1
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Mehryar MM, Shi X, Li J, Wu Q. DNA polymerases in precise and predictable CRISPR/Cas9-mediated chromosomal rearrangements. BMC Biol 2023; 21:288. [PMID: 38066536 PMCID: PMC10709867 DOI: 10.1186/s12915-023-01784-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Recent studies have shown that, owning to its cohesive cleavage, Cas9-mediated CRISPR gene editing outcomes at junctions of chromosomal rearrangements or DNA-fragment editing are precise and predictable; however, the underlying mechanisms are poorly understood due to lack of suitable assay system and analysis tool. RESULTS Here we developed a customized computer program to take account of staggered or cohesive Cas9 cleavage and to rapidly process large volumes of junctional sequencing reads from chromosomal rearrangements or DNA-fragment editing, including DNA-fragment inversions, duplications, and deletions. We also established a sensitive assay system using HPRT1 and DCK as reporters for cell growth during DNA-fragment editing by Cas9 with dual sgRNAs and found prominent large resections or long deletions at junctions of chromosomal rearrangements. In addition, we found that knockdown of PolQ (encoding Polθ polymerase), which has a prominent role in theta-mediated end joining (TMEJ) or microhomology-mediated end joining (MMEJ), results in increased large resections but decreased small deletions. We also found that the mechanisms for generating small deletions of 1bp and >1bp during DNA-fragment editing are different with regard to their opposite dependencies on Polθ and Polλ (encoded by the PolL gene). Specifically, Polθ suppresses 1bp deletions but promotes >1bp deletions, whereas Polλ promotes 1bp deletions but suppresses >1bp deletions. Finally, we found that Polλ is the main DNA polymerase responsible for fill-in of the 5' overhangs of staggered Cas9 cleavage ends. CONCLUSIONS These findings contribute to our understanding of the molecular mechanisms of CRISPR/Cas9-mediated DNA-fragment editing and have important implications for controllable, precise, and predictable gene editing.
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Affiliation(s)
- Mohammadreza M Mehryar
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- WLA Laboratories, Shanghai, 201203, China
| | - Xin Shi
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- WLA Laboratories, Shanghai, 201203, China
| | - Jingwei Li
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- WLA Laboratories, Shanghai, 201203, China
| | - Qiang Wu
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, School of Life Sciences and Biotechnology, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
- WLA Laboratories, Shanghai, 201203, China.
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2
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Heyza JR, Mikhova M, Schmidt JC. Live cell single-molecule imaging to study DNA repair in human cells. DNA Repair (Amst) 2023; 129:103540. [PMID: 37467632 PMCID: PMC10530516 DOI: 10.1016/j.dnarep.2023.103540] [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: 03/31/2023] [Revised: 06/29/2023] [Accepted: 07/05/2023] [Indexed: 07/21/2023]
Abstract
The genetic material in human cells is continuously exposed to a wide variety of insults that can induce different DNA lesions. To maintain genomic stability and prevent potentially deleterious genetic changes caused by DNA damage, mammalian cells have evolved a number of pathways that repair specific types of DNA damage. These DNA repair pathways vary in their accuracy, some providing high-fidelity repair while others are error-prone and are only activated as a last resort. Adding additional complexity to cellular mechanisms of DNA repair is the DNA damage response which is a sophisticated a signaling network that coordinates repair outcomes, cell-cycle checkpoint activation, and cell fate decisions. As a result of the sheer complexity of the various DNA repair pathways and the DNA damage response there are large gaps in our understanding of the molecular mechanisms underlying DNA damage repair in human cells. A key unaddressed question is how the dynamic recruitment of DNA repair factors contributes to repair kinetics and repair pathway choice in human cells. Methodological advances in live cell single-molecule imaging over the last decade now allow researchers to directly observe and analyze the dynamics of DNA repair proteins in living cells with high spatiotemporal resolution. Live cell single-molecule imaging combined with single-particle tracking can provide direct insight into the biochemical reactions that control DNA repair and has the power to identify previously unobservable processes in living cells. This review summarizes the main considerations for experimental design and execution for live cell single-molecule imaging experiments and describes how they can be used to define the molecular mechanisms of DNA damage repair in mammalian cells.
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Affiliation(s)
- Joshua R Heyza
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - Mariia Mikhova
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Jens C Schmidt
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA; Department of Obstetrics, Gynecology, and Reproductive Biology, Michigan State University, East Lansing, MI, USA.
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3
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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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4
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Chen X, McAndrew MJ, Lapinaite A. Unlocking the secrets of ABEs: the molecular mechanism behind their specificity. Biochem Soc Trans 2023; 51:1635-1646. [PMID: 37526140 PMCID: PMC10586758 DOI: 10.1042/bst20221508] [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: 04/13/2023] [Revised: 07/13/2023] [Accepted: 07/18/2023] [Indexed: 08/02/2023]
Abstract
CRISPR-Cas, the bacterial immune systems, have transformed the field of genome editing by providing efficient, easily programmable, and accessible tools for targeted genome editing. DNA base editors (BE) are state-of-the-art CRISPR-based technology, allowing for targeted modifications of individual nucleobases within the genome. Among the BEs, adenine base editors (ABEs) have shown great potential due to their ability to convert A-to-G with high efficiency. However, current ABEs have limitations in terms of their specificity and targeting range. In this review, we provide an overview of the molecular mechanism of ABEs, with a focus on the mechanism of deoxyadenosine deamination by evolved tRNA-specific adenosine deaminase (TadA). We discuss how mutations and adjustments introduced via both directed evolution as well as rational design have improved ABE efficiency and specificity. This review offers insights into the molecular mechanism of ABEs, providing a roadmap for future developments in the precision genome editing field.
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Affiliation(s)
- Xiaoyu Chen
- School of Molecular Sciences, Arizona State University, Tempe, AZ, U.S.A
| | | | - Audrone Lapinaite
- School of Molecular Sciences, Arizona State University, Tempe, AZ, U.S.A
- Arizona State University-Banner Neurodegenerative Disease Research Center at the Biodesign Institute, Arizona State University, Tempe, AZ, U.S.A
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, U.S.A
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5
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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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6
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Multifaceted Nature of DNA Polymerase θ. Int J Mol Sci 2023; 24:ijms24043619. [PMID: 36835031 PMCID: PMC9962433 DOI: 10.3390/ijms24043619] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/26/2023] [Accepted: 02/02/2023] [Indexed: 02/15/2023] Open
Abstract
DNA polymerase θ belongs to the A family of DNA polymerases and plays a key role in DNA repair and damage tolerance, including double-strand break repair and DNA translesion synthesis. Pol θ is often overexpressed in cancer cells and promotes their resistance to chemotherapeutic agents. In this review, we discuss unique biochemical properties and structural features of Pol θ, its multiple roles in protection of genome stability and the potential of Pol θ as a target for cancer treatment.
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7
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Wang S, Meyer DH, Schumacher B. Inheritance of paternal DNA damage by histone-mediated repair restriction. Nature 2023; 613:365-374. [PMID: 36544019 PMCID: PMC9834056 DOI: 10.1038/s41586-022-05544-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 11/08/2022] [Indexed: 12/24/2022]
Abstract
How paternal exposure to ionizing radiation affects genetic inheritance and disease risk in the offspring has been a long-standing question in radiation biology. In humans, nearly 80% of transmitted mutations arise in the paternal germline1, but the transgenerational effects of ionizing radiation exposure has remained controversial and the mechanisms are unknown. Here we show that in sex-separated Caenorhabditis elegans strains, paternal, but not maternal, exposure to ionizing radiation leads to transgenerational embryonic lethality. The offspring of irradiated males displayed various genome instability phenotypes, including DNA fragmentation, chromosomal rearrangement and aneuploidy. Paternal DNA double strand breaks were repaired by maternally provided error-prone polymerase theta-mediated end joining. Mechanistically, we show that depletion of an orthologue of human histone H1.0, HIS-24, or the heterochromatin protein HPL-1, could significantly reverse the transgenerational embryonic lethality. Removal of HIS-24 or HPL-1 reduced histone 3 lysine 9 dimethylation and enabled error-free homologous recombination repair in the germline of the F1 generation from ionizing radiation-treated P0 males, consequently improving the viability of the F2 generation. This work establishes the mechanistic underpinnings of the heritable consequences of paternal radiation exposure on the health of offspring, which may lead to congenital disorders and cancer in humans.
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Affiliation(s)
- Siyao Wang
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University Hospital and University of Cologne, Cologne, Germany.
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
| | - David H Meyer
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University Hospital and University of Cologne, Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University Hospital and University of Cologne, Cologne, Germany.
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
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8
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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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9
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Hanscom T, Woodward N, Batorsky R, Brown AJ, Roberts SA, McVey M. Characterization of sequence contexts that favor alternative end joining at Cas9-induced double-strand breaks. Nucleic Acids Res 2022; 50:7465-7478. [PMID: 35819195 PMCID: PMC9303309 DOI: 10.1093/nar/gkac575] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/16/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Alternative end joining (alt-EJ) mechanisms, such as polymerase theta-mediated end joining, are increasingly recognized as important contributors to inaccurate double-strand break repair. We previously proposed an alt-EJ model whereby short DNA repeats near a double-strand break anneal to form secondary structures that prime limited DNA synthesis. The nascent DNA then pairs with microhomologous sequences on the other break end. This synthesis-dependent microhomology-mediated end joining (SD-MMEJ) explains many of the alt-EJ repair products recovered following I-SceI nuclease cutting in Drosophila. However, sequence-specific factors that influence SD-MMEJ repair remain to be fully characterized. Here, we expand the utility of the SD-MMEJ model through computational analysis of repair products at Cas9-induced double-strand breaks for 1100 different sequence contexts. We find evidence at single nucleotide resolution for sequence characteristics that drive successful SD-MMEJ repair. These include optimal primer repeat length, distance of repeats from the break, flexibility of DNA sequence between primer repeats, and positioning of microhomology templates relative to preferred primer repeats. In addition, we show that DNA polymerase theta is necessary for most SD-MMEJ repair at Cas9 breaks. The analysis described here includes a computational pipeline that can be utilized to characterize preferred mechanisms of alt-EJ repair in any sequence context.
