISPR/Cas9-mediated gene targeting. G3 (BETHESDA, MD.) 2021; 11:jkab114. [PMID: 33836052 PMCID: PMC8495919 DOI: 10.1093/g3journal/jkab114] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/18/2021] [Indexed: 02/06/2023]
Abstract
The use of CRISPR/Cas endonucleases has revolutionized gene editing techniques for research on Chlamydomonas reinhardtii. To better utilize the CRISPR/Cas system, it is essential to develop a more comprehensive understanding of the DNA repair pathways involved in genome editing. In this study, we have analyzed contributions from canonical KU80/KU70-dependent nonhomologous end-joining (cNHEJ) and DNA polymerase theta (POLQ)-mediated end joining on SpCas9-mediated untemplated mutagenesis and homology-directed repair (HDR)/gene inactivation in Chlamydomonas. Using CRISPR/SpCas9 technology, we generated DNA repair-defective mutants ku80, ku70, polQ for gene targeting experiments. Our results show that untemplated repair of SpCas9-induced double strand breaks results in mutation spectra consistent with an involvement of both KU80/KU70 and POLQ. In addition, the inactivation of POLQ was found to negatively affect HDR of the inactivated paromomycin-resistant mut-aphVIII gene when donor single-stranded oligos were used. Nevertheless, mut-aphVIII was still repaired by homologous recombination in these mutants. POLQ inactivation suppressed random integration of transgenes co-transformed with the donor ssDNA. KU80 deficiency did not affect these events but instead was surprisingly found to stimulate HDR/gene inactivation. Our data suggest that in Chlamydomonas, POLQ is the main contributor to CRISPR/Cas-induced HDR and random integration of transgenes, whereas KU80/KU70 potentially plays a secondary role. We expect our results will lead to improvement of genome editing in C. reinhardtii and can be used for future development of algal biotechnology.
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Affiliation(s)
- Irina Sizova
- Experimental Biophysics, Institute of Biology, Humboldt University of Berlin, Berlin D-10099, Germany
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre “Kurchatov Institute”, Gatchina 188300, Russia
- Kurchatov Genome Center - PNPI, Gatchina 188300, Russia
| | - Simon Kelterborn
- Experimental Biophysics, Institute of Biology, Humboldt University of Berlin, Berlin D-10099, Germany
| | - Valeriy Verbenko
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre “Kurchatov Institute”, Gatchina 188300, Russia
- Kurchatov Genome Center - PNPI, Gatchina 188300, Russia
| | - Suneel Kateriya
- Laboratory of Optobiology School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Peter Hegemann
- Experimental Biophysics, Institute of Biology, Humboldt University of Berlin, Berlin D-10099, Germany
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18
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Canedo A, Rocha TL. Zebrafish (Danio rerio) using as model for genotoxicity and DNA repair assessments: Historical review, current status and trends. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 762:144084. [PMID: 33383303 DOI: 10.1016/j.scitotenv.2020.144084] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/18/2020] [Accepted: 11/21/2020] [Indexed: 06/12/2023]
Abstract
Genotoxic pollutants lead to both DNA damage and changes in cell repair mechanisms. Selecting suitable biomonitors is a fundamental step in genotoxicity studies. Thus, zebrafish have become a popular model used to assess the genotoxicity of different pollutants in recent years. They have orthologous genes with humans and hold almost all genes involved in different repair pathways. Therefore, the aim of the current study is to summarize the existing literature on zebrafish using as model system to assess the genotoxicity of different pollutants. Revised data have shown that comet assay is the main technique adopted in these studies. However, it is necessary standardizing the technique applied to zebrafish in order to enable better result interpretation and comparisons. Overall, pollutants lead to single-strand breaks (SSB), double-strand breaks (DSB), adduct formation, as well as to changes in the expression of genes involved in repair mechanisms. Although analyzing repair mechanisms is essential to better understand the genotoxic effects caused by pollutants, few studies have analyzed repair capacity. The current review reinforces the need of conducting further studies on the role played by repair pathways in zebrafish subjected to DNA damage. Revised data have shown that zebrafish are a suitable model to assess pollutant-induced genotoxicity.
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Affiliation(s)
- Aryelle Canedo
- Laboratory of Environmental Biotechnology and Ecotoxicology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiania, Goiás, Brazil
| | - Thiago Lopes Rocha
- Laboratory of Environmental Biotechnology and Ecotoxicology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiania, Goiás, Brazil..
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19
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Carvajal-Garcia J, Crown KN, Ramsden DA, Sekelsky J. DNA polymerase theta suppresses mitotic crossing over. PLoS Genet 2021; 17:e1009267. [PMID: 33750946 PMCID: PMC8016270 DOI: 10.1371/journal.pgen.1009267] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 04/01/2021] [Accepted: 02/27/2021] [Indexed: 12/16/2022] Open
Abstract
Polymerase theta-mediated end joining (TMEJ) is a chromosome break repair pathway that is able to rescue the lethality associated with the loss of proteins involved in early steps in homologous recombination (e.g., BRCA1/2). This is due to the ability of polymerase theta (Pol θ) to use resected, 3' single stranded DNA tails to repair chromosome breaks. These resected DNA tails are also the starting substrate for homologous recombination. However, it remains unknown if TMEJ can compensate for the loss of proteins involved in more downstream steps during homologous recombination. Here we show that the Holliday junction resolvases SLX4 and GEN1 are required for viability in the absence of Pol θ in Drosophila melanogaster, and lack of all three proteins results in high levels of apoptosis. Flies deficient in Pol θ and SLX4 are extremely sensitive to DNA damaging agents, and mammalian cells require either Pol θ or SLX4 to survive. Our results suggest that TMEJ and Holliday junction formation/resolution share a common DNA substrate, likely a homologous recombination intermediate, that when left unrepaired leads to cell death. One major consequence of Holliday junction resolution by SLX4 and GEN1 is cancer-causing loss of heterozygosity due to mitotic crossing over. We measured mitotic crossovers in flies after a Cas9-induced chromosome break, and observed that this mutagenic form of repair is increased in the absence of Pol θ. This demonstrates that TMEJ can function upstream of the Holiday junction resolvases to protect cells from loss of heterozygosity. Our work argues that Pol θ can thus compensate for the loss of the Holliday junction resolvases by using homologous recombination intermediates, suppressing mitotic crossing over and preserving the genomic stability of cells.
