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Coulson-Gilmer C, Littler S, Barnes B, Brady R, Anagho H, Pillay N, Dey M, Macmorland W, Bronder D, Nelson L, Tighe A, Lin WH, Morgan R, Unwin R, Nielsen M, McGrail J, Taylor S. Intrinsic PARG inhibitor sensitivity is mimicked by TIMELESS haploinsufficiency and rescued by nucleoside supplementation. NAR Cancer 2024; 6:zcae030. [PMID: 39015544 PMCID: PMC11249981 DOI: 10.1093/narcan/zcae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 06/20/2024] [Accepted: 06/26/2024] [Indexed: 07/18/2024] Open
Abstract
A subset of cancer cells are intrinsically sensitive to inhibitors targeting PARG, the poly(ADP-ribose) glycohydrolase that degrades PAR chains. Sensitivity is accompanied by persistent DNA replication stress, and can be induced by inhibition of TIMELESS, a replisome accelerator. However, the nature of the vulnerability responsible for intrinsic sensitivity remains undetermined. To understand PARG activity dependency, we analysed Timeless model systems and intrinsically sensitive ovarian cancer cells. We show that nucleoside supplementation rescues all phenotypes associated with PARG inhibitor sensitivity, including replisome speed and fork stalling, S-phase completion and mitotic entry, proliferation dynamics and clonogenic potential. Importantly nucleoside supplementation restores PARG inhibitor resistance despite the continued presence of PAR chains, indicating that sensitivity does not correlate with PAR levels. In addition, we show that inhibition of thymidylate synthase, an enzyme required for dNTP homeostasis, induces PARG-dependency. Together, these observations suggest that PARG inhibitor sensitivity reflects an inability to control replisome speed and/or maintain helicase-polymerase coupling in response to nucleotide imbalances.
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Affiliation(s)
- Camilla Coulson-Gilmer
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
| | - Samantha Littler
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
| | - Bethany M Barnes
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
| | - Rosie M Brady
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
| | - Holda A Anagho
- Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nisha Pillay
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
| | - Malini Dey
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
| | - William Macmorland
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
| | - Daniel Bronder
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
| | - Louisa Nelson
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
| | - Anthony Tighe
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
| | - Wei-Hsiang Lin
- Genome Editing Unit, Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Dover Street, Manchester M13 9PT, UK
| | - Robert D Morgan
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Rd, Manchester M20 4BX, UK
| | - Richard D Unwin
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
| | - Michael L Nielsen
- Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Joanne C McGrail
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
| | - Stephen S Taylor
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4GJ, UK
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Ouyang Y, Al-Amodi A, Tehseen M, Alhudhali L, Shirbini A, Takahashi M, Raducanu VS, Yi G, Danazumi AU, De Biasio A, Hamdan SM. Single-molecule characterization of SV40 replisome and novel factors: human FPC and Mcm10. Nucleic Acids Res 2024:gkae565. [PMID: 38967018 DOI: 10.1093/nar/gkae565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 06/06/2024] [Accepted: 06/18/2024] [Indexed: 07/06/2024] Open
Abstract
The simian virus 40 (SV40) replisome only encodes for its helicase; large T-antigen (L-Tag), while relying on the host for the remaining proteins, making it an intriguing model system. Despite being one of the earliest reconstituted eukaryotic systems, the interactions coordinating its activities and the identification of new factors remain largely unexplored. Herein, we in vitro reconstituted the SV40 replisome activities at the single-molecule level, including DNA unwinding by L-Tag and the single-stranded DNA-binding protein Replication Protein A (RPA), primer extension by DNA polymerase δ, and their concerted leading-strand synthesis. We show that RPA stimulates the processivity of L-Tag without altering its rate and that DNA polymerase δ forms a stable complex with L-Tag during leading-strand synthesis. Furthermore, similar to human and budding yeast Cdc45-MCM-GINS helicase, L-Tag uses the fork protection complex (FPC) and the mini-chromosome maintenance protein 10 (Mcm10) during synthesis. Hereby, we demonstrate that FPC increases this rate, and both FPC and Mcm10 increase the processivity by stabilizing stalled replisomes and increasing their chances of restarting synthesis. The detailed kinetics and novel factors of the SV40 replisome establish it as a closer mimic of the host replisome and expand its application as a model replication system.
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Affiliation(s)
- Yujing Ouyang
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Amani Al-Amodi
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Muhammad Tehseen
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Lubna Alhudhali
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Afnan Shirbini
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Masateru Takahashi
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Vlad-Stefan Raducanu
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Gang Yi
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Ammar Usman Danazumi
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Alfredo De Biasio
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Samir M Hamdan
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
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3
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Tribe AKW, Peng L, Teesdale-Spittle PH, McConnell MJ. BCL6 is a context-dependent mediator of the glioblastoma response to irradiation therapy. Int J Biol Macromol 2024; 270:131782. [PMID: 38734343 DOI: 10.1016/j.ijbiomac.2024.131782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 12/14/2023] [Accepted: 04/21/2024] [Indexed: 05/13/2024]
Abstract
Glioblastoma is a rapidly fatal brain cancer that does not respond to therapy. Previous research showed that the transcriptional repressor protein BCL6 is upregulated by chemo and radiotherapy in glioblastoma, and inhibition of BCL6 enhances the effectiveness of these therapies. Therefore, BCL6 is a promising target to improve the efficacy of current glioblastoma treatment. BCL6 acts as a transcriptional repressor in germinal centre B cells and as an oncogene in lymphoma and other cancers. However, in glioblastoma, BCL6 induced by therapy may not be able to repress transcription. Using a BCL6 inhibitor, the whole proteome response to irradiation was compared with and without BCL6 activity. Acute high dose irradiation caused BCL6 to switch from repressing the DNA damage response to promoting stress response signalling. Rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME) enabled comparison of BCL6 partner proteins between untreated and irradiated glioblastoma cells. BCL6 was associated with transcriptional coregulators in untreated glioblastoma including the known partner NCOR2. However, this association was lost in response to acute irradiation, where BCL6 unexpectedly associated with synaptic and plasma membrane proteins. These results reveal the activity of BCL6 under therapy-induced stress is context-dependent, and potentially altered by the intensity of that stress.
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Affiliation(s)
- Anna K W Tribe
- School of Biological Sciences, Te Herenga Waka Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand.
| | - Lifeng Peng
- School of Biological Sciences, Te Herenga Waka Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand.
| | - Paul H Teesdale-Spittle
- School of Biological Sciences, Te Herenga Waka Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand.
| | - Melanie J McConnell
- School of Biological Sciences, Te Herenga Waka Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand.
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Prorok P, Wolf E, Cardoso MC. Timeless-Tipin interactions with MCM and RPA mediate DNA replication stress response. Front Cell Dev Biol 2024; 12:1346534. [PMID: 38487270 PMCID: PMC10939015 DOI: 10.3389/fcell.2024.1346534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024] Open
Abstract
The accuracy of replication is one of the most important mechanisms ensuring the stability of the genome. The fork protection complex prevents premature replisome stalling and/or premature disassembly upon stress. Here, we characterize the Timeless-Tipin complex, a component of the fork protection complex. We used microscopy approaches, including colocalization analysis and proximity ligation assay, to investigate the spatial localization of the complex during ongoing replication in human cells. Taking advantage of the replication stress induction and the ensuing polymerase-helicase uncoupling, we characterized the Timeless-Tipin localization within the replisome. Replication stress was induced using hydroxyurea (HU) and aphidicolin (APH). While HU depletes the substrate for DNA synthesis, APH binds directly inside the catalytic pocket of DNA polymerase and inhibits its activity. Our data revealed that the Timeless-Tipin complex, independent of the stress, remains bound on chromatin upon stress induction and progresses together with the replicative helicase. This is accompanied by the spatial dissociation of the complex from the blocked replication machinery. Additionally, after stress induction, Timeless interaction with RPA, which continuously accumulates on ssDNA, was increased. Taken together, the Timeless-Tipin complex acts as a universal guardian of the mammalian replisome in an unperturbed S-phase progression as well as during replication stress.
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Affiliation(s)
- Paulina Prorok
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Eva Wolf
- Institute of Molecular Physiology (IMP), Johannes Gutenberg-University Mainz, Mainz, Germany
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
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5
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Vipat S, Moiseeva TN. The TIMELESS Roles in Genome Stability and Beyond. J Mol Biol 2024; 436:168206. [PMID: 37481157 DOI: 10.1016/j.jmb.2023.168206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/20/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023]
Abstract
TIMELESS protein (TIM) protects replication forks from stalling at difficult-to-replicate regions and plays an important role in DNA damage response, including checkpoint signaling, protection of stalled replication forks and DNA repair. Loss of TIM causes severe replication stress, while its overexpression is common in various types of cancer, providing protection from DNA damage and resistance to chemotherapy. Although TIM has mostly been studied for its part in replication stress response, its additional roles in supporting genome stability and a wide variety of other cellular pathways are gradually coming to light. This review discusses the diverse functions of TIM and its orthologs in healthy and cancer cells, open questions, and potential future directions.
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Affiliation(s)
- Sameera Vipat
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn 12618, Estonia
| | - Tatiana N Moiseeva
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn 12618, Estonia.
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Yang Y, Tang X, Lin Z, Zheng T, Zhang S, Liu T, Yang X. An integrative evaluation of circadian gene TIMELESS as a pan-cancer immunological and predictive biomarker. Eur J Med Res 2023; 28:563. [PMID: 38053143 DOI: 10.1186/s40001-023-01519-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/09/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND The gene TIMELESS, which is involved in the circadian clock and the cell cycle, has recently been linked to various human cancers. Nevertheless, the association between TIMELESS expression and the prognosis of individuals afflicted with pan-cancer remains largely unknown. OBJECTIVES The present study aims to exhaustively scrutinize the expression patterns, functional attributes, prognostic implications, and immunological contributions of TIMELESS across diverse types of human cancer. METHODS The expression of TIMELESS in normal and malignant tissues was examined, as well as their clinicopathologic and survival data. The characteristics of genetic alteration and molecular subtypes of cancers were also investigated. In addition, the relationship of TIMELESS with immune infiltration, tumor mutation burden (TMB), microsatellite instability (MSI), and drug sensitivity was illustrated. Immunohistochemistry (IHC) was used to validate the expression of TIMELESS in clinical patients with several types of cancer. RESULTS In contrast to the matching normal controls, most tumor types were found to often overexpress TIMELESS. Abnormal expression of TIMELESS was significantly related to more advanced tumor stage and poorer prognosis of breast cancer, as well as infiltrating immune cells such as cancer-associated fibroblast infiltration in various tumors. Multiple cancer types exhibited abnormal expression of TIMELESS, which was also highly correlated with MSI and TMB. More crucially, TIMELESS showed promise in predicting the effectiveness of immunotherapy and medication sensitivity in cancer therapy. Moreover, cell cycle, DNA replication, circadian rhythm, and mismatch repair were involved in the functional mechanisms of TIMELESS on carcinogenesis. Furthermore, immunohistochemical results manifested that the TIMELESS expression was abnormal in some cancers. CONCLUSIONS This study provides new insights into the link between the circadian gene TIMELESS and the development of various malignant tumors. The findings suggest that TIMELESS could be a prospective prognostic and immunological biomarker for pan-cancer.
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Affiliation(s)
- Yaocheng Yang
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, 136 Renmin Middle Road, Changsha, Hunan, 410011, People's Republic of China
| | - Xianzhe Tang
- Department of Orthopedics, Chenzhou First People's Hospital, Chenzhou, Hunan, China
| | - Zhengjun Lin
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, 136 Renmin Middle Road, Changsha, Hunan, 410011, People's Republic of China
| | - Tao Zheng
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, 136 Renmin Middle Road, Changsha, Hunan, 410011, People's Republic of China
| | - Sheng Zhang
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Tang Liu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, 136 Renmin Middle Road, Changsha, Hunan, 410011, People's Republic of China
| | - Xiaolun Yang
- Department of Stomatology, The Second Xiangya Hospital, Central South University, 136 Renmin Middle Road, Changsha, Hunan, 410011, People's Republic of China.
