1
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Bahap Y, Kayhan G. A Cockayne-Syndrome-Like Phenotype with a Homozygous Truncating UVSSA Variant: Might This Be a New Cause? Mol Syndromol 2024; 15:324-327. [PMID: 39119453 PMCID: PMC11305656 DOI: 10.1159/000536420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 01/18/2024] [Indexed: 08/10/2024] Open
Abstract
Introduction UV-sensitive syndrome and Cockayne syndrome (CS) are rare autosomal recessive and transcription-coupled nucleotide excision repair disorders with different clinical manifestations, although some types are allelic. Case Presentation We report on a patient who passed away at 15 years old with a progeroid-like appearance, cachexia, hearing loss, and dental anomalies, which led us to the diagnosis of Cockayne-like progeroid syndromes. Our clinical exome sequencing including all the known genes of progeroid syndromes revealed a homozygous stop-gain variant in the UVSSA gene. Conclusion Although truncating variants in the UVSSA are known to cause UVsS3, their association with CS has not yet been defined. This case might be the first report of a CS-like phenotype caused by a defective UVSSA.
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Affiliation(s)
- Yusuf Bahap
- Medical Genetics Department, Gazi University Hospital, Ankara, Turkey
| | - Gulsum Kayhan
- Medical Genetics Department, Gazi University Hospital, Ankara, Turkey
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2
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Llerena Schiffmacher DA, Lee SH, Kliza KW, Theil AF, Akita M, Helfricht A, Bezstarosti K, Gonzalo-Hansen C, van Attikum H, Verlaan-de Vries M, Vertegaal ACO, Hoeijmakers JHJ, Marteijn JA, Lans H, Demmers JAA, Vermeulen M, Sixma TK, Ogi T, Vermeulen W, Pines A. The small CRL4 CSA ubiquitin ligase component DDA1 regulates transcription-coupled repair dynamics. Nat Commun 2024; 15:6374. [PMID: 39075067 PMCID: PMC11286758 DOI: 10.1038/s41467-024-50584-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 07/16/2024] [Indexed: 07/31/2024] Open
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 apply a single-step protein-complex isolation coupled to mass spectrometry analysis and identified DDA1 as a CSA interacting protein. Cryo-EM analysis shows that DDA1 is an integral component of the CRL4CSA complex. Functional analysis reveals 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 A Llerena Schiffmacher
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Shun-Hsiao Lee
- Division of Biochemistry and Oncode institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - 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
- 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 GD, Rotterdam, The Netherlands
| | - Masaki Akita
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
| | - Angela Helfricht
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Karel Bezstarosti
- Proteomics Center, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Camila Gonzalo-Hansen
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Oncode Institute, Erasmus University Medical Center, 3015 GD, 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 GD, 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, Oncode Institute, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Oncode 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
| | - Jeroen A A Demmers
- Proteomics Center, Erasmus University Medical Center, 3015 GD, 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
| | - Titia K Sixma
- Division of Biochemistry and Oncode institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, 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 GD, Rotterdam, The Netherlands.
| | - Alex Pines
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands.
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3
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Gonzalo-Hansen C, Steurer B, Janssens RC, Zhou D, van Sluis M, Lans H, Marteijn JA. Differential processing of RNA polymerase II at DNA damage correlates with transcription-coupled repair syndrome severity. Nucleic Acids Res 2024:gkae618. [PMID: 39021334 DOI: 10.1093/nar/gkae618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 06/25/2024] [Accepted: 07/10/2024] [Indexed: 07/20/2024] Open
Abstract
DNA damage severely impedes gene transcription by RNA polymerase II (Pol II), causing cellular dysfunction. Transcription-Coupled Nucleotide Excision Repair (TC-NER) specifically removes such transcription-blocking damage. TC-NER initiation relies on the CSB, CSA and UVSSA proteins; loss of any results in complete TC-NER deficiency. Strikingly, UVSSA deficiency results in UV-Sensitive Syndrome (UVSS), with mild cutaneous symptoms, while loss of CSA or CSB activity results in the severe Cockayne Syndrome (CS), characterized by neurodegeneration and premature aging. Thus far the underlying mechanism for these contrasting phenotypes remains unclear. Live-cell imaging approaches reveal that in TC-NER proficient cells, lesion-stalled Pol II is swiftly resolved, while in CSA and CSB knockout (KO) cells, elongating Pol II remains damage-bound, likely obstructing other DNA transacting processes and shielding the damage from alternative repair pathways. In contrast, in UVSSA KO cells, Pol II is cleared from the damage via VCP-mediated proteasomal degradation which is fully dependent on the CRL4CSA ubiquitin ligase activity. This Pol II degradation might provide access for alternative repair mechanisms, such as GG-NER, to remove the damage. Collectively, our data indicate that the inability to clear lesion-stalled Pol II from the chromatin, rather than TC-NER deficiency, causes the severe phenotypes observed in CS.
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Affiliation(s)
- Camila Gonzalo-Hansen
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Barbara Steurer
- 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
| | - Di Zhou
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marjolein van Sluis
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, 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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4
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Zhang X, Xu J, Hu J, Zhang S, Hao Y, Zhang D, Qian H, Wang D, Fu XD. Cockayne Syndrome Linked to Elevated R-Loops Induced by Stalled RNA Polymerase II during Transcription Elongation. Nat Commun 2024; 15:6031. [PMID: 39019869 PMCID: PMC11255242 DOI: 10.1038/s41467-024-50298-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/04/2024] [Indexed: 07/19/2024] Open
Abstract
Mutations in the Cockayne Syndrome group B (CSB) gene cause cancer in mice, but premature aging and severe neurodevelopmental defects in humans. CSB, a member of the SWI/SNF family of chromatin remodelers, plays diverse roles in regulating gene expression and transcription-coupled nucleotide excision repair (TC-NER); however, these functions do not explain the distinct phenotypic differences observed between CSB-deficient mice and humans. During investigating Cockayne Syndrome-associated genome instability, we uncover an intrinsic mechanism that involves elongating RNA polymerase II (RNAPII) undergoing transient pauses at internal T-runs where CSB is required to propel RNAPII forward. Consequently, CSB deficiency retards RNAPII elongation in these regions, and when coupled with G-rich sequences upstream, exacerbates genome instability by promoting R-loop formation. These R-loop prone motifs are notably abundant in relatively long genes related to neuronal functions in the human genome, but less prevalent in the mouse genome. These findings provide mechanistic insights into differential impacts of CSB deficiency on mice versus humans and suggest that the manifestation of the Cockayne Syndrome phenotype in humans results from the progressive evolution of mammalian genomes.
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Affiliation(s)
- Xuan Zhang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Jun Xu
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Genetics and Metabolism Department, The Children's Hospital, School of Medicine, Zhejiang University, National Clinical Research Center for Child Health, Hangzhou, China
- The Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jing Hu
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Sitao Zhang
- National Institute of Biological Sciences,7 Science Park Road, Beijing, China
| | - Yajing Hao
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- China National Center for Bioinformation, Beijing, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Dongyang Zhang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Hao Qian
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Dong Wang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
| | - Xiang-Dong Fu
- Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences and School of Medicine, Westlake University, Hangzhou, Zhejiang, China.
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5
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Luo Y, Li J, Li X, Lin H, Mao Z, Xu Z, Li S, Nie C, Zhou XA, Liao J, Xiong Y, Xu X, Wang J. The ARK2N-CK2 complex initiates transcription-coupled repair through enhancing the interaction of CSB with lesion-stalled RNAPII. Proc Natl Acad Sci U S A 2024; 121:e2404383121. [PMID: 38843184 PMCID: PMC11181095 DOI: 10.1073/pnas.2404383121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/08/2024] [Indexed: 06/19/2024] Open
Abstract
Transcription is extremely important for cellular processes but can be hindered by RNA polymerase II (RNAPII) pausing and stalling. Cockayne syndrome protein B (CSB) promotes the progression of paused RNAPII or initiates transcription-coupled nucleotide excision repair (TC-NER) to remove stalled RNAPII. However, the specific mechanism by which CSB initiates TC-NER upon damage remains unclear. In this study, we identified the indispensable role of the ARK2N-CK2 complex in the CSB-mediated initiation of TC-NER. The ARK2N-CK2 complex is recruited to damage sites through CSB and then phosphorylates CSB. Phosphorylation of CSB enhances its binding to stalled RNAPII, prolonging the association of CSB with chromatin and promoting CSA-mediated ubiquitination of stalled RNAPII. Consistent with this finding, Ark2n-/- mice exhibit a phenotype resembling Cockayne syndrome. These findings shed light on the pivotal role of the ARK2N-CK2 complex in governing the fate of RNAPII through CSB, bridging a critical gap necessary for initiating TC-NER.
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Affiliation(s)
- Yefei Luo
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Jia Li
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Xiaoman Li
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Haodong Lin
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Zuchao Mao
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Zhanzhan Xu
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Shiwei Li
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Chen Nie
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Xiao Albert Zhou
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Junwei Liao
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Yundong Xiong
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen518055, China
| | - Jiadong Wang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
- Department of Gastrointestinal Translational Research, Peking University Cancer Hospital, Beijing100142, China
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6
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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; 26:770-783. [PMID: 38600236 PMCID: PMC11098752 DOI: 10.1038/s41556-024-01394-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [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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7
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Hozhabrpour A, Mojbafan M, Palizban F, Vahidnezhad F, Talebi S, Amani M, Garshasbi M, Naghavi A, Khalesi R, Mansouri P, Sotoudeh S, Mahmoudi H, Varghaei A, Daneshpazhooh M, Karimi F, Zeinali S, Kalamati E, Uitto J, Youssefian L, Vahidnezhad H. DNA repair-related heritable photosensitivity syndromes: Mutation landscape in a multiethnic cohort of 17 multigenerational families with high degree of consanguinity. DNA Repair (Amst) 2024; 136:103633. [PMID: 38422792 DOI: 10.1016/j.dnarep.2024.103633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 12/30/2023] [Accepted: 01/19/2024] [Indexed: 03/02/2024]
Abstract
Inherited photosensitivity syndromes are a heterogeneous group of genetic skin disorders with tremendous phenotypic variability, characterized by photosensitivity and defective DNA repair, especially nucleotide excision repair. A cohort of 17 Iranian families with heritable photosensitivity syndromes was evaluated to identify their genetic defect. The patients' DNA was analyzed with either whole-exome sequencing or RNA sequencing (RNA-Seq). The interpretations of the genomic results were guided by genome-wide homozygosity mapping. Haplotype analysis was performed for cases with recurrent mutations. RNA-Seq, in addition to mutation detection, was also utilized to confirm the pathogenicity. Thirteen sequence variants, including six previously unreported pathogenic variants, were disclosed in 17 Iranian families, with XPC as the most common mutated gene in 10 families (59%). In one patient, RNA-Seq, as a first-tier diagnostic approach, revealed a non-canonical homozygous germline variant: XPC:c.413-9 T > A. The Sashimi plot showed skipping of exon 4 with dramatic XPC down-expression. Haplotype analysis of XPC:c.2251-1 G>C and XPC:1243 C>T in four families showed common haplotypes of 1.7 Mb and 2.6 Mb, respectively, denoting a founder effect. Lastly, two extremely rare cases were presented in this report: a homozygous UVSSA:c .1990 C>T was disclosed, and ERCC2-related cerebro-oculo-facio-skeletal (COFS) syndrome with an early childhood death. A direct comparison of our data with the results of previously reported cohorts demonstrates the international mutation landscape of DNA repair-related photosensitivity disorders, although population-specific differences were observed.
