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Braun H, Xu Z, Chang F, Viceconte N, Rane G, Levin M, Lototska L, Roth F, Hillairet A, Fradera-Sola A, Khanchandani V, Sin ZW, Yong WK, Dreesen O, Yang Y, Shi Y, Li F, Butter F, Kappei D. ZNF524 directly interacts with telomeric DNA and supports telomere integrity. Nat Commun 2023; 14:8252. [PMID: 38086788 PMCID: PMC10716145 DOI: 10.1038/s41467-023-43397-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/08/2023] [Indexed: 12/18/2023] Open
Abstract
Telomeres are nucleoprotein structures at the ends of linear chromosomes. In humans, they consist of TTAGGG repeats, which are bound by dedicated proteins such as the shelterin complex. This complex blocks unwanted DNA damage repair at telomeres, e.g. by suppressing nonhomologous end joining (NHEJ) through its subunit TRF2. Here, we describe ZNF524, a zinc finger protein that directly binds telomeric repeats with nanomolar affinity, and reveal base-specific sequence recognition by cocrystallization with telomeric DNA. ZNF524 localizes to telomeres and specifically maintains the presence of the TRF2/RAP1 subcomplex at telomeres without affecting other shelterin members. Loss of ZNF524 concomitantly results in an increase in DNA damage signaling and recombination events. Overall, ZNF524 is a direct telomere-binding protein involved in the maintenance of telomere integrity.
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Affiliation(s)
- Hanna Braun
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Institute of Molecular Biology (IMB), Mainz, 55128, Germany
| | - Ziyan Xu
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Fiona Chang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | | | - Grishma Rane
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Michal Levin
- Institute of Molecular Biology (IMB), Mainz, 55128, Germany
| | | | - Franziska Roth
- Institute of Molecular Biology (IMB), Mainz, 55128, Germany
| | - Alexia Hillairet
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | | | - Vartika Khanchandani
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Zi Wayne Sin
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Wai Khang Yong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore
| | - Oliver Dreesen
- Cell Aging Laboratory, A*STAR Skin Research Labs, Singapore, 138648, Singapore
| | - Yang Yang
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yunyu Shi
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Fudong Li
- MOE Key Laboratory for Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Falk Butter
- Institute of Molecular Biology (IMB), Mainz, 55128, Germany.
- Institute of Molecular Virology and Cell Biology (IMVZ), Friedrich Loeffler Institute, Greifswald, 17493, Germany.
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore.
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
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2
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Laberthonnière C, Delourme M, Chevalier R, Dion C, Ganne B, Hirst D, Caron L, Perrin P, Adélaïde J, Chaffanet M, Xue S, Nguyen K, Reversade B, Déjardin J, Baudot A, Robin J, Magdinier F. In skeletal muscle and neural crest cells, SMCHD1 regulates biological pathways relevant for Bosma syndrome and facioscapulohumeral dystrophy phenotype. Nucleic Acids Res 2023; 51:7269-7287. [PMID: 37334829 PMCID: PMC10415154 DOI: 10.1093/nar/gkad523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/15/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023] Open
Abstract
Many genetic syndromes are linked to mutations in genes encoding factors that guide chromatin organization. Among them, several distinct rare genetic diseases are linked to mutations in SMCHD1 that encodes the structural maintenance of chromosomes flexible hinge domain containing 1 chromatin-associated factor. In humans, its function as well as the impact of its mutations remains poorly defined. To fill this gap, we determined the episignature associated with heterozygous SMCHD1 variants in primary cells and cell lineages derived from induced pluripotent stem cells for Bosma arhinia and microphthalmia syndrome (BAMS) and type 2 facioscapulohumeral dystrophy (FSHD2). In human tissues, SMCHD1 regulates the distribution of methylated CpGs, H3K27 trimethylation and CTCF at repressed chromatin but also at euchromatin. Based on the exploration of tissues affected either in FSHD or in BAMS, i.e. skeletal muscle fibers and neural crest stem cells, respectively, our results emphasize multiple functions for SMCHD1, in chromatin compaction, chromatin insulation and gene regulation with variable targets or phenotypical outcomes. We concluded that in rare genetic diseases, SMCHD1 variants impact gene expression in two ways: (i) by changing the chromatin context at a number of euchromatin loci or (ii) by directly regulating some loci encoding master transcription factors required for cell fate determination and tissue differentiation.
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Affiliation(s)
| | - Mégane Delourme
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, Marseille 13005, France
| | - Raphaël Chevalier
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, Marseille 13005, France
| | - Camille Dion
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, Marseille 13005, France
| | - Benjamin Ganne
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, Marseille 13005, France
| | - David Hirst
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, Marseille 13005, France
| | - Leslie Caron
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, Marseille 13005, France
| | - Pierre Perrin
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, Marseille 13005, France
| | - José Adélaïde
- Aix Marseille Univ, INSERM, CNRS, Institut Paoli Calmette, Centre de Recherche en Cancérologie de Marseille, Laboratory of predictive Oncology, Marseille 13009, France
| | - Max Chaffanet
- Aix Marseille Univ, INSERM, CNRS, Institut Paoli Calmette, Centre de Recherche en Cancérologie de Marseille, Laboratory of predictive Oncology, Marseille 13009, France
| | - Shifeng Xue
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Karine Nguyen
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, Marseille 13005, France
- Département de Génétique Médicale, AP-HM, Hôpital d’enfants de la Timone, Marseille 13005, France
| | - Bruno Reversade
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Medical Genetics, Koç University, School of Medicine, Istanbul, Turkey
- Department of Physiology, Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Laboratory of Human Genetics & Therapeutics, Smart-Health Initiative, BESE, KAUST, Thuwal, Saudi Arabia
| | - Jérôme Déjardin
- Institut de Génétique Humaine, UMR 9002, CNRS–Université de Montpellier, Montpellier 34000, France
| | - Anaïs Baudot
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, Marseille 13005, France
| | - Jérôme D Robin
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, Marseille 13005, France
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3
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Fernandes RV, Lingner J. The THO complex counteracts TERRA R-loop-mediated telomere fragility in telomerase+ cells and telomeric recombination in ALT+ cells. Nucleic Acids Res 2023; 51:6702-6722. [PMID: 37246640 PMCID: PMC10359610 DOI: 10.1093/nar/gkad448] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 04/26/2023] [Accepted: 05/14/2023] [Indexed: 05/30/2023] Open
Abstract
Telomeres are the nucleoprotein structures at the ends of linear chromosomes. Telomeres are transcribed into long non-coding Telomeric Repeat-Containing RNA (TERRA), whose functions rely on its ability to associate with telomeric chromatin. The conserved THO complex (THOC) was previously identified at human telomeres. It links transcription with RNA processing, decreasing the accumulation of co-transcriptional DNA:RNA hybrids throughout the genome. Here, we explore the role of THOC at human telomeres, as a regulator of TERRA localization to chromosome ends. We show that THOC counteracts TERRA association with telomeres via R-loops formed co-transcriptionally and also post-transcriptionally, in trans. We demonstrate that THOC binds nucleoplasmic TERRA, and that RNaseH1 loss, which increases telomeric R-loops, promotes THOC occupancy at telomeres. Additionally, we show that THOC counteracts lagging and mainly leading strand telomere fragility, suggesting that TERRA R-loops can interfere with replication fork progression. Finally, we observed that THOC suppresses telomeric sister-chromatid exchange and C-circle accumulation in ALT cancer cells, which maintain telomeres by recombination. Altogether, our findings reveal crucial roles of THOC in telomeric homeostasis through the co- and post-transcriptional regulation of TERRA R-loops.
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Affiliation(s)
- Rita Valador Fernandes
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Joachim Lingner
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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Storchova R, Palek M, Palkova N, Veverka P, Brom T, Hofr C, Macurek L. Phosphorylation of TRF2 promotes its interaction with TIN2 and regulates DNA damage response at telomeres. Nucleic Acids Res 2023; 51:1154-1172. [PMID: 36651296 PMCID: PMC9943673 DOI: 10.1093/nar/gkac1269] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/25/2022] [Accepted: 12/23/2022] [Indexed: 01/19/2023] Open
Abstract
Protein phosphatase magnesium-dependent 1 delta (PPM1D) terminates the cell cycle checkpoint by dephosphorylating the tumour suppressor protein p53. By targeting additional substrates at chromatin, PPM1D contributes to the control of DNA damage response and DNA repair. Using proximity biotinylation followed by proteomic analysis, we identified a novel interaction between PPM1D and the shelterin complex that protects telomeric DNA. In addition, confocal microscopy revealed that endogenous PPM1D localises at telomeres. Further, we found that ATR phosphorylated TRF2 at S410 after induction of DNA double strand breaks at telomeres and this modification increased after inhibition or loss of PPM1D. TRF2 phosphorylation stimulated its interaction with TIN2 both in vitro and at telomeres. Conversely, induced expression of PPM1D impaired localisation of TIN2 and TPP1 at telomeres. Finally, recruitment of the DNA repair factor 53BP1 to the telomeric breaks was strongly reduced after inhibition of PPM1D and was rescued by the expression of TRF2-S410A mutant. Our results suggest that TRF2 phosphorylation promotes the association of TIN2 within the shelterin complex and regulates DNA repair at telomeres.
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Affiliation(s)
- Radka Storchova
- Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague CZ-14220, Czech Republic
| | - Matous Palek
- Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague CZ-14220, Czech Republic
| | - Natalie Palkova
- Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague CZ-14220, Czech Republic
| | - Pavel Veverka
- LifeB, Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
| | - Tomas Brom
- LifeB, Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
| | - Ctirad Hofr
- LifeB, Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno CZ-62500, Czech Republic
| | - Libor Macurek
- Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague CZ-14220, Czech Republic
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5
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Vulsteke JB, Smith V, Bonroy C, Derua R, Blockmans D, De Haes P, Vanderschueren S, Lenaerts JL, Claeys KG, Wuyts WA, Verschueren P, Vanhandsaeme G, Piette Y, De Langhe E, Bossuyt X. Identification of new telomere- and telomerase-associated autoantigens in systemic sclerosis. J Autoimmun 2023; 135:102988. [PMID: 36634459 DOI: 10.1016/j.jaut.2022.102988] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 12/16/2022] [Indexed: 01/12/2023]
Abstract
PURPOSE In up to 20% of patients with systemic sclerosis (SSc) no known autoantibody specificity can be identified. Recently discovered autoantigens, such as telomeric repeat binding factor 1 (TERF1), as well as established autoantigens, like RuvBL1/2, are associated with telomere and telomerase biology. We aimed to identify new telomere- and telomerase-associated autoantigens in patients with SSc without known autoantibody specificity. METHODS Unlabelled protein immunoprecipitation combined with gel-free liquid chromatography-tandem mass spectrometry (IP-MS) was performed with sera of 106 patients with SSc from two tertiary referral centres that had a nuclear pattern on HEp-2 indirect immunofluorescence without previously identified autoantibody. Telomere- or telomerase-associated proteins or protein complexes precipitated by individual sera were identified. Candidate autoantigens were confirmed through immunoprecipitation-western blot (IP-WB). A custom Luminex xMAP assay for 5 proteins was evaluated with sera from persons with SSc (n = 467), other systemic autoimmune rheumatic diseases (n = 923), non-rheumatic disease controls (n = 187) and healthy controls (n = 199). RESULTS Eight telomere- and telomerase-associated autoantigens were identified in a total of 11 index patients, including the THO complex (n = 3, all with interstitial lung disease and two with cardiac involvement), telomeric repeat-binding factor 2 (TERF2, n = 1), homeobox-containing protein 1 (HMBOX1, n = 2), regulator of chromosome condensation 1 (RCC1, n = 1), nucleolar and coiled-body phosphoprotein 1 (NOLC1, n = 1), dyskerin (DKC1, n = 1), probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase (NOP2, n = 1) and nuclear valosin-containing protein-like (NVL, n = 2). A Luminex xMAP assay for THO complex subunit 1 (THOC1), TERF2, NOLC1, NOP2 and NVL revealed high reactivity in all index patients, but also in other patients with SSc and disease controls. However, the reactivity by xMAP assay in these other patients was not confirmed by IP-WB. CONCLUSION IP-MS revealed key telomere- and telomerase-associated proteins and protein complexes as autoantigens in patients with SSc.
