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Yu J, Li M, Ju L, Zhou F, Wang Y, Zhang Y, Zhang R, Du W, Huang R, Qian K, Wang G, Xiao Y, Wang X. TRAIP suppresses bladder cancer progression by catalyzing K48-linked polyubiquitination of MYC. Oncogene 2024; 43:470-483. [PMID: 38123820 DOI: 10.1038/s41388-023-02922-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023]
Abstract
TRAF-interacting protein (TRAIP), an E3 ligase containing a RING domain, has emerged as a significant contributor to maintaining genome integrity and is closely associated with cancer. Our study reveals that TRAIP shows reduced expression in bladder cancer (BLCA), which correlates with an unfavorable prognosis. In vitro and in vivo, TRAIP inhibits proliferation and migration of BLCA cells. MYC has been identified as a novel target for TRAIP, wherein direct interaction promotes K48-linked polyubiquitination at neighboring K428 and K430 residues, ultimately resulting in proteasome-dependent degradation and downregulation of MYC transcriptional activity. This mechanism effectively impedes the progression of BLCA. Restoring MYC expression reverses suppressed proliferation and migration of BLCA cells induced by TRAIP. Moreover, our results suggest that MYC may bind to the transcriptional start region of TRAIP, thereby exerting regulatory control over TRAIP transcription. Consequently, this interaction establishes a negative feedback loop that regulates MYC expression, preventing excessive levels. Taken together, this study reveals a mechanism that TRAIP inhibits proliferation and migration of BLCA by promoting ubiquitin-mediated degradation of MYC.
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Affiliation(s)
- Jingtian Yu
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Mingxing Li
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Lingao Ju
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Fenfang Zhou
- Department of Radiology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yejinpeng Wang
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yi Zhang
- Euler Technology, ZGC Life Sciences Park, Beijing, China
- Center for Quantitative Biology, School of Life Sciences, Peking University, Beijing, China
| | - Renjie Zhang
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Wenzhi Du
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Urology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Ruoyu Huang
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kaiyu Qian
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Gang Wang
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yu Xiao
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China.
| | - Xinghuan Wang
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China.
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China.
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Scaramuzza S, Jones RM, Sadurni MM, Reynolds-Winczura A, Poovathumkadavil D, Farrell A, Natsume T, Rojas P, Cuesta CF, Kanemaki MT, Saponaro M, Gambus A. TRAIP resolves DNA replication-transcription conflicts during the S-phase of unperturbed cells. Nat Commun 2023; 14:5071. [PMID: 37604812 PMCID: PMC10442450 DOI: 10.1038/s41467-023-40695-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: 04/04/2022] [Accepted: 08/08/2023] [Indexed: 08/23/2023] Open
Abstract
Cell division is the basis for the propagation of life and requires accurate duplication of all genetic information. DNA damage created during replication (replication stress) is a major cause of cancer, premature aging and a spectrum of other human disorders. Over the years, TRAIP E3 ubiquitin ligase has been shown to play a role in various cellular processes that govern genome integrity and faultless segregation. TRAIP is essential for cell viability, and mutations in TRAIP ubiquitin ligase activity lead to primordial dwarfism in patients. Here, we have determined the mechanism of inhibition of cell proliferation in TRAIP-depleted cells. We have taken advantage of the auxin induced degron system to rapidly degrade TRAIP within cells and to dissect the importance of various functions of TRAIP in different stages of the cell cycle. We conclude that upon rapid TRAIP degradation, specifically in S-phase, cells cease to proliferate, arrest in G2 stage of the cell cycle and undergo senescence. Our findings reveal that TRAIP works in S-phase to prevent DNA damage at transcription start sites, caused by replication-transcription conflicts.
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Affiliation(s)
- Shaun Scaramuzza
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK
- Cancer Research UK - Manchester Institute, Manchester Cancer Research Centre, Manchester, UK
| | - Rebecca M Jones
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK
| | - Martina Muste Sadurni
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK
| | - Alicja Reynolds-Winczura
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK
| | - Divyasree Poovathumkadavil
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK
| | - Abigail Farrell
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK
| | - Toyoaki Natsume
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
- Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Patricia Rojas
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK
| | - Cyntia Fernandez Cuesta
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK
| | - Masato T Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
- Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan
| | - Marco Saponaro
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK
| | - Agnieszka Gambus
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK.
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Chung HJ, Lee JR, Kim TM, Kim S, Park K, Kim MJ, Jung E, Kim S, Lee EA, Ra JS, Hwang S, Lee JY, Schärer OD, Kim Y, Myung K, Kim H. ZNF212 promotes genomic integrity through direct interaction with TRAIP. Nucleic Acids Res 2023; 51:631-649. [PMID: 36594163 PMCID: PMC9881131 DOI: 10.1093/nar/gkac1226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 12/04/2022] [Accepted: 12/09/2022] [Indexed: 01/04/2023] Open
Abstract
TRAIP is a key factor involved in the DNA damage response (DDR), homologous recombination (HR) and DNA interstrand crosslink (ICL) repair. However, the exact functions of TRAIP in these processes in mammalian cells are not fully understood. Here we identify the zinc finger protein 212, ZNF212, as a novel binding partner for TRAIP and find that ZNF212 colocalizes with sites of DNA damage. The recruitment of TRAIP or ZNF212 to sites of DNA damage is mutually interdependent. We show that depletion of ZNF212 causes defects in the DDR and HR-mediated repair in a manner epistatic to TRAIP. In addition, an epistatic analysis of Zfp212, the mouse homolog of human ZNF212, in mouse embryonic stem cells (mESCs), shows that it appears to act upstream of both the Neil3 and Fanconi anemia (FA) pathways of ICLs repair. We find that human ZNF212 interacted directly with NEIL3 and promotes its recruitment to ICL lesions. Collectively, our findings identify ZNF212 as a new factor involved in the DDR, HR-mediated repair and ICL repair though direct interaction with TRAIP.
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Affiliation(s)
| | | | | | | | | | - Myung-Jin Kim
- Department of Biological Sciences, Research Institute of Women's Health and Digital Humanity Center, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Eunyoung Jung
- Department of Biological Sciences, Research Institute of Women's Health and Digital Humanity Center, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Subin Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Eun A Lee
- Center for Genomic Integrity Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Jae Sun Ra
- Center for Genomic Integrity Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Sunyoung Hwang
- Center for Genomic Integrity Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Ja Yil Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Orlando D Schärer
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea,Center for Genomic Integrity Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Yonghwan Kim
- Correspondence may also be addressed to Yonghwan Kim. Tel: +82 2 710 9552;
| | - Kyungjae Myung
- Correspondence may also be addressed to Kyungjae Myung. Tel: +82 52 217 5323; Fax: +82 52 217 5519;
| | - Hongtae Kim
- To whom correspondence should be addressed. Tel: +82 52 217 5404; Fax: +82 52 217 5519;
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4
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Lee SA, Lee D, Kang M, Kim S, Kwon SJ, Lee HS, Seo HR, Kaushal P, Lee NS, Kim H, Lee C, Kwon J. BAP1 promotes the repair of UV-induced DNA damage via PARP1-mediated recruitment to damage sites and control of activity and stability. Cell Death Differ 2022; 29:2381-2398. [PMID: 35637285 PMCID: PMC9751128 DOI: 10.1038/s41418-022-01024-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: 10/13/2021] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 01/31/2023] Open
Abstract
BRCA1-associated protein-1 (BAP1) is a ubiquitin C-terminal hydrolase domain-containing deubiquitinase with tumor suppressor activity. The gene encoding BAP1 is mutated in various human cancers, with particularly high frequency in kidney and skin cancers, and BAP1 is involved in many cancer-related cellular functions, such as DNA repair and genome stability. Although BAP1 stimulates DNA double-strand break repair, whether it functions in nucleotide excision repair (NER) is unknown. Here, we show that BAP1 promotes the repair of ultraviolet (UV)-induced DNA damage via its deubiquitination activity in various cell types, including primary melanocytes. Poly(ADP-ribose) polymerase 1 (PARP1) interacts with and recruits BAP1 to damage sites, with BAP1 recruitment peaking after the DDB2 and XPC damage sensors. BAP1 recruitment also requires histone H2A monoubiquitinated at Lys119, which accumulates at damage sites. PARP1 transiently poly(ADP-ribosyl)ates (PARylates) BAP1 at multiple sites after UV damage and stimulates the deubiquitination activity of BAP1 both intrinsically and via PARylation. PARP1 also promotes BAP1 stability via crosstalk between PARylation and ubiquitination. Many PARylation sites in BAP1 are mutated in various human cancers, among which the glutamic acid (Glu) residue at position 31, with particularly frequent mutation in kidney cancer, plays a critical role in BAP1 stabilization and promotes UV-induced DNA damage repair. Glu31 also participates in reducing the viability of kidney cancer cells. This study therefore reveals that BAP1 functions in the NER pathway and that PARP1 plays a role as a novel factor that regulates BAP1 enzymatic activity, protein stability, and recruitment to damage sites. This activity of BAP1 in NER, along with its cancer cell viability-reducing activity, may account for its tumor suppressor function.
