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Muniesa-Vargas A, Davó-Martínez C, Ribeiro-Silva C, van der Woude M, Thijssen KL, Haspels B, Häckes D, Kaynak ÜU, Kanaar R, Marteijn JA, Theil AF, Kuijten MMP, Vermeulen W, Lans H. Persistent TFIIH binding to non-excised DNA damage causes cell and developmental failure. Nat Commun 2024; 15:3490. [PMID: 38664429 PMCID: PMC11045817 DOI: 10.1038/s41467-024-47935-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Congenital nucleotide excision repair (NER) deficiency gives rise to several cancer-prone and/or progeroid disorders. It is not understood how defects in the same DNA repair pathway cause different disease features and severity. Here, we show that the absence of functional ERCC1-XPF or XPG endonucleases leads to stable and prolonged binding of the transcription/DNA repair factor TFIIH to DNA damage, which correlates with disease severity and induces senescence features in human cells. In vivo, in C. elegans, this prolonged TFIIH binding to non-excised DNA damage causes developmental arrest and neuronal dysfunction, in a manner dependent on transcription-coupled NER. NER factors XPA and TTDA both promote stable TFIIH DNA binding and their depletion therefore suppresses these severe phenotypical consequences. These results identify stalled NER intermediates as pathogenic to cell functionality and organismal development, which can in part explain why mutations in XPF or XPG cause different disease features than mutations in XPA or TTDA.
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Affiliation(s)
- Alba Muniesa-Vargas
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Carlota Davó-Martínez
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Cristina Ribeiro-Silva
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Melanie van der Woude
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Karen L Thijssen
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Ben Haspels
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Oncode Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - David Häckes
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Ülkem U Kaynak
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Oncode Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Oncode Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Arjan F Theil
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Maayke M P Kuijten
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Oncode Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands.
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2
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van Sluis M, Yu Q, van der Woude M, Gonzalo-Hansen C, Dealy SC, Janssens RC, Somsen HB, Ramadhin AR, Dekkers DHW, Wienecke HL, Demmers JJPG, Raams A, Davó-Martínez C, Llerena Schiffmacher DA, van Toorn M, Häckes D, Thijssen KL, Zhou D, Lammers JG, Pines A, Vermeulen W, Pothof J, Demmers JAA, van den Berg DLC, Lans H, Marteijn JA. Transcription-coupled DNA-protein crosslink repair by CSB and CRL4 CSA-mediated degradation. Nat Cell Biol 2024:10.1038/s41556-024-01394-y. [PMID: 38600236 DOI: 10.1038/s41556-024-01394-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 03/01/2024] [Indexed: 04/12/2024]
Abstract
DNA-protein crosslinks (DPCs) arise from enzymatic intermediates, metabolism or chemicals like chemotherapeutics. DPCs are highly cytotoxic as they impede DNA-based processes such as replication, which is counteracted through proteolysis-mediated DPC removal by spartan (SPRTN) or the proteasome. However, whether DPCs affect transcription and how transcription-blocking DPCs are repaired remains largely unknown. Here we show that DPCs severely impede RNA polymerase II-mediated transcription and are preferentially repaired in active genes by transcription-coupled DPC (TC-DPC) repair. TC-DPC repair is initiated by recruiting the transcription-coupled nucleotide excision repair (TC-NER) factors CSB and CSA to DPC-stalled RNA polymerase II. CSA and CSB are indispensable for TC-DPC repair; however, the downstream TC-NER factors UVSSA and XPA are not, a result indicative of a non-canonical TC-NER mechanism. TC-DPC repair functions independently of SPRTN but is mediated by the ubiquitin ligase CRL4CSA and the proteasome. Thus, DPCs in genes are preferentially repaired in a transcription-coupled manner to facilitate unperturbed transcription.
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Affiliation(s)
- Marjolein van Sluis
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Qing Yu
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Melanie van der Woude
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Camila Gonzalo-Hansen
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Shannon C Dealy
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Roel C Janssens
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Hedda B Somsen
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Anisha R Ramadhin
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Dick H W Dekkers
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Hannah Lena Wienecke
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joris J P G Demmers
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Anja Raams
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Carlota Davó-Martínez
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Diana A Llerena Schiffmacher
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marvin van Toorn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - David Häckes
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Karen L Thijssen
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Di Zhou
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Judith G Lammers
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Alex Pines
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joris Pothof
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jeroen A A Demmers
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Hannes Lans
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
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3
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Zhou D, Yu Q, Janssens RC, Marteijn JA. Live-cell imaging of endogenous CSB-mScarletI as a sensitive marker for DNA-damage-induced transcription stress. Cell Rep Methods 2024; 4:100674. [PMID: 38176411 PMCID: PMC10831951 DOI: 10.1016/j.crmeth.2023.100674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/13/2023] [Accepted: 12/11/2023] [Indexed: 01/06/2024]
Abstract
Transcription by RNA polymerase II (RNA Pol II) is crucial for cellular function, but DNA damage severely impedes this process. Thus far, transcription-blocking DNA lesions (TBLs) and their repair have been difficult to quantify in living cells. To overcome this, we generated, using CRISPR-Cas9-mediated gene editing, mScarletI-tagged Cockayne syndrome group B protein (CSB) and UV-stimulated scaffold protein A (UVSSA) knockin cells. These cells allowed us to study the binding dynamics of CSB and UVSSA to lesion-stalled RNA Pol II using fluorescence recovery after photobleaching (FRAP). We show that especially CSB mobility is a sensitive transcription stress marker at physiologically relevant DNA damage levels. Transcription-coupled nucleotide excision repair (TC-NER)-mediated repair can be assessed by studying CSB immobilization over time. Additionally, flow cytometry reveals the regulation of CSB protein levels by CRL4CSA-mediated ubiquitylation and deubiquitylation by USP7. This approach allows the sensitive detection of TBLs and their repair and the study of TC-NER complex assembly and stability in living cells.
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Affiliation(s)
- Di Zhou
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Qing Yu
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Roel C Janssens
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands.
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4
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Schiffmacher DL, Lee SH, Kliza KW, Theil AF, Akita M, Helfricht A, Bezstarosti K, Gonzalo-Hansen C, van Attikum H, Verlaan-de Vries M, Vertegaal AC, Hoeijmakers JH, Marteijn JA, Lans H, Demmers JA, Vermeulen M, Sixma T, Ogi T, Vermeulen W, Pines A. DDA1, a novel factor in transcription-coupled repair, modulates CRL4 CSA dynamics at DNA damage-stalled RNA polymerase II. Res Sq 2023:rs.3.rs-3385435. [PMID: 37886519 PMCID: PMC10602077 DOI: 10.21203/rs.3.rs-3385435/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Transcription-blocking DNA lesions are specifically targeted by transcription-coupled nucleotide excision repair (TC-NER), which removes a broad spectrum of DNA lesions to preserve transcriptional output and thereby cellular homeostasis to counteract aging. TC-NER is initiated by the stalling of RNA polymerase II at DNA lesions, which triggers the assembly of the TC-NER-specific proteins CSA, CSB and UVSSA. CSA, a WD40-repeat containing protein, is the substrate receptor subunit of a cullin-RING ubiquitin ligase complex composed of DDB1, CUL4A/B and RBX1 (CRL4CSA). Although ubiquitination of several TC-NER proteins by CRL4CSA has been reported, it is still unknown how this complex is regulated. To unravel the dynamic molecular interactions and the regulation of this complex, we applied a single-step protein-complex isolation coupled to mass spectrometry analysis and identified DDA1 as a CSA interacting protein. Cryo-EM analysis showed that DDA1 is an integral component of the CRL4CSA complex. Functional analysis revealed that DDA1 coordinates ubiquitination dynamics during TC-NER and is required for efficient turnover and progression of this process.
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Affiliation(s)
- Diana Llerena Schiffmacher
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
- These authors contributed equally
| | - Shun-Hsiao Lee
- Division of Biochemistry and Oncode institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
- Oncode Institute, The Netherlands
- These authors contributed equally
| | - Katarzyna W. Kliza
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
- Current address: Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Arjan F. Theil
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Masaki Akita
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
- Current address: Department of Biology and National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A7, Brno, Czech Republic
| | - Angela Helfricht
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Karel Bezstarosti
- Proteomics Center, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Camila Gonzalo-Hansen
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Matty Verlaan-de Vries
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Alfred C.O. Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Jan H.J. Hoeijmakers
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
- University Hospital of Cologne, CECAD Forschungszentrum, Institute for Genome Stability in Aging and Disease, Joseph Stelzmann Strasse 26, 50931 Köln, Germany
- Princess Maxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands
- Oncode Institute, The Netherlands
| | - Jurgen A. Marteijn
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
- Oncode Institute, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Jeroen A.A. Demmers
- Proteomics Center, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
- Division of Molecular Genetics and Oncode institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands
- Oncode Institute, The Netherlands
| | - Titia Sixma
- Division of Biochemistry and Oncode institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
- Oncode Institute, The Netherlands
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Wim Vermeulen
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Alex Pines
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
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5
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Zaunz S, De Smedt J, Lauwereins L, Cleuren L, Laffeber C, Bajaj M, Lebbink JHG, Marteijn JA, De Keersmaecker K, Verfaillie C. APEX1 Nuclease and Redox Functions are Both Essential for Adult Mouse Hematopoietic Stem and Progenitor Cells. Stem Cell Rev Rep 2023:10.1007/s12015-023-10550-0. [PMID: 37266894 PMCID: PMC10390635 DOI: 10.1007/s12015-023-10550-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2023] [Indexed: 06/03/2023]
Abstract
Self-renewal and differentiation of hematopoietic stem and progenitor cells (HSPCs) are carefully controlled by extrinsic and intrinsic factors, to ensure the lifelong process of hematopoiesis. Apurinic/apyrimidinic endonuclease 1 (APEX1) is a multifunctional protein implicated in DNA repair and transcriptional regulation. Although previous studies have emphasized the necessity of studying APEX1 in a lineage-specific context and its role in progenitor differentiation, no studies have assessed the role of APEX1, nor its two enzymatic domains, in supporting adult HSPC function. In this study, we demonstrated that complete loss of APEX1 from murine bone marrow HSPCs (induced by CRISPR/Cas9) caused severe hematopoietic failure following transplantation, as well as a HSPC expansion defect in culture conditions maintaining in vivo HSC functionality. Using specific inhibitors against either the nuclease or redox domains of APEX1 in combination with single cell transcriptomics (CITE-seq), we found that both APEX1 nuclease and redox domains are regulating mouse HSPCs, but through distinct underlying transcriptional changes. Inhibition of the APEX1 nuclease function resulted in loss of HSPCs accompanied by early activation of differentiation programs and enhanced lineage commitment. By contrast, inhibition of the APEX1 redox function significantly downregulated interferon-stimulated genes and regulons in expanding HSPCs and their progeny, resulting in dysfunctional megakaryocyte-biased HSPCs, as well as loss of monocytes and lymphoid progenitor cells. In conclusion, we demonstrate that APEX1 is a key regulator for adult regenerative hematopoiesis, and that the APEX1 nuclease and redox domains differently impact proliferating HSPCs.