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Affiliation(s)
- Amir Hozhabrpour
- Department of Medical Genetics, School of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Marzieh Mojbafan
- Department of Medical Genetics, School of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Fahimeh Palizban
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Saeed Talebi
- Department of Medical Genetics, School of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Maliheh Amani
- Clinical Research Development Unit of Allameh Bohlool Gonabadi Hospital, Gonabad University of Medical Sciences, Gonabad, Iran; Department of Dermatology, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Anoosh Naghavi
- Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Raziyeh Khalesi
- Department of Medical Genetics, DeNA Laboratory, Tehran, Iran
| | - Parvin Mansouri
- Skin and Stem Cell Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Soheila Sotoudeh
- Department of Dermatology, Children's Medical Center, Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamidreza Mahmoudi
- Department of Dermatology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Aida Varghaei
- Department of Dermatology, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Maryam Daneshpazhooh
- Department of Dermatology, Autoimmune Bullous Diseases Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | | | | | - Elnaz Kalamati
- Department of Obstetrics and Gynecology, Imam Zaman Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jouni Uitto
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA; Department of Dermatology and Cutaneous Biology, Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - Leila Youssefian
- Department of Pathology and Laboratory Medicine, UCLA Clinical Genomics Center, University of California, Los Angeles, David Geffen School of Medicine, Los Angeles, CA, USA.
| | - Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA; Department of Dermatology and Cutaneous Biology, Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA; Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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8
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Guo NJ, Wang B, Zhang Y, Kang HQ, Nie HQ, Feng MK, Zhang XY, Zhao LJ, Wang N, Liu HM, Zheng YC, Li W, Gao Y. USP7 as an emerging therapeutic target: A key regulator of protein homeostasis. Int J Biol Macromol 2024; 263:130309. [PMID: 38382779 DOI: 10.1016/j.ijbiomac.2024.130309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/19/2024] [Accepted: 02/18/2024] [Indexed: 02/23/2024]
Abstract
Maintaining protein balance within a cell is essential for proper cellular function, and disruptions in the ubiquitin-proteasome pathway, which is responsible for degrading and recycling unnecessary or damaged proteins, can lead to various diseases. Deubiquitinating enzymes play a vital role in regulating protein homeostasis by removing ubiquitin chains from substrate proteins, thereby controlling important cellular processes, such as apoptosis and DNA repair. Among these enzymes, ubiquitin-specific protease 7 (USP7) is of particular interest. USP7 is a cysteine protease consisting of a TRAF region, catalytic region, and C-terminal ubiquitin-like (UBL) region, and it interacts with tumor suppressors, transcription factors, and other key proteins involved in cell cycle regulation and epigenetic control. Moreover, USP7 has been implicated in the pathogenesis and progression of various diseases, including cancer, inflammation, neurodegenerative conditions, and viral infections. Overall, characterizing the functions of USP7 is crucial for understanding the pathophysiology of diverse diseases and devising innovative therapeutic strategies. This article reviews the structure and function of USP7 and its complexes, its association with diseases, and its known inhibitors and thus represents a valuable resource for advancing USP7 inhibitor development and promoting potential future treatment options for a wide range of diseases.
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Affiliation(s)
- Ning-Jie Guo
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Henan Province, Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Bo Wang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Henan Province, Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Yu Zhang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Henan Province, Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Hui-Qin Kang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Henan Province, Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Hai-Qian Nie
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Henan Province, Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Meng-Kai Feng
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Henan Province, Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Xi-Ya Zhang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Henan Province, Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Li-Juan Zhao
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Henan Province, Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Ning Wang
- The School of Chinese Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Hong-Min Liu
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Henan Province, Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Yi-Chao Zheng
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Henan Province, Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China.
| | - Wen Li
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Henan Province, Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China.
| | - Ya Gao
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Henan Province, Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China.
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9
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Kokic G, Yakoub G, van den Heuvel D, Wondergem AP, van der Meer PJ, van der Weegen Y, Chernev A, Fianu I, Fokkens TJ, Lorenz S, Urlaub H, Cramer P, Luijsterburg MS. Structural basis for RNA polymerase II ubiquitylation and inactivation in transcription-coupled repair. Nat Struct Mol Biol 2024; 31:536-547. [PMID: 38316879 PMCID: PMC10948364 DOI: 10.1038/s41594-023-01207-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 12/21/2023] [Indexed: 02/07/2024]
Abstract
During transcription-coupled DNA repair (TCR), RNA polymerase II (Pol II) transitions from a transcriptionally active state to an arrested state that allows for removal of DNA lesions. This transition requires site-specific ubiquitylation of Pol II by the CRL4CSA ubiquitin ligase, a process that is facilitated by ELOF1 in an unknown way. Using cryogenic electron microscopy, biochemical assays and cell biology approaches, we found that ELOF1 serves as an adaptor to stably position UVSSA and CRL4CSA on arrested Pol II, leading to ligase neddylation and activation of Pol II ubiquitylation. In the presence of ELOF1, a transcription factor IIS (TFIIS)-like element in UVSSA gets ordered and extends through the Pol II pore, thus preventing reactivation of Pol II by TFIIS. Our results provide the structural basis for Pol II ubiquitylation and inactivation in TCR.
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Affiliation(s)
- Goran Kokic
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Division of Structural Biology and Protein Therapeutics, Odyssey Therapeutics GmbH, Frankfurt am Main, Germany
| | - George Yakoub
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Diana van den Heuvel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Annelotte P Wondergem
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Paula J van der Meer
- 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
| | - Aleksandar Chernev
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Isaac Fianu
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Thornton J Fokkens
- Ubiquitin Signaling Specificity, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Sonja Lorenz
- Ubiquitin Signaling Specificity, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Bioanalytics Group, University Medical Center Göttingen, Institute of Clinical Chemistry, Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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10
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Waters KL, Spratt DE. New Discoveries on Protein Recruitment and Regulation during the Early Stages of the DNA Damage Response Pathways. Int J Mol Sci 2024; 25:1676. [PMID: 38338953 PMCID: PMC10855619 DOI: 10.3390/ijms25031676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/26/2024] [Accepted: 01/28/2024] [Indexed: 02/12/2024] Open
Abstract
Maintaining genomic stability and properly repairing damaged DNA is essential to staying healthy and preserving cellular homeostasis. The five major pathways involved in repairing eukaryotic DNA include base excision repair (BER), nucleotide excision repair (NER), mismatch repair (MMR), non-homologous end joining (NHEJ), and homologous recombination (HR). When these pathways do not properly repair damaged DNA, genomic stability is compromised and can contribute to diseases such as cancer. It is essential that the causes of DNA damage and the consequent repair pathways are fully understood, yet the initial recruitment and regulation of DNA damage response proteins remains unclear. In this review, the causes of DNA damage, the various mechanisms of DNA damage repair, and the current research regarding the early steps of each major pathway were investigated.
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Affiliation(s)
| | - Donald E. Spratt
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main St., Worcester, MA 01610, USA;
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11
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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 REPORTS 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] [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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12
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Liebau RC, Waters C, Ahmed A, Soni RK, Gautier J. Transcription-Coupled Repair of DNA Interstrand Crosslinks by UVSSA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.10.538304. [PMID: 37214867 PMCID: PMC10197625 DOI: 10.1101/2023.05.10.538304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
DNA interstrand crosslinks (ICLs) are covalent bonds between bases on opposing strands of the DNA helix which prevent DNA melting and subsequent DNA replication or RNA transcription. Here, we show that Ultraviolet Stimulated Scaffold Protein A (UVSSA) participates in transcription-coupled repair of ICLs in human cells. Inactivation of UVSSA sensitizes human cells to ICL-inducing drugs, and delays ICL repair. UVSSA is required for transcription-coupled repair of a single ICL in a fluorescence-based reporter assay. UVSSA localizes to chromatin following ICL damage, and interacts with transcribing Pol II, CSA, CSB, and TFIIH. Specifically, UVSSA interaction with TFIIH is required for ICL repair. Finally, UVSSA expression positively correlates with ICL chemotherapy resistance in human cancer cell lines. Our data strongly suggest that transcription-coupled ICL repair (TC-ICR) is a bona fide ICL repair mechanism that contributes to crosslinker drug resistance independently of replication-coupled ICL repair.
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Affiliation(s)
- Rowyn C Liebau
- Institute for Cancer Genetics, Graduate School of Arts and Sciences, Columbia University, New York, NY, 10027, United States of America
| | - Crystal Waters
- Institute of Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, United States of America
- Agilent Technologies, La Jolla CA, 92037, United States of America
| | - Arooba Ahmed
- Institute of Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, United States of America
| | - Rajesh K Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, United States of America
| | - Jean Gautier
- Institute of Cancer Genetics, Columbia University Irving Medical Center, New York, NY 10032, United States of America
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13
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Theil AF, Häckes D, Lans H. TFIIH central activity in nucleotide excision repair to prevent disease. DNA Repair (Amst) 2023; 132:103568. [PMID: 37977600 DOI: 10.1016/j.dnarep.2023.103568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/22/2023] [Accepted: 09/03/2023] [Indexed: 11/19/2023]
Abstract
The heterodecameric transcription factor IIH (TFIIH) functions in multiple cellular processes, foremost in nucleotide excision repair (NER) and transcription initiation by RNA polymerase II. TFIIH is essential for life and hereditary mutations in TFIIH cause the devastating human syndromes xeroderma pigmentosum, Cockayne syndrome or trichothiodystrophy, or combinations of these. In NER, TFIIH binds to DNA after DNA damage is detected and, using its translocase and helicase subunits XPB and XPD, opens up the DNA and checks for the presence of DNA damage. This central activity leads to dual incision and removal of the DNA strand containing the damage, after which the resulting DNA gap is restored. In this review, we discuss new structural and mechanistic insights into the central function of TFIIH in NER. Moreover, we provide an elaborate overview of all currently known patients and diseases associated with inherited TFIIH mutations and describe how our understanding of TFIIH function in NER and transcription can explain the different disease features caused by TFIIH deficiency.
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Affiliation(s)
- Arjan F Theil
- Department of Molecular Genetics, Erasmus MC Cancer 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
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, the Netherlands.
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14
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Huang Y, Gu L, Li GM. Heat shock protein DNAJA2 regulates transcription-coupled repair by triggering CSB degradation via chaperone-mediated autophagy. Cell Discov 2023; 9:107. [PMID: 37907457 PMCID: PMC10618452 DOI: 10.1038/s41421-023-00601-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/01/2023] [Indexed: 11/02/2023] Open
Abstract
Transcription-coupled nucleotide excision repair (TC-NER) is an important genome maintenance system that preferentially removes DNA lesions on the transcribed strand of actively transcribed genes, including non-coding genes. TC-NER involves lesion recognition by the initiation complex consisting of RNA polymerase II (Pol II) and Cockayne syndrome group B (CSB), followed by NER-catalyzed lesion removal. However, the efficient lesion removal requires the initiation complex to yield the right of way to the excision machinery, and how this occurs in a timely manner is unknown. Here we show that heat shock protein DNAJA2 facilitates the HSC70 chaperone-mediated autophagy (CMA) to degrade CSB during TC-NER. DNAJA2 interacts with and enables HSC70 to recognize sumoylated CSB. This triggers the removal of both CSB and Pol II from the lesion site in a manner dependent on lysosome receptor LAMP2A. Defects in DNAJA2, HSC70 or LAMP2A abolish CSB degradation and block TC-NER. Our findings discover DNAJA2-mediated CMA as a critical regulator of TC-NER, implicating the DNAJA2-HSC70-CMA axis factors in genome maintenance.