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Affiliation(s)
- Juan Carvajal-Garcia
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - K. Nicole Crown
- Department of Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Dale A. Ramsden
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Jeff Sekelsky
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Integrative Program in Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina, United States of America
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20
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Geisinger JM, Stearns T. CRISPR/Cas9 treatment causes extended TP53-dependent cell cycle arrest in human cells. Nucleic Acids Res 2020; 48:9067-9081. [PMID: 32687165 PMCID: PMC7498335 DOI: 10.1093/nar/gkaa603] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/02/2020] [Accepted: 07/07/2020] [Indexed: 12/30/2022] Open
Abstract
While the mechanism of CRISPR/Cas9 cleavage is understood, the basis for the large variation in mutant recovery for a given target sequence between cell lines is much less clear. We hypothesized that this variation may be due to differences in how the DNA damage response affects cell cycle progression. We used incorporation of EdU as a marker of cell cycle progression to analyze the response of several human cell lines to CRISPR/Cas9 treatment with a single guide directed to a unique locus. Cell lines with functionally wild-type TP53 exhibited higher levels of cell cycle arrest compared to lines without. Chemical inhibition of TP53 protein combined with TP53 and RB1 transcript silencing alleviated induced arrest in TP53+/+ cells. Using dCas9, we determined this arrest is driven in part by Cas9 binding to DNA. Additionally, wild-type Cas9 induced fewer 53BP1 foci in TP53+/+ cells compared to TP53−/− cells and DD-Cas9, suggesting that differences in break sensing are responsible for cell cycle arrest variation. We conclude that CRISPR/Cas9 treatment induces a cell cycle arrest dependent on functional TP53 as well as Cas9 DNA binding and cleavage. Our findings suggest that transient inhibition of TP53 may increase genome editing recovery in primary and TP53+/+ cell lines.
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Affiliation(s)
| | - Tim Stearns
- Department of Biology, Stanford University, Stanford, CA 94305, USA.,Department of Genetics, Stanford University Medical School, Stanford, CA 94305, USA
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21
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Wienert B, Nguyen DN, Guenther A, Feng SJ, Locke MN, Wyman SK, Shin J, Kazane KR, Gregory GL, Carter MAM, Wright F, Conklin BR, Marson A, Richardson CD, Corn JE. Timed inhibition of CDC7 increases CRISPR-Cas9 mediated templated repair. Nat Commun 2020; 11:2109. [PMID: 32355159 PMCID: PMC7193628 DOI: 10.1038/s41467-020-15845-1] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/12/2020] [Indexed: 12/11/2022] Open
Abstract
Repair of double strand DNA breaks (DSBs) can result in gene disruption or gene modification via homology directed repair (HDR) from donor DNA. Altering cellular responses to DSBs may rebalance editing outcomes towards HDR and away from other repair outcomes. Here, we utilize a pooled CRISPR screen to define host cell involvement in HDR between a Cas9 DSB and a plasmid double stranded donor DNA (dsDonor). We find that the Fanconi Anemia (FA) pathway is required for dsDonor HDR and that other genes act to repress HDR. Small molecule inhibition of one of these repressors, CDC7, by XL413 and other inhibitors increases the efficiency of HDR by up to 3.5 fold in many contexts, including primary T cells. XL413 stimulates HDR during a reversible slowing of S-phase that is unexplored for Cas9-induced HDR. We anticipate that XL413 and other such rationally developed inhibitors will be useful tools for gene modification.
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Affiliation(s)
- Beeke Wienert
- Innovative Genomics Institute, University of California, Berkeley, CA, 94703, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94703, USA
- Gladstone Institutes, San Francisco, CA, 94158, USA
| | - David N Nguyen
- Department of Microbiology and Immunology, University of California, San Francisco, CA, 94143, USA
- Diabetes Center, University of California, San Francisco, CA, 94143, USA
- Department of Medicine, University of California, San Francisco, CA, 94143, USA
| | - Alexis Guenther
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Sharon J Feng
- Innovative Genomics Institute, University of California, Berkeley, CA, 94703, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94703, USA
| | - Melissa N Locke
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94703, USA
| | - Stacia K Wyman
- Innovative Genomics Institute, University of California, Berkeley, CA, 94703, USA
| | - Jiyung Shin
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093, Zurich, Switzerland
| | - Katelynn R Kazane
- Innovative Genomics Institute, University of California, Berkeley, CA, 94703, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94703, USA
| | | | | | - Francis Wright
- Department of Microbiology and Immunology, University of California, San Francisco, CA, 94143, USA
| | - Bruce R Conklin
- Gladstone Institutes, San Francisco, CA, 94158, USA
- Departments of Medicine, Ophthalmology, and Pharmacology, University of California, San Francisco, CA, 94143, USA
| | - Alex Marson
- Innovative Genomics Institute, University of California, Berkeley, CA, 94703, USA
- Department of Microbiology and Immunology, University of California, San Francisco, CA, 94143, USA
- Diabetes Center, University of California, San Francisco, CA, 94143, USA
- Department of Medicine, University of California, San Francisco, CA, 94143, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, 94129, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Chris D Richardson
- Innovative Genomics Institute, University of California, Berkeley, CA, 94703, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94703, USA.