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Affiliation(s)
- Samantha Zaunz
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, O&N IV Herestraat 49, 3000, Louvain, Belgium.
| | - Jonathan De Smedt
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, O&N IV Herestraat 49, 3000, Louvain, Belgium
- GlaxoSmithKline Biologicals SA, 1300, Wavre, Belgium
| | - Lukas Lauwereins
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, O&N IV Herestraat 49, 3000, Louvain, Belgium
| | - Lana Cleuren
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, O&N IV Herestraat 49, 3000, Louvain, Belgium
| | - Charlie Laffeber
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Manmohan Bajaj
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, O&N IV Herestraat 49, 3000, Louvain, Belgium
| | - Joyce H G Lebbink
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Radiotherapy, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Kim De Keersmaecker
- Laboratory for Disease Mechanisms in Cancer, Department of Oncology, KU Leuven, Louvain, Belgium
| | - Catherine Verfaillie
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, O&N IV Herestraat 49, 3000, Louvain, Belgium
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6
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van Toorn M, Turkyilmaz Y, Han S, Zhou D, Kim HS, Salas-Armenteros I, Kim M, Akita M, Wienholz F, Raams A, Ryu E, Kang S, Theil AF, Bezstarosti K, Tresini M, Giglia-Mari G, Demmers JA, Schärer OD, Choi JH, Vermeulen W, Marteijn JA. Active DNA damage eviction by HLTF stimulates nucleotide excision repair. Mol Cell 2022; 82:1343-1358.e8. [PMID: 35271816 PMCID: PMC9473497 DOI: 10.1016/j.molcel.2022.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/15/2021] [Accepted: 02/10/2022] [Indexed: 10/18/2022]
Abstract
Nucleotide excision repair (NER) counteracts the onset of cancer and aging by removing helix-distorting DNA lesions via a "cut-and-patch"-type reaction. The regulatory mechanisms that drive NER through its successive damage recognition, verification, incision, and gap restoration reaction steps remain elusive. Here, we show that the RAD5-related translocase HLTF facilitates repair through active eviction of incised damaged DNA together with associated repair proteins. Our data show a dual-incision-dependent recruitment of HLTF to the NER incision complex, which is mediated by HLTF's HIRAN domain that binds 3'-OH single-stranded DNA ends. HLTF's translocase motor subsequently promotes the dissociation of the stably damage-bound incision complex together with the incised oligonucleotide, allowing for an efficient PCNA loading and initiation of repair synthesis. Our findings uncover HLTF as an important NER factor that actively evicts DNA damage, thereby providing additional quality control by coordinating the transition between the excision and DNA synthesis steps to safeguard genome integrity.
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Affiliation(s)
- Marvin van Toorn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Yasemin Turkyilmaz
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Sueji Han
- Center for Bioanalysis, Korea Research Institute of Standards and Science, Daejeon 305-340, Republic of Korea; Department of Bio-Analytical Science, University of Science & Technology, Daejeon 305-350, Republic of Korea
| | - Di Zhou
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Hyun-Suk Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Irene Salas-Armenteros
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Mihyun Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea; Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Masaki Akita
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Franziska Wienholz
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Anja Raams
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Eunjin Ryu
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea; Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Arjan F Theil
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Karel Bezstarosti
- Proteomics Centre, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Maria Tresini
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Giuseppina Giglia-Mari
- Institut NeuroMyoGène (INMG), CNRS UMR 5310, INSERM U1217, Université de Lyon, Université Claude Bernard Lyon1, 16 rue Dubois, 69622 Villeurbanne Cedex, France
| | - Jeroen A Demmers
- Proteomics Centre, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea; Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jun-Hyuk Choi
- Center for Bioanalysis, Korea Research Institute of Standards and Science, Daejeon 305-340, Republic of Korea; Department of Bio-Analytical Science, University of Science & Technology, Daejeon 305-350, Republic of Korea
| | - Wim Vermeulen
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Centre, Rotterdam, the Netherlands.
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7
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Geijer ME, Zhou D, Selvam K, Steurer B, Mukherjee C, Evers B, Cugusi S, van Toorn M, van der Woude M, Janssens RC, Kok YP, Gong W, Raams A, Lo CSY, Lebbink JHG, Geverts B, Plummer DA, Bezstarosti K, Theil AF, Mitter R, Houtsmuller AB, Vermeulen W, Demmers JAA, Li S, van Vugt MATM, Lans H, Bernards R, Svejstrup JQ, Ray Chaudhuri A, Wyrick JJ, Marteijn JA. Publisher Correction: Elongation factor ELOF1 drives transcription-coupled repair and prevents genome instability. Nat Cell Biol 2021; 23:809. [PMID: 34163038 DOI: 10.1038/s41556-021-00720-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Marit E Geijer
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Di Zhou
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Kathiresan Selvam
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Barbara Steurer
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Chirantani Mukherjee
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bastiaan Evers
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Simona Cugusi
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London, UK
| | - Marvin van Toorn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Melanie van der Woude
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Roel C Janssens
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Yannick P Kok
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Wenzhi Gong
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Anja Raams
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Calvin S Y Lo
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joyce H G Lebbink
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Radiation Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bart Geverts
- Erasmus Optical Imaging Center, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Dalton A Plummer
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Karel Bezstarosti
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Arjan F Theil
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Richard Mitter
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Adriaan B Houtsmuller
- Erasmus Optical Imaging Center, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jeroen A A Demmers
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Shisheng Li
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Marcel A T M van Vugt
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - René Bernards
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London, UK
| | - Arnab Ray Chaudhuri
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John J Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
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8
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Geijer ME, Zhou D, Selvam K, Steurer B, Mukherjee C, Evers B, Cugusi S, van Toorn M, van der Woude M, Janssens RC, Kok YP, Gong W, Raams A, Lo CSY, Lebbink JHG, Geverts B, Plummer DA, Bezstarosti K, Theil AF, Mitter R, Houtsmuller AB, Vermeulen W, Demmers JAA, Li S, van Vugt MATM, Lans H, Bernards R, Svejstrup JQ, Ray Chaudhuri A, Wyrick JJ, Marteijn JA. Elongation factor ELOF1 drives transcription-coupled repair and prevents genome instability. Nat Cell Biol 2021; 23:608-619. [PMID: 34108662 PMCID: PMC7611218 DOI: 10.1038/s41556-021-00692-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 04/29/2021] [Indexed: 02/05/2023]
Abstract
Correct transcription is crucial for life. However, DNA damage severely impedes elongating RNA polymerase II, causing transcription inhibition and transcription-replication conflicts. Cells are equipped with intricate mechanisms to counteract the severe consequence of these transcription-blocking lesions. However, the exact mechanism and factors involved remain largely unknown. Here, using a genome-wide CRISPR-Cas9 screen, we identified the elongation factor ELOF1 as an important factor in the transcription stress response following DNA damage. We show that ELOF1 has an evolutionarily conserved role in transcription-coupled nucleotide excision repair (TC-NER), where it promotes recruitment of the TC-NER factors UVSSA and TFIIH to efficiently repair transcription-blocking lesions and resume transcription. Additionally, ELOF1 modulates transcription to protect cells against transcription-mediated replication stress, thereby preserving genome stability. Thus, ELOF1 protects the transcription machinery from DNA damage via two distinct mechanisms.
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Affiliation(s)
- Marit E Geijer
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Di Zhou
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Kathiresan Selvam
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Barbara Steurer
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Chirantani Mukherjee
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bastiaan Evers
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Simona Cugusi
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London, UK
| | - Marvin van Toorn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Melanie van der Woude
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Roel C Janssens
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Yannick P Kok
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Wenzhi Gong
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Anja Raams
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Calvin S Y Lo
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joyce H G Lebbink
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Radiation Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bart Geverts
- Erasmus Optical Imaging Center, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Dalton A Plummer
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Karel Bezstarosti
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Arjan F Theil
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Richard Mitter
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Adriaan B Houtsmuller
- Erasmus Optical Imaging Center, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jeroen A A Demmers
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Shisheng Li
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Marcel A T M van Vugt
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - René Bernards
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London, UK
| | - Arnab Ray Chaudhuri
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John J Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
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9
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Lo CSY, van Toorn M, Gaggioli V, Paes Dias M, Zhu Y, Manolika EM, Zhao W, van der Does M, Mukherjee C, G S C Souto Gonçalves J, van Royen ME, French PJ, Demmers J, Smal I, Lans H, Wheeler D, Jonkers J, Chaudhuri AR, Marteijn JA, Taneja N. SMARCAD1-mediated active replication fork stability maintains genome integrity. Sci Adv 2021; 7:7/19/eabe7804. [PMID: 33952518 PMCID: PMC8099181 DOI: 10.1126/sciadv.abe7804] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 03/16/2021] [Indexed: 05/17/2023]
Abstract
The stalled fork protection pathway mediated by breast cancer 1/2 (BRCA1/2) proteins is critical for replication fork stability. However, it is unclear whether additional mechanisms are required to maintain replication fork stability. We describe a hitherto unknown mechanism, by which the SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily-A containing DEAD/H box-1 (SMARCAD1) stabilizes active replication forks, that is essential to maintaining resistance towards replication poisons. We find that SMARCAD1 prevents accumulation of 53BP1-associated nucleosomes to preclude toxic enrichment of 53BP1 at the forks. In the absence of SMARCAD1, 53BP1 mediates untimely dissociation of PCNA via the PCNA-unloader ATAD5, causing frequent fork stalling, inefficient fork restart, and accumulation of single-stranded DNA. Although loss of 53BP1 in SMARCAD1 mutants rescues these defects and restores genome stability, this rescued stabilization also requires BRCA1-mediated fork protection. Notably, fork protection-challenged BRCA1-deficient naïve- or chemoresistant tumors require SMARCAD1-mediated active fork stabilization to maintain unperturbed fork progression and cellular proliferation.
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Affiliation(s)
- Calvin Shun Yu Lo
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, Netherlands
| | - Marvin van Toorn
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, Netherlands
- Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, Netherlands
| | - Vincent Gaggioli
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, Netherlands
| | - Mariana Paes Dias
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
| | - Yifan Zhu
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, Netherlands
| | - Eleni Maria Manolika
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, Netherlands
| | - Wei Zhao
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, Netherlands
| | - Marit van der Does
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, Netherlands
| | - Chirantani Mukherjee
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, Netherlands
| | - João G S C Souto Gonçalves
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Martin E van Royen
- Department of Pathology, Cancer Treatment Screening Facility (CTSF), Erasmus Optical Imaging Centre (OIC), Erasmus University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands
| | - Pim J French
- Department of Neurology and Cancer Treatment Screening Facility (CTSF), Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Jeroen Demmers
- Proteomics Center and Department of Biochemistry, Erasmus University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, Netherlands
| | - Ihor Smal
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, Netherlands
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
| | - Arnab Ray Chaudhuri
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, Netherlands
- Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, Netherlands
| | - Nitika Taneja
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, Netherlands.