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Affiliation(s)
- Yaping Huang
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Liya Gu
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guo-Min Li
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Chinese Institutes for Medical Research, Beijing, China.
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15
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Llerena Schiffmacher DA, Kliza KW, Theil AF, Kremers GJ, Demmers JAA, Ogi T, Vermeulen M, Vermeulen W, Pines A. Live cell transcription-coupled nucleotide excision repair dynamics revisited. DNA Repair (Amst) 2023; 130:103566. [PMID: 37716192 DOI: 10.1016/j.dnarep.2023.103566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/23/2023] [Accepted: 09/03/2023] [Indexed: 09/18/2023]
Abstract
Transcription-blocking lesions are specifically targeted by transcription-coupled nucleotide excision repair (TC-NER), which prevents DNA damage-induced cellular toxicity and maintains proper transcriptional processes. TC-NER is initiated by the stalling of RNA polymerase II (RNAPII), which triggers the assembly of TC-NER-specific proteins, namely CSB, CSA and UVSSA, which collectively control and drive TC-NER progression. Previous research has revealed molecular functions for these proteins, however, exact mechanisms governing the initiation and regulation of TC-NER, particularly at low UV doses have remained elusive, partly due to technical constraints. In this study, we employ knock-in cell lines designed to target the endogenous CSB gene locus with mClover, a GFP variant. Through live cell imaging, we uncover the intricate molecular dynamics of CSB in response to physiologically relevant UV doses. We showed that the DNA damage-induced association of CSB with chromatin is tightly regulated by the CSA-containing ubiquitin-ligase CRL complex (CRL4CSA). Combining the CSB-mClover knock-in cell line with SILAC-based GFP-mediated complex isolation and mass-spectrometry-based proteomics, revealed novel putative CSB interactors as well as discernible variations in complex composition during distinct stages of TC-NER progression. Our work not only provides molecular insight into TC-NER, but also illustrates the versatility of endogenously tagging fluorescent and affinity tags.
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Affiliation(s)
- Diana A Llerena Schiffmacher
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Dr Molewaterplein 40, Rotterdam 3015 GD, the Netherlands
| | - Katarzyna W Kliza
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, Geert Grooteplein Zuid 28, Nijmegen 6525 GA, the Netherlands
| | - Arjan F Theil
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Dr Molewaterplein 40, Rotterdam 3015 GD, the Netherlands
| | - Gert-Jan Kremers
- Optical Imaging Centre, Erasmus University Medical Center, Dr Molewaterplein 40, Rotterdam 3015 GD, the Netherlands
| | - Jeroen A A Demmers
- Proteomics Center, Erasmus University Medical Center, Dr Molewaterplein 40, Rotterdam 3015 GD, the Netherland
| | - Tomoo Ogi
- Department of Human Genetics and Molecular Biology, Graduate School of Medicine, Nagoya University, Nagoya, Japan; Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, Geert Grooteplein Zuid 28, Nijmegen 6525 GA, the Netherlands; Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Dr Molewaterplein 40, Rotterdam 3015 GD, the Netherlands.
| | - Alex Pines
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Dr Molewaterplein 40, Rotterdam 3015 GD, the Netherlands.
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16
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Wang J, Muste Sadurni M, Saponaro M. RNAPII response to transcription-blocking DNA lesions in mammalian cells. FEBS J 2023; 290:4382-4394. [PMID: 35731652 PMCID: PMC10952651 DOI: 10.1111/febs.16561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 05/15/2022] [Accepted: 06/21/2022] [Indexed: 09/21/2023]
Abstract
RNA polymerase II moves along genes to decode genetic information stored in the mammalian genome into messenger RNA and different forms of non-coding RNA. However, the transcription process is frequently challenged by DNA lesions caused by exogenous and endogenous insults, among which helix-distorting DNA lesions and double-stranded DNA breaks are particularly harmful for cell survival. In response to such DNA damage, RNA polymerase II transcription is regulated both locally and globally by multi-layer mechanisms, whereas transcription-blocking lesions are repaired before transcription can recover. Failure in DNA damage repair will cause genome instability and cell death. Although recent studies have expanded our understanding of RNA polymerase II regulation confronting DNA lesions, it is still not always clear what the direct contribution of RNA polymerase II is in the DNA damage repair processes. In this review, we focus on how RNA polymerase II and transcription are both repressed by transcription stalling lesions such as DNA-adducts and double strand breaks, as well as how they are actively regulated to support the cellular response to DNA damage and favour the repair of lesions.
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Affiliation(s)
- Jianming Wang
- Transcription Associated Genome Instability Laboratory, Institute of Cancer and Genomic SciencesUniversity of BirminghamUK
| | - Martina Muste Sadurni
- Transcription Associated Genome Instability Laboratory, Institute of Cancer and Genomic SciencesUniversity of BirminghamUK
| | - Marco Saponaro
- Transcription Associated Genome Instability Laboratory, Institute of Cancer and Genomic SciencesUniversity of BirminghamUK
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17
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Mistry H, Kumari S, Aswal VK, Gupta GD. Structural characterization of transcription-coupled repair protein UVSSA and its interaction with TFIIH protein. Int J Biol Macromol 2023; 247:125792. [PMID: 37442507 DOI: 10.1016/j.ijbiomac.2023.125792] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/29/2023] [Accepted: 07/09/2023] [Indexed: 07/15/2023]
Abstract
UV-stimulated scaffold protein A (UVSSA) is a key protein in the Transcription-Coupled Nucleotide Excision Repair (TC-NER) pathway. UVSSA, an intrinsically disordered protein, interacts with multiple members of the pathway, tethering them into the complex. Several studies have reported that UVSSA recruits Transcription Factor IIH (TFIIH) via direct interaction, following which CSB is degraded and the lesion recognition TC-NER complex dissociates from the damage site to facilitate the DNA repair. Structural insights into these events remain largely unknown. Herein, we have investigated the interaction of human UVSSA with the Pleckstrin-Homology-domain of p62 subunit of TFIIH (p62-PHD) using biophysical techniques. We observed that UVSSA forms a stable complex with the p62-PHD in vitro. Small-angle scattering measurements using X-rays and neutrons revealed a significant change in pair-distance distribution function for UVSSA662/p62-PHD complex compared to UVSSA alone. Additionally, a significant decrease was observed in the radius of gyration of the complex. Our findings suggest that TFIIH binding to UVSSA causes significant conformational changes in UVSSA. We hypothesize that these conformational changes play an important role in the dissociation of the lesion recognition TC-NER complex.
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Affiliation(s)
- Hiral Mistry
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
| | - Shweta Kumari
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
| | - Vinod K Aswal
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
| | - Gagan D Gupta
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India.
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18
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Shen J, Lin X, Dai F, Chen G, Lin H, Fang B, Liu H. Ubiquitin-specific peptidases: Players in bone metabolism. Cell Prolif 2023:e13444. [PMID: 36883930 PMCID: PMC10392067 DOI: 10.1111/cpr.13444] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/22/2023] [Accepted: 02/28/2023] [Indexed: 03/09/2023] Open
Abstract
Osteoporosis is an ageing-related disease, that has become a major public health problem and its pathogenesis has not yet been fully elucidated. Substantial evidence suggests a strong link between overall age-related disease progression and epigenetic modifications throughout the life cycle. As an important epigenetic modification, ubiquitination is extensively involved in various physiological processes, and its role in bone metabolism has attracted increasing attention. Ubiquitination can be reversed by deubiquitinases, which counteract protein ubiquitination degradation. As the largest and most structurally diverse cysteinase family of deubiquitinating enzymes, ubiquitin-specific proteases (USPs), comprising the largest and most structurally diverse cysteine kinase family of deubiquitinating enzymes, have been found to be important players in maintaining the balance between bone formation and resorption. The aim of this review is to explore recent findings highlighting the regulatory functions of USPs in bone metabolism and provide insight into the molecular mechanisms governing their actions during bone loss. An in-deep understanding of USPs-mediated regulation of bone formation and bone resorption will provide a scientific rationale for the discovery and development of novel USP-targeted therapeutic strategies for osteoporosis.
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Affiliation(s)
- Jianlin Shen
- Department of Orthopaedics, Affiliated Hospital of Putian University, Putian, China
| | - Xiaoning Lin
- Department of Orthopaedics, Affiliated Hospital of Putian University, Putian, China
| | - Feifei Dai
- School of Medicine, Putian Universtiy, Putian, China
| | - Guoli Chen
- Department of Orthopaedics, Affiliated Hospital of Putian University, Putian, China
| | - Haibin Lin
- Department of Orthopaedics, Affiliated Hospital of Putian University, Putian, China
| | - Bangjiang Fang
- Department of Emergency, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Emergency and Critical Care Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Huan Liu
- Department of Orthopaedics, Affiliated Hospital of Putian University, Putian, China
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19
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Mistry H, Gupta GD. Transcription coupled DNA repair protein UVSSA binds to DNA and RNA: Mapping of nucleic acid interaction sites on human UVSSA. Arch Biochem Biophys 2023; 735:109515. [PMID: 36623745 DOI: 10.1016/j.abb.2023.109515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/09/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023]
Abstract
Transcription-coupled repair (TCR) is a dedicated pathway for the preferential repair of bulky transcription-blocking DNA lesions. These lesions stall the elongating RNA-polymerase II (RNAPII) triggering the recruitment of TCR proteins at the damaged site. UV-stimulated scaffold protein A (UVSSA) is a recently identified cofactor which is involved in stabilization of the TCR complex, recruitment of DNA-repair machinery and removal/restoration of RNAPII from the lesion site. Mutations in UVSSA render the cells TCR-deficient and have been linked to UV-sensitive syndrome. Human UVSSA is a 709-residue long protein with two short conserved domains; an N-terminal (residues 1-150) and a C-terminal (residues 495-605) domain, while the rest of the protein is predicted to be intrinsically disordered. The protein is well conserved in eukaryotes, however; none of its homologs have been characterized yet. Here, we have purified the recombinant human UVSSA and have characterized it using bioinformatics, biophysical and biochemical techniques. Using EMSA, SPR and fluorescence-based methods, we have shown that human UVSSA interacts with DNA and RNA. Furthermore, we have mapped the nucleic acid binding regions using several recombinant protein fragments containing either the N-terminal or the C-terminal domains. Our data indicate that UVSSA possesses at least two nucleic acid binding regions; the N-terminal domain and a C-terminal tail region (residues 606-662). These regions, far apart in sequence space, are predicted to be in close proximity in structure-space suggesting a coherent interaction with target DNA/RNA. The study may provide functional clues about the novel family of UVSSA proteins.
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Affiliation(s)
- Hiral Mistry
- Radiation Biology & Health Science Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
| | - Gagan Deep Gupta
- Radiation Biology & Health Science Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India.