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA.
| | - Jacob E Corn
- Innovative Genomics Institute, University of California, Berkeley, CA, 94703, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94703, USA.
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093, Zurich, Switzerland.
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22
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Brambati A, Barry RM, Sfeir A. DNA polymerase theta (Polθ) - an error-prone polymerase necessary for genome stability. Curr Opin Genet Dev 2020; 60:119-126. [PMID: 32302896 PMCID: PMC7230004 DOI: 10.1016/j.gde.2020.02.017] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 12/21/2022]
Abstract
Mammalian cells have evolved multiple pathways to repair DNA double strand breaks (DSBs) and ensure genome stability. In addition to non-homologous end-joining (NHEJ) and homologous recombination (HR), cells evolved an error-prone repair pathway termed microhomology-mediated end joining (MMEJ). The mutagenic outcome of MMEJ derives from the activity of DNA polymerase theta (Polθ) - a multidomain enzyme that is minimally expressed in normal tissue but overexpressed in tumors. Polθ expression is particularly crucial for the proliferation of HR deficient cancer cells. As a result, this mutagenic repair emerged as an attractive target for cancer therapy, and inhibitors are currently in pre-clinical development. Here, we review the multifunctionality of this enigmatic polymerase, focusing on its role during DSB repair in mammalian cells and its impact on cancer genomes.
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Affiliation(s)
- Alessandra Brambati
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY 10016, USA
| | - Raymond Mario Barry
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY 10016, USA
| | - Agnel Sfeir
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY 10016, USA.
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23
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Wierson WA, Simone BW, WareJoncas Z, Mann C, Welker JM, Kar B, Emch MJ, Friedberg I, Gendron WA, Barry MA, Clark KJ, Dobbs DL, McGrail MA, Ekker SC, Essner JJ. Expanding the CRISPR Toolbox with ErCas12a in Zebrafish and Human Cells. CRISPR J 2019; 2:417-433. [PMID: 31742435 PMCID: PMC6919245 DOI: 10.1089/crispr.2019.0026] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
CRISPR and CRISPR-Cas effector proteins enable the targeting of DNA double-strand breaks to defined loci based on a variable length RNA guide specific to each effector. The guide RNAs are generally similar in size and form, consisting of a ∼20 nucleotide sequence complementary to the DNA target and an RNA secondary structure recognized by the effector. However, the effector proteins vary in protospacer adjacent motif requirements, nuclease activities, and DNA binding kinetics. Recently, ErCas12a, a new member of the Cas12a family, was identified in Eubacterium rectale. Here, we report the first characterization of ErCas12a activity in zebrafish and expand on previously reported activity in human cells. Using a fluorescent reporter system, we show that CRISPR-ErCas12a elicits strand annealing mediated DNA repair more efficiently than CRISPR-Cas9. Further, using our previously reported gene targeting method that utilizes short homology, GeneWeld, we demonstrate the use of CRISPR-ErCas12a to integrate reporter alleles into the genomes of both zebrafish and human cells. Together, this work provides methods for deploying an additional CRISPR-Cas system, thus increasing the flexibility researchers have in applying genome engineering technologies.
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Affiliation(s)
- Wesley A. Wierson
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa
| | - Brandon W. Simone
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Zachary WareJoncas
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Carla Mann
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa
| | - Jordan M. Welker
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa
| | - Bibekananda Kar
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Michael J. Emch
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Iddo Friedberg
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, Iowa
| | - William A.C. Gendron
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Michael A. Barry
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Karl J. Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Drena L. Dobbs
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa
| | - Maura A. McGrail
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa
| | - Stephen C. Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Jeffrey J. Essner
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa
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24
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Schimmel J, van Schendel R, den Dunnen JT, Tijsterman M. Templated Insertions: A Smoking Gun for Polymerase Theta-Mediated End Joining. Trends Genet 2019; 35:632-644. [PMID: 31296341 DOI: 10.1016/j.tig.2019.06.001] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/27/2019] [Accepted: 06/06/2019] [Indexed: 01/23/2023]
Abstract
A recognized source of disease-causing genome alterations is erroneous repair of broken chromosomes, which can be executed by two distinct mechanisms: non-homologous end joining (NHEJ) and the recently discovered polymerase theta-mediated end joining (TMEJ) pathway. While TMEJ has previously been considered to act as an alternative mechanism backing up NHEJ, recent work points to a role for TMEJ in the repair of replication-associated DNA breaks that are excluded from repair through homologous recombination. Because of its mode of action, TMEJ is intrinsically mutagenic and sometimes leaves behind a recognizable genomic scar when joining chromosome break ends (i.e., 'templated insertions'). This review article focuses on the intriguing observation that this polymerase theta signature is frequently observed in disease alleles, arguing for a prominent role of this double-strand break repair pathway in genome diversification and disease-causing spontaneous mutagenesis in humans.
