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Guo X, Ren J, Zhou X, Zhang M, Lei C, Chai R, Zhang L, Lu D. Strategies to improve the efficiency and quality of mutant breeding using heavy-ion beam irradiation. Crit Rev Biotechnol 2024; 44:735-752. [PMID: 37455421 DOI: 10.1080/07388551.2023.2226339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 04/15/2023] [Indexed: 07/18/2023]
Abstract
Heavy-ion beam irradiation (HIBI) is useful for generating new germplasm in plants and microorganisms due to its ability to induce high mutagenesis rate, broad mutagenesis spectrum, and excellent stability of mutants. However, due to the random mutagenesis and associated mutant breeding modalities, it is imperative to improve HIBI-based mutant breeding efficiency and quality. This review discusses and summarizes the findings of existing theoretical and technical studies and presents a set of tandem strategies to enable efficient and high-quality HIBI-based mutant breeding practices. These strategies: adjust the mutation-inducing techniques, regulate cellular response states, formulate high-throughput screening schemes, and apply the generated superior genetic elements to genetic engineering approaches, thereby, improving the implications and expanding the scope of HIBI-based mutant breeding. These strategies aim to improve the mutagenesis rate, screening efficiency, and utilization of positive mutations. Here, we propose a model based on the integration of these strategies that would leverage the advantages of HIBI while compensating for its present shortcomings. Owing to the unique advantages of HIBI in creating high-quality genetic resources, we believe this review will contribute toward improving HIBI-based breeding.
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Affiliation(s)
- Xiaopeng Guo
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Junle Ren
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiang Zhou
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Miaomiao Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cairong Lei
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ran Chai
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Lingxi Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Dong Lu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
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2
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Li J, Xiong N, West KL, Leung M, Ching YP, Huang J, Yuan J, Yu CH, Leung J, Huen M. Nuclear F-actin assembly on damaged chromatin is regulated by DYRK1A and Spir1 phosphorylation. Nucleic Acids Res 2024:gkae574. [PMID: 38966995 DOI: 10.1093/nar/gkae574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 06/11/2024] [Accepted: 06/20/2024] [Indexed: 07/06/2024] Open
Abstract
Nuclear actin-based movements support DNA double-strand break (DSB) repair. However, molecular determinants that promote filamentous actin (F-actin) formation on the damaged chromatin remain undefined. Here we describe the DYRK1A kinase as a nuclear activity that promotes local F-actin assembly to support DSB mobility and repair, accomplished in part by its targeting of actin nucleator spire homolog 1 (Spir1). Indeed, perturbing DYRK1A-dependent phosphorylation of S482 mis-regulated Spir1 accumulation at damaged-modified chromatin, and led to compromised DSB-associated actin polymerization and attenuated DNA repair. Our findings uncover a role of the DYRK1A-Spir1 axis in nuclear actin dynamics during early DSB responses, and highlight the intricate details of nuclear cytoskeletal network in DSB repair and genome stability maintenance.
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Affiliation(s)
- Junshi Li
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, S.A.R
- State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong, S.A.R
| | - Nan Xiong
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, S.A.R
- State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong, S.A.R
| | - Kirk L West
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Manton Leung
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, S.A.R
| | - Yick Pang Ching
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, S.A.R
| | - Jun Huang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
- Cancer Center, Zhejiang University, Hangzhou 310058, China
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jian Yuan
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, China
| | - Cheng-Han Yu
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, S.A.R
| | - Justin Leung
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Michael Huen
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, S.A.R
- State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong, S.A.R
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3
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He X, Brakebusch C. Regulation of Precise DNA Repair by Nuclear Actin Polymerization: A Chance for Improving Gene Therapy? Cells 2024; 13:1093. [PMID: 38994946 PMCID: PMC11240418 DOI: 10.3390/cells13131093] [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: 05/12/2024] [Revised: 06/18/2024] [Accepted: 06/20/2024] [Indexed: 07/13/2024] Open
Abstract
Although more difficult to detect than in the cytoplasm, it is now clear that actin polymerization occurs in the nucleus and that it plays a role in the specific processes of the nucleus such as transcription, replication, and DNA repair. A number of studies suggest that nuclear actin polymerization is promoting precise DNA repair by homologous recombination, which could potentially be of help for precise genome editing and gene therapy. This review summarizes the findings and describes the challenges and chances in the field.
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Affiliation(s)
| | - Cord Brakebusch
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark;
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Korabel N, Warmenhoven JW, Henthorn NT, Ingram S, Fedotov S, Heaven CJ, Kirkby KJ, Taylor MJ, Merchant MJ. Modelling Heterogeneous Anomalous Dynamics of Radiation-Induced Double-Strand Breaks in DNA during Non-Homologous End-Joining Pathway. ENTROPY (BASEL, SWITZERLAND) 2024; 26:502. [PMID: 38920510 PMCID: PMC11202905 DOI: 10.3390/e26060502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/30/2024] [Accepted: 06/06/2024] [Indexed: 06/27/2024]
Abstract
The process of end-joining during nonhomologous repair of DNA double-strand breaks (DSBs) after radiation damage is considered. Experimental evidence has revealed that the dynamics of DSB ends exhibit subdiffusive motion rather than simple diffusion with rare directional movement. Traditional models often overlook the rare long-range directed motion. To address this limitation, we present a heterogeneous anomalous diffusion model consisting of subdiffusive fractional Brownian motion interchanged with short periods of long-range movement. Our model sheds light on the underlying mechanisms of heterogeneous diffusion in DSB repair and could be used to quantify the DSB dynamics on a time scale inaccessible to single particle tracking analysis. The model predicts that the long-range movement of DSB ends is responsible for the misrepair of DSBs in the form of dicentric chromosome lesions.
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Affiliation(s)
- Nickolay Korabel
- Department of Mathematics, The University of Manchester, Manchester M13 9PL, UK;
| | - John W. Warmenhoven
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.I.); (C.J.H.); (K.J.K.); (M.J.T.); (M.J.M.)
- The Christie NHS Foundation Trust, Manchester M20 4BX, UK
| | - Nicholas T. Henthorn
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.I.); (C.J.H.); (K.J.K.); (M.J.T.); (M.J.M.)
- The Christie NHS Foundation Trust, Manchester M20 4BX, UK
| | - Samuel Ingram
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.I.); (C.J.H.); (K.J.K.); (M.J.T.); (M.J.M.)
- Christie Medical Physics and Engineering, The Christie NHS Foundation Trust, Manchester M20 4BX, UK
| | - Sergei Fedotov
- Department of Mathematics, The University of Manchester, Manchester M13 9PL, UK;
| | - Charlotte J. Heaven
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.I.); (C.J.H.); (K.J.K.); (M.J.T.); (M.J.M.)
- The Christie NHS Foundation Trust, Manchester M20 4BX, UK
| | - Karen J. Kirkby
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.I.); (C.J.H.); (K.J.K.); (M.J.T.); (M.J.M.)
- The Christie NHS Foundation Trust, Manchester M20 4BX, UK
| | - Michael J. Taylor
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.I.); (C.J.H.); (K.J.K.); (M.J.T.); (M.J.M.)
- The Christie NHS Foundation Trust, Manchester M20 4BX, UK
| | - Michael J. Merchant
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK; (J.W.W.); (N.T.H.); (S.I.); (C.J.H.); (K.J.K.); (M.J.T.); (M.J.M.)
- The Christie NHS Foundation Trust, Manchester M20 4BX, UK
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5
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Vivo M, Rosti V, Cervone S, Lanzuolo C. Chromatin plasticity in mechanotransduction. Curr Opin Cell Biol 2024; 88:102376. [PMID: 38810318 DOI: 10.1016/j.ceb.2024.102376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/24/2024] [Accepted: 05/07/2024] [Indexed: 05/31/2024]
Abstract
Living organisms can detect and respond to physical forces at the cellular level. The pathways that transmit these forces to the nucleus allow cells to react quickly and consistently to environmental changes. Mechanobiology involves the interaction between physical forces and biological processes and is crucial for driving embryonic development and adapting to environmental cues during adulthood. Molecular studies have shown that cells can sense mechanical signals directly through membrane receptors linked to the cytoskeleton or indirectly through biochemical cascades that can influence gene expression for environmental adaptation. This review will explore the role of epigenetic modifications, emphasizing the 3D genome architecture and nuclear structures as responders to mechanical stimuli, which ensure cellular memory and adaptability. Understanding how mechanical cues are transduced and regulate cell functioning, governing processes such as cell programming and reprogramming, is essential for advancing our knowledge of human diseases.
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Affiliation(s)
- Maria Vivo
- Università degli Studi di Salerno, Fisciano, Italy.
| | - Valentina Rosti
- Institute of Biomedical Technologies, National Research Council (CNR), Milan, Italy; INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Sara Cervone
- INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Chiara Lanzuolo
- Institute of Biomedical Technologies, National Research Council (CNR), Milan, Italy; INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy.
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Wang F, Yu X, Qian J, Cao Y, Dong S, Zhan S, Lu Z, Bast RC, Song Q, Chen Y, Zhang Y, Zhou J. A novel SIK2 inhibitor SIC-19 exhibits synthetic lethality with PARP inhibitors in ovarian cancer. Drug Resist Updat 2024; 74:101077. [PMID: 38518726 DOI: 10.1016/j.drup.2024.101077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/28/2023] [Accepted: 02/29/2024] [Indexed: 03/24/2024]
Abstract
PURPOSE Ovarian cancer patients with HR proficiency (HRP) have had limited benefits from PARP inhibitor treatment, highlighting the need for improved therapeutic strategies. In this study, we developed a novel SIK2 inhibitor, SIC-19, and investigated its potential to enhance the sensitivity and expand the clinical utility of PARP inhibitors in ovarian cancer. METHODS The SIK2 protein was modeled using a Molecular Operating Environment (MOE), and the most favorable model was selected based on a GBVI/WSA dG scoring function. The Chembridge Compound Library was screened, and the top 20 candidate compounds were tested for their interaction with SIK2 and downstream substrates, AKT-pS473 and MYLK-pS343. SIC-19 emerged as the most promising drug candidate and was further evaluated using multiple assays. RESULTS SIC-19 exhibited selective and potent inhibition of SIK2, leading to its degradation through the ubiquitination pathway. The IC50 of SIC-19 correlated inversely with endogenous SIK2 expression in ovarian cancer cell lines. Treatment with SIC-19 significantly inhibited cancer cell growth and sensitized cells to PARP inhibitors in vitro, as well as in ovarian cancer organoids and xenograft models. Mechanistically, SIK2 knockdown and SIC-19 treatment reduced RAD50 phosphorylation at Ser635, prevented nuclear translocation of RAD50, disrupted nuclear filament assembly, and impaired DNA homologous recombination repair, ultimately inducing apoptosis. These findings highlight the crucial role of SIK2 in the DNA HR repair pathway and demonstrate the significant PARP inhibitor sensitization achieved by SIC-19 in ovarian cancer. CONCLUSIONS SIC-19, a novel SIK2 inhibitor, effectively inhibits tumor cell growth in ovarian cancer by interfering with RAD50-mediated DNA HR repair. Furthermore, SIC-19 enhances the efficacy of PARP inhibitors, providing a promising therapeutic strategy to improve outcomes for ovarian cancer patients.
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Affiliation(s)
- Fang Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xuejiao Yu
- Department of Imaging Department, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jun Qian
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yumin Cao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Shunli Dong
- Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Shenghua Zhan
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhen Lu
- Department of Experimental Therapeutics, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Robert C Bast
- Department of Experimental Therapeutics, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Qingxia Song
- Department of Obstetrics and Gynecology, Nanjing University of Chinese Medicine Affiliated Suzhou Hospital, Suzhou, China
| | - Youguo Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China.
| | - Yi Zhang
- Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, Suzhou, China.
| | - Jinhua Zhou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China.