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20
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Okuda M, Tsunaka Y, Nishimura Y. Dynamic structures of intrinsically disordered proteins related to the general transcription factor TFIIH, nucleosomes, and histone chaperones. Biophys Rev 2022; 14:1449-1472. [PMID: 36659983 PMCID: PMC9842849 DOI: 10.1007/s12551-022-01014-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/06/2022] [Indexed: 11/19/2022] Open
Abstract
Advances in structural analysis by cryogenic electron microscopy (cryo-EM) and X-ray crystallography have revealed the tertiary structures of various chromatin-related proteins, including transcription factors, RNA polymerases, nucleosomes, and histone chaperones; however, the dynamic structures of intrinsically disordered regions (IDRs) in these proteins remain elusive. Recent studies using nuclear magnetic resonance (NMR), together with molecular dynamics (MD) simulations, are beginning to reveal dynamic structures of the general transcription factor TFIIH complexed with target proteins including the general transcription factor TFIIE, the tumor suppressor p53, the cell cycle protein DP1, the DNA repair factors XPC and UVSSA, and three RNA polymerases, in addition to the dynamics of histone tails in nucleosomes and histone chaperones. In complexes of TFIIH, the PH domain of the p62 subunit binds to an acidic string formed by the IDR in TFIIE, p53, XPC, UVSSA, DP1, and the RPB6 subunit of three RNA polymerases by a common interaction mode, namely extended string-like binding of the IDR on the positively charged surface of the PH domain. In the nucleosome, the dynamic conformations of the N-tails of histones H2A and H2B are correlated, while the dynamic conformations of the N-tails of H3 and H4 form a histone tail network dependent on their modifications and linker DNA. The acidic IDRs of the histone chaperones of FACT and NAP1 play important roles in regulating the accessibility to histone proteins in the nucleosome.
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Affiliation(s)
- Masahiko Okuda
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-Cho, Tsurumi-Ku, Yokohama, 230-0045 Japan
| | - Yasuo Tsunaka
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-Cho, Tsurumi-Ku, Yokohama, 230-0045 Japan
| | - Yoshifumi Nishimura
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-Cho, Tsurumi-Ku, Yokohama, 230-0045 Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, 739-8528 Japan
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21
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Muñoz JC, Beckerman I, Choudhary R, Bouvier LA, Muñoz MJ. DNA Damage-Induced RNAPII Degradation and Its Consequences in Gene Expression. Genes (Basel) 2022; 13:1951. [PMID: 36360188 PMCID: PMC9689695 DOI: 10.3390/genes13111951] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/13/2022] [Accepted: 10/20/2022] [Indexed: 08/27/2023] Open
Abstract
RPB1, the major and catalytic subunit of human RNA Polymerase II (RNAPII), is specifically degraded by the ubiquitin-proteasome system upon induction of DNA damage by different agents, such as ultraviolet (UV) light. The "last resort" model of RNAPII degradation states that a persistently stalled RNAPII is degraded at the site of the DNA lesion in order to facilitate access to Nucleotide Excision Repair (NER) factors, thereby promoting repair in template strands of active genes. Recent identification and mutation of the lysine residue involved in RPB1 ubiquitylation and degradation unveiled the relevance of RNAPII levels in the control of gene expression. Inhibition of RNAPII degradation after UV light exposure enhanced RNAPII loading onto chromatin, demonstrating that the mere concentration of RNAPII shapes the gene expression response. In this review, we discuss the role of RNAPII ubiquitylation in NER-dependent repair, recent advances in RPB1 degradation mechanisms and its consequences in gene expression under stress, both in normal and repair deficient cells.
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Affiliation(s)
- Juan Cristobal Muñoz
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Ciudad Universitaria, Buenos Aires C1428EHA, Argentina
| | - Inés Beckerman
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Ciudad Universitaria, Buenos Aires C1428EHA, Argentina
| | - Ramveer Choudhary
- IFOM ETS—The AIRC Institute of Molecular Oncology, Via Adamello, 16, 20139 Milan, Italy
| | - León Alberto Bouvier
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Ciudad Universitaria, Buenos Aires C1428EHA, Argentina
| | - Manuel J. Muñoz
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Ciudad Universitaria, Buenos Aires C1428EHA, Argentina
- IFOM ETS—The AIRC Institute of Molecular Oncology, Via Adamello, 16, 20139 Milan, Italy
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires C1428EHA, Argentina
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22
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Natural Killer cells demonstrate distinct eQTL and transcriptome-wide disease associations, highlighting their role in autoimmunity. Nat Commun 2022; 13:4073. [PMID: 35835762 PMCID: PMC9283523 DOI: 10.1038/s41467-022-31626-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/24/2022] [Indexed: 12/13/2022] Open
Abstract
Natural Killer cells are innate lymphocytes with central roles in immunosurveillance and are implicated in autoimmune pathogenesis. The degree to which regulatory variants affect Natural Killer cell gene expression is poorly understood. Here we perform expression quantitative trait locus mapping of negatively selected Natural Killer cells from a population of healthy Europeans (n = 245). We find a significant subset of genes demonstrate expression quantitative trait loci specific to Natural Killer cells and these are highly informative of human disease, in particular autoimmunity. A Natural Killer cell transcriptome-wide association study across five common autoimmune diseases identifies further novel associations at 27 genes. In addition to these cis observations, we find novel master-regulatory regions impacting expression of trans gene networks at regions including 19q13.4, the Killer cell Immunoglobulin-like Receptor region, GNLY, MC1R and UVSSA. Our findings provide new insights into the unique biology of Natural Killer cells, demonstrating markedly different expression quantitative trait loci from other immune cells, with implications for disease mechanisms. Natural Killer cells are key mediators of anti-tumour immunosurveillance and anti-viral immunity. Here, the authors map regulatory genetic variation in primary Natural Killer cells, providing new insights into their role in human health and disease.
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23
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Li X, Cao G, Liu X, Tang TS, Guo C, Liu H. Polymerases and DNA Repair in Neurons: Implications in Neuronal Survival and Neurodegenerative Diseases. Front Cell Neurosci 2022; 16:852002. [PMID: 35846567 PMCID: PMC9279898 DOI: 10.3389/fncel.2022.852002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/23/2022] [Indexed: 12/22/2022] Open
Abstract
Most of the neurodegenerative diseases and aging are associated with reactive oxygen species (ROS) or other intracellular damaging agents that challenge the genome integrity of the neurons. As most of the mature neurons stay in G0/G1 phase, replication-uncoupled DNA repair pathways including BER, NER, SSBR, and NHEJ, are pivotal, efficient, and economic mechanisms to maintain genomic stability without reactivating cell cycle. In these progresses, polymerases are prominent, not only because they are responsible for both sensing and repairing damages, but also for their more diversified roles depending on the cell cycle phase and damage types. In this review, we summarized recent knowledge on the structural and biochemical properties of distinct polymerases, including DNA and RNA polymerases, which are known to be expressed and active in nervous system; the biological relevance of these polymerases and their interactors with neuronal degeneration would be most graphically illustrated by the neurological abnormalities observed in patients with hereditary diseases associated with defects in DNA repair; furthermore, the vicious cycle of the trinucleotide repeat (TNR) and impaired DNA repair pathway is also discussed. Unraveling the mechanisms and contextual basis of the role of the polymerases in DNA damage response and repair will promote our understanding about how long-lived postmitotic cells cope with DNA lesions, and why disrupted DNA repair contributes to disease origin, despite the diversity of mutations in genes. This knowledge may lead to new insight into the development of targeted intervention for neurodegenerative diseases.
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Affiliation(s)
- Xiaoling Li
- Nano-Biotechnology Key Lab of Hebei Province, Yanshan University, Qinhuangdao, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
- Xiaoling Li
| | - Guanghui Cao
- Nano-Biotechnology Key Lab of Hebei Province, Yanshan University, Qinhuangdao, China
| | - Xiaokang Liu
- Nano-Biotechnology Key Lab of Hebei Province, Yanshan University, Qinhuangdao, China
| | - Tie-Shan Tang
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Caixia Guo
- Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
- *Correspondence: Caixia Guo
| | - Hongmei Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Hongmei Liu
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24
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Zhang X, Yin M, Hu J. Nucleotide excision repair: a versatile and smart toolkit. Acta Biochim Biophys Sin (Shanghai) 2022; 54:807-819. [PMID: 35975604 PMCID: PMC9828404 DOI: 10.3724/abbs.2022054] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Nucleotide excision repair (NER) is a major pathway to deal with bulky adducts induced by various environmental toxins in all cellular organisms. The two sub-pathways of NER, global genome repair (GGR) and transcription-coupled repair (TCR), differ in the damage recognition modes. In this review, we describe the molecular mechanism of NER in mammalian cells, especially the details of damage recognition steps in both sub-pathways. We also introduce new sequencing methods for genome-wide mapping of NER, as well as recent advances about NER in chromatin by these methods. Finally, the roles of NER factors in repairing oxidative damages and resolving R-loops are discussed.
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Affiliation(s)
| | | | - Jinchuan Hu
- Correspondence address. Tel: +86-21-54237702; E-mail:
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25
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Sakasai R, Wakasugi M, Matsui T, Sunatani Y, Saijo M, Matsunaga T, Iwabuchi K. Camptothecin compromises transcription recovery and cell survival against cisplatin and ultraviolet irradiation regardless of transcription-coupled nucleotide excision repair. DNA Repair (Amst) 2022; 113:103318. [PMID: 35325630 DOI: 10.1016/j.dnarep.2022.103318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 02/18/2022] [Accepted: 03/07/2022] [Indexed: 11/28/2022]
Abstract
DNA-damaging anti-cancer drugs are used clinically to induce cell death by causing DNA strand breaks or DNA replication stress. Camptothecin (CPT) and cisplatin are commonly used anti-cancer drugs, and their combined use enhances the anti-tumour effects. However, the mechanism underlying this enhanced effect has not been well studied. In this study, we analysed the combined effect of CPT and cisplatin or ultraviolet (UV) and found that CPT suppresses transcription recovery after UV damage and induces the disappearance of the Cockayne syndrome group B (CSB) protein, a transcription-coupled nucleotide excision repair (TC-NER) factor. This CPT-induced disappearance of CSB expression was suppressed by proteasome and transcription inhibitors. Moreover, CSB ubiquitination was detected after CPT treatment in a transcription-dependent manner, suggesting that the transcription stress caused by CPT induces CSB ubiquitination, resulting in CSB undetectability. However, Cockayne syndrome group A (CSA) and CUL4A were not involved in the CPT-induced CSB undetectability, suggesting that CSB ubiquitination caused by CPT is regulated differently from the UV response. However, cisplatin or UV sensitivity was enhanced by CPT even in CSB- or CSA-knockout cells. Furthermore, the excessive CSB expression, which suppressed CSB ubiquitination, did not cancel the combined effect of CPT. These results suggest that CPT blocks the repair of cisplatin or UV-induced DNA damage regardless of TC-NER status. CPT possibly compromised the alternative repair pathways other than TC-NER, leading to the suppression of transcription recovery and enhancement of cell killing.