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Affiliation(s)
- Joost Schimmel
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Robin van Schendel
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Johan T den Dunnen
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands.
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25
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Kurosawa A, Kuboshima H, Adachi N. Complex genetic interactions between DNA polymerase β and the NHEJ ligase. FEBS J 2019; 287:377-385. [PMID: 31330087 DOI: 10.1111/febs.15012] [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: 03/04/2019] [Revised: 06/05/2019] [Accepted: 07/19/2019] [Indexed: 12/19/2022]
Abstract
Mammalian cells possess multiple pathways for repairing various types of DNA damage. Although the molecular mechanisms of each DNA repair pathway have been analyzed by biochemical analysis and cell biological analysis, interplay between different pathways has not been fully elucidated. In this study, using human Nalm-6-mutant cell lines, we analyzed the relationship between the base excision repair factor DNA polymerase β (POLβ) and DNA ligase IV (LIG4), which is essential for DNA double-strand break (DSB) repair by non-homologous end-joining (NHEJ). We found that cells lacking both POLβ and LIG4 grew significantly more slowly than either single mutant, indicating cooperative functions of the two proteins in normal cell growth. To further investigate the genetic interaction between POLβ and LIG4, we examined DNA damage sensitivity of the mutant cell lines. Our results suggested that NHEJ acts as a backup pathway for repairing alkylation damage (when converted into DSBs) in the absence of POLβ. Surprisingly, despite the critical role of POLβ in alkylation damage repair, cells lacking POLβ exhibited increased resistance to camptothecin (a topoisomerase I inhibitor that induces DNA single-strand breaks), irrespective of the presence or absence of LIG4. A LIG4-independent increased resistance associated with POLβ loss was also observed with ionizing radiation; however, cells lacking both POLβ and LIG4 were more radiosensitive than either single mutant. Taken together, our findings provide novel insight into the complex interplay between different DNA repair pathways.
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Affiliation(s)
- Aya Kurosawa
- Graduate School of Nanobioscience, Yokohama City University, Japan
| | | | - Noritaka Adachi
- Graduate School of Nanobioscience, Yokohama City University, Japan
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26
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Genomic non-redundancy of the mir-183/96/182 cluster and its requirement for hair cell maintenance. Sci Rep 2019; 9:10302. [PMID: 31311951 PMCID: PMC6635406 DOI: 10.1038/s41598-019-46593-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 07/02/2019] [Indexed: 01/02/2023] Open
Abstract
microRNAs are important regulators of gene expression. In the retina, the mir-183/96/182 cluster is of particular interest due to its robust expression and studies in which loss of the cluster caused photoreceptor degeneration. However, it is unclear which of the three miRNAs in the cluster are ultimately required in photoreceptors, whether each may have independent, contributory roles, or whether a single miRNA from the cluster compensates for the loss of another. These are important questions that will not only help us to understand the role of these particular miRNAs in the retina, but will deepen our understanding of how clustered microRNAs evolve and operate. To that end, we have developed a complete panel of single, double, and triple mir-183/96/182 mutant zebrafish. While the retinas of all mutant animals were normal, the triple mutants exhibited acute hair cell degeneration which corresponded with impaired swimming and death at a young age. By measuring the penetrance of this phenotype in each mutant line, we determine which of the three miRNAs in the cluster are necessary and/or sufficient to ensure normal hair cell development and function.
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27
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Xu L, Zhao J, Wang Z. Genotoxic response and damage recovery of macrophages to graphene quantum dots. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 664:536-545. [PMID: 30759415 DOI: 10.1016/j.scitotenv.2019.01.356] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 01/24/2019] [Accepted: 01/27/2019] [Indexed: 05/20/2023]
Abstract
The potential adverse effects of graphene quantum dots (GQDs) have increasingly attracted attention. Our present study revealed the genotoxic responses of rat alveolar macrophages (NR8383) to aminated graphene QDs (AG-QDs) and detected the cellular recovery after removing AG-QDs. Global gene expression analysis from RNA-sequencing showed that AG-QDs (100 μg/mL) caused significant alterations in expression of 2898 genes after exposure for 24 h. Among these, 1335 and 1563 genes were up-regulated and down-regulated, respectively. Based on the Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genomes (KEGG) analysis, we found that most of the down-regulated genes were responsive to "cell cycle", which correlated well with the cell cycle arrest data that AG-QDs triggered cell cycle arrest at S (synthesis) and G2/M (second gap/mitosis) phase. The percentages of cells in S and G2/M phase were increased by 4.5%, and 29.0%, respectively. In addition, the up-regulated genes related with "endocytosis" and "phagocytosis" were identified, which could regulate the internalization of AG-QDs by endocytosis and phagocytosis. After removing exposed AG-QDs and re-incubating the cells in fresh medium, the arrest of S and G2/M phase in NR8383 cells was reduced, and the cell cycle gradually recovered. This cellular recovery could be attributed to the cellular excretion of AG-QDs and the up-regulation of the DNA-repair-related genes (Rad51, Brca2, and Atm). The current work provides insights into the potential hazards of AG-QDs in transcriptional level and presented the long-term effects of AG-QDs on organisms in environment.
