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Currò R, Dominik N, Facchini S, Vegezzi E, Sullivan R, Galassi Deforie V, Fernández-Eulate G, Traschütz A, Rossi S, Garibaldi M, Kwarciany M, Taroni F, Brusco A, Good JM, Cavalcanti F, Hammans S, Ravenscroft G, Roxburgh RH, Parolin Schnekenberg R, Rugginini B, Abati E, Manini A, Quartesan I, Ghia A, Lòpez de Munaìn A, Manganelli F, Kennerson M, Santorelli FM, Infante J, Marques W, Jokela M, Murphy SM, Mandich P, Fabrizi GM, Briani C, Gosal D, Pareyson D, Ferrari A, Prados F, Yousry T, Khurana V, Kuo SH, Miller J, Troakes C, Jaunmuktane Z, Giunti P, Hartmann A, Basak N, Synofzik M, Stojkovic T, Hadjivassiliou M, Reilly MM, Houlden H, Cortese A. Role of the repeat expansion size in predicting age of onset and severity in RFC1 disease. Brain 2024; 147:1887-1898. [PMID: 38193360 PMCID: PMC11068103 DOI: 10.1093/brain/awad436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/04/2023] [Accepted: 12/10/2023] [Indexed: 01/10/2024] Open
Abstract
RFC1 disease, caused by biallelic repeat expansion in RFC1, is clinically heterogeneous in terms of age of onset, disease progression and phenotype. We investigated the role of the repeat size in influencing clinical variables in RFC1 disease. We also assessed the presence and role of meiotic and somatic instability of the repeat. In this study, we identified 553 patients carrying biallelic RFC1 expansions and measured the repeat expansion size in 392 cases. Pearson's coefficient was calculated to assess the correlation between the repeat size and age at disease onset. A Cox model with robust cluster standard errors was adopted to describe the effect of repeat size on age at disease onset, on age at onset of each individual symptoms, and on disease progression. A quasi-Poisson regression model was used to analyse the relationship between phenotype and repeat size. We performed multivariate linear regression to assess the association of the repeat size with the degree of cerebellar atrophy. Meiotic stability was assessed by Southern blotting on first-degree relatives of 27 probands. Finally, somatic instability was investigated by optical genome mapping on cerebellar and frontal cortex and unaffected peripheral tissue from four post-mortem cases. A larger repeat size of both smaller and larger allele was associated with an earlier age at neurological onset [smaller allele hazard ratio (HR) = 2.06, P < 0.001; larger allele HR = 1.53, P < 0.001] and with a higher hazard of developing disabling symptoms, such as dysarthria or dysphagia (smaller allele HR = 3.40, P < 0.001; larger allele HR = 1.71, P = 0.002) or loss of independent walking (smaller allele HR = 2.78, P < 0.001; larger allele HR = 1.60; P < 0.001) earlier in disease course. Patients with more complex phenotypes carried larger expansions [smaller allele: complex neuropathy rate ratio (RR) = 1.30, P = 0.003; cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS) RR = 1.34, P < 0.001; larger allele: complex neuropathy RR = 1.33, P = 0.008; CANVAS RR = 1.31, P = 0.009]. Furthermore, larger repeat expansions in the smaller allele were associated with more pronounced cerebellar vermis atrophy (lobules I-V β = -1.06, P < 0.001; lobules VI-VII β = -0.34, P = 0.005). The repeat did not show significant instability during vertical transmission and across different tissues and brain regions. RFC1 repeat size, particularly of the smaller allele, is one of the determinants of variability in RFC1 disease and represents a key prognostic factor to predict disease onset, phenotype and severity. Assessing the repeat size is warranted as part of the diagnostic test for RFC1 expansion.
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Affiliation(s)
- Riccardo Currò
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Natalia Dominik
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Stefano Facchini
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | | | - Roisin Sullivan
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | | | - Gorka Fernández-Eulate
- Nord/Est/Ile-de-France Neuromuscular Reference Center, Institute of Myology, Pitié-Salpêtrière Hospital, APHP, 75013 Paris, France
| | - Andreas Traschütz
- Research Division ‘Translational Genomics of Neurodegenerative Diseases’, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, 72076 Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, 72076 Tübingen, Germany
| | - Salvatore Rossi
- Dipartimento di Scienze dell'Invecchiamento, Neurologiche, Ortopediche e della Testa-Collo, UOC Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Facoltà di Medicina e Chirurgia, Dipartimento di Neuroscienze, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Matteo Garibaldi
- Neuromuscular and Rare Disease Center, Department of Neuroscience, Mental Health and Sensory Organs (NESMOS), Sant'Andrea Hospital, Sapienza University of Rome, 00189 Rome, Italy
| | - Mariusz Kwarciany
- Department of Adult Neurology, Medical University of Gdańsk, 80-952 Gdańsk, Poland
| | - Franco Taroni
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20133, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, 10124 Turin, Italy
| | - Jean-Marc Good
- Division of Genetic Medicine, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Francesca Cavalcanti
- Institute for Biomedical Research and Innovation (IRIB), Italian National Research Council (CNR), 87050 Mangone, Italy
| | - Simon Hammans
- Wessex Neurological Centre, Southampton General Hospital, Southampton, SO16 6YD, UK
| | - Gianina Ravenscroft
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, Nedland, WA 6009, Australia
| | - Richard H Roxburgh
- Neurology Department, Auckland City Hospital, New Zealand and the Centre for Brain Research, University of Auckland, Auckland 1142, New Zealand
| | | | - Bianca Rugginini
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Elena Abati
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
| | - Arianna Manini
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
| | - Ilaria Quartesan
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Arianna Ghia
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Adolfo Lòpez de Munaìn
- Neurology Department, Donostia University Hospital, University of the Basque Country-Osakidetza-CIBERNED-Biodonostia, 20014 Donostia-San Sebastián, Spain
| | - Fiore Manganelli
- Department of Neuroscience and Reproductive and Odontostomatological Sciences, University of Naples Federico II, 80131 Naples, Italy
| | - Marina Kennerson
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2050, Australia
| | - Filippo Maria Santorelli
- IRCCS Stella Maris Foundation, Molecular Medicine for Neurodegenerative and Neuromuscular Disease Unit, 56128 Pisa, Italy
| | - Jon Infante
- University Hospital Marquès de Valdecilla-IDIVAL, University of Cantabria, 39008 Santander, Spain
| | - Wilson Marques
- Department of Neurology, School of Medicine of Ribeirão Preto, University of São Paulo, 2650 Ribeirão Preto, Brazil
| | - Manu Jokela
- Neuromuscular Research Center, Department of Neurology, Tampere University and University Hospital, 33520 Tampere, Finland
- Neurocenter, Department of Neurology, Clinical Neurosciences, Turku University Hospital and University of Turku, 20014 Turku, Finland
| | - Sinéad M Murphy
- Department of Neurology, Tallaght University Hospital, D24 NR0A Dublin, Ireland
- Academic Unit of Neurology, Trinity College Dublin, D02 R590 Dublin, Ireland
| | - Paola Mandich
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, 16132 Genoa, Italy
- IRCCS Ospedale Policlinico San Martino-UOC Genetica Medica, 16132 Genova, Italy
| | - Gian Maria Fabrizi
- Department of Neurosciences, Biomedicine, and Movement Sciences, University of Verona, 37134 Verona, Italy
| | - Chiara Briani
- Department of Neurosciences, ERN Neuromuscular Unit, University of Padova, 35100 Padova, Italy
| | - David Gosal
- Manchester Centre for Clinical Neurosciences, Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Greater Manchester, M6 8HD, UK
| | - Davide Pareyson
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20133, Italy
| | | | - Ferran Prados
- Centre for Medical Image Computing (CMIC), Department of Medical Physics and Biomedical Engineering, University College London, London, WC1V 6LJ, UK
- NMR Research Unit, Institute of Neurology, University College London (UCL), London, WC1N 3BG, UK
- e-Health Centre, Universitat Oberta de Catalunya, 08018 Barcelona, Spain
| | - Tarek Yousry
- Neuroradiological Academic Unit, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Vikram Khurana
- Division of Movement Disorders and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sheng-Han Kuo
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - James Miller
- Department of Neurology, Royal Victoria Hospitals, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, NE1 4LP, UK
| | - Claire Troakes
- London Neurodegenerative Diseases Brain Bank, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, SE21 8EA, UK
| | - Zane Jaunmuktane
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Paola Giunti
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Annette Hartmann
- Division of General Psychiatry, Medical University of Vienna, 1090 Vienna, Austria
| | - Nazli Basak