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Affiliation(s)
- Jean-Baptiste Vulsteke
- KU Leuven, Department of Development and Regeneration, Skeletal Biology and Engineering Research Center, Leuven, Belgium; Rheumatology, University Hospitals Leuven, Leuven, Belgium
| | - Vanessa Smith
- Ghent University, Department of Internal Medicine, Ghent, Belgium; Unit for Molecular Immunology and Inflammation, VIB Inflammation Research Center (IRC), Ghent, Belgium; Rheumatology, Ghent University Hospital, Ghent, Belgium; European Reference Network on Rare and Complex Connective Tissue and Musculoskeletal Diseases (ERN ReCONNET), Belgium
| | - Carolien Bonroy
- Ghent University, Department of Diagnostic Sciences, Ghent, Belgium; Laboratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Rita Derua
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Protein Phosphorylation and Proteomics, Leuven, Belgium; KU Leuven, SyBioMa, Leuven, Belgium
| | - Daniel Blockmans
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory for Clinical Infectious and Inflammatory Disorders, Leuven, Belgium; General Internal Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Petra De Haes
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Leuven, Belgium; Dermatology, University Hospitals Leuven, Leuven, Belgium
| | - Steven Vanderschueren
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory for Clinical Infectious and Inflammatory Disorders, Leuven, Belgium; General Internal Medicine, University Hospitals Leuven, Leuven, Belgium; European Reference Network on Rare Immunodeficiency, Autoinflammatory and Autoimmune Diseases (ERN RITA), Belgium
| | - Jan L Lenaerts
- Rheumatology, University Hospitals Leuven, Leuven, Belgium
| | - Kristl G Claeys
- KU Leuven, Department of Neurosciences, Laboratory for Muscle Diseases and Neuropathies, Neurology, University Hospitals Leuven, Leuven, Belgium; European Reference Network on Rare Neuromuscular Diseases (ERN EURO-NMD), Belgium
| | - Wim A Wuyts
- KU Leuven, Department of Chronic Diseases and Metabolism, Laboratory of Respiratory Diseases and Thoracic Surgery, Unit for Interstitial Lung Diseases, Respiratory Medicine, University Hospitals Leuven, Leuven, Belgium; European Reference Network on Rare Respiratory Diseases (ERN LUNG), Belgium
| | - Patrick Verschueren
- KU Leuven, Department of Development and Regeneration, Skeletal Biology and Engineering Research Center, Leuven, Belgium; Rheumatology, University Hospitals Leuven, Leuven, Belgium
| | | | - Yves Piette
- Ghent University, Department of Internal Medicine, Ghent, Belgium; Rheumatology, Ghent University Hospital, Ghent, Belgium
| | - Ellen De Langhe
- KU Leuven, Department of Development and Regeneration, Skeletal Biology and Engineering Research Center, Leuven, Belgium; Rheumatology, University Hospitals Leuven, Leuven, Belgium; European Reference Network on Rare and Complex Connective Tissue and Musculoskeletal Diseases (ERN ReCONNET), Belgium; European Reference Network on Rare Immunodeficiency, Autoinflammatory and Autoimmune Diseases (ERN RITA), Belgium
| | - Xavier Bossuyt
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Clinical and Diagnostic Immunology, Leuven, Belgium; Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium.
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6
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Mendez-Bermudez A, Lototska L, Pousse M, Tessier F, Croce O, Latrick CM, Cherdyntseva V, Nassour J, Xiaohua J, Lu Y, Abbadie C, Gagos S, Ye J, Gilson E. Selective pericentromeric heterochromatin dismantling caused by TP53 activation during senescence. Nucleic Acids Res 2022; 50:7493-7510. [PMID: 35819196 PMCID: PMC9303393 DOI: 10.1093/nar/gkac603] [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: 12/13/2021] [Revised: 06/17/2022] [Accepted: 07/01/2022] [Indexed: 11/13/2022] Open
Abstract
Cellular senescence triggers various types of heterochromatin remodeling that contribute to aging. However, the age-related mechanisms that lead to these epigenetic alterations remain elusive. Here, we asked how two key aging hallmarks, telomere shortening and constitutive heterochromatin loss, are mechanistically connected during senescence. We show that, at the onset of senescence, pericentromeric heterochromatin is specifically dismantled consisting of chromatin decondensation, accumulation of DNA breakages, illegitimate recombination and loss of DNA. This process is caused by telomere shortening or genotoxic stress by a sequence of events starting from TP53-dependent downregulation of the telomere protective protein TRF2. The resulting loss of TRF2 at pericentromeres triggers DNA breaks activating ATM, which in turn leads to heterochromatin decondensation by releasing KAP1 and Lamin B1, recombination and satellite DNA excision found in the cytosol associated with cGAS. This TP53–TRF2 axis activates the interferon response and the formation of chromosome rearrangements when the cells escape the senescent growth arrest. Overall, these results reveal the role of TP53 as pericentromeric disassembler and define the basic principles of how a TP53-dependent senescence inducer hierarchically leads to selective pericentromeric dismantling through the downregulation of TRF2.
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Affiliation(s)
- Aaron Mendez-Bermudez
- Department of Geriatrics, Medical center on Aging of Shanghai Ruijin Hospital, Shanghai Jiaotong University school of Medicine; International laboratory in Hematology, Cancer and Aging, Pôle Sino-Français de Recherches en Sciences du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; CNRS/INSERM/University Côte d'Azur.,Université Côte d'Azur, CNRS, INSERM, IRCAN, Faculty of Medicine Nice, France
| | - Liudmyla Lototska
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Faculty of Medicine Nice, France
| | - Melanie Pousse
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Faculty of Medicine Nice, France
| | - Florent Tessier
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Faculty of Medicine Nice, France
| | - Oliver Croce
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Faculty of Medicine Nice, France
| | - Chrysa M Latrick
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Faculty of Medicine Nice, France
| | - Veronica Cherdyntseva
- Laboratory of Genetics, Center of Experimental Medicine and Translational Research, Biomedical Research Foundation of the Academy of Athens, Greece
| | - Joe Nassour
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020-U1277, CANTHER, Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Jiang Xiaohua
- School of Biomedical Sciences, The Chinese University of Hong Kong
| | - Yiming Lu
- Department of Geriatrics, Medical center on Aging of Shanghai Ruijin Hospital, Shanghai Jiaotong University school of Medicine; International laboratory in Hematology, Cancer and Aging, Pôle Sino-Français de Recherches en Sciences du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; CNRS/INSERM/University Côte d'Azur
| | - Corinne Abbadie
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020-U1277, CANTHER, Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Sarantis Gagos
- Laboratory of Genetics, Center of Experimental Medicine and Translational Research, Biomedical Research Foundation of the Academy of Athens, Greece
| | - Jing Ye
- Department of Geriatrics, Medical center on Aging of Shanghai Ruijin Hospital, Shanghai Jiaotong University school of Medicine; International laboratory in Hematology, Cancer and Aging, Pôle Sino-Français de Recherches en Sciences du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; CNRS/INSERM/University Côte d'Azur
| | - Eric Gilson
- Department of Geriatrics, Medical center on Aging of Shanghai Ruijin Hospital, Shanghai Jiaotong University school of Medicine; International laboratory in Hematology, Cancer and Aging, Pôle Sino-Français de Recherches en Sciences du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; CNRS/INSERM/University Côte d'Azur.,Université Côte d'Azur, CNRS, INSERM, IRCAN, Faculty of Medicine Nice, France.,Department of medical genetics, CHU, Nice, France
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7
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Sigismondo G, Papageorgiou DN, Krijgsveld J. Cracking chromatin with proteomics: From chromatome to histone modifications. Proteomics 2022; 22:e2100206. [PMID: 35633285 DOI: 10.1002/pmic.202100206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 11/10/2022]
Abstract
Chromatin is the assembly of genomic DNA and proteins packaged in the nucleus of eukaryotic cells, which together are crucial in regulating a plethora of cellular processes. Histones may be the best known class of protein constituents in chromatin, which are decorated by a range of post-translational modifications to recruit accessory proteins and protein complexes to execute specific functions, ranging from DNA compaction, repair, transcription and duplication, all in a dynamic fashion and depending on the cellular state. The key role of chromatin in cellular fitness is emphasized by the deregulation of chromatin determinants predisposing to different diseases, including cancer. For this reason, deep investigation of chromatin composition is fundamental to better understand cellular physiology. Proteomic approaches have played a crucial role to understand critical aspects of this complex interplay, benefiting from the ability to identify and quantify proteins and their modifications in an unbiased manner. This review gives an overview of the proteomic approaches that have been developed by combining mass spectrometry-based with tailored biochemical and genetic methods to examine overall protein make-up of chromatin, to characterize chromatin domains, to determine protein interactions, and to decipher the broad spectrum of histone modifications that represent the quintessence of chromatin function. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Gianluca Sigismondo
- German Cancer Research Center (DKFZ), Division of Proteomics of Stem Cells and Cancer, Heidelberg, Germany
| | - Dimitris N Papageorgiou
- German Cancer Research Center (DKFZ), Division of Proteomics of Stem Cells and Cancer, Heidelberg, Germany.,Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Division of Proteomics of Stem Cells and Cancer, Heidelberg, Germany.,Medical Faculty, Heidelberg University, Heidelberg, Germany
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8
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Ge F, Pan Q, Qin Y, Jia M, Ruan C, Wei X, Jing Q, Zhi X, Wang X, Jiang L, Osto E, Guo J, Meng D. Single-Cell Analysis Identify Transcription Factor BACH1 as a Master Regulator Gene in Vascular Cells During Aging. Front Cell Dev Biol 2022; 9:786496. [PMID: 35004685 PMCID: PMC8740196 DOI: 10.3389/fcell.2021.786496] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/23/2021] [Indexed: 12/13/2022] Open
Abstract
Vascular aging is a potent driver of cardiovascular and cerebrovascular diseases. Vascular aging features cellular and functional changes, while its molecular mechanisms and the cell heterogeneity are poorly understood. This study aims to 1) explore the cellular and molecular properties of aged cardiac vasculature in monkey and mouse and 2) demonstrate the role of transcription factor BACH1 in the regulation of endothelial cell (EC) senescence and its mechanisms. Here we analyzed published single-cell RNA sequencing (scRNA-seq) data from monkey coronary arteries and aortic arches and mouse hearts. We revealed that the gene expression of YAP1, insulin receptor, and VEGF receptor 2 was downregulated in both aged ECs of coronary arteries’ of monkey and aged cardiac capillary ECs of mouse, and proliferation-related cardiac capillary ECs were significantly decreased in aged mouse. Increased interaction of ECs and immunocytes was observed in aged vasculature of both monkey and mouse. Gene regulatory network analysis identified BACH1 as a master regulator of aging-related genes in both coronary and aorta ECs of monkey and cardiac ECs of mouse. The expression of BACH1 was upregulated in aged cardiac ECs and aortas of mouse. BACH1 aggravated endothelial cell senescence under oxidative stress. Mechanistically, BACH1 occupied at regions of open chromatin and bound to CDKN1A (encoding for P21) gene enhancers, activating its transcription in senescent human umbilical vein endothelial cells (HUVECs). Thus, these findings demonstrate that BACH1 plays an important role in endothelial cell senescence and vascular aging.
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Affiliation(s)
- Fei Ge
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Department of Rheumatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qi Pan
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Department of Rheumatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yue Qin
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Department of Rheumatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Mengping Jia
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Department of Rheumatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chengchao Ruan
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Department of Rheumatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiangxiang Wei
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Department of Rheumatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qing Jing
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiuling Zhi
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Department of Rheumatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xinhong Wang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Department of Rheumatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lindi Jiang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Department of Rheumatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Elena Osto
- Institute of Clinical Chemistry and Department of Cardiology, University Heart Center, University and University Hospital Zurich, Zurich, Switzerland
| | - Jieyu Guo
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Department of Rheumatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Dan Meng
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Department of Rheumatology, Zhongshan Hospital, Fudan University, Shanghai, China
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9
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Barroso-González J, García-Expósito L, Galaviz P, Lynskey ML, Allen JAM, Hoang S, Watkins SC, Pickett HA, O'Sullivan RJ. Anti-recombination function of MutSα restricts telomere extension by ALT-associated homology-directed repair. Cell Rep 2021; 37:110088. [PMID: 34879271 PMCID: PMC8724847 DOI: 10.1016/j.celrep.2021.110088] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/13/2021] [Accepted: 11/10/2021] [Indexed: 01/02/2023] Open
Abstract
Alternative lengthening of telomeres (ALT) is a telomere-elongation mechanism observed in ~15% of cancer subtypes. Current models indicate that ALT is mediated by homology-directed repair mechanisms. By disrupting MSH6 gene expression, we show that the deficiency of MutSα (MSH2/MSH6) DNA mismatch repair complex causes striking telomere hyperextension. Mechanistically, we show MutSα is specifically recruited to telomeres in ALT cells by associating with the proliferating-cell nuclear antigen (PCNA) subunit of the ALT telomere replisome. We also provide evidence that MutSα counteracts Bloom (BLM) helicase, which adopts a crucial role in stabilizing hyper-extended telomeres and maintaining the survival of MutSα-deficient ALT cancer cells. Lastly, we propose a model in which MutSα deficiency impairs heteroduplex rejection, leading to premature initiation of telomere DNA synthesis that coincides with an accumulation of telomere variant repeats (TVRs). These findings provide evidence that the MutSα DNA mismatch repair complex acts to restrain unwarranted ALT. Barroso-Gonzalez et al. show that the mismatch repair complex MutSα restricts the alternative lengthening of telomeres (ALT) pathway in cancer cells. MutSα has an anti-recombination function and limits recombination between heteroduplex sequences at telomeres, in part by counteracting the Bloom helicase (BLM).