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Affiliation(s)
- Lina Xu
- Institute of Environmental Processes and Pollution Control, and School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China; Institute of Coastal Environmental Pollution Control, and College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Jian Zhao
- Institute of Coastal Environmental Pollution Control, and College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control, and School of Environmental and Civil Engineering, Jiangnan University, Wuxi 214122, China.
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28
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Mara K, Charlot F, Guyon-Debast A, Schaefer DG, Collonnier C, Grelon M, Nogué F. POLQ plays a key role in the repair of CRISPR/Cas9-induced double-stranded breaks in the moss Physcomitrella patens. THE NEW PHYTOLOGIST 2019; 222:1380-1391. [PMID: 30636294 DOI: 10.1111/nph.15680] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 01/05/2019] [Indexed: 05/19/2023]
Abstract
Double-stranded breaks can be repaired by different mechanisms such as homologous recombination (HR), classical nonhomologous end joining (C-NHEJ) and alternative end joining (Alt-EJ). Polymerase Q (POLQ) has been proposed to be the main factor involved in Alt-EJ-mediated DNA repair. Here we describe the role of POLQ in DNA repair and gene targeting in Physcomitrella patens. The disruption of the POLQ gene does not influence the genetic stability of P. patens nor its development. The polq mutant shows the same sensitivity as wild-type towards most of the genotoxic agents tested (ultraviolet (UV), methyl methanesulfonate (MMS) and cisplatin) with the notable exception of bleomycin for which it shows less sensitivity than the wild-type. Furthermore, we show that POLQ is involved in the repair of CRISPR-Cas9-induced double-stranded breaks in P. patens. We also demonstrate that POLQ is a potential competitor and/or inhibitor of the HR repair pathway. This finding has a consequence in terms of genetic engineering, as in the absence of POLQ the frequency of gene targeting is significantly increased and the number of clean two-sided HR-mediated insertions is enhanced. Therefore, the control of POLQ activity in plants could be a useful strategy to optimize the tools of genome engineering for plant breeding.
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Affiliation(s)
- Kostlend Mara
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, 78000, France
| | - Florence Charlot
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, 78000, France
| | - Anouchka Guyon-Debast
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, 78000, France
| | - Didier G Schaefer
- Laboratory of Cell and Molecular Biology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, CH-2009 Neuchâtel, Switzerland
| | - Cécile Collonnier
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, 78000, France
| | - Mathilde Grelon
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, 78000, France
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, 78000, France
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29
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Cayuela ML, Claes KBM, Ferreira MG, Henriques CM, van Eeden F, Varga M, Vierstraete J, Mione MC. The Zebrafish as an Emerging Model to Study DNA Damage in Aging, Cancer and Other Diseases. Front Cell Dev Biol 2019; 6:178. [PMID: 30687705 PMCID: PMC6335974 DOI: 10.3389/fcell.2018.00178] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 12/22/2018] [Indexed: 12/17/2022] Open
Abstract
Cancer is a disease of the elderly, and old age is its largest risk factor. With age, DNA damage accumulates continuously, increasing the chance of malignant transformation. The zebrafish has emerged as an important vertebrate model to study these processes. Key mechanisms such as DNA damage responses and cellular senescence can be studied in zebrafish throughout its life course. In addition, the zebrafish is becoming an important resource to study telomere biology in aging, regeneration and cancer. Here we review some of the tools and resources that zebrafish researchers have developed and discuss their potential use in the study of DNA damage, cancer and aging related diseases.
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Affiliation(s)
- Maria Luisa Cayuela
- Telomerase, Cancer and Aging Group, Surgery Unit, Instituto Murciano de Investigación Biosanitaria-Arrixaca, Murcia, Spain
| | | | | | - Catarina Martins Henriques
- Department of Oncology and Metabolism, Bateson Centre, University of Sheffield, Sheffield, United Kingdom
| | | | - Máté Varga
- Department of Genetics, Eötvös Loránd University, Budapest, Hungary
- MTA-SE Lendület Nephrogenetic Laboratory, Budapest, Hungary
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30
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Momose T, De Cian A, Shiba K, Inaba K, Giovannangeli C, Concordet JP. High doses of CRISPR/Cas9 ribonucleoprotein efficiently induce gene knockout with low mosaicism in the hydrozoan Clytia hemisphaerica through microhomology-mediated deletion. Sci Rep 2018; 8:11734. [PMID: 30082705 PMCID: PMC6078951 DOI: 10.1038/s41598-018-30188-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/24/2018] [Indexed: 12/16/2022] Open
Abstract
Targeted mutagenesis using CRISPR/Cas9 technology has been shown to be a powerful approach to examine gene function in diverse metazoan species. One common drawback is that mixed genotypes, and thus variable phenotypes, arise in the F0 generation because incorrect DNA repair produces different mutations amongst cells of the developing embryo. We report here an effective method for gene knockout (KO) in the hydrozoan Clytia hemisphaerica, by injection into the egg of Cas9/sgRNA ribonucleoprotein complex (RNP). Expected phenotypes were observed in the F0 generation when targeting endogenous GFP genes, which abolished fluorescence in embryos, or CheRfx123 (that codes for a conserved master transcriptional regulator for ciliogenesis) which caused sperm motility defects. When high concentrations of Cas9 RNP were used, the mutations in target genes at F0 polyp or jellyfish stages were not random but consisted predominantly of one or two specific deletions between pairs of short microhomologies flanking the cleavage site. Such microhomology-mediated (MM) deletion is most likely caused by microhomology-mediated end-joining (MMEJ), which may be favoured in early stage embryos. This finding makes it very easy to isolate uniform, largely non-mosaic mutants with predictable genotypes in the F0 generation in Clytia, allowing rapid and reliable phenotype assessment.