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Affiliation(s)
- Shin-Ai Lee
- Department of Life Science, The Research Center for Cellular Homeostasis, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Korea
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, Building 37, Room 1068, Bethesda, MD, 20892-4263, USA
| | - Daye Lee
- Department of Life Science, The Research Center for Cellular Homeostasis, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Korea
| | - Minhwa Kang
- Department of Life Science, The Research Center for Cellular Homeostasis, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Korea
| | - Sora Kim
- Department of Life Science, The Research Center for Cellular Homeostasis, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Korea
| | - Su-Jung Kwon
- Department of Life Science, The Research Center for Cellular Homeostasis, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Korea
| | - Han-Sae Lee
- Department of Life Science, The Research Center for Cellular Homeostasis, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Korea
| | - Hye-Ran Seo
- Department of Life Science, The Research Center for Cellular Homeostasis, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Korea
| | - Prashant Kaushal
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul, 02792, Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul, 02792, Korea
| | - Nam Soo Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Hongtae Kim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, 44919, Korea
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul, 02792, Korea
- KHU-KIST Department of Converging Science and Technology, Kyung Hee University, 26 Kyunghee-daero, Dongdaemun-gu, Seoul, 02447, Korea
| | - Jongbum Kwon
- Department of Life Science, The Research Center for Cellular Homeostasis, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Korea.
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5
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Sagkrioti E, Biz GM, Takan I, Asfa S, Nikitaki Z, Zanni V, Kars RH, Hellweg CE, Azzam EI, Logotheti S, Pavlopoulou A, Georgakilas AG. Radiation Type- and Dose-Specific Transcriptional Responses across Healthy and Diseased Mammalian Tissues. Antioxidants (Basel) 2022; 11:2286. [PMID: 36421472 PMCID: PMC9687520 DOI: 10.3390/antiox11112286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/12/2022] [Accepted: 11/15/2022] [Indexed: 08/30/2023] Open
Abstract
Ionizing radiation (IR) is a genuine genotoxic agent and a major modality in cancer treatment. IR disrupts DNA sequences and exerts mutagenic and/or cytotoxic properties that not only alter critical cellular functions but also impact tissues proximal and distal to the irradiated site. Unveiling the molecular events governing the diverse effects of IR at the cellular and organismal levels is relevant for both radiotherapy and radiation protection. Herein, we address changes in the expression of mammalian genes induced after the exposure of a wide range of tissues to various radiation types with distinct biophysical characteristics. First, we constructed a publicly available database, termed RadBioBase, which will be updated at regular intervals. RadBioBase includes comprehensive transcriptomes of mammalian cells across healthy and diseased tissues that respond to a range of radiation types and doses. Pertinent information was derived from a hybrid analysis based on stringent literature mining and transcriptomic studies. An integrative bioinformatics methodology, including functional enrichment analysis and machine learning techniques, was employed to unveil the characteristic biological pathways related to specific radiation types and their association with various diseases. We found that the effects of high linear energy transfer (LET) radiation on cell transcriptomes significantly differ from those caused by low LET and are consistent with immunomodulation, inflammation, oxidative stress responses and cell death. The transcriptome changes also depend on the dose since low doses up to 0.5 Gy are related with cytokine cascades, while higher doses with ROS metabolism. We additionally identified distinct gene signatures for different types of radiation. Overall, our data suggest that different radiation types and doses can trigger distinct trajectories of cell-intrinsic and cell-extrinsic pathways that hold promise to be manipulated toward improving radiotherapy efficiency and reducing systemic radiotoxicities.
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Affiliation(s)
- Eftychia Sagkrioti
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou, 15780 Athens, Greece
- Biology Department, National and Kapodistrian University of Athens (NKUA), 15784 Athens, Greece
| | - Gökay Mehmet Biz
- Department of Technical Programs, Izmir Vocational School, Dokuz Eylül University, Buca, Izmir 35380, Turkey
| | - Işıl Takan
- Izmir Biomedicine and Genome Center (IBG), Balcova, Izmir 35340, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, Izmir 35340, Turkey
| | - Seyedehsadaf Asfa
- Izmir Biomedicine and Genome Center (IBG), Balcova, Izmir 35340, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, Izmir 35340, Turkey
| | - Zacharenia Nikitaki
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou, 15780 Athens, Greece
| | - Vassiliki Zanni
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou, 15780 Athens, Greece
| | - Rumeysa Hanife Kars
- Department of Biomedical Engineering, Istanbul Medipol University, Istanbul 34810, Turkey
| | - Christine E. Hellweg
- German Aerospace Center (DLR), Institute of Aerospace Medicine, Radiation Biology, Linder Höhe, D-51147 Köln, Germany
| | | | - Stella Logotheti
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou, 15780 Athens, Greece
| | - Athanasia Pavlopoulou
- Izmir Biomedicine and Genome Center (IBG), Balcova, Izmir 35340, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Balcova, Izmir 35340, Turkey
| | - Alexandros G. Georgakilas
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou, 15780 Athens, Greece
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Zhang M, Su L, Wang W, Li C, Liang Q, Ji F, Jiao J. Endothelial cells regulated by RNF20 orchestrate the proliferation and differentiation of neural precursor cells during embryonic development. Cell Rep 2022; 40:111350. [PMID: 36103829 DOI: 10.1016/j.celrep.2022.111350] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/10/2022] [Accepted: 08/22/2022] [Indexed: 11/03/2022] Open
Abstract
The intimate communication between the vascular and nervous systems is critical for maintaining central nervous system (CNS) development. However, whether cerebrovascular endothelial cells (ECs) can orchestrate neural precursor cell (NPC) proliferation and differentiation, and the identity of the signals involved therein, is unclear. Here, we find that the development of ECs is often accompanied by DNA damage. RNF20, an E3 ubiquitin ligase, is required for the DNA damage response (DDR). The deletion of RNF20 causes the accumulation of DNA damage in ECs, which fails to secrete cartilage intermediate layer protein 2 (CILP2). Moreover, the loss of endothelium-derived CILP2 alters the downstream cascade signaling of Wnt signaling pathways through the interaction with Wnt3a, which disturbs the NPC fate and causes autism-like behaviors in mice. Therefore, the close and refined controlled neurovascular interactions ensure the normal operation of neurogenesis during embryonic development.
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Affiliation(s)
- Mengtian Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute for Stem Cell and Regenerative Medicine, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Libo Su
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute for Stem Cell and Regenerative Medicine, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | - Wenwen Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Chenxiao Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute for Stem Cell and Regenerative Medicine, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Qingli Liang
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fen Ji
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute for Stem Cell and Regenerative Medicine, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianwei Jiao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute for Stem Cell and Regenerative Medicine, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
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Roemer A, Mohammed L, Strickfaden H, Underhill DA, Hendzel MJ. Mechanisms governing the accessibility of DNA damage proteins to constitutive heterochromatin. Front Genet 2022; 13:876862. [PMID: 36092926 PMCID: PMC9458887 DOI: 10.3389/fgene.2022.876862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 07/18/2022] [Indexed: 12/05/2022] Open
Abstract
Chromatin is thought to regulate the accessibility of the underlying DNA sequence to machinery that transcribes and repairs the DNA. Heterochromatin is chromatin that maintains a sufficiently high density of DNA packing to be visible by light microscopy throughout the cell cycle and is thought to be most restrictive to transcription. Several studies have suggested that larger proteins and protein complexes are attenuated in their access to heterochromatin. In addition, heterochromatin domains may be associated with phase separated liquid condensates adding further complexity to the regulation of protein concentration within chromocenters. This provides a solvent environment distinct from the nucleoplasm, and proteins that are not size restricted in accessing this liquid environment may partition between the nucleoplasm and heterochromatin based on relative solubility. In this study, we assessed the accessibility of constitutive heterochromatin in mouse cells, which is organized into large and easily identifiable chromocenters, to fluorescently tagged DNA damage response proteins. We find that proteins larger than the expected 10 nm size limit can access the interior of heterochromatin. We find that the sensor proteins Ku70 and PARP1 enrich in mouse chromocenters. At the same time, MRE11 shows variability within an asynchronous population that ranges from depleted to enriched but is primarily homogeneously distribution between chromocenters and the nucleoplasm. While larger downstream proteins such as ATM, BRCA1, and 53BP1 are commonly depleted in chromocenters, they show a wide range of concentrations, with none being depleted beyond approximately 75%. Contradicting exclusively size-dependent accessibility, many smaller proteins, including EGFP, are also depleted in chromocenters. Our results are consistent with minimal size-dependent selectivity but a distinct solvent environment explaining reduced concentrations of diffusing nucleoplasmic proteins within the volume of the chromocenter.
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Ju MK, Lee JR, Choi Y, Park SY, Sul HJ, Chung HJ, An S, Lee S, Jung E, Kim B, Choi BY, Kim BJ, Kim HS, Lim H, Kang HS, Soh JS, Myung K, Kim KC, Cho JW, Seo J, Kim TM, Lee JY, Kim Y, Kim H, Zang DY. PWWP2B promotes DNA end resection and homologous recombination. EMBO Rep 2022; 23:e53492. [PMID: 35582821 PMCID: PMC9253748 DOI: 10.15252/embr.202153492] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 04/18/2022] [Accepted: 05/02/2022] [Indexed: 11/15/2023] Open
Abstract
Genome instability is one of the leading causes of gastric cancers. However, the mutational landscape of driver genes in gastric cancer is poorly understood. Here, we investigate somatic mutations in 25 Korean gastric adenocarcinoma patients using whole-exome sequencing and show that PWWP2B is one of the most frequently mutated genes. PWWP2B mutation correlates with lower cancer patient survival. We find that PWWP2B has a role in DNA double-strand break repair. As a nuclear protein, PWWP2B moves to sites of DNA damage through its interaction with UHRF1. Depletion of PWWP2B enhances cellular sensitivity to ionizing radiation (IR) and impairs IR-induced foci formation of RAD51. PWWP2B interacts with MRE11 and participates in homologous recombination via promoting DNA end-resection. Taken together, our data show that PWWP2B facilitates the recruitment of DNA repair machinery to sites of DNA damage and promotes HR-mediated DNA double-strand break repair. Impaired PWWP2B function might thus cause genome instability and promote gastric cancer development.