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7
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Ulferts S, Lopes M, Miyamoto K, Grosse R. Nuclear actin dynamics and functions at a glance. J Cell Sci 2024; 137:jcs261630. [PMID: 38563209 DOI: 10.1242/jcs.261630] [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] [Indexed: 04/04/2024] Open
Abstract
Actin is well known for its cytoskeletal functions, where it helps to control and maintain cell shape and architecture, as well as regulating cell migration and intracellular cargo transport, among others. However, actin is also prevalent in the nucleus, where genome-regulating roles have been described, including it being part of chromatin-remodeling complexes. More recently, with the help of advances in microscopy techniques and specialized imaging probes, direct visualization of nuclear actin filament dynamics has helped elucidate new roles for nuclear actin, such as in cell cycle regulation, DNA replication and repair, chromatin organization and transcriptional condensate formation. In this Cell Science at a Glance article, we summarize the known signaling events driving the dynamic assembly of actin into filaments of various structures within the nuclear compartment for essential genome functions. Additionally, we highlight the physiological role of nuclear F-actin in meiosis and early embryonic development.
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Affiliation(s)
- Svenja Ulferts
- Institute for Clinical and Experimental Pharmacology and Toxicology I, Medical Faculty, University of Freiburg, 79104 Freiburg, Germany
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland
| | - Kei Miyamoto
- Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama 649-6493, Japan
| | - Robert Grosse
- Institute for Clinical and Experimental Pharmacology and Toxicology I, Medical Faculty, University of Freiburg, 79104 Freiburg, Germany
- Centre for Integrative Biological Signalling Studies (CIBSS), 79104 Freiburg, Germany
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8
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Hu J, Crickard JB. All who wander are not lost: the search for homology during homologous recombination. Biochem Soc Trans 2024; 52:367-377. [PMID: 38323621 PMCID: PMC10903458 DOI: 10.1042/bst20230705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 02/08/2024]
Abstract
Homologous recombination (HR) is a template-based DNA double-strand break repair pathway that functions to maintain genomic integrity. A vital component of the HR reaction is the identification of template DNA to be used during repair. This occurs through a mechanism known as the homology search. The homology search occurs in two steps: a collision step in which two pieces of DNA are forced to collide and a selection step that results in homologous pairing between matching DNA sequences. Selection of a homologous template is facilitated by recombinases of the RecA/Rad51 family of proteins in cooperation with helicases, translocases, and topoisomerases that determine the overall fidelity of the match. This menagerie of molecular machines acts to regulate critical intermediates during the homology search. These intermediates include recombinase filaments that probe for short stretches of homology and early strand invasion intermediates in the form of displacement loops (D-loops) that stabilize paired DNA. Here, we will discuss recent advances in understanding how these specific intermediates are regulated on the molecular level during the HR reaction. We will also discuss how the stability of these intermediates influences the ultimate outcomes of the HR reaction. Finally, we will discuss recent physiological models developed to explain how the homology search protects the genome.
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Affiliation(s)
- Jingyi Hu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, U.S.A
| | - J Brooks Crickard
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, U.S.A
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9
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Chappidi N, Quail T, Doll S, Vogel LT, Aleksandrov R, Felekyan S, Kühnemuth R, Stoynov S, Seidel CAM, Brugués J, Jahnel M, Franzmann TM, Alberti S. PARP1-DNA co-condensation drives DNA repair site assembly to prevent disjunction of broken DNA ends. Cell 2024; 187:945-961.e18. [PMID: 38320550 DOI: 10.1016/j.cell.2024.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 10/27/2023] [Accepted: 01/12/2024] [Indexed: 02/08/2024]
Abstract
DNA double-strand breaks (DSBs) are repaired at DSB sites. How DSB sites assemble and how broken DNA is prevented from separating is not understood. Here we uncover that the synapsis of broken DNA is mediated by the DSB sensor protein poly(ADP-ribose) (PAR) polymerase 1 (PARP1). Using bottom-up biochemistry, we reconstitute functional DSB sites and show that DSB sites form through co-condensation of PARP1 multimers with DNA. The co-condensates exert mechanical forces to keep DNA ends together and become enzymatically active for PAR synthesis. PARylation promotes release of PARP1 from DNA ends and the recruitment of effectors, such as Fused in Sarcoma, which stabilizes broken DNA ends against separation, revealing a finely orchestrated order of events that primes broken DNA for repair. We provide a comprehensive model for the hierarchical assembly of DSB condensates to explain DNA end synapsis and the recruitment of effector proteins for DNA damage repair.
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Affiliation(s)
- Nagaraja Chappidi
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Thomas Quail
- Max Planck Institute of Cell Biology and Genetics (MPI-CBG), Pfotenhauerstr. 108, 01307 Dresden, Germany; Cluster of Excellence Physics of Life, TU Dresden, Arnoldstraße 18, 01307 Dresden, Germany; Max Planck Institute for the Physics of Complex Systems (MPI-PKS), Nöthnitzer Str. 38, 01187 Dresden, Germany; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Simon Doll
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany; Cluster of Excellence Physics of Life, TU Dresden, Arnoldstraße 18, 01307 Dresden, Germany
| | - Laura T Vogel
- Department of Molecular Physical Chemistry, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Radoslav Aleksandrov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str, bl.21, 1113 Sofia, Bulgaria
| | - Suren Felekyan
- Department of Molecular Physical Chemistry, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Ralf Kühnemuth
- Department of Molecular Physical Chemistry, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Stoyno Stoynov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str, bl.21, 1113 Sofia, Bulgaria
| | - Claus A M Seidel
- Department of Molecular Physical Chemistry, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Jan Brugués
- Max Planck Institute of Cell Biology and Genetics (MPI-CBG), Pfotenhauerstr. 108, 01307 Dresden, Germany; Cluster of Excellence Physics of Life, TU Dresden, Arnoldstraße 18, 01307 Dresden, Germany; Max Planck Institute for the Physics of Complex Systems (MPI-PKS), Nöthnitzer Str. 38, 01187 Dresden, Germany
| | - Marcus Jahnel
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany; Cluster of Excellence Physics of Life, TU Dresden, Arnoldstraße 18, 01307 Dresden, Germany
| | - Titus M Franzmann
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Simon Alberti
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany.
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10
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Perdyan A, Jąkalski M, Horbacz M, Beheshti A, Mieczkowski J. Chromosomal positioning and epigenetic architecture influence DNA methylation patterns triggered by galactic cosmic radiation. Sci Rep 2024; 14:1324. [PMID: 38225252 PMCID: PMC10789781 DOI: 10.1038/s41598-024-51756-7] [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: 09/27/2023] [Accepted: 01/09/2024] [Indexed: 01/17/2024] Open
Abstract
Despite surging interest in space travel in recent decades, the impacts of prolonged, elevated exposure to galactic cosmic radiation (GCR) on human health remain poorly understood. This form of ionizing radiation causes significant changes to biological systems including damage to DNA structure by altering epigenetic phenotype with emphasis on DNA methylation. Building on previous work by Kennedy et al. (Sci Rep 8(1): 6709. 10.1038/S41598-018-24755-8), we evaluated spatial DNA methylation patterns triggered by high-LET (56Fe, 28Si) and low-LET (X-ray) radiation and the influence of chromosome positioning and epigenetic architecture in distinct radial layers of cell nucleus. Next, we validated our results using gene expression data of mice irradiated with simulated GCR and JAXA astronauts. We showed that primarily 56Fe induces a persistent DNA methylation increase whereas 28Si and X-ray induce a decrease DNA methylation which is not persistent with time. Moreover, we highlighted the role of nuclear chromatin architecture in cell response to external radiation. In summary, our study provides novel insights towards epigenetic and transcriptomic response as well as chromatin multidimensional structure influence on galactic cosmic radiation damage.
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Affiliation(s)
- Adrian Perdyan
- International Research Agenda 3P - Medicine Laboratory, Medical University of Gdansk, Marii Sklodowskiej Curie 3a, 80-210, Gdansk, Poland
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Marcin Jąkalski
- International Research Agenda 3P - Medicine Laboratory, Medical University of Gdansk, Marii Sklodowskiej Curie 3a, 80-210, Gdansk, Poland
| | - Monika Horbacz
- International Research Agenda 3P - Medicine Laboratory, Medical University of Gdansk, Marii Sklodowskiej Curie 3a, 80-210, Gdansk, Poland
| | - Afshin Beheshti
- Space Biosciences Division, NASA Ames Research Center, Blue Marble Space Institute of Science, Moffett Field, CA, 94035, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jakub Mieczkowski
- International Research Agenda 3P - Medicine Laboratory, Medical University of Gdansk, Marii Sklodowskiej Curie 3a, 80-210, Gdansk, Poland.
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11
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Verma N, Renauer PA, Dong C, Xin S, Lin Q, Zhang F, Glazer PM, Chen S. Genome scale CRISPR screens identify actin capping proteins as key modulators of therapeutic responses to radiation and immunotherapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.14.575614. [PMID: 38293095 PMCID: PMC10827061 DOI: 10.1101/2024.01.14.575614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Radiotherapy (RT), is a fundamental treatment for malignant tumors and is used in over half of cancer patients. As radiation can promote anti-tumor immune effects, a promising therapeutic strategy is to combine radiation with immune checkpoint inhibitors (ICIs). However, the genetic determinants that impact therapeutic response in the context of combination therapy with radiation and ICI have not been systematically investigated. To unbiasedly identify the tumor intrinsic genetic factors governing such responses, we perform a set of genome-scale CRISPR screens in melanoma cells for cancer survival in response to low-dose genotoxic radiation treatment, in the context of CD8 T cell co-culture and with anti-PD1 checkpoint blockade antibody. Two actin capping proteins, Capza3 and Capg, emerge as top hits that upon inactivation promote the survival of melanoma cells in such settings. Capza3 and Capg knockouts (KOs) in mouse and human cancer cells display persistent DNA damage due to impaired homology directed repair (HDR); along with increased radiation, chemotherapy, and DNA repair inhibitor sensitivity. However, when cancer cells with these genes inactivated were exposed to sublethal radiation, inactivation of such actin capping protein promotes activation of the STING pathway, induction of inhibitory CEACAM1 ligand expression and resistance to CD8 T cell killing. Patient cancer genomics analysis reveals an increased mutational burden in patients with inactivating mutations in CAPG and/or CAPZA3, at levels comparable to other HDR associated genes. There is also a positive correlation between CAPG expression and activation of immune related pathways and CD8 T cell tumor infiltration. Our results unveil the critical roles of actin binding proteins for efficient HDR within cancer cells and demonstrate a previously unrecognized regulatory mechanism of therapeutic response to radiation and immunotherapy.
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Affiliation(s)
- Nipun Verma
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Department of Therapeutic Radiology, Yale University, New Haven, Connecticut, USA
| | - Paul A. Renauer
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Chuanpeng Dong
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Shan Xin
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Qianqian Lin
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Feifei Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
| | - Peter M. Glazer
- Department of Therapeutic Radiology, Yale University, New Haven, Connecticut, USA
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Immunobiology Program, Yale University, New Haven, Connecticut, USA
- Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, Connecticut, USA
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, USA
- Yale Center for Biomedical Data Science, Yale University School of Medicine, New Haven, Connecticut, USA
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12
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van Bueren MAE, Janssen A. The impact of chromatin on double-strand break repair: Imaging tools and discoveries. DNA Repair (Amst) 2024; 133:103592. [PMID: 37976899 DOI: 10.1016/j.dnarep.2023.103592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/16/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023]
Abstract
Eukaryotic nuclei are constantly being exposed to factors that break or chemically modify the DNA. Accurate repair of this DNA damage is crucial to prevent DNA mutations and maintain optimal cell function. To overcome the detrimental effects of DNA damage, a multitude of repair pathways has evolved. These pathways need to function properly within the different chromatin domains present in the nucleus. Each of these domains exhibit distinct molecular- and bio-physical characteristics that can influence the response to DNA damage. In particular, chromatin domains highly enriched for repetitive DNA sequences, such as nucleoli, centromeres and pericentromeric heterochromatin require tailored repair mechanisms to safeguard genome stability. Work from the past decades has led to the development of innovative imaging tools as well as inducible DNA damage techniques to gain new insights into the impact of these repetitive chromatin domains on the DNA repair process. Here we summarize these tools with a particular focus on Double-Strand Break (DSB) repair, and discuss the insights gained into our understanding of the influence of chromatin domains on DSB -dynamics and -repair pathway choice.