- Koç University, School of Medicine, Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Research Center for Translational Medicine, 34010 Istanbul, Turkey
| | - Matthis Synofzik
- Research Division ‘Translational Genomics of Neurodegenerative Diseases’, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, 72076 Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, 72076 Tübingen, Germany
| | - Tanya Stojkovic
- Nord/Est/Ile-de-France Neuromuscular Reference Center, Institute of Myology, Pitié-Salpêtrière Hospital, APHP, 75013 Paris, France
| | - Marios Hadjivassiliou
- Academic Department of Neurosciences, Sheffield Teaching Hospitals NHS Trust and University of Sheffield, Sheffield, S10 2JF, UK
| | - Mary M Reilly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Andrea Cortese
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
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Pellerin D, Heindl F, Traschütz A, Rujescu D, Hartmann AM, Brais B, Houlden H, Dufke C, Riess O, Haack T, Strupp M, Synofzik M. RFC1 repeat expansions in downbeat nystagmus syndromes: frequency and phenotypic profile. J Neurol 2024; 271:2886-2892. [PMID: 38381176 PMCID: PMC11055689 DOI: 10.1007/s00415-024-12229-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/26/2024] [Accepted: 01/27/2024] [Indexed: 02/22/2024]
Abstract
OBJECTIVES The cause of downbeat nystagmus (DBN) remains unknown in a substantial number of patients ("idiopathic"), although intronic GAA expansions in FGF14 have recently been shown to account for almost 50% of yet idiopathic cases. Here, we hypothesized that biallelic RFC1 expansions may also represent a recurrent cause of DBN syndrome. METHODS We genotyped the RFC1 repeat and performed in-depth phenotyping in 203 patients with DBN, including 65 patients with idiopathic DBN, 102 patients carrying an FGF14 GAA expansion, and 36 patients with presumed secondary DBN. RESULTS Biallelic RFC1 AAGGG expansions were identified in 15/65 patients with idiopathic DBN (23%). None of the 102 GAA-FGF14-positive patients, but 2/36 (6%) of patients with presumed secondary DBN carried biallelic RFC1 expansions. The DBN syndrome in RFC1-positive patients was characterized by additional cerebellar impairment in 100% (15/15), bilateral vestibulopathy (BVP) in 100% (15/15), and polyneuropathy in 80% (12/15) of cases. Compared to GAA-FGF14-positive and genetically unexplained patients, RFC1-positive patients had significantly more frequent neuropathic features on examination and BVP. Furthermore, vestibular function, as measured by the video head impulse test, was significantly more impaired in RFC1-positive patients. DISCUSSION Biallelic RFC1 expansions are a common monogenic cause of DBN syndrome.
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Affiliation(s)
- David Pellerin
- Department of Neurology and Neurosurgery, Montreal Neurological Hospital and Institute, McGill University, Montreal, QC, Canada
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, University College London, London, UK
| | - Felix Heindl
- Department of Neurology and German Center for Vertigo and Balance Disorders, University Hospital, Ludwig-Maximilians University, Munich, Germany
| | - Andreas Traschütz
- Division Translational Genomics of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Dan Rujescu
- Department of Psychiatry and Psychotherapy, Comprehensive Center for Clinical Neurosciences and Mental Health (C3NMH), Medical University of Vienna, Vienna, Austria
| | - Annette M Hartmann
- Department of Psychiatry and Psychotherapy, Comprehensive Center for Clinical Neurosciences and Mental Health (C3NMH), Medical University of Vienna, Vienna, Austria
| | - Bernard Brais
- Department of Neurology and Neurosurgery, Montreal Neurological Hospital and Institute, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Centre de Réadaptation Lucie-Bruneau, Montreal, QC, Canada
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, University College London, London, UK
| | - Claudia Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Tobias Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Michael Strupp
- Department of Neurology and German Center for Vertigo and Balance Disorders, University Hospital, Ludwig-Maximilians University, Munich, Germany
| | - Matthis Synofzik
- Division Translational Genomics of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, Tübingen, Germany.
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany.
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Landeck JT, Pajak J, Norman EK, Sedivy EL, Kelch BA. Differences between bacteria and eukaryotes in clamp loader mechanism, a conserved process underlying DNA replication. J Biol Chem 2024; 300:107166. [PMID: 38490435 PMCID: PMC11044049 DOI: 10.1016/j.jbc.2024.107166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/23/2024] [Accepted: 03/01/2024] [Indexed: 03/17/2024] Open
Abstract
Clamp loaders are pentameric ATPases that place circular sliding clamps onto DNA, where they function in DNA replication and genome integrity. The central activity of a clamp loader is the opening of the ring-shaped sliding clamp and the subsequent binding to primer-template (p/t)-junctions. The general architecture of clamp loaders is conserved across all life, suggesting that their mechanism is retained. Recent structural studies of the eukaryotic clamp loader replication factor C (RFC) revealed that it functions using a crab-claw mechanism, where clamp opening is coupled to a massive conformational change in the loader. Here we investigate the clamp loading mechanism of the Escherichia coli clamp loader at high resolution using cryo-electron microscopy. We find that the E. coli clamp loader opens the clamp using a crab-claw motion at a single pivot point, whereas the eukaryotic RFC loader uses motions distributed across the complex. Furthermore, we find clamp opening occurs in multiple steps, starting with a partly open state with a spiral conformation, and proceeding to a wide open clamp in a surprising planar geometry. Finally, our structures in the presence of p/t-junctions illustrate how the clamp closes around p/t-junctions and how the clamp loader initiates release from the loaded clamp. Our results reveal mechanistic distinctions in a macromolecular machine that is conserved across all domains of life.
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Affiliation(s)
- Jacob T Landeck
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Joshua Pajak
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Emily K Norman
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Emma L Sedivy
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Brian A Kelch
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA.
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Kudo K, Hori K, Asamitsu S, Maeda K, Aida Y, Hokimoto M, Matsuo K, Yabuki Y, Shioda N. Structural polymorphism of the nucleic acids in pentanucleotide repeats associated with the neurological disorder CANVAS. J Biol Chem 2024; 300:107138. [PMID: 38447794 PMCID: PMC10999818 DOI: 10.1016/j.jbc.2024.107138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 02/15/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024] Open
Abstract
Short tandem repeats are inherently unstable during DNA replication depending on repeat length, and the expansion of the repeat length in the human genome is responsible for repeat expansion disorders. Pentanucleotide AAGGG and ACAGG repeat expansions in intron 2 of the gene encoding replication factor C subunit 1 (RFC1) cause cerebellar ataxia, neuropathy, vestibular areflexia syndrome (CANVAS) and other phenotypes of late-onset cerebellar ataxia. Herein, we reveal the structural polymorphism of the RFC1 repeats associated with CANVAS in vitro. Single-stranded AAGGG repeat DNA formed a hybrid-type G-quadruplex, whereas its RNA formed a parallel-type G-quadruplex with three layers. The RNA of the ACAGG repeat formed hairpin structure comprising C-G and G-C base pairs with A:A and GA:AG mismatched repeats. Furthermore, both pathogenic repeat RNAs formed more rigid structures than those of the nonpathogenic repeat RNAs. These findings provide novel insights into the structural polymorphism of the RFC1 repeats, which may be closely related to the disease mechanism of CANVAS.
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Affiliation(s)
- Kenta Kudo
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan; Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Karin Hori
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan
| | - Sefan Asamitsu
- Laboratory for Functional Non-coding Genomics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Kohei Maeda
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan; Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yukari Aida
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan; Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Mei Hokimoto
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan; Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Kazuya Matsuo
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan
| | - Yasushi Yabuki
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan; Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Norifumi Shioda
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG), Kumamoto University, Kumamoto, Japan; Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan.