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Affiliation(s)
- Jonathan Barroso-González
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Laura García-Expósito
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Pablo Galaviz
- Bioinformatics Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Michelle Lee Lynskey
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Joshua A M Allen
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - SongMy Hoang
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Simon C Watkins
- Department of Cell Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Roderick J O'Sullivan
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.
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10
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Sepe S, Rossiello F, Cancila V, Iannelli F, Matti V, Cicio G, Cabrini M, Marinelli E, Alabi BR, di Lillo A, Di Napoli A, Shay JW, Tripodo C, d'Adda di Fagagna F. DNA damage response at telomeres boosts the transcription of SARS-CoV-2 receptor ACE2 during aging. EMBO Rep 2021; 23:e53658. [PMID: 34854526 PMCID: PMC8811650 DOI: 10.15252/embr.202153658] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 01/08/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) causes the coronavirus disease 2019 (COVID‐19), known to be more common in the elderly, who also show more severe symptoms and are at higher risk of hospitalization and death. Here, we show that the expression of the angiotensin converting enzyme 2 (ACE2), the SARS‐CoV‐2 cell receptor, increases during aging in mouse and human lungs. ACE2 expression increases upon telomere shortening or dysfunction in both cultured mammalian cells and in vivo in mice. This increase is controlled at the transcriptional level, and Ace2 promoter activity is DNA damage response (DDR)‐dependent. Both pharmacological global DDR inhibition of ATM kinase activity and selective telomeric DDR inhibition by the use of antisense oligonucleotides prevent Ace2 upregulation following telomere damage in cultured cells and in mice. We propose that during aging telomere dysfunction due to telomeric shortening or damage triggers DDR activation and this causes the upregulation of ACE2, the SARS‐CoV‐2 cell receptor, thus contributing to make the elderly more susceptible to the infection.
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Affiliation(s)
- Sara Sepe
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Milan, Italy
| | - Francesca Rossiello
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Milan, Italy
| | - Valeria Cancila
- Tumor Immunology Unit, Department of Health Sciences, University of Palermo, Palermo, Italy
| | - Fabio Iannelli
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Milan, Italy
| | - Valentina Matti
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Milan, Italy
| | - Giada Cicio
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Milan, Italy.,Tumor Immunology Unit, Department of Health Sciences, University of Palermo, Palermo, Italy
| | - Matteo Cabrini
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Milan, Italy.,Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Pavia, Italy
| | - Eugenia Marinelli
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Milan, Italy.,Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Pavia, Italy
| | - Busola R Alabi
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Alessia di Lillo
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Milan, Italy
| | - Arianna Di Napoli
- Department of Clinical and Molecular Medicine, Pathology Unit, Sant'Andrea Hospital, Sapienza University, Rome, Italy
| | - Jerry W Shay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Claudio Tripodo
- Tumor Immunology Unit, Department of Health Sciences, University of Palermo, Palermo, Italy
| | - Fabrizio d'Adda di Fagagna
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Milan, Italy.,Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Pavia, Italy
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11
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ATRX proximal protein associations boast roles beyond histone deposition. PLoS Genet 2021; 17:e1009909. [PMID: 34780483 PMCID: PMC8629390 DOI: 10.1371/journal.pgen.1009909] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/29/2021] [Accepted: 10/23/2021] [Indexed: 12/31/2022] Open
Abstract
The ATRX ATP-dependent chromatin remodelling/helicase protein associates with the DAXX histone chaperone to deposit histone H3.3 over repetitive DNA regions. Because ATRX-protein interactions impart functions, such as histone deposition, we used proximity-dependent biotinylation (BioID) to identify proximal associations for ATRX. The proteomic screen captured known interactors, such as DAXX, NBS1, and PML, but also identified a range of new associating proteins. To gauge the scope of their roles, we examined three novel ATRX-associating proteins that likely differed in function, and for which little data were available. We found CCDC71 to associate with ATRX, but also HP1 and NAP1, suggesting a role in chromatin maintenance. Contrastingly, FAM207A associated with proteins involved in ribosome biosynthesis and localized to the nucleolus. ATRX proximal associations with the SLF2 DNA damage response factor help inhibit telomere exchanges. We further screened for the proteomic changes at telomeres when ATRX, SLF2, or both proteins were deleted. The loss caused important changes in the abundance of chromatin remodelling, DNA replication, and DNA repair factors at telomeres. Interestingly, several of these have previously been implicated in alternative lengthening of telomeres. Altogether, this study expands the repertoire of ATRX-associating proteins and functions. ATRX is a protein that is needed to keep repetitive DNA regions organized. It does so in part by binding the DAXX histone chaperone to deposit histone proteins on DNA and assemble structures known as nucleosomes. While important, ATRX has additional functions that remain understudied. To better understand its various biological roles, we first identified the other proteins that are found in its proximity. ATRX-associating proteins were implicated in a range of functions, in addition to histone deposition. Our results suggest that ATRX-associating proteins likely help compact DNA after it is assembled into nucleosomes, and also promote its stability. We then examined the effect of ATRX on telomeres (repetitive DNA regions at the end of chromosomes). ATRX and at least one of its associating proteins suppressed spurious DNA exchanges at telomeres. To understand why, we then identified proteomic changes that occur at telomeres when ATRX was deleted. Loss of ATRX altered the enrichment of a surprising number of proteins at telomeres, including several DNA damage response and chromatin remodelling proteins.
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12
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Lin CYG, Näger AC, Lunardi T, Vančevska A, Lossaint G, Lingner J. The human telomeric proteome during telomere replication. Nucleic Acids Res 2021; 49:12119-12135. [PMID: 34747482 PMCID: PMC8643687 DOI: 10.1093/nar/gkab1015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/07/2021] [Accepted: 10/13/2021] [Indexed: 11/13/2022] Open
Abstract
Telomere shortening can cause detrimental diseases and contribute to aging. It occurs due to the end replication problem in cells lacking telomerase. Furthermore, recent studies revealed that telomere shortening can be attributed to difficulties of the semi-conservative DNA replication machinery to replicate the bulk of telomeric DNA repeats. To investigate telomere replication in a comprehensive manner, we develop QTIP-iPOND - Quantitative Telomeric chromatin Isolation Protocol followed by isolation of Proteins On Nascent DNA - which enables purification of proteins that associate with telomeres specifically during replication. In addition to the core replisome, we identify a large number of proteins that specifically associate with telomere replication forks. Depletion of several of these proteins induces telomere fragility validating their importance for telomere replication. We also find that at telomere replication forks the single strand telomere binding protein POT1 is depleted, whereas histone H1 is enriched. Our work reveals the dynamic changes of the telomeric proteome during replication, providing a valuable resource of telomere replication proteins. To our knowledge, this is the first study that examines the replisome at a specific region of the genome.
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Affiliation(s)
- Chih-Yi Gabriela Lin
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Anna Christina Näger
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Thomas Lunardi
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Aleksandra Vančevska
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Gérald Lossaint
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Joachim Lingner
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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13
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Current Analytical Strategies in Studying Chromatin-Associated-Proteome (Chromatome). Molecules 2021; 26:molecules26216694. [PMID: 34771102 PMCID: PMC8588255 DOI: 10.3390/molecules26216694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/01/2021] [Accepted: 11/03/2021] [Indexed: 11/25/2022] Open
Abstract
Chromatin is a dynamic structure comprising of DNA and proteins. Its unique nature not only help to pack the DNA tightly within the cell but also is pivotal in regulating gene expression DNA replication. Furthermore it also protects the DNA from being damaged. Various proteins are involved in making a specific complex within a chromatin and the knowledge about these interacting partners is helpful to enhance our understanding about the pathophysiology of various chromatin associated diseases. Moreover, it could also help us to identify new drug targets and design more effective remedies. Due to the existence of chromatin in different forms under various physiological conditions it is hard to develop a single strategy to study chromatin associated proteins under all conditions. In our current review, we tried to provide an overview and comparative analysis of the strategies currently adopted to capture the DNA bounded protein complexes and their mass spectrometric identification and quantification. Precise information about the protein partners and their function in the DNA-protein complexes is crucial to design new and more effective therapeutic molecules against chromatin associated diseases.
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14
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Ide S, Sasaki A, Kawamoto Y, Bando T, Sugiyama H, Maeshima K. Telomere-specific chromatin capture using a pyrrole-imidazole polyamide probe for the identification of proteins and non-coding RNAs. Epigenetics Chromatin 2021; 14:46. [PMID: 34627342 PMCID: PMC8502363 DOI: 10.1186/s13072-021-00421-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/23/2021] [Indexed: 11/25/2022] Open
Abstract
Background Knowing chromatin components at a DNA regulatory element at any given time is essential for understanding how the element works during cellular proliferation, differentiation and development. A region-specific chromatin purification is an invaluable approach to dissecting the comprehensive chromatin composition at a particular region. Several methods (e.g., PICh, enChIP, CAPTURE and CLASP) have been developed for isolating and analyzing chromatin components. However, all of them have some shortcomings in identifying non-coding RNA associated with DNA regulatory elements. Results We have developed a new approach for affinity purification of specific chromatin segments employing an N-methyl pyrrole (P)-N-methylimidazole (I) (PI) polyamide probe, which binds to a specific sequence in double-stranded DNA via Watson–Crick base pairing as a minor groove binder. This new technique is called proteomics and RNA-omics of isolated chromatin segments (PI-PRICh). Using PI-PRICh to isolate mouse and human telomeric components, we found enrichments of shelterin proteins, the well-known telomerase RNA component (TERC) and telomeric repeat-containing RNA (TERRA). When PI-PRICh was performed for alternative lengthening of telomere (ALT) cells with highly recombinogenic telomeres, in addition to the conventional telomeric chromatin, we obtained chromatin regions containing telomeric repeat insertions scattered in the genome and their associated RNAs. Conclusion PI-PRICh reproducibly identified both the protein and RNA components of telomeric chromatin when targeting telomere repeats. PI polyamide is a promising alternative to simultaneously isolate associated proteins and RNAs of sequence-specific chromatin regions under native conditions, allowing better understanding of chromatin organization and functions within the cell. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00421-8.
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Affiliation(s)
- Satoru Ide
- Genome Dynamics Laboratory, National Institute of Genetics, ROIS, Mishima, Shizuoka, 411-8540, Japan. .,Department of Genetics, School of Life Science, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan.
| | - Asuka Sasaki
- Genome Dynamics Laboratory, National Institute of Genetics, ROIS, Mishima, Shizuoka, 411-8540, Japan.,Department of Genetics, School of Life Science, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
| | - Yusuke Kawamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, ROIS, Mishima, Shizuoka, 411-8540, Japan.,Department of Genetics, School of Life Science, SOKENDAI, Mishima, Shizuoka, 411-8540, Japan
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15
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Glousker G, Lingner J. Challenging endings: How telomeres prevent fragility. Bioessays 2021; 43:e2100157. [PMID: 34436787 DOI: 10.1002/bies.202100157] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/23/2022]
Abstract
It has become apparent that difficulties to replicate telomeres concern not only the very ends of eukaryotic chromosomes. The challenges already start when the replication fork enters the telomeric repeats. The obstacles encountered consist mainly of noncanonical nucleic acid structures that interfere with replication if not resolved. Replication stress at telomeres promotes the formation of so-called fragile telomeres displaying an abnormal appearance in metaphase chromosomes though their exact molecular nature remains to be elucidated. A substantial number of factors is required to counteract fragility. In this review we promote the hypothesis that telomere fragility is not caused directly by an initial insult during replication but it results as a secondary consequence of DNA repair of damaged replication forks by the homologous DNA recombination machinery. Incomplete DNA synthesis at repair sites or partial chromatin condensation may become apparent as telomere fragility. Fragility and DNA repair during telomere replication emerges as a common phenomenon which exacerbates in multiple disease conditions.