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Affiliation(s)
- Marit A E van Bueren
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Aniek Janssen
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands.
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13
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Spegg V, Altmeyer M. Genome maintenance meets mechanobiology. Chromosoma 2024; 133:15-36. [PMID: 37581649 PMCID: PMC10904543 DOI: 10.1007/s00412-023-00807-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/20/2023] [Accepted: 07/26/2023] [Indexed: 08/16/2023]
Abstract
Genome stability is key for healthy cells in healthy organisms, and deregulated maintenance of genome integrity is a hallmark of aging and of age-associated diseases including cancer and neurodegeneration. To maintain a stable genome, genome surveillance and repair pathways are closely intertwined with cell cycle regulation and with DNA transactions that occur during transcription and DNA replication. Coordination of these processes across different time and length scales involves dynamic changes of chromatin topology, clustering of fragile genomic regions and repair factors into nuclear repair centers, mobilization of the nuclear cytoskeleton, and activation of cell cycle checkpoints. Here, we provide a general overview of cell cycle regulation and of the processes involved in genome duplication in human cells, followed by an introduction to replication stress and to the cellular responses elicited by perturbed DNA synthesis. We discuss fragile genomic regions that experience high levels of replication stress, with a particular focus on telomere fragility caused by replication stress at the ends of linear chromosomes. Using alternative lengthening of telomeres (ALT) in cancer cells and ALT-associated PML bodies (APBs) as examples of replication stress-associated clustered DNA damage, we discuss compartmentalization of DNA repair reactions and the role of protein properties implicated in phase separation. Finally, we highlight emerging connections between DNA repair and mechanobiology and discuss how biomolecular condensates, components of the nuclear cytoskeleton, and interfaces between membrane-bound organelles and membraneless macromolecular condensates may cooperate to coordinate genome maintenance in space and time.
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Affiliation(s)
- Vincent Spegg
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.
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14
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Bader AS, Bushell M. iMUT-seq: high-resolution DSB-induced mutation profiling reveals prevalent homologous-recombination dependent mutagenesis. Nat Commun 2023; 14:8419. [PMID: 38110444 PMCID: PMC10728174 DOI: 10.1038/s41467-023-44167-1] [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: 04/01/2022] [Accepted: 12/04/2023] [Indexed: 12/20/2023] Open
Abstract
DNA double-strand breaks (DSBs) are the most mutagenic form of DNA damage, and play a significant role in cancer biology, neurodegeneration and aging. However, studying DSB-induced mutagenesis is limited by our current approaches. Here, we describe iMUT-seq, a technique that profiles DSB-induced mutations at high-sensitivity and single-nucleotide resolution around endogenous DSBs. By depleting or inhibiting 20 DSB-repair factors we define their mutational signatures in detail, revealing insights into the mechanisms of DSB-induced mutagenesis. Notably, we find that homologous-recombination (HR) is more mutagenic than previously thought, inducing prevalent base substitutions and mononucleotide deletions at distance from the break due to DNA-polymerase errors. Simultaneously, HR reduces translocations, suggesting a primary role of HR is specifically the prevention of genomic rearrangements. The results presented here offer fundamental insights into DSB-induced mutagenesis and have significant implications for our understanding of cancer biology and the development of DDR-targeting chemotherapeutics.
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Affiliation(s)
- Aldo S Bader
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK.
- Cancer Research UK/CI, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK.
- The Gurdon Institute, University of Cambridge, Biochemistry, Cambridge, UK.
| | - Martin Bushell
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK.
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15
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Colding-Christensen CS, Kakulidis ES, Arroyo-Gomez J, Hendriks IA, Arkinson C, Fábián Z, Gambus A, Mailand N, Duxin JP, Nielsen ML. Profiling ubiquitin signalling with UBIMAX reveals DNA damage- and SCF β-Trcp1-dependent ubiquitylation of the actin-organizing protein Dbn1. Nat Commun 2023; 14:8293. [PMID: 38097601 PMCID: PMC10721886 DOI: 10.1038/s41467-023-43873-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023] Open
Abstract
Ubiquitin widely modifies proteins, thereby regulating most cellular functions. The complexity of ubiquitin signalling necessitates unbiased methods enabling global detection of dynamic protein ubiquitylation. Here, we describe UBIMAX (UBiquitin target Identification by Mass spectrometry in Xenopus egg extracts), which enriches ubiquitin-conjugated proteins and quantifies regulation of protein ubiquitylation under precise and adaptable conditions. We benchmark UBIMAX by investigating DNA double-strand break-responsive ubiquitylation events, identifying previously known targets and revealing the actin-organizing protein Dbn1 as a major target of DNA damage-induced ubiquitylation. We find that Dbn1 is targeted for proteasomal degradation by the SCFβ-Trcp1 ubiquitin ligase, in a conserved mechanism driven by ATM-mediated phosphorylation of a previously uncharacterized β-Trcp1 degron containing an SQ motif. We further show that this degron is sufficient to induce DNA damage-dependent protein degradation of a model substrate. Collectively, we demonstrate UBIMAX's ability to identify targets of stimulus-regulated ubiquitylation and reveal an SCFβ-Trcp1-mediated ubiquitylation mechanism controlled directly by the apical DNA damage response kinases.
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Affiliation(s)
- Camilla S Colding-Christensen
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Ellen S Kakulidis
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Javier Arroyo-Gomez
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Ivo A Hendriks
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Connor Arkinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- California Institute for Quantitative Biosciences and Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Zita Fábián
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Agnieszka Gambus
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Niels Mailand
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Julien P Duxin
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark.
| | - Michael L Nielsen
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark.
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16
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Girasol MJ, Krasilnikova M, Marques CA, Damasceno JD, Lapsley C, Lemgruber L, Burchmore R, Beraldi D, Carruthers R, Briggs EM, McCulloch R. RAD51-mediated R-loop formation acts to repair transcription-associated DNA breaks driving antigenic variation in Trypanosoma brucei. Proc Natl Acad Sci U S A 2023; 120:e2309306120. [PMID: 37988471 PMCID: PMC10691351 DOI: 10.1073/pnas.2309306120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/13/2023] [Indexed: 11/23/2023] Open
Abstract
RNA-DNA hybrids are epigenetic features of all genomes that intersect with many processes, including transcription, telomere homeostasis, and centromere function. Increasing evidence suggests that RNA-DNA hybrids can provide two conflicting roles in the maintenance and transmission of genomes: They can be the triggers of DNA damage, leading to genome change, or can aid the DNA repair processes needed to respond to DNA lesions. Evasion of host immunity by African trypanosomes, such as Trypanosoma brucei, relies on targeted recombination of silent Variant Surface Glycoprotein (VSG) genes into a specialized telomeric locus that directs transcription of just one VSG from thousands. How such VSG recombination is targeted and initiated is unclear. Here, we show that a key enzyme of T. brucei homologous recombination, RAD51, interacts with RNA-DNA hybrids. In addition, we show that RNA-DNA hybrids display a genome-wide colocalization with DNA breaks and that this relationship is impaired by mutation of RAD51. Finally, we show that RAD51 acts to repair highly abundant, localised DNA breaks at the single transcribed VSG and that mutation of RAD51 alters RNA-DNA hybrid abundance at 70 bp repeats both around the transcribed VSG and across the silent VSG archive. This work reveals a widespread, generalised role for RNA-DNA hybrids in directing RAD51 activity during recombination and uncovers a specialised application of this interplay during targeted DNA break repair needed for the critical T. brucei immune evasion reaction of antigenic variation.
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Affiliation(s)
- Mark John Girasol
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
- Faculty of the MD-PhD in Molecular Medicine Program, College of Medicine, University of the Philippines Manila, Manila1000, Philippines
| | - Marija Krasilnikova
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Catarina A. Marques
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Jeziel D. Damasceno
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Craig Lapsley
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Leandro Lemgruber
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Richard Burchmore
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Dario Beraldi
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
| | - Ross Carruthers
- College of Medical, Veterinary and Life Sciences, School of Cancer Sciences, University of Glasgow, GlasgowG12 0YN, United Kingdom
| | - Emma M. Briggs
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, EdinburghEH9 3FL, United Kingdom
| | - Richard McCulloch
- College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, University of Glasgow, GlasgowG12 8TA, United Kingdom
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17
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Palumbieri MD, Merigliano C, González-Acosta D, Kuster D, Krietsch J, Stoy H, von Känel T, Ulferts S, Welter B, Frey J, Doerdelmann C, Sanchi A, Grosse R, Chiolo I, Lopes M. Nuclear actin polymerization rapidly mediates replication fork remodeling upon stress by limiting PrimPol activity. Nat Commun 2023; 14:7819. [PMID: 38016948 PMCID: PMC10684888 DOI: 10.1038/s41467-023-43183-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/02/2023] [Indexed: 11/30/2023] Open
Abstract
Cells rapidly respond to replication stress actively slowing fork progression and inducing fork reversal. How replication fork plasticity is achieved in the context of nuclear organization is currently unknown. Using nuclear actin probes in living and fixed cells, we visualized nuclear actin filaments in unperturbed S phase and observed their rapid extension in number and length upon genotoxic treatments, frequently taking contact with replication factories. Chemically or genetically impairing nuclear actin polymerization shortly before these treatments prevents active fork slowing and abolishes fork reversal. Defective fork remodeling is linked to deregulated chromatin loading of PrimPol, which promotes unrestrained and discontinuous DNA synthesis and limits the recruitment of RAD51 and SMARCAL1 to nascent DNA. Moreover, defective nuclear actin polymerization upon mild replication interference induces chromosomal instability in a PRIMPOL-dependent manner. Hence, by limiting PrimPol activity, nuclear F-actin orchestrates replication fork plasticity and is a key molecular determinant in the rapid cellular response to genotoxic treatments.
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Affiliation(s)
| | - Chiara Merigliano
- Molecular and Computational Biology Department, University of Southern California, Los Angeles, CA, USA
| | | | - Danina Kuster
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Jana Krietsch
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Henriette Stoy
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
- Department of Cellular and Molecular Medicine, Copenhagen University, Copenhagen, Denmark
| | - Thomas von Känel
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Svenja Ulferts
- Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany
| | - Bettina Welter
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Joël Frey
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Cyril Doerdelmann
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Andrea Sanchi
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Robert Grosse
- Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany
- CIBSS - Centre for Integrative Biological Signaling Studies, University of Freiburg, Freiburg im Breisgau, Germany
| | - Irene Chiolo
- Molecular and Computational Biology Department, University of Southern California, Los Angeles, CA, USA.