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10
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Zhang Y, Mandemaker IK, Matsumoto S, Foreman O, Holland CP, Lloyd WR, Sugasawa K, Vermeulen W, Marteijn JA, Galardy PJ. USP44 Stabilizes DDB2 to Facilitate Nucleotide Excision Repair and Prevent Tumors. Front Cell Dev Biol 2021; 9:663411. [PMID: 33937266 PMCID: PMC8085418 DOI: 10.3389/fcell.2021.663411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/29/2021] [Indexed: 02/02/2023] Open
Abstract
Nucleotide excision repair (NER) is a pathway involved in the repair of a variety of potentially mutagenic lesions that distort the DNA double helix. The ubiquitin E3-ligase complex UV-DDB is required for the recognition and repair of UV-induced cyclobutane pyrimidine dimers (CPDs) lesions through NER. DDB2 directly binds CPDs and subsequently undergoes ubiquitination and proteasomal degradation. DDB2 must remain on damaged chromatin, however, for sufficient time to recruit and hand-off lesions to XPC, a factor essential in the assembly of downstream repair components. Here we show that the tumor suppressor USP44 directly deubiquitinates DDB2 to prevent its premature degradation and is selectively required for CPD repair. Cells lacking USP44 have impaired DDB2 accumulation on DNA lesions with subsequent defects in XPC retention. The physiological importance of this mechanism is evident in that mice lacking Usp44 are prone to tumors induced by NER lesions introduced by DMBA or UV light. These data reveal the requirement for highly regulated ubiquitin addition and removal in the recognition and repair of helix-distorting DNA damage and identify another mechanism by which USP44 protects genomic integrity and prevents tumors.
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Affiliation(s)
- Ying Zhang
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, United States
| | - Imke K Mandemaker
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, Rotterdam, Netherlands
| | | | - Oded Foreman
- Department of Pathology, Genentech, South San Francisco, CA, United States
| | - Christopher P Holland
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, United States
| | - Whitney R Lloyd
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, United States
| | - Kaoru Sugasawa
- Biosignal Research Center, Kobe University, Hyogo, Japan
| | - Wim Vermeulen
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, Rotterdam, Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, Rotterdam, Netherlands
| | - Paul J Galardy
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, United States.,Division of Pediatric Hematology-Oncology, Mayo Clinic, Rochester, MN, United States.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
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11
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van den Heuvel D, Spruijt CG, González-Prieto R, Kragten A, Paulsen MT, Zhou D, Wu H, Apelt K, van der Weegen Y, Yang K, Dijk M, Daxinger L, Marteijn JA, Vertegaal ACO, Ljungman M, Vermeulen M, Luijsterburg MS. A CSB-PAF1C axis restores processive transcription elongation after DNA damage repair. Nat Commun 2021; 12:1342. [PMID: 33637760 PMCID: PMC7910549 DOI: 10.1038/s41467-021-21520-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 01/28/2021] [Indexed: 02/06/2023] Open
Abstract
Bulky DNA lesions in transcribed strands block RNA polymerase II (RNAPII) elongation and induce a genome-wide transcriptional arrest. The transcription-coupled repair (TCR) pathway efficiently removes transcription-blocking DNA lesions, but how transcription is restored in the genome following DNA repair remains unresolved. Here, we find that the TCR-specific CSB protein loads the PAF1 complex (PAF1C) onto RNAPII in promoter-proximal regions in response to DNA damage. Although dispensable for TCR-mediated repair, PAF1C is essential for transcription recovery after UV irradiation. We find that PAF1C promotes RNAPII pause release in promoter-proximal regions and subsequently acts as a processivity factor that stimulates transcription elongation throughout genes. Our findings expose the molecular basis for a non-canonical PAF1C-dependent pathway that restores transcription throughout the human genome after genotoxic stress. The transcription-coupled repair pathway removes transcription-blocking DNA lesions, but how transcription is restored following DNA repair is not clear. Here the authors reveal that the PAF1 complex, while dispensable for the repair process, restores transcription after DNA damage.
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Affiliation(s)
- Diana van den Heuvel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Cornelia G Spruijt
- Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands.,Prinses Maxima Center, Utrecht, The Netherlands
| | - Román González-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Angela Kragten
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Michelle T Paulsen
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Di Zhou
- Department of Molecular Genetics, Oncode Institute, Rotterdam, The Netherlands
| | - Haoyu Wu
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Katja Apelt
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Yana van der Weegen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Kevin Yang
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Madelon Dijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Rotterdam, The Netherlands
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA.,Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Michiel Vermeulen
- Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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12
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Mandemaker IK, Zhou D, Bruens ST, Dekkers DH, Verschure PJ, Edupuganti RR, Meshorer E, Demmers JAA, Marteijn JA. Histone H1 eviction by the histone chaperone SET reduces cell survival following DNA damage. J Cell Sci 2020; 133:jcs235473. [PMID: 32184266 DOI: 10.1242/jcs.235473] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 02/27/2020] [Indexed: 08/31/2023] Open
Abstract
Many chromatin remodeling and modifying proteins are involved in the DNA damage response, where they stimulate repair or induce DNA damage signaling. Interestingly, we identified that downregulation of the histone H1 (H1)-interacting protein SET results in increased resistance to a wide variety of DNA damaging agents. We found that this increased resistance does not result from alleviation of an inhibitory effect of SET on DNA repair but, rather, is the consequence of a suppressed apoptotic response to DNA damage. Furthermore, we provide evidence that the histone chaperone SET is responsible for the eviction of H1 from chromatin. Knockdown of H1 in SET-depleted cells resulted in re-sensitization of cells to DNA damage, suggesting that the increased DNA damage resistance in SET-depleted cells is the result of enhanced retention of H1 on chromatin. Finally, clonogenic survival assays showed that SET and p53 act epistatically in the attenuation of DNA damage-induced cell death. Taken together, our data indicate a role for SET in the DNA damage response as a regulator of cell survival following genotoxic stress.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Imke K Mandemaker
- Erasmus MC, University Medical Center Rotterdam, Department of Molecular Genetics, Oncode Institute, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Di Zhou
- Erasmus MC, University Medical Center Rotterdam, Department of Molecular Genetics, Oncode Institute, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Serena T Bruens
- Erasmus MC, University Medical Center Rotterdam, Department of Molecular Genetics, Oncode Institute, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Dick H Dekkers
- Proteomics Center, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Pernette J Verschure
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Raghu R Edupuganti
- The Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra campus, 91904 Jerusalem, Israel
| | - Eran Meshorer
- The Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra campus, 91904 Jerusalem, Israel
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Jeroen A A Demmers
- Proteomics Center, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Jurgen A Marteijn
- Erasmus MC, University Medical Center Rotterdam, Department of Molecular Genetics, Oncode Institute, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
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13
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Kochan JA, van den Belt M, von der Lippe J, Desclos ECB, Steurer B, Hoebe RA, Scutigliani EM, Verhoeven J, Stap J, Bosch R, Rijpkema M, van Oven C, van Veen HA, Stellingwerf I, Vriend LEM, Marteijn JA, Aten JA, Krawczyk PM. Ultra-soft X-ray system for imaging the early cellular responses to X-ray induced DNA damage. Nucleic Acids Res 2019; 47:e100. [PMID: 31318974 PMCID: PMC6753493 DOI: 10.1093/nar/gkz609] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 06/18/2019] [Accepted: 07/10/2019] [Indexed: 11/14/2022] Open
Abstract
The majority of the proteins involved in processing of DNA double-strand breaks (DSBs) accumulate at the damage sites. Real-time imaging and analysis of these processes, triggered by the so-called microirradiation using UV lasers or heavy particle beams, yielded valuable insights into the underlying DSB repair mechanisms. To study the temporal organization of DSB repair responses triggered by a more clinically-relevant DNA damaging agent, we developed a system coined X-ray multi-microbeam microscope (XM3), capable of simultaneous high dose-rate (micro)irradiation of large numbers of cells with ultra-soft X-rays and imaging of the ensuing cellular responses. Using this setup, we analyzed the changes in real-time kinetics of MRE11, MDC1, RNF8, RNF168 and 53BP1—proteins involved in the signaling axis of mammalian DSB repair—in response to X-ray and UV laser-induced DNA damage, in non-cancerous and cancer cells and in the presence or absence of a photosensitizer. Our results reveal, for the first time, the kinetics of DSB signaling triggered by X-ray microirradiation and establish XM3 as a powerful platform for real-time analysis of cellular DSB repair responses.
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Affiliation(s)
- Jakub A Kochan
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands.,Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Matthias van den Belt
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Julia von der Lippe
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Emilie C B Desclos
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Barbara Steurer
- Erasmus MC, University Medical Center Rotterdam, Department of Molecular Genetics, Oncode Institute, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Ron A Hoebe
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Enzo M Scutigliani
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Jan Verhoeven
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Jan Stap
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Ruben Bosch
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Meindert Rijpkema
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Carel van Oven
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Henk A van Veen
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Irene Stellingwerf
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Lianne E M Vriend
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Jurgen A Marteijn
- Erasmus MC, University Medical Center Rotterdam, Department of Molecular Genetics, Oncode Institute, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Jacob A Aten
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Przemek M Krawczyk
- Department of Medical Biology, Amsterdam University Medical Centers (location AMC), Cancer Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
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14
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Wienholz F, Zhou D, Turkyilmaz Y, Schwertman P, Tresini M, Pines A, van Toorn M, Bezstarosti K, Demmers JAA, Marteijn JA. FACT subunit Spt16 controls UVSSA recruitment to lesion-stalled RNA Pol II and stimulates TC-NER. Nucleic Acids Res 2019; 47:4011-4025. [PMID: 30715484 PMCID: PMC6486547 DOI: 10.1093/nar/gkz055] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 01/18/2019] [Accepted: 01/22/2019] [Indexed: 11/15/2022] Open
Abstract
Transcription-coupled nucleotide excision repair (TC-NER) is a dedicated DNA repair pathway that removes transcription-blocking DNA lesions (TBLs). TC-NER is initiated by the recognition of lesion-stalled RNA Polymerase II by the joint action of the TC-NER factors Cockayne Syndrome protein A (CSA), Cockayne Syndrome protein B (CSB) and UV-Stimulated Scaffold Protein A (UVSSA). However, the exact recruitment mechanism of these factors toward TBLs remains elusive. Here, we study the recruitment mechanism of UVSSA using live-cell imaging and show that UVSSA accumulates at TBLs independent of CSA and CSB. Furthermore, using UVSSA deletion mutants, we could separate the CSA interaction function of UVSSA from its DNA damage recruitment activity, which is mediated by the UVSSA VHS and DUF2043 domains, respectively. Quantitative interaction proteomics showed that the Spt16 subunit of the histone chaperone FACT interacts with UVSSA, which is mediated by the DUF2043 domain. Spt16 is recruited to TBLs, independently of UVSSA, to stimulate UVSSA recruitment and TC-NER-mediated repair. Spt16 specifically affects UVSSA, as Spt16 depletion did not affect CSB recruitment, highlighting that different chromatin-modulating factors regulate different reaction steps of the highly orchestrated TC-NER pathway.