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Yin H, Wang Z, Wang D, Nuer M, Han M, Ren P, Ma S, Lin C, Chen J, Xian H, Ai D, Li X, Ma S, Lin Z, Pan Y. TIMELESS promotes the proliferation and migration of lung adenocarcinoma cells by activating EGFR through AMPK and SPHK1 regulation. Eur J Pharmacol 2023; 955:175883. [PMID: 37433364 DOI: 10.1016/j.ejphar.2023.175883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/13/2023]
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) has high morbidity and is prone to recurrence. TIMELESS (TIM), which regulates circadian rhythms in Drosophila, is highly expressed in various tumors. Its role in LUAD has gained attention, but the detailed function and mechanism have not been clarified completely at present. METHODS Tumor samples from patients with LUAD patient data from public databases were used to confirm the relationship of TIM expression with lung cancer. LUAD cell lines were used and siRNA of TIM was adopted to knock down TIM expression in LUAD cells, and further cell proliferation, migration and colony formation were analyzed. By using Western blot and qPCR, we detected the influence of TIM on epidermal growth factor receptor (EGFR), sphingosine kinase 1 (SPHK1) and AMP-activated protein kinase (AMPK). With proteomics analysis, we comprehensively inspected the different changed proteins influenced by TIM and did global bioinformatic analysis. RESULTS We found that TIM expression was elevated in LUAD and that this high expression was positively correlated with more advanced tumor pathological stages and shorter overall and disease-free survival. TIM knockdown inhibited EGFR activation and also AKT/mTOR phosphorylation. We also clarified that TIM regulated the activation of SPHK1 in LUAD cells. And with SPHK1 siRNA to knock down the expression level of SPHK1, we found that EGFR activation were inhibited greatly too. Quantitative proteomics techniques combined with bioinformatics analysis clarified the global molecular mechanisms regulated by TIM in LUAD. The results of proteomics suggested that mitochondrial translation elongation and termination were altered, which were closely related to the process of mitochondrial oxidative phosphorylation. We further confirmed that TIM knockdown reduced ATP content and promoted AMPK activation in LUAD cells. CONCLUSIONS Our study revealed that siTIM could inhibit EGFR activation through activating AMPK and inhibiting SPHK1 expression, as well as influencing mitochondrial function and altering the ATP level; TIM's high expression in LUAD is an important factor and a potential key target in LUAD.
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Affiliation(s)
- Houqing Yin
- Department of Pharmacology, School of Basic Medical Sciences, Health Science Center, Peking University, Beijing, 100191, China
| | - Zequn Wang
- Department of Pharmacology, School of Basic Medical Sciences, Health Science Center, Peking University, Beijing, 100191, China
| | - Dan Wang
- Department of Pharmacology, School of Basic Medical Sciences, Health Science Center, Peking University, Beijing, 100191, China
| | - Muhadaisi Nuer
- Department of Pharmacology, Xinjiang Medical University, Urumqi, Xinjiang, 830011, China
| | - Mengyuan Han
- Department of Pharmacology, Xinjiang Medical University, Urumqi, Xinjiang, 830011, China
| | - Peng Ren
- Peking University Third Hospital Thoracic Surgery Department, China
| | - Shanwu Ma
- Peking University Third Hospital Thoracic Surgery Department, China
| | - Chutong Lin
- Peking University Third Hospital Thoracic Surgery Department, China
| | - Jingjing Chen
- Department of Pharmacology, Changzhi Medical College, Changzhi City, Shanxi Province, 046000, China
| | - Haocheng Xian
- Department of Pharmacology, School of Basic Medical Sciences, Health Science Center, Peking University, Beijing, 100191, China
| | - Dongmei Ai
- School of Mathematics and Physics, University of Science and Technology Beijing, Beijing, 100083, China
| | - Xuejun Li
- Department of Pharmacology, School of Basic Medical Sciences, Health Science Center, Peking University, Beijing, 100191, China; Beijing Key Laboratory of Tumor Systems Biology, Peking University, Beijing, 100191, China
| | - Shaohua Ma
- Peking University Third Hospital Thoracic Surgery Department, China.
| | - Zhiqiang Lin
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
| | - Yan Pan
- Department of Pharmacology, School of Basic Medical Sciences, Health Science Center, Peking University, Beijing, 100191, China; Beijing Key Laboratory of Tumor Systems Biology, Peking University, Beijing, 100191, China.
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Patel JA, Kim H. The TIMELESS effort for timely DNA replication and protection. Cell Mol Life Sci 2023; 80:84. [PMID: 36892674 PMCID: PMC9998586 DOI: 10.1007/s00018-023-04738-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/16/2023] [Accepted: 02/24/2023] [Indexed: 03/10/2023]
Abstract
Accurate replication of the genome is fundamental to cellular survival and tumor prevention. The DNA replication fork is vulnerable to DNA lesions and damages that impair replisome progression, and improper control over DNA replication stress inevitably causes fork stalling and collapse, a major source of genome instability that fuels tumorigenesis. The integrity of the DNA replication fork is maintained by the fork protection complex (FPC), in which TIMELESS (TIM) constitutes a key scaffold that couples the CMG helicase and replicative polymerase activities, in conjunction with its interaction with other proteins associated with the replication machinery. Loss of TIM or the FPC in general results in impaired fork progression, elevated fork stalling and breakage, and a defect in replication checkpoint activation, thus underscoring its pivotal role in protecting the integrity of both active and stalled replication forks. TIM is upregulated in multiple cancers, which may represent a replication vulnerability of cancer cells that could be exploited for new therapies. Here, we discuss recent advances on our understanding of the multifaceted roles of TIM in DNA replication and stalled fork protection, and how its complex functions are engaged in collaboration with other genome surveillance and maintenance factors.
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Affiliation(s)
- Jinal A Patel
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Basic Sciences Tower 8-125, 101 Nicolls Rd, Stony Brook, NY, 11794, USA
| | - Hyungjin Kim
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Basic Sciences Tower 8-125, 101 Nicolls Rd, Stony Brook, NY, 11794, USA.
- Stony Brook Cancer Center and Renaissance School of Medicine, Stony Brook University, Basic Sciences Tower 8-125, 101 Nicolls Rd, Stony Brook, NY, 11794, USA.
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9
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Clyne CD, Kusnadi KP, Cowcher A, Morgan J, Yang J, Fuller PJ, Young MJ. Regulation of mineralocorticoid receptor activation by circadian protein TIMELESS. J Mol Endocrinol 2023; 70:JME-21-0279. [PMID: 36099062 DOI: 10.1530/jme-21-0279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/13/2022] [Indexed: 01/19/2023]
Abstract
The mineralocorticoid receptor (MR) is a ligand-activated transcription factor that regulates cardiorenal physiology and disease. Ligand-dependent MR transactivation involves a conformational change in the MR and recruitment of coregulatory proteins to form a unique DNA-binding complex at the hormone response element in target gene promoters. Differences in the recruitment of coregulatory proteins can promote tissue-, ligand- or gene-specific transcriptional outputs. The goal of this study was to evaluate the circadian protein TIMELESS as a selective regulator of MR transactivation. TIMELESS has an established role in cell cycle regulation and DNA repair. TIMELESS may not be central to mammalian clock function and does not bind DNA; however, RNA and protein levels oscillate over 24 h. Co-expression of TIMELESS down-regulated MR transactivation of an MR-responsive reporter in HEK293 cells, yet enhanced transactivation mediated by other steroid receptors. TIMELESS markedly inhibited MR transactivation of synthetic and native gene promoters and expression of MR target genes in H9c2 cardiac myoblasts. Immunofluorescence showed aldosterone induces colocalisation of TIMELESS and MR, although a direct interaction was not confirmed by coimmunoprecipitation. Potential regulation of circadian clock targets cryptochrome 1 and 2 by TIMELESS was not detected. However, our data suggest that these effects may involve TIMELESS coactivation of oestrogen receptor alpha (ERα). Taken together, these data suggest that TIMELESS may contribute to MR transcriptional outputs via enhancing ERα inhibitory actions on MR transactivation. Given the variable expression of TIMELESS in different cell types, these data offer new opportunities for the development of MR modulators with selective actions.
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Affiliation(s)
- Colin D Clyne
- Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, Clayton, Australia
| | - Kevin P Kusnadi
- Cardiovascular Endocrinology Laboratory, Baker Heart and Diabetes Institute, Melbourne, Australia
| | - Alexander Cowcher
- Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, Clayton, Australia
| | - James Morgan
- Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, Clayton, Australia
| | - Jun Yang
- Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, Clayton, Australia
| | - Peter J Fuller
- Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, Clayton, Australia
| | - Morag J Young
- Cardiovascular Endocrinology Laboratory, Baker Heart and Diabetes Institute, Melbourne, Australia
- University of Melbourne and Baker HDI Department of Cardiometabolic Health and Disease, Melbourne, Australia
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10
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Identification of replication fork-associated proteins in Drosophila embryos and cultured cells using iPOND coupled to quantitative mass spectrometry. Sci Rep 2022; 12:6903. [PMID: 35484306 PMCID: PMC9050644 DOI: 10.1038/s41598-022-10821-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 04/13/2022] [Indexed: 12/02/2022] Open
Abstract
Replication of the eukaryotic genome requires the formation of thousands of replication forks that must work in concert to accurately replicate the genetic and epigenetic information. Defining replication fork-associated proteins is a key step in understanding how genomes are replicated and repaired in the context of chromatin to maintain genome stability. To identify replication fork-associated proteins, we performed iPOND (Isolation of Proteins on Nascent DNA) coupled to quantitative mass spectrometry in Drosophila embryos and cultured cells. We identified 76 and 278 fork-associated proteins in post-MZT embryos and Drosophila cultured S2 cells, respectively. By performing a targeted screen of a subset of these proteins, we demonstrate that BRWD3, a targeting specificity factor for the DDB1/Cul4 ubiquitin ligase complex (CRL4), functions at or in close proximity to replication forks to promote fork progression and maintain genome stability. Altogether, our work provides a valuable resource for those interested in DNA replication, repair and chromatin assembly during development.
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11
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Xian H, Li Y, Zou B, Chen Y, Yin H, Li X, Pan Y. Identification of TIMELESS and RORA as key clock molecules of non-small cell lung cancer and the comprehensive analysis. BMC Cancer 2022; 22:107. [PMID: 35078435 PMCID: PMC8788117 DOI: 10.1186/s12885-022-09203-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/13/2022] [Indexed: 12/21/2022] Open
Abstract
Background The incidence rate of non-small cell lung cancer (NSCLC) has been increasing worldwide, and the correlation of circadian rhythm disruption with a raised risk of cancer and worse prognosis has been shown by accumulating evidences recently. On the other hand, drug resistance and the impact of tumor heterogeneity have been inevitable in NSCLC therapy. These both lead to an urgent need to identify more useful prognostic and predictive markers for NSCLC diagnosis and treatment, especially on the aspect of circadian clock genes. Methods The expression of the main clock genes in cancer was probed with TIMER and Oncomine databases. The prognostic value of key clock genes was probed systematically with the Kaplan–Meier estimate and Cox regression on samples from TCGA database. RT-qPCR was performed on patient tissue samples to further validate the results from databases. The functional enrichment analysis was performed using the “ClusterProfiler” R package, and the correlation of key clock genes with tumor mutation burden, immune checkpoint, and immune infiltration levels were also assessed using multiple algorithms including TIDE, TIMER2.0, and XCELL. Results TIMELESS was significantly upregulated in lung tissue of clinical lung cancer patients as well as TCGA and Oncomine databases, while RORA was downregulated. Multivariate Cox regression analysis indicated that TIMELESS (P = 0.004, HR = 1.21 [1.06, 1.38]) and RORA (P = 0.047, HR = 0.868 [0.755, 0.998]) has a significant correlation with overall survival in NSCLC. Genes related to TIMELESS were enriched in the cell cycle and immune system, and the function of RORA was mainly focused on oncogenic signaling pathways or glycosylation and protein activation. Also, TIMELESS was positively correlated with tumor mutation burden while RORA was negatively correlated with it. TIMELESS and RORA were also significantly correlated with immune checkpoint and immune infiltration levels in NSCLC. Additionally, TIMELESS showed a significant positive relationship with lipid metabolism. Conclusions TIMELESS and RORA were identified as key clock genes in NSCLC, and were independent prognostic factors for overall survival in NSCLC. The function of them were assessed in many aspects, indicating the strong potential of the two genes to serve as biomarkers for NSCLC progression and prognosis. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09203-1.