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Affiliation(s)
- Tsuyoshi Momose
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV) 181 Chemin du Lazaret, 06230, Villefranche-sur-Mer, France.
| | - Anne De Cian
- Laboratoire Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Museum National d'Histoire Naturelle 43 rue Cuvier, 75005, Paris, France
| | - Kogiku Shiba
- Shimoda Marine Research Centre, University of Tsukuba, 5-10-1 Shimoda, Shizuoka, 415-0025, Japan
| | - Kazuo Inaba
- Shimoda Marine Research Centre, University of Tsukuba, 5-10-1 Shimoda, Shizuoka, 415-0025, Japan
| | - Carine Giovannangeli
- Laboratoire Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Museum National d'Histoire Naturelle 43 rue Cuvier, 75005, Paris, France
| | - Jean-Paul Concordet
- Laboratoire Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Museum National d'Histoire Naturelle 43 rue Cuvier, 75005, Paris, France
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31
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Simone BW, Martínez-Gálvez G, WareJoncas Z, Ekker SC. Fishing for understanding: Unlocking the zebrafish gene editor's toolbox. Methods 2018; 150:3-10. [PMID: 30076892 DOI: 10.1016/j.ymeth.2018.07.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/23/2018] [Accepted: 07/30/2018] [Indexed: 02/06/2023] Open
Abstract
The rapid growth of the field of gene editing can largely be attributed to the discovery and optimization of designer endonucleases. These include zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regular interspersed short palindromic repeat (CRISPR) systems including Cas9, Cas12a, and structure-guided nucleases. Zebrafish (Danio rerio) have proven to be a powerful model system for genome engineering testing and applications due to their external development, high fecundity, and ease of housing. As the zebrafish gene editing toolkit continues to grow, it is becoming increasingly important to understand when and how to utilize which of these technologies for maximum efficacy in a particular project. While CRISPR-Cas9 has brought broad attention to the field of genome engineering in recent years, designer endonucleases have been utilized in genome engineering for more than two decades. This chapter provides a brief overview of designer endonuclease and other gene editing technologies in zebrafish as well as some of their known functional benefits and limitations depending on specific project goals. Finally, selected prospects for additional gene editing tools are presented, promising additional options for directed genomic programming of this versatile animal model system.
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Affiliation(s)
- Brandon W Simone
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Zachary WareJoncas
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Stephen C Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA.
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32
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Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain. Nat Biotechnol 2018; 36:442-450. [PMID: 29608178 PMCID: PMC5938111 DOI: 10.1038/nbt.4103] [Citation(s) in RCA: 374] [Impact Index Per Article: 62.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 02/15/2018] [Indexed: 12/25/2022]
Abstract
The lineage relationships among the hundreds of cell types generated during development are difficult to reconstruct. A recent method, GESTALT, used CRISPR-Cas9 barcode editing for large-scale lineage tracing, but was restricted to early development and did not identify cell types. Here we present scGESTALT, which combines the lineage recording capabilities of GESTALT with cell-type identification by single-cell RNA sequencing. The method relies on an inducible system that enables barcodes to be edited at multiple time points, capturing lineage information from later stages of development. Sequencing of ~60,000 transcriptomes from the juvenile zebrafish brain identifies >100 cell types and marker genes. Using these data, we generate lineage trees with hundreds of branches that help uncover restrictions at the level of cell types, brain regions, and gene expression cascades during differentiation. scGESTALT can be applied to other multicellular organisms to simultaneously characterize molecular identities and lineage histories of thousands of cells during development and disease.
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33
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Bewg WP, Ci D, Tsai CJ. Genome Editing in Trees: From Multiple Repair Pathways to Long-Term Stability. FRONTIERS IN PLANT SCIENCE 2018; 9:1732. [PMID: 30532764 PMCID: PMC6265510 DOI: 10.3389/fpls.2018.01732] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 11/07/2018] [Indexed: 05/19/2023]
Abstract
The CRISPR technology continues to diversify with a broadening array of applications that touch all kingdoms of life. The simplicity, versatility and species-independent nature of the CRISPR system offers researchers a previously unattainable level of precision and control over genomic modifications. Successful applications in forest, fruit and nut trees have demonstrated the efficacy of CRISPR technology at generating null mutations in the first generation. This eliminates the lengthy process of multigenerational crosses to obtain homozygous knockouts (KO). The high degree of genome heterozygosity in outcrossing trees is both a challenge and an opportunity for genome editing: a challenge because sequence polymorphisms at the target site can render CRISPR editing ineffective; yet an opportunity because the power and specificity of CRISPR can be harnessed for allele-specific editing. Examination of CRISPR/Cas9-induced mutational profiles from published tree studies reveals the potential involvement of multiple DNA repair pathways, suggesting that the influence of sequence context at or near the target sites can define mutagenesis outcomes. For commercial production of elite trees that rely on vegetative propagation, available data suggest an excellent outlook for stable CRISPR-induced mutations and associated phenotypes over multiple clonal generations.