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Affiliation(s)
- Franziska Wienholz
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Di Zhou
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Yasemin Turkyilmaz
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Petra Schwertman
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Maria Tresini
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Alex Pines
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Marvin van Toorn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Karel Bezstarosti
- Proteomics Centre, Erasmus University Medical Center, P.O. Box 1738, 3000 DR, Rotterdam, the Netherlands
| | - Jeroen A A Demmers
- Proteomics Centre, Erasmus University Medical Center, P.O. Box 1738, 3000 DR, Rotterdam, the Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
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15
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Steurer B, Turkyilmaz Y, van Toorn M, van Leeuwen W, Escudero-Ferruz P, Marteijn JA. Fluorescently-labelled CPD and 6-4PP photolyases: new tools for live-cell DNA damage quantification and laser-assisted repair. Nucleic Acids Res 2019; 47:3536-3549. [PMID: 30698791 PMCID: PMC6468286 DOI: 10.1093/nar/gkz035] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 11/29/2018] [Accepted: 01/15/2019] [Indexed: 01/02/2023] Open
Abstract
UV light induces cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone (6-4) photoproducts (6-4PPs), which can result in carcinogenesis and aging, if not properly repaired by nucleotide excision repair (NER). Assays to determine DNA damage load and repair rates are invaluable tools for fundamental and clinical NER research. However, most current assays to quantify DNA damage and repair cannot be performed in real time. To overcome this limitation, we made use of the damage recognition characteristics of CPD and 6-4PP photolyases (PLs). Fluorescently-tagged PLs efficiently recognize UV-induced DNA damage without blocking NER activity, and therefore can be used as sensitive live-cell damage sensors. Importantly, FRAP-based assays showed that PLs bind to damaged DNA in a highly sensitive and dose-dependent manner, and can be used to quantify DNA damage load and to determine repair kinetics in real time. Additionally, PLs can instantly reverse DNA damage by 405 nm laser-assisted photo-reactivation during live-cell imaging, opening new possibilities to study lesion-specific NER dynamics and cellular responses to damage removal. Our results show that fluorescently-tagged PLs can be used as a versatile tool to sense, quantify and repair DNA damage, and to study NER kinetics and UV-induced DNA damage response in living cells.
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Affiliation(s)
- Barbara Steurer
- Erasmus MC, University Medical Center Rotterdam, Department of Molecular Genetics, Oncode Institute, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Yasemin Turkyilmaz
- Erasmus MC, University Medical Center Rotterdam, Department of Molecular Genetics, Oncode Institute, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Marvin van Toorn
- Erasmus MC, University Medical Center Rotterdam, Department of Molecular Genetics, Oncode Institute, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Wessel van Leeuwen
- Erasmus MC, University Medical Center Rotterdam, Department of Molecular Genetics, Oncode Institute, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Paula Escudero-Ferruz
- Erasmus MC, University Medical Center Rotterdam, Department of Molecular Genetics, Oncode Institute, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Jurgen A Marteijn
- Erasmus MC, University Medical Center Rotterdam, Department of Molecular Genetics, Oncode Institute, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
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16
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Lans H, Hoeijmakers JHJ, Vermeulen W, Marteijn JA. The DNA damage response to transcription stress. Nat Rev Mol Cell Biol 2019; 20:766-784. [DOI: 10.1038/s41580-019-0169-4] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2019] [Indexed: 12/30/2022]
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17
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Menoni H, Wienholz F, Theil AF, Janssens RC, Lans H, Campalans A, Radicella JP, Marteijn JA, Vermeulen W. The transcription-coupled DNA repair-initiating protein CSB promotes XRCC1 recruitment to oxidative DNA damage. Nucleic Acids Res 2019; 46:7747-7756. [PMID: 29955842 PMCID: PMC6125634 DOI: 10.1093/nar/gky579] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 06/22/2018] [Indexed: 02/05/2023] Open
Abstract
Transcription-coupled nucleotide excision repair factor Cockayne syndrome protein B (CSB) was suggested to function in the repair of oxidative DNA damage. However thus far, no clear role for CSB in base excision repair (BER), the dedicated pathway to remove abundant oxidative DNA damage, could be established. Using live cell imaging with a laser-assisted procedure to locally induce 8-oxo-7,8-dihydroguanine (8-oxoG) lesions, we previously showed that CSB is recruited to these lesions in a transcription-dependent but NER-independent fashion. Here we showed that recruitment of the preferred 8-oxoG-glycosylase 1 (OGG1) is independent of CSB or active transcription. In contrast, recruitment of the BER-scaffolding protein, X-ray repair cross-complementing protein 1 (XRCC1), to 8-oxoG lesions is stimulated by CSB and transcription. Remarkably, recruitment of XRCC1 to BER-unrelated single strand breaks (SSBs) does not require CSB or transcription. Together, our results suggest a specific transcription-dependent role for CSB in recruiting XRCC1 to BER-generated SSBs, whereas XRCC1 recruitment to SSBs generated independently of BER relies predominantly on PARP activation. Based on our results, we propose a model in which CSB plays a role in facilitating BER progression at transcribed genes, probably to allow XRCC1 recruitment to BER-intermediates masked by RNA polymerase II complexes stalled at these intermediates.
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Affiliation(s)
- Hervé Menoni
- Department of Molecular Genetics, Oncode Institute, Cancer Genomics Netherlands, Erasmus MC, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands.,Laboratoire de Biologie et Modélisation de la Cellule (LBMC) CNRS, ENSL, UCBL UMR 5239, Université de Lyon, Ecole Normale Supérieure de Lyon, 69007 Lyon
| | - Franziska Wienholz
- Department of Molecular Genetics, Oncode Institute, Cancer Genomics Netherlands, Erasmus MC, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Arjan F Theil
- Department of Molecular Genetics, Oncode Institute, Cancer Genomics Netherlands, Erasmus MC, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Roel C Janssens
- Department of Molecular Genetics, Oncode Institute, Cancer Genomics Netherlands, Erasmus MC, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Oncode Institute, Cancer Genomics Netherlands, Erasmus MC, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Anna Campalans
- CEA, Institute of Cellular and Molecular Radiobiology, F-96265 Fontenay aux Roses, France.,UMR967 CEA, INSERM, Universités Paris-Diderot et Paris-Sud, F-92265 Fontenay aux Roses, France
| | - J Pablo Radicella
- CEA, Institute of Cellular and Molecular Radiobiology, F-96265 Fontenay aux Roses, France.,UMR967 CEA, INSERM, Universités Paris-Diderot et Paris-Sud, F-92265 Fontenay aux Roses, France
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Cancer Genomics Netherlands, Erasmus MC, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Oncode Institute, Cancer Genomics Netherlands, Erasmus MC, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
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18
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Ribeiro-Silva C, Aydin ÖZ, Mesquita-Ribeiro R, Slyskova J, Helfricht A, Marteijn JA, Hoeijmakers JHJ, Lans H, Vermeulen W. DNA damage sensitivity of SWI/SNF-deficient cells depends on TFIIH subunit p62/GTF2H1. Nat Commun 2018; 9:4067. [PMID: 30287812 PMCID: PMC6172278 DOI: 10.1038/s41467-018-06402-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 09/03/2018] [Indexed: 12/11/2022] Open
Abstract
Mutations in SWI/SNF genes are amongst the most common across all human cancers, but efficient therapeutic approaches that exploit vulnerabilities caused by SWI/SNF mutations are currently lacking. Here, we show that the SWI/SNF ATPases BRM/SMARCA2 and BRG1/SMARCA4 promote the expression of p62/GTF2H1, a core subunit of the transcription factor IIH (TFIIH) complex. Inactivation of either ATPase subunit downregulates GTF2H1 and therefore compromises TFIIH stability and function in transcription and nucleotide excision repair (NER). We also demonstrate that cells with permanent BRM or BRG1 depletion have the ability to restore GTF2H1 expression. As a consequence, the sensitivity of SWI/SNF-deficient cells to DNA damage induced by UV irradiation and cisplatin treatment depends on GTF2H1 levels. Together, our results expose GTF2H1 as a potential novel predictive marker of platinum drug sensitivity in SWI/SNF-deficient cancer cells. SWI/SNF genes are commonly found to be mutated in different cancers. Here the authors report that the remodelers BRM and BRG1 are necessary for efficient nucleotide excision repair by promoting the expression of TFIIH subunit GTF2H1.
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Affiliation(s)
- Cristina Ribeiro-Silva
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Özge Z Aydin
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.,Molecular Biology and Genetics Department, Koç University, Istanbul, 34450, Turkey
| | | | - Jana Slyskova
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Angela Helfricht
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Jan H J Hoeijmakers
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.
| | - Wim Vermeulen
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.
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19
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Mandemaker IK, Geijer ME, Kik I, Bezstarosti K, Rijkers E, Raams A, Janssens RC, Lans H, Hoeijmakers JH, Demmers JA, Vermeulen W, Marteijn JA. DNA damage-induced replication stress results in PA200-proteasome-mediated degradation of acetylated histones. EMBO Rep 2018; 19:embr.201745566. [PMID: 30104204 PMCID: PMC6172457 DOI: 10.15252/embr.201745566] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 07/06/2018] [Accepted: 07/16/2018] [Indexed: 12/21/2022] Open
Abstract
Histone acetylation influences protein interactions and chromatin accessibility and plays an important role in the regulation of transcription, replication, and DNA repair. Conversely, DNA damage affects these crucial cellular processes and induces changes in histone acetylation. However, a comprehensive overview of the effects of DNA damage on the histone acetylation landscape is currently lacking. To quantify changes in histone acetylation, we developed an unbiased quantitative mass spectrometry analysis on affinity‐purified acetylated histone peptides, generated by differential parallel proteolysis. We identify a large number of histone acetylation sites and observe an overall reduction of acetylated histone residues in response to DNA damage, indicative of a histone‐wide loss of acetyl modifications. This decrease is mainly caused by DNA damage‐induced replication stress coupled to specific proteasome‐dependent loss of acetylated histones. Strikingly, this degradation of acetylated histones is independent of ubiquitylation but requires the PA200‐proteasome activator, a complex that specifically targets acetylated histones for degradation. The uncovered replication stress‐induced degradation of acetylated histones represents an important chromatin‐modifying response to cope with replication stress.