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Affiliation(s)
- Galina Glousker
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
| | - Joachim Lingner
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
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16
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Abstract
Telomeres protect chromosome ends from nucleolytic degradation, uncontrolled recombination by DNA repair enzymes and checkpoint signaling, and they provide mechanisms for their maintenance by semiconservative DNA replication, telomerase and homologous recombination. The telomeric long noncoding RNA TERRA is transcribed from a large number of chromosome ends. TERRA has been implicated in modulating telomeric chromatin structure and checkpoint signaling, and in telomere maintenance by homology directed repair, and telomerase – when telomeres are damaged or very short. Recent work indicates that TERRA association with telomeres involves the formation of DNA:RNA hybrid structures that can be formed post transcription by the RAD51 DNA recombinase, which in turn may trigger homologous recombination between telomeric repeats and telomere elongation. In this review, we describe the mechanisms of TERRA recruitment to telomeres, R-loop formation and its regulation by shelterin proteins. We discuss the consequences of R-loop formation, with regard to telomere maintenance by DNA recombination and how this may impinge on telomere replication while counteracting telomere shortening in normal cells and in ALT cancer cells, which maintain telomeres in the absence of telomerase.
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Affiliation(s)
- Rita Valador Fernandes
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
| | - Marianna Feretzaki
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
| | - Joachim Lingner
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Swiss Institute for Experimental Cancer Research (ISREC), Lausanne, Switzerland
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17
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The nuclear kinesin KIF18B promotes 53BP1-mediated DNA double-strand break repair. Cell Rep 2021; 35:109306. [PMID: 34192545 DOI: 10.1016/j.celrep.2021.109306] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 04/29/2021] [Accepted: 06/03/2021] [Indexed: 12/13/2022] Open
Abstract
53BP1 is recruited to chromatin in the vicinity of DNA double-strand breaks (DSBs). We identify the nuclear kinesin, KIF18B, as a 53BP1-interacting protein and define its role in 53BP1-mediated DSB repair. KIF18B is a molecular motor protein involved in destabilizing astral microtubules during mitosis. It is primarily nuclear throughout the interphase and is constitutively chromatin bound. Our observations indicate a nuclear function during the interphase for a kinesin previously implicated in mitosis. We identify a central motif in KIF18B, which we term the Tudor-interacting motif (TIM), because of its interaction with the Tudor domain of 53BP1. TIM enhances the interaction between the 53BP1 Tudor domain and dimethylated lysine 20 of histone H4. TIM and the motor function of KIF18B are both required for efficient 53BP1 focal recruitment in response to damage and for fusion of dysfunctional telomeres. Our data suggest a role for KIF18B in efficient 53BP1-mediated end-joining of DSBs.
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18
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Bauwens S, Lototska L, Koundrioukoff S, Debatisse M, Ye J, Gilson E, Mendez-Bermudez A. The Telomeric Protein TRF2 Regulates Replication Origin Activity within Pericentromeric Heterochromatin. Life (Basel) 2021; 11:life11040267. [PMID: 33804994 PMCID: PMC8063955 DOI: 10.3390/life11040267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/12/2021] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
Heterochromatic regions render the replication process particularly difficult due to the high level of chromatin compaction and the presence of repeated DNA sequences. In humans, replication through pericentromeric heterochromatin requires the binding of a complex formed by the telomeric factor TRF2 and the helicase RTEL1 in order to relieve topological barriers blocking fork progression. Since TRF2 is known to bind the Origin Replication Complex (ORC), we hypothesized that this factor could also play a role at the replication origins (ORI) of these heterochromatin regions. By performing DNA combing analysis, we found that the ORI density is higher within pericentromeric satellite DNA repeats than within bulk genomic DNA and decreased upon TRF2 downregulation. Moreover, we showed that TRF2 and ORC2 interact in pericentromeric DNA, providing a mechanism by which TRF2 is involved in ORI activity. Altogether, our findings reveal an essential role for TRF2 in pericentromeric heterochromatin replication by regulating both replication initiation and elongation.
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Affiliation(s)
- Serge Bauwens
- Faculty of Medicine Nice, Institute for Research on Cancer and Aging (IRCAN), CNRS, INSERM, Université Côte d’Azur, 06107 Nice, France; (S.B.); (L.L.)
| | - Liudmyla Lototska
- Faculty of Medicine Nice, Institute for Research on Cancer and Aging (IRCAN), CNRS, INSERM, Université Côte d’Azur, 06107 Nice, France; (S.B.); (L.L.)
| | - Stephane Koundrioukoff
- Institut Gustave Roussy, Sorbonne Université, UPMC University, 94805 Villejuif, France; (S.K.); (M.D.)
| | - Michelle Debatisse
- Institut Gustave Roussy, Sorbonne Université, UPMC University, 94805 Villejuif, France; (S.K.); (M.D.)
| | - Jing Ye
- International Laboratory in Hematology, Cancer and Aging, Pôle Sino-Français de Recherches en Sciences du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China;
| | - Eric Gilson
- Faculty of Medicine Nice, Institute for Research on Cancer and Aging (IRCAN), CNRS, INSERM, Université Côte d’Azur, 06107 Nice, France; (S.B.); (L.L.)
- International Laboratory in Hematology, Cancer and Aging, Pôle Sino-Français de Recherches en Sciences du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China;
- Correspondence: (E.G.); (A.M.-B.)
| | - Aaron Mendez-Bermudez
- Faculty of Medicine Nice, Institute for Research on Cancer and Aging (IRCAN), CNRS, INSERM, Université Côte d’Azur, 06107 Nice, France; (S.B.); (L.L.)
- International Laboratory in Hematology, Cancer and Aging, Pôle Sino-Français de Recherches en Sciences du Vivant et Génomique, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China;
- Correspondence: (E.G.); (A.M.-B.)
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19
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Burlet B, Ramla S, Fournier C, Abrey-Recalde MJ, Sauter C, Chrétien ML, Rossi C, Duffourd Y, Ragot S, Buriller C, Tournier B, Chapusot C, Nadal N, Racine J, Guy J, Bailly F, Martin L, Casasnovas O, Bastie JN, Caillot D, Albuisson J, Broccardo C, Thieblemont C, Delva L, Maynadié M, Aucagne R, Callanan MB. Identification of novel, clonally stable, somatic mutations targeting transcription factors PAX5 and NKX2-3, the epigenetic regulator LRIF1, and BRAF in a case of atypical B-cell chronic lymphocytic leukemia harboring a t(14;18)(q32;q21). Cold Spring Harb Mol Case Stud 2021; 7:mcs.a005934. [PMID: 33608382 PMCID: PMC7903887 DOI: 10.1101/mcs.a005934] [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: 10/21/2020] [Accepted: 02/06/2021] [Indexed: 12/15/2022] Open
Abstract
Diagnosis of B-cell chronic lymphocytic leukemia (B-CLL) is usually straightforward, involving clinical, immunophenotypic (Matutes score), and (immuno)genetic analyses (to refine patient prognosis for treatment). CLL cases with atypical presentation (e.g., Matutes ≤ 3) are also encountered, and for these diseases, biology and prognostic impact are less clear. Here we report the genomic characterization of a case of atypical B-CLL in a 70-yr-old male patient; B-CLL cells showed a Matutes score of 3, chromosomal translocation t(14;18)(q32;q21) (BCL2/IGH), mutated IGHV, deletion 17p, and mutations in BCL2, NOTCH1 (subclonal), and TP53 (subclonal). Quite strikingly, a novel PAX5 mutation that was predicted to be loss of function was also seen. Exome sequencing identified, in addition, a potentially actionable BRAF mutation, together with novel somatic mutations affecting the homeobox transcription factor NKX2-3, known to control B-lymphocyte development and homing, and the epigenetic regulator LRIF1, which is implicated in chromatin compaction and gene silencing. Neither NKX2-3 nor LRIF1 mutations, predicted to be loss of function, have previously been reported in B-CLL. Sequencing confirmed the presence of these mutations together with BCL2, NOTCH1, and BRAF mutations, with the t(14;18)(q32;q21) translocation, in the initial diagnostic sample obtained 12 yr prior. This is suggestive of a role for these novel mutations in B-CLL initiation and stable clonal evolution, including upon treatment withdrawal. This case extends the spectrum of atypical B-CLL with t(14;18)(q32;q21) and highlights the value of more global precision genomics for patient follow-up and treatment in these patients.
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Affiliation(s)
- Bénédicte Burlet
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Unit for innovation in genetics and epigenetics in oncology, Dijon University Hospital, 21079 Dijon, France
| | - Selim Ramla
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Department of Pathology, Dijon University Hospital, 21079 Dijon, France
| | - Cyril Fournier
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Unit for innovation in genetics and epigenetics in oncology, Dijon University Hospital, 21079 Dijon, France
| | - Maria Jimena Abrey-Recalde
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France
| | - Camille Sauter
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France
| | - Marie-Lorraine Chrétien
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Hematology Laboratory, Dijon University Hospital, 21079 Dijon, France
| | - Cédric Rossi
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Department of Clinical Hematology, Dijon University Hospital, 21079 Dijon, France
| | - Yannis Duffourd
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France
| | - Sylviane Ragot
- Unit for innovation in genetics and epigenetics in oncology, Dijon University Hospital, 21079 Dijon, France
| | - Céline Buriller
- Genetics Laboratory, Dijon University Hospital, 21079 Dijon, France
| | - Benjamin Tournier
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Unit for innovation in genetics and epigenetics in oncology, Dijon University Hospital, 21079 Dijon, France.,Department of Pathology, Dijon University Hospital, 21079 Dijon, France
| | - Caroline Chapusot
- Department of Pathology, Dijon University Hospital, 21079 Dijon, France
| | - Nathalie Nadal
- Genetics Laboratory, Dijon University Hospital, 21079 Dijon, France
| | - Jessica Racine
- Hematology Laboratory, Dijon University Hospital, 21079 Dijon, France
| | - Julien Guy
- Hematology Laboratory, Dijon University Hospital, 21079 Dijon, France
| | - François Bailly
- Hematology Laboratory, Dijon University Hospital, 21079 Dijon, France
| | - Laurent Martin
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Department of Pathology, Dijon University Hospital, 21079 Dijon, France
| | - Olivier Casasnovas
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Department of Clinical Hematology, Dijon University Hospital, 21079 Dijon, France
| | - Jean-Noël Bastie
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Department of Clinical Hematology, Dijon University Hospital, 21079 Dijon, France
| | - Denis Caillot
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Department of Clinical Hematology, Dijon University Hospital, 21079 Dijon, France
| | - Juliette Albuisson
- Oncogenetics laboratory, Centre George François Leclerc, 21079 Dijon, France
| | - Cyril Broccardo
- Centre de Recherches en Cancérologie de Toulouse, Inserm UMR1037, Université de Toulouse III - Paul Sabatier, 31037 Toulouse, France
| | - Catherine Thieblemont
- Department of Hemato-oncology, Hôpital Saint-Louis, AP-HP, 75010 Paris, France.,Université de Paris, NF-kappaB, Différenciation et Cancer, 75006 Paris, France
| | - Laurent Delva
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France
| | - Marc Maynadié
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Hematology Laboratory, Dijon University Hospital, 21079 Dijon, France.,Registre des hémopathies malignes de Côte d'Or, University of Burgundy, Faculty of Medicine, 21079 Dijon, France
| | - Romain Aucagne
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Unit for innovation in genetics and epigenetics in oncology, Dijon University Hospital, 21079 Dijon, France
| | - Mary B Callanan
- University of Burgundy-ISITE-BFC-Institut national de la santé et de la recherche médicale (Inserm) UMR1231, Faculty of Medicine, 21079 Dijon, France.,Unit for innovation in genetics and epigenetics in oncology, Dijon University Hospital, 21079 Dijon, France
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20
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Lim CJ, Cech TR. Shaping human telomeres: from shelterin and CST complexes to telomeric chromatin organization. Nat Rev Mol Cell Biol 2021; 22:283-298. [PMID: 33564154 DOI: 10.1038/s41580-021-00328-y] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2021] [Indexed: 01/14/2023]
Abstract
The regulation of telomere length in mammals is crucial for chromosome end-capping and thus for maintaining genome stability and cellular lifespan. This process requires coordination between telomeric protein complexes and the ribonucleoprotein telomerase, which extends the telomeric DNA. Telomeric proteins modulate telomere architecture, recruit telomerase to accessible telomeres and orchestrate the conversion of the newly synthesized telomeric single-stranded DNA tail into double-stranded DNA. Dysfunctional telomere maintenance leads to telomere shortening, which causes human diseases including bone marrow failure, premature ageing and cancer. Recent studies provide new insights into telomerase-related interactions (the 'telomere replisome') and reveal new challenges for future telomere structural biology endeavours owing to the dynamic nature of telomere architecture and the great number of structures that telomeres form. In this Review, we discuss recently determined structures of the shelterin and CTC1-STN1-TEN1 (CST) complexes, how they may participate in the regulation of telomere replication and chromosome end-capping, and how disease-causing mutations in their encoding genes may affect specific functions. Major outstanding questions in the field include how all of the telomere components assemble relative to each other and how the switching between different telomere structures is achieved.
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Affiliation(s)
- Ci Ji Lim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA. .,Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA. .,BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA.
| | - Thomas R Cech
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA. .,BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA. .,Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA.