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12
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Grabarczyk DB. The Fork Protection Complex: A Regulatory Hub at the Head of the Replisome. Subcell Biochem 2022; 99:83-107. [PMID: 36151374 DOI: 10.1007/978-3-031-00793-4_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
As well as accurately duplicating DNA, the eukaryotic replisome performs a variety of other crucial tasks to maintain genomic stability. For example, organizational elements, like cohesin, must be transferred from the front of the fork to the new strands, and when there is replication stress, forks need to be protected and checkpoint signalling activated. The Tof1-Csm3 (or Timeless-Tipin in humans) Fork Protection Complex (FPC) ensures efficient replisome progression and is required for a range of replication-associated activities. Recent studies have begun to reveal the structure of this complex, and how it functions within the replisome to perform its diverse roles. The core of the FPC acts as a DNA grip on the front of the replisome to regulate fork progression. Other flexibly linked domains and motifs mediate interactions with proteins and specific DNA structures, enabling the FPC to act as a hub at the head of the replication fork.
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Affiliation(s)
- Daniel B Grabarczyk
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, Würzburg, Germany.
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria.
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13
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Cai YD, Chiu JC. Timeless in animal circadian clocks and beyond. FEBS J 2021; 289:6559-6575. [PMID: 34699674 PMCID: PMC9038958 DOI: 10.1111/febs.16253] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 10/09/2021] [Accepted: 10/26/2021] [Indexed: 12/13/2022]
Abstract
TIMELESS (TIM) was first identified as a molecular cog in the Drosophila circadian clock. Almost three decades of investigations have resulted in an insightful model describing the critical role of Drosophila TIM (dTIM) in circadian timekeeping in insects, including its function in mediating light entrainment and temperature compensation of the molecular clock. Furthermore, exciting discoveries on its sequence polymorphism and thermosensitive alternative RNA splicing have also established its role in regulating seasonal biology. Although mammalian TIM (mTIM), its mammalian paralog, was first identified as a potential circadian clock component in 1990s due to sequence similarity to dTIM, its role in clock regulation has been more controversial. Mammalian TIM has now been characterized as a DNA replication fork component and has been shown to promote fork progression and participate in cell cycle checkpoint signaling in response to DNA damage. Despite defective circadian rhythms displayed by mtim mutants, it remains controversial whether the regulation of circadian clocks by mTIM is direct, especially given the interconnection between the cell cycle and circadian clocks. In this review, we provide a historical perspective on the identification of animal tim genes, summarize the roles of TIM proteins in biological timing and genomic stability, and draw parallels between dTIM and mTIM despite apparent functional divergence.
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Affiliation(s)
- Yao D Cai
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, CA, USA
| | - Joanna C Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, CA, USA
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14
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Ren Z, Ma S, Cheng X, Guo Y, Liu Z. Expression and clinical significance of TIMELESS in glioma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2021; 14:938-955. [PMID: 34646412 PMCID: PMC8493260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
In recent years, studies have shown that TIMELESS, as an oncogene, is involved in progression of cancers. However, its relationship with prognosis in glioma patients is rarely reported. Our purpose was to explore the role of TIMELESS in glioma. Based on 1814 glioma samples from multiple databases such as The Cancer Genome Atlas (TCGA), The Chinese Glioma Genome Atlas (CGGA), and The Gene Expression Omnibus (GEO), we use a variety of bioinformatics methods to verify the mechanism of action of TIMELESS in glioma from mRNA to protein, from appearance to mechanism analysis, from clinical features to prognosis. Then, the connectivity map (CMap) tool was used to predict drugs that inhibit the expression of TIMELESS. First, we found TIMELESS is highly expressed in glioma at mRNA and protein levels. Second, TIMELESS is an independent risk factor in prognosis and has suitable clinical diagnostic value in glioma. It was also positively correlated with World Health Organization (WHO) grade, age, and histology, and negatively correlated with isocitrate dehydrogenase (IDH) 1 mutation and 1p19q codeletion. Third, base excision, cell cycle, and mismatch repair pathway were activated by TIMELESS in glioma. We predict small molecules to inhibit TIMELESS such as 8-azaguanine, gw8510, 6-thioguanosine, and ursodeoxycholic acid. This study is the first comprehensive analysis of TIMELESS, revealing a relationship between this novel oncogene, clinical characteristics of patients with glioma, and a mechanism leading to poor prognosis. It also provides a biomarker for diagnosis and treatment of glioma and reveal the pathologic progress of glioma at the genetic level.
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Affiliation(s)
- Zhishuai Ren
- Zhengzhou University People’s Hospital, Henan Provincial People’s HospitalZhengzhou 450003, Henan, China
| | - Shenqian Ma
- Zhengzhou University People’s Hospital, Henan Provincial People’s HospitalZhengzhou 450003, Henan, China
| | - Xingbo Cheng
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical UniversityHarbin 150001, Heilongjiang, China
| | - Yuqi Guo
- Department of Obstetrics and Gynecology, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou UniversityZhengzhou 450003, Henan, China
- Henan International Joint Laboratory for Gynecological Oncology and NanomedicineZhengzhou 450003, Henan, China
| | - Zhendong Liu
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou UniversityZhengzhou 450003, Henan, China
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15
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Fan Y, Köberlin MS, Ratnayeke N, Liu C, Deshpande M, Gerhardt J, Meyer T. LRR1-mediated replisome disassembly promotes DNA replication by recycling replisome components. J Cell Biol 2021; 220:212186. [PMID: 34037657 PMCID: PMC8160578 DOI: 10.1083/jcb.202009147] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 03/30/2021] [Accepted: 05/04/2021] [Indexed: 11/22/2022] Open
Abstract
After two converging DNA replication forks meet, active replisomes are disassembled and unloaded from chromatin. A key process in replisome disassembly is the unloading of CMG helicases (CDC45–MCM–GINS), which is initiated in Caenorhabditis elegans and Xenopus laevis by the E3 ubiquitin ligase CRL2LRR1. Here, we show that human cells lacking LRR1 fail to unload CMG helicases and accumulate increasing amounts of chromatin-bound replisome components as cells progress through S phase. Markedly, we demonstrate that the failure to disassemble replisomes reduces the rate of DNA replication increasingly throughout S phase by sequestering rate-limiting replisome components on chromatin and blocking their recycling. Continued binding of CMG helicases to chromatin during G2 phase blocks mitosis by activating an ATR-mediated G2/M checkpoint. Finally, we provide evidence that LRR1 is an essential gene for human cell division, suggesting that CRL2LRR1 enzyme activity is required for the proliferation of cancer cells and is thus a potential target for cancer therapy.
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Affiliation(s)
- Yilin Fan
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA.,Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY
| | - Marielle S Köberlin
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA
| | - Nalin Ratnayeke
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA.,Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY
| | - Chad Liu
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA
| | - Madhura Deshpande
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY
| | - Jeannine Gerhardt
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY.,Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY
| | - Tobias Meyer
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA.,Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY
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16
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Rageul J, Park JJ, Zeng PP, Lee EA, Yang J, Hwang S, Lo N, Weinheimer AS, Schärer OD, Yeo JE, Kim H. SDE2 integrates into the TIMELESS-TIPIN complex to protect stalled replication forks. Nat Commun 2020; 11:5495. [PMID: 33127907 PMCID: PMC7603486 DOI: 10.1038/s41467-020-19162-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 09/28/2020] [Indexed: 01/07/2023] Open
Abstract
Protecting replication fork integrity during DNA replication is essential for maintaining genome stability. Here, we report that SDE2, a PCNA-associated protein, plays a key role in maintaining active replication and counteracting replication stress by regulating the replication fork protection complex (FPC). SDE2 directly interacts with the FPC component TIMELESS (TIM) and enhances its stability, thereby aiding TIM localization to replication forks and the coordination of replisome progression. Like TIM deficiency, knockdown of SDE2 leads to impaired fork progression and stalled fork recovery, along with a failure to activate CHK1 phosphorylation. Moreover, loss of SDE2 or TIM results in an excessive MRE11-dependent degradation of reversed forks. Together, our study uncovers an essential role for SDE2 in maintaining genomic integrity by stabilizing the FPC and describes a new role for TIM in protecting stalled replication forks. We propose that TIM-mediated fork protection may represent a way to cooperate with BRCA-dependent fork stabilization. The fork protection complex (FPC), including the proteins TIMELESS and TIPIN, stabilizes the replisome to ensure unperturbed fork progression during DNA replication. Here the authors reveal that that SDE2, a PCNA-associated protein, plays an important role in maintaining active replication and protecting stalled forks by regulating the replication fork protection complex (FPC).
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Affiliation(s)
- Julie Rageul
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, New York, 11794, USA
| | - Jennifer J Park
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, New York, 11794, USA
| | - Ping Ping Zeng
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, New York, 11794, USA
| | - Eun-A Lee
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea
| | - Jihyeon Yang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea
| | - Sunyoung Hwang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea
| | - Natalie Lo
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, New York, 11794, USA
| | - Alexandra S Weinheimer
- Department of Biochemistry and Cell Biology, State University of New York at Stony Brook, Stony Brook, New York, 11794, USA
| | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Jung-Eun Yeo
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea.
| | - Hyungjin Kim
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, New York, 11794, USA. .,Stony Brook Cancer Center, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York, 11794, USA.
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17
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Lerner LK, Holzer S, Kilkenny ML, Šviković S, Murat P, Schiavone D, Eldridge CB, Bittleston A, Maman JD, Branzei D, Stott K, Pellegrini L, Sale JE. Timeless couples G-quadruplex detection with processing by DDX11 helicase during DNA replication. EMBO J 2020; 39:e104185. [PMID: 32705708 PMCID: PMC7506991 DOI: 10.15252/embj.2019104185] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/27/2022] Open
Abstract
Regions of the genome with the potential to form secondary DNA structures pose a frequent and significant impediment to DNA replication and must be actively managed in order to preserve genetic and epigenetic integrity. How the replisome detects and responds to secondary structures is poorly understood. Here, we show that a core component of the fork protection complex in the eukaryotic replisome, Timeless, harbours in its C-terminal region a previously unappreciated DNA-binding domain that exhibits specific binding to G-quadruplex (G4) DNA structures. We show that this domain contributes to maintaining processive replication through G4-forming sequences, and exhibits partial redundancy with an adjacent PARP-binding domain. Further, this function of Timeless requires interaction with and activity of the helicase DDX11. Loss of both Timeless and DDX11 causes epigenetic instability at G4-forming sequences and DNA damage. Our findings indicate that Timeless contributes to the ability of the replisome to sense replication-hindering G4 formation and ensures the prompt resolution of these structures by DDX11 to maintain processive DNA synthesis.
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Affiliation(s)
- Leticia K Lerner
- MRC Laboratory of Molecular BiologyCambridgeUK
- Present address:
Centre de Recherche des CordeliersCell Death and Drug Resistance in Hematological Disorders TeamINSERM UMRS 1138Sorbonne UniversitéParisFrance
| | - Sandro Holzer
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | | | | | | | | | | | - Joseph D Maman
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Dana Branzei
- IFOMFondazione Italiana per la Ricerca sul CancroInstitute of Molecular OncologyMilanItaly
| | - Katherine Stott
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Luca Pellegrini
- Department of BiochemistryUniversity of CambridgeCambridgeUK
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18
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Grabarczyk DB. Crystal structure and interactions of the Tof1-Csm3 (Timeless-Tipin) fork protection complex. Nucleic Acids Res 2020; 48:6996-7004. [PMID: 32469068 PMCID: PMC7337906 DOI: 10.1093/nar/gkaa456] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/14/2020] [Accepted: 05/20/2020] [Indexed: 11/13/2022] Open
Abstract
The Tof1-Csm3 fork protection complex has a central role in the replisome-it promotes the progression of DNA replication forks and protects them when they stall, while also enabling cohesion establishment and checkpoint responses. Here, I present the crystal structure of the Tof1-Csm3 complex from Chaetomium thermophilum at 3.1 Å resolution. The structure reveals that both proteins together form an extended alpha helical repeat structure, which suggests a mechanical or scaffolding role for the complex. Expanding on this idea, I characterize a DNA interacting region and a cancer-associated Mrc1 binding site. This study provides the molecular basis for understanding the functions of the Tof1-Csm3 complex, its human orthologue the Timeless-Tipin complex and additionally the Drosophila circadian rhythm protein Timeless.