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Affiliation(s)
- Min Kyung Ju
- Department of Biological SciencesUlsan National Institute of Science and TechnologyUlsanKorea
| | - Joo Rak Lee
- Department of Biological SciencesUlsan National Institute of Science and TechnologyUlsanKorea
| | - Yeonsong Choi
- Department of Biomedical EngineeringUlsan National Institute of Science and TechnologyUlsanKorea
| | - Seon Young Park
- Department of Biological SciencesResearch Institute of Women’s HealthSookmyung Women's UniversitySeoulKorea
| | - Hee Jung Sul
- Hallym Translational Research InstituteHallym University Sacred Heart HospitalAnyang‐siKorea
| | - Hee Jin Chung
- Department of Biological SciencesUlsan National Institute of Science and TechnologyUlsanKorea
| | - Soyeong An
- Department of Biological SciencesUlsan National Institute of Science and TechnologyUlsanKorea
| | - Semin Lee
- Department of Biomedical EngineeringUlsan National Institute of Science and TechnologyUlsanKorea
| | - Eunyoung Jung
- Department of Biological SciencesResearch Institute of Women’s HealthSookmyung Women's UniversitySeoulKorea
| | - Bohyun Kim
- Hallym Translational Research InstituteHallym University Sacred Heart HospitalAnyang‐siKorea
| | - Bo Youn Choi
- Hallym Translational Research InstituteHallym University Sacred Heart HospitalAnyang‐siKorea
| | - Bum Jun Kim
- Department of Internal MedicineHallym University Sacred Heart HospitalHallym University College of MedicineAnyang‐siKorea
| | - Hyeong Su Kim
- Department of Internal MedicineHallym University Sacred Heart HospitalHallym University College of MedicineAnyang‐siKorea
| | - Hyun Lim
- Department of Internal MedicineHallym University Sacred Heart HospitalHallym University College of MedicineAnyang‐siKorea
| | - Ho Suk Kang
- Department of Internal MedicineHallym University Sacred Heart HospitalHallym University College of MedicineAnyang‐siKorea
| | - Jae Seung Soh
- Department of Internal MedicineHallym University Sacred Heart HospitalHallym University College of MedicineAnyang‐siKorea
| | - Kyungjae Myung
- Department of Biological SciencesUlsan National Institute of Science and TechnologyUlsanKorea
- Center for Genomic Integrity Institute for Basic Science (IBS)UlsanKorea
| | - Kab Choong Kim
- Department of SurgeryHallym University Medical CenterHallym University College of MedicineAnyang‐siKorea
| | - Ji Woong Cho
- Department of SurgeryHallym University Medical CenterHallym University College of MedicineAnyang‐siKorea
| | - Jinwon Seo
- Department of PathologyHallym University Sacred Heart HospitalHallym University College of MedicineAnyang‐siKorea
| | - Tae Moon Kim
- Center for Genomic Integrity Institute for Basic Science (IBS)UlsanKorea
| | - Ja Yil Lee
- Department of Biological SciencesUlsan National Institute of Science and TechnologyUlsanKorea
- Center for Genomic Integrity Institute for Basic Science (IBS)UlsanKorea
| | - Yonghwan Kim
- Department of Biological SciencesResearch Institute of Women’s HealthSookmyung Women's UniversitySeoulKorea
| | - Hongtae Kim
- Department of Biological SciencesUlsan National Institute of Science and TechnologyUlsanKorea
- Center for Genomic Integrity Institute for Basic Science (IBS)UlsanKorea
| | - Dae Young Zang
- Hallym Translational Research InstituteHallym University Sacred Heart HospitalAnyang‐siKorea
- Department of Internal MedicineHallym University Sacred Heart HospitalHallym University College of MedicineAnyang‐siKorea
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9
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O'Neill RS, Rusan NM. Traip controls mushroom body size by suppressing mitotic defects. Development 2022; 149:dev199987. [PMID: 35297981 PMCID: PMC8995085 DOI: 10.1242/dev.199987] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 02/28/2022] [Indexed: 05/12/2024]
Abstract
Microcephaly is a failure to develop proper brain size and neuron number. Mutations in diverse genes are linked to microcephaly, including several with DNA damage repair (DDR) functions; however, it is not well understood how these DDR gene mutations limit brain size. One such gene is TRAIP, which has multiple functions in DDR. We characterized the Drosophila TRAIP homolog nopo, hereafter traip, and found that traip mutants (traip-) have a brain-specific defect in the mushroom body (MB). traip- MBs were smaller and contained fewer neurons, but no neurodegeneration, consistent with human primary microcephaly. Reduced neuron numbers in traip- were explained by premature loss of MB neuroblasts (MB-NBs), in part via caspase-dependent cell death. Many traip- MB-NBs had prominent chromosome bridges in anaphase, along with polyploidy, aneuploidy or micronuclei. Traip localization during mitosis is sufficient for MB development, suggesting that Traip can repair chromosome bridges during mitosis if necessary. Our results suggest that proper brain size is ensured by the recently described role for TRAIP in unloading stalled replication forks in mitosis, which suppresses DNA bridges and premature neural stem cell loss to promote proper neuron number.
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Affiliation(s)
- Ryan S. O'Neill
- Cell and Developmental Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nasser M. Rusan
- Cell and Developmental Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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10
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Yasuhara T, Kato R, Yamauchi M, Uchihara Y, Zou L, Miyagawa K, Shibata A. RAP80 suppresses the vulnerability of R-loops during DNA double-strand break repair. Cell Rep 2022; 38:110335. [PMID: 35108530 DOI: 10.1016/j.celrep.2022.110335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 12/08/2021] [Accepted: 01/12/2022] [Indexed: 01/15/2023] Open
Abstract
Single-stranded DNA (ssDNA) arising as an intermediate of cellular processes on DNA is a potential vulnerability of the genome unless it is appropriately protected. Recent evidence suggests that R-loops, consisting of ssDNA and DNA-RNA hybrids, can form in the proximity of DNA double-strand breaks (DSBs) within transcriptionally active regions. However, how the vulnerability of ssDNA in R-loops is overcome during DSB repair remains unclear. Here, we identify RAP80 as a factor suppressing the vulnerability of ssDNA in R-loops, chromosome translocations, and deletions during DSB repair. Mechanistically, RAP80 prevents unscheduled nucleolytic processing of ssDNA in R-loops by CtIP. This mechanism promotes efficient DSB repair via transcription-associated end joining dependent on BRCA1, Polθ, and LIG1/3. Thus, RAP80 suppresses the vulnerability of R-loops during DSB repair, thereby precluding genomic abnormalities in a critical component of the genome caused by deleterious R-loop processing.
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Affiliation(s)
- Takaaki Yasuhara
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA.
| | - Reona Kato
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Motohiro Yamauchi
- Hospital Campus Laboratory, Radioisotope Center, Central Institute of Radioisotope Science and Safety Management, Kyushu University, Fukuoka, Japan
| | - Yuki Uchihara
- Gunma University Initiative for Advanced Research, Gunma University, Maebashi, Gunma, Japan
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Kiyoshi Miyagawa
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
| | - Atsushi Shibata
- Gunma University Initiative for Advanced Research, Gunma University, Maebashi, Gunma, Japan.
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11
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Bhat EA, Sajjad N, Rather IA, Sabir JSM, Hor YY. In vitro assembly complex formation of TRAIP CC and RAP 80 zinc finger motif revealed by our study. Saudi J Biol Sci 2021; 28:7511-7516. [PMID: 34867056 PMCID: PMC8626312 DOI: 10.1016/j.sjbs.2021.08.083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 08/10/2021] [Accepted: 08/23/2021] [Indexed: 11/17/2022] Open
Abstract
Background Tumor necrosis factor interacting protein (TRAIP/TRIP) is an important cell-signaling molecule that prevents the TNF-induced-nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) activation via direct interaction with TRAF 2 protein. TRAIP is a crucial downstream signaling molecule, implicated in several signaling pathways. Due to these multifunctional effects, TRAIP is more related to cellular mitosis, chromosome segregation, and DNA damage response. Tumor necrosis factor interacting protein is a downstream signaling molecule that contains a RING domain with E3 ubiquitin ligase activity at the N terminal side followed by coiled-coil and C terminal leucine zipper domain. Human TRAIP is constituted of 469 amino acids with 76% sequence similarity with the mouse TRAIP protein. Although, the main inhibitory function of TRAIP has been known for decades, however, in vitro interaction of TRAIPCC domain with RAP80 Zinc finger motif has not been reported yet. Besides, RAP80, the binding partner of TRAIPCC protein has been implicated in DNA damage response. Results Our in vitro study shows that the TRAIP CC (64-166) associates with the RAP80 zinc finger of corresponding amino acid 490-584. However, TRAIP CCLZ (66-260) and TRAIP RINGCC (1 = 157) failed to interact with the RAP80 zinc finger of corresponding amino acid 490-584. The current study reinforces TRAIP CC (64-166) and RAP80 zinc finger of corresponding amino acid 490-584 associates to form a complex. Moreover, SDS PAGE arbitrated the homogeneity of RAP80 Zinc finger and TRAIP CC of corresponding amino acid 490-584 and 64-166, respectively. Conclusion In vitro, a specific interaction was observed between the TRAIP CC (64-166) and the RAP80 zinc finger of the corresponding amino acid 490-584 and a specific binding area of the RAP80 zinc finger motif were investigated. The TRAIPCC region is required for the complex to bind to the RAP80-Zn finger motif. This strategy may be necessary for the RAP80 zinc finger activity to the TRAIP CC protein.