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5
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Guo Z, Guo L. Abnormal activation of RFC3, A YAP1/TEAD downstream target, promotes gastric cancer progression. Int J Clin Oncol 2024; 29:442-455. [PMID: 38383698 DOI: 10.1007/s10147-024-02478-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 01/11/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND Gastric cancer (GC) is a malignant tumor with a high mortality rate, and thus, it is necessary to explore molecular mechanisms underlying its progression. While replication factor C subunit 3 (RFC3) has been demonstrated to function as an oncogene in many cancers, its role in GC remains unclear. METHODS Tumor tissues were collected from clinical GC patients, and the expression of RFC3 was analyzed. NCI-N87 and HGC-27 cells were infected with lentivirus sh-RFC3 to knock down RFC3 expression. RFC3 expression levels were determined, in addition to cell biological behaviors both in vitro and in vivo. The relationship between RFC3 and the YAP1/TEAD signaling pathway was detected by dual luciferase reporter assay. RESULTS RFC3 was upregulated in GC tumor tissues. RFC3 knockdown inhibited cell proliferation, promoted cell apoptosis of GC cells, and suppressed cell migration and invasion. Moreover, depleted RFC3 suppressed tumor growth and metastasis in vivo. Mechanistically, the YAP1/TEAD axis activated RFC3 expression transcriptionally by binding to the RFC3 promoter. CONCLUSIONS RFC3 was transcriptional activated by the YAP1/TEAD signaling pathway, thus promoting GC progression. RFC3 may be a promising therapeutic target for GC.
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Affiliation(s)
- Zijun Guo
- Department of Operating Room, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, People's Republic of China
| | - Lin Guo
- Department of General Surgery, Shengjing Hospital of China Medical University, 36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, People's Republic of China.
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Wang Y, Wang J, Yan Z, Hou J, Wan L, Yang Y, Liu Y, Yi J, Guo P, Han D. Structural investigation of pathogenic RFC1 AAGGG pentanucleotide repeats reveals a role of G-quadruplex in dysregulated gene expression in CANVAS. Nucleic Acids Res 2024; 52:2698-2710. [PMID: 38266156 PMCID: PMC10954463 DOI: 10.1093/nar/gkae032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/26/2024] Open
Abstract
An expansion of AAGGG pentanucleotide repeats in the replication factor C subunit 1 (RFC1) gene is the genetic cause of cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS), and it also links to several other neurodegenerative diseases including the Parkinson's disease. However, the pathogenic mechanism of RFC1 AAGGG repeat expansion remains enigmatic. Here, we report that the pathogenic RFC1 AAGGG repeats form DNA and RNA parallel G-quadruplex (G4) structures that play a role in impairing biological processes. We determine the first high-resolution nuclear magnetic resonance (NMR) structure of a bimolecular parallel G4 formed by d(AAGGG)2AA and reveal how AAGGG repeats fold into a higher-order structure composed of three G-tetrad layers, and further demonstrate the formation of intramolecular G4s in longer DNA and RNA repeats. The pathogenic AAGGG repeats, but not the nonpathogenic AAAAG repeats, form G4 structures to stall DNA replication and reduce gene expression via impairing the translation process in a repeat-length-dependent manner. Our results provide an unprecedented structural basis for understanding the pathogenic mechanism of AAGGG repeat expansion associated with CANVAS. In addition, the high-resolution structures resolved in this study will facilitate rational design of small-molecule ligands and helicases targeting G4s formed by AAGGG repeats for therapeutic interventions.
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Affiliation(s)
- Yang Wang
- School of Materials Science and Engineering, Tianjin University, Tianjin 300350, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Junyan Wang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Zhenzhen Yan
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Jianing Hou
- Institute of Molecular Medicine (IMM) Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Liqi Wan
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yingquan Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Yu Liu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Jie Yi
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Pei Guo
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Da Han
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Institute of Molecular Medicine (IMM) Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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7
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Misbah M, Kumar M, Najmi AK, Akhtar M. Identification of expression profiles and prognostic value of RFCs in colorectal cancer. Sci Rep 2024; 14:6607. [PMID: 38504096 PMCID: PMC10951252 DOI: 10.1038/s41598-024-56361-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/05/2024] [Indexed: 03/21/2024] Open
Abstract
Colorectal cancer (CRC) ranks among the most prevalent cancers globally, with its incidence closely tied to DNA damage. The Replication Factor C (RFC) complexes comprises five protein subunits: RFC1, RFC2, RFC3, RFC4, and RFC5. These RFC complexes play crucial roles in DNA replication, repair pathways, activities post DNA damage, and ATP-dependent processes during DNA synthesis. However, the impact of RFC complexes proteins on CRC prognosis remains unclear. To explore this, we employed a computational analysis approach, utilizing platforms such as the DepMap portal, GEPIA, DAVID Bioinformatics for KEGG pathway analysis, Human Protein Atlas (HPA), STRING, and TIMER. Our results indicate that the mRNA levels of RFC1 and RFC5 were the least expressed among CRC cell lines compared to other RFC complex subunits. Notably, low RFC1 and RFC5 expression was correlated with poor prognosis in terms of CRC patients' overall survival (OS). Immunohistochemical results from the Human Protein Atlas demonstrated medium staining for RFC1, RFC2, and RFC5 in CRC tissues. Furthermore, the low expression of RFC1 and RFC5 showed a significant correlation with high expression levels of miR-26a-5p and miR-636, impacting cell proliferation through mismatch repair, DNA replication, and the nucleotide excision repair pathway. Although the precise functions of RFC1 in cancer are still unknown, our findings suggest that the small-molecule single target, CHEMBL430483, and multiple target molecules could be potential treatments for CRC. In conclusion, the elevated expression of miR-26a-5p and miR-636 targeting RFC1 and RFC5 expression holds promise as a potential biomarker for early-stage CRC detection. These insights provide novel directions and strategies for CRC therapies.
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Affiliation(s)
- Md Misbah
- International Ph.D. Program in Medicine, College of Medicine, Taipei Medical University, Taipei, 110, Taiwan.
- Bioinformatics Infrastructure Facility, Jamia Hamdard, New Delhi, India.
- Kusumraj Institute of Pharmacy, Bikram, Patna, Bihar, India, 801104.
| | - Manoj Kumar
- Centre for Translational and Clinical Research, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, 110062, India
| | - Abul Kalam Najmi
- Department of Pharmacology, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
| | - Mymoona Akhtar
- Bioinformatics Infrastructure Facility, Jamia Hamdard, New Delhi, India.
- Drug Design and Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India.
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8
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Tsuchiya M, Bunai T, Watanabe K, Saitsu H, Goshima S. Cerebellar Ataxia With Neuropathy and Vestibular Areflexia Syndrome Due to Replication Factor C Subunit 1 Gene Repeat Expansion. Clin Nucl Med 2024; 49:242-243. [PMID: 38306376 DOI: 10.1097/rlu.0000000000005047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
Abstract
ABSTRACT A 56-year-old man was born to consanguineous parents. He experienced slow-progressing sensory disturbances in the upper extremities. T1-weighted images showed cerebellar atrophy. 123I-IMP SPECT revealed reduced cerebral blood flow in the cerebellum. 123I-FP-CIT SPECT showed low uptake of dopamine transporter in the bilateral tail of the striatum. 123I-MIBG scintigraphy shows a decreased heart-to-mediastinum ratio. Flanking polymerase chain reaction suggested biallelic repeat expansion in intron 2 of RFC1, and subsequent repeat-primed polymerase chain reaction revealed ACAGG repeat expansion. Thus, he was diagnosed as cerebellar ataxia with neuropathy and vestibular areflexia syndrome.
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Affiliation(s)
| | | | | | - Hirotomo Saitsu
- Biochemistry, Hamamatsu University School of Medicine, Shizuoka, Japan
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9
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Kawasoe Y, Shimokawa S, Gillespie PJ, Blow JJ, Tsurimoto T, Takahashi TS. The Atad5 RFC-like complex is the major unloader of proliferating cell nuclear antigen in Xenopus egg extracts. J Biol Chem 2024; 300:105588. [PMID: 38141767 PMCID: PMC10827553 DOI: 10.1016/j.jbc.2023.105588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 12/25/2023] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is a homo-trimeric clamp complex that serves as the molecular hub for various DNA transactions, including DNA synthesis and post-replicative mismatch repair. Its timely loading and unloading are critical for genome stability. PCNA loading is catalyzed by Replication factor C (RFC) and the Ctf18 RFC-like complex (Ctf18-RLC), and its unloading is catalyzed by Atad5/Elg1-RLC. However, RFC, Ctf18-RLC, and even some subcomplexes of their shared subunits are capable of unloading PCNA in vitro, leaving an ambiguity in the division of labor in eukaryotic clamp dynamics. By using a system that specifically detects PCNA unloading, we show here that Atad5-RLC, which accounts for only approximately 3% of RFC/RLCs, nevertheless provides the major PCNA unloading activity in Xenopus egg extracts. RFC and Ctf18-RLC each account for approximately 40% of RFC/RLCs, while immunodepletion of neither Rfc1 nor Ctf18 detectably affects the rate of PCNA unloading in our system. PCNA unloading is dependent on the ATP-binding motif of Atad5, independent of nicks on DNA and chromatin assembly, and inhibited effectively by PCNA-interacting peptides. These results support a model in which Atad5-RLC preferentially unloads DNA-bound PCNA molecules that are free from their interactors.