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Affiliation(s)
- Terrence Hanscom
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155, USA
| | - Nicholas Woodward
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155, USA
| | - Rebecca Batorsky
- Data Intensive Studies Center, Tufts University, 177 College Ave, Medford, MA 02155, USA
| | - Alexander J Brown
- School of Molecular Biosciences, Washington State University, P100 Dairy Road, Pullman, WA 99164, USA
| | - Steven A Roberts
- School of Molecular Biosciences, Washington State University, P100 Dairy Road, Pullman, WA 99164, USA
| | - Mitch McVey
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155, USA
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10
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Huang J, Cook DE. The contribution of DNA repair pathways to genome editing and evolution in filamentous pathogens. FEMS Microbiol Rev 2022; 46:6638986. [PMID: 35810003 PMCID: PMC9779921 DOI: 10.1093/femsre/fuac035] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/29/2022] [Accepted: 07/06/2022] [Indexed: 01/09/2023] Open
Abstract
DNA double-strand breaks require repair or risk corrupting the language of life. To ensure genome integrity and viability, multiple DNA double-strand break repair pathways function in eukaryotes. Two such repair pathways, canonical non-homologous end joining and homologous recombination, have been extensively studied, while other pathways such as microhomology-mediated end joint and single-strand annealing, once thought to serve as back-ups, now appear to play a fundamental role in DNA repair. Here, we review the molecular details and hierarchy of these four DNA repair pathways, and where possible, a comparison for what is known between animal and fungal models. We address the factors contributing to break repair pathway choice, and aim to explore our understanding and knowledge gaps regarding mechanisms and regulation in filamentous pathogens. We additionally discuss how DNA double-strand break repair pathways influence genome engineering results, including unexpected mutation outcomes. Finally, we review the concept of biased genome evolution in filamentous pathogens, and provide a model, termed Biased Variation, that links DNA double-strand break repair pathways with properties of genome evolution. Despite our extensive knowledge for this universal process, there remain many unanswered questions, for which the answers may improve genome engineering and our understanding of genome evolution.
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Affiliation(s)
- Jun Huang
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, Throckmorton Hall, Manhattan, KS 66506, United States
| | - David E Cook
- Corresponding author: 1712 Claflin Road, 4004 Throckmorton Hall, Manhattan, KS 66502, United States. E-mail:
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11
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Kamp JA, Lemmens BBLG, Romeijn RJ, González-Prieto R, Olsen J, Vertegaal ACO, van Schendel R, Tijsterman M. THO complex deficiency impairs DNA double-strand break repair via the RNA surveillance kinase SMG-1. Nucleic Acids Res 2022; 50:6235-6250. [PMID: 35670662 PMCID: PMC9226523 DOI: 10.1093/nar/gkac472] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 05/11/2022] [Accepted: 06/02/2022] [Indexed: 12/25/2022] Open
Abstract
The integrity and proper expression of genomes are safeguarded by DNA and RNA surveillance pathways. While many RNA surveillance factors have additional functions in the nucleus, little is known about the incidence and physiological impact of converging RNA and DNA signals. Here, using genetic screens and genome-wide analyses, we identified unforeseen SMG-1-dependent crosstalk between RNA surveillance and DNA repair in living animals. Defects in RNA processing, due to viable THO complex or PNN-1 mutations, induce a shift in DNA repair in dividing and non-dividing tissues. Loss of SMG-1, an ATM/ATR-like kinase central to RNA surveillance by nonsense-mediated decay (NMD), restores DNA repair and radio-resistance in THO-deficient animals. Mechanistically, we find SMG-1 and its downstream target SMG-2/UPF1, but not NMD per se, to suppress DNA repair by non-homologous end-joining in favour of single strand annealing. We postulate that moonlighting proteins create short-circuits in vivo, allowing aberrant RNA to redirect DNA repair.
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Affiliation(s)
| | | | - Ron J Romeijn
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Román González-Prieto
- Department of Cell & Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Alfred C O Vertegaal
- Department of Cell & Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Robin van Schendel
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
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12
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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: 65] [Impact Index Per Article: 32.5] [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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13
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Sharma VK, Marla S, Zheng W, Mishra D, Huang J, Zhang W, Morris GP, Cook DE. CRISPR guides induce gene silencing in plants in the absence of Cas. Genome Biol 2022; 23:6. [PMID: 34980227 PMCID: PMC8722000 DOI: 10.1186/s13059-021-02586-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 12/17/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND RNA-targeting CRISPR-Cas can provide potential advantages over DNA editing, such as avoiding pleiotropic effects of genome editing, providing precise spatiotemporal regulation, and expanded function including antiviral immunity. RESULTS Here, we report the use of CRISPR-Cas13 in plants to reduce both viral and endogenous RNA. Unexpectedly, we observe that crRNA designed to guide Cas13 could, in the absence of the Cas13 protein, cause substantial reduction in RNA levels as well. We demonstrate Cas13-independent guide-induced gene silencing (GIGS) in three plant species, including stable transgenic Arabidopsis. Small RNA sequencing during GIGS identifies the production of small RNA that extend beyond the crRNA expressed sequence in samples expressing multi-guide crRNA. Additionally, we demonstrate that mismatches in guide sequences at position 10 and 11 abolish GIGS. Finally, we show that GIGS is elicited by guides that lack the Cas13 direct repeat and can extend to Cas9 designed crRNA of at least 28 base pairs, indicating that GIGS can be elicited through a variety of guide designs and is not dependent on Cas13 crRNA sequences or design. CONCLUSIONS Collectively, our results suggest that GIGS utilizes endogenous RNAi machinery despite the fact that crRNA are unlike canonical triggers of RNAi such as miRNA, hairpins, or long double-stranded RNA. Given similar evidence of Cas13-independent silencing in an insect system, it is likely GIGS is active across many eukaryotes. Our results show that GIGS offers a novel and flexible approach to RNA reduction with potential benefits over existing technologies for crop improvement and functional genomics.
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Affiliation(s)
| | - Sandeep Marla
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Wenguang Zheng
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Divya Mishra
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Jun Huang
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Wei Zhang
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | | | - David Edward Cook
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.
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14
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van Tol N, van Schendel R, Bos A, van Kregten M, de Pater S, Hooykaas PJ, Tijsterman M. Gene targeting in polymerase theta-deficient Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:112-125. [PMID: 34713516 PMCID: PMC9299229 DOI: 10.1111/tpj.15557] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 10/19/2021] [Accepted: 10/25/2021] [Indexed: 05/26/2023]
Abstract
Agrobacterium tumefaciens-mediated transformation has been for decades the preferred tool to generate transgenic plants. During this process, a T-DNA carrying transgenes is transferred from the bacterium to plant cells, where it randomly integrates into the genome via polymerase theta (Polθ)-mediated end joining (TMEJ). Targeting of the T-DNA to a specific genomic locus via homologous recombination (HR) is also possible, but such gene targeting (GT) events occur at low frequency and are almost invariably accompanied by random integration events. An additional complexity is that the product of recombination between T-DNA and target locus may not only map to the target locus (true GT), but also to random positions in the genome (ectopic GT). In this study, we have investigated how TMEJ functionality affects the biology of GT in plants, by using Arabidopsis thaliana mutated for the TEBICHI gene, which encodes for Polθ. Whereas in TMEJ-proficient plants we predominantly found GT events accompanied by random T-DNA integrations, GT events obtained in the teb mutant background lacked additional T-DNA copies, corroborating the essential role of Polθ in T-DNA integration. Polθ deficiency also prevented ectopic GT events, suggesting that the sequence of events leading up to this outcome requires TMEJ. Our findings provide insights that can be used for the development of strategies to obtain high-quality GT events in crop plants.