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Affiliation(s)
- William Patrick Bewg
- Warnell School of Forestry and Natural Resources, Department of Genetics, and Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Dong Ci
- Warnell School of Forestry and Natural Resources, Department of Genetics, and Department of Plant Biology, University of Georgia, Athens, GA, United States
- Department of Bioscience and Biotechnology, Beijing Forestry University, Beijing, China
| | - Chung-Jui Tsai
- Warnell School of Forestry and Natural Resources, Department of Genetics, and Department of Plant Biology, University of Georgia, Athens, GA, United States
- *Correspondence: Chung-Jui Tsai,
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34
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Mateos-Gomez PA, Kent T, Deng SK, McDevitt S, Kashkina E, Hoang TM, Pomerantz RT, Sfeir A. The helicase domain of Polθ counteracts RPA to promote alt-NHEJ. Nat Struct Mol Biol 2017; 24:1116-1123. [PMID: 29058711 PMCID: PMC6047744 DOI: 10.1038/nsmb.3494] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 09/22/2017] [Indexed: 12/15/2022]
Abstract
Mammalian polymerase theta (Polθ) is a multifunctional enzyme that promotes error-prone DNA repair by alternative nonhomologous end joining (alt-NHEJ). Here we present structure-function analyses that reveal that, in addition to the polymerase domain, Polθ-helicase activity plays a central role during double-strand break (DSB) repair. Our results show that the helicase domain promotes chromosomal translocations by alt-NHEJ in mouse embryonic stem cells and also suppresses CRISPR-Cas9- mediated gene targeting by homologous recombination (HR). In vitro assays demonstrate that Polθ-helicase activity facilitates the removal of RPA from resected DSBs to allow their annealing and subsequent joining by alt-NHEJ. Consistent with an antagonistic role for RPA during alt-NHEJ, inhibition of RPA1 enhances end joining and suppresses recombination. Taken together, our results reveal that the balance between HR and alt-NHEJ is controlled by opposing activities of Polθ and RPA, providing further insight into the regulation of repair-pathway choice in mammalian cells.
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Affiliation(s)
- Pedro A. Mateos-Gomez
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, USA
- Department of Cell Biology, New York University School of Medicine, New York, USA
| | - Tatiana Kent
- Temple University Lewis Katz School of Medicine, Philadelphia, USA
| | - Sarah K. Deng
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, USA
- Department of Cell Biology, New York University School of Medicine, New York, USA
| | - Shane McDevitt
- Temple University Lewis Katz School of Medicine, Philadelphia, USA
| | | | - Trung M. Hoang
- Temple University Lewis Katz School of Medicine, Philadelphia, USA
| | | | - Agnel Sfeir
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, USA
- Department of Cell Biology, New York University School of Medicine, New York, USA
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35
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Beagan K, Armstrong RL, Witsell A, Roy U, Renedo N, Baker AE, Schärer OD, McVey M. Drosophila DNA polymerase theta utilizes both helicase-like and polymerase domains during microhomology-mediated end joining and interstrand crosslink repair. PLoS Genet 2017; 13:e1006813. [PMID: 28542210 PMCID: PMC5466332 DOI: 10.1371/journal.pgen.1006813] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 06/09/2017] [Accepted: 05/12/2017] [Indexed: 11/20/2022] Open
Abstract
Double strand breaks (DSBs) and interstrand crosslinks (ICLs) are toxic DNA lesions that can be repaired through multiple pathways, some of which involve shared proteins. One of these proteins, DNA Polymerase θ (Pol θ), coordinates a mutagenic DSB repair pathway named microhomology-mediated end joining (MMEJ) and is also a critical component for bypass or repair of ICLs in several organisms. Pol θ contains both polymerase and helicase-like domains that are tethered by an unstructured central region. While the role of the polymerase domain in promoting MMEJ has been studied extensively both in vitro and in vivo, a function for the helicase-like domain, which possesses DNA-dependent ATPase activity, remains unclear. Here, we utilize genetic and biochemical analyses to examine the roles of the helicase-like and polymerase domains of Drosophila Pol θ. We demonstrate an absolute requirement for both polymerase and ATPase activities during ICL repair in vivo. However, similar to mammalian systems, polymerase activity, but not ATPase activity, is required for ionizing radiation-induced DSB repair. Using a site-specific break repair assay, we show that overall end-joining efficiency is not affected in ATPase-dead mutants, but there is a significant decrease in templated insertion events. In vitro, Pol θ can efficiently bypass a model unhooked nitrogen mustard crosslink and promote DNA synthesis following microhomology annealing, although ATPase activity is not required for these functions. Together, our data illustrate the functional importance of the helicase-like domain of Pol θ and suggest that its tethering to the polymerase domain is important for its multiple functions in DNA repair and damage tolerance. Error-prone DNA Polymerase θ (Pol θ) plays a conserved role in a mutagenic DNA double-strand break repair mechanism called microhomology-mediated end joining (MMEJ). In many organisms, it also participates in a process crucial to the removal/repair of DNA interstrand crosslinks. The exact mechanism by which Pol θ promotes these processes is unclear, but a clue may lie in its dual-domain structure. While the role of its polymerase domain has been well-studied, the function of its helicase-like domain remains an open question. Here we report an absolute requirement for ATPase activity of the helicase-like domain during interstrand crosslink repair in Drosophila melanogaster. We also find that although end joining frequency does not decrease in ATPase-dead mutants, ATPase activity is critical for generating templated insertions. Using purified Pol θ protein, we show that it can bypass synthetic substrates mimicking interstrand crosslink intermediates and can promote MMEJ-like reactions with partial double-stranded and single-stranded DNA. Together, these data demonstrate a novel function for the helicase-like domain of Pol θ in both interstrand crosslink repair and MMEJ and provide insight into why the dual-domain structure has been conserved throughout evolution.