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
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18
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Wollscheid HP, Ulrich HD. Chromatin meets the cytoskeleton: the importance of nuclear actin dynamics and associated motors for genome stability. DNA Repair (Amst) 2023; 131:103571. [PMID: 37738698 DOI: 10.1016/j.dnarep.2023.103571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 09/24/2023]
Abstract
The actin cytoskeleton is of fundamental importance for numerous cellular processes, including intracellular transport, cell plasticity, and cell migration. However, functions of filamentous actin (F-actin) in the nucleus remain understudied due to the comparatively low abundance of nuclear actin and the resulting experimental limitations to its visualization. Owing to recent technological advances such as super-resolution microscopy and the development of nuclear-specific actin probes, essential roles of the actin cytoskeleton in the context of genome maintenance are now emerging. In addition to the contributions of monomeric actin as a component of multiple important nuclear protein complexes, nuclear actin has been found to undergo polymerization in response to DNA damage and DNA replication stress. Consequently, nuclear F-actin plays important roles in the regulation of intra-nuclear mobility of repair and replication foci as well as the maintenance of nuclear shape, two important aspects of efficient stress tolerance. Beyond actin itself, there is accumulating evidence for the participation of multiple actin-binding proteins (ABPs) in the surveillance of genome integrity, including nucleation factors and motor proteins of the myosin family. Here we summarize recent findings highlighting the importance of actin cytoskeletal factors within the nucleus in key genome maintenance pathways.
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Affiliation(s)
- Hans-Peter Wollscheid
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, Mainz D - 55128, Germany.
| | - Helle D Ulrich
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, Mainz D - 55128, Germany.
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19
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Heemskerk T, van de Kamp G, Essers J, Kanaar R, Paul MW. Multi-scale cellular imaging of DNA double strand break repair. DNA Repair (Amst) 2023; 131:103570. [PMID: 37734176 DOI: 10.1016/j.dnarep.2023.103570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023]
Abstract
Live-cell and high-resolution fluorescence microscopy are powerful tools to study the organization and dynamics of DNA double-strand break repair foci and specific repair proteins in single cells. This requires specific induction of DNA double-strand breaks and fluorescent markers to follow the DNA lesions in living cells. In this review, where we focused on mammalian cell studies, we discuss different methods to induce DNA double-strand breaks, how to visualize and quantify repair foci in living cells., We describe different (live-cell) imaging modalities that can reveal details of the DNA double-strand break repair process across multiple time and spatial scales. In addition, recent developments are discussed in super-resolution imaging and single-molecule tracking, and how these technologies can be applied to elucidate details on structural compositions or dynamics of DNA double-strand break repair.
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Affiliation(s)
- Tim Heemskerk
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Gerarda van de Kamp
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jeroen Essers
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands; Department of Vascular Surgery, Erasmus University Medical Center, Rotterdam, the Netherlands; Department of Radiotherapy, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Maarten W Paul
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands.
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20
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Arnould C, Rocher V, Saur F, Bader AS, Muzzopappa F, Collins S, Lesage E, Le Bozec B, Puget N, Clouaire T, Mangeat T, Mourad R, Ahituv N, Noordermeer D, Erdel F, Bushell M, Marnef A, Legube G. Chromatin compartmentalization regulates the response to DNA damage. Nature 2023; 623:183-192. [PMID: 37853125 PMCID: PMC10620078 DOI: 10.1038/s41586-023-06635-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 09/12/2023] [Indexed: 10/20/2023]
Abstract
The DNA damage response is essential to safeguard genome integrity. Although the contribution of chromatin in DNA repair has been investigated1,2, the contribution of chromosome folding to these processes remains unclear3. Here we report that, after the production of double-stranded breaks (DSBs) in mammalian cells, ATM drives the formation of a new chromatin compartment (D compartment) through the clustering of damaged topologically associating domains, decorated with γH2AX and 53BP1. This compartment forms by a mechanism that is consistent with polymer-polymer phase separation rather than liquid-liquid phase separation. The D compartment arises mostly in G1 phase, is independent of cohesin and is enhanced after pharmacological inhibition of DNA-dependent protein kinase (DNA-PK) or R-loop accumulation. Importantly, R-loop-enriched DNA-damage-responsive genes physically localize to the D compartment, and this contributes to their optimal activation, providing a function for DSB clustering in the DNA damage response. However, DSB-induced chromosome reorganization comes at the expense of an increased rate of translocations, also observed in cancer genomes. Overall, we characterize how DSB-induced compartmentalization orchestrates the DNA damage response and highlight the critical impact of chromosome architecture in genomic instability.
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Affiliation(s)
- Coline Arnould
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Vincent Rocher
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Florian Saur
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Aldo S Bader
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Fernando Muzzopappa
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Sarah Collins
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Emma Lesage
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Benjamin Le Bozec
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Nadine Puget
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Thomas Clouaire
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Thomas Mangeat
- LITC Core Facility, Centre de Biologie Integrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Raphael Mourad
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Daan Noordermeer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Fabian Erdel
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Martin Bushell
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Aline Marnef
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Gaëlle Legube
- MCD, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France.
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21
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Kovacs MT, Vallette M, Wiertsema P, Dingli F, Loew D, Nader GPDF, Piel M, Ceccaldi R. DNA damage induces nuclear envelope rupture through ATR-mediated phosphorylation of lamin A/C. Mol Cell 2023; 83:3659-3668.e10. [PMID: 37832547 PMCID: PMC10597398 DOI: 10.1016/j.molcel.2023.09.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 08/01/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023]
Abstract
The integrity of the nuclear envelope (NE) is essential for maintaining the structural stability of the nucleus. Rupture of the NE has been frequently observed in cancer cells, especially in the context of mechanical challenges, such as physical confinement and migration. However, spontaneous NE rupture events, without any obvious physical challenges to the cell, have also been described. The molecular mechanism(s) of these spontaneous NE rupture events remain to be explored. Here, we show that DNA damage and subsequent ATR activation leads to NE rupture. Upon DNA damage, lamin A/C is phosphorylated in an ATR-dependent manner, leading to changes in lamina assembly and, ultimately, NE rupture. In addition, we show that cancer cells with intrinsic DNA repair defects undergo frequent events of DNA-damage-induced NE rupture, which renders them extremely sensitive to further NE perturbations. Exploiting this NE vulnerability could provide a new angle to complement traditional, DNA-damage-based chemotherapy.
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Affiliation(s)
| | - Marie Vallette
- Inserm U830, PSL Research University, Institut Curie, 75005 Paris, France
| | - Pauline Wiertsema
- Inserm U830, PSL Research University, Institut Curie, 75005 Paris, France
| | - Florent Dingli
- Institut Curie, PSL Research University, Centre de Recherche, CurieCoreTech Spectrométrie de Masse Protéomique, 26 rue d'Ulm, Paris 75248 Cedex 05, France
| | - Damarys Loew
- Institut Curie, PSL Research University, Centre de Recherche, CurieCoreTech Spectrométrie de Masse Protéomique, 26 rue d'Ulm, Paris 75248 Cedex 05, France
| | | | - Matthieu Piel
- Institut Curie and Institut Pierre Gilles de Gennes, PSL Research University, CNRS, UMR 144, Paris, France
| | - Raphael Ceccaldi
- Inserm U830, PSL Research University, Institut Curie, 75005 Paris, France.
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22
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Yang H, Lachtara EM, Ran X, Hopkins J, Patel PS, Zhu X, Xiao Y, Phoon L, Gao B, Zou L, Lawrence MS, Lan L. The RNA m5C modification in R-loops as an off switch of Alt-NHEJ. Nat Commun 2023; 14:6114. [PMID: 37777505 PMCID: PMC10542358 DOI: 10.1038/s41467-023-41790-w] [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: 02/01/2023] [Accepted: 09/19/2023] [Indexed: 10/02/2023] Open
Abstract
The roles of R-loops and RNA modifications in homologous recombination (HR) and other DNA double-stranded break (DSB) repair pathways remain poorly understood. Here, we find that DNA damage-induced RNA methyl-5-cytosine (m5C) modification in R-loops plays a crucial role to regulate PARP1-mediated poly ADP-ribosylation (PARylation) and the choice of DSB repair pathways at sites of R-loops. Through bisulfite sequencing, we discover that the methyltransferase TRDMT1 preferentially generates m5C after DNA damage in R-loops across the genome. In the absence of m5C, R-loops activate PARP1-mediated PARylation both in vitro and in cells. Concurrently, m5C promotes transcription-coupled HR (TC-HR) while suppressing PARP1-dependent alternative non-homologous end joining (Alt-NHEJ), favoring TC-HR over Alt-NHEJ in transcribed regions as the preferred repair pathway. Importantly, simultaneous disruption of both TC-HR and Alt-NHEJ with TRDMT1 and PARP or Polymerase θ inhibitors prevents alternative DSB repair and exhibits synergistic cytotoxic effects on cancer cells, suggesting an effective strategy to exploit genomic instability in cancer therapy.
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Affiliation(s)
- Haibo Yang
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Emily M Lachtara
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiaojuan Ran
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Jessica Hopkins
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Parasvi S Patel
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Xueping Zhu
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Yao Xiao
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Laiyee Phoon
- Departments of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA
| | - Boya Gao
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Li Lan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA.
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Departments of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA.
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23
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Dileep V, Boix CA, Mathys H, Marco A, Welch GM, Meharena HS, Loon A, Jeloka R, Peng Z, Bennett DA, Kellis M, Tsai LH. Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration. Cell 2023; 186:4404-4421.e20. [PMID: 37774679 PMCID: PMC10697236 DOI: 10.1016/j.cell.2023.08.038] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 04/02/2023] [Accepted: 08/29/2023] [Indexed: 10/01/2023]
Abstract
Persistent DNA double-strand breaks (DSBs) in neurons are an early pathological hallmark of neurodegenerative diseases including Alzheimer's disease (AD), with the potential to disrupt genome integrity. We used single-nucleus RNA-seq in human postmortem prefrontal cortex samples and found that excitatory neurons in AD were enriched for somatic mosaic gene fusions. Gene fusions were particularly enriched in excitatory neurons with DNA damage repair and senescence gene signatures. In addition, somatic genome structural variations and gene fusions were enriched in neurons burdened with DSBs in the CK-p25 mouse model of neurodegeneration. Neurons enriched for DSBs also had elevated levels of cohesin along with progressive multiscale disruption of the 3D genome organization aligned with transcriptional changes in synaptic, neuronal development, and histone genes. Overall, this study demonstrates the disruption of genome stability and the 3D genome organization by DSBs in neurons as pathological steps in the progression of neurodegenerative diseases.
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Affiliation(s)
- Vishnu Dileep
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Carles A Boix
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hansruedi Mathys
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Asaf Marco
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gwyneth M Welch
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hiruy S Meharena
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anjanet Loon
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ritika Jeloka
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zhuyu Peng
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Li-Huei Tsai
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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24
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Han Z, Moore GA, Mitter R, Lopez Martinez D, Wan L, Dirac Svejstrup AB, Rueda DS, Svejstrup JQ. DNA-directed termination of RNA polymerase II transcription. Mol Cell 2023; 83:3253-3267.e7. [PMID: 37683646 PMCID: PMC7615648 DOI: 10.1016/j.molcel.2023.08.007] [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: 03/23/2023] [Revised: 06/27/2023] [Accepted: 08/09/2023] [Indexed: 09/10/2023]
Abstract
RNA polymerase II (RNAPII) transcription involves initiation from a promoter, transcriptional elongation through the gene, and termination in the terminator region. In bacteria, terminators often contain specific DNA elements provoking polymerase dissociation, but RNAPII transcription termination is thought to be driven entirely by protein co-factors. We used biochemical reconstitution, single-molecule studies, and genome-wide analysis in yeast to study RNAPII termination. Transcription into natural terminators by pure RNAPII results in spontaneous termination at specific sequences containing T-tracts. Single-molecule analysis indicates that termination involves pausing without backtracking. The "torpedo" Rat1-Rai1 exonuclease (XRN2 in humans) greatly stimulates spontaneous termination but is ineffectual on other paused RNAPIIs. By contrast, elongation factor Spt4-Spt5 (DSIF) suppresses termination. Genome-wide analysis further indicates that termination occurs by transcript cleavage at the poly(A) site exposing a new 5' RNA-end that allows Rat1-Rai1 loading, which then catches up with destabilized RNAPII at specific termination sites to end transcription.