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21
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van Mierlo G, Vermeulen M. Chromatin Proteomics to Study Epigenetics - Challenges and Opportunities. Mol Cell Proteomics 2021; 20:100056. [PMID: 33556626 PMCID: PMC7973309 DOI: 10.1074/mcp.r120.002208] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Regulation of gene expression is essential for the functioning of all eukaryotic organisms. Understanding gene expression regulation requires determining which proteins interact with regulatory elements in chromatin. MS-based analysis of chromatin has emerged as a powerful tool to identify proteins associated with gene regulation, as it allows studying protein function and protein complex formation in their in vivo chromatin-bound context. Total chromatin isolated from cells can be directly analyzed using MS or further fractionated into transcriptionally active and inactive chromatin prior to MS-based analysis. Newly formed chromatin that is assembled during DNA replication can also be specifically isolated and analyzed. Furthermore, capturing specific chromatin domains facilitates the identification of previously unknown transcription factors interacting with these domains. Finally, in recent years, advances have been made toward identifying proteins that interact with a single genomic locus of interest. In this review, we highlight the power of chromatin proteomics approaches and how these provide complementary alternatives compared with conventional affinity purification methods. Furthermore, we discuss the biochemical challenges that should be addressed to consolidate and expand the role of chromatin proteomics as a key technology in the context of gene expression regulation and epigenetics research in health and disease. An overview of proteomics methods to study chromatin and gene regulation. Strength and limitations of the different approaches are highlighted. An outlook on the outstanding challenges for chromatin proteomics. Future directions for chromatin proteomics are discussed.
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Affiliation(s)
- Guido van Mierlo
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands.
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands.
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22
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Glousker G, Briod A, Quadroni M, Lingner J. Human shelterin protein POT1 prevents severe telomere instability induced by homology-directed DNA repair. EMBO J 2020; 39:e104500. [PMID: 33073402 PMCID: PMC7705456 DOI: 10.15252/embj.2020104500] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 01/05/2023] Open
Abstract
The evolutionarily conserved POT1 protein binds single-stranded G-rich telomeric DNA and has been implicated in contributing to telomeric DNA maintenance and the suppression of DNA damage checkpoint signaling. Here, we explore human POT1 function through genetics and proteomics, discovering that a complete absence of POT1 leads to severe telomere maintenance defects that had not been anticipated from previous depletion studies in human cells. Conditional deletion of POT1 in HEK293E cells gives rise to rapid telomere elongation and length heterogeneity, branched telomeric DNA structures, telomeric R-loops, and telomere fragility. We determine the telomeric proteome upon POT1-loss, implementing an improved telomeric chromatin isolation protocol. We identify a large set of proteins involved in nucleic acid metabolism that engage with telomeres upon POT1-loss. Inactivation of the homology-directed repair machinery suppresses POT1-loss-mediated telomeric DNA defects. Our results unravel as major function of human POT1 the suppression of telomere instability induced by homology-directed repair.
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Affiliation(s)
- Galina Glousker
- School of Life SciencesSwiss Institute for Experimental Cancer Research (ISREC)Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Anna‐Sophia Briod
- School of Life SciencesSwiss Institute for Experimental Cancer Research (ISREC)Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | | | - Joachim Lingner
- School of Life SciencesSwiss Institute for Experimental Cancer Research (ISREC)Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
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23
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Ahmed W, Lingner J. PRDX1 Counteracts Catastrophic Telomeric Cleavage Events That Are Triggered by DNA Repair Activities Post Oxidative Damage. Cell Rep 2020; 33:108347. [DOI: 10.1016/j.celrep.2020.108347] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 08/26/2020] [Accepted: 10/13/2020] [Indexed: 01/03/2023] Open
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24
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Replication stress conferred by POT1 dysfunction promotes telomere relocalization to the nuclear pore. Genes Dev 2020; 34:1619-1636. [PMID: 33122293 PMCID: PMC7706707 DOI: 10.1101/gad.337287.120] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 09/21/2020] [Indexed: 12/31/2022]
Abstract
In this study, Pinzaru et al. set out to uncover the pathways that enable the proliferation of cells expressing cancer-associated POT1 mutations. Using complementary genetic and proteomic approaches, the authors identify a conserved function for the NPC in resolving replication defects at telomere loci. Mutations in the telomere-binding protein POT1 are associated with solid tumors and leukemias. POT1 alterations cause rapid telomere elongation, ATR kinase activation, telomere fragility, and accelerated tumor development. Here, we define the impact of mutant POT1 alleles through complementary genetic and proteomic approaches based on CRISPR interference and biotin-based proximity labeling, respectively. These screens reveal that replication stress is a major vulnerability in cells expressing mutant POT1, which manifests as increased telomere mitotic DNA synthesis at telomeres. Our study also unveils a role for the nuclear pore complex in resolving replication defects at telomeres. Depletion of nuclear pore complex subunits in the context of POT1 dysfunction increases DNA damage signaling, telomere fragility and sister chromatid exchanges. Furthermore, we observed telomere repositioning to the nuclear periphery driven by nuclear F-actin polymerization in cells with POT1 mutations. In conclusion, our study establishes that relocalization of dysfunctional telomeres to the nuclear periphery is critical to preserve telomere repeat integrity.
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25
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Feretzaki M, Pospisilova M, Valador Fernandes R, Lunardi T, Krejci L, Lingner J. RAD51-dependent recruitment of TERRA lncRNA to telomeres through R-loops. Nature 2020; 587:303-308. [PMID: 33057192 PMCID: PMC7116795 DOI: 10.1038/s41586-020-2815-6] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 07/16/2020] [Indexed: 12/12/2022]
Abstract
Telomeres which are present at the ends of eukaryotic chromosomes mediate genome stability and determine cellular lifespan1. Telomeric repeat containing RNAs (TERRA) are long noncoding RNAs transcribed from chromosome ends2,3, which regulate telomeric chromatin structure and telomere maintenance via telomerase and homology directed repair (HDR)4,5. The mechanisms by which TERRA is recruited to chromosome ends remain poorly defined. Here we develop a reporter system to dissect the underlying mechanisms and demonstrate that the UUAGGG-repeats of TERRA are both necessary and sufficient to target TERRA to chromosome ends. TERRA preferentially associates with short telomeres through the formation of telomeric DNA:RNA hybrid (R-loop) structures that can form in trans. Telomere association and R-loop formation triggers telomere fragility and is promoted by the RAD51 recombinase and its interacting partner BRCA2 but counteracted by RNA surveillance factors, RNaseH1 and TRF1. RAD51 physically interacts with TERRA and catalyzes R-loop formation with TERRA in vitro supporting a direct involvement of this DNA recombinase in TERRA recruitment by strand invasion. Together, our findings reveal a RAD51-dependent pathway that governs TERRA mediated R-loop formation post transcription providing a mechanism of how lncRNAs can be recruited to new loci in trans.
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Affiliation(s)
- Marianna Feretzaki
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Michaela Pospisilova
- Department of Biology and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Rita Valador Fernandes
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Thomas Lunardi
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Lumir Krejci
- Department of Biology and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic. .,International Clinical Research Center, St Anne's University Hospital, Brno, Czech Republic.
| | - Joachim Lingner
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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26
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Kroustallaki P, Lirussi L, Carracedo S, You P, Esbensen QY, Götz A, Jobert L, Alsøe L, Sætrom P, Gagos S, Nilsen H. SMUG1 Promotes Telomere Maintenance through Telomerase RNA Processing. Cell Rep 2020; 28:1690-1702.e10. [PMID: 31412240 DOI: 10.1016/j.celrep.2019.07.040] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 05/28/2019] [Accepted: 07/14/2019] [Indexed: 12/13/2022] Open
Abstract
Telomerase biogenesis is a complex process where several steps remain poorly understood. Single-strand-selective uracil-DNA glycosylase (SMUG1) associates with the DKC1-containing H/ACA ribonucleoprotein complex, which is essential for telomerase biogenesis. Herein, we show that SMUG1 interacts with the telomeric RNA component (hTERC) and is required for co-transcriptional processing of the nascent transcript into mature hTERC. We demonstrate that SMUG1 regulates the presence of base modifications in hTERC, in a region between the CR4/CR5 domain and the H box. Increased levels of hTERC base modifications are accompanied by reduced DKC1 binding. Loss of SMUG1 leads to an imbalance between mature hTERC and its processing intermediates, leading to the accumulation of 3'-polyadenylated and 3'-extended intermediates that are degraded in an EXOSC10-independent RNA degradation pathway. Consequently, SMUG1-deprived cells exhibit telomerase deficiency, leading to impaired bone marrow proliferation in Smug1-knockout mice.
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Affiliation(s)
- Penelope Kroustallaki
- Department of Clinical Molecular Biology, University of Oslo, 0318 Oslo, Norway; Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, 1478 Lørenskog, Norway
| | - Lisa Lirussi
- Department of Clinical Molecular Biology, University of Oslo, 0318 Oslo, Norway; Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, 1478 Lørenskog, Norway
| | - Sergio Carracedo
- Department of Clinical Molecular Biology, University of Oslo, 0318 Oslo, Norway; Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, 1478 Lørenskog, Norway
| | - Panpan You
- Department of Clinical Molecular Biology, University of Oslo, 0318 Oslo, Norway; Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, 1478 Lørenskog, Norway
| | - Q Ying Esbensen
- Department of Clinical Molecular Biology, University of Oslo, 0318 Oslo, Norway; Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, 1478 Lørenskog, Norway
| | - Alexandra Götz
- Department of Clinical Molecular Biology, University of Oslo, 0318 Oslo, Norway; Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, 1478 Lørenskog, Norway
| | - Laure Jobert
- Department of Clinical Molecular Biology, University of Oslo, 0318 Oslo, Norway
| | - Lene Alsøe
- Department of Clinical Molecular Biology, University of Oslo, 0318 Oslo, Norway; Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, 1478 Lørenskog, Norway
| | - Pål Sætrom
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, 7491 Trondheim, Norway; Department of Computer Science, Norwegian University of Science and Technology, NTNU, 7491 Trondheim, Norway; Bioinformatics Core Facility-BioCore, Norwegian University of Science and Technology, NTNU, 7491 Trondheim, Norway; K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, NTNU, 7491 Trondheim, Norway
| | - Sarantis Gagos
- Center of Clinical, Experimental Surgery & Translational Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, University of Oslo, 0318 Oslo, Norway; Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, 1478 Lørenskog, Norway.
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27
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Aeby E, Lee HG, Lee YW, Kriz A, del Rosario BC, Oh HJ, Boukhali M, Haas W, Lee JT. Decapping enzyme 1A breaks X-chromosome symmetry by controlling Tsix elongation and RNA turnover. Nat Cell Biol 2020; 22:1116-1129. [PMID: 32807903 DOI: 10.1038/s41556-020-0558-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/09/2020] [Indexed: 12/27/2022]
Abstract
How allelic asymmetry is generated remains a major unsolved problem in epigenetics. Here we model the problem using X-chromosome inactivation by developing "BioRBP", an enzymatic RNA-proteomic method that enables probing of low-abundance interactions and an allelic RNA-depletion and -tagging system. We identify messenger RNA-decapping enzyme 1A (DCP1A) as a key regulator of Tsix, a noncoding RNA implicated in allelic choice through X-chromosome pairing. DCP1A controls Tsix half-life and transcription elongation. Depleting DCP1A causes accumulation of X-X pairs and perturbs the transition to monoallelic Tsix expression required for Xist upregulation. While ablating DCP1A causes hyperpairing, forcing Tsix degradation resolves pairing and enables Xist upregulation. We link pairing to allelic partitioning of CCCTC-binding factor (CTCF) and show that tethering DCP1A to one Tsix allele is sufficient to drive monoallelic Xist expression. Thus, DCP1A flips a bistable switch for the mutually exclusive determination of active and inactive Xs.
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28
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Guo T, Dong Y, Chen Y, Liu L, Sun H. Development and optimization of a cascade of screening assays for inhibitors of TRF2. Anal Biochem 2020; 602:113796. [PMID: 32485162 DOI: 10.1016/j.ab.2020.113796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 05/20/2020] [Accepted: 05/22/2020] [Indexed: 11/30/2022]
Abstract
TRF2 is a telomere associated protein which plays an important role in telomere maintenance. Knockdown of TRF2 can cause chromosomal end to end fusions and induce DNA damage responses. TRF2 exerts its functions partially by recruiting a number of accessory proteins through its TRF homology domain (TRFH), therefore identification of small molecular compounds which can bind to the TRFH domain of TRF2 and block the interactions of TRF2 with its associated proteins is important to elucidate the molecular mechanism of these protein-protein interactions. Development of robust and sensitive screening and evaluation assays is critical to the identification of TRF2 inhibitors, in this paper we reported the development and optimization of a cascade of screening and binding affinity evaluation assays, including a competitive FP (Fluorescence Polarization) assay utilized in our previous research, and two novel label-free DSF (Differential Scanning Fluorescence) and BLI (Biolayer Interferometry) assays. A previously identified TRF2 inhibitor TRF2-27 was used as an internal reference compound and evaluated in all of these assays. According to the results, DSF assay is not suitable for TRF2 screening because of the low ΔTm, while the optimized labeled-free BLI assay was demonstrated to be an accurate and reproducible assay for TRF2 inhibitor screening and characterization.