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Affiliation(s)
- Ryo Sakasai
- Department of Biochemistry I, Kanazawa Medical University, Kahoku, Ishikawa 920-0293, Japan.
| | - Mitsuo Wakasugi
- Laboratory of Human Molecular Genetics, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Tadashi Matsui
- Department of Biochemistry I, Kanazawa Medical University, Kahoku, Ishikawa 920-0293, Japan
| | - Yumi Sunatani
- Department of Biochemistry I, Kanazawa Medical University, Kahoku, Ishikawa 920-0293, Japan
| | - Masafumi Saijo
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Tsukasa Matsunaga
- Laboratory of Human Molecular Genetics, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Kuniyoshi Iwabuchi
- Department of Biochemistry I, Kanazawa Medical University, Kahoku, Ishikawa 920-0293, Japan.
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26
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Abstract
The XPG/ERCC5 endonuclease was originally identified as the causative gene for Xeroderma Pigmentosum complementation group G. Ever since its discovery, in depth biochemical, structural and cell biological studies have provided detailed mechanistic insight into its function in excising DNA damage in nucleotide excision repair, together with the ERCC1–XPF endonuclease. In recent years, it has become evident that XPG has additional important roles in genome maintenance that are independent of its function in NER, as XPG has been implicated in protecting replication forks by promoting homologous recombination as well as in resolving R-loops. Here, we provide an overview of the multitasking of XPG in genome maintenance, by describing in detail how its activity in NER is regulated and the evidence that points to important functions outside of NER. Furthermore, we present the various disease phenotypes associated with inherited XPG deficiency and discuss current ideas on how XPG deficiency leads to these different types of disease.
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27
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Di Genova A, Nardocci G, Maldonado-Agurto R, Hodar C, Valdivieso C, Morales P, Gajardo F, Marina R, Gutiérrez RA, Orellana A, Cambiazo V, González M, Glavic A, Mendez MA, Maass A, Allende ML, Montecino MA. Genome sequencing and transcriptomic analysis of the Andean killifish Orestias ascotanensis reveals adaptation to high-altitude aquatic life. Genomics 2021; 114:305-315. [PMID: 34954349 DOI: 10.1016/j.ygeno.2021.12.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/26/2021] [Accepted: 12/17/2021] [Indexed: 12/21/2022]
Abstract
Orestias ascotanensis (Cyprinodontidae) is a teleost pupfish endemic to springs feeding into the Ascotan saltpan in the Chilean Altiplano (3,700 m.a.s.l.) and represents an opportunity to study adaptations to high-altitude aquatic environments. We have de novo assembled the genome of O. ascotanensis at high coverage. Comparative analysis of the O. ascotanensis genome showed an overall process of contraction, including loss of genes related to G-protein signaling, chemotaxis and signal transduction, while there was expansion of gene families associated with microtubule-based movement and protein ubiquitination. We identified 818 genes under positive selection, many of which are involved in DNA repair. Additionally, we identified novel and conserved microRNAs expressed in O. ascotanensis and its closely-related species, Orestias gloriae. Our analysis suggests that positive selection and expansion of genes that preserve genome stability are a potential adaptive mechanism to cope with the increased solar UV radiation to which high-altitude animals are exposed to.
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Affiliation(s)
- Alex Di Genova
- FONDAP Center for Genome Regulation, Santiago, Chile; Center for Mathematical Modeling, Department of Mathematical Engineering, Faculty of Physical and Mathematical Sciences, Universidad de Chile and IRL CNRS, 2807 Santiago, Chile
| | - Gino Nardocci
- FONDAP Center for Genome Regulation, Santiago, Chile; Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Rodrigo Maldonado-Agurto
- FONDAP Center for Genome Regulation, Santiago, Chile; Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Christian Hodar
- FONDAP Center for Genome Regulation, Santiago, Chile; Institute of Nutrition and Food Technology, Universidad de Chile, Santiago, Chile
| | - Camilo Valdivieso
- FONDAP Center for Genome Regulation, Santiago, Chile; Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | - Pamela Morales
- FONDAP Center for Genome Regulation, Santiago, Chile; Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | - Felipe Gajardo
- FONDAP Center for Genome Regulation, Santiago, Chile; Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | - Raquel Marina
- FONDAP Center for Genome Regulation, Santiago, Chile; Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Rodrigo A Gutiérrez
- FONDAP Center for Genome Regulation, Santiago, Chile; Department of Molecular Genetics and Microbiology, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Ariel Orellana
- FONDAP Center for Genome Regulation, Santiago, Chile; Center of Plant Biotechnology, Universidad Andres Bello, Santiago, Chile
| | - Veronica Cambiazo
- FONDAP Center for Genome Regulation, Santiago, Chile; Institute of Nutrition and Food Technology, Universidad de Chile, Santiago, Chile
| | - Mauricio González
- FONDAP Center for Genome Regulation, Santiago, Chile; Institute of Nutrition and Food Technology, Universidad de Chile, Santiago, Chile
| | - Alvaro Glavic
- FONDAP Center for Genome Regulation, Santiago, Chile; Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | - Marco A Mendez
- FONDAP Center for Genome Regulation, Santiago, Chile; Faculty of Sciences, Universidad de Chile, Santiago, Chile; Center of Applied Ecology and Sustainability (CAPES), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Chile; Institute of Ecology and Biodiversity, Chile
| | - Alejandro Maass
- FONDAP Center for Genome Regulation, Santiago, Chile; Center for Mathematical Modeling, Department of Mathematical Engineering, Faculty of Physical and Mathematical Sciences, Universidad de Chile and IRL CNRS, 2807 Santiago, Chile
| | - Miguel L Allende
- FONDAP Center for Genome Regulation, Santiago, Chile; Faculty of Sciences, Universidad de Chile, Santiago, Chile.
| | - Martin A Montecino
- FONDAP Center for Genome Regulation, Santiago, Chile; Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.
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28
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Zhou L, Ouyang T, Li M, Hong T, Mhs A, Meng W, Zhang N. Ubiquitin-Specific Peptidase 7: A Novel Deubiquitinase That Regulates Protein Homeostasis and Cancers. Front Oncol 2021; 11:784672. [PMID: 34869041 PMCID: PMC8640129 DOI: 10.3389/fonc.2021.784672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 10/26/2021] [Indexed: 12/23/2022] Open
Abstract
Ubiquitin-Specific Peptidase 7 (USP7), or herpes virus-associated protease (HAUSP), is the largest family of the deubiquitinating enzymes (DUBs). Recent studies have shown that USP7 plays a vital role in regulating various physiological and pathological processes. Dysregulation of these processes mediated by USP7 may contribute to many diseases, such as cancers. Moreover, USP7 with aberrant expression levels and abnormal activity are found in cancers. Therefore, given the association between USP7 and cancers, targeting USP7 could be considered as an attractive and potential therapeutic approach in cancer treatment. This review describes the functions of USP7 and the regulatory mechanisms of its expression and activity, aiming to emphasize the necessity of research on USP7, and provide a better understanding of USP7-related biological processes and cancer.
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Affiliation(s)
- Lin Zhou
- First Clinical Medical College, Nanchang University, Nanchang, China
| | - Taohui Ouyang
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Meihua Li
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Tao Hong
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Alriashy Mhs
- Department of Neurosurgery, Huashan Hospital of Fudan University, Shanghai, China
| | - Wei Meng
- Department of Neurosurgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Na Zhang
- Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang, China
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29
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Akinniyi OT, Reese JC. DEF1: Much more than an RNA polymerase degradation factor. DNA Repair (Amst) 2021; 107:103202. [PMID: 34419700 PMCID: PMC8879385 DOI: 10.1016/j.dnarep.2021.103202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/28/2021] [Accepted: 08/03/2021] [Indexed: 01/14/2023]
Abstract
Degradation Factor 1 was discovered 20 years ago as a yeast protein copurifying with Rad26, a helicase involved in transcription-coupled DNA repair. It was subsequently shown to control the ubiquitylation and destruction of the large subunit of DNA damage-arrested RNA Polymerase II. Since that time, much has been learned about Def1's role in polymerase destruction and new functions of the protein have been revealed. We now understand that Def1 is involved in more than just RNA polymerase II regulation. Most of its known functions are associated with maintaining chromosome and genomic integrity, but other exciting activities outside this realm have been suggested. Here we review this fascinating protein, describe its regulation and present a hypothesis that Def1 is a central coordinator of ubiquitin signaling pathways in cells.
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Affiliation(s)
- Oluwasegun T Akinniyi
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Joseph C Reese
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
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30
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Gaul L, Svejstrup JQ. Transcription-coupled repair and the transcriptional response to UV-Irradiation. DNA Repair (Amst) 2021; 107:103208. [PMID: 34416541 DOI: 10.1016/j.dnarep.2021.103208] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 02/07/2023]
Abstract
Lesions in genes that result in RNA polymerase II (RNAPII) stalling or arrest are particularly toxic as they are a focal point of genome instability and potently block further transcription of the affected gene. Thus, cells have evolved the transcription-coupled nucleotide excision repair (TC-NER) pathway to identify damage-stalled RNAPIIs, so that the lesion can be rapidly repaired and transcription can continue. However, despite the identification of several factors required for TC-NER, how RNAPII is remodelled, modified, removed, or whether this is even necessary for repair remains enigmatic, and theories are intensely contested. Recent studies have further detailed the cellular response to UV-induced ubiquitylation and degradation of RNAPII and its consequences for transcription and repair. These advances make it pertinent to revisit the TC-NER process in general and with specific discussion of the fate of RNAPII stalled at DNA lesions.
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Affiliation(s)
- Liam Gaul
- Department of Cellular and Molecular Medicine, Panum Institute, Blegdamsvej 3B, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Jesper Q Svejstrup
- Department of Cellular and Molecular Medicine, Panum Institute, Blegdamsvej 3B, University of Copenhagen, 2200, Copenhagen N, Denmark.
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31
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Abstract
Transcription-coupled DNA repair removes bulky DNA lesions from the genome1,2 and protects cells against ultraviolet (UV) irradiation3. Transcription-coupled DNA repair begins when RNA polymerase II (Pol II) stalls at a DNA lesion and recruits the Cockayne syndrome protein CSB, the E3 ubiquitin ligase, CRL4CSA and UV-stimulated scaffold protein A (UVSSA)3. Here we provide five high-resolution structures of Pol II transcription complexes containing human transcription-coupled DNA repair factors and the elongation factors PAF1 complex (PAF) and SPT6. Together with biochemical and published3,4 data, the structures provide a model for transcription–repair coupling. Stalling of Pol II at a DNA lesion triggers replacement of the elongation factor DSIF by CSB, which binds to PAF and moves upstream DNA to SPT6. The resulting elongation complex, ECTCR, uses the CSA-stimulated translocase activity of CSB to pull on upstream DNA and push Pol II forward. If the lesion cannot be bypassed, CRL4CSA spans over the Pol II clamp and ubiquitylates the RPB1 residue K1268, enabling recruitment of TFIIH to UVSSA and DNA repair. Conformational changes in CRL4CSA lead to ubiquitylation of CSB and to release of transcription-coupled DNA repair factors before transcription may continue over repaired DNA. The authors resolve the structure of five complexes containing RNA polymerase II and the CSA and CSB proteins, offering insight into how the repair of DNA lesions is coupled to transcription.