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Affiliation(s)
- Eijaz Ahmed Bhat
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, PR China.,Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Nasreena Sajjad
- Department of Biochemistry, University of Kashmir, Hazratbal, Jammu and Kashmir, India
| | - Irfan A Rather
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Jamal S M Sabir
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Yan-Yan Hor
- Department of Biotechnology, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, Republic of Korea
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12
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Krais JJ, Wang Y, Patel P, Basu J, Bernhardy AJ, Johnson N. RNF168-mediated localization of BARD1 recruits the BRCA1-PALB2 complex to DNA damage. Nat Commun 2021; 12:5016. [PMID: 34408138 PMCID: PMC8373961 DOI: 10.1038/s41467-021-25346-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/30/2021] [Indexed: 12/19/2022] Open
Abstract
DNA damage prompts a diverse range of alterations to the chromatin landscape. The RNF168 E3 ubiquitin ligase catalyzes the mono-ubiquitination of histone H2A at lysine (K)13/15 (mUb-H2A), forming a binding module for DNA repair proteins. BRCA1 promotes homologous recombination (HR), in part, through its interaction with PALB2, and the formation of a larger BRCA1-PALB2-BRCA2-RAD51 (BRCA1-P) complex. The mechanism by which BRCA1-P is recruited to chromatin surrounding DNA breaks is unclear. In this study, we reveal that an RNF168-governed signaling pathway is responsible for localizing the BRCA1-P complex to DNA damage. Using mice harboring a Brca1CC (coiled coil) mutation that blocks the Brca1-Palb2 interaction, we uncovered an epistatic relationship between Rnf168− and Brca1CC alleles, which disrupted development, and reduced the efficiency of Palb2-Rad51 localization. Mechanistically, we show that RNF168-generated mUb-H2A recruits BARD1 through a BRCT domain ubiquitin-dependent recruitment motif (BUDR). Subsequently, BARD1-BRCA1 accumulate PALB2-RAD51 at DNA breaks via the CC domain-mediated BRCA1-PALB2 interaction. Together, these findings establish a series of molecular interactions that connect the DNA damage signaling and HR repair machinery. The BRCA1-PALB2-BRCA2-RAD51 (BRCA1-P) complex is well known to play a fundamental role in DNA repair, but how the complex recruitment is regulated is still a matter of interest. Here the authors reveal mechanistic insights into RNF168 activity being responsible for PALB2 recruitment, through BARD1-BRCA1 during homologous recombination repair.
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Affiliation(s)
- John J Krais
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Yifan Wang
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Pooja Patel
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Jayati Basu
- Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Andrea J Bernhardy
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Neil Johnson
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA.
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13
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Ju MK, Shin KJ, Lee JR, Khim KW, A Lee E, Ra JS, Kim BG, Jo HS, Yoon JH, Kim TM, Myung K, Choi JH, Kim H, Chae YC. NSMF promotes the replication stress-induced DNA damage response for genome maintenance. Nucleic Acids Res 2021; 49:5605-5622. [PMID: 33963872 PMCID: PMC8191778 DOI: 10.1093/nar/gkab311] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 11/14/2022] Open
Abstract
Proper activation of DNA repair pathways in response to DNA replication stress is critical for maintaining genomic integrity. Due to the complex nature of the replication fork (RF), problems at the RF require multiple proteins, some of which remain unidentified, for resolution. In this study, we identified the N-methyl-D-aspartate receptor synaptonuclear signaling and neuronal migration factor (NSMF) as a key replication stress response factor that is important for ataxia telangiectasia and Rad3-related protein (ATR) activation. NSMF localizes rapidly to stalled RFs and acts as a scaffold to modulate replication protein A (RPA) complex formation with cell division cycle 5-like (CDC5L) and ATR/ATR-interacting protein (ATRIP). Depletion of NSMF compromised phosphorylation and ubiquitination of RPA2 and the ATR signaling cascade, resulting in genomic instability at RFs under DNA replication stress. Consistently, NSMF knockout mice exhibited increased genomic instability and hypersensitivity to genotoxic stress. NSMF deficiency in human and mouse cells also caused increased chromosomal instability. Collectively, these findings demonstrate that NSMF regulates the ATR pathway and the replication stress response network for genome maintenance and cell survival.
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Affiliation(s)
- Min Kyung Ju
- Department of Life Sciences, Ulsan National University of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Kyeong Jin Shin
- Department of Life Sciences, Ulsan National University of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Joo Rak Lee
- Department of Life Sciences, Ulsan National University of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Keon Woo Khim
- Department of Life Sciences, Ulsan National University of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Eun A Lee
- Center for Genomic Integrity Institute for Basic Science (IBS), UNIST, Ulsan 44919, Republic of Korea
| | - Jae Sun Ra
- Center for Genomic Integrity Institute for Basic Science (IBS), UNIST, Ulsan 44919, Republic of Korea
| | - Byung-Gyu Kim
- Center for Genomic Integrity Institute for Basic Science (IBS), UNIST, Ulsan 44919, Republic of Korea
| | - Han-Seul Jo
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Jong Hyuk Yoon
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Tae Moon Kim
- Center for Genomic Integrity Institute for Basic Science (IBS), UNIST, Ulsan 44919, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity Institute for Basic Science (IBS), UNIST, Ulsan 44919, Republic of Korea.,Department of Biomedical Engineering, Ulsan National University of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jang Hyun Choi
- Department of Life Sciences, Ulsan National University of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Hongtae Kim
- Department of Life Sciences, Ulsan National University of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.,Center for Genomic Integrity Institute for Basic Science (IBS), UNIST, Ulsan 44919, Republic of Korea
| | - Young Chan Chae
- Department of Life Sciences, Ulsan National University of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
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14
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Villa F, Fujisawa R, Ainsworth J, Nishimura K, Lie‐A‐Ling M, Lacaud G, Labib KPM. CUL2 LRR1 , TRAIP and p97 control CMG helicase disassembly in the mammalian cell cycle. EMBO Rep 2021; 22:e52164. [PMID: 33590678 PMCID: PMC7926238 DOI: 10.15252/embr.202052164] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/16/2020] [Accepted: 01/07/2021] [Indexed: 11/26/2022] Open
Abstract
The eukaryotic replisome is disassembled in each cell cycle, dependent upon ubiquitylation of the CMG helicase. Studies of Saccharomyces cerevisiae, Caenorhabditis elegans and Xenopus laevis have revealed surprising evolutionary diversity in the ubiquitin ligases that control CMG ubiquitylation, but regulated disassembly of the mammalian replisome has yet to be explored. Here, we describe a model system for studying the ubiquitylation and chromatin extraction of the mammalian CMG replisome, based on mouse embryonic stem cells. We show that the ubiquitin ligase CUL2LRR1 is required for ubiquitylation of the CMG-MCM7 subunit during S-phase, leading to disassembly by the p97 ATPase. Moreover, a second pathway of CMG disassembly is activated during mitosis, dependent upon the TRAIP ubiquitin ligase that is mutated in primordial dwarfism and mis-regulated in various cancers. These findings indicate that replisome disassembly in diverse metazoa is regulated by a conserved pair of ubiquitin ligases, distinct from those present in other eukaryotes.