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Affiliation(s)
- Tianyue Guo
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, PR China
| | - Yao Dong
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, PR China
| | - Yong Chen
- State Key Laboratory of Molecular Biology, National Center for Protein Science, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 333 Haike Road, Shanghai, 201210, PR China
| | - Liu Liu
- Pharmablock Sciences (Nanjing), Inc., 10 XueFu Road, Jiangbei New District, Nanjing, 210032, PR China.
| | - Haiying Sun
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, PR China.
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29
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TCGA Pan-Cancer Genomic Analysis of Alternative Lengthening of Telomeres (ALT) Related Genes. Genes (Basel) 2020; 11:genes11070834. [PMID: 32708340 PMCID: PMC7397314 DOI: 10.3390/genes11070834] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/15/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023] Open
Abstract
Telomere maintenance mechanisms (TMM) are used by cancer cells to avoid apoptosis, 85–90% reactivate telomerase, while 10–15% use the alternative lengthening of telomeres (ALT). Due to anti-telomerase-based treatments, some tumors switch from a telomerase-dependent mechanism to ALT; in fact, the co-existence between both mechanisms has been observed in some cancers. Although different elements in the ALT pathway are uncovered, some molecular mechanisms are still poorly understood. Therefore, with the aim to identify potential molecular markers for the study of ALT, we combined in silico approaches in a 411 telomere maintenance gene set. As a consequence, we conducted a genomic analysis of these genes in 31 Pan-Cancer Atlas studies from The Cancer Genome Atlas and found 325,936 genomic alterations; from which, we identified 20 genes highly mutated in the cancer studies. Finally, we made a protein-protein interaction network and enrichment analysis to observe the main pathways of these genes and discuss their role in ALT-related processes, like homologous recombination and homology directed repair. Overall, due to the lack of understanding of the molecular mechanisms of ALT cancers, we proposed a group of genes, which after ex vivo validations, could represent new potential therapeutic markers in the study of ALT.
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30
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Roake CM, Artandi SE. Regulation of human telomerase in homeostasis and disease. Nat Rev Mol Cell Biol 2020; 21:384-397. [PMID: 32242127 DOI: 10.1038/s41580-020-0234-z] [Citation(s) in RCA: 158] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2020] [Indexed: 12/14/2022]
Abstract
Telomerase is a ribonucleoprotein complex, the catalytic core of which includes the telomerase reverse transcriptase (TERT) and the non-coding human telomerase RNA (hTR), which serves as a template for the addition of telomeric repeats to chromosome ends. Telomerase expression is restricted in humans to certain cell types, and telomerase levels are tightly controlled in normal conditions. Increased levels of telomerase are found in the vast majority of human cancers, and we have recently begun to understand the mechanisms by which cancer cells increase telomerase activity. Conversely, germline mutations in telomerase-relevant genes that decrease telomerase function cause a range of genetic disorders, including dyskeratosis congenita, idiopathic pulmonary fibrosis and bone marrow failure. In this Review, we discuss the transcriptional regulation of human TERT, hTR processing, assembly of the telomerase complex, the cellular localization of telomerase and its recruitment to telomeres, and the regulation of telomerase activity. We also discuss the disease relevance of each of these steps of telomerase biogenesis.
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Affiliation(s)
- Caitlin M Roake
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.,Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Steven E Artandi
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
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31
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Katahira J, Senokuchi K, Hieda M. Human THO maintains the stability of repetitive DNA. Genes Cells 2020; 25:334-342. [PMID: 32065701 DOI: 10.1111/gtc.12760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 01/31/2023]
Abstract
The evolutionarily conserved multiprotein complex THO/TREX is required for pre-mRNA processing, mRNA export and the maintenance of genome stability. In this study, we analyzed the genome-wide distribution of human THOC7, a component of human THO, by chromatin immunoprecipitation sequencing. The analysis revealed that human THOC7 occupies repetitive sequences, which include microsatellite repeats in genic and intergenic regions and telomeric repeats. The majority of the THOC7 ChIP peaks overlapped with those of the elongating form of RNA polymerase II and R-loops, indicating that THOC7 accumulates in transcriptionally active repeat regions. Knocking down THOC5, an RNA-binding component of human THO, by siRNA induced the accumulation of γH2AX in the repeat regions. We also observed an aberration in the telomeres in the THOC5-depleted condition. These results suggest that human THO restrains the transcription-associated instability of repeat regions in the human genome.
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Affiliation(s)
- Jun Katahira
- Laboratory of Cellular and Molecular Biology, Department of Veterinary Sciences, Osaka Prefecture University, Izumisano, Japan
| | - Kohei Senokuchi
- Laboratory of Cellular and Molecular Biology, Department of Veterinary Sciences, Osaka Prefecture University, Izumisano, Japan
| | - Miki Hieda
- Graduate School of Health Sciences, Ehime Prefectural University of Health Sciences, Iyo-gun, Japan
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32
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Purification and enrichment of specific chromatin loci. Nat Methods 2020; 17:380-389. [PMID: 32152500 DOI: 10.1038/s41592-020-0765-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/29/2020] [Indexed: 12/20/2022]
Abstract
Understanding how chromatin is regulated is essential to fully grasp genome biology, and establishing the locus-specific protein composition is a major step toward this goal. Here we explain why the isolation and analysis of a specific chromatin segment are technically challenging, independently of the method. We then describe the published strategies and discuss their advantages and limitations. We conclude by discussing why significant technology developments are required to unambiguously describe the composition of small single loci.
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33
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Vančevska A, Ahmed W, Pfeiffer V, Feretzaki M, Boulton SJ, Lingner J. SMCHD1 promotes ATM-dependent DNA damage signaling and repair of uncapped telomeres. EMBO J 2020; 39:e102668. [PMID: 32080884 DOI: 10.15252/embj.2019102668] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 01/30/2020] [Accepted: 01/31/2020] [Indexed: 12/13/2022] Open
Abstract
Structural maintenance of chromosomes flexible hinge domain-containing protein 1 (SMCHD1) has been implicated in X-chromosome inactivation, imprinting, and DNA damage repair, and mutations in SMCHD1 can cause facioscapulohumeral muscular dystrophy. More recently, SMCHD1 has also been identified as a component of telomeric chromatin. Here, we report that SMCHD1 is required for DNA damage signaling and non-homologous end joining (NHEJ) at unprotected telomeres. Co-depletion of SMCHD1 and the shelterin subunit TRF2 reduced telomeric 3'-overhang removal in time-course experiments, as well as the number of chromosome end fusions. SMCHD1-deficient cells displayed reduced ATM S1981 phosphorylation and diminished formation of γH2AX foci and of 53BP1-containing telomere dysfunction-induced foci (TIFs), indicating defects in DNA damage checkpoint signaling. Removal of TPP1 and subsequent activation of ATR signaling rescued telomere fusion events in TRF2-depleted SMCHD1 knockout cells. Together, these data indicate that SMCHD1 depletion reduces telomere fusions in TRF2-depleted cells due to defects in ATM-dependent checkpoint signaling and that SMCHD1 mediates DNA damage response activation upstream of ATM phosphorylation at uncapped telomeres.
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Affiliation(s)
- Aleksandra Vančevska
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,The Francis Crick Institute, London, UK
| | - Wareed Ahmed
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Verena Pfeiffer
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Marianna Feretzaki
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Joachim Lingner
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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34
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Lalonde M, Chartrand P. TERRA, a Multifaceted Regulator of Telomerase Activity at Telomeres. J Mol Biol 2020; 432:4232-4243. [PMID: 32084415 DOI: 10.1016/j.jmb.2020.02.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 02/06/2020] [Accepted: 02/10/2020] [Indexed: 02/07/2023]
Abstract
In eukaryotes, telomeres are repetitive sequences at the end of chromosomes, which are maintained in a constitutive heterochromatin state. It is now known that telomeres can be actively transcribed, leading to the production of a telomeric repeat-containing noncoding RNA called TERRA. Due to its sequence complementarity to the telomerase template, it was suggested early on that TERRA could be an inhibitor of telomerase. Since then, TERRA has been shown to be involved in heterochromatin formation at telomeres, to invade telomeric dsDNA and form R-loops, and even to promote telomerase recruitment at short telomeres. All these functions depend on the diverse capacities of this lncRNA to bind various cofactors, act as a scaffold, and promote higher-order complexes in cells. In this review, it will be highlighted as to how these properties of TERRA work together to regulate telomerase activity at telomeres.
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Affiliation(s)
- Maxime Lalonde
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Quebec, Canada
| | - Pascal Chartrand
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Quebec, Canada.
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35
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Dion C, Roche S, Laberthonnière C, Broucqsault N, Mariot V, Xue S, Gurzau AD, Nowak A, Gordon CT, Gaillard MC, El-Yazidi C, Thomas M, Schlupp-Robaglia A, Missirian C, Malan V, Ratbi L, Sefiani A, Wollnik B, Binetruy B, Salort Campana E, Attarian S, Bernard R, Nguyen K, Amiel J, Dumonceaux J, Murphy JM, Déjardin J, Blewitt ME, Reversade B, Robin JD, Magdinier F. SMCHD1 is involved in de novo methylation of the DUX4-encoding D4Z4 macrosatellite. Nucleic Acids Res 2019; 47:2822-2839. [PMID: 30698748 PMCID: PMC6451109 DOI: 10.1093/nar/gkz005] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/26/2018] [Accepted: 01/03/2019] [Indexed: 12/11/2022] Open
Abstract
The DNA methylation epigenetic signature is a key determinant during development. Rules governing its establishment and maintenance remain elusive especially at repetitive sequences, which account for the majority of methylated CGs. DNA methylation is altered in a number of diseases including those linked to mutations in factors that modify chromatin. Among them, SMCHD1 (Structural Maintenance of Chromosomes Hinge Domain Containing 1) has been of major interest following identification of germline mutations in Facio-Scapulo-Humeral Dystrophy (FSHD) and in an unrelated developmental disorder, Bosma Arhinia Microphthalmia Syndrome (BAMS). By investigating why germline SMCHD1 mutations lead to these two different diseases, we uncovered a role for this factor in de novo methylation at the pluripotent stage. SMCHD1 is required for the dynamic methylation of the D4Z4 macrosatellite upon reprogramming but seems dispensable for methylation maintenance. We find that FSHD and BAMS patient's cells carrying SMCHD1 mutations are both permissive for DUX4 expression, a transcription factor whose regulation has been proposed as the main trigger for FSHD. These findings open new questions as to what is the true aetiology for FSHD, the epigenetic events associated with the disease thus calling the current model into question and opening new perspectives for understanding repetitive DNA sequences regulation.