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Affiliation(s)
- Zhong Han
- Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark; Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - George A Moore
- Single Molecule Imaging group, MRC-London Institute of Medical Sciences, and Section of Virology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London W12 0NN, UK
| | - Richard Mitter
- Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David Lopez Martinez
- Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark; Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Li Wan
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - A Barbara Dirac Svejstrup
- Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark; Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David S Rueda
- Single Molecule Imaging group, MRC-London Institute of Medical Sciences, and Section of Virology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London W12 0NN, UK
| | - Jesper Q Svejstrup
- Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark; Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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25
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Canoy RJ, Shmakova A, Karpukhina A, Lomov N, Tiukacheva E, Kozhevnikova Y, André F, Germini D, Vassetzky Y. Specificity of cancer-related chromosomal translocations is linked to proximity after the DNA double-strand break and subsequent selection. NAR Cancer 2023; 5:zcad049. [PMID: 37750169 PMCID: PMC10518054 DOI: 10.1093/narcan/zcad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 08/01/2023] [Accepted: 09/14/2023] [Indexed: 09/27/2023] Open
Abstract
Most cancer-related chromosomal translocations appear to be cell type specific. It is currently unknown why different chromosomal translocations occur in different cells. This can be due to either the occurrence of particular translocations in specific cell types or adaptive survival advantage conferred by translocations only in specific cells. We experimentally addressed this question by double-strand break (DSB) induction at MYC, IGH, AML and ETO loci in the same cell to generate chromosomal translocations in different cell lineages. Our results show that any translocation can potentially arise in any cell type. We have analyzed different factors that could affect the frequency of the translocations, and only the spatial proximity between gene loci after the DSB induction correlated with the resulting translocation frequency, supporting the 'breakage-first' model. Furthermore, upon long-term culture of cells with the generated chromosomal translocations, only oncogenic MYC-IGH and AML-ETO translocations persisted over a 60-day period. Overall, the results suggest that chromosomal translocation can be generated after DSB induction in any type of cell, but whether the cell with the translocation would persist in a cell population depends on the cell type-specific selective survival advantage that the chromosomal translocation confers to the cell.
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Affiliation(s)
- Reynand Jay Canoy
- UMR 9018, CNRS, Univ. Paris-Sud, Université Paris Saclay, Institut Gustave Roussy, F-94805 Villejuif, France
- Institute of Human Genetics, National Institutes of Health, University of the Philippines Manila, 1000 Manila, The Philippines
| | - Anna Shmakova
- UMR 9018, CNRS, Univ. Paris-Sud, Université Paris Saclay, Institut Gustave Roussy, F-94805 Villejuif, France
- Laboratory of Molecular Endocrinology, Institute of Experimental Cardiology, Federal State Budgetary Organization ‘National Cardiology Research Center’ of the Ministry of Health of the Russian Federation, 127994 Moscow, Russia
- Koltzov Institute of Developmental Biology, 117334 Moscow, Russia
| | - Anna Karpukhina
- UMR 9018, CNRS, Univ. Paris-Sud, Université Paris Saclay, Institut Gustave Roussy, F-94805 Villejuif, France
- Koltzov Institute of Developmental Biology, 117334 Moscow, Russia
| | - Nikolai Lomov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Eugenia Tiukacheva
- UMR 9018, CNRS, Univ. Paris-Sud, Université Paris Saclay, Institut Gustave Roussy, F-94805 Villejuif, France
- Koltzov Institute of Developmental Biology, 117334 Moscow, Russia
| | - Yana Kozhevnikova
- UMR 9018, CNRS, Univ. Paris-Sud, Université Paris Saclay, Institut Gustave Roussy, F-94805 Villejuif, France
| | - Franck André
- UMR 9018, CNRS, Univ. Paris-Sud, Université Paris Saclay, Institut Gustave Roussy, F-94805 Villejuif, France
| | - Diego Germini
- UMR 9018, CNRS, Univ. Paris-Sud, Université Paris Saclay, Institut Gustave Roussy, F-94805 Villejuif, France
| | - Yegor Vassetzky
- UMR 9018, CNRS, Univ. Paris-Sud, Université Paris Saclay, Institut Gustave Roussy, F-94805 Villejuif, France
- Koltzov Institute of Developmental Biology, 117334 Moscow, Russia
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26
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Min J, Zhao J, Zagelbaum J, Lee J, Takahashi S, Cummings P, Schooley A, Dekker J, Gottesman ME, Rabadan R, Gautier J. Mechanisms of insertions at a DNA double-strand break. Mol Cell 2023; 83:2434-2448.e7. [PMID: 37402370 PMCID: PMC10527084 DOI: 10.1016/j.molcel.2023.06.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 04/06/2023] [Accepted: 06/08/2023] [Indexed: 07/06/2023]
Abstract
Insertions and deletions (indels) are common sources of structural variation, and insertions originating from spontaneous DNA lesions are frequent in cancer. We developed a highly sensitive assay called insertion and deletion sequencing (Indel-seq) to monitor rearrangements in human cells at the TRIM37 acceptor locus that reports indels stemming from experimentally induced and spontaneous genome instability. Templated insertions, which derive from sequences genome wide, require contact between donor and acceptor loci, require homologous recombination, and are stimulated by DNA end-processing. Insertions are facilitated by transcription and involve a DNA/RNA hybrid intermediate. Indel-seq reveals that insertions are generated via multiple pathways. The broken acceptor site anneals with a resected DNA break or invades the displaced strand of a transcription bubble or R-loop, followed by DNA synthesis, displacement, and then ligation by non-homologous end joining. Our studies identify transcription-coupled insertions as a critical source of spontaneous genome instability that is distinct from cut-and-paste events.
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Affiliation(s)
- Jaewon Min
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
| | - Junfei Zhao
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jennifer Zagelbaum
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jina Lee
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Sho Takahashi
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Portia Cummings
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Allana Schooley
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Max E Gottesman
- Department of Biochemistry and Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Raul Rabadan
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jean Gautier
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Genetics and Development, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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27
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Lomov NA, Viushkov VS, Rubtsov MA. Mechanisms of Secondary Leukemia Development Caused by Treatment with DNA Topoisomerase Inhibitors. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:892-911. [PMID: 37751862 DOI: 10.1134/s0006297923070040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/14/2023] [Accepted: 04/20/2023] [Indexed: 09/28/2023]
Abstract
Leukemia is a blood cancer originating in the blood and bone marrow. Therapy-related leukemia is associated with prior chemotherapy. Although cancer therapy with DNA topoisomerase II inhibitors is one of the most effective cancer treatments, its side effects include development of secondary leukemia characterized by the chromosomal rearrangements affecting AML1 or MLL genes. Recurrent chromosomal translocations in the therapy-related leukemia differ from chromosomal rearrangements associated with other neoplasias. Here, we reviewed the factors that drive chromosomal translocations induced by cancer treatment with DNA topoisomerase II inhibitors, such as mobility of ends of double-strand DNA breaks formed before the translocation and gain of function of fusion proteins generated as a result of translocation.
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Affiliation(s)
- Nikolai A Lomov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Vladimir S Viushkov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Mikhail A Rubtsov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Department of Biochemistry, Center for Industrial Technologies and Entrepreneurship Sechenov First Moscow State Medical University (Sechenov University), Moscow, 119435, Russia
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28
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Shi J, Hauschulte K, Mikicic I, Maharjan S, Arz V, Strauch T, Heidelberger JB, Schaefer JV, Dreier B, Plückthun A, Beli P, Ulrich HD, Wollscheid HP. Nuclear myosin VI maintains replication fork stability. Nat Commun 2023; 14:3787. [PMID: 37355687 PMCID: PMC10290672 DOI: 10.1038/s41467-023-39517-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 06/09/2023] [Indexed: 06/26/2023] Open
Abstract
The actin cytoskeleton is of fundamental importance for cellular structure and plasticity. However, abundance and function of filamentous actin in the nucleus are still controversial. Here we show that the actin-based molecular motor myosin VI contributes to the stabilization of stalled or reversed replication forks. In response to DNA replication stress, myosin VI associates with stalled replication intermediates and cooperates with the AAA ATPase Werner helicase interacting protein 1 (WRNIP1) in protecting these structures from DNA2-mediated nucleolytic attack. Using functionalized affinity probes to manipulate myosin VI levels in a compartment-specific manner, we provide evidence for the direct involvement of myosin VI in the nucleus and against a contribution of the abundant cytoplasmic pool during the replication stress response.
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Affiliation(s)
- Jie Shi
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Kristine Hauschulte
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Ivan Mikicic
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Srijana Maharjan
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
- Mainz Biomed N.V., Robert-Koch-Str. 50, D - 55129, Mainz, Germany
| | - Valerie Arz
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Tina Strauch
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Jan B Heidelberger
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
- Max Planck School Matter to Life, Jahnstr. 29, D - 69120, Heidelberg, Germany
| | - Jonas V Schaefer
- University of Zurich, Department of Biochemistry, Winterthurerstr. 190, CH - 8057, Zurich, Switzerland
| | - Birgit Dreier
- University of Zurich, Department of Biochemistry, Winterthurerstr. 190, CH - 8057, Zurich, Switzerland
| | - Andreas Plückthun
- University of Zurich, Department of Biochemistry, Winterthurerstr. 190, CH - 8057, Zurich, Switzerland
| | - Petra Beli
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
- Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University, Hanns-Dieter-Hüsch-Weg 15, D - 55128, Mainz, Germany
| | - Helle D Ulrich
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany.
| | - Hans-Peter Wollscheid
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany.
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29
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Debaugnies M, Rodríguez-Acebes S, Blondeau J, Parent MA, Zocco M, Song Y, de Maertelaer V, Moers V, Latil M, Dubois C, Coulonval K, Impens F, Van Haver D, Dufour S, Uemura A, Sotiropoulou PA, Méndez J, Blanpain C. RHOJ controls EMT-associated resistance to chemotherapy. Nature 2023; 616:168-175. [PMID: 36949199 PMCID: PMC10076223 DOI: 10.1038/s41586-023-05838-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 02/14/2023] [Indexed: 03/24/2023]
Abstract
The resistance of cancer cells to therapy is responsible for the death of most patients with cancer1. Epithelial-to-mesenchymal transition (EMT) has been associated with resistance to therapy in different cancer cells2,3. However, the mechanisms by which EMT mediates resistance to therapy remain poorly understood. Here, using a mouse model of skin squamous cell carcinoma undergoing spontaneous EMT during tumorigenesis, we found that EMT tumour cells are highly resistant to a wide range of anti-cancer therapies both in vivo and in vitro. Using gain and loss of function studies in vitro and in vivo, we found that RHOJ-a small GTPase that is preferentially expressed in EMT cancer cells-controls resistance to therapy. Using genome-wide transcriptomic and proteomic profiling, we found that RHOJ regulates EMT-associated resistance to chemotherapy by enhancing the response to replicative stress and activating the DNA-damage response, enabling tumour cells to rapidly repair DNA lesions induced by chemotherapy. RHOJ interacts with proteins that regulate nuclear actin, and inhibition of actin polymerization sensitizes EMT tumour cells to chemotherapy-induced cell death in a RHOJ-dependent manner. Together, our study uncovers the role and the mechanisms through which RHOJ acts as a key regulator of EMT-associated resistance to chemotherapy.