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Affiliation(s)
- Daniel B Grabarczyk
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg, Josef-Schneider-Str. 2, Würzburg, Germany
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19
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Chakraborty A, Aziz F, Roh E, Le LTM, Dey R, Zhang T, Rathore MG, Biswas AS, Bode AM, Dong Z. Knock-down of the TIM/TIPIN complex promotes apoptosis in melanoma cells. Oncotarget 2020; 11:1846-1861. [PMID: 32499870 PMCID: PMC7244016 DOI: 10.18632/oncotarget.27572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/10/2020] [Indexed: 11/25/2022] Open
Abstract
The Timeless (TIM) and it's interacting partner TIPIN protein complex is well known for its role in replication checkpoints and normal DNA replication processes. Recent studies revealed the involvement of TIM and TIPIN in human malignancies; however, no evidence is available regarding the expression of the TIM/TIPIN protein complex or its potential role in melanoma. Therefore, we investigated the role of this complex in melanoma. To assess the role of the TIM/TIPIN complex in melanoma, we analyzed TIM/TIPIN expression data from the publicly accessible TCGA online database, Western blot analysis, and RT-qPCR in a panel of melanoma cell lines. Lentivirus-mediated TIM/TIPIN knockdown in A375 melanoma cells was used to examine proliferation, colony formation, and apoptosis. A xenograft tumor formation assay was also performed. The TIM/TIPIN complex is frequently overexpressed in melanoma cells compared to normal melanocytes. We also discovered that the overexpression of TIM and TIPIN was significantly associated with poorer prognosis of melanoma patients. Furthermore, we observed that shRNA-mediated knockdown of TIM and TIPIN reduced cell viability and proliferation due to the induction of apoptosis and increased levels of γH2AX, a marker of DNA damage. In a xenograft tumor nude mouse model, shRNA-knockdown of TIM/TIPIN significantly reduced tumor growth. Our results suggest that the TIM/TIPIN complex plays an important role in tumorigenesis of melanoma, which might reveal novel approaches for the development of new melanoma therapies. Our studies also provide a beginning structural basis for understanding the assembly of the TIM/TIPIN complex. Further mechanistic investigations are needed to determine the complex’s potential as a biomarker of melanoma susceptibility. Targeting TIM/TIPIN might be a potential therapeutic strategy against melanoma.
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Affiliation(s)
- Abhijit Chakraborty
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA.,Immunology, Allergy and Rheumatology Section, Baylor College of Medicine, Houston, TX 77030, USA
| | - Faisal Aziz
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Eunmiri Roh
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Le Thi My Le
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Raja Dey
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Tianshun Zhang
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Moeez G Rathore
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Aalekhya Sharma Biswas
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA.,Pediatric Gastroenterology and Liver Center, Baylor College of Medicine, Houston, Texas, Houston, TX 77030, USA
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Zigang Dong
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA.,College of Medicine, Zhengzhou University, Zhengzhou, Henan Province 450052, China
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20
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Schneck DT, Barreto FS. Phenotypic Variation in Growth and Gene Expression Under Different Photoperiods in Allopatric Populations of the Copepod Tigriopus californicus. THE BIOLOGICAL BULLETIN 2020; 238:106-118. [PMID: 32412840 DOI: 10.1086/708678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Daylength is a major environmental condition that varies seasonally and predictably along a latitudinal cline, where higher latitudes exhibit greater ranges in total daylengths. Generally, the circadian clock acts as a network of genes whose expression dynamics are known to control daily rhythms in response to daylength, and it enables the control of many physiological processes such as growth and development. While well studied in many model animals, the influence of daylength variation on phenotypic evolution is poorly examined in marine species. In this study we demonstrate that two allopatric populations of the intertidal crustacean Tigriopus californicus exhibit plastic and divergent phenotypic responses to changes in daylength. Using common-garden experiments, we discovered that shorter daylengths promoted decreased adult body size and faster growth rates in the two divergent populations, suggesting a plastic response to shortened days. In addition, the higher-latitude population exhibited a faster growth rate at any daylength condition, indicating a fixed response, possibly as a result of adaptation to respective natural light regimes. Gene expression profiles of several circadian clock genes, monitored throughout the day by quantitative polymerase chain reaction, revealed that the key core clock genes reach higher daily transcription maxima in the southern population compared to the northern population, pointing to divergent strategies used to respond to changes in daylength. Many modifier genes to the circadian clock showed similar plastic responses to the different daylengths, supporting the existence of at least some conserved gene expression across both populations. Ultimately, our results suggest that photoperiod and daylength exert a potent selective pressure underexplored in marine systems and warranting further future research.
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21
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Zhou J, Zhang Y, Zou X, Kuai L, Wang L, Wang J, Shen F, Hu J, Zhang X, Huang Y, Chen Y. Aberrantly Expressed Timeless Regulates Cell Proliferation and Cisplatin Efficacy in Cervical Cancer. Hum Gene Ther 2020; 31:385-395. [PMID: 31870179 DOI: 10.1089/hum.2019.080] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Timeless is a regulator of molecular clockwork in Drosophila and related to cancer development in mammals. This study aimed to investigate the effect of Timeless on cell proliferation and cisplatin sensitivity in cervical cancer. Timeless expression was determined by bioinformatics analysis, immunohistochemistry, and quantitative polymerase chain reaction (qPCR). Chromatin immunoprecipitation assays and reporter gene assays were applied to determine the transcriptional factor contributing to Timeless upregulation. The effects of Timeless depletion on cell proliferation and cisplatin sensitivity were determined through in vitro and in vivo experiments. Cell apoptosis and senescence were assessed by flow cytometry and β-galactosidase staining. DNA damage and DNA repair pathways were determined by comet assay, immunofluorescent staining, and Western blot analysis. Timeless is aberrantly expressed in ∼52.5% of cervical cancer tissues. E2F1 and E2F4 contribute to the transcriptional activation of Timeless. Timeless depletion inhibits cell proliferation and increases cisplatin sensitivity in vitro and in vivo. Knockdown of Timeless induces cell apoptosis and cell senescence. Mechanically, Timeless silencing leads to DNA damage and impairs the activation of the ATR/CHK1 pathway in response to cisplatin in cervical cancer. Timeless is overexpressed in cervical cancer and regulates cell proliferation and cisplatin sensitivity, presenting an attractive target for cisplatin sensitizer in cervical cancer.
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Affiliation(s)
- Jinhua Zhou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China.,Clinical Research Center of Obstetrics and Gynecology, Jiangsu Key Laboratory of Clinical Immunology, Soochow University, Suzhou, China.,Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yinghui Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xinwei Zou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Lingling Kuai
- Department of Obstetrics and Gynecology, Nanjing Maternity and Child Health Hospital, Nanjing, China
| | - Li Wang
- Department of Gynecology and Obstetrics, Changzhou Maternal and Child Health Care Hospital Affiliated Nanjing Medical University, Changzhou, China
| | - Juan Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Fangrong Shen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jinghui Hu
- Department of Gynecology, The First Affiliated Hospital of Zhejiang University Medical College, Hangzhou, China
| | - Xia Zhang
- Department of Obstetrics and Gynecology, TuHa Petroleum Hospital, Xinjiang, China
| | - Yazhen Huang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Youguo Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China.,Clinical Research Center of Obstetrics and Gynecology, Jiangsu Key Laboratory of Clinical Immunology, Soochow University, Suzhou, China.,Jiangsu Institute of Clinical Immunology, The First Affiliated Hospital of Soochow University, Suzhou, China
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22
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Gellon L, Kaushal S, Cebrián J, Lahiri M, Mirkin SM, Freudenreich CH. Mrc1 and Tof1 prevent fragility and instability at long CAG repeats by their fork stabilizing function. Nucleic Acids Res 2019; 47:794-805. [PMID: 30476303 PMCID: PMC6344861 DOI: 10.1093/nar/gky1195] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 11/13/2018] [Indexed: 12/14/2022] Open
Abstract
Fork stabilization at DNA impediments is key to maintaining replication fork integrity and preventing chromosome breaks. Mrc1 and Tof1 are two known stabilizers that travel with the replication fork. In addition to a structural role, Mrc1 has a DNA damage checkpoint function. Using a yeast model system, we analyzed the role of Mrc1 and Tof1 at expanded CAG repeats of medium and long lengths, which are known to stall replication forks and cause trinucleotide expansion diseases such as Huntington's disease and myotonic dystrophy. We demonstrate that the fork stabilizer but not the checkpoint activation function of Mrc1 is key for preventing DNA breakage and death of cells containing expanded CAG tracts. In contrast, both Mrc1 functions are important in preventing repeat length instability. Mrc1 has a general fork protector role that is evident at forks traversing both repetitive and non-repetitive DNA, though it becomes crucial at long CAG repeat lengths. In contrast, the role of Tof1 in preventing fork breakage is specific to long CAG tracts of 85 or more repeats. Our results indicate that long CAG repeats have a particular need for Tof1 and highlight the importance of fork stabilizers in maintaining fork integrity during replication of structure-forming repeats.
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Affiliation(s)
- Lionel Gellon
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave, Medford, MA 02155, USA
| | - Simran Kaushal
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave, Medford, MA 02155, USA
| | - Jorge Cebrián
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave, Medford, MA 02155, USA
| | - Mayurika Lahiri
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave, Medford, MA 02155, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave, Medford, MA 02155, USA
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23
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Neilsen BK, Frodyma DE, McCall JL, Fisher KW, Lewis RE. ERK-mediated TIMELESS expression suppresses G2/M arrest in colon cancer cells. PLoS One 2019; 14:e0209224. [PMID: 30629587 PMCID: PMC6328106 DOI: 10.1371/journal.pone.0209224] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/30/2018] [Indexed: 01/04/2023] Open
Abstract
The cell cycle is under circadian regulation. Oncogenes can dysregulate circadian-regulated genes to disrupt the cell cycle, promoting tumor cell proliferation. As a regulator of G2/M arrest in response to DNA damage, the circadian gene Timeless Circadian Clock (TIMELESS) coordinates this connection and is a potential locus for oncogenic manipulation. TIMELESS expression was evaluated using RNASeq data from TCGA and by RT-qPCR and western blot analysis in a panel of colon cancer cell lines. TIMELESS expression following ERK inhibition was examined via western blot. Cell metabolic capacity, propidium iodide, and CFSE staining were used to evaluate the effect of TIMELESS depletion on colon cancer cell survival and proliferation. Cell metabolic capacity following TIMELESS depletion in combination with Wee1 or CHK1 inhibition was assessed. TIMELESS is overexpressed in cancer and required for increased cancer cell proliferation. ERK activation promotes TIMELESS expression. TIMELESS depletion increases γH2AX, a marker of DNA damage, and triggers G2/M arrest via increased CHK1 and CDK1 phosphorylation. TIMELESS depletion in combination with Wee1 or CHK1 inhibition causes an additive decrease in cancer cell metabolic capacity with limited effects in non-transformed human colon epithelial cells. The data show that ERK activation contributes to the overexpression of TIMELESS in cancer. Depletion of TIMELESS increases γH2AX and causes G2/M arrest, limiting cell proliferation. These results demonstrate a role for TIMELESS in cancer and encourage further examination of the link between circadian rhythm dysregulation and cancer cell proliferation.