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Affiliation(s)
- Fabrizio Villa
- The MRC Protein Phosphorylation and Ubiquitylation UnitSchool of Life SciencesUniversity of DundeeDundeeUK
| | - Ryo Fujisawa
- The MRC Protein Phosphorylation and Ubiquitylation UnitSchool of Life SciencesUniversity of DundeeDundeeUK
| | - Johanna Ainsworth
- The MRC Protein Phosphorylation and Ubiquitylation UnitSchool of Life SciencesUniversity of DundeeDundeeUK
| | - Kohei Nishimura
- The MRC Protein Phosphorylation and Ubiquitylation UnitSchool of Life SciencesUniversity of DundeeDundeeUK
- Division of Biological ScienceGraduate School of ScienceNagoya UniversityNagoyaJapan
| | - Michael Lie‐A‐Ling
- Cancer Research U.K. Manchester InstituteThe University of ManchesterAlderley ParkUK
| | - Georges Lacaud
- Cancer Research U.K. Manchester InstituteThe University of ManchesterAlderley ParkUK
| | - Karim PM Labib
- The MRC Protein Phosphorylation and Ubiquitylation UnitSchool of Life SciencesUniversity of DundeeDundeeUK
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15
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Cuella-Martin R, Hayward SB, Fan X, Chen X, Huang JW, Taglialatela A, Leuzzi G, Zhao J, Rabadan R, Lu C, Shen Y, Ciccia A. Functional interrogation of DNA damage response variants with base editing screens. Cell 2021; 184:1081-1097.e19. [PMID: 33606978 PMCID: PMC8018281 DOI: 10.1016/j.cell.2021.01.041] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 11/16/2020] [Accepted: 01/22/2021] [Indexed: 12/13/2022]
Abstract
Mutations in DNA damage response (DDR) genes endanger genome integrity and predispose to cancer and genetic disorders. Here, using CRISPR-dependent cytosine base editing screens, we identify > 2,000 sgRNAs that generate nucleotide variants in 86 DDR genes, resulting in altered cellular fitness upon DNA damage. Among those variants, we discover loss- and gain-of-function mutants in the Tudor domain of the DDR regulator 53BP1 that define a non-canonical surface required for binding the deubiquitinase USP28. Moreover, we characterize variants of the TRAIP ubiquitin ligase that define a domain, whose loss renders cells resistant to topoisomerase I inhibition. Finally, we identify mutations in the ATM kinase with opposing genome stability phenotypes and loss-of-function mutations in the CHK2 kinase previously categorized as variants of uncertain significance for breast cancer. We anticipate that this resource will enable the discovery of additional DDR gene functions and expedite studies of DDR variants in human disease.
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Affiliation(s)
- Raquel Cuella-Martin
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Samuel B Hayward
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xiao Fan
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xiao Chen
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jen-Wei Huang
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Angelo Taglialatela
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Giuseppe Leuzzi
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Junfei Zhao
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA; Program for Mathematical Genomics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Raul Rabadan
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA; Program for Mathematical Genomics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Chao Lu
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
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16
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Wu RA, Pellman DS, Walter JC. The Ubiquitin Ligase TRAIP: Double-Edged Sword at the Replisome. Trends Cell Biol 2021; 31:75-85. [PMID: 33317933 PMCID: PMC7856240 DOI: 10.1016/j.tcb.2020.11.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/09/2020] [Accepted: 11/16/2020] [Indexed: 12/12/2022]
Abstract
In preparation for cell division, the genome must be copied with high fidelity. However, replisomes often encounter obstacles, including bulky DNA lesions caused by reactive metabolites and chemotherapeutics, as well as stable nucleoprotein complexes. Here, we discuss recent advances in our understanding of TRAIP, a replisome-associated E3 ubiquitin ligase that is mutated in microcephalic primordial dwarfism. In interphase, TRAIP helps replisomes overcome DNA interstrand crosslinks and DNA-protein crosslinks, whereas in mitosis it triggers disassembly of all replisomes that remain on chromatin. We describe a model to explain how TRAIP performs these disparate functions and how they help maintain genome integrity.
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Affiliation(s)
- R Alex Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA 02115, USA
| | - David S Pellman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Blavatnik Institute, Boston, MA 02115, USA; Howard Hughes Medical Institute, Cambridge, MA, 02139, USA
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA 02115, USA; Howard Hughes Medical Institute, Cambridge, MA, 02139, USA.
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17
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Epigenetic modification and a role for the E3 ligase RNF40 in cancer development and metastasis. Oncogene 2020; 40:465-474. [PMID: 33199825 PMCID: PMC7819849 DOI: 10.1038/s41388-020-01556-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 10/15/2020] [Accepted: 11/02/2020] [Indexed: 12/19/2022]
Abstract
RNF40 (OMIM: 607700) is a really interesting new gene (RING) finger E3 ubiquitin ligase containing multiple coiled-coil domains and a C-terminal RING finger motif, which engage in protein–DNA and protein–protein interactions. RNF40 encodes a polypeptide of 1001 amino acids with a predicted molecular mass of 113,678 Da. RNF40 and its paralog RNF20 form a stable heterodimer complex that can monoubiquitylate histone H2B at lysine 120 as well as other nonhistone proteins. Cancer is a major public health problem and the second leading cause of death. Through its protein ubiquitylation activity, RNF40 acts as a tumor suppressor or oncogene to play major epigenetic roles in cancer development, progression, and metastasis, highlighting the essential function of RNF40 and the importance of studying it. In this review, we summarize current knowledge about RNF40 gene structure and the role of RNF40 in histone H2B monoubiquitylation, DNA damage repair, apoptosis, cancer development, and metastasis. We also underscore challenges in applying this information to cancer prognosis and prevention and highlight the urgent need for additional investigations of RNF40 as a potential target for cancer therapeutics.
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18
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Hwang JW, Kim SN, Myung N, Song D, Han G, Bae GU, Bedford MT, Kim YK. PRMT5 promotes DNA repair through methylation of 53BP1 and is regulated by Src-mediated phosphorylation. Commun Biol 2020; 3:428. [PMID: 32759981 PMCID: PMC7406651 DOI: 10.1038/s42003-020-01157-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 07/16/2020] [Indexed: 02/07/2023] Open
Abstract
PRMT5 participates in various cellular processes, including transcription regulation, signal transduction, mRNA splicing, and DNA repair; however, its mechanism of regulation is poorly understood. Here, we demonstrate that PRMT5 is phosphorylated at residue Y324 by Src kinase, a negative regulator of its activity. Either phosphorylation or substitution of the Y324 residue suppresses PRMT5 activity by preventing its binding with the methyl donor S-adenosyl-L-methionine. Additionally, we show that PRMT5 activity is associated with non-homologous end joining (NHEJ) repair by methylating and stabilizing p53-binding protein 1 (53BP1), which promotes cellular survival after DNA damage. Src-mediated phosphorylation of PRMT5 and the subsequent inhibition of its activity during the DNA damage process blocks NHEJ repair, leading to apoptotic cell death. Altogether, our findings suggest that PRMT5 regulates DNA repair through Src-mediated Y324 phosphorylation in response to DNA damage. Hwang et al. show that the activity of PRMT5 methyltransferase is regulated by Src kinase-mediated phosphorylation at Y324 in response to DNA damage. They also show that PRMT5 participates in NHEJ repair by regulating 53BP1 protein levels and is critical for cellular survival after DNA damage.
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Affiliation(s)
- Jee Won Hwang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Su-Nam Kim
- Natural Product Research Institute, Korea Institute of Science and Technology, Gangneung, 25451, Republic of Korea
| | - Nayeon Myung
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Doona Song
- Department of Biotechnology, Department of Biomedical Sciences, Yonsei University, Seoul, 03722, Republic of Korea
| | - Gyoonhee Han
- Department of Biotechnology, Department of Biomedical Sciences, Yonsei University, Seoul, 03722, Republic of Korea
| | - Gyu-Un Bae
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA.
| | - Yong Kee Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul, 04310, Republic of Korea.
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19
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Li Y, Ma X, Wu W, Chen Z, Meng G. PML Nuclear Body Biogenesis, Carcinogenesis, and Targeted Therapy. Trends Cancer 2020; 6:889-906. [PMID: 32527650 DOI: 10.1016/j.trecan.2020.05.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/20/2020] [Accepted: 05/11/2020] [Indexed: 01/16/2023]
Abstract
Targeted therapy has become increasingly important in cancer therapy. For example, targeting the promyelocytic leukemia PML protein in leukemia has proved to be an effective treatment. PML is the core component of super-assembled structures called PML nuclear bodies (NBs). Although this nuclear megaDalton complex was first observed in the 1960s, the mechanism of its assembly remains poorly understood. We review recent breakthroughs in the PML field ranging from a revised assembly mechanism to PML-driven genome organization and carcinogenesis. In addition, we highlight that oncogenic oligomerization might also represent a promising target in the treatment of leukemias and solid tumors.
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Affiliation(s)
- Yuwen Li
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiaodan Ma
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Wenyu Wu
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhu Chen
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Guoyu Meng
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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20
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Kong LR, Ong RW, Tan TZ, Mohamed Salleh NAB, Thangavelu M, Chan JV, Koh LYJ, Periyasamy G, Lau JA, Le TBU, Wang L, Lee M, Kannan S, Verma CS, Lim CM, Chng WJ, Lane DP, Venkitaraman A, Hung HT, Cheok CF, Goh BC. Targeting codon 158 p53-mutant cancers via the induction of p53 acetylation. Nat Commun 2020; 11:2086. [PMID: 32350249 PMCID: PMC7190866 DOI: 10.1038/s41467-020-15608-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 03/19/2020] [Indexed: 12/14/2022] Open
Abstract
Gain of function (GOF) DNA binding domain (DBD) mutations of TP53 upregulate chromatin regulatory genes that promote genome-wide histone methylation and acetylation. Here, we therapeutically exploit the oncogenic GOF mechanisms of p53 codon 158 (Arg158) mutation, a DBD mutant found to be prevalent in lung carcinomas. Using high throughput compound screening and combination analyses, we uncover that acetylating mutp53R158G could render cancers susceptible to cisplatin-induced DNA stress. Acetylation of mutp53R158G alters DNA binding motifs and upregulates TRAIP, a RING domain-containing E3 ubiquitin ligase which dephosphorylates IĸB and impedes nuclear translocation of RelA (p65), thus repressing oncogenic nuclear factor kappa-B (NF-ĸB) signaling and inducing apoptosis. Given that this mechanism of cytotoxic vulnerability appears inapt in p53 wild-type (WT) or other hotspot GOF mutp53 cells, our work provides a therapeutic opportunity specific to Arg158-mutp53 tumors utilizing a regimen consisting of DNA-damaging agents and mutp53 acetylators, which is currently being pursued clinically. Codon 158 gain-of-function mutant p53 (158-mutp53) promotes tumourigenesis in lung cancer. Here, the authors show that 158-mutp53 render cancers sensitive to cisplatin and p53 acetylation agents through a mechanism where acetylated mutant p53 upregulates TRAIP and inhibits NF-ĸB signaling.