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Affiliation(s)
- Camille Dion
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
| | - Stéphane Roche
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
| | | | - Natacha Broucqsault
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
| | - Virginie Mariot
- NIHR Biomedical Research Centre, University College London, Great Ormond Street Institute of Child Health and Great Ormond Street Hospital NHS Trust, 30 Guilford Street, London WC1N 1EH, UK
| | - Shifeng Xue
- Institute of Molecular and Cell Biology, A*STAR, Singapore. Institute of Medical Biology, A*STAR, Singapore
| | - Alexandra D Gurzau
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; The Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Agnieszka Nowak
- Institut de Génétique Humaine UMR9002 CNRS-Université de Montpellier. France
| | - Christopher T Gordon
- Laboratory of Embryology and Genetics of Human Malformation, INSERM UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | | | - Claire El-Yazidi
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
| | - Morgane Thomas
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
| | - Andrée Schlupp-Robaglia
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France.,Département de Génétique Médicale et Biologie Cellulaire, AP-HM, Hôpital de la Timone enfants, Marseille, France.,Centre de ressources biologiques, AP-HM, Hôpital de la Timone enfants, Marseille, France
| | - Chantal Missirian
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France.,Département de Génétique Médicale et Biologie Cellulaire, AP-HM, Hôpital de la Timone enfants, Marseille, France
| | - Valérie Malan
- Laboratory of Embryology and Genetics of Human Malformation, INSERM UMR 1163, Institut Imagine, Paris, France.,Département de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Liham Ratbi
- Centre de Génomique Humaine et Genopath, Faculté de Médecine et de Pharmacie, Université Mohammed V, 10100 Rabat, Morocco
| | - Abdelaziz Sefiani
- Centre de Génomique Humaine et Genopath, Faculté de Médecine et de Pharmacie, Université Mohammed V, 10100 Rabat, Morocco
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Campus Göttingen, 37073 Göttingen, Germany
| | - Bernard Binetruy
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
| | - Emmanuelle Salort Campana
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France.,Centre de références pour les maladies neuromusculaires et la SLA, AP-HM, Hôpital de la Timone, Marseille, France
| | - Shahram Attarian
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France.,Centre de références pour les maladies neuromusculaires et la SLA, AP-HM, Hôpital de la Timone, Marseille, France
| | - Rafaelle Bernard
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France.,Département de Génétique Médicale et Biologie Cellulaire, AP-HM, Hôpital de la Timone enfants, Marseille, France
| | - Karine Nguyen
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France.,Département de Génétique Médicale et Biologie Cellulaire, AP-HM, Hôpital de la Timone enfants, Marseille, France
| | - Jeanne Amiel
- Laboratory of Embryology and Genetics of Human Malformation, INSERM UMR 1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France.,Département de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Julie Dumonceaux
- NIHR Biomedical Research Centre, University College London, Great Ormond Street Institute of Child Health and Great Ormond Street Hospital NHS Trust, 30 Guilford Street, London WC1N 1EH, UK
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; The Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Jérôme Déjardin
- Institut de Génétique Humaine UMR9002 CNRS-Université de Montpellier. France
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; The Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Bruno Reversade
- Institute of Molecular and Cell Biology, A*STAR, Singapore. Institute of Medical Biology, A*STAR, Singapore.,Department of Paediatrics, National University of Singapore, Singapore, Singapore.,Medical Genetics Department, Koç University School of Medicine (KUSOM), Istanbul, Turkey.,Reproductive Biology Laboratory, Academic Medical Center (AMC), Amsterdam-Zuidoost, The Netherlands
| | - Jérôme D Robin
- Aix Marseille Univ, INSERM MMG, Nerve and Muscle Department, Marseille, France
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36
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Feretzaki M, Renck Nunes P, Lingner J. Expression and differential regulation of human TERRA at several chromosome ends. RNA (NEW YORK, N.Y.) 2019; 25:1470-1480. [PMID: 31350341 PMCID: PMC6795134 DOI: 10.1261/rna.072322.119] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 07/25/2019] [Indexed: 05/07/2023]
Abstract
The telomeric long noncoding RNA TERRA has been implicated in regulating telomere maintenance by telomerase and homologous recombination, and in influencing telomeric protein composition during the cell cycle and the telomeric DNA damage response. TERRA transcription starts at subtelomeric regions resembling the CpG islands of eukaryotic genes extending toward chromosome ends. TERRA contains chromosome-specific subtelomeric sequences at its 5' end and long tracts of UUAGGG-repeats toward the 3' end. Conflicting studies have been published as to whether TERRA is expressed from one or several chromosome ends. Here, we quantify TERRA species by RT-qPCR in normal and several cancerous human cell lines. By using chromosome-specific subtelomeric DNA primers, we demonstrate that TERRA is expressed from a large number of telomeres. Deficiency in DNA methyltransferases leads to TERRA up-regulation only at the subset of chromosome ends that contain CpG-island sequences, revealing differential regulation of TERRA promoters by DNA methylation. However, independently of the differences in TERRA expression, short telomeres were uniformly present in a DNA methyltransferase deficient cell line, indicating that telomere length was not dictated by TERRA expression in cis Bioinformatic analyses indicated the presence of a large number of putative transcription factors binding sites at TERRA promoters, and we identified a subset of them that repress TERRA expression. Altogether, our study confirms that TERRA corresponds to a large gene family transcribed from multiple chromosome ends where we identified two types of TERRA promoters, only one of which is regulated by DNA methylation.
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Affiliation(s)
- Marianna Feretzaki
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Patricia Renck Nunes
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Joachim Lingner
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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37
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Vaquero-Sedas MI, Vega-Palas MA. Assessing the Epigenetic Status of Human Telomeres. Cells 2019; 8:cells8091050. [PMID: 31500249 PMCID: PMC6770363 DOI: 10.3390/cells8091050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/29/2019] [Accepted: 09/05/2019] [Indexed: 12/21/2022] Open
Abstract
The epigenetic modifications of human telomeres play a relevant role in telomere functions and cell proliferation. Therefore, their study is becoming an issue of major interest. These epigenetic modifications are usually analyzed by microscopy or by chromatin immunoprecipitation (ChIP). However, these analyses could be challenged by subtelomeres and/or interstitial telomeric sequences (ITSs). Whereas telomeres and subtelomeres cannot be differentiated by microscopy techniques, telomeres and ITSs might not be differentiated in ChIP analyses. In addition, ChIP analyses of telomeres should be properly controlled. Hence, studies focusing on the epigenetic features of human telomeres have to be carefully designed and interpreted. Here, we present a comprehensive discussion on how subtelomeres and ITSs might influence studies of human telomere epigenetics. We specially focus on the influence of ITSs and some experimental aspects of the ChIP technique on ChIP analyses. In addition, we propose a specific pipeline to accurately perform these studies. This pipeline is very simple and can be applied to a wide variety of cells, including cancer cells. Since the epigenetic status of telomeres could influence cancer cells proliferation, this pipeline might help design precise epigenetic treatments for specific cancer types.
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Affiliation(s)
- María I Vaquero-Sedas
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 41092 Seville, Spain.
| | - Miguel A Vega-Palas
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 41092 Seville, Spain.
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38
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Abstract
Facioscapulohumeral muscular dystrophy (FSHD), a progressive myopathy that afflicts individuals of all ages, provides a powerful model of the complex interplay between genetic and epigenetic mechanisms of chromatin regulation. FSHD is caused by dysregulation of a macrosatellite repeat, either by contraction of the repeat or by mutations in silencing proteins. Both cases lead to chromatin relaxation and, in the context of a permissive allele, aberrant expression of the DUX4 gene in skeletal muscle. DUX4 is a pioneer transcription factor that activates a program of gene expression during early human development, after which its expression is silenced in most somatic cells. When misexpressed in FSHD skeletal muscle, the DUX4 program leads to accumulated muscle pathology. Epigenetic regulators of the disease locus represent particularly attractive therapeutic targets for FSHD, as many are not global modifiers of the genome, and altering their expression or activity should allow correction of the underlying defect.
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MESH Headings
- CRISPR-Cas Systems
- Chromatin/chemistry
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomes, Human, Pair 4
- DNA (Cytosine-5-)-Methyltransferases/genetics
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- DNA Methylation
- Epigenesis, Genetic
- Gene Editing
- Genetic Loci
- Genome, Human
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/pathology
- Muscular Dystrophy, Facioscapulohumeral/classification
- Muscular Dystrophy, Facioscapulohumeral/genetics
- Muscular Dystrophy, Facioscapulohumeral/metabolism
- Muscular Dystrophy, Facioscapulohumeral/pathology
- Mutation
- Severity of Illness Index
- DNA Methyltransferase 3B
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Affiliation(s)
- Charis L Himeda
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, Nevada 89557, USA;
| | - Peter L Jones
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, Nevada 89557, USA;
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39
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CSL controls telomere maintenance and genome stability in human dermal fibroblasts. Nat Commun 2019; 10:3884. [PMID: 31467287 PMCID: PMC6715699 DOI: 10.1038/s41467-019-11785-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/31/2019] [Indexed: 12/31/2022] Open
Abstract
Genomic instability is a hallmark of cancer. Whether it also occurs in Cancer Associated Fibroblasts (CAFs) remains to be carefully investigated. Loss of CSL/RBP-Jκ, the effector of canonical NOTCH signaling with intrinsic transcription repressive function, causes conversion of dermal fibroblasts into CAFs. Here, we find that CSL down-modulation triggers DNA damage, telomere loss and chromosome end fusions that also occur in skin Squamous Cell Carcinoma (SCC)-associated CAFs, in which CSL is decreased. Separately from its role in transcription, we show that CSL is part of a multiprotein telomere protective complex, binding directly and with high affinity to telomeric DNA as well as to UPF1 and Ku70/Ku80 proteins and being required for their telomere association. Taken together, the findings point to a central role of CSL in telomere homeostasis with important implications for genomic instability of cancer stromal cells and beyond. Conversion of dermal fibroblasts into Cancer Associated Fibroblasts (CAFs) can play an important role in keratinocyte tumour development. Here the authors reveal that CSL plays a role in maintenance of telomeres and genomic integrity in both dermal fibroblasts and CAFs.
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40
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Li P, Meng Y, Wang Y, Li J, Lam M, Wang L, Di LJ. Nuclear localization of Desmoplakin and its involvement in telomere maintenance. Int J Biol Sci 2019; 15:2350-2362. [PMID: 31595153 PMCID: PMC6775319 DOI: 10.7150/ijbs.34450] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 04/28/2019] [Indexed: 12/21/2022] Open
Abstract
The interaction between genomic DNA and protein fundamentally determines the activity and the function of DNA elements. Capturing the protein complex and identifying the proteins associated with a specific DNA locus is difficult. Herein, we employed CRISPR, the well-known gene-targeting tool in combination with the proximity-dependent labeling tool BioID to capture a specific genome locus associated proteins and to uncover the novel functions of these proteins. By applying this research tool on telomeres, we identified DSP, out of many others, as a convincing telomere binding protein validated by both biochemical and cell-biological approaches. We also provide evidence to demonstrate that the C-terminal domain of DSP is required for its binding to telomere after translocating to the nucleus mediated by NLS sequence of DSP. In addition, we found that the telomere binding of DSP is telomere length dependent as hTERT inhibition or knockdown caused a decrease of telomere length and diminished DSP binding to the telomere. Knockdown of TRF2 also negatively influenced DSP binding to the telomere. Functionally, loss of DSP resulted in the shortened telomere DNA and induced the DNA damage response and cell apoptosis. In conclusion, our studies identified DSP as a novel potential telomere binding protein and highlighted its role in protecting against telomere DNA damage and resultant cell apoptosis.
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Affiliation(s)
- Peipei Li
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, SAR of China
| | - Yuan Meng
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, SAR of China
| | - Yuan Wang
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, SAR of China.,Metabolomics Core, Faculty of Health Sciences, University of Macau, Macau, SAR of China
| | - Jingjing Li
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, SAR of China.,Metabolomics Core, Faculty of Health Sciences, University of Macau, Macau, SAR of China
| | - Manting Lam
- Metabolomics Core, Faculty of Health Sciences, University of Macau, Macau, SAR of China
| | - Li Wang
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, SAR of China.,Metabolomics Core, Faculty of Health Sciences, University of Macau, Macau, SAR of China
| | - Li-Jun Di
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, SAR of China
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Bilgili H, Białas AJ, Górski P, Piotrowski WJ. Telomere Abnormalities in the Pathobiology of Idiopathic Pulmonary Fibrosis. J Clin Med 2019; 8:jcm8081232. [PMID: 31426295 PMCID: PMC6723768 DOI: 10.3390/jcm8081232] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/12/2019] [Accepted: 08/13/2019] [Indexed: 12/14/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) occurs primarily in older adults and the incidence is clearly associated with aging. This disease seems to be associated with several hallmarks of aging, including telomere attrition and cellular senescence. Increasing evidence suggests that abnormalities involving telomeres and their proteome play a significant role in the pathobiology of IPF. The aim of this study is to summarize present knowledge in the field, as well as to discuss its possible clinical implications. Numerous mutations in genes associated with telomere functioning were studied in the context of IPF, mainly for Telomerase Reverse Transcriptase (TERT) and Telomerase RNA Component (TERC). Such mutations may lead to telomere shortening, which seems to increase the risk of IPF, negatively influence disease progression, and contribute to worse prognosis after lung transplantation. Some evidence indicates the possibility for the use of telomerase activators as potential therapeutic agents in pulmonary fibrosis. To sum up, increasing evidence suggests the role of telomere abnormalities in the pathobiology of IPF, natural history and prognosis of the disease. There are also possibilities for telomerase targeting in the potential development of new treatment agents. However, all these aspects require further research.