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Affiliation(s)
| | - Sakiko Shimokawa
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Peter J Gillespie
- Division of Molecular, Cell & Developmental Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | - J Julian Blow
- Division of Molecular, Cell & Developmental Biology, School of Life Sciences, University of Dundee, Dundee, UK
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10
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Zhu J, Ye L, Sun S, Yuan J, Huang J, Zeng Z. Involvement of RFC3 in tamoxifen resistance in ER-positive breast cancer through the cell cycle. Aging (Albany NY) 2023; 15:13738-13752. [PMID: 38059884 PMCID: PMC10756131 DOI: 10.18632/aging.205260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 10/17/2023] [Indexed: 12/08/2023]
Abstract
Since the establishment of the molecular subtyping system, ER positive breast cancer was considered to be the most prevalent type of breast cancer, and endocrine therapy was a very important solution. However, numerous studies have shown that the cell cycle plays a key role in the progression and metastasis of breast cancer. The present study showed that RFC3 was involved in the cell cycle through DNA replication. Furthermore, RFC3 expression was significantly higher in breast cancer-resistant cells than in parental cells, which correlated with the cell cycle. We confirmed these results by established drug-resistant cell lines for breast cancer, raw letter analysis and immunohistochemical analysis of primary and recurrent tissues from three ER+ breast cancers. In addition, analysis of the results through an online database revealed that RFC3 expression was significantly associated with poor prognosis in ER+ breast cancer. We also demonstrated that in ER positive breast cancer-resistant cells, knockdown of RFC3 blocked the S-phase of cells and significantly attenuated cell proliferation, migration and invasion. Furthermore, RFC3 overexpression in ER positive breast cancer cells enhanced cell proliferation, migration and invasion. Taking all these findings into account, we could conclude that RFC3 was involved in endocrine resistance in breast cancer through the cell cycle. Thus, RFC3 may be a target to address endocrine therapy resistance in ER positive breast cancer and may be an independent prognostic factor in ER positive breast cancer.
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Affiliation(s)
- Jintao Zhu
- Department of Breast, Foshan Fosun Chancheng Hospital, Foshan, Guangdong, China
| | - Lei Ye
- Foshan Clinical Medical School of Guangzhou University of Chinese Medicine, Foshan, Guangdong, China
| | - Shishen Sun
- Foshan Clinical Medical School of Guangzhou University of Chinese Medicine, Foshan, Guangdong, China
| | - Jie Yuan
- Department of General Surgery, Foshan Fosun Chancheng Hospital, Foshan, Guangdong, China
| | - Jianfeng Huang
- Department of General Surgery, Foshan Fosun Chancheng Hospital, Foshan, Guangdong, China
| | - Zhiqiang Zeng
- Department of Breast, Foshan Fosun Chancheng Hospital, Foshan, Guangdong, China
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11
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Miranda C M, Diaz M, Hughes G R, Barreto Y M, Nakousi C N, Campero S M. [Late-Onset Cerebellar Ataxia with Neuropathy: Uncovering the Role of RFC1 Gene Mutations]. Rev Med Chil 2023; 151:524-529. [PMID: 38687529 DOI: 10.4067/s0034-98872023000400524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
We report two unrelated patients with late-onset cerebellar ataxia associated with neuropathy and a long-standing dry cough. One patient had two siblings affected with sensory neuropathy and cough. Both probands had extensive investigations including genetics testing negative for most common ataxias as well as testing for paraneoplasic and other immunologic causes. Both patients showed an abnormal intronic expansion in the pentanucleotide AAGGG of the gene RFC1. This etiology is being reported as frequent cause of adult-onset ataxia; the presence of cough may lead to the correct diagnosis.
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Affiliation(s)
| | - Mario Diaz
- Facultad Medicina, Universidad de Santiago, Santiago, Chile
| | - Ricardo Hughes G
- Departamento Neurología, Hospital Clínico, Universidad de Chile, Santiago, Chile
| | | | - Nicole Nakousi C
- Genetista Clínica Hospital Carlos Van Buren, Facultad de Ingeniería, Universidad Andrés Bello, Santiago, Chile
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12
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Arteche-López A, Avila-Fernandez A, Damian A, Soengas-Gonda E, de la Fuente RP, Gómez PR, Merlo JG, Burgos LH, Fernández CC, Rosales JML, Martínez JFG, Quesada-Espinosa JF, Corton M, Guerrero-Molina MP. New Cerebellar Ataxia, Neuropathy, Vestibular Areflexia Syndrome cases are caused by the presence of a nonsense variant in compound heterozygosity with the pathogenic repeat expansion in the RFC1 gene. Clin Genet 2023; 103:236-241. [PMID: 36250766 DOI: 10.1111/cge.14249] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/28/2022] [Accepted: 10/07/2022] [Indexed: 01/20/2023]
Abstract
The biallelic pathogenic repeat (AAGGG)400-2000 intronic expansion in the RFC1 gene has been recently described as the cause of cerebellar ataxia, neuropathy, vestibular areflexia syndrome (CANVAS) and as a major cause of late-onset ataxia. Since then, many heterozygous carriers have been identified, with an estimated allele frequency of 0.7% to 4% in the healthy population. Here, we describe in two affected CANVAS sisters the presence of the nonsense c.724C > T p.(Arg242*) variant in compound heterozygosity with the pathogenic repeat expansion in the RFC1 gene. Further RNA analysis demonstrated a reduced expression of the p.Arg242* allele in patients confirming an efficient nonsense-mediated mRNA decay. We also highlight the importance of considering the sequencing of the RFC1 gene for the diagnosis, especially in patients with CANVAS diagnosis carriers of the AAGGG repeat expansion.
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Affiliation(s)
- Ana Arteche-López
- Genetics Department, 12 de Octubre University Hospital, Madrid, Spain
- UDISGEN (Unidad de Dismorfología y Genética), 12 de Octubre University Hospital, Madrid, Spain
| | - Almudena Avila-Fernandez
- Genetics Department, Health Research Institute-Jimenez Diaz Foundation University Hospital, Universidad Autónoma de Madrid (IIS-FJD-UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Alejandra Damian
- Genetics Department, Health Research Institute-Jimenez Diaz Foundation University Hospital, Universidad Autónoma de Madrid (IIS-FJD-UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Emma Soengas-Gonda
- Genetics Department, 12 de Octubre University Hospital, Madrid, Spain
- UDISGEN (Unidad de Dismorfología y Genética), 12 de Octubre University Hospital, Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Rubén Pérez de la Fuente
- Genetics Department, 12 de Octubre University Hospital, Madrid, Spain
- UDISGEN (Unidad de Dismorfología y Genética), 12 de Octubre University Hospital, Madrid, Spain
| | | | - Jesús Gallego Merlo
- Genetics Department, Health Research Institute-Jimenez Diaz Foundation University Hospital, Universidad Autónoma de Madrid (IIS-FJD-UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Laura Horcajada Burgos
- Genetics Department, Health Research Institute-Jimenez Diaz Foundation University Hospital, Universidad Autónoma de Madrid (IIS-FJD-UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Jose Miguel Lezana Rosales
- Genetics Department, 12 de Octubre University Hospital, Madrid, Spain
- UDISGEN (Unidad de Dismorfología y Genética), 12 de Octubre University Hospital, Madrid, Spain
| | | | - Juan Francisco Quesada-Espinosa
- Genetics Department, 12 de Octubre University Hospital, Madrid, Spain
- UDISGEN (Unidad de Dismorfología y Genética), 12 de Octubre University Hospital, Madrid, Spain
| | - Marta Corton
- Genetics Department, Health Research Institute-Jimenez Diaz Foundation University Hospital, Universidad Autónoma de Madrid (IIS-FJD-UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
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13
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Guan S, Feng L, Wei J, Wang G, Wu L. Knockdown of RFC4 inhibits the cell proliferation of nasopharyngeal carcinoma in vitro and in vivo. Front Med 2023; 17:132-142. [PMID: 36562948 DOI: 10.1007/s11684-022-0938-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 05/10/2022] [Indexed: 12/24/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is a malignant tumor that mainly occurs in East and Southeast Asia. Although patients benefit from the main NPC treatments (e.g., radiotherapy and concurrent chemotherapy), persistent and recurrent diseases still occur in some NPC patients. Therefore, investigating the pathogenesis of NPC is of great clinical significance. In the present study, replication factor c subunit 4 (RFC4) is a key potential target involved in NPC progression via bioinformatics analysis. Furthermore, the expression and mechanism of RFC4 in NPC were investigated in vitro and in vivo. Our results revealed that RFC4 was more elevated in NPC tumor tissues than in normal tissues. RFC4 knockdown induced G2/M cell cycle arrest and inhibited NPC cell proliferation in vitro and in vivo. Interestingly, HOXA10 was confirmed as a downstream target of RFC4, and the overexpression of HOXA10 attenuated the silencing of RFC4-induced cell proliferation, colony formation inhibition, and cell cycle arrest. For the first time, this study reveals that RFC4 is required for NPC cell proliferation and may play a pivotal role in NPC tumorigenesis.