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Affiliation(s)
- Niels van Tol
- Institute of Biology LeidenLeiden UniversitySylviusweg 72Leiden2333 BEThe Netherlands
| | - Robin van Schendel
- Department of Human GeneticsLeiden University Medical CenterEinthovenweg 20Leiden2300 RCThe Netherlands
| | - Alex Bos
- Institute of Biology LeidenLeiden UniversitySylviusweg 72Leiden2333 BEThe Netherlands
| | - Maartje van Kregten
- Institute of Biology LeidenLeiden UniversitySylviusweg 72Leiden2333 BEThe Netherlands
| | - Sylvia de Pater
- Institute of Biology LeidenLeiden UniversitySylviusweg 72Leiden2333 BEThe Netherlands
| | - Paul J.J. Hooykaas
- Institute of Biology LeidenLeiden UniversitySylviusweg 72Leiden2333 BEThe Netherlands
| | - Marcel Tijsterman
- Institute of Biology LeidenLeiden UniversitySylviusweg 72Leiden2333 BEThe Netherlands
- Department of Human GeneticsLeiden University Medical CenterEinthovenweg 20Leiden2300 RCThe Netherlands
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15
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Helicase Q promotes homology-driven DNA double-strand break repair and prevents tandem duplications. Nat Commun 2021; 12:7126. [PMID: 34880204 PMCID: PMC8654963 DOI: 10.1038/s41467-021-27408-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 11/16/2021] [Indexed: 11/09/2022] Open
Abstract
DNA double-strand breaks are a major threat to cellular survival and genetic integrity. In addition to high fidelity repair, three intrinsically mutagenic DNA break repair routes have been described, i.e. single-strand annealing (SSA), polymerase theta-mediated end-joining (TMEJ) and residual ill-defined microhomology-mediated end-joining (MMEJ) activity. Here, we identify C. elegans Helicase Q (HELQ-1) as being essential for MMEJ as well as for SSA. We also find HELQ-1 to be crucial for the synthesis-dependent strand annealing (SDSA) mode of homologous recombination (HR). Loss of HELQ-1 leads to increased genome instability: patchwork insertions arise at deletion junctions due to abortive rounds of polymerase theta activity, and tandem duplications spontaneously accumulate in genomes of helq-1 mutant animals as a result of TMEJ of abrogated HR intermediates. Our work thus implicates HELQ activity for all DSB repair modes guided by complementary base pairs and provides mechanistic insight into mutational signatures common in HR-defective cancers.
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16
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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: 9] [Impact Index Per Article: 3.0] [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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17
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Zatreanu D, Robinson HMR, Alkhatib O, Boursier M, Finch H, Geo L, Grande D, Grinkevich V, Heald RA, Langdon S, Majithiya J, McWhirter C, Martin NMB, Moore S, Neves J, Rajendra E, Ranzani M, Schaedler T, Stockley M, Wiggins K, Brough R, Sridhar S, Gulati A, Shao N, Badder LM, Novo D, Knight EG, Marlow R, Haider S, Callen E, Hewitt G, Schimmel J, Prevo R, Alli C, Ferdinand A, Bell C, Blencowe P, Bot C, Calder M, Charles M, Curry J, Ekwuru T, Ewings K, Krajewski W, MacDonald E, McCarron H, Pang L, Pedder C, Rigoreau L, Swarbrick M, Wheatley E, Willis S, Wong AC, Nussenzweig A, Tijsterman M, Tutt A, Boulton SJ, Higgins GS, Pettitt SJ, Smith GCM, Lord CJ. Polθ inhibitors elicit BRCA-gene synthetic lethality and target PARP inhibitor resistance. Nat Commun 2021; 12:3636. [PMID: 34140467 PMCID: PMC8211653 DOI: 10.1038/s41467-021-23463-8] [Citation(s) in RCA: 144] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 04/30/2021] [Indexed: 02/05/2023] Open
Abstract
To identify approaches to target DNA repair vulnerabilities in cancer, we discovered nanomolar potent, selective, low molecular weight (MW), allosteric inhibitors of the polymerase function of DNA polymerase Polθ, including ART558. ART558 inhibits the major Polθ-mediated DNA repair process, Theta-Mediated End Joining, without targeting Non-Homologous End Joining. In addition, ART558 elicits DNA damage and synthetic lethality in BRCA1- or BRCA2-mutant tumour cells and enhances the effects of a PARP inhibitor. Genetic perturbation screening revealed that defects in the 53BP1/Shieldin complex, which cause PARP inhibitor resistance, result in in vitro and in vivo sensitivity to small molecule Polθ polymerase inhibitors. Mechanistically, ART558 increases biomarkers of single-stranded DNA and synthetic lethality in 53BP1-defective cells whilst the inhibition of DNA nucleases that promote end-resection reversed these effects, implicating these in the synthetic lethal mechanism-of-action. Taken together, these observations describe a drug class that elicits BRCA-gene synthetic lethality and PARP inhibitor synergy, as well as targeting a biomarker-defined mechanism of PARPi-resistance.
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Affiliation(s)
- Diana Zatreanu
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Helen M R Robinson
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Omar Alkhatib
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Marie Boursier
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Harry Finch
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Lerin Geo
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Diego Grande
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Vera Grinkevich
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Robert A Heald
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Sophie Langdon
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Jayesh Majithiya
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Claire McWhirter
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Niall M B Martin
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Shaun Moore
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Joana Neves
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Eeson Rajendra
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Marco Ranzani
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Theresia Schaedler
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Martin Stockley
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Kimberley Wiggins
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Rachel Brough
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Sandhya Sridhar
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Aditi Gulati
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Nan Shao
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Luned M Badder
- The Breast Cancer Now Research Unit, King's College London, London, UK
| | - Daniela Novo
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Eleanor G Knight
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Rebecca Marlow
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Research Unit, King's College London, London, UK
| | - Syed Haider
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Joost Schimmel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Remko Prevo
- Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, UK
| | - Christina Alli
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Amanda Ferdinand
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Cameron Bell
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Peter Blencowe
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Chris Bot
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Mathew Calder
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Mark Charles
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Jayne Curry
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Tennyson Ekwuru
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Katherine Ewings
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Wojciech Krajewski
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Ellen MacDonald
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Hollie McCarron
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Leon Pang
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Chris Pedder
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Laurent Rigoreau
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Martin Swarbrick
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Ed Wheatley
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Simon Willis
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Ai Ching Wong
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Andre Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Andrew Tutt
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Research Unit, King's College London, London, UK
| | - Simon J Boulton
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
- The Francis Crick Institute, London, UK
| | - Geoff S Higgins
- Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, UK
| | - Stephen J Pettitt
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK.
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
| | - Graeme C M Smith
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK.
| | - Christopher J Lord
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK.
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
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18
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Froehlich JJ, Uyar B, Herzog M, Theil K, Glažar P, Akalin A, Rajewsky N. Parallel genetics of regulatory sequences using scalable genome editing in vivo. Cell Rep 2021; 35:108988. [PMID: 33852857 DOI: 10.1016/j.celrep.2021.108988] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 01/13/2021] [Accepted: 03/23/2021] [Indexed: 12/27/2022] Open
Abstract
How regulatory sequences control gene expression is fundamental for explaining phenotypes in health and disease. Regulatory elements must ultimately be understood within their genomic environment and development- or tissue-specific contexts. Because this is technically challenging, few regulatory elements have been characterized in vivo. Here, we use inducible Cas9 and multiplexed guide RNAs to create hundreds of mutations in enhancers/promoters and 3' UTRs of 16 genes in C. elegans. Our software crispr-DART analyzes indel mutations in targeted DNA sequencing. We quantify the impact of mutations on expression and fitness by targeted RNA sequencing and DNA sampling. When applying our approach to the lin-41 3' UTR, generating hundreds of mutants, we find that the two adjacent binding sites for the miRNA let-7 can regulate lin-41 expression independently of each other. Finally, we map regulatory genotypes to phenotypic traits for several genes. Our approach enables parallel analysis of regulatory sequences directly in animals.
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Affiliation(s)
- Jonathan J Froehlich
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Bora Uyar
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Margareta Herzog
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Kathrin Theil
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Petar Glažar
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Altuna Akalin
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Nikolaus Rajewsky
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany.
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19
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Suehiro Y, Yoshina S, Motohashi T, Iwata S, Dejima K, Mitani S. Efficient collection of a large number of mutations by mutagenesis of DNA damage response defective animals. Sci Rep 2021; 11:7630. [PMID: 33828169 PMCID: PMC8027614 DOI: 10.1038/s41598-021-87226-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/24/2021] [Indexed: 02/01/2023] Open
Abstract
With the development of massive parallel sequencing technology, it has become easier to establish new model organisms that are ideally suited to the specific biological phenomena of interest. Considering the history of research using classical model organisms, we believe that the efficient construction and sharing of gene mutation libraries will facilitate the progress of studies using these new model organisms. Using C. elegans, we applied the TMP/UV mutagenesis method to animals lacking function in the DNA damage response genes atm-1 and xpc-1. This method produces genetic mutations three times more efficiently than mutagenesis of wild-type animals. Furthermore, we confirmed that the use of next-generation sequencing and the elimination of false positives through machine learning could automate the process of mutation identification with an accuracy of over 95%. Eventually, we sequenced the whole genomes of 488 strains and isolated 981 novel mutations generated by the present method; these strains have been made available to anyone who wants to use them. Since the targeted DNA damage response genes are well conserved and the mutagens used in this study are also effective in a variety of species, we believe that our method is generally applicable to a wide range of animal species.
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Affiliation(s)
- Yuji Suehiro
- Department of Physiology, Tokyo Women's Medical University, Shinjuku, Tokyo, Japan
| | - Sawako Yoshina
- Department of Physiology, Tokyo Women's Medical University, Shinjuku, Tokyo, Japan
| | - Tomoko Motohashi
- Department of Physiology, Tokyo Women's Medical University, Shinjuku, Tokyo, Japan
| | - Satoru Iwata
- Chubu University Center for Education in Laboratory Animal Research, Kasugai, Aichi, Japan
| | - Katsufumi Dejima
- Department of Physiology, Tokyo Women's Medical University, Shinjuku, Tokyo, Japan
| | - Shohei Mitani
- Department of Physiology, Tokyo Women's Medical University, Shinjuku, Tokyo, Japan.
- Tokyo Women's Medical University Institute for Integrated Medical Sciences, Shinjuku, Tokyo, Japan.