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Affiliation(s)
- Imke K Mandemaker
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marit E Geijer
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Iris Kik
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Karel Bezstarosti
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Erikjan Rijkers
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Anja Raams
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Roel C Janssens
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jan Hj Hoeijmakers
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.,CECAD Forschungszentrum, Köln, Germany.,Princess Máxima Center for Pediatric Oncology, Bilthoven, The Netherlands
| | - Jeroen Aa Demmers
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
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20
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Theil AF, Mandemaker IK, van den Akker E, Swagemakers SMA, Raams A, Wüst T, Marteijn JA, Giltay JC, Colombijn RM, Moog U, Kotzaeridou U, Ghazvini M, von Lindern M, Hoeijmakers JHJ, Jaspers NGJ, van der Spek PJ, Vermeulen W. Trichothiodystrophy causative TFIIEβ mutation affects transcription in highly differentiated tissue. Hum Mol Genet 2018; 26:4689-4698. [PMID: 28973399 PMCID: PMC5886110 DOI: 10.1093/hmg/ddx351] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 08/29/2017] [Indexed: 01/01/2023] Open
Abstract
The rare recessive developmental disorder Trichothiodystrophy (TTD) is characterized by brittle hair and nails. Patients also present a variable set of poorly explained additional clinical features, including ichthyosis, impaired intelligence, developmental delay and anemia. About half of TTD patients are photosensitive due to inherited defects in the DNA repair and transcription factor II H (TFIIH). The pathophysiological contributions of unrepaired DNA lesions and impaired transcription have not been dissected yet. Here, we functionally characterize the consequence of a homozygous missense mutation in the general transcription factor II E, subunit 2 (GTF2E2/TFIIEβ) of two unrelated non-photosensitive TTD (NPS-TTD) families. We demonstrate that mutant TFIIEβ strongly reduces the total amount of the entire TFIIE complex, with a remarkable temperature-sensitive transcription defect, which strikingly correlates with the phenotypic aggravation of key clinical symptoms after episodes of high fever. We performed induced pluripotent stem (iPS) cell reprogramming of patient fibroblasts followed by in vitro erythroid differentiation to translate the intriguing molecular defect to phenotypic expression in relevant tissue, to disclose the molecular basis for some specific TTD features. We observed a clear hematopoietic defect during late-stage differentiation associated with hemoglobin subunit imbalance. These new findings of a DNA repair-independent transcription defect and tissue-specific malfunctioning provide novel mechanistic insight into the etiology of TTD.
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Affiliation(s)
- Arjan F Theil
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus MC, Rotterdam, The Netherlands
| | - Imke K Mandemaker
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus MC, Rotterdam, The Netherlands
| | - Emile van den Akker
- Sanquin Research, Department of Hematopoiesis/Landsteiner Laboratory, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Anja Raams
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus MC, Rotterdam, The Netherlands
| | - Tatjana Wüst
- Sanquin Research, Department of Hematopoiesis/Landsteiner Laboratory, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus MC, Rotterdam, The Netherlands
| | - Jacques C Giltay
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Ute Moog
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | | | - Mehrnaz Ghazvini
- Department of Developmental Biology, iPS Core Facility, Erasmus MC, Rotterdam, The Netherlands
| | - Marieke von Lindern
- Sanquin Research, Department of Hematopoiesis/Landsteiner Laboratory, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Jan H J Hoeijmakers
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus MC, Rotterdam, The Netherlands
| | - Nicolaas G J Jaspers
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus MC, Rotterdam, The Netherlands
| | | | - Wim Vermeulen
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus MC, Rotterdam, The Netherlands
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21
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Wienholz F, Vermeulen W, Marteijn JA. Amplification of unscheduled DNA synthesis signal enables fluorescence-based single cell quantification of transcription-coupled nucleotide excision repair. Nucleic Acids Res 2017; 45:e68. [PMID: 28088761 PMCID: PMC5436002 DOI: 10.1093/nar/gkw1360] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 01/02/2017] [Indexed: 12/14/2022] Open
Abstract
Nucleotide excision repair (NER) comprises two damage recognition pathways: global genome NER (GG-NER) and transcription-coupled NER (TC-NER), which remove a wide variety of helix-distorting lesions including UV-induced damage. During NER, a short stretch of single-stranded DNA containing damage is excised and the resulting gap is filled by DNA synthesis in a process called unscheduled DNA synthesis (UDS). UDS is measured by quantifying the incorporation of nucleotide analogues into repair patches to provide a measure of NER activity. However, this assay is unable to quantitatively determine TC-NER activity due to the low contribution of TC-NER to the overall NER activity. Therefore, we developed a user-friendly, fluorescence-based single-cell assay to measure TC-NER activity. We combined the UDS assay with tyramide-based signal amplification to greatly increase the UDS signal, thereby allowing UDS to be quantified at low UV doses, as well as DNA-repair synthesis of other excision-based repair mechanisms such as base excision repair and mismatch repair. Importantly, we demonstrated that the amplified UDS is sufficiently sensitive to quantify TC-NER-derived repair synthesis in GG-NER-deficient cells. This assay is important as a diagnostic tool for NER-related disorders and as a research tool for obtaining new insights into the mechanism and regulation of excision repair.
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Affiliation(s)
- Franziska Wienholz
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
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22
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Abstract
Environmental genotoxins and metabolic byproducts generate DNA lesions that can cause genomic instability and disrupt tissue homeostasis. To ensure genomic integrity, cells employ mechanisms that convert signals generated by stochastic DNA damage into organized responses, including activation of repair systems, cell cycle checkpoints, and apoptotic mechanisms. DNA damage response (DDR) signaling pathways coordinate these responses and determine cellular fates in part, by transducing signals that modulate RNA metabolism. One of the master DDR coordinators, the Ataxia Telangiectasia Mutated (ATM) kinase, has a fundamental role in mediating DNA damage-induced changes in mRNA synthesis. ATM acts by modulating a variety of RNA metabolic pathways including nascent RNA splicing, a process catalyzed by the spliceosome. Interestingly, ATM and the spliceosome influence each other's activity in a reciprocal manner by a pathway that initiates when transcribing RNA polymerase II (RNAPII) encounters DNA lesions that prohibit forward translocation. In response to stalling of RNAPII assembly of late-stage spliceosomes is disrupted resulting in increased splicing factor mobility. Displacement of spliceosomes from lesion-arrested RNA polymerases facilitates formation of R-loops between the nascent RNA and DNA adjacent to the transcription bubble. R-loops signal for noncanonical ATM activation which in quiescent cells occurs in absence of detectable dsDNA breaks. In turn, activated ATM signals to regulate spliceosome dynamics and AS genome wide.This chapter describes the use of fluorescence microscopy methods that can be used to evaluate noncanonical ATM activation by transcription-blocking DNA damage. First, we present an immunofluorescence-detection method that can be used to evaluate ATM activation by autophosphorylation, in fixed cells. Second, we present a protocol for Fluorescence Recovery After Photobleaching (FRAP) of GFP-tagged splicing factors, a highly sensitive and reproducible readout to measure in living cells, the ATM influence on the spliceosome. These approaches have been extensively used in our laboratory for a number of cell lines of various origins and are particularly informative when used in primary cells that can be synchronized in quiescence, to avoid generation of replication stress-induced dsDNA breaks and consequent ATM activation through its canonical pathway.
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Affiliation(s)
- Jurgen A Marteijn
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Maria Tresini
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
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23
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Steurer B, Marteijn JA. Traveling Rocky Roads: The Consequences of Transcription-Blocking DNA Lesions on RNA Polymerase II. J Mol Biol 2016; 429:3146-3155. [PMID: 27851891 DOI: 10.1016/j.jmb.2016.11.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 11/04/2016] [Accepted: 11/04/2016] [Indexed: 12/13/2022]
Abstract
The faithful transcription of eukaryotic genes by RNA polymerase II (RNAP2) is crucial for proper cell function and tissue homeostasis. However, transcription-blocking DNA lesions of both endogenous and environmental origin continuously challenge the progression of elongating RNAP2. The stalling of RNAP2 on a transcription-blocking lesion triggers a series of highly regulated events, including RNAP2 processing to make the lesion accessible for DNA repair, R-loop-mediated DNA damage signaling, and the initiation of transcription-coupled DNA repair. The correct execution and coordination of these processes is vital for resuming transcription following the successful repair of transcription-blocking lesions. Here, we outline recent insights into the molecular consequences of RNAP2 stalling on transcription-blocking DNA lesions and how these lesions are resolved to restore mRNA synthesis.
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Affiliation(s)
- Barbara Steurer
- Department of Molecular Genetics, Erasmus MC, Wytemaweg 80, Rotterdam 3015 CN, The Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Erasmus MC, Wytemaweg 80, Rotterdam 3015 CN, The Netherlands.
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Abstract
In response to DNA damage cells activate intricate protein networks to ensure genomic fidelity and tissue homeostasis. DNA damage response signaling pathways coordinate these networks and determine cellular fates, in part, by modulating RNA metabolism. Here we discuss a replication-independent pathway activated by transcription-blocking DNA lesions, which utilizes the ATM signaling kinase to regulate spliceosome function in a reciprocal manner. We present a model according to which, displacement of co-transcriptional spliceosomes from lesion-arrested RNA polymerases, culminates in R-loop formation and non-canonical ATM activation. ATM signals in a feed-forward fashion to further impede spliceosome organization and regulates UV-induced gene expression and alternative splicing genome-wide. This reciprocal coupling between ATM and the spliceosome highlights the importance of ATM signaling in the cellular response to transcription-blocking lesions and supports a key role of the splicing machinery in this process.
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Affiliation(s)
- Maria Tresini
- a Department of Genetics , Cancer Genomics Netherlands, Erasmus University Medical Center , Rotterdam , The Netherlands
| | - Jurgen A Marteijn
- a Department of Genetics , Cancer Genomics Netherlands, Erasmus University Medical Center , Rotterdam , The Netherlands
| | - Wim Vermeulen
- a Department of Genetics , Cancer Genomics Netherlands, Erasmus University Medical Center , Rotterdam , The Netherlands
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25
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Abstract
In this issue, Li et al. (2015) uncover roles for the XPB and XPD helicases and for XPA during damage verification in nucleotide excision repair, supporting a novel tripartite damage checking mechanism that combines extreme versatility with narrow specificity.
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Affiliation(s)
- Jurgen A Marteijn
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Jan H J Hoeijmakers
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands.
| | - Wim Vermeulen
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
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Tresini M, Warmerdam DO, Kolovos P, Snijder L, Vrouwe MG, Demmers JAA, van IJcken WFJ, Grosveld FG, Medema RH, Hoeijmakers JHJ, Mullenders LHF, Vermeulen W, Marteijn JA. The core spliceosome as target and effector of non-canonical ATM signalling. Nature 2015; 523:53-8. [PMID: 26106861 PMCID: PMC4501432 DOI: 10.1038/nature14512] [Citation(s) in RCA: 182] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 05/11/2015] [Indexed: 01/19/2023]
Abstract
In response to DNA damage, tissue homoeostasis is ensured by protein networks promoting DNA repair, cell cycle arrest or apoptosis. DNA damage response signalling pathways coordinate these processes, partly by propagating gene-expression-modulating signals. DNA damage influences not only the abundance of messenger RNAs, but also their coding information through alternative splicing. Here we show that transcription-blocking DNA lesions promote chromatin displacement of late-stage spliceosomes and initiate a positive feedback loop centred on the signalling kinase ATM. We propose that initial spliceosome displacement and subsequent R-loop formation is triggered by pausing of RNA polymerase at DNA lesions. In turn, R-loops activate ATM, which signals to impede spliceosome organization further and augment ultraviolet-irradiation-triggered alternative splicing at the genome-wide level. Our findings define R-loop-dependent ATM activation by transcription-blocking lesions as an important event in the DNA damage response of non-replicating cells, and highlight a key role for spliceosome displacement in this process.