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Affiliation(s)
- Shuzhen Guan
- Medical College of Guangxi University, Nanning, 530004, China
| | - Lin Feng
- Department of Pathology, The First Medical Center of PLA General Hospital, Beijing, 100853, China
| | - Jinrui Wei
- Guangxi Scientific Research Center of Traditional Chinese Medicine, Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Guizhen Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Lichuan Wu
- Medical College of Guangxi University, Nanning, 530004, China.
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14
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Aoki M, Maruta K, Almansour MA. [Vestibular Dysfunction in Replication Factor C Subunit 1 (RFC1) Spectrum Disorder]. Brain Nerve 2022; 74:1261-1266. [PMID: 36343930 DOI: 10.11477/mf.1416202225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
More than 90% of replication factor c subunit 1 (RFC1) gene-related spectrum disorders such as cerebellar ataxia with neuropathy and vestibular areflexia syndrome (CANVAS) have bilateral vestibular dysfunction. A case with CANVAS presented in this paper showed repeat extension of AAGGG in the intron region of the RFC1 gene, and showed bilateral vestibular dysfunction in caloric test, vestibular evoked myogenic potential, video Head Impulse Test and rotary chair test. Visual enhanced vestibulo-ocular reflex tests also revealed abnormalities, suggesting the presence of combined lesions of the cerebellum and brainstem including vestibular nuclei.
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Affiliation(s)
- Mitsuhiro Aoki
- Center for Dizziness and Deafness, Department of Otolaryngology, Ogaki Tokushukai Hospital
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15
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Cui K, Qin L, Tang X, Nong J, Chen J, Wu N, Gong X, Yi L, Yang C, Xia S. A Single Amino Acid Substitution in RFC4 Leads to Endoduplication and Compromised Resistance to DNA Damage in Arabidopsis thaliana. Genes (Basel) 2022; 13:genes13061037. [PMID: 35741798 PMCID: PMC9223238 DOI: 10.3390/genes13061037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 02/04/2023] Open
Abstract
Replication factor C (RFC) is a heteropentameric ATPase associated with the diverse cellular activities (AAA+ATPase) protein complex, which is composed of one large subunit, known as RFC1, and four small subunits, RFC2/3/4/5. Among them, RFC1 and RFC3 were previously reported to mediate genomic stability and resistance to pathogens in Arabidopsis. Here, we generated a viable rfc4e (rfc4-1/RFC4G54E) mutant with a single amino acid substitution by site-directed mutagenesis. Three of six positive T2 mutants with the same amino acid substitution, but different insertion loci, were sequenced to identify homozygotes, and the three homozygote mutants showed dwarfism, early flowering, and a partially sterile phenotype. RNA sequencing revealed that genes related to DNA repair and replication were highly upregulated. Moreover, the frequency of DNA lesions was found to be increased in rfc4e mutants. Consistent with this, the rfc4e mutants were very sensitive to DSB-inducing genotoxic agents. In addition, the G54E amino acid substitution in AtRFC4 delayed cell cycle progression and led to endoduplication. Overall, our study provides evidence supporting the notion that RFC4 plays an important role in resistance to genotoxicity and cell proliferation by regulating DNA damage repair in Arabidopsis thaliana.
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Affiliation(s)
- Kan Cui
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (K.C.); (L.Q.); (X.T.); (J.N.); (N.W.); (X.G.); (C.Y.)
| | - Lei Qin
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (K.C.); (L.Q.); (X.T.); (J.N.); (N.W.); (X.G.); (C.Y.)
| | - Xianyu Tang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (K.C.); (L.Q.); (X.T.); (J.N.); (N.W.); (X.G.); (C.Y.)
| | - Jieying Nong
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (K.C.); (L.Q.); (X.T.); (J.N.); (N.W.); (X.G.); (C.Y.)
| | - Jin Chen
- Hunan Academy of Agricultural Sciences, Changsha 410125, China; (J.C.); (L.Y.)
- Changsha Technology Innovation Center for Phytoremediation of Heavy Metal Contaminated Soil, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Nan Wu
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (K.C.); (L.Q.); (X.T.); (J.N.); (N.W.); (X.G.); (C.Y.)
| | - Xin Gong
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (K.C.); (L.Q.); (X.T.); (J.N.); (N.W.); (X.G.); (C.Y.)
| | - Lixiong Yi
- Hunan Academy of Agricultural Sciences, Changsha 410125, China; (J.C.); (L.Y.)
| | - Chenghuizi Yang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (K.C.); (L.Q.); (X.T.); (J.N.); (N.W.); (X.G.); (C.Y.)
| | - Shitou Xia
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (K.C.); (L.Q.); (X.T.); (J.N.); (N.W.); (X.G.); (C.Y.)
- Correspondence:
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16
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Zheng F, Georgescu RE, Yao NY, O'Donnell ME, Li H. DNA is loaded through the 9-1-1 DNA checkpoint clamp in the opposite direction of the PCNA clamp. Nat Struct Mol Biol 2022; 29:376-385. [PMID: 35314830 PMCID: PMC9010301 DOI: 10.1038/s41594-022-00742-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 02/11/2022] [Indexed: 12/11/2022]
Abstract
The 9-1-1 DNA checkpoint clamp is loaded onto 5'-recessed DNA to activate the DNA damage checkpoint that arrests the cell cycle. The 9-1-1 clamp is a heterotrimeric ring that is loaded in Saccharomyces cerevisiae by Rad24-RFC (hRAD17-RFC), an alternate clamp loader in which Rad24 replaces Rfc1 in the RFC1-5 clamp loader of proliferating cell nuclear antigen (PCNA). The 9-1-1 clamp loading mechanism has been a mystery, because, unlike RFC, which loads PCNA onto a 3'-recessed junction, Rad24-RFC loads the 9-1-1 ring onto a 5'-recessed DNA junction. Here we report two cryo-EM structures of Rad24-RFC-DNA with a closed or 27-Å open 9-1-1 clamp. The structures reveal a completely unexpected mechanism by which a clamp can be loaded onto DNA. Unlike RFC, which encircles DNA, Rad24 binds 5'-DNA on its surface, not inside the loader, and threads the 3' ssDNA overhang into the 9-1-1 clamp from above the ring.