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20
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Zahn KE, Jensen RB, Wood RD, Doublié S. WITHDRAWN: Human DNA polymerase θ harbors DNA end-trimming activity critical for DNA repair. Mol Cell 2021; 81:1534-1547.e4. [PMID: 33577776 PMCID: PMC8231307 DOI: 10.1016/j.molcel.2021.01.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/24/2020] [Accepted: 01/15/2021] [Indexed: 12/12/2022]
Abstract
Cancers with hereditary defects in homologous recombination rely on DNA polymerase θ (pol θ) for repair of DNA double-strand breaks. During end joining, pol θ aligns microhomology tracts internal to 5'-resected broken ends. An unidentified nuclease trims the 3' ends before synthesis can occur. Here we report that a nuclease activity, which differs from the proofreading activity often associated with DNA polymerases, is intrinsic to the polymerase domain of pol θ. Like the DNA synthesis activity, the nuclease activity requires conserved metal-binding residues, metal ions, and dNTPs and is inhibited by ddNTPs or chain-terminated DNA. Our data indicate that pol θ repurposes metal ions in the polymerase active site for endonucleolytic cleavage and that the polymerase-active and end-trimming conformations of the enzyme are distinct. We reveal a nimble strategy of substrate processing that allows pol θ to trim or extend DNA depending on the DNA repair context.
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Affiliation(s)
- Karl E Zahn
- Department of Microbiology and Molecular Genetics, University of Vermont, 89 Beaumont Ave., Burlington, VT 05405, USA; Department of Therapeutic Radiology, Yale University, New Haven, CT 06510, USA
| | - Ryan B Jensen
- Department of Therapeutic Radiology, Yale University, New Haven, CT 06510, USA
| | - Richard D Wood
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 78957, USA.
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, 89 Beaumont Ave., Burlington, VT 05405, USA.
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21
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Toraason E, Horacek A, Clark C, Glover ML, Adler VL, Premkumar T, Salagean A, Cole F, Libuda DE. Meiotic DNA break repair can utilize homolog-independent chromatid templates in C. elegans. Curr Biol 2021; 31:1508-1514.e5. [PMID: 33740427 DOI: 10.1016/j.cub.2021.03.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 02/09/2021] [Accepted: 03/02/2021] [Indexed: 02/06/2023]
Abstract
During meiosis, the maintenance of genome integrity is critical for generating viable haploid gametes.1 In meiotic prophase I, double-strand DNA breaks (DSBs) are induced and a subset of these DSBs are repaired as interhomolog crossovers to ensure proper chromosome segregation. DSBs not resolved as crossovers with the homolog must be repaired by other pathways to ensure genome integrity.2 To determine if alternative repair templates can be engaged for meiotic DSB repair during oogenesis, we developed an assay to detect sister and/or intra-chromatid repair events at a defined DSB site during Caenorhabditis elegans meiosis. Using this assay, we directly demonstrate that the sister chromatid or the same DNA molecule can be engaged as a meiotic repair template for both crossover and noncrossover recombination, with noncrossover events being the predominant recombination outcome. We additionally find that the sister or intra-chromatid substrate is available as a recombination partner for DSBs induced throughout meiotic prophase I, including late prophase when the homolog is unavailable. Analysis of noncrossover conversion tract sequences reveals that DSBs are processed similarly throughout prophase I. We further present data indicating that the XPF-1 nuclease functions in late prophase to promote sister or intra-chromatid repair at steps of recombination following joint molecule processing. Despite its function in sister or intra-chromatid repair, we find that xpf-1 mutants do not exhibit severe defects in progeny viability following exposure to ionizing radiation. Overall, we propose that C. elegans XPF-1 may assist as an intersister or intrachromatid resolvase only in late prophase I.
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Affiliation(s)
- Erik Toraason
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1229 Franklin Boulevard, Eugene, OR 97403, USA
| | - Anna Horacek
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1229 Franklin Boulevard, Eugene, OR 97403, USA
| | - Cordell Clark
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1229 Franklin Boulevard, Eugene, OR 97403, USA
| | - Marissa L Glover
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1229 Franklin Boulevard, Eugene, OR 97403, USA
| | - Victoria L Adler
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1229 Franklin Boulevard, Eugene, OR 97403, USA
| | - Tolkappiyan Premkumar
- Department of Epigenetics and Molecular Carcinogenesis, MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX 78957, USA
| | - Alina Salagean
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1229 Franklin Boulevard, Eugene, OR 97403, USA
| | - Francesca Cole
- Department of Epigenetics and Molecular Carcinogenesis, MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX 78957, USA
| | - Diana E Libuda
- Institute of Molecular Biology, Department of Biology, University of Oregon, 1229 Franklin Boulevard, Eugene, OR 97403, USA.
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22
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Chandramouly G, Liao S, Rusanov T, Borisonnik N, Calbert ML, Kent T, Sullivan-Reed K, Vekariya U, Kashkina E, Skorski T, Yan H, Pomerantz RT. Polθ promotes the repair of 5'-DNA-protein crosslinks by microhomology-mediated end-joining. Cell Rep 2021; 34:108820. [PMID: 33691100 PMCID: PMC8565190 DOI: 10.1016/j.celrep.2021.108820] [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: 03/16/2020] [Revised: 11/23/2020] [Accepted: 02/12/2021] [Indexed: 12/25/2022] Open
Abstract
DNA polymerase θ (Polθ) confers resistance to chemotherapy agents that cause DNA-protein crosslinks (DPCs) at double-strand breaks (DSBs), such as topoisomerase inhibitors. This suggests Polθ might facilitate DPC repair by microhomology-mediated end-joining (MMEJ). Here, we investigate Polθ repair of DSBs carrying DPCs by monitoring MMEJ in Xenopus egg extracts. MMEJ in extracts is dependent on Polθ, exhibits the MMEJ repair signature, and efficiently repairs 5' terminal DPCs independently of non-homologous end-joining and the replisome. We demonstrate that Polθ promotes the repair of 5' terminal DPCs in mammalian cells by using an MMEJ reporter and find that Polθ confers resistance to formaldehyde in addition to topoisomerase inhibitors. Dual deficiency in Polθ and tyrosyl-DNA phosphodiesterase 2 (TDP2) causes severe cellular sensitivity to etoposide, which demonstrates MMEJ as an independent DPC repair pathway. These studies recapitulate MMEJ in vitro and elucidate how Polθ confers resistance to etoposide.
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Affiliation(s)
- Gurushankar Chandramouly
- Thomas Jefferson University, Sidney Kimmel Cancer Center, Department of Biochemistry and Molecular Biology, Philadelphia, PA 19107, USA
| | - Shuren Liao
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Timur Rusanov
- Washington University School of Medicine, Department of Pathology & Immunology, St. Louis, MO 63110, USA
| | - Nikita Borisonnik
- Thomas Jefferson University, Sidney Kimmel Cancer Center, Department of Biochemistry and Molecular Biology, Philadelphia, PA 19107, USA
| | - Marissa L Calbert
- Thomas Jefferson University, Sidney Kimmel Cancer Center, Department of Biochemistry and Molecular Biology, Philadelphia, PA 19107, USA; Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Tatiana Kent
- Thomas Jefferson University, Sidney Kimmel Cancer Center, Department of Biochemistry and Molecular Biology, Philadelphia, PA 19107, USA
| | - Katherine Sullivan-Reed
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Umeshkumar Vekariya
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Ekaterina Kashkina
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Tomasz Skorski
- Fels Cancer Institute for Personalized Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Hong Yan
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Richard T Pomerantz
- Thomas Jefferson University, Sidney Kimmel Cancer Center, Department of Biochemistry and Molecular Biology, Philadelphia, PA 19107, USA.
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23
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Faure D. Is there a unique integration mechanism of Agrobacterium T-DNA into a plant genome? THE NEW PHYTOLOGIST 2021; 229:2386-2388. [PMID: 33616946 DOI: 10.1111/nph.17184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This article is a Commentary on Nishizawa‐Yokoi et al. (2021), 229: 2859–2872.
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Affiliation(s)
- Denis Faure
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Paris-Saclay University, 91 190, Gif-sur-Yvette, France
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24
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Vicencio J, Cerón J. A Living Organism in your CRISPR Toolbox: Caenorhabditis elegans Is a Rapid and Efficient Model for Developing CRISPR-Cas Technologies. CRISPR J 2021; 4:32-42. [PMID: 33538637 DOI: 10.1089/crispr.2020.0103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Cas9 nuclease from Streptococcus pyogenes (SpCas9) is the most popular enzyme for CRISPR technologies. However, considering the wide diversity of microorganisms (discovered and still unknown), a massive number of CRISPR effectors are being and will be identified and characterized in the search of optimal Cas variants for each of the many applications of CRISPR. In this context, a versatile and efficient multicellular system for CRISPR editing such as Caenorhabditis elegans would be of great help in the development of these effectors. Here, we highlight the benefits of using C. elegans for the rapid evaluation of new CRISPR effectors, and for optimizing CRISPR efficiency in animals in several ways such as by modulating the balance between repair pathways, modifying chromatin accessibility, or controlling the expression and activity of nucleases and guide RNAs.