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Affiliation(s)
- Kelly Beagan
- Department of Biology, Tufts University, Medford, Massachusetts
| | | | - Alice Witsell
- Department of Biology, Tufts University, Medford, Massachusetts
| | - Upasana Roy
- Department of Chemistry and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, United States of America
| | - Nikolai Renedo
- Department of Biology, Tufts University, Medford, Massachusetts
| | - Amy E. Baker
- Department of Biology, Tufts University, Medford, Massachusetts
| | - Orlando D. Schärer
- Department of Chemistry and Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, United States of America
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Korea and Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Mitch McVey
- Department of Biology, Tufts University, Medford, Massachusetts
- * E-mail:
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36
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Albadri S, Del Bene F, Revenu C. Genome editing using CRISPR/Cas9-based knock-in approaches in zebrafish. Methods 2017; 121-122:77-85. [PMID: 28300641 DOI: 10.1016/j.ymeth.2017.03.005] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/13/2017] [Accepted: 03/03/2017] [Indexed: 12/19/2022] Open
Abstract
With its variety of applications, the CRISPR/Cas9 genome editing technology has been rapidly evolving in the last few years. In the zebrafish community, knock-out reports are constantly increasing but insertion studies have been so far more challenging. With this review, we aim at giving an overview of the homologous directed repair (HDR)-based knock-in generation in zebrafish. We address the critical points and limitations of the procedure such as cutting efficiency of the chosen single guide RNA, use of cas9 mRNA or Cas9 protein, homology arm size etc. but also ways to circumvent encountered issues with HDR insertions by the development of non-homologous dependent strategies. While imprecise, these homology-independent mechanisms based on non-homologous-end-joining (NHEJ) repair have been employed in zebrafish to generate reporter lines or to accurately edit an open reading frame by the use of intron-targeting modifications. Therefore, with higher efficiency and insertion rate, NHEJ-based knock-in seems to be a promising approach to target endogenous loci and to circumvent the limitations of HDR whenever it is possible and appropriate. In this perspective, we propose new strategies to generate cDNA edited or tagged insertions, which once established will constitute a new and versatile toolbox for CRISPR/Cas9-based knock-ins in zebrafish.
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Affiliation(s)
- Shahad Albadri
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, 75248 Paris Cedex 05, France
| | - Filippo Del Bene
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, 75248 Paris Cedex 05, France.
| | - Céline Revenu
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, 75248 Paris Cedex 05, France
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37
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van Bostelen I, Tijsterman M. Combined loss of three DNA damage response pathways renders C. elegans intolerant to light. DNA Repair (Amst) 2017; 54:55-62. [PMID: 28472716 DOI: 10.1016/j.dnarep.2017.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/17/2017] [Accepted: 04/10/2017] [Indexed: 12/20/2022]
Abstract
Infliction of DNA damage initiates a complex cellular reaction - the DNA damage response - that involves both signaling and DNA repair networks with many redundancies and parallel pathways. Here, we reveal the three strategies that the simple multicellular eukaryote, C. elegans, uses to deal with DNA damage induced by light. Separately inactivating repair or replicative bypass of photo-lesions results in cellular hypersensitivity towards UV-light, but impeding repair of replication associated DNA breaks does not. Yet, we observe an unprecedented synergistic relationship when these pathways are inactivated in combination. C. elegans mutants that lack nucleotide excision repair (NER), translesion synthesis (TLS) and alternative end joining (altEJ) grow undisturbed in the dark, but become sterile when grown in light. Even exposure to very low levels of normal daylight impedes animal growth. We show that NER and TLS operate to suppress the formation of lethal DNA breaks that require polymerase theta-mediated end joining (TMEJ) for their repair. Our data testifies to the enormous genotoxicity of light and to the demand of multiple layers of protection against an environmental threat that is so common.
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Affiliation(s)
- Ivo van Bostelen
- Department of Human Genetics, Leiden University Medical Centre, 2300 RC, Leiden, The Netherlands
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Centre, 2300 RC, Leiden, The Netherlands.
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Li M, Zhao L, Page-McCaw PS, Chen W. Zebrafish Genome Engineering Using the CRISPR-Cas9 System. Trends Genet 2016; 32:815-827. [PMID: 27836208 DOI: 10.1016/j.tig.2016.10.005] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 10/05/2016] [Accepted: 10/10/2016] [Indexed: 12/21/2022]
Abstract
Geneticists have long sought the ability to manipulate vertebrate genomes by directly altering the information encoded in specific genes. The recently discovered clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 endonuclease has the ability to bind single loci within vertebrate genomes and generate double-strand breaks (DSBs) at those sites. These DSBs induce an endogenous DSB repair response that results in small insertions or deletions at the targeted site. Alternatively, a template can be supplied, in which case homology-directed repair results in the generation of engineered alleles at the break site. These changes alter the function of the targeted gene facilitating the analysis of gene function. This tool has been widely adopted in the zebrafish model; we discuss the development of this system in the zebrafish and how it can be manipulated to facilitate genome engineering.
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Affiliation(s)
- Mingyu Li
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Liyuan Zhao
- Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, China
| | - Patrick S Page-McCaw
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Division of Nephrology and Hypertension, Vanderbilt Center for Kidney Disease, Vanderbilt University Medical Center, Nashville, TN.
| | - Wenbiao Chen
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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