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Affiliation(s)
- Li Ren Kong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore. .,Medical Research Council Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, UK.
| | - Richard Weijie Ong
- Laboratory of Molecular Endocrinology, National Cancer Centre Singapore, Singapore, Singapore
| | - Tuan Zea Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | | | - Matan Thangavelu
- Genome Institute of Singapore, Agency for Science, Technology & Research (A*STAR), Singapore, 138672, Singapore
| | - Jane Vin Chan
- Genome Institute of Singapore, Agency for Science, Technology & Research (A*STAR), Singapore, 138672, Singapore
| | - Lie Yong Judice Koh
- Genome Institute of Singapore, Agency for Science, Technology & Research (A*STAR), Singapore, 138672, Singapore
| | - Giridharan Periyasamy
- Genome Institute of Singapore, Agency for Science, Technology & Research (A*STAR), Singapore, 138672, Singapore
| | - Jieying Amelia Lau
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Thi Bich Uyen Le
- Laboratory of Molecular Endocrinology, National Cancer Centre Singapore, Singapore, Singapore
| | - Lingzhi Wang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.,Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Miyoung Lee
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Srinivasaraghavan Kannan
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR), Singapore, 138671, Singapore
| | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR), Singapore, 138671, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - Chwee Ming Lim
- Division of Surgical Oncology (Head and Neck Surgery), National University Cancer Institute, Singapore (NCIS), Singapore, 119074, Singapore
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.,Department of Haematology-Oncology, National University Cancer Institute, Singapore, 119074, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - David P Lane
- p53 Laboratory (p53Lab), Agency for Science, Technology, and Research (A*STAR), Singapore, 138648, Singapore
| | - Ashok Venkitaraman
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Huynh The Hung
- Laboratory of Molecular Endocrinology, National Cancer Centre Singapore, Singapore, Singapore
| | - Chit Fang Cheok
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology, and Research (A*STAR), Singapore, 138673, Singapore.,Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119074, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore
| | - Boon Cher Goh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore. .,Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore. .,Department of Haematology-Oncology, National University Cancer Institute, Singapore, 119074, Singapore.
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21
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Sonneville R, Bhowmick R, Hoffmann S, Mailand N, Hickson ID, Labib K. TRAIP drives replisome disassembly and mitotic DNA repair synthesis at sites of incomplete DNA replication. eLife 2019; 8:e48686. [PMID: 31545170 PMCID: PMC6773462 DOI: 10.7554/elife.48686] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 09/20/2019] [Indexed: 11/13/2022] Open
Abstract
The faithful segregation of eukaryotic chromosomes in mitosis requires that the genome be duplicated completely prior to anaphase. However, cells with large genomes sometimes fail to complete replication during interphase and instead enter mitosis with regions of incompletely replicated DNA. These regions are processed in early mitosis via a process known as mitotic DNA repair synthesis (MiDAS), but little is known about how cells switch from conventional DNA replication to MiDAS. Using the early embryo of the nematode Caenorhabditis elegans as a model system, we show that the TRAIP ubiquitin ligase drives replisome disassembly in response to incomplete DNA replication, thereby providing access to replication forks for other factors. Moreover, TRAIP is essential for MiDAS in human cells, and is important in both systems to prevent mitotic segregation errors. Our data indicate that TRAIP is a master regulator of the processing of incomplete DNA replication during mitosis in metazoa.
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Affiliation(s)
- Remi Sonneville
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
| | - Rahul Bhowmick
- Department of Cellular and Molecular Medicine, Center for Chromosome StabilityUniversity of CopenhagenCopenhagenDenmark
| | - Saskia Hoffmann
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Niels Mailand
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Ian D Hickson
- Department of Cellular and Molecular Medicine, Center for Chromosome StabilityUniversity of CopenhagenCopenhagenDenmark
| | - Karim Labib
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
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22
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Chen Y, Li J, Cao F, Lam J, Cheng CC, Yu CH, Huen MS. Nucleolar residence of the seckel syndrome protein TRAIP is coupled to ribosomal DNA transcription. Nucleic Acids Res 2019; 46:10119-10131. [PMID: 30165463 PMCID: PMC6212796 DOI: 10.1093/nar/gky775] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 08/16/2018] [Indexed: 12/30/2022] Open
Abstract
The RING finger protein TRAIP protects genome integrity and its mutation causes Seckel syndrome. TRAIP encodes a nucleolar protein that migrates to UV-induced DNA lesions via a direct interaction with the DNA replication clamp PCNA. Thus far, mechanistically how UV mobilizes TRAIP from the nucleoli remains unknown. We found that PCNA binding is dispensable for the nucleolus-nucleoplasm shuttling of TRAIP following cell exposure to UV irradiation, and that its redistribution did not rely on the master DNA damage kinases ATM and ATR. Interestingly, I-PpoI-induced ribosomal DNA damage led to TRAIP exclusion from the nucleoli, raising the possibility that active ribosomal DNA transcription may underlie TRAIP retention in the nuclear sub-compartments. Accordingly, chemical inhibition of RNA polymerase I activity led to TRAIP diffusion into the nucleoplasm, and was coupled with marked reduction of DNA/RNA hybrids in the nucleoli, suggesting that TRAIP may be sequestered via binding to nucleic acid structures in the nucleoli. Consistently, cell pre-treatment with DNase/RNase effectively released TRAIP from the nucleoli. Taken together, our study defines a bipartite mechanism that drives TRAIP trafficking in response to UV damage, and highlights the nucleolus as a stress sensor that contributes to orchestrating DNA damage responses.
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Affiliation(s)
- Yangzi Chen
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R
| | - Junshi Li
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R
| | - Fakun Cao
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R
| | - Jason Lam
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R
| | - Clooney Cy Cheng
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R
| | - Cheng-Han Yu
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R
| | - Michael Sy Huen
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong S.A.R.,Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, PR China.,State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong S.A.R
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23
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Priego Moreno S, Jones RM, Poovathumkadavil D, Scaramuzza S, Gambus A. Mitotic replisome disassembly depends on TRAIP ubiquitin ligase activity. Life Sci Alliance 2019; 2:2/2/e201900390. [PMID: 30979826 PMCID: PMC6464043 DOI: 10.26508/lsa.201900390] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 01/08/2023] Open
Abstract
Analysis of the mitotic replisome disassembly pathway in X. laevis egg extract shows that any replisomes retained on chromatin past S-phase are unloaded through formation of K6- and K63-linked ubiquitin chains on Mcm7 by TRAIP ubiquitin ligase and p97/VCP activity. We have shown previously that the process of replication machinery (replisome) disassembly at the termination of DNA replication forks in the S-phase is driven through polyubiquitylation of one of the replicative helicase subunits (Mcm7) by Cul2LRR1 ubiquitin ligase. Interestingly, upon inhibition of this pathway in Caenorhabditis elegans embryos, the replisomes retained on chromatin were unloaded in the subsequent mitosis. Here, we show that this mitotic replisome disassembly pathway exists in Xenopus laevis egg extract and we determine the first elements of its regulation. The mitotic disassembly pathway depends on the formation of K6- and K63-linked ubiquitin chains on Mcm7 by TRAIP ubiquitin ligase and the activity of p97/VCP protein segregase. Unlike in lower eukaryotes, however, it does not require SUMO modifications. Importantly, we also show that this process can remove all replisomes from mitotic chromatin, including stalled ones, which indicates a wide application for this pathway over being just a “backup” for terminated replisomes. Finally, we characterise the composition of the replisome retained on chromatin until mitosis.
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Affiliation(s)
- Sara Priego Moreno
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Rebecca M Jones
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Divyasree Poovathumkadavil
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Shaun Scaramuzza
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Agnieszka Gambus
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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24
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Deng L, Wu RA, Sonneville R, Kochenova OV, Labib K, Pellman D, Walter JC. Mitotic CDK Promotes Replisome Disassembly, Fork Breakage, and Complex DNA Rearrangements. Mol Cell 2019; 73:915-929.e6. [PMID: 30849395 PMCID: PMC6410736 DOI: 10.1016/j.molcel.2018.12.021] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 10/03/2018] [Accepted: 12/21/2018] [Indexed: 12/27/2022]
Abstract
DNA replication errors generate complex chromosomal rearrangements and thereby contribute to tumorigenesis and other human diseases. One mechanism that triggers these errors is mitotic entry before the completion of DNA replication. To address how mitosis might affect DNA replication, we used Xenopus egg extracts. When mitotic CDK (Cyclin B1-CDK1) is used to drive interphase egg extracts into a mitotic state, the replicative CMG (CDC45/MCM2-7/GINS) helicase undergoes ubiquitylation on its MCM7 subunit, dependent on the E3 ubiquitin ligase TRAIP. Whether replisomes have stalled or undergone termination, CMG ubiquitylation is followed by its extraction from chromatin by the CDC48/p97 ATPase. TRAIP-dependent CMG unloading during mitosis is also seen in C. elegans early embryos. At stalled forks, CMG removal results in fork breakage and end joining events involving deletions and templated insertions. Our results identify a mitotic pathway of global replisome disassembly that can trigger replication fork collapse and DNA rearrangements.