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Affiliation(s)
- Jeremy Vicencio
- Modeling human diseases in C. elegans Group, Genes, Disease and Therapy Program, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Julián Cerón
- Modeling human diseases in C. elegans Group, Genes, Disease and Therapy Program, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
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25
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Sankaranarayanan G, Coghlan A, Driguez P, Lotkowska ME, Sanders M, Holroyd N, Tracey A, Berriman M, Rinaldi G. Large CRISPR-Cas-induced deletions in the oxamniquine resistance locus of the human parasite Schistosoma mansoni. Wellcome Open Res 2021; 5:178. [PMID: 32789192 PMCID: PMC7405262 DOI: 10.12688/wellcomeopenres.16031.2] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2020] [Indexed: 12/18/2022] Open
Abstract
Background. At least 250 million people worldwide suffer from schistosomiasis, caused by Schistosoma worms. Genome sequences for several Schistosoma species are available, including a high-quality annotated reference for Schistosoma mansoni. There is a pressing need to develop a reliable functional toolkit to translate these data into new biological insights and targets for intervention. CRISPR-Cas9 was recently demonstrated for the first time in S. mansoni, to produce somatic mutations in the omega-1 ( ω1) gene. Methods. We employed CRISPR-Cas9 to introduce somatic mutations in a second gene, SULT-OR, a sulfotransferase expressed in the parasitic stages of S. mansoni, in which mutations confer resistance to the drug oxamniquine. A 262-bp PCR product spanning the region targeted by the gRNA against SULT-OR was amplified, and mutations identified in it by high-throughput sequencing. Results. We found that 0.3-2.0% of aligned reads from CRISPR-Cas9-treated adult worms showed deletions spanning the predicted Cas9 cut site, compared to 0.1-0.2% for sporocysts, while deletions were extremely rare in eggs. The most common deletion observed in adults and sporocysts was a 34 bp-deletion directly upstream of the predicted cut site, but rarer deletions reaching as far as 102 bp upstream of the cut site were also detected. The CRISPR-Cas9-induced deletions, if homozygous, are predicted to cause resistance to oxamniquine by producing frameshifts, ablating SULT-OR transcription, or leading to mRNA degradation via the nonsense-mediated mRNA decay pathway. However, no SULT-OR knock down at the mRNA level was observed, presumably because the cells in which CRISPR-Cas9 did induce mutations represented a small fraction of all cells expressing SULT-OR. Conclusions. Further optimisation of CRISPR-Cas protocols for different developmental stages and particular cell types, including germline cells, will contribute to the generation of a homozygous knock-out in any gene of interest, and in particular the SULT-OR gene to derive an oxamniquine-resistant stable transgenic line.
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Affiliation(s)
| | | | | | | | | | | | - Alan Tracey
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
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26
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Panigrahi R, Glover JNM. Structural insights into DNA double-strand break signaling. Biochem J 2021; 478:135-156. [PMID: 33439989 DOI: 10.1042/bcj20200066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 12/10/2020] [Accepted: 12/15/2020] [Indexed: 12/14/2022]
Abstract
Genomic integrity is most threatened by double-strand breaks, which, if left unrepaired, lead to carcinogenesis or cell death. The cell generates a network of protein-protein signaling interactions that emanate from the DNA damage which are now recognized as a rich basis for anti-cancer therapy development. Deciphering the structures of signaling proteins has been an uphill task owing to their large size and complex domain organization. Recent advances in mammalian protein expression/purification and cryo-EM-based structure determination have led to significant progress in our understanding of these large multidomain proteins. This review is an overview of the structural principles that underlie some of the key signaling proteins that function at the double-strand break site. We also discuss some plausible ideas that could be considered for future structural approaches to visualize and build a more complete understanding of protein dynamics at the break site.
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Affiliation(s)
- Rashmi Panigrahi
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - J N Mark Glover
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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27
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Unravelling roles of error-prone DNA polymerases in shaping cancer genomes. Oncogene 2021; 40:6549-6565. [PMID: 34663880 PMCID: PMC8639439 DOI: 10.1038/s41388-021-02032-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/01/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022]
Abstract
Mutagenesis is a key hallmark and enabling characteristic of cancer cells, yet the diverse underlying mutagenic mechanisms that shape cancer genomes are not understood. This review will consider the emerging challenge of determining how DNA damage response pathways-both tolerance and repair-act upon specific forms of DNA damage to generate mutations characteristic of tumors. DNA polymerases are typically the ultimate mutagenic effectors of DNA repair pathways. Therefore, understanding the contributions of DNA polymerases is critical to develop a more comprehensive picture of mutagenic mechanisms in tumors. Selection of an appropriate DNA polymerase-whether error-free or error-prone-for a particular DNA template is critical to the maintenance of genome stability. We review different modes of DNA polymerase dysregulation including mutation, polymorphism, and over-expression of the polymerases themselves or their associated activators. Based upon recent findings connecting DNA polymerases with specific mechanisms of mutagenesis, we propose that compensation for DNA repair defects by error-prone polymerases may be a general paradigm molding the mutational landscape of cancer cells. Notably, we demonstrate that correlation of error-prone polymerase expression with mutation burden in a subset of patient tumors from The Cancer Genome Atlas can identify mechanistic hypotheses for further testing. We contrast experimental approaches from broad, genome-wide strategies to approaches with a narrower focus on a few hundred base pairs of DNA. In addition, we consider recent developments in computational annotation of patient tumor data to identify patterns of mutagenesis. Finally, we discuss the innovations and future experiments that will develop a more comprehensive portrait of mutagenic mechanisms in human tumors.
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28
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Elsakrmy N, Zhang-Akiyama QM, Ramotar D. The Base Excision Repair Pathway in the Nematode Caenorhabditis elegans. Front Cell Dev Biol 2020; 8:598860. [PMID: 33344454 PMCID: PMC7744777 DOI: 10.3389/fcell.2020.598860] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/09/2020] [Indexed: 12/12/2022] Open
Abstract
Exogenous and endogenous damage to the DNA is inevitable. Several DNA repair pathways including base excision, nucleotide excision, mismatch, homologous and non-homologous recombinations are conserved across all organisms to faithfully maintain the integrity of the genome. The base excision repair (BER) pathway functions to repair single-base DNA lesions and during the process creates the premutagenic apurinic/apyrimidinic (AP) sites. In this review, we discuss the components of the BER pathway in the nematode Caenorhabditis elegans and delineate the different phenotypes caused by the deletion or the knockdown of the respective DNA repair gene, as well as the implications. To date, two DNA glycosylases have been identified in C. elegans, the monofunctional uracil DNA glycosylase-1 (UNG-1) and the bifunctional endonuclease III-1 (NTH-1) with associated AP lyase activity. In addition, the animal possesses two AP endonucleases belonging to the exonuclease-3 and endonuclease IV families and in C. elegans these enzymes are called EXO-3 and APN-1, respectively. In mammalian cells, the DNA polymerase, Pol beta, that is required to reinsert the correct bases for DNA repair synthesis is not found in the genome of C. elegans and the evidence indicates that this role could be substituted by DNA polymerase theta (POLQ), which is known to perform a function in the microhomology-mediated end-joining pathway in human cells. The phenotypes observed by the C. elegans mutant strains of the BER pathway raised many challenging questions including the possibility that the DNA glycosylases may have broader functional roles, as discuss in this review.
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Affiliation(s)
- Noha Elsakrmy
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar
| | - Qiu-Mei Zhang-Akiyama
- Laboratory of Stress Response Biology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Dindial Ramotar
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Qatar
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29
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Du X, McManus DP, French JD, Jones MK, You H. CRISPR/Cas9: A new tool for the study and control of helminth parasites. Bioessays 2020; 43:e2000185. [PMID: 33145822 DOI: 10.1002/bies.202000185] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 12/17/2022]
Abstract
Recent reports of CRISPR/Cas9 genome editing in parasitic helminths open up new avenues for research on these dangerous pathogens. However, the complex morphology and life cycles inherent to these parasites present obstacles for the efficient application of CRISPR/Cas9-targeted mutagenesis. This is especially true with the trematode flukes where only modest levels of gene mutation efficiency have been achieved. Current major challenges in the application of CRISPR/Cas9 for study of parasitic worms thus lie in enhancing gene mutation efficiency and overcoming issues involved in host passage so that mutated parasites survive. Strategies developed for CRISPR/Cas9 studies on Caenorhabditis elegans, protozoa and mammalian cells, including novel delivery methods, the choice of selectable markers, and refining mutation precision represent novel tactics whereby these impediments can be overcome. Furthermore, employing CRISPR/Cas9-mediated gene drive to interfere with vector transmission represents a novel approach for the control of parasitic worms that is worthy of further exploration.
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Affiliation(s)
- Xiaofeng Du
- Immunology Department, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia.,Faculty of Medicine, The University of Queensland, Herston, Brisbane, Queensland, Australia
| | - Donald P McManus
- Immunology Department, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia.,Faculty of Medicine, The University of Queensland, Herston, Brisbane, Queensland, Australia
| | - Juliet D French
- Genetics & Computational Biology Department, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Malcolm K Jones
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
| | - Hong You
- Immunology Department, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
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30
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The molecular basis and disease relevance of non-homologous DNA end joining. Nat Rev Mol Cell Biol 2020; 21:765-781. [PMID: 33077885 DOI: 10.1038/s41580-020-00297-8] [Citation(s) in RCA: 201] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2020] [Indexed: 12/26/2022]
Abstract
Non-homologous DNA end joining (NHEJ) is the predominant repair mechanism of any type of DNA double-strand break (DSB) during most of the cell cycle and is essential for the development of antigen receptors. Defects in NHEJ result in sensitivity to ionizing radiation and loss of lymphocytes. The most critical step of NHEJ is synapsis, or the juxtaposition of the two DNA ends of a DSB, because all subsequent steps rely on it. Recent findings show that, like the end processing step, synapsis can be achieved through several mechanisms. In this Review, we first discuss repair pathway choice between NHEJ and other DSB repair pathways. We then integrate recent insights into the mechanisms of NHEJ synapsis with updates on other steps of NHEJ, such as DNA end processing and ligation. Finally, we discuss NHEJ-related human diseases, including inherited disorders and neoplasia, which arise from rare failures at different NHEJ steps.