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Jia N, Guo C, Nakazawa Y, van den Heuvel D, Luijsterburg MS, Ogi T. Dealing with transcription-blocking DNA damage: Repair mechanisms, RNA polymerase II processing and human disorders. DNA Repair (Amst) 2021; 106:103192. [PMID: 34358806 DOI: 10.1016/j.dnarep.2021.103192] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/23/2021] [Accepted: 07/25/2021] [Indexed: 12/15/2022]
Abstract
Transcription-blocking DNA lesions (TBLs) in genomic DNA are triggered by a wide variety of DNA-damaging agents. Such lesions cause stalling of elongating RNA polymerase II (RNA Pol II) enzymes and fully block transcription when unresolved. The toxic impact of DNA damage on transcription progression is commonly referred to as transcription stress. In response to RNA Pol II stalling, cells activate and employ transcription-coupled repair (TCR) machineries to repair cytotoxic TBLs and resume transcription. Increasing evidence indicates that the modification and processing of stalled RNA Pol II is an integral component of the cellular response to and the repair of TBLs. If TCR pathways fail, the prolonged stalling of RNA Pol II will impede global replication and transcription as well as block the access of other DNA repair pathways that may act upon the TBL. Consequently, such prolonged stalling will trigger profound genome instability and devastating clinical features. In this review, we will discuss the mechanisms by which various types of TBLs are repaired by distinct TCR pathways and how RNA Pol II processing is regulated during these processes. We will also discuss the clinical consequences of transcription stress and genotype-phenotype correlations of related TCR-deficiency disorders.
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Affiliation(s)
- Nan Jia
- Department of Allergy and Clinical Immunology, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China; 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
| | - Chaowan Guo
- 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
| | - Yuka Nakazawa
- 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
| | - Diana van den Heuvel
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, 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.
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ELOF1 is a transcription-coupled DNA repair factor that directs RNA polymerase II ubiquitylation. Nat Cell Biol 2021; 23:595-607. [PMID: 34108663 PMCID: PMC8890769 DOI: 10.1038/s41556-021-00688-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 04/26/2021] [Indexed: 02/05/2023]
Abstract
Cells employ transcription-coupled repair (TCR) to eliminate transcription-blocking DNA lesions. DNA damage-induced binding of the TCR-specific repair factor CSB to RNA polymerase II (RNAPII) triggers RNAPII ubiquitylation of a single lysine (K1268) by the CRL4CSA ubiquitin ligase. How CRL4CSA is specifically directed towards K1268 is unknown. Here, we identify ELOF1 as the missing link that facilitates RNAPII ubiquitylation, a key signal for the assembly of downstream repair factors. This function requires its constitutive interaction with RNAPII close to K1268, revealing ELOF1 as a specificity factor that binds and positions CRL4CSA for optimal RNAPII ubiquitylation. Drug-genetic interaction screening also revealed a CSB-independent pathway in which ELOF1 prevents R-loops in active genes and protects cells against DNA replication stress. Our study offers key insights into the molecular mechanisms of TCR and provides a genetic framework of the interplay between transcriptional stress responses and DNA replication.
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34
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Chauhan AK, Sun Y, Zhu Q, Wani AA. Timely upstream events regulating nucleotide excision repair by ubiquitin-proteasome system: ubiquitin guides the way. DNA Repair (Amst) 2021; 103:103128. [PMID: 33991872 DOI: 10.1016/j.dnarep.2021.103128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/15/2021] [Accepted: 05/04/2021] [Indexed: 12/11/2022]
Abstract
The ubiquitin-proteasome system (UPS) plays crucial roles in regulation of multiple DNA repair pathways, including nucleotide excision repair (NER), which eliminates a broad variety of helix-distorting DNA lesions that can otherwise cause deleterious mutations and genomic instability. In mammalian NER, DNA damage sensors, DDB and XPC acting in global genomic NER (GG-NER), and, CSB and RNAPII acting in transcription-coupled NER (TC-NER) sub-pathways, undergo an array of post-translational ubiquitination at the DNA lesion sites. Accumulating evidence indicates that ubiquitination orchestrates the productive assembly of NER preincision complex by driving well-timed compositional changes in DNA damage-assembled sensor complexes. Conversely, the deubiquitination is also intimately involved in regulating the damage sensing aftermath, via removal of degradative ubiquitin modification on XPC and CSB to prevent their proteolysis for the factor recycling. This review summaries the relevant research efforts and latest findings in our understanding of ubiquitin-mediated regulation of NER and active participation by new regulators of NER, e.g., Cullin-Ring ubiquitin ligases (CRLs), ubiquitin-specific proteases (USPs) and ubiquitin-dependent segregase, valosin-containing protein (VCP)/p97. We project hypothetical step-by-step models in which VCP/p97-mediated timely extraction of damage sensors is integral to overall productive NER. The USPs and proteasome subtly counteract in fine-tuning the vital stability and function of NER damage sensors.
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Affiliation(s)
- Anil K Chauhan
- Department of Radiology, The Ohio State University, Columbus, OH, 43210, United States
| | - Yingming Sun
- Department of Radiology, The Ohio State University, Columbus, OH, 43210, United States
| | - Qianzheng Zhu
- Department of Radiology, The Ohio State University, Columbus, OH, 43210, United States.
| | - Altaf A Wani
- Department of Radiology, The Ohio State University, Columbus, OH, 43210, United States; Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, OH, 43210, United States; James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, OH, 43210, United States.
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35
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Tiwari V, Baptiste BA, Okur MN, Bohr VA. Current and emerging roles of Cockayne syndrome group B (CSB) protein. Nucleic Acids Res 2021; 49:2418-2434. [PMID: 33590097 DOI: 10.1093/nar/gkab085] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/26/2021] [Accepted: 02/01/2021] [Indexed: 12/11/2022] Open
Abstract
Cockayne syndrome (CS) is a segmental premature aging syndrome caused primarily by defects in the CSA or CSB genes. In addition to premature aging, CS patients typically exhibit microcephaly, progressive mental and sensorial retardation and cutaneous photosensitivity. Defects in the CSB gene were initially thought to primarily impair transcription-coupled nucleotide excision repair (TC-NER), predicting a relatively consistent phenotype among CS patients. In contrast, the phenotypes of CS patients are pleiotropic and variable. The latter is consistent with recent work that implicates CSB in multiple cellular systems and pathways, including DNA base excision repair, interstrand cross-link repair, transcription, chromatin remodeling, RNAPII processing, nucleolin regulation, rDNA transcription, redox homeostasis, and mitochondrial function. The discovery of additional functions for CSB could potentially explain the many clinical phenotypes of CSB patients. This review focuses on the diverse roles played by CSB in cellular pathways that enhance genome stability, providing insight into the molecular features of this complex premature aging disease.
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Affiliation(s)
- Vinod Tiwari
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Beverly A Baptiste
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Mustafa N Okur
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Vilhelm A Bohr
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
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van den Heuvel D, van der Weegen Y, Boer DEC, Ogi T, Luijsterburg MS. Transcription-Coupled DNA Repair: From Mechanism to Human Disorder. Trends Cell Biol 2021; 31:359-371. [PMID: 33685798 DOI: 10.1016/j.tcb.2021.02.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 12/13/2022]
Abstract
DNA lesions pose a major obstacle during gene transcription by RNA polymerase II (RNAPII) enzymes. The transcription-coupled DNA repair (TCR) pathway eliminates such DNA lesions. Inherited defects in TCR cause severe clinical syndromes, including Cockayne syndrome (CS). The molecular mechanism of TCR and the molecular origin of CS have long remained enigmatic. Here we explore new advances in our understanding of how TCR complexes assemble through cooperative interactions between repair factors stimulated by RNAPII ubiquitylation. Mounting evidence suggests that RNAPII ubiquitylation activates TCR complex assembly during repair and, in parallel, promotes processing and degradation of RNAPII to prevent prolonged stalling. The fate of stalled RNAPII is therefore emerging as a crucial link between TCR and associated human diseases.
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Affiliation(s)
- Diana van den Heuvel
- 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
| | - Daphne E C Boer
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan.
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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37
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Sato M, Liebau RC, Liu Z, Liu L, Rabadan R, Gautier J. The UVSSA complex alleviates MYC-driven transcription stress. J Cell Biol 2021; 220:e201807163. [PMID: 33404608 PMCID: PMC7791342 DOI: 10.1083/jcb.201807163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 10/05/2020] [Accepted: 11/25/2020] [Indexed: 01/05/2023] Open
Abstract
Cancer cells develop strong genetic dependencies, enabling survival under oncogenic stress. MYC is a key oncogene activated across most cancers, and identifying associated synthetic lethality or sickness can provide important clues about its activity and potential therapeutic strategies. On the basis of previously conducted genome-wide screenings in MCF10A cells expressing MYC fused to an estrogen receptor fragment, we identified UVSSA, a gene involved in transcription-coupled repair, whose knockdown or knockout decreased cell viability when combined with MYC expression. Synthetic sick interactions between MYC expression and UVSSA down-regulation correlated with ATM/CHK2 activation, suggesting increased genome instability. We show that the synthetic sick interaction is diminished by attenuating RNA polymerase II (RNAPII) activity; yet, it is independent of UV-induced damage repair, suggesting that UVSSA has a critical function in regulating RNAPII in the absence of exogenous DNA damage. Supporting this hypothesis, RNAPII ChIP-seq revealed that MYC-dependent increases in RNAPII promoter occupancy are reduced or abrogated by UVSSA knockdown, suggesting that UVSSA influences RNAPII dynamics during MYC-dependent transcription. Taken together, our data show that the UVSSA complex has a significant function in supporting MYC-dependent RNAPII dynamics and maintaining cell survival during MYC addiction. While the role of UVSSA in regulating RNAPII has been documented thus far only in the context of UV-induced DNA damage repair, we propose that its activity is also required to cope with transcriptional changes induced by oncogene activation.
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Affiliation(s)
- Mai Sato
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY
| | - Rowyn C. Liebau
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY
- Department of Biology, Columbia University, New York, NY
| | - Zhaoqi Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, China
- Program for Mathematical Genomics, Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY
| | - Lizhi Liu
- Department of Biology, Columbia University, New York, NY
| | - Raul Rabadan
- Program for Mathematical Genomics, Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY
| | - Jean Gautier
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY
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38
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Oh J, Xu J, Chong J, Wang D. Molecular basis of transcriptional pausing, stalling, and transcription-coupled repair initiation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194659. [PMID: 33271312 DOI: 10.1016/j.bbagrm.2020.194659] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/21/2020] [Accepted: 11/23/2020] [Indexed: 12/24/2022]
Abstract
Transcription elongation by RNA polymerase II (Pol II) is constantly challenged by numerous types of obstacles that lead to transcriptional pausing or stalling. These obstacles include DNA lesions, DNA epigenetic modifications, DNA binding proteins, and non-B form DNA structures. In particular, lesion-induced prolonged transcriptional blockage or stalling leads to genome instability, cellular dysfunction, and cell death. Transcription-coupled nucleotide excision repair (TC-NER) pathway is the first line of defense that detects and repairs these transcription-blocking DNA lesions. In this review, we will first summarize the recent research progress toward understanding the molecular basis of transcriptional pausing and stalling by different kinds of obstacles. We will then discuss new insights into Pol II-mediated lesion recognition and the roles of CSB in TC-NER.
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Affiliation(s)
- Juntaek Oh
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences; University of California, San Diego, La Jolla, CA 92093, United States
| | - Jun Xu
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences; University of California, San Diego, La Jolla, CA 92093, United States
| | - Jenny Chong
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences; University of California, San Diego, La Jolla, CA 92093, United States
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences; University of California, San Diego, La Jolla, CA 92093, United States; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, United States; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, United States.