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Affiliation(s)
- Lin Deng
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Blavatnik Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA 02115, USA
| | - R Alex Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA 02115, USA
| | - Remi Sonneville
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Olga V Kochenova
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA 02115, USA
| | - Karim Labib
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - David Pellman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Blavatnik Institute, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA.
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA.
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25
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Yates M, Maréchal A. Ubiquitylation at the Fork: Making and Breaking Chains to Complete DNA Replication. Int J Mol Sci 2018; 19:E2909. [PMID: 30257459 PMCID: PMC6213728 DOI: 10.3390/ijms19102909] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 09/20/2018] [Accepted: 09/24/2018] [Indexed: 12/11/2022] Open
Abstract
The complete and accurate replication of the genome is a crucial aspect of cell proliferation that is often perturbed during oncogenesis. Replication stress arising from a variety of obstacles to replication fork progression and processivity is an important contributor to genome destabilization. Accordingly, cells mount a complex response to this stress that allows the stabilization and restart of stalled replication forks and enables the full duplication of the genetic material. This response articulates itself on three important platforms, Replication Protein A/RPA-coated single-stranded DNA, the DNA polymerase processivity clamp PCNA and the FANCD2/I Fanconi Anemia complex. On these platforms, the recruitment, activation and release of a variety of genome maintenance factors is regulated by post-translational modifications including mono- and poly-ubiquitylation. Here, we review recent insights into the control of replication fork stability and restart by the ubiquitin system during replication stress with a particular focus on human cells. We highlight the roles of E3 ubiquitin ligases, ubiquitin readers and deubiquitylases that provide the required flexibility at stalled forks to select the optimal restart pathways and rescue genome stability during stressful conditions.
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Affiliation(s)
- Maïlyn Yates
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada.
| | - Alexandre Maréchal
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada.
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26
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Zheng X, Chen K, Liu X, Pan Y, Liu H. High RNF40 expression indicates poor prognosis of hepatocellular carcinoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:2901-2906. [PMID: 31938414 PMCID: PMC6958262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 03/28/2018] [Indexed: 06/10/2023]
Abstract
Human RING-finger protein 40 (RNF40) is reported as an E3 ligase of H2B ubiquitination. RNF40 needs to couple with its homolog RNF20 to format a complex to regulate DNA double strand break (DSB) response and chromatin stability. Deficient expression of RNF40 might cause incorrect DNA repair and contribute to genomic instability, leading to an abnormal transcriptional program. Incorrect DSB repair and aberrant gene transcription play important roles in tumorigenesis. The role in primary hepatocellular carcinoma (HCC), however, remains unclear. In this study, we selected 103 cases of HCC for immunohistochemistry to explore the role of RNF40 in HCC. The relationship between RNF40 expression and clinicopathological features of HCC was evaluated. RNF40 was mainly localized in the nucleus, where the percentage of low and high staining of RNF40 in tumor tissues was 50.4% (53/103) and 49.6% (50/103), respectively. By contrast, in para-normal tissues the percentage was 92.2% (95/103) and 7.8% (8/103) respectively. Expression of RNF40 in tumor tissues was significantly higher than that in para-normal tissues (P>0.01). Expression of RNF40 had significant association with AFP and TNM tumor stage (both P>0.01). However, age, gender, Hepatitis B Virus infection, liver cirrhosis, tumor size, tumor number, differential stage, and tumor thrombosis were not associated with RNF40 expression. Meanwhile, HCC patients with high expression of RNF40 had lower 5 year overall survival rates and disease-free survival rates (P>0.05). RNF40 is, potentially, an independent prognostic factor for survival in HCC.
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Affiliation(s)
- Xueyong Zheng
- Department of General Surgery, Institute of Minimally Invasive Surgery, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang UniversityHangzhou, China
| | - Ke Chen
- Department of General Surgery, Institute of Minimally Invasive Surgery, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang UniversityHangzhou, China
| | - Xiaolong Liu
- Department of General Surgery, Institute of Minimally Invasive Surgery, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang UniversityHangzhou, China
| | - Yu Pan
- Department of General Surgery, Institute of Minimally Invasive Surgery, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang UniversityHangzhou, China
| | - Hui Liu
- Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang UniversityHangzhou, Zhejiang, China
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27
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Kochan JA, Desclos EC, Bosch R, Meister L, Vriend LE, van Attikum H, Krawczyk PM. Meta-analysis of DNA double-strand break response kinetics. Nucleic Acids Res 2017; 45:12625-12637. [PMID: 29182755 PMCID: PMC5728399 DOI: 10.1093/nar/gkx1128] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/24/2017] [Accepted: 11/13/2017] [Indexed: 12/12/2022] Open
Abstract
Most proteins involved in the DNA double-strand break response (DSBR) accumulate at the damage sites, where they perform functions related to damage signaling, chromatin remodeling and repair. Over the last two decades, studying the accumulation of many DSBR proteins provided information about their functionality and underlying mechanisms of action. However, comparison and systemic interpretation of these data is challenging due to their scattered nature and differing experimental approaches. Here, we extracted, analyzed and compared the available results describing accumulation of 79 DSBR proteins at sites of DNA damage, which can be further explored using Cumulus (http://www.dna-repair.live/cumulus/)-the accompanying interactive online application. Despite large inter-study variability, our analysis revealed that the accumulation of most proteins starts immediately after damage induction, occurs in parallel and peaks within 15-20 min. Various DSBR pathways are characterized by distinct accumulation kinetics with major non-homologous end joining proteins being generally faster than those involved in homologous recombination, and signaling and chromatin remodeling factors accumulating with varying speeds. Our meta-analysis provides, for the first time, comprehensive overview of the temporal organization of the DSBR in mammalian cells and could serve as a reference for future mechanistic studies of this complex process.
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Affiliation(s)
- Jakub A. Kochan
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Emilie C.B. Desclos
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Ruben Bosch
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Luna Meister
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Lianne E.M. Vriend
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Przemek M. Krawczyk
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
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28
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Lombardi PM, Matunis MJ, Wolberger C. RAP80, ubiquitin and SUMO in the DNA damage response. J Mol Med (Berl) 2017; 95:799-807. [PMID: 28681078 DOI: 10.1007/s00109-017-1561-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 06/07/2017] [Accepted: 06/13/2017] [Indexed: 12/28/2022]
Abstract
A decade has passed since the first reported connection between RAP80 and BRCA1 in DNA double-strand break repair. Despite the initial identification of RAP80 as a factor localizing BRCA1 to DNA double-strand breaks and potentially promoting homologous recombination, there is increasing evidence that RAP80 instead suppresses homologous recombination to fine-tune the balance of competing DNA repair processes during the S/G2 phase of the cell cycle. RAP80 opposes homologous recombination by inhibiting DNA end-resection and sequestering BRCA1 into the BRCA1-A complex. Ubiquitin and SUMO modifications of chromatin at DNA double-strand breaks recruit RAP80, which contains distinct sequence motifs that recognize ubiquitin and SUMO. Here, we review RAP80's role in repressing homologous recombination at DNA double-strand breaks and how this role is facilitated by its ability to bind ubiquitin and SUMO modifications.
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Affiliation(s)
- Patrick M Lombardi
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Michael J Matunis
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA.
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29
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Chang HR, Munkhjargal A, Kim MJ, Park SY, Jung E, Ryu JH, Yang Y, Lim JS, Kim Y. The functional roles of PML nuclear bodies in genome maintenance. Mutat Res 2017; 809:99-107. [PMID: 28521962 DOI: 10.1016/j.mrfmmm.2017.05.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/28/2017] [Accepted: 05/04/2017] [Indexed: 02/07/2023]
Abstract
In the nucleus, there are several membraneless structures called nuclear bodies. Among them, promyelocytic leukemia nuclear bodies (PML-NBs) are involved in multiple genome maintenance pathways including the DNA damage response, DNA repair, telomere homeostasis, and p53-associated apoptosis. In response to DNA damage, PML-NBs are coalesced and divided by a fission mechanism, thus increasing their number. PML-NBs also play a role in repairing DNA double-strand breaks (DSBs) by homologous recombination (HR). Clinically, the dominant negative PML-RARα fusion protein expressed in acute promyelocytic leukemia (APL) inhibits the transactivation of downstream factors and disrupts PML function, revealing the tumor suppressor role of PML-NBs. All-trans retinoic acid and arsenic trioxide treatment has been implemented for promyelocytic leukemia to target the PML-RARα fusion protein. PML-NBs are associated with various factors implicated in genome maintenance, and are found at the sites of DNA damage. Their interaction with proteins such as p53 indicates that PML-NBs may play a significant role in apoptosis and cancer. Decades of research have revealed the importance of PML-NBs in diverse cellular pathways, yet the underlying molecular mechanisms and exact functions of PML-NBs remain elusive. In this review, PML protein modifications and the functional relevance of PML-NB and its associated factors in genome maintenance will be discussed.
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Affiliation(s)
- Hae Ryung Chang
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Anudari Munkhjargal
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Myung-Jin Kim
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Seon Young Park
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Eunyoung Jung
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Jae-Ha Ryu
- Research Center for Cell Fate Control, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Young Yang
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Jong-Seok Lim
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Yonghwan Kim
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea.