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Affiliation(s)
- Beth K. Neilsen
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Danielle E. Frodyma
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Jamie L. McCall
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Kurt W. Fisher
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Robert E. Lewis
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- * E-mail:
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24
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Liao H, Xie X, Xu Y, Huang G. Identification of driver genes associated with chemotherapy resistance of Ewing's sarcoma. Onco Targets Ther 2018; 11:6947-6956. [PMID: 30410352 PMCID: PMC6199211 DOI: 10.2147/ott.s172190] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Background The aim of this study was to identify the driver genes associated with chemotherapy resistance of Ewing’s sarcoma and potential targets for Ewing’s sarcoma treatment. Methods Two mRNA microarray datasets, GSE12102 and GSE17679, were downloaded from the Gene Expression Omnibus database, which contain 94 human Ewing’s sarcoma samples, including 65 from those who experienced a relapse and 29 from those with no evidence of disease. The differen tially expressed genes (DEGs) were identified using LIMMA package R. Subsequently, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed for DEGs using Database for Annotation, Visualization and Integrated Analysis. The protein–protein interaction network was constructed using Cytoscape software, and module analysis was performed using Molecular Complex Detection. Results A total of 206 upregulated DEGs and 141 downregulated DEGs were identified. Upregulated DEGs were primarily enriched in DNA replication, nucleoplasm and protein kinase binding for biological processes, cellular component and molecular functions, respectively. Downregulated DEGs were predominantly involved in receptor clustering, membrane raft, and ligand-dependent nuclear receptor binding. The protein–protein interaction network of DEGs consisted of 150 nodes and 304 interactions. Thirteen hub genes were identified, and biological analysis revealed that these genes were primarily enriched in cell division, cell cycle, and mitosis. Furthermore, based on closeness centrality, betweenness centrality, and degree centrality, the three most significant genes were identified as GAPDH, AURKA, and EHMT2. Furthermore, the significant network module was composed of nine genes. These genes were primarily enriched in mitotic nuclear division, mitotic chromosome condensation, and nucleoplasm. Conclusion These hub genes, especially GAPDH, AURKA, and EHMT2, may be closely associated with the progression of Ewing’s sarcoma chemotherapy resistance, and further experiments are needed for confirmation.
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Affiliation(s)
- Hongyi Liao
- Department of Orthopedic Surgery, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, People's Republic of China
| | - Xianbiao Xie
- Department of Orthopedic Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China,
| | - Yuanyuan Xu
- Department of Pediatrics, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Gang Huang
- Department of Orthopedic Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China,
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25
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Mazzoccoli G, Colangelo T, Panza A, Rubino R, Tiberio C, Palumbo O, Carella M, Trombetta D, Gentile A, Tavano F, Valvano MR, Storlazzi CT, Macchia G, De Cata A, Bisceglia G, Capocefalo D, Colantuoni V, Sabatino L, Piepoli A, Mazza T. Analysis of clock gene-miRNA correlation networks reveals candidate drivers in colorectal cancer. Oncotarget 2018; 7:45444-45461. [PMID: 27323779 PMCID: PMC5216733 DOI: 10.18632/oncotarget.9989] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 05/29/2016] [Indexed: 12/20/2022] Open
Abstract
Altered functioning of the biological clock is involved in cancer onset and progression. MicroRNAs (miRNAs) interact with the clock genes modulating the function of genetically encoded molecular clockworks. Collaborative interactions may take place within the coding-noncoding RNA regulatory networks. We aimed to evaluate the cross-talk among miRNAs and clock genes in colorectal cancer (CRC). We performed an integrative analysis of miRNA-miRNA and miRNA-mRNA interactions on high-throughput molecular profiling of matched human CRC tissue and non-tumor mucosa, pinpointing core clock genes and their targeting miRNAs. Data obtained in silico were validated in CRC patients and human colon cancer cell lines. In silico we found severe alterations of clock gene–related coding-noncoding RNA regulatory networks in tumor tissues, which were later corroborated by the analysis of human CRC specimens and experiments performed in vitro. In conclusion, specific miRNAs target and regulate the transcription/translation of clock genes and clock gene-related miRNA-miRNA as well as mRNA-miRNA interactions are altered in colorectal cancer. Exploration of the interplay between specific miRNAs and genes, which are critically involved in the functioning of the biological clock, provides a better understanding of the importance of the miRNA-clock genes axis and its derangement in colorectal cancer.
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Affiliation(s)
- Gianluigi Mazzoccoli
- Division of Internal Medicine and Chronobiology Unit, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Tommaso Colangelo
- Department of Sciences and Technologies, University of Sannio, Benevento, Italy
| | - Anna Panza
- Division of Gastroenterology and Research Laboratory, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Rosa Rubino
- Division of Internal Medicine and Chronobiology Unit, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Cristiana Tiberio
- Division of Internal Medicine and Chronobiology Unit, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Orazio Palumbo
- Medical Genetics Service, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Massimo Carella
- Medical Genetics Service, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Domenico Trombetta
- Oncology-Research Laboratory, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Annamaria Gentile
- Division of Gastroenterology and Research Laboratory, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Francesca Tavano
- Division of Gastroenterology and Research Laboratory, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Maria Rosa Valvano
- Division of Gastroenterology and Research Laboratory, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | | | - Gemma Macchia
- Department of Biology, University of Bari, Bari, Italy
| | - Angelo De Cata
- Division of Internal Medicine and Chronobiology Unit, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Giovanni Bisceglia
- Department of Surgical Sciences, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Daniele Capocefalo
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Vittorio Colantuoni
- Department of Sciences and Technologies, University of Sannio, Benevento, Italy
| | - Lina Sabatino
- Department of Sciences and Technologies, University of Sannio, Benevento, Italy
| | - Ada Piepoli
- Division of Epidemiology and Health Statistics, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Tommaso Mazza
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
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26
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Kottemann MC, Conti BA, Lach FP, Smogorzewska A. Removal of RTF2 from Stalled Replisomes Promotes Maintenance of Genome Integrity. Mol Cell 2017; 69:24-35.e5. [PMID: 29290612 DOI: 10.1016/j.molcel.2017.11.035] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 09/25/2017] [Accepted: 11/29/2017] [Indexed: 11/27/2022]
Abstract
The protection and efficient restart of stalled replication forks is critical for the maintenance of genome integrity. Here, we identify a regulatory pathway that promotes stalled forks recovery from replication stress. We show that the mammalian replisome component C20orf43/RTF2 (homologous to S. pombe Rtf2) must be removed for fork restart to be optimal. We further show that the proteasomal shuttle proteins DDI1 and DDI2 are required for RTF2 removal from stalled forks. Persistence of RTF2 at stalled forks results in fork restart defects, hyperactivation of the DNA damage signal, accumulation of single-stranded DNA (ssDNA), sensitivity to replication drugs, and chromosome instability. These results establish that RTF2 removal is a key determinant for the ability of cells to manage replication stress and maintain genome integrity.
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Affiliation(s)
- Molly C Kottemann
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY 10065, USA
| | - Brooke A Conti
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY 10065, USA
| | - Francis P Lach
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY 10065, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY 10065, USA.
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27
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Chastain M, Zhou Q, Shiva O, Fadri-Moskwik M, Whitmore L, Jia P, Dai X, Huang C, Ye P, Chai W. Human CST Facilitates Genome-wide RAD51 Recruitment to GC-Rich Repetitive Sequences in Response to Replication Stress. Cell Rep 2017; 16:1300-1314. [PMID: 27487043 DOI: 10.1016/j.celrep.2016.06.077] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 05/23/2016] [Accepted: 06/17/2016] [Indexed: 11/25/2022] Open
Abstract
The telomeric CTC1/STN1/TEN1 (CST) complex has been implicated in promoting replication recovery under replication stress at genomic regions, yet its precise role is unclear. Here, we report that STN1 is enriched at GC-rich repetitive sequences genome-wide in response to hydroxyurea (HU)-induced replication stress. STN1 deficiency exacerbates the fragility of these sequences under replication stress, resulting in chromosome fragmentation. We find that upon fork stalling, CST proteins form distinct nuclear foci that colocalize with RAD51. Furthermore, replication stress induces physical association of CST with RAD51 in an ATR-dependent manner. Strikingly, CST deficiency diminishes HU-induced RAD51 foci formation and reduces RAD51 recruitment to telomeres and non-telomeric GC-rich fragile sequences. Collectively, our findings establish that CST promotes RAD51 recruitment to GC-rich repetitive sequences in response to replication stress to facilitate replication restart, thereby providing insights into the mechanism underlying genome stability maintenance.
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Affiliation(s)
- Megan Chastain
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99210, USA
| | - Qing Zhou
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99210, USA
| | - Olga Shiva
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99210, USA
| | - Maria Fadri-Moskwik
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99210, USA
| | - Leanne Whitmore
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Pingping Jia
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99210, USA
| | - Xueyu Dai
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99210, USA
| | - Chenhui Huang
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99210, USA
| | - Ping Ye
- Department of Molecular and Experimental Medicine, Avera Cancer Institute, 1000 E 23rd Street, Suite 370, Sioux Falls, SD 57105, USA; Department of Pharmacy Practice, South Dakota State University, Brookings, SD 57007, USA
| | - Weihang Chai
- Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99210, USA.
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28
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Holzer S, Degliesposti G, Kilkenny ML, Maslen SL, Matak-Vinkovíc D, Skehel M, Pellegrini L. Crystal structure of the N-terminal domain of human Timeless and its interaction with Tipin. Nucleic Acids Res 2017; 45:5555-5563. [PMID: 28334766 PMCID: PMC5605233 DOI: 10.1093/nar/gkx139] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 02/24/2017] [Indexed: 11/13/2022] Open
Abstract
Human Timeless is involved in replication fork stabilization, S-phase checkpoint activation and establishment of sister chromatid cohesion. In the cell, Timeless forms a constitutive heterodimeric complex with Tipin. Here we present the 1.85 Å crystal structure of a large N-terminal segment of human Timeless, spanning amino acids 1-463, and we show that this region of human Timeless harbours a partial binding site for Tipin. Furthermore, we identify minimal regions of the two proteins that are required for the formation of a stable Timeless-Tipin complex and provide evidence that the Timeless-Tipin interaction is based on a composite binding interface comprising different domains of Timeless.
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Affiliation(s)
- Sandro Holzer
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | | | - Mairi L Kilkenny
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Sarah L Maslen
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Mark Skehel
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Luca Pellegrini
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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29
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Escorcia W, Forsburg SL. Destabilization of the replication fork protection complex disrupts meiotic chromosome segregation. Mol Biol Cell 2017; 28:2978-2997. [PMID: 28855376 PMCID: PMC5662257 DOI: 10.1091/mbc.e17-02-0101] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 08/21/2017] [Accepted: 08/23/2017] [Indexed: 12/17/2022] Open
Abstract
The replication fork protection complex (FPC) coordinates multiple processes that are crucial for unimpeded passage of the replisome through various barriers and difficult to replicate areas of the genome. We examine the function of Swi1 and Swi3, fission yeast's primary FPC components, to elucidate how replication fork stability contributes to DNA integrity in meiosis. We report that destabilization of the FPC results in reduced spore viability, delayed replication, changes in recombination, and chromosome missegregation in meiosis I and meiosis II. These phenotypes are linked to accumulation and persistence of DNA damage markers in meiosis and to problems with cohesion stability at the centromere. These findings reveal an important connection between meiotic replication fork stability and chromosome segregation, two processes with major implications to human reproductive health.
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Affiliation(s)
- Wilber Escorcia
- Program in Molecular & Computational Biology, University of Southern California, Los Angeles, CA 90089-2910
| | - Susan L Forsburg
- Program in Molecular & Computational Biology, University of Southern California, Los Angeles, CA 90089-2910
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30
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Liu X, Dang Y, Matsu-Ura T, He Y, He Q, Hong CI, Liu Y. DNA Replication Is Required for Circadian Clock Function by Regulating Rhythmic Nucleosome Composition. Mol Cell 2017. [PMID: 28648778 DOI: 10.1016/j.molcel.2017.05.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Although the coupling between circadian and cell cycles allows circadian clocks to gate cell division and DNA replication in many organisms, circadian clocks were thought to function independently of cell cycle. Here, we show that DNA replication is required for circadian clock function in Neurospora. Genetic and pharmacological inhibition of DNA replication abolished both overt and molecular rhythmicities by repressing frequency (frq) gene transcription. DNA replication is essential for the rhythmic changes of nucleosome composition at the frq promoter. The FACT complex, known to be involved in histone disassembly/reassembly, is required for clock function and is recruited to the frq promoter in a replication-dependent manner to promote replacement of histone H2A.Z by H2A. Finally, deletion of H2A.Z uncoupled the dependence of the circadian clock on DNA replication. Together, these results establish circadian clock and cell cycle as interdependent coupled oscillators and identify DNA replication as a critical process in the circadian mechanism.