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39
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Das S, Chandrasekaran AP, Jo KS, Ko NR, Oh SJ, Kim KS, Ramakrishna S. HAUSP stabilizes Cdc25A and protects cervical cancer cells from DNA damage response. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118835. [PMID: 32860838 DOI: 10.1016/j.bbamcr.2020.118835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 08/14/2020] [Accepted: 08/19/2020] [Indexed: 12/21/2022]
Abstract
Resistance to DNA-damaging agents is one of the main reasons for the low survival of cervical cancer patients. Previous reports have suggested that the Cdc25A oncoprotein significantly affects the level of susceptibility to DNA-damaging agents, but the molecular mechanism remains unclear. In this study, we used Western blot and flow cytometry analyses to demonstrate that the deubiquitinating enzyme HAUSP stabilizes Cdc25A protein level. Furthermore, in a co-immunoprecipitation assay, we found that HAUSP interacts with and deubiquitinates Cdc25A both exogenously and endogenously. HAUSP extends the half-life of the Cdc25A protein by circumventing turnover. HAUSP knockout in HeLa cells using the CRISPR/Cas9 system caused a significant delay in Cdc25A-mediated cell cycle progression, cell migration, and colony formation and attenuated tumor progression in a mouse xenograft model. Furthermore, HAUSP-mediated stabilization of the Cdc25A protein produced enhanced resistance to DNA-damaging agents. Overall, our study suggests that targeting Cdc25A and HAUSP could be a promising combinatorial approach to halt progression and minimize antineoplastic resistance in cervical cancer.
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Affiliation(s)
- Soumyadip Das
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea
| | | | - Ki-Sang Jo
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea
| | - Na Re Ko
- Biomedical Research Center, Asan Institute for Life Sciences, Seoul, South Korea; Department of Nuclear Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Seung Jun Oh
- Department of Nuclear Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea.
| | - Kye-Seong Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea; College of Medicine, Hanyang University, Seoul, South Korea.
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea; College of Medicine, Hanyang University, Seoul, South Korea.
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40
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Valles GJ, Bezsonova I, Woodgate R, Ashton NW. USP7 Is a Master Regulator of Genome Stability. Front Cell Dev Biol 2020; 8:717. [PMID: 32850836 PMCID: PMC7419626 DOI: 10.3389/fcell.2020.00717] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/13/2020] [Indexed: 12/25/2022] Open
Abstract
Genetic alterations, including DNA mutations and chromosomal abnormalities, are primary drivers of tumor formation and cancer progression. These alterations can endow cells with a selective growth advantage, enabling cancers to evade cell death, proliferation limits, and immune checkpoints, to metastasize throughout the body. Genetic alterations occur due to failures of the genome stability pathways. In many cancers, the rate of alteration is further accelerated by the deregulation of these processes. The deubiquitinating enzyme ubiquitin specific protease 7 (USP7) has recently emerged as a key regulator of ubiquitination in the genome stability pathways. USP7 is also deregulated in many cancer types, where deviances in USP7 protein levels are correlated with cancer progression. In this work, we review the increasingly evident role of USP7 in maintaining genome stability, the links between USP7 deregulation and cancer progression, as well as the rationale of targeting USP7 in cancer therapy.
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Affiliation(s)
- Gabrielle J Valles
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Irina Bezsonova
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Nicholas W Ashton
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
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41
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Vessoni AT, Guerra CCC, Kajitani GS, Nascimento LLS, Garcia CCM. Cockayne Syndrome: The many challenges and approaches to understand a multifaceted disease. Genet Mol Biol 2020; 43:e20190085. [PMID: 32453336 PMCID: PMC7250278 DOI: 10.1590/1678-4685-gmb-2019-0085] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 01/15/2020] [Indexed: 01/04/2023] Open
Abstract
The striking and complex phenotype of Cockayne syndrome (CS) patients combines progeria-like features with developmental deficits. Since the establishment of the in vitro culture of skin fibroblasts derived from patients with CS in the 1970s, significant progress has been made in the understanding of the genetic alterations associated with the disease and their impact on molecular, cellular, and organismal functions. In this review, we provide a historic perspective on the research into CS by revisiting seminal papers in this field. We highlighted the great contributions of several researchers in the last decades, ranging from the cloning and characterization of CS genes to the molecular dissection of their roles in DNA repair, transcription, redox processes and metabolism control. We also provide a detailed description of all pathological mutations in genes ERCC6 and ERCC8 reported to date and their impact on CS-related proteins. Finally, we review the contributions (and limitations) of many genetic animal models to the study of CS and how cutting-edge technologies, such as cell reprogramming and state-of-the-art genome editing, are helping us to address unanswered questions.
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Affiliation(s)
| | - Camila Chaves Coelho Guerra
- Universidade Federal de Ouro Preto, Instituto de Ciências Exatas e
Biológicas, Núcleo de Pesquisa em Ciências Biológicas & Departamento de Ciências
Biológicas, Ouro Preto, MG, Brazil
| | - Gustavo Satoru Kajitani
- Universidade Federal de Ouro Preto, Instituto de Ciências Exatas e
Biológicas, Núcleo de Pesquisa em Ciências Biológicas & Departamento de Ciências
Biológicas, Ouro Preto, MG, Brazil
- Universidade de São Paulo, Instituto de Ciências Biomédicas,
Departamento de Microbiologia, São Paulo,SP, Brazil
| | - Livia Luz Souza Nascimento
- Universidade de São Paulo, Instituto de Ciências Biomédicas,
Departamento de Microbiologia, São Paulo,SP, Brazil
| | - Camila Carrião Machado Garcia
- Universidade Federal de Ouro Preto, Instituto de Ciências Exatas e
Biológicas, Núcleo de Pesquisa em Ciências Biológicas & Departamento de Ciências
Biológicas, Ouro Preto, MG, Brazil
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42
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van der Weegen Y, Golan-Berman H, Mevissen TET, Apelt K, González-Prieto R, Goedhart J, Heilbrun EE, Vertegaal ACO, van den Heuvel D, Walter JC, Adar S, Luijsterburg MS. The cooperative action of CSB, CSA, and UVSSA target TFIIH to DNA damage-stalled RNA polymerase II. Nat Commun 2020; 11:2104. [PMID: 32355176 PMCID: PMC7192910 DOI: 10.1038/s41467-020-15903-8] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 03/27/2020] [Indexed: 12/13/2022] Open
Abstract
The response to DNA damage-stalled RNA polymerase II (RNAPIIo) involves the assembly of the transcription-coupled repair (TCR) complex on actively transcribed strands. The function of the TCR proteins CSB, CSA and UVSSA and the manner in which the core DNA repair complex, including transcription factor IIH (TFIIH), is recruited are largely unknown. Here, we define the assembly mechanism of the TCR complex in human isogenic knockout cells. We show that TCR is initiated by RNAPIIo-bound CSB, which recruits CSA through a newly identified CSA-interaction motif (CIM). Once recruited, CSA facilitates the association of UVSSA with stalled RNAPIIo. Importantly, we find that UVSSA is the key factor that recruits the TFIIH complex in a manner that is stimulated by CSB and CSA. Together these findings identify a sequential and highly cooperative assembly mechanism of TCR proteins and reveal the mechanism for TFIIH recruitment to DNA damage-stalled RNAPIIo to initiate repair. The response to DNA damage-stalled RNA polymerase II leads to the assembly of the transcription-coupled repair (TCR) complex on actively transcribed strands. Here, the authors reveal the complex assembly mechanism of the TCR complex in human cells.
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Affiliation(s)
- Yana van der Weegen
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands
| | - Hadar Golan-Berman
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, 91120, Israel
| | - Tycho E T Mevissen
- Howard Hughes Medical Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Katja Apelt
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands
| | - Román González-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands
| | - Joachim Goedhart
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
| | - Elisheva E Heilbrun
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, 91120, Israel
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands
| | - Diana van den Heuvel
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands
| | - Johannes C Walter
- Howard Hughes Medical Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Sheera Adar
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, 91120, Israel
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands.
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43
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Liebelt F, Schimmel J, Verlaan-de Vries M, Klemann E, van Royen ME, van der Weegen Y, Luijsterburg MS, Mullenders LH, Pines A, Vermeulen W, Vertegaal ACO. Transcription-coupled nucleotide excision repair is coordinated by ubiquitin and SUMO in response to ultraviolet irradiation. Nucleic Acids Res 2020; 48:231-248. [PMID: 31722399 PMCID: PMC7145520 DOI: 10.1093/nar/gkz977] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/08/2019] [Accepted: 10/14/2019] [Indexed: 12/04/2022] Open
Abstract
Cockayne Syndrome (CS) is a severe neurodegenerative and premature aging autosomal-recessive disease, caused by inherited defects in the CSA and CSB genes, leading to defects in transcription-coupled nucleotide excision repair (TC-NER) and consequently hypersensitivity to ultraviolet (UV) irradiation. TC-NER is initiated by lesion-stalled RNA polymerase II, which stabilizes the interaction with the SNF2/SWI2 ATPase CSB to facilitate recruitment of the CSA E3 Cullin ubiquitin ligase complex. However, the precise biochemical connections between CSA and CSB are unknown. The small ubiquitin-like modifier SUMO is important in the DNA damage response. We found that CSB, among an extensive set of other target proteins, is the most dynamically SUMOylated substrate in response to UV irradiation. Inhibiting SUMOylation reduced the accumulation of CSB at local sites of UV irradiation and reduced recovery of RNA synthesis. Interestingly, CSA is required for the efficient clearance of SUMOylated CSB. However, subsequent proteomic analysis of CSA-dependent ubiquitinated substrates revealed that CSA does not ubiquitinate CSB in a UV-dependent manner. Surprisingly, we found that CSA is required for the ubiquitination of the largest subunit of RNA polymerase II, RPB1. Combined, our results indicate that the CSA, CSB, RNA polymerase II triad is coordinated by ubiquitin and SUMO in response to UV irradiation. Furthermore, our work provides a resource of SUMO targets regulated in response to UV or ionizing radiation.
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Affiliation(s)
- Frauke Liebelt
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Joost Schimmel
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands.,Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Matty Verlaan-de Vries
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Esra Klemann
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - 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, The Netherlands
| | - Yana van der Weegen
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
| | - Leon H Mullenders
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands.,Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Japan
| | - Alex Pines
- 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
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, Leiden 2333 ZC, The Netherlands
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44
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Nakazawa Y, Hara Y, Oka Y, Komine O, van den Heuvel D, Guo C, Daigaku Y, Isono M, He Y, Shimada M, Kato K, Jia N, Hashimoto S, Kotani Y, Miyoshi Y, Tanaka M, Sobue A, Mitsutake N, Suganami T, Masuda A, Ohno K, Nakada S, Mashimo T, Yamanaka K, Luijsterburg MS, Ogi T. Ubiquitination of DNA Damage-Stalled RNAPII Promotes Transcription-Coupled Repair. Cell 2020; 180:1228-1244.e24. [PMID: 32142649 DOI: 10.1016/j.cell.2020.02.010] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 12/16/2019] [Accepted: 02/04/2020] [Indexed: 02/06/2023]
Abstract
Transcription-coupled nucleotide excision repair (TC-NER) is initiated by the stalling of elongating RNA polymerase II (RNAPIIo) at DNA lesions. The ubiquitination of RNAPIIo in response to DNA damage is an evolutionarily conserved event, but its function in mammals is unknown. Here, we identified a single DNA damage-induced ubiquitination site in RNAPII at RPB1-K1268, which regulates transcription recovery and DNA damage resistance. Mechanistically, RPB1-K1268 ubiquitination stimulates the association of the core-TFIIH complex with stalled RNAPIIo through a transfer mechanism that also involves UVSSA-K414 ubiquitination. We developed a strand-specific ChIP-seq method, which revealed RPB1-K1268 ubiquitination is important for repair and the resolution of transcriptional bottlenecks at DNA lesions. Finally, RPB1-K1268R knockin mice displayed a short life-span, premature aging, and neurodegeneration. Our results reveal RNAPII ubiquitination provides a two-tier protection mechanism by activating TC-NER and, in parallel, the processing of DNA damage-stalled RNAPIIo, which together prevent prolonged transcription arrest and protect against neurodegeneration.