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Affiliation(s)
- Fengwei Zheng
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Roxana E Georgescu
- DNA Replication Laboratory, The Rockefeller University, New York, NY, USA
| | - Nina Y Yao
- DNA Replication Laboratory, The Rockefeller University, New York, NY, USA
| | - Michael E O'Donnell
- DNA Replication Laboratory, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
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17
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Fargeot G, Humbert M, Echaniz-Laguna A. RFC1 gene intronic repeat expansion and unexplained chronic cough: A pathophysiological conundrum. Respir Med Res 2021; 80:100831. [PMID: 34146893 DOI: 10.1016/j.resmer.2021.100831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 11/18/2022]
Affiliation(s)
- G Fargeot
- Neurophysiology Department, Pitié-Salpêtrière Hospital, AP-HP, Paris, France.
| | - M Humbert
- Inserm U999, service de pneumologie et soins intensifs respiratoires, université Paris-Saclay, hôpital Bicêtre, AP-HP, Le-Kremlin-Bicêtre, France
| | - A Echaniz-Laguna
- Neurology Department, CHU de Bicêtre, AP-HP, Le-Kremlin-Bicêtre, France; French National Reference Center for Rare Neuropathies (NNERF), 94276 Le-Kremlin-Bicêtre, France; Inserm U1195, Paris-Saclay University, Le-Kremlin-Bicêtre, France
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18
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Liu L, Tao T, Liu S, Yang X, Chen X, Liang J, Hong R, Wang W, Yang Y, Li X, Zhang Y, Li Q, Liang S, Yu H, Wu Y, Guo X, Lai Y, Ding X, Guan H, Wu J, Zhu X, Yuan J, Li J, Su S, Li M, Cai X, Cai J, Tian H. An RFC4/Notch1 signaling feedback loop promotes NSCLC metastasis and stemness. Nat Commun 2021; 12:2693. [PMID: 33976158 PMCID: PMC8113560 DOI: 10.1038/s41467-021-22971-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 04/09/2021] [Indexed: 12/11/2022] Open
Abstract
Notch signaling represents a key mechanism mediating cancer metastasis and stemness. To understand how Notch signaling is overactivated to couple tumor metastasis and self-renewal in NSCLC cells, we performed the current study and showed that RFC4, a DNA replication factor amplified in more than 40% of NSCLC tissues, directly binds to the Notch1 intracellular domain (NICD1) to competitively abrogate CDK8/FBXW7-mediated degradation of NICD1. Moreover, RFC4 is a functional transcriptional target gene of Notch1 signaling, forming a positive feedback loop between high RFC4 and NICD1 levels and sustained overactivation of Notch signaling, which not only leads to NSCLC tumorigenicity and metastasis but also confers NSCLC cell resistance to treatment with the clinically tested drug DAPT against NICD1 synthesis. Furthermore, together with our study, analysis of two public datasets involving more than 1500 NSCLC patients showed that RFC4 gene amplification, and high RFC4 and NICD1 levels were tightly correlated with NSCLC metastasis, progression and poor patient prognosis. Therefore, our study characterizes the pivotal roles of the positive feedback loop between RFC4 and NICD1 in coupling NSCLC metastasis and stemness properties and suggests its therapeutic and diagnostic/prognostic potential for NSCLC therapy.
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MESH Headings
- A549 Cells
- Animals
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/metabolism
- Carcinoma, Non-Small-Cell Lung/therapy
- Cell Line, Tumor
- Feedback, Physiological
- Female
- Gene Expression Regulation, Neoplastic
- HEK293 Cells
- Humans
- Kaplan-Meier Estimate
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/therapy
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Mice, Nude
- Neoplasm Metastasis
- Receptor, Notch1/genetics
- Receptor, Notch1/metabolism
- Replication Protein C/genetics
- Replication Protein C/metabolism
- Signal Transduction/genetics
- Xenograft Model Antitumor Assays/methods
- Mice
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Affiliation(s)
- Lei Liu
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Chongqing Key Laboratory of Molecular Oncology and Epigenetics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Tianyu Tao
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Shihua Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xia Yang
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Xuwei Chen
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Jiaer Liang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Ruohui Hong
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Wenting Wang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Yi Yang
- Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Xiaoyi Li
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Youhong Zhang
- Cancer Institute, Southern Medical University, Guangzhou, China
| | - Quanfeng Li
- Cancer Institute, Southern Medical University, Guangzhou, China
| | - Shujun Liang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Haocheng Yu
- Guangzhou No. 2 High School, Guangzhou, China
| | - Yun Wu
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Xinyu Guo
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Yan Lai
- State Key Laboratory of Respiratory Diseases and Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaofan Ding
- Department of Surgery at the Sir YK Pao Centre for Cancer, The Chinese University of Hong Kong, Hong Kong, China
| | - Hongyu Guan
- Department of Endocrinology and Diabetes Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jueheng Wu
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Xun Zhu
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Jie Yuan
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Jun Li
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Shicheng Su
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Mengfeng Li
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Cancer Institute, Southern Medical University, Guangzhou, China
| | - Xiuyu Cai
- Department of General Internal Medicine, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Junchao Cai
- Department of Immunology, Sun Yat-sen University Zhongshan School of Medicine, Guangzhou, China.
- Guangdong Engineering & Technology Research Center for Disease-Model Animals, Sun Yat-sen University, Guangzhou, China.
| | - Han Tian
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
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19
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Zhang J, Wang L, Xie X. RFC4 promotes the progression and growth of Oral Tongue squamous cell carcinoma in vivo and vitro. J Clin Lab Anal 2021; 35:e23761. [PMID: 33783864 PMCID: PMC8128301 DOI: 10.1002/jcla.23761] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/28/2021] [Accepted: 03/02/2021] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVE Currently, many studies have found that RFC4 was up-regulated in various cancers, and related to the progression and development. While the effects of RFC4 in oral tongue squamous cell carcinoma remain unclear, the main purpose of this research is to explore the role of RFC4 in oral tongue squamous cell carcinoma. METHODS The expression of RFC4 in various cancers was analyzed in GEPIA database, and the results were further verified by IHC assay. The relationship between RFC4 and several clinical parameters was analyzed; the proliferation was further observed by knockdown RFC4 in vitro. Finally, we constructed related nude mouse models by planting cells subcutaneous of nude mice, and the discrepancy was observed. RESULTS Based on GEPIA database, RFC4 was up-regulated in various cancers, including colorectal cancer, breast cancer, prostate cancer, lung cancer, and liver cancer. RFC4 was up-regulated in oral tongue squamous cell carcinoma compared with the normal tissue from GEPIA online database; we further found that the expression of RFC4 was tightly associated with TNM stage (p = 0.005), but not with age, gender, and differentiation (p > 0.05). We further found that the proliferation of oral tongue squamous cell carcinoma was obviously restrained in vitro, and the carcinogenesis was also inhibited in vivo. CONCLUSIONS We found that RFC4 was up-regulated and related to the progression of oral tongue squamous cell carcinoma, and knockdown RFC4 could restrain the proliferation and progression. RFC4 might serve a potential biomarker and provide a new treatment strategy for lots of patients with oral tongue squamous cell carcinoma.
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Affiliation(s)
- Jian Zhang
- Head and Neck Tumor SurgerySecond People's Hospital of Lianyungang CityLianyungang CityChina
| | - Linlin Wang
- The Department of OncologySecond People's Hospital of Lianyungang CityLianyungang CityChina
| | - Xiao Xie
- Head and Neck Tumor SurgerySecond People's Hospital of Lianyungang CityLianyungang CityChina
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20
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Beecroft SJ, Cortese A, Sullivan R, Yau WY, Dyer Z, Wu TY, Mulroy E, Pelosi L, Rodrigues M, Taylor R, Mossman S, Leadbetter R, Cleland J, Anderson T, Ravenscroft G, Laing NG, Houlden H, Reilly MM, Roxburgh RH. A Māori specific RFC1 pathogenic repeat configuration in CANVAS, likely due to a founder allele. Brain 2020; 143:2673-2680. [PMID: 32851396 PMCID: PMC7526724 DOI: 10.1093/brain/awaa203] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 04/12/2020] [Accepted: 05/07/2020] [Indexed: 12/15/2022] Open
Abstract
Cerebellar ataxia with neuropathy and bilateral vestibular areflexia syndrome (CANVAS) is a recently recognized neurodegenerative disease with onset in mid- to late adulthood. The genetic basis for a large proportion of Caucasian patients was recently shown to be the biallelic expansion of a pentanucleotide (AAGGG)n repeat in RFC1. Here, we describe the first instance of CANVAS genetic testing in New Zealand Māori and Cook Island Māori individuals. We show a novel, possibly population-specific CANVAS configuration (AAAGG)10-25(AAGGG)exp, which was the cause of CANVAS in all patients. There were no apparent phenotypic differences compared with European CANVAS patients. Presence of a common disease haplotype among this cohort suggests this novel repeat expansion configuration is a founder effect in this population, which may indicate that CANVAS will be especially prevalent in this group. Haplotype dating estimated the most recent common ancestor at ∼1430 ce. We also show the same core haplotype as previously described, supporting a single origin of the CANVAS mutation.