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Affiliation(s)
- Xiao Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA
| | - Yunkun Dang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA
| | - Toru Matsu-Ura
- Department of Molecular and Cellular Physiology, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Yubo He
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA; Department of Biochemistry and Cell Biology, McMurtry College, Rice University, Houston, TX 77005, USA
| | - Qun He
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Christian I Hong
- Department of Molecular and Cellular Physiology, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA.
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31
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Dewar JM, Low E, Mann M, Räschle M, Walter JC. CRL2 Lrr1 promotes unloading of the vertebrate replisome from chromatin during replication termination. Genes Dev 2017; 31:275-290. [PMID: 28235849 PMCID: PMC5358724 DOI: 10.1101/gad.291799.116] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 01/30/2017] [Indexed: 01/26/2023]
Abstract
Here, Dewar et al. use a proteomic screen in Xenopus egg extracts to identify factors that are enriched on chromatin when CMG unloading from chromatin, which is a key event during eukaryotic replication termination, is blocked. Their results show that CRL2Lrr1 is a master regulator of replisome disassembly during vertebrate DNA replication termination. A key event during eukaryotic replication termination is the removal of the CMG helicase from chromatin. CMG unloading involves ubiquitylation of its Mcm7 subunit and the action of the p97 ATPase. Using a proteomic screen in Xenopus egg extracts, we identified factors that are enriched on chromatin when CMG unloading is blocked. This approach identified the E3 ubiquitin ligase CRL2Lrr1, a specific p97 complex, other potential regulators of termination, and many replisome components. We show that Mcm7 ubiquitylation and CRL2Lrr1 binding to chromatin are temporally linked and occur only during replication termination. In the absence of CRL2Lrr1, Mcm7 is not ubiquitylated, CMG unloading is inhibited, and a large subcomplex of the vertebrate replisome that includes DNA Pol ε is retained on DNA. Our data identify CRL2Lrr1 as a master regulator of replisome disassembly during vertebrate DNA replication termination.
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Affiliation(s)
- James M Dewar
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Emily Low
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Markus Räschle
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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Zhang W, He W, Shi Y, Zhao J, Liu S, Zhang F, Yang J, Xie C, Zhang Y. Aberrant TIMELESS expression is associated with poor clinical survival and lymph node metastasis in early-stage cervical carcinoma. Int J Oncol 2016; 50:173-184. [DOI: 10.3892/ijo.2016.3784] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 11/22/2016] [Indexed: 11/06/2022] Open
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33
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Solovyov IA, Dobrovol’skaya EV, Moskalev AA. Genetic control of circadian rhythms and aging. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416040104] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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34
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A Timeless Link Between Circadian Patterns and Disease. Trends Mol Med 2016; 22:68-81. [DOI: 10.1016/j.molmed.2015.11.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/16/2015] [Accepted: 11/18/2015] [Indexed: 02/06/2023]
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35
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Li D, Su Y, Tu J, Wei R, Fan X, Yin H, Hu Y, Xu H, Yao Y, Yang D, Yang M. Evolutionary conservation of the circadian gene timeout in Metazoa. ANIM BIOL 2016. [DOI: 10.1163/15707563-00002482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Timeless (Tim) is considered to function as an essential circadian clock gene in Drosophila. Putative homologues of the Drosophila timeless gene have been identified in both mice and humans. While Drosophila contains two paralogs, timeless and timeout, acting in clock/light entrainment and chromosome integrity/photoreception, respectively, mammals contain only one Tim homolog. In this paper, we study the phylogeny of the timeless/timeout family in 48 species [including 1 protozoan (Guillardia theta), 1 nematode (Caenorhabditis elegans), 8 arthropods and 38 chordates], for which whole genome data are available by using MEGA (Molecular Evolutionary Genetics Analysis). Phylogenetic Analysis by Maximum Likelihood (PAML) was used to analyze the selective pressure acting on metazoan timeless/timeout genes. Our phylogeny clearly separates insect timeless and timeout lineages and shows that non-insect animal Tim genes are homologs of insect timeout. In this study, we explored the relatively rapidly evolving timeless lineage that was apparently lost from most deuterostomes, including chordates, and from Caenorhabditis elegans. In contrast, we found that the timeout protein, often confusingly called “timeless” in the vertebrate literature, is present throughout the available animal genomes. Selection results showed that timeout is under weaker negative selection than timeless. Finally, our phylogeny of timeless/timeout showed an evolutionary conservation of the circadian clock gene timeout in Metazoa. This conservation is in line with its multifunctionality, being essential for embryonic development and maintenance of chromosome integrity, among others.
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Affiliation(s)
- Diyan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P. R. China
| | - Yuan Su
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P. R. China
| | - Jianbo Tu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P. R. China
| | - Ranlei Wei
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P. R. China
| | - Xiaolan Fan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P. R. China
| | - Huadong Yin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P. R. China
| | - Yaodong Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P. R. China
| | - Huailiang Xu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P. R. China
| | - Yongfang Yao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P. R. China
| | - Deying Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P. R. China
| | - Mingyao Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P. R. China
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Calì F, Bharti SK, Di Perna R, Brosh RM, Pisani FM. Tim/Timeless, a member of the replication fork protection complex, operates with the Warsaw breakage syndrome DNA helicase DDX11 in the same fork recovery pathway. Nucleic Acids Res 2015; 44:705-17. [PMID: 26503245 PMCID: PMC4737141 DOI: 10.1093/nar/gkv1112] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 10/13/2015] [Indexed: 11/15/2022] Open
Abstract
We present evidence that Tim establishes a physical and functional interaction with DDX11, a super-family 2 iron-sulfur cluster DNA helicase genetically linked to the chromosomal instability disorder Warsaw breakage syndrome. Tim stimulates DDX11 unwinding activity on forked DNA substrates up to 10-fold and on bimolecular anti-parallel G-quadruplex DNA structures and three-stranded D-loop approximately 4–5-fold. Electrophoretic mobility shift assays revealed that Tim enhances DDX11 binding to DNA, suggesting that the observed stimulation derives from an improved ability of DDX11 to interact with the nucleic acid substrate. Surface plasmon resonance measurements indicate that DDX11 directly interacts with Tim. DNA fiber track assays with HeLa cells exposed to hydroxyurea demonstrated that Tim or DDX11 depletion significantly reduced replication fork progression compared to control cells; whereas no additive effect was observed by co-depletion of both proteins. Moreover, Tim and DDX11 are epistatic in promoting efficient resumption of stalled DNA replication forks in hydroxyurea-treated cells. This is consistent with the finding that association of the two endogenous proteins in the cell extract chromatin fraction is considerably increased following hydroxyurea exposure. Overall, our studies provide evidence that Tim and DDX11 physically and functionally interact and act in concert to preserve replication fork progression in perturbed conditions.
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Affiliation(s)
- Federica Calì
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via Pietro Castellino, 111. 80131 - Napoli, Italy
| | - Sanjay Kumar Bharti
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, 251 Bayview Blvd, Baltimore, MD 21224 USA
| | - Roberta Di Perna
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via Pietro Castellino, 111. 80131 - Napoli, Italy
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, 251 Bayview Blvd, Baltimore, MD 21224 USA
| | - Francesca M Pisani
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via Pietro Castellino, 111. 80131 - Napoli, Italy
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Xie S, Mortusewicz O, Ma HT, Herr P, Poon RYC, Poon RRY, Helleday T, Qian C. Timeless Interacts with PARP-1 to Promote Homologous Recombination Repair. Mol Cell 2015; 60:163-76. [PMID: 26344098 DOI: 10.1016/j.molcel.2015.07.031] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 05/01/2015] [Accepted: 07/29/2015] [Indexed: 12/21/2022]
Abstract
Human Timeless helps stabilize replication forks during normal DNA replication and plays a critical role in activation of the S phase checkpoint and proper establishment of sister chromatid cohesion. However, it remains elusive whether Timeless is involved in the repair of damaged DNA. Here, we identify that Timeless physically interacts with PARP-1 independent of poly(ADP-ribosyl)ation. We present high-resolution crystal structures of Timeless PAB (PARP-1-binding domain) in free form and in complex with PARP-1 catalytic domain. Interestingly, Timeless PAB domain specifically recognizes PARP-1, but not PARP-2 or PARP-3. Timeless-PARP-1 interaction does not interfere with PARP-1 enzymatic activity. We demonstrate that rapid and transient accumulation of Timeless at laser-induced DNA damage sites requires PARP-1, but not poly(ADP-ribosyl)ation and that Timeless is co-trapped with PARP-1 at DNA lesions upon PARP inhibition. Furthermore, we show that Timeless and PARP-1 interaction is required for efficient homologous recombination repair.
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Affiliation(s)
- Si Xie
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong
| | - Oliver Mortusewicz
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 21 Stockholm, Sweden
| | - Hoi Tang Ma
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong
| | - Patrick Herr
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 21 Stockholm, Sweden
| | - Randy Y C Poon
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong
| | - Randy R Y Poon
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong
| | - Thomas Helleday
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 21 Stockholm, Sweden.
| | - Chengmin Qian
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong.
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Cenci G, Ciapponi L, Marzullo M, Raffa GD, Morciano P, Raimondo D, Burla R, Saggio I, Gatti M. The Analysis of Pendolino (peo) Mutants Reveals Differences in the Fusigenic Potential among Drosophila Telomeres. PLoS Genet 2015; 11:e1005260. [PMID: 26110638 PMCID: PMC4481407 DOI: 10.1371/journal.pgen.1005260] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 05/04/2015] [Indexed: 01/08/2023] Open
Abstract
Drosophila telomeres are sequence-independent structures that are maintained by transposition to chromosome ends of three specialized retroelements (HeT-A, TART and TAHRE; collectively designated as HTT) rather than telomerase activity. Fly telomeres are protected by the terminin complex (HOAP-HipHop-Moi-Ver) that localizes and functions exclusively at telomeres and by non-terminin proteins that do not serve telomere-specific functions. Although all Drosophila telomeres terminate with HTT arrays and are capped by terminin, they differ in the type of subtelomeric chromatin; the Y, XR, and 4L HTT are juxtaposed to constitutive heterochromatin, while the XL, 2L, 2R, 3L and 3R HTT are linked to the TAS repetitive sequences; the 4R HTT is associated with a chromatin that has features common to both euchromatin and heterochromatin. Here we show that mutations in pendolino (peo) cause telomeric fusions (TFs). The analysis of several peo mutant combinations showed that these TFs preferentially involve the Y, XR and 4th chromosome telomeres, a TF pattern never observed in the other 10 telomere-capping mutants so far characterized. peo encodes a non-terminin protein homologous to the E2 variant ubiquitin-conjugating enzymes. The Peo protein directly interacts with the terminin components, but peo mutations do not affect telomeric localization of HOAP, Moi, Ver and HP1a, suggesting that the peo-dependent telomere fusion phenotype is not due to loss of terminin from chromosome ends. peo mutants are also defective in DNA replication and PCNA recruitment. However, our results suggest that general defects in DNA replication are unable to induce TFs in Drosophila cells. We thus hypothesize that DNA replication in Peo-depleted cells results in specific fusigenic lesions concentrated in heterochromatin-associated telomeres. Alternatively, it is possible that Peo plays a dual function being independently required for DNA replication and telomere capping. Telomeres are specialized structures that protect chromosome ends from incomplete replication, degradation and end-to-end fusion. Abnormalities in telomere structure or maintenance can promote a variety of human diseases including premature aging and cancer. Although all human telomeres contain the same DNA sequences, they differ from each other in the subtelomeric regions or subtelomeres. Recent work has shown that human subtelomeres control telomere replication and that abnormalities in these structures can lead to localized chromosome instability and disease. However, the relationships between subtelomeres and telomeres are currently poorly understood. Here, we have addressed this problem using the fruit fly Drosophila melanogaster as model system. Drosophila subtelomers are very different from each other as they contain different types of chromatin. We have found that mutations in a gene we called pendolino (peo) cause telomeric fusions (TFs) and that these fusions preferentially involve the telomeres associated with a tightly packed form of chromatin called heterochromatin. Interestingly, none of the 10 mutants with TFs so far described in Drosophila shows the pattern of TFs observed in peo mutants. Thus, our data provide the first demonstration that subtelomeres can affect telomere fusion. We believe that these results will stimulate further studies on the role of subtelomeres in the maintenance of genome stability.