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31
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Sankaranarayanan G, Coghlan A, Driguez P, Lotkowska ME, Sanders M, Holroyd N, Tracey A, Berriman M, Rinaldi G. Large CRISPR-Cas-induced deletions in the oxamniquine resistance locus of the human parasite Schistosoma mansoni. Wellcome Open Res 2020; 5:178. [PMID: 32789192 PMCID: PMC7405262 DOI: 10.12688/wellcomeopenres.16031.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2020] [Indexed: 12/29/2022] Open
Abstract
Background. At least 250 million people worldwide suffer from schistosomiasis, caused by Schistosoma worms. Genome sequences for several Schistosoma species are available, including a high-quality annotated reference for Schistosoma mansoni. There is a pressing need to develop a reliable functional toolkit to translate these data into new biological insights and targets for intervention. CRISPR-Cas9 was recently demonstrated for the first time in S. mansoni, to produce somatic mutations in the omega-1 ( ω1) gene. Methods. We employed CRISPR-Cas9 to introduce somatic mutations in a second gene, SULT-OR, a sulfotransferase expressed in the parasitic stages of S. mansoni, in which mutations confer resistance to the drug oxamniquine. A 262-bp PCR product spanning the region targeted by the gRNA against SULT-OR was amplified, and mutations identified in it by high-throughput sequencing. Results. We found that 0.3-2.0% of aligned reads from CRISPR-Cas9-treated adult worms showed deletions spanning the predicted Cas9 cut site, compared to 0.1-0.2% for sporocysts, while deletions were extremely rare in eggs. The most common deletion observed in adults and sporocysts was a 34 bp-deletion directly upstream of the predicted cut site, but rarer deletions reaching as far as 102 bp upstream of the cut site were also detected. The CRISPR-Cas9-induced deletions, if homozygous, are predicted to cause resistance to oxamniquine by producing frameshifts, ablating SULT-OR transcription, or leading to mRNA degradation via the nonsense-mediated mRNA decay pathway. However, no SULT-OR knock down at the mRNA level was observed, presumably because the cells in which CRISPR-Cas9 did induce mutations represented a small fraction of all cells expressing SULT-OR. Conclusions. Further optimisation of CRISPR-Cas protocols for different developmental stages and particular cell types, including germline cells, will contribute to the generation of a homozygous knock-out in any gene of interest, and in particular the SULT-OR gene to derive an oxamniquine-resistant stable transgenic line.
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Affiliation(s)
| | | | | | | | | | | | - Alan Tracey
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
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32
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Kamp JA, van Schendel R, Dilweg IW, Tijsterman M. BRCA1-associated structural variations are a consequence of polymerase theta-mediated end-joining. Nat Commun 2020; 11:3615. [PMID: 32680986 PMCID: PMC7368036 DOI: 10.1038/s41467-020-17455-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 07/01/2020] [Indexed: 12/03/2022] Open
Abstract
Failure to preserve the integrity of the genome is a hallmark of cancer. Recent studies have revealed that loss of the capacity to repair DNA breaks via homologous recombination (HR) results in a mutational profile termed BRCAness. The enzymatic activity that repairs HR substrates in BRCA-deficient conditions to produce this profile is currently unknown. We here show that the mutational landscape of BRCA1 deficiency in C. elegans closely resembles that of BRCA1-deficient tumours. We identify polymerase theta-mediated end-joining (TMEJ) to be responsible: knocking out polq-1 suppresses the accumulation of deletions and tandem duplications in brc-1 and brd-1 animals. We find no additional back-up repair in HR and TMEJ compromised animals; non-homologous end-joining does not affect BRCAness. The notion that TMEJ acts as an alternative to HR, promoting the genome alteration of HR-deficient cells, supports the idea that polymerase theta is a promising therapeutic target for HR-deficient tumours.
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Affiliation(s)
- J A Kamp
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - R van Schendel
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - I W Dilweg
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - M Tijsterman
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands.
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
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33
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Hanscom T, McVey M. Regulation of Error-Prone DNA Double-Strand Break Repair and Its Impact on Genome Evolution. Cells 2020; 9:E1657. [PMID: 32660124 PMCID: PMC7407515 DOI: 10.3390/cells9071657] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/17/2022] Open
Abstract
Double-strand breaks are one of the most deleterious DNA lesions. Their repair via error-prone mechanisms can promote mutagenesis, loss of genetic information, and deregulation of the genome. These detrimental outcomes are significant drivers of human diseases, including many cancers. Mutagenic double-strand break repair also facilitates heritable genetic changes that drive organismal adaptation and evolution. In this review, we discuss the mechanisms of various error-prone DNA double-strand break repair processes and the cellular conditions that regulate them, with a focus on alternative end joining. We provide examples that illustrate how mutagenic double-strand break repair drives genome diversity and evolution. Finally, we discuss how error-prone break repair can be crucial to the induction and progression of diseases such as cancer.
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Affiliation(s)
| | - Mitch McVey
- Department. of Biology, Tufts University, Medford, MA 02155, USA;
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34
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van Bostelen I, van Schendel R, Romeijn R, Tijsterman M. Translesion synthesis polymerases are dispensable for C. elegans reproduction but suppress genome scarring by polymerase theta-mediated end joining. PLoS Genet 2020; 16:e1008759. [PMID: 32330130 PMCID: PMC7202663 DOI: 10.1371/journal.pgen.1008759] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/06/2020] [Accepted: 04/06/2020] [Indexed: 12/30/2022] Open
Abstract
Bases within DNA are frequently damaged, producing obstacles to efficient and accurate DNA replication by replicative polymerases. Translesion synthesis (TLS) polymerases, via their ability to catalyze nucleotide additions to growing DNA chains across DNA lesions, promote replication of damaged DNA, thus preventing checkpoint activation, genome instability and cell death. In this study, we used C. elegans to determine the contribution of TLS activity on long-term stability of an animal genome. We monitored and compared the types of mutations that accumulate in REV1, REV3, POLH1 and POLK deficient animals that were grown under unchallenged conditions. We also addressed redundancies in TLS activity by combining all deficiencies. Remarkably, animals that are deficient for all Y-family polymerases as well as animals that have lost all TLS activity are viable and produce progeny, demonstrating that TLS is not essential for animal life. Whole genome sequencing analyses, however, reveal that TLS is needed to prevent genomic scars from accumulating. These scars, which are the product of polymerase theta-mediated end joining (TMEJ), are found overrepresented at guanine bases, consistent with TLS suppressing DNA double-strand breaks (DSBs) from occurring at replication-blocking guanine adducts. We found that in C. elegans, TLS across spontaneous damage is predominantly error free and anti-clastogenic, and thus ensures preservation of genetic information.
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Affiliation(s)
- Ivo van Bostelen
- 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
| | - Ron Romeijn
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
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35
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Atkins PA, Voytas DF. Overcoming bottlenecks in plant gene editing. CURRENT OPINION IN PLANT BIOLOGY 2020; 54:79-84. [PMID: 32143167 DOI: 10.1016/j.pbi.2020.01.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/30/2019] [Accepted: 01/22/2020] [Indexed: 05/06/2023]
Abstract
Agriculture has reached a technological inflection point. The development of novel gene editing tools and methods for their delivery to plant cells promises to increase genome malleability and transform plant biology. Whereas gene editing is capable of making a myriad of DNA sequence modifications, its widespread adoption has been hindered by a number of factors, particularly inefficiencies in creating precise DNA sequence modifications and ineffective methods for delivering gene editing reagents to plant cells. Here, we briefly overview the principles of plant genome editing and highlight a subset of the most recent advances that promise to overcome current limitations.
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Affiliation(s)
- Paul Ap Atkins
- Center for Genome Engineering, Center for Precision Plant Genomics and Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA
| | - Daniel F Voytas
- Center for Genome Engineering, Center for Precision Plant Genomics and Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA.
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36
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Castelletto ML, Gang SS, Hallem EA. Recent advances in functional genomics for parasitic nematodes of mammals. ACTA ACUST UNITED AC 2020; 223:223/Suppl_1/jeb206482. [PMID: 32034038 DOI: 10.1242/jeb.206482] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Human-parasitic nematodes infect over a quarter of the world's population and are a major cause of morbidity in low-resource settings. Currently available treatments have not been sufficient to eliminate infections in endemic areas, and drug resistance is an increasing concern, making new treatment options a priority. The development of new treatments requires an improved understanding of the basic biology of these nematodes. Specifically, a better understanding of parasitic nematode development, reproduction and behavior may yield novel drug targets or new opportunities for intervention such as repellents or traps. Until recently, our ability to study parasitic nematode biology was limited because few tools were available for their genetic manipulation. This is now changing as a result of recent advances in the large-scale sequencing of nematode genomes and the development of new techniques for their genetic manipulation. Notably, skin-penetrating gastrointestinal nematodes in the genus Strongyloides are now amenable to transgenesis, RNAi and CRISPR/Cas9-mediated targeted mutagenesis, positioning the Strongyloides species as model parasitic nematode systems. A number of other mammalian-parasitic nematodes, including the giant roundworm Ascaris suum and the tissue-dwelling filarial nematode Brugia malayi, are also now amenable to transgenesis and/or RNAi in some contexts. Using these tools, recent studies of Strongyloides species have already provided insight into the molecular pathways that control the developmental decision to form infective larvae and that drive the host-seeking behaviors of infective larvae. Ultimately, a mechanistic understanding of these processes could lead to the development of new avenues for nematode control.