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Affiliation(s)
- Maud Debaugnies
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
- CHU Saint-Pierre, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Sara Rodríguez-Acebes
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Jeremy Blondeau
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
| | - Marie-Astrid Parent
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
| | - Manuel Zocco
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
| | - Yura Song
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
| | - Viviane de Maertelaer
- Institute of Interdisciplinary Research (IRIBHM), Université Libre de Bruxelles (ULB), Brussels, Belgium
- ULB-Cancer Research Center (U-crc), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Virginie Moers
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
| | - Mathilde Latil
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
| | - Christine Dubois
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
| | - Katia Coulonval
- Institute of Interdisciplinary Research (IRIBHM), Université Libre de Bruxelles (ULB), Brussels, Belgium
- ULB-Cancer Research Center (U-crc), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Francis Impens
- VIB Center for Medical Biotechnology, VIB Proteomics Core, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Delphi Van Haver
- VIB Center for Medical Biotechnology, VIB Proteomics Core, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Sara Dufour
- VIB Center for Medical Biotechnology, VIB Proteomics Core, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Akiyoshi Uemura
- Department of Retinal Vascular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | | | - Juan Méndez
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Cédric Blanpain
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium.
- WELBIO, Université Libre de Bruxelles (ULB), Brussels, Belgium.
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30
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Palumbieri MD, Merigliano C, Acosta DG, von Känel T, Welter B, Stoy H, Krietsch J, Ulferts S, Sanchi A, Grosse R, Chiolo I, Lopes M. Replication fork plasticity upon replication stress requires rapid nuclear actin polymerization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.24.534097. [PMID: 36993227 PMCID: PMC10055433 DOI: 10.1101/2023.03.24.534097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Cells rapidly respond to replication stress actively slowing fork progression and inducing fork reversal. How replication fork plasticity is achieved in the context of nuclear organization is currently unknown. Using nuclear actin probes in living and fixed cells, we visualized nuclear actin filaments in unperturbed S phase, rapidly extending in number and thickness upon genotoxic treatments, and taking frequent contact with replication factories. Chemically or genetically impairing nuclear actin polymerization shortly before these treatments prevents active fork slowing and abolishes fork reversal. Defective fork plasticity is linked to reduced recruitment of RAD51 and SMARCAL1 to nascent DNA. Conversely, PRIMPOL gains access to replicating chromatin, promoting unrestrained and discontinuous DNA synthesis, which is associated with increased chromosomal instability and decreased cellular resistance to replication stress. Hence, nuclear F-actin orchestrates replication fork plasticity and is a key molecular determinant in the rapid cellular response to genotoxic treatments.
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31
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Faustini E, Panza A, Longaretti M, Lottersberger F. Quantitative analysis of nuclear deformations and DNA damage foci dynamics by live-cell imaging. Methods Cell Biol 2023; 182:247-263. [PMID: 38359981 DOI: 10.1016/bs.mcb.2022.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The correct repair of DNA Double Strand Breaks (DSBs) is fundamental to prevent the loss of genetic information, mutations, and chromosome rearrangements. An emerging determinant of DNA repair is chromatin mobility. However, how chromatin mobility can influence DSBs repair is still poorly understood. While increased mobility is generally associated with the correct repair by Homologous Recombination (HR) of DSBs generated in heterochromatin, it promotes the mis-repair of multiple distal DSBs by Non-Homologous End Joining (NHEJ). Here we describe a method for detecting and quantifying DSBs mobility by live-cell imaging in the context of multiple DSBs prone to mis-repair by NHEJ. In addition, we discuss a set of parameters that can be used for quantitative and qualitative analysis of nuclear deformations and to discard nuclei where the deformation could affect the analysis of DSBs mobility. While this method is based on the visualization of DSBs with the mCherry-53BP1-2 fusion protein, we believe that it can also be used to analyze the mobility of nuclear foci formed by different fluorescent proteins.
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Affiliation(s)
- Elena Faustini
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden; Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
| | - Andrea Panza
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden; Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
| | - Matteo Longaretti
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden; Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
| | - Francisca Lottersberger
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden; Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden.
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32
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Zagelbaum J, Gautier J. Double-strand break repair and mis-repair in 3D. DNA Repair (Amst) 2023; 121:103430. [PMID: 36436496 PMCID: PMC10799305 DOI: 10.1016/j.dnarep.2022.103430] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]
Abstract
DNA double-strand breaks (DSBs) are lesions that arise frequently from exposure to damaging agents as well as from ongoing physiological DNA transactions. Mis-repair of DSBs leads to rearrangements and structural variations in chromosomes, including insertions, deletions, and translocations implicated in disease. The DNA damage response (DDR) limits pathologic mutations and large-scale chromosome rearrangements. DSB repair initiates in 2D at DNA lesions with the stepwise recruitment of repair proteins and local chromatin remodeling which facilitates break accessibility. More complex structures are then formed via protein assembly into nanodomains and via genome folding into chromatin loops. Subsequently, 3D reorganization of DSBs is guided by clustering forces which drive the assembly of repair domains harboring multiple lesions. These domains are further stabilized and insulated into condensates via liquid-liquid phase-separation. Here, we discuss the benefits and risks associated with this 3D reorganization of the broken genome.
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Affiliation(s)
- Jennifer Zagelbaum
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jean Gautier
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Genetics and Development, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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33
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Zagelbaum J, Schooley A, Zhao J, Schrank BR, Callen E, Zha S, Gottesman ME, Nussenzweig A, Rabadan R, Dekker J, Gautier J. Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin polymerization. Nat Struct Mol Biol 2023; 30:99-106. [PMID: 36564591 PMCID: PMC10104780 DOI: 10.1038/s41594-022-00893-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/04/2022] [Indexed: 12/24/2022]
Abstract
Nuclear actin-based movements have been shown to orchestrate clustering of DNA double-strand breaks (DSBs) into homology-directed repair domains. Here we describe multiscale three-dimensional genome reorganization following DNA damage and analyze the contribution of the nuclear WASP-ARP2/3-actin pathway toward chromatin topology alterations and pathologic repair. Hi-C analysis reveals genome-wide, DNA damage-induced chromatin compartment flips facilitated by ARP2/3 that enrich for open, A compartments. Damage promotes interactions between DSBs, which in turn facilitate aberrant, actin-dependent intra- and inter-chromosomal rearrangements. Our work establishes that clustering of resected DSBs into repair domains by nuclear actin assembly is coordinated with multiscale alterations in genome architecture that enable homology-directed repair while also increasing nonhomologous end-joining-dependent translocation frequency.
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Affiliation(s)
- Jennifer Zagelbaum
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Allana Schooley
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Junfei Zhao
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Benjamin R Schrank
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Elsa Callen
- Laboratory of Genome Integrity, National Institutes of Health, Bethesda, MD, USA
| | - Shan Zha
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Pathology and Cell Biology and Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Max E Gottesman
- Department of Biochemistry and Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Institutes of Health, Bethesda, MD, USA
| | - Raul Rabadan
- Department of Systems Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Jean Gautier
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Department of Genetics and Development, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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34
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Actin up: shifting chromosomes toward repair, but also translocations. Nat Struct Mol Biol 2023; 30:2-4. [PMID: 36577921 DOI: 10.1038/s41594-022-00906-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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35
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Viushkov VS, Lomov NA, Rubtsov MA, Vassetzky YS. Visualizing the Genome: Experimental Approaches for Live-Cell Chromatin Imaging. Cells 2022; 11:cells11244086. [PMID: 36552850 PMCID: PMC9776900 DOI: 10.3390/cells11244086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/07/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
Over the years, our vision of the genome has changed from a linear molecule to that of a complex 3D structure that follows specific patterns and possesses a hierarchical organization. Currently, genomics is becoming "four-dimensional": our attention is increasingly focused on the study of chromatin dynamics over time, in the fourth dimension. Recent methods for visualizing the movements of chromatin loci in living cells by targeting fluorescent proteins can be divided into two groups. The first group requires the insertion of a special sequence into the locus of interest, to which proteins that recognize the sequence are recruited (e.g., FROS and ParB-INT methods). In the methods of the second approach, "programmed" proteins are targeted to the locus of interest (i.e., systems based on CRISPR/Cas, TALE, and zinc finger proteins). In the present review, we discuss these approaches, examine their strengths and weaknesses, and identify the key scientific problems that can be studied using these methods.
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Affiliation(s)
- Vladimir S. Viushkov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Nikolai A. Lomov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Mikhail A. Rubtsov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Department of Biochemistry, Center for Industrial Technologies and Entrepreneurship, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119435 Moscow, Russia
| | - Yegor S. Vassetzky
- CNRS UMR9018, Université Paris-Saclay, Gustave Roussy, 94805 Villejuif, France
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
- Correspondence:
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36
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Kaminski N, Wondisford AR, Kwon Y, Lynskey ML, Bhargava R, Barroso-González J, García-Expósito L, He B, Xu M, Mellacheruvu D, Watkins SC, Modesti M, Miller KM, Nesvizhskii AI, Zhang H, Sung P, O'Sullivan RJ. RAD51AP1 regulates ALT-HDR through chromatin-directed homeostasis of TERRA. Mol Cell 2022; 82:4001-4017.e7. [PMID: 36265488 PMCID: PMC9713952 DOI: 10.1016/j.molcel.2022.09.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 08/10/2022] [Accepted: 09/23/2022] [Indexed: 11/05/2022]
Abstract
Alternative lengthening of telomeres (ALT) is a homology-directed repair (HDR) mechanism of telomere elongation that controls proliferation in subsets of aggressive cancer. Recent studies have revealed that telomere repeat-containing RNA (TERRA) promotes ALT-associated HDR (ALT-HDR). Here, we report that RAD51AP1, a crucial ALT factor, interacts with TERRA and utilizes it to generate D- and R-loop HR intermediates. We also show that RAD51AP1 binds to and might stabilize TERRA-containing R-loops as RAD51AP1 depletion reduces R-loop formation at telomere DNA breaks. Proteomic analyses uncover a role for RAD51AP1-mediated TERRA R-loop homeostasis in a mechanism of chromatin-directed suppression of TERRA and prevention of transcription-replication collisions (TRCs) during ALT-HDR. Intriguingly, we find that both TERRA binding and this non-canonical function of RAD51AP1 require its intrinsic SUMO-SIM regulatory axis. These findings provide insights into the multi-contextual functions of RAD51AP1 within the ALT mechanism and regulation of TERRA.
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Affiliation(s)
- Nicole Kaminski
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Anne R Wondisford
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Youngho Kwon
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, USA
| | - Michelle Lee Lynskey
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ragini Bhargava
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jonathan Barroso-González
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Laura García-Expósito
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Boxue He
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, USA; Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Meng Xu
- Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Dattatreya Mellacheruvu
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Simon C Watkins
- Department of Cell Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mauro Modesti
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm UMR1068, Aix Marseille Université U105, Institut Paoli Calmettes, 27 Boulevard Lei Roure CS30059, 13273 Marseille Cedex 09, France
| | - Kyle M Miller
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2506 Speedway, Austin, TX 78712, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Huaiying Zhang
- Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, USA
| | - Roderick J O'Sullivan
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.
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37
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Min S, Ji JH, Heo Y, Cho H. Transcriptional regulation and chromatin dynamics at DNA double-strand breaks. Exp Mol Med 2022; 54:1705-1712. [PMID: 36229590 PMCID: PMC9636152 DOI: 10.1038/s12276-022-00862-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/27/2022] [Accepted: 08/01/2022] [Indexed: 12/29/2022] Open
Abstract
In eukaryotic cells, DNA damage can occur at any time and at any chromatin locus, including loci at which active transcription is taking place. DNA double-strand breaks affect chromatin integrity and elicit a DNA damage response to facilitate repair of the DNA lesion. Actively transcribed genes near DNA lesions are transiently suppressed by crosstalk between DNA damage response factors and polycomb repressive complexes. Epigenetic modulation of the chromatin environment also contributes to efficient DNA damage response signaling and transcriptional repression. On the other hand, RNA transcripts produced in the G1 phase, as well as the active chromatin context of the lesion, appear to drive homologous recombination repair. Here, we discuss how the ISWI family of chromatin remodeling factors coordinates the DNA damage response and transcriptional repression, especially in transcriptionally active regions, highlighting the direct modulation of the epigenetic environment.