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Affiliation(s)
- Maria Tresini
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | - Daniël O Warmerdam
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands
| | - Petros Kolovos
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | - Loes Snijder
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | - Mischa G Vrouwe
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, The Netherlands
| | - Jeroen A A Demmers
- Erasmus MC Proteomics Center, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | - Wilfred F J van IJcken
- Erasmus Center for Biomics, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | - Frank G Grosveld
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | - René H Medema
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, 1066 CX, The Netherlands
| | - Jan H J Hoeijmakers
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | - Leon H F Mullenders
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, The Netherlands
| | - Wim Vermeulen
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | - Jurgen A Marteijn
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
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van Cuijk L, Vermeulen W, Marteijn JA. Ubiquitin at work: The ubiquitous regulation of the damage recognition step of NER. Exp Cell Res 2014; 329:101-9. [DOI: 10.1016/j.yexcr.2014.07.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 07/14/2014] [Indexed: 12/28/2022]
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Gourdin AM, van Cuijk L, Tresini M, Luijsterburg MS, Nigg AL, Giglia-Mari G, Houtsmuller AB, Vermeulen W, Marteijn JA. Differential binding kinetics of replication protein A during replication and the pre- and post-incision steps of nucleotide excision repair. DNA Repair (Amst) 2014; 24:46-56. [PMID: 25453469 DOI: 10.1016/j.dnarep.2014.09.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 09/24/2014] [Accepted: 09/26/2014] [Indexed: 11/17/2022]
Abstract
The ability of replication protein A (RPA) to bind single-stranded DNA (ssDNA) underlines its crucial roles during DNA replication and repair. A combination of immunofluorescence and live cell imaging of GFP-tagged RPA70 revealed that RPA, in contrast to other replication factors, does not cluster into replication foci, which is explained by its short residence time at ssDNA. In addition to replication, RPA also plays a crucial role in both the pre- and post-incision steps of nucleotide excision repair (NER). Pre-incision factors like XPC and TFIIH accumulate rapidly at locally induced UV-damage and remain visible up to 4h. However, RPA did not reach its maximum accumulation level until 3h after DNA damage infliction and a chromatin-bound pool remained detectable up to 8h, probably reflecting its role during the post-incision step of NER. During the pre-incision steps of NER, RPA could only be visualized at DNA lesions in incision deficient XP-F cells, however without a substantial increase in residence time at DNA damage. Together our data show that RPA is an intrinsically highly dynamic ssDNA-binding complex during both replication and distinct steps of NER.
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Affiliation(s)
- Audrey M Gourdin
- Department of Genetics, Cancer Genomics Netherlands, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Loes van Cuijk
- Department of Genetics, Cancer Genomics Netherlands, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Maria Tresini
- Department of Genetics, Cancer Genomics Netherlands, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Martijn S Luijsterburg
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 SM Amsterdam, The Netherlands; Swammerdam Institute for Life Sciences, University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands
| | - Alex L Nigg
- Department of Pathology, Josephine Nefkens Institute, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Guiseppina Giglia-Mari
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route de Narbonne, F-31077 Toulouse, France
| | - Adriaan B Houtsmuller
- Department of Pathology, Josephine Nefkens Institute, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Genetics, Cancer Genomics Netherlands, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands.
| | - Jurgen A Marteijn
- Department of Genetics, Cancer Genomics Netherlands, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands.
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Aydin ÖZ, Marteijn JA, Ribeiro-Silva C, Rodríguez López A, Wijgers N, Smeenk G, van Attikum H, Poot RA, Vermeulen W, Lans H. Human ISWI complexes are targeted by SMARCA5 ATPase and SLIDE domains to help resolve lesion-stalled transcription. Nucleic Acids Res 2014; 42:8473-85. [PMID: 24990377 PMCID: PMC4117783 DOI: 10.1093/nar/gku565] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Chromatin compaction of deoxyribonucleic acid (DNA) presents a major challenge to the detection and removal of DNA damage. Helix-distorting DNA lesions that block transcription are specifically repaired by transcription-coupled nucleotide excision repair, which is initiated by binding of the CSB protein to lesion-stalled RNA polymerase II. Using live cell imaging, we identify a novel function for two distinct mammalian ISWI adenosine triphosphate (ATP)-dependent chromatin remodeling complexes in resolving lesion-stalled transcription. Human ISWI isoform SMARCA5/SNF2H and its binding partners ACF1 and WSTF are rapidly recruited to UV-C induced DNA damage to specifically facilitate CSB binding and to promote transcription recovery. SMARCA5 targeting to UV-C damage depends on transcription and histone modifications and requires functional SWI2/SNF2-ATPase and SLIDE domains. After initial recruitment to UV damage, SMARCA5 re-localizes away from the center of DNA damage, requiring its HAND domain. Our studies support a model in which SMARCA5 targeting to DNA damage-stalled transcription sites is controlled by an ATP-hydrolysis-dependent scanning and proofreading mechanism, highlighting how SWI2/SNF2 chromatin remodelers identify and bind nucleosomes containing damaged DNA.
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Affiliation(s)
- Özge Z Aydin
- Department of Genetics, Medical Genetics Cluster, Cancer Genomics Netherlands, Erasmus MC, Rotterdam, 3015 GE, The Netherlands
| | - Jurgen A Marteijn
- Department of Genetics, Medical Genetics Cluster, Cancer Genomics Netherlands, Erasmus MC, Rotterdam, 3015 GE, The Netherlands
| | - Cristina Ribeiro-Silva
- Department of Genetics, Medical Genetics Cluster, Cancer Genomics Netherlands, Erasmus MC, Rotterdam, 3015 GE, The Netherlands
| | - Aida Rodríguez López
- Department of Genetics, Medical Genetics Cluster, Cancer Genomics Netherlands, Erasmus MC, Rotterdam, 3015 GE, The Netherlands
| | - Nils Wijgers
- Department of Genetics, Medical Genetics Cluster, Cancer Genomics Netherlands, Erasmus MC, Rotterdam, 3015 GE, The Netherlands
| | - Godelieve Smeenk
- Department of Toxicogenetics, Leiden University Medical Center, Leiden, 2333 ZC, The Netherlands
| | - Haico van Attikum
- Department of Toxicogenetics, Leiden University Medical Center, Leiden, 2333 ZC, The Netherlands
| | - Raymond A Poot
- Department of Cell Biology, Medical Genetics Cluster, Erasmus MC, Rotterdam, 3015 GE, The Netherlands
| | - Wim Vermeulen
- Department of Genetics, Medical Genetics Cluster, Cancer Genomics Netherlands, Erasmus MC, Rotterdam, 3015 GE, The Netherlands
| | - Hannes Lans
- Department of Genetics, Medical Genetics Cluster, Cancer Genomics Netherlands, Erasmus MC, Rotterdam, 3015 GE, The Netherlands
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30
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Abstract
During transcription, RNA polymerase may encounter DNA lesions, which causes stalling of transcription. To overcome the RNA polymerase blocking lesions, the transcribed strand is repaired by a dedicated repair mechanism, called transcription coupled nucleotide excision repair (TC-NER). After repair is completed, it is essential that transcription restarts. So far, the regulation and exact molecular mechanism of this transcriptional restart upon genotoxic damage has remained elusive. Recently, three different chromatin remodeling factors, HIRA, FACT, and Dot1L, were identified to stimulate transcription restart after DNA damage. These factors either incorporate new histones or establish specific chromatin marks that will gear up the chromatin to subsequently promote transcription recovery. This adds a new layer to the current model of chromatin remodeling necessary for repair and indicates that this specific form of transcription, i.e., the transcriptional restart upon DNA damage, needs specific chromatin remodeling events.
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Affiliation(s)
- Imke K Mandemaker
- Department of Genetics; Erasmus Medical Centre; Rotterdam, the Netherlands
| | - Wim Vermeulen
- Department of Genetics; Erasmus Medical Centre; Rotterdam, the Netherlands
| | - Jurgen A Marteijn
- Department of Genetics; Erasmus Medical Centre; Rotterdam, the Netherlands
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31
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Dinant C, Ampatziadis-Michailidis G, Lans H, Tresini M, Lagarou A, Grosbart M, Theil AF, van Cappellen WA, Kimura H, Bartek J, Fousteri M, Houtsmuller AB, Vermeulen W, Marteijn JA. Enhanced chromatin dynamics by FACT promotes transcriptional restart after UV-induced DNA damage. Mol Cell 2013; 51:469-79. [PMID: 23973375 DOI: 10.1016/j.molcel.2013.08.007] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 06/07/2013] [Accepted: 07/17/2013] [Indexed: 02/05/2023]
Abstract
Chromatin remodeling is tightly linked to all DNA-transacting activities. To study chromatin remodeling during DNA repair, we established quantitative fluorescence imaging methods to measure the exchange of histones in chromatin in living cells. We show that particularly H2A and H2B are evicted and replaced at an accelerated pace at sites of UV-induced DNA damage. This accelerated exchange of H2A/H2B is facilitated by SPT16, one of the two subunits of the histone chaperone FACT (facilitates chromatin transcription) but largely independent of its partner SSRP1. Interestingly, SPT16 is targeted to sites of UV light-induced DNA damage-arrested transcription and is required for efficient restart of RNA synthesis upon damage removal. Together, our data uncover an important role for chromatin dynamics at the crossroads of transcription and the UV-induced DNA damage response.