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Affiliation(s)
- Michelle L Castelletto
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Spencer S Gang
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92161, USA
| | - Elissa A Hallem
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
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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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The effect of inhibitors of phosphatidylinositol 3-kinase-related kinases on dibenzo[def,p]chrysene genotoxicity measured by γH2AX levels and neutral comet assay in HepG2 human hepatocellular cancer cells. Toxicol In Vitro 2019; 63:104749. [PMID: 31838185 DOI: 10.1016/j.tiv.2019.104749] [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: 07/02/2019] [Revised: 12/11/2019] [Accepted: 12/11/2019] [Indexed: 12/12/2022]
Abstract
In the study the modulating effect of inhibition of phosphatidylinositol 3-kinase-related kinases (PIKK): ATM (Ataxia Telangiectasia Mutated), ATR (Ataxia Telangiectasia and Rad3 Related) and DNA-PK (DNA-dependent protein kinase) on genotoxicity of dibenzo[def,p]chrysene (DBC) in HepG2 human hepatocellular cancer cells was investigated. The cytotoxicity of DBC was determined, also in combination with PIKK inhibitors, using the MTT reduction assay. The high cytotoxicity of DBC was observed after 72 h incubation (IC50 = 0.06 μM). The PIKK inhibitors applied at non-cytotoxic concentrations: caffeine (1 mM) and KU55933 (2.5 μM) had no significant influence on the DBC cytotoxicity, however NU7026 (5 μM) caused significant increase in the cell viability by about 25%. The combinations of the inhibitors (double or triple) where NU7026 was present also caused increase in the cell viability (i.e. cytoprotective effect) compared to the effect of DBC. The level of damage to the genetic material (DNA double strand breaks, DSB) was assessed by measuring levels of phosphorylated form of H2A histone (γH2AX) and neutral comet assay. DBC induced DSB in a concentration and time-dependent manner. NU7026 considerably reduced the level of DSB level measured by γH2AX and comet assay. The obtained results confirm that DBC is cytotoxic and causes damage to the genetic material including DSB. The DNA-PK inhibitor NU7026 increases cell viability after exposure to DBC and reduces DNA damage, what indicates an important role of the sensor kinase in mediating the effect.
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Pilzecker B, Buoninfante OA, Jacobs H. DNA damage tolerance in stem cells, ageing, mutagenesis, disease and cancer therapy. Nucleic Acids Res 2019; 47:7163-7181. [PMID: 31251805 PMCID: PMC6698745 DOI: 10.1093/nar/gkz531] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 05/22/2019] [Accepted: 06/26/2019] [Indexed: 12/12/2022] Open
Abstract
The DNA damage response network guards the stability of the genome from a plethora of exogenous and endogenous insults. An essential feature of the DNA damage response network is its capacity to tolerate DNA damage and structural impediments during DNA synthesis. This capacity, referred to as DNA damage tolerance (DDT), contributes to replication fork progression and stability in the presence of blocking structures or DNA lesions. Defective DDT can lead to a prolonged fork arrest and eventually cumulate in a fork collapse that involves the formation of DNA double strand breaks. Four principal modes of DDT have been distinguished: translesion synthesis, fork reversal, template switching and repriming. All DDT modes warrant continuation of replication through bypassing the fork stalling impediment or repriming downstream of the impediment in combination with filling of the single-stranded DNA gaps. In this way, DDT prevents secondary DNA damage and critically contributes to genome stability and cellular fitness. DDT plays a key role in mutagenesis, stem cell maintenance, ageing and the prevention of cancer. This review provides an overview of the role of DDT in these aspects.
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Affiliation(s)
- Bas Pilzecker
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Olimpia Alessandra Buoninfante
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Heinz Jacobs
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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Feng W, Simpson DA, Carvajal-Garcia J, Price BA, Kumar RJ, Mose LE, Wood RD, Rashid N, Purvis JE, Parker JS, Ramsden DA, Gupta GP. Genetic determinants of cellular addiction to DNA polymerase theta. Nat Commun 2019; 10:4286. [PMID: 31537809 PMCID: PMC6753077 DOI: 10.1038/s41467-019-12234-1] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 08/22/2019] [Indexed: 02/07/2023] Open
Abstract
Polymerase theta (Pol θ, gene name Polq) is a widely conserved DNA polymerase that mediates a microhomology-mediated, error-prone, double strand break (DSB) repair pathway, referred to as Theta Mediated End Joining (TMEJ). Cells with homologous recombination deficiency are reliant on TMEJ for DSB repair. It is unknown whether deficiencies in other components of the DNA damage response (DDR) also result in Pol θ addiction. Here we use a CRISPR genetic screen to uncover 140 Polq synthetic lethal (PolqSL) genes, the majority of which were previously unknown. Functional analyses indicate that Pol θ/TMEJ addiction is associated with increased levels of replication-associated DSBs, regardless of the initial source of damage. We further demonstrate that approximately 30% of TCGA breast cancers have genetic alterations in PolqSL genes and exhibit genomic scars of Pol θ/TMEJ hyperactivity, thereby substantially expanding the subset of human cancers for which Pol θ inhibition represents a promising therapeutic strategy.
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Affiliation(s)
- Wanjuan Feng
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Dennis A Simpson
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Juan Carvajal-Garcia
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Brandon A Price
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Rashmi J Kumar
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Lisle E Mose
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Richard D Wood
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Naim Rashid
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jeremy E Purvis
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Dale A Ramsden
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Gaorav P Gupta
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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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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42
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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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Vicencio J, Martínez-Fernández C, Serrat X, Cerón J. Efficient Generation of Endogenous Fluorescent Reporters by Nested CRISPR in Caenorhabditis elegans. Genetics 2019; 211:1143-1154. [PMID: 30696716 PMCID: PMC6456308 DOI: 10.1534/genetics.119.301965] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/25/2019] [Indexed: 12/27/2022] Open
Abstract
CRISPR-based genome-editing methods in model organisms are evolving at an extraordinary speed. Whereas the generation of deletion or missense mutants is quite straightforward, the production of endogenous fluorescent reporters is more challenging. We have developed Nested CRISPR, a cloning-free ribonucleoprotein-driven method that robustly produces endogenous fluorescent reporters with EGFP, mCherry or wrmScarlet in Caenorhabditis elegans This method is based on the division of the fluorescent protein (FP) sequence in three fragments. In the first step, single-stranded DNA (ssDNA) donors (≤200 bp) are used to insert the 5' and 3' fragments of the FP in the locus of interest. In the second step, these sequences act as homology regions for homology-directed repair using a double-stranded DNA (dsDNA) donor (PCR product) containing the middle fragment, thus completing the FP sequence. In Nested CRISPR, the first step involving ssDNA donors is a well-established method that yields high editing efficiencies, and the second step is reliable because it uses universal CRISPR RNAs (crRNAs) and PCR products. We have also used Nested CRISPR in a nonessential gene to produce a deletion mutant in the first step and a transcriptional reporter in the second step. In the search for modifications to optimize the method, we tested synthetic single guide RNAs (sgRNAs), but did not observe a significant increase in efficiency. To streamline the approach, we combined all step 1 and step 2 reagents in a single injection and were successful in three of five loci tested with editing efficiencies of up to 20%. Finally, we discuss the prospects of this method in the future.
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Affiliation(s)
- Jeremy Vicencio
- Genes, Diseases, and Therapies Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Carmen Martínez-Fernández
- Genes, Diseases, and Therapies Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Xènia Serrat
- Genes, Diseases, and Therapies Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Julián Cerón
- Genes, Diseases, and Therapies Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908 Barcelona, Spain
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44
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CRISPR/Cas9 Methodology for the Generation of Knockout Deletions in Caenorhabditis elegans. G3-GENES GENOMES GENETICS 2019; 9:135-144. [PMID: 30420468 PMCID: PMC6325907 DOI: 10.1534/g3.118.200778] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The Caenorhabditis elegans Gene Knockout Consortium is tasked with obtaining null mutations in each of the more than 20,000 open reading frames (ORFs) of this organism. To date, approximately 15,000 ORFs have associated putative null alleles. As there has been substantial success in using CRISPR/Cas9 in C. elegans, this appears to be the most promising technique to complete the task. To enhance the efficiency of using CRISPR/Cas9 to generate gene deletions in C. elegans we provide a web-based interface to access our database of guide RNAs (http://genome.sfu.ca/crispr). When coupled with previously developed selection vectors, optimization for homology arm length, and the use of purified Cas9 protein, we demonstrate a robust and effective protocol for generating deletions for this large-scale project. Debate and speculation in the larger scientific community concerning off-target effects due to non-specific Cas9 cutting has prompted us to investigate through whole genome sequencing the occurrence of single nucleotide variants and indels accompanying targeted deletions. We did not detect any off-site variants above the natural spontaneous mutation rate and therefore conclude that this modified protocol does not generate off-target events to any significant degree in C. elegans. We did, however, observe a number of non-specific alterations at the target site itself following the Cas9-induced double-strand break and offer a protocol for best practice quality control for such events.
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45
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Bianchi FT, Berto GE, Di Cunto F. Impact of DNA repair and stability defects on cortical development. Cell Mol Life Sci 2018; 75:3963-3976. [PMID: 30116853 PMCID: PMC11105354 DOI: 10.1007/s00018-018-2900-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/16/2018] [Accepted: 08/08/2018] [Indexed: 02/07/2023]
Abstract
Maintenance of genome stability is a crucial cellular function for normal mammalian development and physiology. However, despite the general relevance of this process, genome stability alteration due to genetic or non-genetic conditions has a particularly profound impact on the developing cerebral cortex. In this review, we will analyze the main pathways involved in maintenance of genome stability, the consequences of their alterations with regard to central nervous system development, as well as the possible molecular and cellular basis of this specificity.