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Affiliation(s)
- Sunwoo Min
- grid.251916.80000 0004 0532 3933Department of Biochemistry, Ajou University School of Medicine, Suwon, 16499 Korea ,grid.251916.80000 0004 0532 3933Genomic Instability Research Center, Ajou University School of Medicine, Suwon, 16499 Korea
| | - Jae-Hoon Ji
- grid.267309.90000 0001 0629 5880Department of Biochemistry and Structural Biology, The University of Texas Health San Antonio, Texas, 78229-3000 USA
| | - Yungyeong Heo
- grid.251916.80000 0004 0532 3933Department of Biochemistry, Ajou University School of Medicine, Suwon, 16499 Korea ,grid.251916.80000 0004 0532 3933Genomic Instability Research Center, Ajou University School of Medicine, Suwon, 16499 Korea
| | - Hyeseong Cho
- grid.251916.80000 0004 0532 3933Department of Biochemistry, Ajou University School of Medicine, Suwon, 16499 Korea ,grid.251916.80000 0004 0532 3933Genomic Instability Research Center, Ajou University School of Medicine, Suwon, 16499 Korea
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38
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García Fernández F, Almayrac E, Carré Simon À, Batrin R, Khalil Y, Boissac M, Fabre E. Global chromatin mobility induced by a DSB is dictated by chromosomal conformation and defines the HR outcome. eLife 2022; 11:78015. [PMID: 36125964 PMCID: PMC9489209 DOI: 10.7554/elife.78015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 09/08/2022] [Indexed: 12/16/2022] Open
Abstract
Repair of DNA double-strand breaks (DSBs) is crucial for genome integrity. A conserved response to DSBs is an increase in chromatin mobility that can be local, at the site of the DSB, or global, at undamaged regions of the genome. Here, we address the function of global chromatin mobility during homologous recombination (HR) of a single, targeted, controlled DSB. We set up a system that tracks HR in vivo over time and show that two types of DSB-induced global chromatin mobility are involved in HR, depending on the position of the DSB. Close to the centromere, a DSB induces global mobility that depends solely on H2A(X) phosphorylation and accelerates repair kinetics, but is not essential. In contrast, the global mobility induced by a DSB away from the centromere becomes essential for HR repair and is triggered by homology search through a mechanism that depends on H2A(X) phosphorylation, checkpoint progression, and Rad51. Our data demonstrate that global mobility is governed by chromosomal conformation and differentially coordinates repair by HR.
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Affiliation(s)
| | - Etienne Almayrac
- Université de Paris, IRSL, INSERM, U944, CNRS, UMR7212, Paris, France
| | - Ànnia Carré Simon
- Université de Paris, IRSL, INSERM, U944, CNRS, UMR7212, Paris, France
| | - Renaud Batrin
- Université de Paris, IRSL, INSERM, U944, CNRS, UMR7212, Paris, France
| | - Yasmine Khalil
- Université de Paris, IRSL, INSERM, U944, CNRS, UMR7212, Paris, France
| | - Michel Boissac
- Université de Paris, IRSL, INSERM, U944, CNRS, UMR7212, Paris, France
| | - Emmanuelle Fabre
- Université de Paris, IRSL, INSERM, U944, CNRS, UMR7212, Paris, France
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39
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Groelly FJ, Dagg RA, Petropoulos M, Rossetti GG, Prasad B, Panagopoulos A, Paulsen T, Karamichali A, Jones SE, Ochs F, Dionellis VS, Puig Lombardi E, Miossec MJ, Lockstone H, Legube G, Blackford AN, Altmeyer M, Halazonetis TD, Tarsounas M. Mitotic DNA synthesis is caused by transcription-replication conflicts in BRCA2-deficient cells. Mol Cell 2022; 82:3382-3397.e7. [PMID: 36002001 PMCID: PMC9631240 DOI: 10.1016/j.molcel.2022.07.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/31/2022] [Accepted: 07/16/2022] [Indexed: 12/24/2022]
Abstract
Aberrant replication causes cells lacking BRCA2 to enter mitosis with under-replicated DNA, which activates a repair mechanism known as mitotic DNA synthesis (MiDAS). Here, we identify genome-wide the sites where MiDAS reactions occur when BRCA2 is abrogated. High-resolution profiling revealed that these sites are different from MiDAS at aphidicolin-induced common fragile sites in that they map to genomic regions replicating in the early S-phase, which are close to early-firing replication origins, are highly transcribed, and display R-loop-forming potential. Both transcription inhibition in early S-phase and RNaseH1 overexpression reduced MiDAS in BRCA2-deficient cells, indicating that transcription-replication conflicts (TRCs) and R-loops are the source of MiDAS. Importantly, the MiDAS sites identified in BRCA2-deficient cells also represent hotspots for genomic rearrangements in BRCA2-mutated breast tumors. Thus, our work provides a mechanism for how tumor-predisposing BRCA2 inactivation links transcription-induced DNA damage with mitotic DNA repair to fuel the genomic instability characteristic of cancer cells.
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Affiliation(s)
- Florian J Groelly
- Genome Stability and Tumourigenesis Group, Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Rebecca A Dagg
- Genome Stability and Tumourigenesis Group, Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | | | - Giacomo G Rossetti
- Department of Molecular Biology, University of Geneva, 1205 Geneva, Switzerland
| | - Birbal Prasad
- Genome Stability and Tumourigenesis Group, Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Andreas Panagopoulos
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
| | - Teressa Paulsen
- Genome Stability and Tumourigenesis Group, Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | | | - Samuel E Jones
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Fena Ochs
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Vasilis S Dionellis
- Department of Molecular Biology, University of Geneva, 1205 Geneva, Switzerland
| | - Emilia Puig Lombardi
- Genome Stability and Tumourigenesis Group, Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Matthieu J Miossec
- Bioinformatics and Statistical Genetics Core, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Helen Lockstone
- Bioinformatics and Statistical Genetics Core, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Gaëlle Legube
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse 31062, France
| | - Andrew N Blackford
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
| | - Thanos D Halazonetis
- Department of Molecular Biology, University of Geneva, 1205 Geneva, Switzerland.
| | - Madalena Tarsounas
- Genome Stability and Tumourigenesis Group, Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK.
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40
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Dubois F, Sidiropoulos N, Weischenfeldt J, Beroukhim R. Structural variations in cancer and the 3D genome. Nat Rev Cancer 2022; 22:533-546. [PMID: 35764888 PMCID: PMC10423586 DOI: 10.1038/s41568-022-00488-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/18/2022] [Indexed: 12/21/2022]
Abstract
Structural variations (SVs) affect more of the cancer genome than any other type of somatic genetic alteration but difficulties in detecting and interpreting them have limited our understanding. Clinical cancer sequencing also increasingly aims to detect SVs, leading to a widespread necessity to interpret their biological and clinical relevance. Recently, analyses of large whole-genome sequencing data sets revealed features that impact rates of SVs across the genome in different cancers. A striking feature has been the extent to which, in both their generation and their influence on the selective fitness of cancer cells, SVs are more specific to individual cancer types than other genetic alterations such as single-nucleotide variants. This Perspective discusses how the folding of the 3D genome, and differences in its folding across cell types, affect observed SV rates in different cancer types as well as how SVs can impact cancer cell fitness.
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Affiliation(s)
- Frank Dubois
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of and Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nikos Sidiropoulos
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- The Finsen Laboratory, Rigshospitalet, Copenhagen, Denmark
| | - Joachim Weischenfeldt
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
- The Finsen Laboratory, Rigshospitalet, Copenhagen, Denmark.
- Department of Urology, Charité-Universitätsmedizin Berlin, Berlin, Germany.
| | - Rameen Beroukhim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of and Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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41
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Recurrent Translocations in Topoisomerase Inhibitor-Related Leukemia Are Determined by the Features of DNA Breaks Rather Than by the Proximity of the Translocating Genes. Int J Mol Sci 2022; 23:ijms23179824. [PMID: 36077220 PMCID: PMC9456246 DOI: 10.3390/ijms23179824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 08/09/2022] [Accepted: 08/21/2022] [Indexed: 11/25/2022] Open
Abstract
Topoisomerase inhibitors are widely used in cancer chemotherapy. However, one of the potential long-term adverse effects of such therapy is acute leukemia. A key feature of such therapy-induced acute myeloid leukemia (t-AML) is recurrent chromosomal translocations involving AML1 (RUNX1) or MLL (KMT2A) genes. The formation of chromosomal translocation depends on the spatial proximity of translocation partners and the mobility of the DNA ends. It is unclear which of these two factors might be decisive for recurrent t-AML translocations. Here, we used fluorescence in situ hybridization (FISH) and chromosome conformation capture followed by sequencing (4C-seq) to investigate double-strand DNA break formation and the mobility of broken ends upon etoposide treatment, as well as contacts between translocation partner genes. We detected the separation of the parts of the broken AML1 gene, as well as the increased mobility of these separated parts. 4C-seq analysis showed no evident contacts of AML1 and MLL with loci, implicated in recurrent t-AML translocations, either before or after etoposide treatment. We suggest that separation of the break ends and their increased non-targeted mobility—but not spatial predisposition of the rearrangement partners—plays a major role in the formation of these translocations.
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42
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Patra SK, Szyf M. Epigenetic perspectives of COVID-19: Virus infection to disease progression and therapeutic control. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166527. [PMID: 36002132 PMCID: PMC9393109 DOI: 10.1016/j.bbadis.2022.166527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/05/2022] [Accepted: 08/18/2022] [Indexed: 11/20/2022]
Abstract
COVID-19 has caused numerous deaths as well as imposed social isolation and upheaval world-wide. Although, the genome and the composition of the virus, the entry process and replication mechanisms are well investigated from by several laboratories across the world, there are many unknown remaining questions. For example, what are the functions of membrane lipids during entry, packaging and exit of virus particles? Also, the metabolic aspects of the infected tissue cells are poorly understood. In the course of virus replication and formation of virus particles within the host cell, the enhanced metabolic activities of the host is directly proportional to viral loads. The epigenetic landscape of the host cells is also altered, particularly the expression/repression of genes associated with cellular metabolism as well as cellular processes that are antagonistic to the virus. Metabolic pathways are enzyme driven processes and the expression profile and mechanism of regulations of the respective genes encoding those enzymes during the course of pathogen invasion might be highly informative on the course of the disease. Recently, the metabolic profile of the patients' sera have been analysed from few patients. In view of this, and to gain further insights into the roles that epigenetic mechanisms might play in this scenario in regulation of metabolic pathways during the progression of COVID-19 are discussed and summarised in this contribution for ensuring best therapy.