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Affiliation(s)
- Yuka Nakazawa
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuichiro Hara
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yasuyoshi Oka
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Okiru Komine
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Neuroscience and Pathobiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Diana van den Heuvel
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, the Netherlands
| | - Chaowan Guo
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yasukazu Daigaku
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Japan; Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Mayu Isono
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuxi He
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mayuko Shimada
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kana Kato
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nan Jia
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Satoru Hashimoto
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuko Kotani
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, Osaka, Japan; Genome Editing Research and Development (R&D) Center, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yuka Miyoshi
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Neuroscience and Pathobiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Miyako Tanaka
- Department of Molecular Medicine and Metabolism, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Immunometabolism, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Akira Sobue
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Neuroscience and Pathobiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Norisato Mitsutake
- Department of Radiation Medical Sciences, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Takayoshi Suganami
- Department of Molecular Medicine and Metabolism, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Immunometabolism, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Akio Masuda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shinichiro Nakada
- Department of Bioregulation and Cellular Response, Graduate School of Medicine, Osaka University, Osaka, Japan; Institute for Advanced Co-Creation Studies, Osaka University, Osaka, Japan
| | - Tomoji Mashimo
- Institute of Experimental Animal Sciences, Graduate School of Medicine, Osaka University, Osaka, Japan; Genome Editing Research and Development (R&D) Center, Graduate School of Medicine, Osaka University, Osaka, Japan; Division of Animal Genetics, Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Koji Yamanaka
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Neuroscience and Pathobiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, the Netherlands
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan.
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45
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Li P, Liu HM. Recent advances in the development of ubiquitin-specific-processing protease 7 (USP7) inhibitors. Eur J Med Chem 2020; 191:112107. [PMID: 32092586 DOI: 10.1016/j.ejmech.2020.112107] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/14/2020] [Accepted: 01/28/2020] [Indexed: 12/16/2022]
Abstract
Ubiquitin-specific-processing protease 7 (USP7) is one among the several deubiquitinating enzymes gaining central attention in the current cancer research. Most recent studies have focused on illustrating how USP7 is involved in the cancer process, while few articles reported the development of small molecule USP7 inhibitors. Although some review articles dealt with USP7, they mainly focused on its physiological role and not on the development of USP7 inhibitors. In this review, we systematically summarise the structures, activities and structure-activity relationship (SAR) of small molecule USP7 inhibitors, recently disclosed in scientific articles and patents from 2000 to 2019. The binding modes of typical compounds and their interactions with USP7 are also presented, while other deubiquitinase inhibitors are described in detail. Meanwhile, we briefly introduce the biochemical and physiological functions of USP7. Finally, challenges and potential strategies in developing small molecule USP7 inhibitors are also discussed.
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Affiliation(s)
- Peng Li
- Key Laboratory of Advanced Technology of Drug Preparation Technologies, Ministry of Education, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, And School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan, 450001, China
| | - Hong-Min Liu
- Key Laboratory of Advanced Technology of Drug Preparation Technologies, Ministry of Education, Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety, And School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan, 450001, China.
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46
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Zhu Q, Ding N, Wei S, Li P, Wani G, He J, Wani AA. USP7-mediated deubiquitination differentially regulates CSB but not UVSSA upon UV radiation-induced DNA damage. Cell Cycle 2019; 19:124-141. [PMID: 31775559 DOI: 10.1080/15384101.2019.1695996] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Cockayne syndrome group B (CSB) protein participates in transcription-coupled nucleotide excision repair. The stability of CSB is known to be regulated by ubiquitin-specific protease 7 (USP7). Yet, whether USP7 acts as a deubiquitinating enzyme for CSB is not clear. Here, we demonstrate that USP7 deubiquitinates CSB to maintain its levels after ultraviolet (UV)-induced DNA damage. While both CSB and UV-stimulated scaffold protein A (UVSSA) exhibit a biphasic decrease and recovery upon UV irradiation, only CSB recovery depends on USP7, which physically interacts with and deubiquitinates CSB. Meanwhile, CSB overexpression stabilizes UVSSA, but decrease UVSSA's presence in nuclease-releasable/soluble chromatin, and increase the presence of ubiquitinated UVSSA in insoluble chromatin alongside CSB-ubiquitin conjugates. Remarkably, CSB overexpression also decreases CSB association with USP7 and UVSSA in soluble chromatin. UVSSA exists in several ubiquitinated forms, of which mono-ubiquitinated form and other ubiquitinated UVSSA forms are detectable upon 6xHistidine tag-based purification. The ubiquitinated UVSSA forms, however, are not cleavable by USP7 in vitro. Furthermore, USP7 disruption does not affect RNA synthesis but decreases the recovery of RNA synthesis following UV exposure. These results reveal a role of USP7 as a CSB deubiquitinating enzyme for fine-tuning the process of TC-NER in human cells.
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Affiliation(s)
- Qianzheng Zhu
- Department of Radiology, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Nan Ding
- Department of Radiology, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Shengcai Wei
- Department of Radiology, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Ping Li
- Department of Radiology, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Gulzar Wani
- Department of Radiology, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Jinshan He
- Department of Radiology, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Altaf A Wani
- Department of Radiology, The Ohio State University College of Medicine, Columbus, OH, USA.,Department of Molecular and Cellular Biochemistry, The Ohio State University College of Medicine, Columbus, OH, USA.,James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, OH, USA
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47
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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] [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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48
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Takahashi TS, Sato Y, Yamagata A, Goto-Ito S, Saijo M, Fukai S. Structural basis of ubiquitin recognition by the winged-helix domain of Cockayne syndrome group B protein. Nucleic Acids Res 2019; 47:3784-3794. [PMID: 30753618 PMCID: PMC6468306 DOI: 10.1093/nar/gkz081] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 01/25/2019] [Accepted: 02/01/2019] [Indexed: 12/18/2022] Open
Abstract
Cockayne syndrome group B (CSB, also known as ERCC6) protein is involved in many DNA repair processes and essential for transcription-coupled repair (TCR). The central region of CSB has the helicase motif, whereas the C-terminal region contains important regulatory elements for repair of UV- and oxidative stress-induced damages and double-strand breaks (DSBs). A previous study suggested that a small part (∼30 residues) within this region was responsible for binding to ubiquitin (Ub). Here, we show that the Ub-binding of CSB requires a larger part of CSB, which was previously identified as a winged-helix domain (WHD) and is involved in the recruitment of CSB to DSBs. We also present the crystal structure of CSB WHD in complex with Ub. CSB WHD folds as a single globular domain, defining a class of Ub-binding domains (UBDs) different from 23 UBD classes identified so far. The second α-helix and C-terminal extremity of CSB WHD interact with Ub. Together with structure-guided mutational analysis, we identified the residues critical for the binding to Ub. CSB mutants defective in the Ub binding reduced repair of UV-induced damage. This study supports the notion that DSB repair and TCR may be associated with the Ub-binding of CSB.
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Affiliation(s)
- Tomio S Takahashi
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo 113-0032, Japan
| | - Yusuke Sato
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo 113-0032, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Atsushi Yamagata
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo 113-0032, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Sakurako Goto-Ito
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo 113-0032, Japan
| | - Masafumi Saijo
- Graduate School of Frontier Biosciences, Osaka University, Yamadaoka 1-3, Suita, Osaka 565-0871, Japan
| | - Shuya Fukai
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo 113-0032, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
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49
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2019] [Indexed: 12/30/2022]
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50
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Ijaz A, Wolf S, Mandukhail SR, Basit S, Betz RC, Wali A. UV-sensitive syndrome: Whole exome sequencing identified a nonsense mutation in the gene UVSSA in two consanguineous pedigrees from Pakistan. J Dermatol Sci 2019; 95:113-118. [PMID: 31421932 DOI: 10.1016/j.jdermsci.2019.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 07/18/2019] [Accepted: 08/07/2019] [Indexed: 11/15/2022]
Abstract
BACKGROUND UV-sensitive syndrome (UVSS) is a rare autosomal recessive genodermatosis characterised by photosensitivity, and hyperpigmentation, freckling, and dryness of sun exposed areas. In contrast to other photosensitivity disorders, affected patients show no predisposition to cutaneous melanoma or neurological dysfunction. UVSS results from a defect in the transcription-coupled nucleotide excision repair (TC-NER) mechanism. UVSS can be caused by mutations in the genes ERCC8, ERCC6, and UVSSA. OBJECTIVE To determine the underlying genetic cause of UVSS and its functional consequences in nine members of two large, unrelated consanguineous pedigrees from Pakistan. METHODS Genomic DNA from one affected member of each family was subjected to whole exome sequencing. The identified mutation was then validated via Sanger sequencing using samples from all available family members. Molecular cloning and mammalian cell cultures were used for the translation and localisation of wild type (WT) and mutant constructs. RESULTS A novel homozygous nonsense mutation, (c.1040G>A [p.(Trp347*)]), was detected in exon 6 of the UVSSA gene in both families. Sanger sequencing revealed co-segregation of the nonsense mutation with the UVSS phenotype. Immunoblotting revealed the anticipated 81kDa band for the WT construct, and a truncated protein of around 39kDa for the mutant. In mutant samples, immunofluorescence revealed mislocalisation of UVSSA from the nucleus to the cytoplasm. CONCLUSIONS This is the first report of UVSS in the Pakistani population and the fourth report of a disease-causing mutation in UVSSA. The study broadens the UVSSA mutational spectrum, and contributes to functional understanding of truncated UVSSA proteins.
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Affiliation(s)
- Ambreen Ijaz
- Department of Biotechnology, Faculty of Life Sciences & Informatics, BUITEMS, 87100, Quetta, Pakistan; Department of Zoology, Sardar Bahadur Khan Women's University, Quetta, Pakistan
| | - Sabrina Wolf
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, D-53127, Bonn, Germany
| | - Safur Rehman Mandukhail
- Department of Biotechnology, Faculty of Life Sciences & Informatics, BUITEMS, 87100, Quetta, Pakistan
| | - Sulman Basit
- Center for Genetics and Inherited Diseases, Taibah University Al Madinah Al Munawarah, Saudi Arabia
| | - Regina C Betz
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, D-53127, Bonn, Germany.
| | - Abdul Wali
- Department of Biotechnology, Faculty of Life Sciences & Informatics, BUITEMS, 87100, Quetta, Pakistan.
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