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Affiliation(s)
- Sarah J Beecroft
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, Nedlands, WA 6009, Australia
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia
| | - Andrea Cortese
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
- Brain and Behavioural Sciences, University of Pavia, Pavia, Italy
| | - Roisin Sullivan
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Wai Yan Yau
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Zoe Dyer
- Neurology Department, Auckland City Hospital, Auckland, New Zealand
| | - Teddy Y Wu
- Department of Neurology, Christchurch Hospital, Christchurch, New Zealand
| | - Eoin Mulroy
- Neurology Department, Auckland City Hospital, Auckland, New Zealand
| | - Luciana Pelosi
- Neurology Department, Auckland City Hospital, Auckland, New Zealand
| | - Miriam Rodrigues
- Neurology Department, Auckland City Hospital, Auckland, New Zealand
| | - Rachael Taylor
- Centre for Brain Research Neurogenetics Research Clinic, University of Auckland, Auckland, New Zealand
| | - Stuart Mossman
- Neurology Department, Wellington Hospital, Wellington, New Zealand
| | - Ruth Leadbetter
- Neurology Department, Wellington Hospital, Wellington, New Zealand
| | - James Cleland
- Neurology Department, Tauranga Hospital, Tauranga, New Zealand
| | - Tim Anderson
- Department of Neurology, Christchurch Hospital, Christchurch, New Zealand
| | - Gianina Ravenscroft
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, Nedlands, WA 6009, Australia
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia
| | - Nigel G Laing
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, Nedlands, WA 6009, Australia
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia
| | - Henry Houlden
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Mary M Reilly
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Richard H Roxburgh
- Neurology Department, Auckland City Hospital, Auckland, New Zealand
- Centre for Brain Research Neurogenetics Research Clinic, University of Auckland, Auckland, New Zealand
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21
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Liu HW, Bouchoux C, Panarotto M, Kakui Y, Patel H, Uhlmann F. Division of Labor between PCNA Loaders in DNA Replication and Sister Chromatid Cohesion Establishment. Mol Cell 2020; 78:725-738.e4. [PMID: 32277910 PMCID: PMC7242910 DOI: 10.1016/j.molcel.2020.03.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/17/2019] [Accepted: 03/10/2020] [Indexed: 01/26/2023]
Abstract
Concomitant with DNA replication, the chromosomal cohesin complex establishes cohesion between newly replicated sister chromatids. Several replication-fork-associated "cohesion establishment factors," including the multifunctional Ctf18-RFC complex, aid this process in as yet unknown ways. Here, we show that Ctf18-RFC's role in sister chromatid cohesion correlates with PCNA loading but is separable from its role in the replication checkpoint. Ctf18-RFC loads PCNA with a slight preference for the leading strand, which is dispensable for DNA replication. Conversely, the canonical Rfc1-RFC complex preferentially loads PCNA onto the lagging strand, which is crucial for DNA replication but dispensable for sister chromatid cohesion. The downstream effector of Ctf18-RFC is cohesin acetylation, which we place toward a late step during replication maturation. Our results suggest that Ctf18-RFC enriches and balances PCNA levels at the replication fork, beyond the needs of DNA replication, to promote establishment of sister chromatid cohesion and possibly other post-replicative processes.
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Affiliation(s)
- Hon Wing Liu
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Céline Bouchoux
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Mélanie Panarotto
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Yasutaka Kakui
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Harshil Patel
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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22
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Li X, Zhang N, Wu N, Li J, Yang J, Yu Y, Zheng J, Li X, Wang X, Gong P, Zhang X. Identification of GdRFC1 as a novel regulator of telomerase in Giardia duodenalis. Parasitol Res 2020; 119:1035-1041. [PMID: 32072328 DOI: 10.1007/s00436-020-06610-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 01/15/2020] [Indexed: 11/25/2022]
Abstract
Telomerase plays a crucial role in ageing and tumourigenesis. However, the regulatory network of its activity is complicated and not fully understood. In the present study, a yeast two-hybrid screen identified a homologue of human replication factor C subunit 1 (RFC1) as a novel interacting protein of Giardia duodenalis GdTRBD (Giardia duodenalis telomerase ribonucleoprotein complex RNA binding domain GdTRBD). This interaction was further verified via GST pull-down in vitro and co-immunoprecipitation (Co-IP) and bimolecular fluorescence complementation (BiFC) in vivo. We also found that GdRFC1 (Giardia duodenalis replication factor C subunit 1) only interacted with GdTRBD in one nucleus in Giardia duodenalis via a proximity ligation assay (PLA). We reasoned that the two nuclei might have significant heterogeneity in their functional activities during the trophozoite stage and that the two molecules might be involved in other unidentified functions in addition to telomerase activity. In addition, knockdown of GdRFC1 decreased telomerase activity. Collectively, our results indicate that GdRFC1 is a novel binding partner and positive regulator of telomerase in Giardia duodenalis.
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Affiliation(s)
- Xianhe Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Nan Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
- The First Bethune Hospital, Jilin University, Changchun, 130021, China
| | - Na Wu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Jianhua Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Ju Yang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Yanhui Yu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Jingtong Zheng
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Xin Li
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Xiaocen Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China
| | - Pengtao Gong
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China.
| | - Xichen Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Institute of Zoonosis, Jilin University, Changchun, 130062, China.
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23
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Varghese VK, Shukla V, Jishnu PV, Kabekkodu SP, Pandey D, Sharan K, Satyamoorthy K. Characterizing methylation regulated miRNA in carcinoma of the human uterine cervix. Life Sci 2019; 232:116668. [PMID: 31326568 DOI: 10.1016/j.lfs.2019.116668] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 07/17/2019] [Indexed: 12/24/2022]
Abstract
Gene regulatory mechanisms determine the multistep carcinogenesis process. Two aspects of epigenetics are microRNA (miRNAs) and DNA methylation that regulate distinct biological mechanisms such as metastasis, apoptosis cell proliferation and induction of senescence. Although critical, the interplay between these two epigenetic mechanisms is yet to be completely understood, particularly in cervical cancer. To study the DNA methylation regulation of miRNAs and its potential role in cervical cancer, we investigated the differential methylation pattern of two candidate miRNAs (miR-375 and miR-196a-1) during cervical cancer progression against normal cervical epithelium (NCE) by bisulfite DNA sequencing. miR-375 and miR-196a-1 were hypermethylated in Squamous Cell Carcinoma (SCC) against NCE and Cervical Intra-Epithelial Neoplasia (CIN) (p < 0.05). Treatment with demethylating agent reactivated the miR-375 and miR-196a-1 expression in SiHa, HeLa and CaSki cells. In vitro artificial methylation by M.SssI followed by dual luciferase assay confirmed miR-375 and miR-196a-1 as methylation regulated miRNAs (P < 0.05). miR-375 and miR-196a-1 expression levels were negatively correlated with methylation levels in clinical specimens. We further identified Replication Factor C Subunit 3 (RFC3) and High Mobility Group AT-Hook 1 (HMGA1) as targets of miR-375 and miR-196a-1 respectively by dual luciferase reporter assay. Our analysis indicates that miR-375 and miR-196a-1 are DNA methylation regulated miRNAs whose deregulation may facilitate pathophysiology of cervical cancer.
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Affiliation(s)
- Vinay Koshy Varghese
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Vaibhav Shukla
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Padacherri Vethil Jishnu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Deeksha Pandey
- Department of Obstetrics and Gynaecology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal 576104, India
| | - Krishna Sharan
- Department of Radiotherapy and Oncology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal 576104, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India.
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24
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Rafehi H, Szmulewicz DJ, Bennett MF, Sobreira NLM, Pope K, Smith KR, Gillies G, Diakumis P, Dolzhenko E, Eberle MA, Barcina MG, Breen DP, Chancellor AM, Cremer PD, Delatycki MB, Fogel BL, Hackett A, Halmagyi GM, Kapetanovic S, Lang A, Mossman S, Mu W, Patrikios P, Perlman SL, Rosemergy I, Storey E, Watson SRD, Wilson MA, Zee DS, Valle D, Amor DJ, Bahlo M, Lockhart PJ. Bioinformatics-Based Identification of Expanded Repeats: A Non-reference Intronic Pentamer Expansion in RFC1 Causes CANVAS. Am J Hum Genet 2019; 105:151-165. [PMID: 31230722 PMCID: PMC6612533 DOI: 10.1016/j.ajhg.2019.05.016] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/21/2019] [Indexed: 01/28/2023] Open
Abstract
Genomic technologies such as next-generation sequencing (NGS) are revolutionizing molecular diagnostics and clinical medicine. However, these approaches have proven inefficient at identifying pathogenic repeat expansions. Here, we apply a collection of bioinformatics tools that can be utilized to identify either known or novel expanded repeat sequences in NGS data. We performed genetic studies of a cohort of 35 individuals from 22 families with a clinical diagnosis of cerebellar ataxia with neuropathy and bilateral vestibular areflexia syndrome (CANVAS). Analysis of whole-genome sequence (WGS) data with five independent algorithms identified a recessively inherited intronic repeat expansion [(AAGGG)exp] in the gene encoding Replication Factor C1 (RFC1). This motif, not reported in the reference sequence, localized to an Alu element and replaced the reference (AAAAG)11 short tandem repeat. Genetic analyses confirmed the pathogenic expansion in 18 of 22 CANVAS-affected families and identified a core ancestral haplotype, estimated to have arisen in Europe more than twenty-five thousand years ago. WGS of the four RFC1-negative CANVAS-affected families identified plausible variants in three, with genomic re-diagnosis of SCA3, spastic ataxia of the Charlevoix-Saguenay type, and SCA45. This study identified the genetic basis of CANVAS and demonstrated that these improved bioinformatics tools increase the diagnostic utility of WGS to determine the genetic basis of a heterogeneous group of clinically overlapping neurogenetic disorders.