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Affiliation(s)
- Giovanni Cenci
- Dipartimento di Biologia e Biotecnologie, Sapienza—Università di Roma, Roma, Italy
- Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza—Università di Roma, Roma, Italy
| | - Laura Ciapponi
- Dipartimento di Biologia e Biotecnologie, Sapienza—Università di Roma, Roma, Italy
- Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza—Università di Roma, Roma, Italy
| | - Marta Marzullo
- Dipartimento di Biologia e Biotecnologie, Sapienza—Università di Roma, Roma, Italy
- Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza—Università di Roma, Roma, Italy
| | - Grazia D. Raffa
- Dipartimento di Biologia e Biotecnologie, Sapienza—Università di Roma, Roma, Italy
- Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza—Università di Roma, Roma, Italy
| | - Patrizia Morciano
- Dipartimento di Biologia e Biotecnologie, Sapienza—Università di Roma, Roma, Italy
- Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza—Università di Roma, Roma, Italy
| | | | - Romina Burla
- Dipartimento di Biologia e Biotecnologie, Sapienza—Università di Roma, Roma, Italy
- Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza—Università di Roma, Roma, Italy
| | - Isabella Saggio
- Dipartimento di Biologia e Biotecnologie, Sapienza—Università di Roma, Roma, Italy
- Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza—Università di Roma, Roma, Italy
- IBPM CNR, Sapienza—Università di Roma, Roma, Italy
| | - Maurizio Gatti
- Dipartimento di Biologia e Biotecnologie, Sapienza—Università di Roma, Roma, Italy
- Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza—Università di Roma, Roma, Italy
- IBPM CNR, Sapienza—Università di Roma, Roma, Italy
- * E-mail:
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Hao J, de Renty C, Li Y, Xiao H, Kemp MG, Han Z, DePamphilis ML, Zhu W. And-1 coordinates with Claspin for efficient Chk1 activation in response to replication stress. EMBO J 2015; 34:2096-110. [PMID: 26082189 DOI: 10.15252/embj.201488016] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Accepted: 05/08/2015] [Indexed: 11/09/2022] Open
Abstract
The replisome is important for DNA replication checkpoint activation, but how specific components of the replisome coordinate with ATR to activate Chk1 in human cells remains largely unknown. Here, we demonstrate that And-1, a replisome component, acts together with ATR to activate Chk1. And-1 is phosphorylated at T826 by ATR following replication stress, and this phosphorylation is required for And-1 to accumulate at the damage sites, where And-1 promotes the interaction between Claspin and Chk1, thereby stimulating efficient Chk1 activation by ATR. Significantly, And-1 binds directly to ssDNA and facilitates the association of Claspin with ssDNA. Furthermore, And-1 associates with replication forks and is required for the recovery of stalled forks. These studies establish a novel ATR-And-1 axis as an important regulator for efficient Chk1 activation and reveal a novel mechanism of how the replisome regulates the replication checkpoint and genomic stability.
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Affiliation(s)
- Jing Hao
- Department of Biochemistry and Molecular Medicine, The George Washington University Medical School, Washington, DC, USA
| | | | - Yongming Li
- Department of Biochemistry and Molecular Medicine, The George Washington University Medical School, Washington, DC, USA
| | - Haijie Xiao
- Department of Biochemistry and Molecular Medicine, The George Washington University Medical School, Washington, DC, USA
| | - Michael G Kemp
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL, USA
| | - Zhiyong Han
- Department of Biochemistry and Molecular Medicine, The George Washington University Medical School, Washington, DC, USA
| | | | - Wenge Zhu
- Department of Biochemistry and Molecular Medicine, The George Washington University Medical School, Washington, DC, USA
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40
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Baldeyron C, Brisson A, Tesson B, Némati F, Koundrioukoff S, Saliba E, De Koning L, Martel E, Ye M, Rigaill G, Meseure D, Nicolas A, Gentien D, Decaudin D, Debatisse M, Depil S, Cruzalegui F, Pierré A, Roman-Roman S, Tucker GC, Dubois T. TIPIN depletion leads to apoptosis in breast cancer cells. Mol Oncol 2015; 9:1580-98. [PMID: 26004086 DOI: 10.1016/j.molonc.2015.04.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 03/10/2015] [Accepted: 04/23/2015] [Indexed: 12/31/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is the breast cancer subgroup with the most aggressive clinical behavior. Alternatives to conventional chemotherapy are required to improve the survival of TNBC patients. Gene-expression analyses for different breast cancer subtypes revealed significant overexpression of the Timeless-interacting protein (TIPIN), which is involved in the stability of DNA replication forks, in the highly proliferative associated TNBC samples. Immunohistochemistry analysis showed higher expression of TIPIN in the most proliferative and aggressive breast cancer subtypes including TNBC, and no TIPIN expression in healthy breast tissues. The depletion of TIPIN by RNA interference impairs the proliferation of both human breast cancer and non-tumorigenic cell lines. However, this effect may be specifically associated with apoptosis in breast cancer cells. TIPIN silencing results in higher levels of single-stranded DNA (ssDNA), indicative of replicative stress (RS), in TNBC compared to non-tumorigenic cells. Upon TIPIN depletion, the speed of DNA replication fork was significantly decreased in all BC cells. However, TIPIN-depleted TNBC cells are unable to fire additional replication origins in response to RS and therefore undergo apoptosis. TIPIN knockdown in TNBC cells decreases tumorigenicity in vitro and delays tumor growth in vivo. Our findings suggest that TIPIN is important for the maintenance of DNA replication and represents a potential treatment target for the worst prognosis associated breast cancers, such as TNBC.
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Affiliation(s)
- Céline Baldeyron
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Breast Cancer Biology Group, Department of Translational Research, Paris, F-75248, France
| | - Amélie Brisson
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Breast Cancer Biology Group, Department of Translational Research, Paris, F-75248, France
| | - Bruno Tesson
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Breast Cancer Biology Group, Department of Translational Research, Paris, F-75248, France; INSERM, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Paris, F-75248, France; Mines ParisTech, Fontainebleau, F-77300, France
| | - Fariba Némati
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Laboratory of Preclinical Investigation, Department of Translational Research, Paris, F-75248, France
| | - Stéphane Koundrioukoff
- Institut Curie, Centre de Recherche, Paris, F-75248, France; CNRS, UMR 3244, Paris, F-75248, France; Université Pierre and Marie Curie Paris VI, Paris, F-75005, France
| | - Elie Saliba
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Breast Cancer Biology Group, Department of Translational Research, Paris, F-75248, France
| | - Leanne De Koning
- Institut Curie, Centre de Recherche, Paris, F-75248, France; RPPA Platform, Department of Translational Research, Paris, F-75248, France
| | - Elise Martel
- Institut Curie, Investigative Pathology Platform, Paris, F-75248, France
| | - Mengliang Ye
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Breast Cancer Biology Group, Department of Translational Research, Paris, F-75248, France
| | - Guillem Rigaill
- Unité de Recherche en Génomique Végétale, INRA-CNRS-Université d'Evry Val d'Essonne, Evry, F-91057, France
| | - Didier Meseure
- Institut Curie, Investigative Pathology Platform, Paris, F-75248, France
| | - André Nicolas
- Institut Curie, Investigative Pathology Platform, Paris, F-75248, France
| | - David Gentien
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Platform of Molecular Biology Facilities, Department of Translational Research, Paris, F-75248, France
| | - Didier Decaudin
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Laboratory of Preclinical Investigation, Department of Translational Research, Paris, F-75248, France
| | - Michelle Debatisse
- Institut Curie, Centre de Recherche, Paris, F-75248, France; CNRS, UMR 3244, Paris, F-75248, France; Université Pierre and Marie Curie Paris VI, Paris, F-75005, France
| | - Stéphane Depil
- Institut de Recherches SERVIER, Pôle Innovation Thérapeutique Oncologie, Croissy-sur-Seine, F-78290, France
| | - Francisco Cruzalegui
- Institut de Recherches SERVIER, Pôle Innovation Thérapeutique Oncologie, Croissy-sur-Seine, F-78290, France
| | - Alain Pierré
- Institut de Recherches SERVIER, Pôle Innovation Thérapeutique Oncologie, Croissy-sur-Seine, F-78290, France
| | - Sergio Roman-Roman
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Breast Cancer Biology Group, Department of Translational Research, Paris, F-75248, France
| | - Gordon C Tucker
- Institut de Recherches SERVIER, Pôle Innovation Thérapeutique Oncologie, Croissy-sur-Seine, F-78290, France
| | - Thierry Dubois
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Breast Cancer Biology Group, Department of Translational Research, Paris, F-75248, France.
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Inaguma Y, Ito H, Hara A, Iwamoto I, Matsumoto A, Yamagata T, Tabata H, Nagata KI. Morphological characterization of mammalian Timeless in the mouse brain development. Neurosci Res 2015; 92:21-8. [DOI: 10.1016/j.neures.2014.10.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 10/24/2014] [Accepted: 10/28/2014] [Indexed: 01/14/2023]
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Gustafson CL, Partch CL. Emerging models for the molecular basis of mammalian circadian timing. Biochemistry 2014; 54:134-49. [PMID: 25303119 PMCID: PMC4303291 DOI: 10.1021/bi500731f] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Mammalian circadian timekeeping arises from a transcription-based feedback loop driven by a set of dedicated clock proteins. At its core, the heterodimeric transcription factor CLOCK:BMAL1 activates expression of Period, Cryptochrome, and Rev-Erb genes, which feed back to repress transcription and create oscillations in gene expression that confer circadian timing cues to cellular processes. The formation of different clock protein complexes throughout this transcriptional cycle helps to establish the intrinsic ∼24 h periodicity of the clock; however, current models of circadian timekeeping lack the explanatory power to fully describe this process. Recent studies confirm the presence of at least three distinct regulatory complexes: a transcriptionally active state comprising the CLOCK:BMAL1 heterodimer with its coactivator CBP/p300, an early repressive state containing PER:CRY complexes, and a late repressive state marked by a poised but inactive, DNA-bound CLOCK:BMAL1:CRY1 complex. In this review, we analyze high-resolution structures of core circadian transcriptional regulators and integrate biochemical data to suggest how remodeling of clock protein complexes may be achieved throughout the 24 h cycle. Defining these detailed mechanisms will provide a foundation for understanding the molecular basis of circadian timing and help to establish new platforms for the discovery of therapeutics to manipulate the clock.
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Affiliation(s)
- Chelsea L Gustafson
- Department of Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
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43
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Potential conservation of circadian clock proteins in the phylum Nematoda as revealed by bioinformatic searches. PLoS One 2014; 9:e112871. [PMID: 25396739 PMCID: PMC4232591 DOI: 10.1371/journal.pone.0112871] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 10/15/2014] [Indexed: 11/19/2022] Open
Abstract
Although several circadian rhythms have been described in C. elegans, its molecular clock remains elusive. In this work we employed a novel bioinformatic approach, applying probabilistic methodologies, to search for circadian clock proteins of several of the best studied circadian model organisms of different taxa (Mus musculus, Drosophila melanogaster, Neurospora crassa, Arabidopsis thaliana and Synechoccocus elongatus) in the proteomes of C. elegans and other members of the phylum Nematoda. With this approach we found that the Nematoda contain proteins most related to the core and accessory proteins of the insect and mammalian clocks, which provide new insights into the nematode clock and the evolution of the circadian system.
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Sancar A, Lindsey-Boltz LA, Gaddameedhi S, Selby CP, Ye R, Chiou YY, Kemp MG, Hu J, Lee JH, Ozturk N. Circadian clock, cancer, and chemotherapy. Biochemistry 2014; 54:110-23. [PMID: 25302769 PMCID: PMC4303322 DOI: 10.1021/bi5007354] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The
circadian clock is a global regulatory system that interfaces
with most other regulatory systems and pathways in mammalian organisms.