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Affiliation(s)
- Christoffel Dinant
- Department of Genetics, Erasmus Medical Centre, Rotterdam 3015 GE, The Netherlands
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32
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Poulsen SL, Hansen RK, Wagner SA, van Cuijk L, van Belle GJ, Streicher W, Wikström M, Choudhary C, Houtsmuller AB, Marteijn JA, Bekker-Jensen S, Mailand N. RNF111/Arkadia is a SUMO-targeted ubiquitin ligase that facilitates the DNA damage response. ACTA ACUST UNITED AC 2013; 201:797-807. [PMID: 23751493 PMCID: PMC3678163 DOI: 10.1083/jcb.201212075] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
RNF111/Arkadia targets SUMOylated XPC for ubiquitylation, negatively regulating its association with damaged DNA Protein modifications by ubiquitin and small ubiquitin-like modifier (SUMO) play key roles in cellular signaling pathways. SUMO-targeted ubiquitin ligases (STUbLs) directly couple these modifications by selectively recognizing SUMOylated target proteins through SUMO-interacting motifs (SIMs), promoting their K48-linked ubiquitylation and degradation. Only a single mammalian STUbL, RNF4, has been identified. We show that human RNF111/Arkadia is a new STUbL, which used three adjacent SIMs for specific recognition of poly-SUMO2/3 chains, and used Ubc13–Mms2 as a cognate E2 enzyme to promote nonproteolytic, K63-linked ubiquitylation of SUMOylated target proteins. We demonstrate that RNF111 promoted ubiquitylation of SUMOylated XPC (xeroderma pigmentosum C) protein, a central DNA damage recognition factor in nucleotide excision repair (NER) extensively regulated by ultraviolet (UV)-induced SUMOylation and ubiquitylation. Moreover, we show that RNF111 facilitated NER by regulating the recruitment of XPC to UV-damaged DNA. Our findings establish RNF111 as a new STUbL that directly links nonproteolytic ubiquitylation and SUMOylation in the DNA damage response.
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Affiliation(s)
- Sara L Poulsen
- Ubiquitin Signaling Group, Department of Disease Biology, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
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Schwertman P, Bezstarosti K, Laffeber C, Vermeulen W, Demmers JAA, Marteijn JA. An immunoaffinity purification method for the proteomic analysis of ubiquitinated protein complexes. Anal Biochem 2013; 440:227-36. [PMID: 23743150 DOI: 10.1016/j.ab.2013.05.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 04/25/2013] [Accepted: 05/13/2013] [Indexed: 01/04/2023]
Abstract
Protein ubiquitination plays an important role in the regulation of many cellular processes, including protein degradation, cell cycle regulation, apoptosis, and DNA repair. To study the ubiquitin proteome we have established an immunoaffinity purification method for the proteomic analysis of endogenously ubiquitinated protein complexes. A strong, specific enrichment of ubiquitinated factors was achieved using the FK2 antibody bound to protein G-beaded agarose, which recognizes monoubiquitinated and polyubiquitinated conjugates. Mass spectrometric analysis of two FK2 immunoprecipitations (IPs) resulted in the identification of 296 FK2-specific proteins in both experiments. The isolation of ubiquitinated and ubiquitination-related proteins was confirmed by pathway analyses (using Ingenuity Pathway Analysis and Gene Ontology-annotation enrichment). Additionally, comparing the proteins that specifically came down in the FK2 IP with databases of ubiquitinated proteins showed that a high percentage of proteins in our enriched fraction was indeed ubiquitinated. Finally, assessment of protein-protein interactions revealed that significantly more FK2-specific proteins were residing in protein complexes than in random protein sets. This method, which is capable of isolating both endogenously ubiquitinated proteins and their interacting proteins, can be widely used for unraveling ubiquitin-mediated protein regulation in various cell systems and tissues when comparing different cellular states.
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Affiliation(s)
- Petra Schwertman
- Department of Genetics and Netherlands Proteomics Centre, Centre for Biomedical Genetics, Erasmus University Medical Centre, 3015 GE Rotterdam, The Netherlands
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Theil AF, Nonnekens J, Steurer B, Mari PO, de Wit J, Lemaitre C, Marteijn JA, Raams A, Maas A, Vermeij M, Essers J, Hoeijmakers JHJ, Giglia-Mari G, Vermeulen W. Disruption of TTDA results in complete nucleotide excision repair deficiency and embryonic lethality. PLoS Genet 2013; 9:e1003431. [PMID: 23637614 PMCID: PMC3630102 DOI: 10.1371/journal.pgen.1003431] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 02/19/2013] [Indexed: 12/01/2022] Open
Abstract
The ten-subunit transcription factor IIH (TFIIH) plays a crucial role in transcription and nucleotide excision repair (NER). Inactivating mutations in the smallest 8-kDa TFB5/TTDA subunit cause the neurodevelopmental progeroid repair syndrome trichothiodystrophy A (TTD-A). Previous studies have shown that TTDA is the only TFIIH subunit that appears not to be essential for NER, transcription, or viability. We studied the consequences of TTDA inactivation by generating a Ttda knock-out (Ttda−/−) mouse-model resembling TTD-A patients. Unexpectedly, Ttda−/− mice were embryonic lethal. However, in contrast to full disruption of all other TFIIH subunits, viability of Ttda−/− cells was not affected. Surprisingly, Ttda−/− cells were completely NER deficient, contrary to the incomplete NER deficiency of TTD-A patient-derived cells. We further showed that TTD-A patient mutations only partially inactivate TTDA function, explaining the relatively mild repair phenotype of TTD-A cells. Moreover, Ttda−/− cells were also highly sensitive to oxidizing agents. These findings reveal an essential role of TTDA for life, nucleotide excision repair, and oxidative DNA damage repair and identify Ttda−/− cells as a unique class of TFIIH mutants. DNA is under constant attack of various environmental and cellular produced DNA damaging agents. DNA damage hampers normal cell function; however, different DNA repair mechanisms protect our genetic information. Nucleotide Excision Repair is one of the most versatile repair processes, as it removes a large variety of DNA helix-distorting lesions induced by UV light and various chemicals. To remove these lesions, the DNA helix needs to be opened by the transcription/repair factor II H (TFIIH). TFIIH is a multifunctional complex that consists of 10 subunits and plays a fundamental role in opening the DNA helix in both NER and transcription. TTDA, the smallest subunit of TFIIH, was thought to be dispensable for both NER and transcription. However, in this paper, we show for the first time that TTDA is in fact a crucial component of TFIIH for NER. We demonstrate that Ttda−/− mice are embryonic lethal. We also show that Ttda−/− mouse cells are the first known viable TFIIH subunit knock-out cells, which are completely NER deficient and sensitive to oxidative agents (showing a new role for TFIIH outside NER and transcription).
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Affiliation(s)
- Arjan F. Theil
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Julie Nonnekens
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
- CNRS, Institut de Pharmacologie et de Biologie Structurale (IPBS) and Université de Toulouse, UPS, Toulouse, France
| | - Barbara Steurer
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Pierre-Olivier Mari
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
- CNRS, Institut de Pharmacologie et de Biologie Structurale (IPBS) and Université de Toulouse, UPS, Toulouse, France
| | - Jan de Wit
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
| | | | | | - Anja Raams
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Alex Maas
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Marcel Vermeij
- Department of Pathology, Erasmus MC, Rotterdam, The Netherlands
| | - Jeroen Essers
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
- Department of Vascular Surgery, Erasmus MC, Rotterdam, The Netherlands
- Department of Radiation Oncology, Erasmus MC, Rotterdam, The Netherlands
| | | | - Giuseppina Giglia-Mari
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
- CNRS, Institut de Pharmacologie et de Biologie Structurale (IPBS) and Université de Toulouse, UPS, Toulouse, France
- * E-mail: (WV); (GG-M)
| | - Wim Vermeulen
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
- * E-mail: (WV); (GG-M)
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Warmerdam DO, Brinkman EK, Marteijn JA, Medema RH, Kanaar R, Smits VAJ. UV-induced G2 checkpoint depends on p38 MAPK and minimal activation of ATR-Chk1 pathway. J Cell Sci 2013; 126:1923-30. [PMID: 23447674 DOI: 10.1242/jcs.118265] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In response to UV light, single-stranded DNA intermediates coated with replication protein A (RPA) are generated, which trigger the ATR-Chk1 checkpoint pathway. Recruitment and/or activation of several checkpoint proteins at the damaged sites is important for the subsequent cell cycle arrest. Surprisingly, upon UV irradiation, Rad9 and RPA only minimally accumulate at DNA lesions in G2 phase, suggesting that only a few single-stranded DNA intermediates are generated. Also, little phosphorylated Chk1 is observed in G2 phase after UV-irradiation, and UV light fails to elicit efficient accumulation of typical DNA damage response proteins at sites of damage in this phase. By contrast, p38 MAPK is phosphorylated in G2 phase cells after UV damage. Interestingly, despite the lack of an obvious activation of the ATR-Chk1 pathway, only the combined inhibition of the ATR- and p38-dependent pathways results in a complete abrogation of the UV-induced G2/M arrest. This suggests that UV light induces less hazardous lesions in G2 phase or that lesions created in this phase are less efficiently processed, resulting in a low activation of the ATR-Chk1 pathway. UV-induced G2 checkpoint activation in this situation therefore relies on signalling via the p38 MAPK and ATR-Chk1 signalling cascades.
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Affiliation(s)
- Daniël O Warmerdam
- Department of Cell Biology and Genetics, Cancer Genomics Center, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands. ;
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Smeenk G, Wiegant WW, Marteijn JA, Luijsterburg MS, Sroczynski N, Costelloe T, Romeijn RJ, Pastink A, Mailand N, Vermeulen W, van Attikum H. Poly(ADP-ribosyl)ation links the chromatin remodeler SMARCA5/SNF2H to RNF168-dependent DNA damage signaling. J Cell Sci 2012; 126:889-903. [PMID: 23264744 DOI: 10.1242/jcs.109413] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Ionizing radiation (IR)-induced DNA double-strand breaks (DSBs) arising in native chromatin elicit an RNF8/RNF168-dependent ubiquitylation response, which triggers the recruitment of various repair factors. Precisely how this response is regulated in the context of chromatin remains largely unexplored. Here, we show that SMARCA5/SNF2H, the catalytic subunit of ISWI chromatin remodeling complexes, is recruited to DSBs in a poly(ADP-ribose) polymerase 1 (PARP1)-dependent manner. Remarkably, PARP activity, although dispensable for the efficient spreading of γH2AX into damaged chromatin, selectively promotes spreading of SMARCA5, the E3 ubiquitin ligase RNF168, ubiquitin conjugates and the ubiquitin-binding factors RAD18 and the RAP80-BRCA1 complex throughout DSB-flanking chromatin. This suggests that PARP regulates the spatial organization of the RNF168-driven ubiquitin response to DNA damage. In support of this, we show that SMARCA5 and RNF168 interact in a DNA damage- and PARP-dependent manner. RNF168 became poly(ADP-ribosyl)ated after DNA damage, while RNF168 and poly(ADP-ribose) chains were required for SMARCA5 binding in vivo, explaining how SMARCA5 is linked to the RNF168 ubiquitin cascade. Moreover, SMARCA5 was found to regulate the ubiquitin response by promoting RNF168 accumulation at DSBs, which subsequently facilitates efficient ubiquitin conjugation and BRCA1 assembly. Underlining the importance of these findings, we show that SMARCA5 depletion renders cells sensitive to IR and results in DSB repair defects. Our study unveils a functional link between DNA damage-induced poly(ADP-ribosyl)ation, SMARCA5-mediated chromatin remodeling and RNF168-dependent signaling and repair of DSBs.