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Affiliation(s)
- Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
| | - Moshe Szyf
- Department of Pharmacology & Therapeutics, McIntyre Medical Sciences Building, McGill University, Montreal, QC H3G 1Y6, Canada
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43
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Oanh N, Lee HS, Kim YH, Min S, Park YJ, Heo J, Park YY, Lim WC, Cho H. Regulation of nuclear DNA damage response by mitochondrial morphofunctional pathway. Nucleic Acids Res 2022; 50:9247-9259. [PMID: 35979947 PMCID: PMC9458461 DOI: 10.1093/nar/gkac690] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/22/2022] [Accepted: 08/03/2022] [Indexed: 12/24/2022] Open
Abstract
Cells are constantly challenged by genotoxic stresses that can lead to genome instability. The integrity of the nuclear genome is preserved by the DNA damage response (DDR) and repair. Additionally, these stresses can induce mitochondria to transiently hyperfuse; however, it remains unclear whether canonical DDR is linked to these mitochondrial morphological changes. Here, we report that the abolition of mitochondrial fusion causes a substantial defect in the ATM-mediated DDR signaling. This deficiency is overcome by the restoration of mitochondria fusion. In cells with fragmented mitochondria, genotoxic stress-induced activation of JNK and its translocation to DNA lesion are lost. Importantly, the mitochondrial fusion machinery of MFN1/MFN2 associates with Sab (SH3BP5) and JNK, and these interactions are indispensable for the Sab-mediated activation of JNK and the ATM-mediated DDR signaling. Accordingly, the formation of BRCA1 and 53BP1 foci, as well as homology and end-joining repair are impaired in cells with fragmented mitochondria. Together, these data show that mitochondrial fusion-dependent JNK signaling is essential for the DDR, providing vital insight into the integration of nuclear and cytoplasmic stress signals.
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Affiliation(s)
| | | | - Yong-Hyun Kim
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, Republic of Korea,Department of Biomedical Sciences, Graduate School of Ajou University, Suwon, Republic of Korea
| | - Sunwoo Min
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Yeon-Ji Park
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - June Heo
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, Republic of Korea,Department of Biomedical Sciences, Graduate School of Ajou University, Suwon, Republic of Korea
| | - Yong-Yea Park
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Won-Chung Lim
- Correspondence may also be addressed to Won-Chung Lim.
| | - Hyeseong Cho
- To whom correspondence should be addressed. Tel: +82 312195052; Fax: +82 312195059;
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44
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Cao H, Zhang Y, Cai Y, Tang L, Gao F, Xu D, Kapranov P. Hotspots of single-strand DNA “breakome” are enriched at transcriptional start sites of genes. Front Mol Biosci 2022; 9:895795. [PMID: 36046604 PMCID: PMC9420937 DOI: 10.3389/fmolb.2022.895795] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/27/2022] [Indexed: 01/01/2023] Open
Abstract
Single-strand breaks (SSBs) represent one of the most common types of DNA damage, yet not much is known about the genome landscapes of this type of DNA lesions in mammalian cells. Here, we found that SSBs are more likely to occur in certain positions of the human genome—SSB hotspots—in different cells of the same cell type and in different cell types. We hypothesize that the hotspots are likely to represent biologically relevant breaks. Furthermore, we found that the hotspots had a prominent tendency to be enriched in the immediate vicinity of transcriptional start sites (TSSs). We show that these hotspots are not likely to represent technical artifacts or be caused by common mechanisms previously found to cause DNA cleavage at promoters, such as apoptotic DNA fragmentation or topoisomerase type II (TOP2) activity. Therefore, such TSS-associated hotspots could potentially be generated using a novel mechanism that could involve preferential cleavage at cytosines, and their existence is consistent with recent studies suggesting a complex relationship between DNA damage and regulation of gene expression.
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45
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Kolobynina KG, Rapp A, Cardoso MC. Chromatin Ubiquitination Guides DNA Double Strand Break Signaling and Repair. Front Cell Dev Biol 2022; 10:928113. [PMID: 35865631 PMCID: PMC9294282 DOI: 10.3389/fcell.2022.928113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
Chromatin is the context for all DNA-based molecular processes taking place in the cell nucleus. The initial chromatin structure at the site of the DNA damage determines both, lesion generation and subsequent activation of the DNA damage response (DDR) pathway. In turn, proceeding DDR changes the chromatin at the damaged site and across large fractions of the genome. Ubiquitination, besides phosphorylation and methylation, was characterized as an important chromatin post-translational modification (PTM) occurring at the DNA damage site and persisting during the duration of the DDR. Ubiquitination appears to function as a highly versatile “signal-response” network involving several types of players performing various functions. Here we discuss how ubiquitin modifiers fine-tune the DNA damage recognition and response and how the interaction with other chromatin modifications ensures cell survival.
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46
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Biswas B, Chaaban R, Chakraborty S, Devaux A, Dian AL, Minello A, Singh JK, Vagner S, Uguen P, Lambert S, Dutertre M, Carreira A. At the crossroads of RNA biology, genome integrity and cancer. Bull Cancer 2022; 109:728-735. [PMID: 35597618 DOI: 10.1016/j.bulcan.2022.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 10/18/2022]
Abstract
This article is the synthesis of the scientific presentations that took place during two international courses at Institute Curie, one on post-transcriptional gene regulation and the other on genome instability and human disease, that were joined together in their 2021 edition. This joined course brought together the knowledge on RNA metabolism and the maintenance of genome stability.
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Affiliation(s)
- Biswendu Biswas
- CNRS UMR 3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Rady Chaaban
- CNRS UMR 3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Shrena Chakraborty
- CNRS UMR 3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Alexandre Devaux
- CNRS UMR 3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Ana Luisa Dian
- CNRS UMR 3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Anna Minello
- CNRS UMR 3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Jenny Kaur Singh
- CNRS UMR 3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Stephan Vagner
- CNRS UMR 3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Patricia Uguen
- CNRS UMR 3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France.
| | - Sarah Lambert
- CNRS UMR 3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Martin Dutertre
- CNRS UMR 3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
| | - Aura Carreira
- CNRS UMR 3348 Genome integrity, RNA and Cancer, Institut Curie, University Paris-Saclay, 91401 Orsay, France
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47
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A POLD3/BLM dependent pathway handles DSBs in transcribed chromatin upon excessive RNA:DNA hybrid accumulation. Nat Commun 2022; 13:2012. [PMID: 35440629 PMCID: PMC9019021 DOI: 10.1038/s41467-022-29629-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 03/25/2022] [Indexed: 12/03/2022] Open
Abstract
Transcriptionally active loci are particularly prone to breakage and mounting evidence suggests that DNA Double-Strand Breaks arising in active genes are handled by a dedicated repair pathway, Transcription-Coupled DSB Repair (TC-DSBR), that entails R-loop accumulation and dissolution. Here, we uncover a function for the Bloom RecQ DNA helicase (BLM) in TC-DSBR in human cells. BLM is recruited in a transcription dependent-manner at DSBs where it fosters resection, RAD51 binding and accurate Homologous Recombination repair. However, in an R-loop dissolution-deficient background, we find that BLM promotes cell death. We report that upon excessive RNA:DNA hybrid accumulation, DNA synthesis is enhanced at DSBs, in a manner that depends on BLM and POLD3. Altogether our work unveils a role for BLM at DSBs in active chromatin, and highlights the toxic potential of RNA:DNA hybrids that accumulate at transcription-associated DSBs. DNA Double Strand breaks in transcriptionally active loci (TC-DSBs) undergo a dedicated repair pathway. Here, the authors show that excessive RNA:DNA hybrid accumulation at TC-DSBs elicits POLD3/BLM-dependent DNA synthesis that induces cell toxicity.
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48
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Lossaint G, Horvat A, Gire V, Bacevic K, Mrouj K, Charrier-Savournin F, Georget V, Fisher D, Dulic V. Reciprocal regulation of p21 and Chk1 controls the Cyclin D1-RB pathway to mediate senescence onset after G2 arrest. J Cell Sci 2022; 135:274865. [PMID: 35343565 DOI: 10.1242/jcs.259114] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 03/18/2022] [Indexed: 11/20/2022] Open
Abstract
Senescence is an irreversible proliferation withdrawal that can be initiated after DNA damage-induced cell cycle arrest in G2 phase to prevent genomic instability. Senescence onset in G2 requires p53 and RB family tumour suppressors, but how they are regulated to convert a temporary cell cycle arrest into a permanent one remains unknown. Here, we show that a previously unrecognised balance between the CDK inhibitor p21 and Chk1 controls D-type cyclin-CDK activity during G2 arrest. In non-transformed cells, p21 activates RB in G2 by inhibiting Cyclin D1-CDK2/CDK4. The resulting G2 exit, which precedes appearance of senescence markers, is associated with a mitotic bypass, Chk1 downregulation and DNA damage foci reduction. In p53/RB-proficient cancer cells, compromised G2 exit correlates with sustained Chk1 activity, delayed p21 induction, untimely Cyclin E1 re-expression and genome reduplication. Conversely, Chk1 depletion promotes senescence by inducing p21 binding to Cyclin D1 and Cyclin E1-CDK complexes and down-regulating CDK6, whereas Chk2 knockdown enables RB phosphorylation and delays G2 exit. In conclusion, p21 and Chk2 oppose Chk1 to maintain RB activity, thus promoting DNA damage-induced senescence onset in G2.
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Affiliation(s)
| | | | | | | | - Karim Mrouj
- IGMM, Univ. Montpellier, CNRS, Montpellier, France
| | | | - Virginie Georget
- CRBM, Univ. Montpellier, CNRS, Montpellier, France.,Montpellier Ressources Imagerie, BioCampus, University of Montpellier, CNRS, INSERM, Montpellier, France
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49
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García Fernández F, Fabre E. The Dynamic Behavior of Chromatin in Response to DNA Double-Strand Breaks. Genes (Basel) 2022; 13:genes13020215. [PMID: 35205260 PMCID: PMC8872016 DOI: 10.3390/genes13020215] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 02/05/2023] Open
Abstract
The primary functions of the eukaryotic nucleus as a site for the storage, retrieval, and replication of information require a highly dynamic chromatin organization, which can be affected by the presence of DNA damage. In response to double-strand breaks (DSBs), the mobility of chromatin at the break site is severely affected and, to a lesser extent, that of other chromosomes. The how and why of such movement has been widely studied over the last two decades, leading to different mechanistic models and proposed potential roles underlying both local and global mobility. Here, we review the state of the knowledge on current issues affecting chromatin mobility upon DSBs, and highlight its role as a crucial step in the DNA damage response (DDR).
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Affiliation(s)
- Fabiola García Fernández
- Institut Curie, CNRS UMR3664, Sorbonne Université, F-75005 Paris, France
- Correspondence: (F.G.F.); (E.F.)
| | - Emmanuelle Fabre
- Génomes Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Université de Paris, F-75010 Paris, France
- Correspondence: (F.G.F.); (E.F.)
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50
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Mirzaei G, Petreaca RC. Distribution of copy number variations and rearrangement endpoints in human cancers with a review of literature. Mutat Res 2022; 824:111773. [PMID: 35091282 PMCID: PMC11301607 DOI: 10.1016/j.mrfmmm.2021.111773] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/08/2021] [Accepted: 12/10/2021] [Indexed: 12/13/2022]
Abstract
Copy number variations (CNVs) which include deletions, duplications, inversions, translocations, and other forms of chromosomal re-arrangements are common to human cancers. In this report we investigated the pattern of these variations with the goal of understanding whether there exist specific cancer signatures. We used re-arrangement endpoint data deposited on the Catalogue of Somatic Mutations in Cancers (COSMIC) for our analysis. Indeed, we find that human cancers are characterized by specific patterns of chromosome rearrangements endpoints which in turn result in cancer specific CNVs. A review of the literature reveals tissue specific mutations which either drive these CNVs or appear as a consequence of CNVs because they confer an advantage to the cancer cell. We also identify several rearrangement endpoints hotspots that were not previously reported. Our analysis suggests that in addition to local chromosomal architecture, CNVs are driven by the internal cellular or nuclear physiology of each cancer tissue.
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Affiliation(s)
- Golrokh Mirzaei
- Department of Computer Science and Engineering, The Ohio State University at Marion, Marion, OH, 43302, USA
| | - Ruben C Petreaca
- Department of Molecular Genetics, The Ohio State University at Marion, Marion, OH, 43302, USA; Cancer Biology Program, The Ohio State University James Comprehensive Cancer Center, Columbus, OH, 43210, USA.
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