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Affiliation(s)
- Hasancan Bilgili
- Department of Pneumology and Allergy, Medical University of Lodz, 90-154 Lodz, Poland
| | - Adam J Białas
- Department of Pneumology and Allergy, Medical University of Lodz, 90-154 Lodz, Poland.
| | - Paweł Górski
- Department of Pneumology and Allergy, Medical University of Lodz, 90-154 Lodz, Poland
| | - Wojciech J Piotrowski
- Department of Pneumology and Allergy, Medical University of Lodz, 90-154 Lodz, Poland
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42
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Genome-wide Control of Heterochromatin Replication by the Telomere Capping Protein TRF2. Mol Cell 2019; 70:449-461.e5. [PMID: 29727617 DOI: 10.1016/j.molcel.2018.03.036] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 02/20/2018] [Accepted: 03/29/2018] [Indexed: 11/22/2022]
Abstract
Hard-to-replicate regions of chromosomes (e.g., pericentromeres, centromeres, and telomeres) impede replication fork progression, eventually leading, in the event of replication stress, to chromosome fragility, aging, and cancer. Our knowledge of the mechanisms controlling the stability of these regions is essentially limited to telomeres, where fragility is counteracted by the shelterin proteins. Here we show that the shelterin subunit TRF2 ensures progression of the replication fork through pericentromeric heterochromatin, but not centromeric chromatin. In a process involving its N-terminal basic domain, TRF2 binds to pericentromeric Satellite III sequences during S phase, allowing the recruitment of the G-quadruplex-resolving helicase RTEL1 to facilitate fork progression. We also show that TRF2 is required for the stability of other heterochromatic regions localized throughout the genome, paving the way for future research on heterochromatic replication and its relationship with aging and cancer.
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43
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Majerska J, Feretzaki M, Glousker G, Lingner J. Transformation-induced stress at telomeres is counteracted through changes in the telomeric proteome including SAMHD1. Life Sci Alliance 2018; 1:e201800121. [PMID: 30456372 PMCID: PMC6238619 DOI: 10.26508/lsa.201800121] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 07/04/2018] [Accepted: 07/05/2018] [Indexed: 12/13/2022] Open
Abstract
The authors apply telomeric chromatin analysis to identify factors that accumulate at telomeres during cellular transformation, promoting telomere replication and repair and counteracting oncogene-borne telomere replication stress. Telomeres play crucial roles during tumorigenesis, inducing cellular senescence upon telomere shortening and extensive chromosome instability during telomere crisis. However, it has not been investigated if and how cellular transformation and oncogenic stress alter telomeric chromatin composition and function. Here, we transform human fibroblasts by consecutive transduction with vectors expressing hTERT, the SV40 early region, and activated H-RasV12. Pairwise comparisons of the telomeric proteome during different stages of transformation reveal up-regulation of proteins involved in chromatin remodeling, DNA repair, and replication at chromosome ends. Depletion of several of these proteins induces telomere fragility, indicating their roles in replication of telomeric DNA. Depletion of SAMHD1, which has reported roles in DNA resection and homology-directed repair, leads to telomere breakage events in cells deprived of the shelterin component TRF1. Thus, our analysis identifies factors, which accumulate at telomeres during cellular transformation to promote telomere replication and repair, resisting oncogene-borne telomere replication stress.
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Affiliation(s)
- Jana Majerska
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute for Experimental Cancer Research, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Marianna Feretzaki
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute for Experimental Cancer Research, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Galina Glousker
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute for Experimental Cancer Research, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Joachim Lingner
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute for Experimental Cancer Research, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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44
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Armstrong CA, Tomita K. Fundamental mechanisms of telomerase action in yeasts and mammals: understanding telomeres and telomerase in cancer cells. Open Biol 2018; 7:rsob.160338. [PMID: 28330934 PMCID: PMC5376709 DOI: 10.1098/rsob.160338] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/20/2017] [Indexed: 12/12/2022] Open
Abstract
Aberrant activation of telomerase occurs in 85–90% of all cancers and underpins the ability of cancer cells to bypass their proliferative limit, rendering them immortal. The activity of telomerase is tightly controlled at multiple levels, from transcriptional regulation of the telomerase components to holoenzyme biogenesis and recruitment to the telomere, and finally activation and processivity. However, studies using cancer cell lines and other model systems have begun to reveal features of telomeres and telomerase that are unique to cancer. This review summarizes our current knowledge on the mechanisms of telomerase recruitment and activation using insights from studies in mammals and budding and fission yeasts. Finally, we discuss the differences in telomere homeostasis between normal cells and cancer cells, which may provide a foundation for telomere/telomerase targeted cancer treatments.
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Affiliation(s)
- Christine A Armstrong
- Chromosome Maintenance Group, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Kazunori Tomita
- Chromosome Maintenance Group, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
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45
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Braun DM, Chung I, Kepper N, Deeg KI, Rippe K. TelNet - a database for human and yeast genes involved in telomere maintenance. BMC Genet 2018; 19:32. [PMID: 29776332 PMCID: PMC5960154 DOI: 10.1186/s12863-018-0617-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 04/30/2018] [Indexed: 02/05/2023] Open
Abstract
Background The ends of linear chromosomes, the telomeres, comprise repetitive DNA sequences in complex with proteins that protects them from being processed by the DNA repair machinery. Cancer cells need to counteract the shortening of telomere repeats during replication for their unlimited proliferation by reactivating the reverse transcriptase telomerase or by using the alternative lengthening of telomeres (ALT) pathway. The different telomere maintenance (TM) mechanisms appear to involve hundreds of proteins but their telomere repeat length related activities are only partly understood. Currently, a database that integrates information on TM relevant genes is missing. Description To provide a resource for studies that dissect TM features, we here introduce the TelNet database at http://www.cancertelsys.org/telnet/. It offers a comprehensive compilation of more than 2000 human and 1100 yeast genes linked to telomere maintenance. These genes were annotated in terms of TM mechanism, associated specific functions and orthologous genes, a TM significance score and information from peer-reviewed literature. This TM information can be retrieved via different search and view modes and evaluated for a set of genes as demonstrated for an exemplary application. Conclusion TelNet supports the annotation of genes identified from bioinformatics analysis pipelines to reveal possible connections with TM networks. We anticipate that TelNet will be a helpful resource for researchers that study telomeres. Electronic supplementary material The online version of this article (10.1186/s12863-018-0617-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Delia M Braun
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) & Bioquant, 69120, Heidelberg, Germany
| | - Inn Chung
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) & Bioquant, 69120, Heidelberg, Germany
| | - Nick Kepper
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) & Bioquant, 69120, Heidelberg, Germany
| | - Katharina I Deeg
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) & Bioquant, 69120, Heidelberg, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) & Bioquant, 69120, Heidelberg, Germany.
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46
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Ahmed W, Lingner J. PRDX1 and MTH1 cooperate to prevent ROS-mediated inhibition of telomerase. Genes Dev 2018; 32:658-669. [PMID: 29773556 PMCID: PMC6004070 DOI: 10.1101/gad.313460.118] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 04/23/2018] [Indexed: 11/29/2022]
Abstract
In this study, Ahmed et al. demonstrate that oxidative damage of telomeres inhibits telomerase activity at chromosome ends in cancer cells. Deletion of two antioxidant enzymes—PRDX1 and MTH1, needed for protecting telomeres from oxidative damage—results in loss of telomeric DNA in an oxygen concentration-dependent manner due to inhibition of telomerase, thus providing new insights into the role of antioxidant systems that are required to protect telomeres from oxidation. Telomerase counteracts telomere shortening and cellular senescence in germ, stem, and cancer cells by adding repetitive DNA sequences to the ends of chromosomes. Telomeres are susceptible to damage by reactive oxygen species (ROS), but the consequences of oxidation of telomeres on telomere length and the mechanisms that protect from ROS-mediated telomere damage are not well understood. In particular, 8-oxoguanine nucleotides at 3′ ends of telomeric substrates inhibit telomerase in vitro, whereas, at internal positions, they suppress G-quadruplex formation and were therefore proposed to promote telomerase activity. Here, we disrupt the peroxiredoxin 1 (PRDX1) and 7,8-dihydro-8-oxoguanine triphosphatase (MTH1) genes in cancer cells and demonstrate that PRDX1 and MTH1 cooperate to prevent accumulation of oxidized guanine in the genome. Concomitant disruption of PRDX1 and MTH1 leads to ROS concentration-dependent continuous shortening of telomeres, which is due to efficient inhibition of telomere extension by telomerase. Our results identify antioxidant systems that are required to protect telomeres from oxidation and are necessary to allow telomere maintenance by telomerase conferring immortality to cancer cells.
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Affiliation(s)
- Wareed Ahmed
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Joachim Lingner
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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47
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Chen X, Liu L, Chen Y, Yang Y, Yang CY, Guo T, Lei M, Sun H, Wang S. Cyclic Peptidic Mimetics of Apollo Peptides Targeting Telomeric Repeat Binding Factor 2 (TRF2) and Apollo Interaction. ACS Med Chem Lett 2018; 9:507-511. [PMID: 29795768 DOI: 10.1021/acsmedchemlett.8b00152] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 04/25/2018] [Indexed: 01/30/2023] Open
Abstract
Telomeric repeat binding factor 2 (TRF2) is a telomere-associated protein that plays an important role in the formation of the 3' single strand DNA overhang and the "T loop", two structures critical for the stability of the telomeres. Apollo is a 5'-exonuclease recruited by TRF2 to the telomere and contributes to the formation of the 3' single strand DNA overhang. Knocking down of Apollo can induce DNA damage response similar to that caused by the knocking down of TRF2. In this Letter, we report the design and synthesis of a class of cyclic peptidic mimetics of the TRFH binding motif of Apollo (ApolloTBM). We found conformational control of the C terminal residues of ApolloTBM can effectively improve the binding affinity. We have obtained a crystal structure of a cyclic peptidic Apollo peptide mimetic (34) complexed with TRF2, which provides valuable guidance to the future design of TRF2 inhibitors.
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Affiliation(s)
- Xia Chen
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | | | - Yong Chen
- State Key Laboratory of Molecular Biology, National Center for Protein Science, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China
| | | | | | - Tianyue Guo
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Ming Lei
- Ninth People’s Hospital, Shanghai Jiaotong University School of Medicine, 639 Zhizaoju Lu, Shanghai 200011, China
- Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Haiying Sun
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
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48
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Tsui C, Inouye C, Levy M, Lu A, Florens L, Washburn MP, Tjian R. dCas9-targeted locus-specific protein isolation method identifies histone gene regulators. Proc Natl Acad Sci U S A 2018; 115:E2734-E2741. [PMID: 29507191 PMCID: PMC5866577 DOI: 10.1073/pnas.1718844115] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eukaryotic gene regulation is a complex process, often coordinated by the action of tens to hundreds of proteins. Although previous biochemical studies have identified many components of the basal machinery and various ancillary factors involved in gene regulation, numerous gene-specific regulators remain undiscovered. To comprehensively survey the proteome directing gene expression at a specific genomic locus of interest, we developed an in vitro nuclease-deficient Cas9 (dCas9)-targeted chromatin-based purification strategy, called "CLASP" (Cas9 locus-associated proteome), to identify and functionally test associated gene-regulatory factors. Our CLASP method, coupled to mass spectrometry and functional screens, can be efficiently adapted for isolating associated regulatory factors in an unbiased manner targeting multiple genomic loci across different cell types. Here, we applied our method to isolate the Drosophila melanogaster histone cluster in S2 cells to identify several factors including Vig and Vig2, two proteins that bind and regulate core histone H2A and H3 mRNA via interaction with their 3' UTRs.
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Affiliation(s)
- Chiahao Tsui
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
| | - Carla Inouye
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
| | - Michaella Levy
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Andrew Lu
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California, Berkeley, CA 94720
| | | | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, MO 64110
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160
| | - Robert Tjian
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California, Berkeley, CA 94720;
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
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49
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Impact of oxidative stress on telomere biology. Differentiation 2018; 99:21-27. [DOI: 10.1016/j.diff.2017.12.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 12/12/2017] [Accepted: 12/13/2017] [Indexed: 12/12/2022]
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50
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Aeby E, Ahmed W, Redon S, Simanis V, Lingner J. Peroxiredoxin 1 Protects Telomeres from Oxidative Damage and Preserves Telomeric DNA for Extension by Telomerase. Cell Rep 2017; 17:3107-3114. [PMID: 28009281 DOI: 10.1016/j.celrep.2016.11.071] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 11/04/2016] [Accepted: 11/22/2016] [Indexed: 01/19/2023] Open
Abstract
Oxidative damage of telomeres can promote cancer, cardiac failure, and muscular dystrophy. Specific mechanisms protecting telomeres from oxidative damage have not been described. We analyzed telomeric chromatin composition during the cell cycle and show that the antioxidant enzyme peroxiredoxin 1 (PRDX1) is enriched at telomeres during S phase. Deletion of the PRDX1 gene leads to damage of telomeric DNA upon oxidative stress, revealing a protective function of PRDX1 against oxidative damage at telomeres. We also show that the oxidized nucleotide 8-oxo-2'deoxyguanosine-5'-triphosphate (8oxodGTP) causes premature chain termination when incorporated by telomerase and that some DNA substrates terminating in 8oxoG prevent extension by telomerase. Thus, PRDX1 safeguards telomeres from oxygen radicals to counteract telomere damage and preserve telomeric DNA for elongation by telomerase.
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Affiliation(s)
- Eric Aeby
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Wareed Ahmed
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Sophie Redon
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Viesturs Simanis
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Joachim Lingner
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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