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Affiliation(s)
- Godelieve Smeenk
- Department of Toxicogenetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
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Mattiroli F, Vissers JHA, van Dijk WJ, Ikpa P, Citterio E, Vermeulen W, Marteijn JA, Sixma TK. RNF168 ubiquitinates K13-15 on H2A/H2AX to drive DNA damage signaling. Cell 2012; 150:1182-95. [PMID: 22980979 DOI: 10.1016/j.cell.2012.08.005] [Citation(s) in RCA: 458] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 05/29/2012] [Accepted: 07/09/2012] [Indexed: 01/01/2023]
Abstract
Ubiquitin-dependent signaling during the DNA damage response (DDR) to double-strand breaks (DSBs) is initiated by two E3 ligases, RNF8 and RNF168, targeting histone H2A and H2AX. RNF8 is the first ligase recruited to the damage site, and RNF168 follows RNF8-dependent ubiquitination. This suggests that RNF8 initiates H2A/H2AX ubiquitination with K63-linked ubiquitin chains and RNF168 extends them. Here, we show that RNF8 is inactive toward nucleosomal H2A, whereas RNF168 catalyzes the monoubiquitination of the histones specifically on K13-15. Structure-based mutagenesis of RNF8 and RNF168 RING domains shows that a charged residue determines whether nucleosomal proteins are recognized. We find that K63 ubiquitin chains are conjugated to RNF168-dependent H2A/H2AX monoubiquitination at K13-15 and not on K118-119. Using a mutant of RNF168 unable to target histones but still catalyzing ubiquitin chains at DSBs, we show that ubiquitin chains per se are insufficient for signaling, but RNF168 target ubiquitination is required for DDR.
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Affiliation(s)
- Francesca Mattiroli
- Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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Pines A, Vrouwe MG, Marteijn JA, Typas D, Luijsterburg MS, Cansoy M, Hensbergen P, Deelder A, de Groot A, Matsumoto S, Sugasawa K, Thoma N, Vermeulen W, Vrieling H, Mullenders L. PARP1 promotes nucleotide excision repair through DDB2 stabilization and recruitment of ALC1. ACTA ACUST UNITED AC 2012; 199:235-49. [PMID: 23045548 PMCID: PMC3471223 DOI: 10.1083/jcb.201112132] [Citation(s) in RCA: 179] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PARP1-mediated poly(ADP-ribosyl)ation of DDB2 prolongs its occupation on UV-damaged chromatin and promotes the recruitment of the chromatin remodeler ALC1. The WD40-repeat protein DDB2 is essential for efficient recognition and subsequent removal of ultraviolet (UV)-induced DNA lesions by nucleotide excision repair (NER). However, how DDB2 promotes NER in chromatin is poorly understood. Here, we identify poly(ADP-ribose) polymerase 1 (PARP1) as a novel DDB2-associated factor. We demonstrate that DDB2 facilitated poly(ADP-ribosyl)ation of UV-damaged chromatin through the activity of PARP1, resulting in the recruitment of the chromatin-remodeling enzyme ALC1. Depletion of ALC1 rendered cells sensitive to UV and impaired repair of UV-induced DNA lesions. Additionally, DDB2 itself was targeted by poly(ADP-ribosyl)ation, resulting in increased protein stability and a prolonged chromatin retention time. Our in vitro and in vivo data support a model in which poly(ADP-ribosyl)ation of DDB2 suppresses DDB2 ubiquitylation and outline a molecular mechanism for PARP1-mediated regulation of NER through DDB2 stabilization and recruitment of the chromatin remodeler ALC1.
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Affiliation(s)
- Alex Pines
- Department of Toxicogenetics, Leiden University Medical Center, Leiden, Netherlands
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Schwertman P, Lagarou A, Dekkers DHW, Raams A, van der Hoek AC, Laffeber C, Hoeijmakers JHJ, Demmers JAA, Fousteri M, Vermeulen W, Marteijn JA. UV-sensitive syndrome protein UVSSA recruits USP7 to regulate transcription-coupled repair. Nat Genet 2012; 44:598-602. [PMID: 22466611 DOI: 10.1038/ng.2230] [Citation(s) in RCA: 180] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 02/29/2012] [Indexed: 02/07/2023]
Abstract
Transcription-coupled nucleotide-excision repair (TC-NER) is a subpathway of NER that efficiently removes the highly toxic RNA polymerase II blocking lesions in DNA. Defective TC-NER gives rise to the human disorders Cockayne syndrome and UV-sensitive syndrome (UV(S)S). NER initiating factors are known to be regulated by ubiquitination. Using a SILAC-based proteomic approach, we identified UVSSA (formerly known as KIAA1530) as part of a UV-induced ubiquitinated protein complex. Knockdown of UVSSA resulted in TC-NER deficiency. UVSSA was found to be the causative gene for UV(S)S, an unresolved NER deficiency disorder. The UVSSA protein interacts with elongating RNA polymerase II, localizes specifically to UV-induced lesions, resides in chromatin-associated TC-NER complexes and is implicated in stabilizing the TC-NER master organizing protein ERCC6 (also known as CSB) by delivering the deubiquitinating enzyme USP7 to TC-NER complexes. Together, these findings indicate that UVSSA-USP7–mediated stabilization of ERCC6 represents a critical regulatory mechanism of TC-NER in restoring gene expression.
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Affiliation(s)
- Petra Schwertman
- Department of Genetics and Netherlands Proteomics Centre, Centre for Biomedical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
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Lans H, Marteijn JA, Vermeulen W. ATP-dependent chromatin remodeling in the DNA-damage response. Epigenetics Chromatin 2012; 5:4. [PMID: 22289628 PMCID: PMC3275488 DOI: 10.1186/1756-8935-5-4] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 01/30/2012] [Indexed: 12/31/2022] Open
Abstract
The integrity of DNA is continuously challenged by metabolism-derived and environmental genotoxic agents that cause a variety of DNA lesions, including base alterations and breaks. DNA damage interferes with vital processes such as transcription and replication, and if not repaired properly, can ultimately lead to premature aging and cancer. Multiple DNA pathways signaling for DNA repair and DNA damage collectively safeguard the integrity of DNA. Chromatin plays a pivotal role in regulating DNA-associated processes, and is itself subject to regulation by the DNA-damage response. Chromatin influences access to DNA, and often serves as a docking or signaling site for repair and signaling proteins. Its structure can be adapted by post-translational histone modifications and nucleosome remodeling, catalyzed by the activity of ATP-dependent chromatin-remodeling complexes. In recent years, accumulating evidence has suggested that ATP-dependent chromatin-remodeling complexes play important, although poorly characterized, roles in facilitating the effectiveness of the DNA-damage response. In this review, we summarize the current knowledge on the involvement of ATP-dependent chromatin remodeling in three major DNA repair pathways: nucleotide excision repair, homologous recombination, and non-homologous end-joining. This shows that a surprisingly large number of different remodeling complexes display pleiotropic functions during different stages of the DNA-damage response. Moreover, several complexes seem to have multiple functions, and are implicated in various mechanistically distinct repair pathways.
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Affiliation(s)
- Hannes Lans
- Department of Genetics, Medical Genetics Center, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands.
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Marteijn JA, Bekker-Jensen S, Mailand N, Lans H, Schwertman P, Gourdin AM, Dantuma NP, Lukas J, Vermeulen W. Nucleotide excision repair-induced H2A ubiquitination is dependent on MDC1 and RNF8 and reveals a universal DNA damage response. ACTA ACUST UNITED AC 2009; 186:835-47. [PMID: 19797077 PMCID: PMC2753161 DOI: 10.1083/jcb.200902150] [Citation(s) in RCA: 148] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The epigenetic mark indicative of DNA UV damage or double-strand breaks is achieved via a common pathway regardless of the cause of damage. Chromatin modifications are an important component of the of DNA damage response (DDR) network that safeguard genomic integrity. Recently, we demonstrated nucleotide excision repair (NER)–dependent histone H2A ubiquitination at sites of ultraviolet (UV)-induced DNA damage. In this study, we show a sustained H2A ubiquitination at damaged DNA, which requires dynamic ubiquitination by Ubc13 and RNF8. Depletion of these enzymes causes UV hypersensitivity without affecting NER, which is indicative of a function for Ubc13 and RNF8 in the downstream UV–DDR. RNF8 is targeted to damaged DNA through an interaction with the double-strand break (DSB)–DDR scaffold protein MDC1, establishing a novel function for MDC1. RNF8 is recruited to sites of UV damage in a cell cycle–independent fashion that requires NER-generated, single-stranded repair intermediates and ataxia telangiectasia–mutated and Rad3-related protein. Our results reveal a conserved pathway of DNA damage–induced H2A ubiquitination for both DSBs and UV lesions, including the recruitment of 53BP1 and Brca1. Although both lesions are processed by independent repair pathways and trigger signaling responses by distinct kinases, they eventually generate the same epigenetic mark, possibly functioning in DNA damage signal amplification.
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Affiliation(s)
- Jurgen A Marteijn
- Department of Genetics, Center for Biomedical Genetics, Erasmus Medical Center, 3015 GE Rotterdam, Netherlands
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Nicassio F, Corrado N, Vissers JHA, Areces LB, Bergink S, Marteijn JA, Geverts B, Houtsmuller AB, Vermeulen W, Di Fiore PP, Citterio E. Human USP3 is a chromatin modifier required for S phase progression and genome stability. Curr Biol 2007; 17:1972-7. [PMID: 17980597 DOI: 10.1016/j.cub.2007.10.034] [Citation(s) in RCA: 218] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2006] [Revised: 10/03/2007] [Accepted: 10/04/2007] [Indexed: 11/16/2022]
Abstract
Protein ubiquitination is critical for numerous cellular functions, including DNA damage response pathways. Histones are the most abundant monoubiquitin conjugates in mammalian cells; however, the regulation and the function of monoubiquitinated H2A (uH2A) and H2B (uH2B) remain poorly understood. In particular, little is known about mammalian deubiquitinating enzymes (DUBs) that catalyze the removal of ubiquitin from uH2A/uH2B. Here we identify the ubiquitin-specific protease 3 USP3 as a deubiquitinating enzyme for uH2A and uH2B. USP3 dynamically associates with chromatin and deubiquitinates H2A/H2B in vivo. The ZnF-UBP domain of USP3 mediates uH2A-USP3 interaction. Functional ablation of USP3 by RNAi leads to delay of S phase progression and to accumulation of DNA breaks, with ensuing activation of DNA damage checkpoint pathways. In addition, we show that in response to ionizing radiation, (1) uH2A redistributes and colocalizes in gamma-H2AX DNA repair foci and (2) USP3 is required for full deubiquitination of ubiquitin-conjugates/uH2A and gamma-H2AX dephosphorylation. Our studies identify USP3 as a novel regulator of H2A and H2B ubiquitination, highlight its role in preventing replication stress, and suggest its involvement in the response to DNA double-strand breaks. Together, our results implicate USP3 as a novel chromatin modifier in the maintenance of genome integrity.
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Affiliation(s)
- Francesco Nicassio
- IFOM, Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy
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