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30
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Ka NL, Na TY, Na H, Lee MH, Park HS, Hwang S, Kim IY, Seong JK, Lee MO. NR1D1 Recruitment to Sites of DNA Damage Inhibits Repair and Is Associated with Chemosensitivity of Breast Cancer. Cancer Res 2017; 77:2453-2463. [PMID: 28249904 DOI: 10.1158/0008-5472.can-16-2099] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/12/2016] [Accepted: 02/16/2017] [Indexed: 11/16/2022]
Abstract
DNA repair capacity is critical for survival of cancer cells upon therapeutic DNA damage and thus is an important determinant of susceptibility to chemotherapy in cancer patients. In this study, we identified a novel function of nuclear receptor NR1D1 in DNA repair, which enhanced chemosensitivity in breast cancer cells. NR1D1 inhibited both nonhomologous end joining and homologous recombination double-strand breaks repair, and delayed the clearance of γH2AX DNA repair foci that formed after treatment of doxorubicin. PARylation of NR1D1 by PARP1 drove its recruitment to damaged DNA lesions. Deletion of the ligand binding domain of NR1D1 that interacted with PARP1, or treatment of 6-(5H)-phenanthridinone, an inhibitor of PARP1, suppressed the recruitment of NR1D1 to DNA damaged sites, indicating PARylation as a critical step for the NR1D1 recruitment. NR1D1 inhibited recruitment of the components of DNA damage response complex such as SIRT6, pNBS1, and BRCA1 to DNA lesions. Downregulation of NR1D1 in MCF7 cells resulted in resistance to doxorubicin, both in vitro and in vivo Analysis of four public patient data sets indicated that NR1D1 expression correlates positively with clinical outcome in breast cancer patients who received chemotherapy. Our findings suggest that NR1D1 and its ligands provide therapeutic options that could enhance the outcomes of chemotherapy in breast cancer patients. Cancer Res; 77(9); 2453-63. ©2017 AACR.
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Affiliation(s)
- Na-Lee Ka
- College of Pharmacy and Bio-MAX Institute, Seoul National University, Gwanak-gu, Seoul, Korea
| | - Tae-Young Na
- College of Pharmacy and Bio-MAX Institute, Seoul National University, Gwanak-gu, Seoul, Korea
| | - Hyelin Na
- College of Pharmacy and Bio-MAX Institute, Seoul National University, Gwanak-gu, Seoul, Korea
| | - Min-Ho Lee
- College of Pharmacy and Bio-MAX Institute, Seoul National University, Gwanak-gu, Seoul, Korea
| | - Han-Su Park
- College of Pharmacy and Bio-MAX Institute, Seoul National University, Gwanak-gu, Seoul, Korea
| | - Sewon Hwang
- College of Pharmacy and Bio-MAX Institute, Seoul National University, Gwanak-gu, Seoul, Korea
| | - Il Yong Kim
- College of Veterinary Medicine, Seoul National University and Korea Mouse Phenotyping Center, Gwanak-gu, Seoul, Korea
| | - Je Kyung Seong
- College of Veterinary Medicine, Seoul National University and Korea Mouse Phenotyping Center, Gwanak-gu, Seoul, Korea
| | - Mi-Ock Lee
- College of Pharmacy and Bio-MAX Institute, Seoul National University, Gwanak-gu, Seoul, Korea.
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31
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Yuan YF, Ren YX, Yuan P, Yan LY, Qiao J. TRAIP is involved in chromosome alignment and SAC regulation in mouse oocyte meiosis. Sci Rep 2016; 6:29735. [PMID: 27405720 PMCID: PMC4942609 DOI: 10.1038/srep29735] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 06/22/2016] [Indexed: 12/14/2022] Open
Abstract
Recent whole-exome sequencing (WES) studies demonstrated that TRAIP is associated with primordial dwarfism. Although TRAIP was partially studied in mitosis, its function in oocyte meiosis remained unknown. In this study, we investigated the roles of TRAIP during mouse oocyte meiosis. TRAIP was stably expressed during oocytes meiosis and co-localized with CREST at the centromere region. Knockdown of TRAIP led to DNA damage, as revealed by the appearance of γH2AX. Although oocytes meiotic maturation was not affected, the proportions of misaligned chromosomes and aneuploidy were elevated after TRAIP knockdown, suggesting TRAIP is required for stable kinetochore–microtubule (K-MT) attachment. TRAIP knockdown decreased the accumulation of Mad2 on centromeres, potentially explaining why oocyte maturation was not affected following formation of DNA lesions. Securin, a protein which was prevent from precocious degradation by Mad2, was down-regulated after TRAIP knockdown. Inhibition of TRAIP by microinjection of antibody into pro-metaphase I (pro-MI) stage oocytes resulted in precocious first polar body (PB1) extrusion, and live-cell imaging clearly revealed misaligned chromosomes after TRAIP knockdown. Taken together, these data indicate that TRAIP plays important roles in oocyte meiosis regulation.
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Affiliation(s)
- Yi-Feng Yuan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49 North HuaYuan Road, HaiDian District, Beijing 100191, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China
| | - Yi-Xin Ren
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China
| | - Peng Yuan
- Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China
| | - Li-Ying Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49 North HuaYuan Road, HaiDian District, Beijing 100191, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49 North HuaYuan Road, HaiDian District, Beijing 100191, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China
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Feng W, Guo Y, Huang J, Deng Y, Zang J, Huen MSY. TRAIP regulates replication fork recovery and progression via PCNA. Cell Discov 2016; 2:16016. [PMID: 27462463 PMCID: PMC4923944 DOI: 10.1038/celldisc.2016.16] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 03/23/2016] [Indexed: 12/24/2022] Open
Abstract
PCNA is a central scaffold that coordinately assembles replication and repair machineries at DNA replication forks for faithful genome duplication. Here, we describe TRAIP (RNF206) as a novel PCNA-interacting factor that has important roles during mammalian replicative stress responses. We show that TRAIP encodes a nucleolar protein that migrates to stalled replication forks, and that this is accomplished by its targeting of PCNA via an evolutionarily conserved PIP box on its C terminus. Accordingly, inactivation of TRAIP or its interaction with the PCNA clamp compromised replication fork recovery and progression, and leads to chromosome instability. Together, our findings establish TRAIP as a component of the mammalian replicative stress response network, and implicate the TRAIP-PCNA axis in recovery of stalled replication forks.
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Affiliation(s)
- Wanjuan Feng
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong S.A.R., China; Centre for Cancer Research, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong S.A.R., China
| | - Yingying Guo
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong S.A.R., China
| | - Jun Huang
- Life Sciences Institute, Zhejiang University, Zhejiang, China
| | - Yiqun Deng
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Jianye Zang
- School of Life Sciences, University of Science of Technology of China , Hefei, China
| | - Michael Shing-Yan Huen
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong S.A.R., China; Centre for Cancer Research, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong S.A.R., China; State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Pokfulam, Hong Kong S.A.R., China
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Interaction of hepatitis B virus X protein with PARP1 results in inhibition of DNA repair in hepatocellular carcinoma. Oncogene 2016; 35:5435-5445. [PMID: 27041572 DOI: 10.1038/onc.2016.82] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 02/05/2016] [Accepted: 02/23/2016] [Indexed: 02/07/2023]
Abstract
Hepatitis B virus X protein (HBx) contributes to the development of hepatocellular carcinoma (HCC), probably by regulating activities of many host or viral proteins through protein-protein interactions. In this study, we identified poly(ADP-ribose) polymerase (PARP1), a crucial factor in DNA repair, as an HBx-interacting protein using a proteomics approach. Coimmunoprecipitation and proximity ligation assays confirmed the binding and colocalization of HBx and PARP1 in the nucleus. The carboxyl-terminus of HBx protein bound to the catalytic domain of PARP1, and this binding reduced the enzymatic activity of PARP1 in both in vitro and in vivo assays. HBx interrupted the binding of PARP1 to Sirt6, which catalyzes the mono-ADP-ribosylation required for DNA repair. Consistently, overexpression of HBx inhibited the clearance of γH2AX DNA repair foci generated under oxidative stress in Chang liver cells. Recruitment of the DNA repair complex to the site-specific double-strand breaks was inhibited in the presence of HBx, when measured by laser microirradiation assay and damage-specific chromatin immunoprecipitation assays. Consequently, HBx increased signs of DNA damage such as accumulation of 8-hydroxy-2'-deoxyguanosine and comet formation, which were reversed by overexpression of PARP1 and/or Sirt6. Finally, the interaction between PARP1 and Sirt6 was markedly lower in the livers of HBx-transgenic mice and specimens obtained from HCC patients to compare with the corresponding control. Our data suggest that the physical interaction of HBx and PARP1 accelerates DNA damage by inhibiting recruitment of the DNA repair complex to the damaged DNA sites, which may lead to the onset of hepatocarcinogenesis.
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Park IS, Han YG, Chung HJ, Jung YW, Kim Y, Kim H. SUMOylation regulates nuclear localization and stability of TRAIP/RNF206. Biochem Biophys Res Commun 2016; 470:881-7. [DOI: 10.1016/j.bbrc.2016.01.141] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 01/22/2016] [Indexed: 12/14/2022]
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