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Affiliation(s)
- Federico T Bianchi
- Neuroscience Institute Cavalieri Ottolenghi, Turin, Italy.
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy.
| | - Gaia E Berto
- Neuroscience Institute Cavalieri Ottolenghi, Turin, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Ferdinando Di Cunto
- Neuroscience Institute Cavalieri Ottolenghi, Turin, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
- Department of Neuroscience, University of Turin, Turin, Italy
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46
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Khodaverdian VY, Hanscom T, Yu AM, Yu TL, Mak V, Brown AJ, Roberts SA, McVey M. Secondary structure forming sequences drive SD-MMEJ repair of DNA double-strand breaks. Nucleic Acids Res 2018; 45:12848-12861. [PMID: 29121353 PMCID: PMC5728401 DOI: 10.1093/nar/gkx1056] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 10/18/2017] [Indexed: 12/29/2022] Open
Abstract
Alternative end-joining (alt-EJ) repair of DNA double-strand breaks is associated with deletions, chromosome translocations, and genome instability. Alt-EJ frequently uses annealing of microhomologous sequences to tether broken ends. When accessible pre-existing microhomologies do not exist, we have postulated that new microhomologies can be created via limited DNA synthesis at secondary-structure forming sequences. This model, called synthesis-dependent microhomology-mediated end joining (SD-MMEJ), predicts that differences between DNA sequences near double-strand breaks should alter repair outcomes in predictable ways. To test this hypothesis, we injected plasmids with sequence variations flanking an I-SceI endonuclease recognition site into I-SceI expressing Drosophila embryos and used Illumina amplicon sequencing to compare repair junctions. As predicted by the model, we found that small changes in sequences near the I-SceI site had major impacts on the spectrum of repair junctions. Bioinformatic analyses suggest that these repair differences arise from transiently forming loops and hairpins within 30 nucleotides of the break. We also obtained evidence for ‘trans SD-MMEJ,’ involving at least two consecutive rounds of microhomology annealing and synthesis across the break site. These results highlight the importance of sequence context for alt-EJ repair and have important implications for genome editing and genome evolution.
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Affiliation(s)
- Varandt Y Khodaverdian
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155, USA
| | - Terrence Hanscom
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155, USA
| | - Amy Marie Yu
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155, USA
| | - Taylor L Yu
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155, USA
| | - Victoria Mak
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155, USA
| | - Alexander J Brown
- School of Molecular Biosciences, Washington State University, P100 Dairy Road, Pullman, WA 99164, USA
| | - Steven A Roberts
- School of Molecular Biosciences, Washington State University, P100 Dairy Road, Pullman, WA 99164, USA
| | - Mitch McVey
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155, USA
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47
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Schimmel J, Kool H, van Schendel R, Tijsterman M. Mutational signatures of non-homologous and polymerase theta-mediated end-joining in embryonic stem cells. EMBO J 2017; 36:3634-3649. [PMID: 29079701 PMCID: PMC5730883 DOI: 10.15252/embj.201796948] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 09/05/2017] [Accepted: 09/29/2017] [Indexed: 12/11/2022] Open
Abstract
Cells employ potentially mutagenic DNA repair mechanisms to avoid the detrimental effects of chromosome breaks on cell survival. While classical non-homologous end-joining (cNHEJ) is largely error-free, alternative end-joining pathways have been described that are intrinsically mutagenic. Which end-joining mechanisms operate in germ and embryonic cells and thus contribute to heritable mutations found in congenital diseases is, however, still largely elusive. Here, we determined the genetic requirements for the repair of CRISPR/Cas9-induced chromosomal breaks of different configurations, and establish the mutational consequences. We find that cNHEJ and polymerase theta-mediated end-joining (TMEJ) act both parallel and redundant in mouse embryonic stem cells and account for virtually all end-joining activity. Surprisingly, mutagenic repair by polymerase theta (Pol θ, encoded by the Polq gene) is most prevalent for blunt double-strand breaks (DSBs), while cNHEJ dictates mutagenic repair of DSBs with protruding ends, in which the cNHEJ polymerases lambda and mu play minor roles. We conclude that cNHEJ-dependent repair of DSBs with protruding ends can explain de novo formation of tandem duplications in mammalian genomes.
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Affiliation(s)
- Joost Schimmel
- 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
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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48
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Gang SS, Castelletto ML, Bryant AS, Yang E, Mancuso N, Lopez JB, Pellegrini M, Hallem EA. Targeted mutagenesis in a human-parasitic nematode. PLoS Pathog 2017; 13:e1006675. [PMID: 29016680 PMCID: PMC5650185 DOI: 10.1371/journal.ppat.1006675] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 10/20/2017] [Accepted: 10/02/2017] [Indexed: 11/19/2022] Open
Abstract
Parasitic nematodes infect over 1 billion people worldwide and cause some of the most common neglected tropical diseases. Despite their prevalence, our understanding of the biology of parasitic nematodes has been limited by the lack of tools for genetic intervention. In particular, it has not yet been possible to generate targeted gene disruptions and mutant phenotypes in any parasitic nematode. Here, we report the development of a method for introducing CRISPR-Cas9-mediated gene disruptions in the human-parasitic threadworm Strongyloides stercoralis. We disrupted the S. stercoralis twitchin gene unc-22, resulting in nematodes with severe motility defects. Ss-unc-22 mutations were resolved by homology-directed repair when a repair template was provided. Omission of a repair template resulted in deletions at the target locus. Ss-unc-22 mutations were heritable; we passed Ss-unc-22 mutants through a host and successfully recovered mutant progeny. Using a similar approach, we also disrupted the unc-22 gene of the rat-parasitic nematode Strongyloides ratti. Our results demonstrate the applicability of CRISPR-Cas9 to parasitic nematodes, and thereby enable future studies of gene function in these medically relevant but previously genetically intractable parasites. Parasitic worms are a widespread public health burden, yet very little is known about the cellular and molecular mechanisms that contribute to their parasitic lifestyle. One of the major barriers to better understanding these mechanisms is that there are currently no available methods for making targeted gene knockouts in any parasitic worm species. Here, we describe the first mutant phenotype in a parasitic worm resulting from a targeted gene disruption. We applied CRISPR-Cas9-mediated mutagenesis to parasitic worms in the genus Strongyloides and developed a method that overcomes many of the challenges that have previously inhibited generating mutant parasitic worms. We characterize heritable mutant phenotypes and outline a toolkit that will be applicable to many other genes with potential roles in parasitism. Importantly, we developed our method for gene knockouts in a human-parasitic worm. By directly investigating the genes and molecular pathways that enable worms to parasitize humans, we may be able to develop novel anthelmintic therapies or other measures for preventing nematode infections.
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Affiliation(s)
- Spencer S. Gang
- Molecular Biology Institute, University of California, Los Angeles, California, United States of America
| | - Michelle L. Castelletto
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, United States of America
| | - Astra S. Bryant
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, United States of America
| | - Emily Yang
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, United States of America
| | - Nicholas Mancuso
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Jacqueline B. Lopez
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, United States of America
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United States of America
| | - Elissa A. Hallem
- Molecular Biology Institute, University of California, Los Angeles, California, United States of America
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California, United States of America
- * E-mail:
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Herbette M, Mercier M, Michal F, Cluet D, Burny C, Yvert G, Robert V, Palladino F. The C. elegans SET-2/SET1 histone H3 Lys4 (H3K4) methyltransferase preserves genome stability in the germline. DNA Repair (Amst) 2017; 57:139-150. [DOI: 10.1016/j.dnarep.2017.07.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/13/2017] [Accepted: 07/13/2017] [Indexed: 10/19/2022]
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Farboud B. Targeted genome editing in Caenorhabditis elegans using CRISPR/Cas9. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 6. [PMID: 28810059 DOI: 10.1002/wdev.287] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 06/04/2017] [Accepted: 07/05/2017] [Indexed: 12/26/2022]
Abstract
Utilization of programmable nucleases to generate DNA lesions at precise endogenous sequences has transformed the ability to edit genomes from microbes to plants and animals. This is especially true in organisms that previously lacked the means to engineer precise genomic changes, like Caenorhabditis elegans. C. elegans is a 1 mm long free-living, nonparasitic, nematode worm, which is easily cultivated in a laboratory. Its detailed genetic map and relatively compact genome (~100 megabases) helped make it the first metazoan to have its entire genome sequenced. With detailed sequence information came development of numerous molecular tools to dissect gene function. Initially absent from this toolbox, however, were methods to make precise edits at chosen endogenous loci. Adapting site-specific nucleases for use in C. elegans, revolutionized studies of C. elegans biology. Zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and then CRISPR-associated protein 9 (Cas9) were used to target specific endogenous DNA sequences to make double-strand DNA breaks (DSBs). Precise changes could be engineered by providing repair templates targeting the DSB in trans. The ease of programming Cas9 to bind and cleave DNA sequences with few limitations has led to its widespread use in C. elegans research and sped the development of strategies to facilitate mutant recovery. Numerous innovative CRISPR/Cas9 methodologies are now primed for use in C. elegans. WIREs Dev Biol 2017, 6:e287. doi: 10.1002/wdev.287 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Behnom Farboud
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
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