Investigations of the circadian clock–DNA damage response connections
have revealed that nucleotide excision repair, DNA damage checkpoints,
and apoptosis are appreciably influenced by the clock. Although several
epidemiological studies in humans and a limited number of genetic
studies in mouse model systems have indicated that clock disruption
may predispose mammals to cancer, well-controlled genetic studies
in mice have not supported the commonly held view that circadian clock
disruption is a cancer risk factor. In fact, in the appropriate genetic
background, clock disruption may instead aid in cancer regression
by promoting intrinsic and extrinsic apoptosis. Finally, the clock
may affect the efficacy of cancer treatment (chronochemotherapy) by
modulating the pharmacokinetics and pharmacodynamics of chemotherapeutic
drugs as well as the activity of the DNA repair enzymes that repair
the DNA damage caused by anticancer drugs.
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Affiliation(s)
- Aziz Sancar
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine , Chapel Hill, North Carolina 27599, United States
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Witosch J, Wolf E, Mizuno N. Architecture and ssDNA interaction of the Timeless-Tipin-RPA complex. Nucleic Acids Res 2014; 42:12912-27. [PMID: 25348395 PMCID: PMC4227788 DOI: 10.1093/nar/gku960] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The Timeless-Tipin (Tim-Tipin) complex, also referred to as the fork protection complex, is involved in coordination of DNA replication. Tim-Tipin is suggested to be recruited to replication forks via Replication Protein A (RPA) but details of the interaction are unknown. Here, using cryo-EM and biochemical methods, we characterized complex formation of Tim-Tipin, RPA and single-stranded DNA (ssDNA). Tim-Tipin and RPA form a 258 kDa complex with a 1:1:1 stoichiometry. The cryo-EM 3D reconstruction revealed a globular architecture of the Tim-Tipin-RPA complex with a ring-like and a U-shaped domain covered by a RPA lid. Interestingly, RPA in the complex adopts a horse shoe-like shape resembling its conformation in the presence of long ssDNA (>30 nucleotides). Furthermore, the recruitment of the Tim-Tipin-RPA complex to ssDNA is modulated by the RPA conformation and requires RPA to be in the more compact 30 nt ssDNA binding mode. The dynamic formation and disruption of the Tim-Tipin-RPA-ssDNA complex implicates the RPA-based recruitment of Tim-Tipin to the replication fork.
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Affiliation(s)
- Justine Witosch
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Eva Wolf
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany Department of Physiological Chemistry and Center For Integrated Protein Science Munich (CIPSM), Butenandt Institute, Ludwig Maximilians University of Munich, Butenandtstrasse 5, 81377 Munich, Germany Institut für allgemeine Botanik, Johannes Gutenberg-University, Johannes-von-Müller-Weg 6, 55128 Mainz, Germany and Institute of Molecular Biology (IMB), Mainz, Germany
| | - Naoko Mizuno
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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Severson AF, Meyer BJ. Divergent kleisin subunits of cohesin specify mechanisms to tether and release meiotic chromosomes. eLife 2014; 3:e03467. [PMID: 25171895 PMCID: PMC4174578 DOI: 10.7554/elife.03467] [Citation(s) in RCA: 57] [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: 05/23/2014] [Accepted: 08/28/2014] [Indexed: 12/22/2022] Open
Abstract
We show that multiple, functionally specialized cohesin complexes mediate the establishment and two-step release of sister chromatid cohesion that underlies the production of haploid gametes. In C. elegans, the kleisin subunits REC-8 and COH-3/4 differ between meiotic cohesins and endow them with distinctive properties that specify how cohesins load onto chromosomes and then trigger and release cohesion. Unlike REC-8 cohesin, COH-3/4 cohesin becomes cohesive through a replication-independent mechanism initiated by the DNA double-stranded breaks that induce crossover recombination. Thus, break-induced cohesion also tethers replicated meiotic chromosomes. Later, recombination stimulates separase-independent removal of REC-8 and COH-3/4 cohesins from reciprocal chromosomal territories flanking the crossover site. This region-specific removal likely underlies the two-step separation of homologs and sisters. Unexpectedly, COH-3/4 performs cohesion-independent functions in synaptonemal complex assembly. This new model for cohesin function diverges from that established in yeast but likely applies directly to plants and mammals, which utilize similar meiotic kleisins.
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Affiliation(s)
- Aaron F Severson
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
- Center for Gene Regulation in Health and Disease and Department of Biological, Geological, and Environmental Sciences, Cleveland State University, Cleveland, United States
| | - Barbara J Meyer
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
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Gu HF, Xiao JH, Niu LM, Wang B, Ma GC, Dunn DW, Huang DW. Adaptive evolution of the circadian gene timeout in insects. Sci Rep 2014; 4:4212. [PMID: 24572761 PMCID: PMC3936262 DOI: 10.1038/srep04212] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 01/28/2014] [Indexed: 12/24/2022] Open
Abstract
Most insects harbor two paralogous circadian genes, namely timeout and timeless. However, in the Hymenoptera only timeout is present. It remains unclear whether both genes, especially timeout in hymenopteran insects, have distinct evolutionary patterns. In this study, we examine the molecular evolution of both genes in 25 arthropod species, for which whole genome data are available, with addition of the daily expression of the timeout gene in a pollinating fig wasp, Ceratosolen solmsi (Hymenoptera: Chalcidoidea: Agaonidae). Timeless is under stronger purifying selection than timeout, and timeout has positively selected sites in insects, especially in the Hymenoptera. Within the Hymenoptera, the function of timeout may be conserved in bees and ants, but still evolving rapidly in some wasps such as the chalcids. In fig wasps, timeout is rhythmically expressed only in females when outside of the fig syconium but arrhythmically in male and female wasps inside the syconium. These plastic gene expressions reflect adaptive differences of males and females to their environment.
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Affiliation(s)
- Hai-Feng Gu
- 1] Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China [2] University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Jin-Hua Xiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Li-Ming Niu
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, China
| | - Bo Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guang-Chang Ma
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan, 571737, China
| | - Derek W Dunn
- Statistics and Mathematics College, Yunnan University of Finance and Economics, Kunming, Yunnan, 650221, China
| | - Da-Wei Huang
- 1] Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China [2] Plant Protection College, Shandong Agricultural University, Tai'an, 271018, China
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Hosono Y, Abe T, Higuchi M, Kajii K, Sakuraba S, Tada S, Enomoto T, Seki M. Tipin functions in the protection against topoisomerase I inhibitor. J Biol Chem 2014; 289:11374-11384. [PMID: 24573676 DOI: 10.1074/jbc.m113.531707] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The replication fork temporarily stalls when encountering an obstacle on the DNA, and replication resumes after the barrier is removed. Simultaneously, activation of the replication checkpoint delays the progression of S phase and inhibits late origin firing. Camptothecin (CPT), a topoisomerase I (Top1) inhibitor, acts as a DNA replication barrier by inducing the covalent retention of Top1 on DNA. The Timeless-Tipin complex, a component of the replication fork machinery, plays a role in replication checkpoint activation and stabilization of the replication fork. However, the role of the Timeless-Tipin complex in overcoming the CPT-induced replication block remains elusive. Here, we generated viable TIPIN gene knock-out (KO) DT40 cells showing delayed S phase progression and increased cell death. TIPIN KO cells were hypersensitive to CPT. However, homologous recombination and replication checkpoint were activated normally, whereas DNA synthesis activity was markedly decreased in CPT-treated TIPIN KO cells. Proteasome-dependent degradation of chromatin-bound Top1 was induced in TIPIN KO cells upon CPT treatment, and pretreatment with aphidicolin, a DNA polymerase inhibitor, suppressed both CPT sensitivity and Top1 degradation. Taken together, our data indicate that replication forks formed without Tipin may collide at a high rate with Top1 retained on DNA by CPT treatment, leading to CPT hypersensitivity and Top1 degradation in TIPIN KO cells.
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Affiliation(s)
- Yoshifumi Hosono
- Molecular Cell Biology Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba 6-3, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Takuya Abe
- Instituto FIRC di Oncologia Molecolare (IFOM), Fondazione Italiana per la Ricerca sul Cancro (FIRC) Institute for Molecular Oncology Foundation, IFOM-Istituto Europeo di Oncologia Campus, Via Adamello 16, 20139 Milan, Italy
| | - Masato Higuchi
- Molecular Cell Biology Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba 6-3, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Kosa Kajii
- Department of Biochemistry, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi 981-8558, Japan
| | - Shuichi Sakuraba
- Molecular Cell Biology Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba 6-3, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Shusuke Tada
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, 4-21-2 Nakano, Nakano-ku, Tokyo 164-8530, Japan, and
| | - Takemi Enomoto
- Molecular Cell Biology Laboratory, Research Institute of Pharmaceutical Sciences, Faculty of Pharmacy, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi, Tokyo 202-8585, Japan
| | - Masayuki Seki
- Department of Biochemistry, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi 981-8558, Japan,.
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Kang TH, Leem SH. Modulation of ATR-mediated DNA damage checkpoint response by cryptochrome 1. Nucleic Acids Res 2014; 42:4427-34. [PMID: 24489120 PMCID: PMC3985666 DOI: 10.1093/nar/gku094] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Mammalian cryptochromes (Crys) are essential circadian clock factors implicated in diverse clock-independent physiological functions, including DNA damage responses. Here we show that Cry1 modulates the ATR-mediated DNA damage checkpoint (DDC) response by interacting with Timeless (Tim) in a time-of-day-dependent manner. The DDC capacity in response to UV irradiation showed a circadian rhythm. Interestingly, clock-deficient Cry1 and Cry2 double knockout (CryDKO) cells retained substantial DDC capacity compared with clock-proficient wild-type cells, although the Cry1-modulated oscillation of the DDC capacity was abolished in CryDKO cells. We found temporal interaction of Cry1 and Tim in the nucleus. When Cry1 was expressed in the nucleus, it was critical for circadian ATR activity. We regenerated rhythmic DDC responses by ectopically expressing Cry1 in CryDKO cells. In addition, we also investigated the DDC capacity in the liver of mice that were intraperitoneally injected with cisplatin at different circadian times (CT). When mice were injected at CT20, about 2-fold higher expression of phosphorylated minichromosome maintenance protein 2 (p-MCM2) was detected compared with mice injected at CT08, which consequently affected the removal rate of cisplatin-DNA adducts from genomic DNA. Taken together, our data demonstrate the intimate interaction between the circadian clock and the DDC system during genotoxic stress in clock-ticking cells.
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Affiliation(s)
- Tae-Hong Kang
- Department of Biological Science, Dong-A University, Hadan2-dong, Saha-gu, Busan 604-714, South Korea
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Mao Y, Fu A, Leaderer D, Zheng T, Chen K, Zhu Y. Potential cancer-related role of circadian gene TIMELESS suggested by expression profiling and in vitro analyses. BMC Cancer 2013; 13:498. [PMID: 24161199 PMCID: PMC3924353 DOI: 10.1186/1471-2407-13-498] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 10/04/2013] [Indexed: 02/08/2023] Open
Abstract
Background The circadian clock and cell cycle are two global regulatory systems that have pervasive behavioral and physiological effects on eukaryotic cells, and both play a role in cancer development. Recent studies have indicated that the circadian and cell cycle regulator, TIMELESS, may serve as a molecular bridge between these two regulatory systems. Methods To assess the role of TIMELESS in tumorigenesis, we analyzed TIMELESS expression data from publically accessible online databases. A loss-of-function analysis was then performed using TIMELESS-targeting siRNA oligos followed by a whole-genome expression microarray and network analysis. We further tested the effect of TIMELESS down-regulation on cell proliferation rates of a breast and cervical cancer cell line, as suggested by the results of our network analysis. Results TIMELESS was found to be frequently overexpressed in different tumor types compared to normal controls. Elevated expression of TIMELESS was significantly associated with more advanced tumor stage and poorer breast cancer prognosis. We identified a cancer-relevant network of transcripts with altered expression following TIMELESS knockdown which contained many genes with known functions in cancer development and progression. Furthermore, we observed that TIMELESS knockdown significantly decreased cell proliferation rate. Conclusions Our results suggest a potential role for TIMELESS in tumorigenesis, which warrants further investigation of TIMELESS expression as a potential biomarker of cancer susceptibility and prognostic outcome.
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Affiliation(s)
| | | | | | | | | | - Yong Zhu
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT 06520, USA.
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