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Affiliation(s)
- Haloom Rafehi
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - David J Szmulewicz
- Cerebellar Ataxia Clinic, Neuroscience Department, Alfred Health, Melbourne, VIC 3004, Australia; Balance Disorders and Ataxia Service, Royal Victorian Eye & Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Mark F Bennett
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC 3052, Australia; Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, 245 Burgundy Street, Heidelberg, VIC 3084, Australia
| | - Nara L M Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kate Pope
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia
| | - Katherine R Smith
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Greta Gillies
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia
| | - Peter Diakumis
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Melbourne, VIC 3000, Australia
| | - Egor Dolzhenko
- Illumina Inc, 5200 Illumina Way, San Diego, CA 92122, USA
| | | | - María García Barcina
- Genetic Unit, Basurto University Hospital, OSI Bilbao-Basurto, avenida Montevideo 18, 48013 Bilbao, Spain
| | - David P Breen
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, Scotland; Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh EH16 4SB, Scotland; Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh EH16 4UX, Scotland
| | - Andrew M Chancellor
- Department of Neurology, Tauranga Hospital, Private Bag, Cameron Road, Tauranga 3171, New Zealand
| | - Phillip D Cremer
- University of Sydney, Camperdown, NSW 2006, Australia; Royal North Shore Hospital, Pacific Hwy, St Leonards, NSW 2065, Australia
| | - Martin B Delatycki
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Rd, Parkville, VIC 3052, Australia
| | - Brent L Fogel
- Departments of Neurology and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Anna Hackett
- Hunter Genetics, Hunter New England Health Service, Waratah, Newcastle, NSW 2300, Australia; University of Newcastle, Newcastle, NSW 2300, Australia
| | - G Michael Halmagyi
- Neurology Department, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia; Central Clinical School, University of Sydney, Camperdown, NSW 2050, Australia
| | - Solange Kapetanovic
- Servicio de Neurología, Hospital de Basurto, Avenida de Montevideo 18, 48013 Bilbao, Bizkaia, Spain
| | - Anthony Lang
- Edmond J. Safra Program in Parkinson disease and the Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital, Toronto, ON M5T 2S8, Canada; Department of Medicine, Division of Neurology, University Health Network and the University of Toronto, Toronto, ON M5T 2S8, Canada
| | - Stuart Mossman
- Department of Neurology, Wellington Hospital, Wellington 6021, New Zealand
| | - Weiyi Mu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Susan L Perlman
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Ian Rosemergy
- Department of Neurology, Wellington Hospital, Newtown, Wellington 6021, New Zealand
| | - Elsdon Storey
- Department of Neuroscience, Central Clinical School, Monash University, Alfred Hospital Campus, Commercial Road, Melbourne, VIC 3004, Australia
| | - Shaun R D Watson
- Institute of Neurological Sciences, Prince of Wales Hospital, Randwick, NSW 2031, Australia
| | - Michael A Wilson
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia
| | - David S Zee
- Department of Neurology, Johns Hopkins Hospital, Baltimore, MD 21287, USA
| | - David Valle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - David J Amor
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Rd, Parkville, VIC 3052, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Flemington Rd, Parkville, VIC 3052, Australia.
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25
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Gali VK, Dickerson D, Katou Y, Fujiki K, Shirahige K, Owen-Hughes T, Kubota T, Donaldson AD. Identification of Elg1 interaction partners and effects on post-replication chromatin re-formation. PLoS Genet 2018; 14:e1007783. [PMID: 30418970 PMCID: PMC6258251 DOI: 10.1371/journal.pgen.1007783] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/26/2018] [Accepted: 10/23/2018] [Indexed: 12/04/2022] Open
Abstract
Elg1, the major subunit of a Replication Factor C-like complex, is critical to ensure genomic stability during DNA replication, and is implicated in controlling chromatin structure. We investigated the consequences of Elg1 loss for the dynamics of chromatin re-formation following DNA replication. Measurement of Okazaki fragment length and the micrococcal nuclease sensitivity of newly replicated DNA revealed a defect in nucleosome organization in the absence of Elg1. Using a proteomic approach to identify Elg1 binding partners, we discovered that Elg1 interacts with Rtt106, a histone chaperone implicated in replication-coupled nucleosome assembly that also regulates transcription. A central role for Elg1 is the unloading of PCNA from chromatin following DNA replication, so we examined the relative importance of Rtt106 and PCNA unloading for chromatin reassembly following DNA replication. We find that the major cause of the chromatin organization defects of an ELG1 mutant is PCNA retention on DNA following replication, with Rtt106-Elg1 interaction potentially playing a contributory role.
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Affiliation(s)
- Vamsi K. Gali
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, Scotland, United Kingdom
| | - David Dickerson
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland, United Kingdom
| | - Yuki Katou
- Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo, Japan
| | - Katsunori Fujiki
- Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo, Japan
| | - Katsuhiko Shirahige
- Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo, Japan
| | - Tom Owen-Hughes
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland, United Kingdom
| | - Takashi Kubota
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, Scotland, United Kingdom
| | - Anne D. Donaldson
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, Scotland, United Kingdom
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Juhász S, Elbakry A, Mathes A, Löbrich M. ATRX Promotes DNA Repair Synthesis and Sister Chromatid Exchange during Homologous Recombination. Mol Cell 2018; 71:11-24.e7. [PMID: 29937341 DOI: 10.1016/j.molcel.2018.05.014] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 03/20/2018] [Accepted: 05/10/2018] [Indexed: 01/15/2023]
Abstract
ATRX is a chromatin remodeler that, together with its chaperone DAXX, deposits the histone variant H3.3 in pericentromeric and telomeric regions. Notably, ATRX is frequently mutated in tumors that maintain telomere length by a specific form of homologous recombination (HR). Surprisingly, in this context, we demonstrate that ATRX-deficient cells exhibit a defect in repairing exogenously induced DNA double-strand breaks (DSBs) by HR. ATRX operates downstream of the Rad51 removal step and interacts with PCNA and RFC-1, which are collectively required for DNA repair synthesis during HR. ATRX depletion abolishes DNA repair synthesis and prevents the formation of sister chromatid exchanges at exogenously induced DSBs. DAXX- and H3.3-depleted cells exhibit identical HR defects as ATRX-depleted cells, and both ATRX and DAXX function to deposit H3.3 during DNA repair synthesis. This suggests that ATRX facilitates the chromatin reconstitution required for extended DNA repair synthesis and sister chromatid exchange during HR.
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Affiliation(s)
- Szilvia Juhász
- Radiation Biology and DNA Repair, Darmstadt University of Technology, 64287 Darmstadt, Germany
| | - Amira Elbakry
- Radiation Biology and DNA Repair, Darmstadt University of Technology, 64287 Darmstadt, Germany
| | - Arthur Mathes
- Radiation Biology and DNA Repair, Darmstadt University of Technology, 64287 Darmstadt, Germany
| | - Markus Löbrich
- Radiation Biology and DNA Repair, Darmstadt University of Technology, 64287 Darmstadt, Germany.
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27
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Aghdam R, Baghfalaki T, Khosravi P, Saberi Ansari E. The Ability of Different Imputation Methods to Preserve the Significant Genes and Pathways in Cancer. Genomics Proteomics Bioinformatics 2017; 15:396-404. [PMID: 29247873 PMCID: PMC5828654 DOI: 10.1016/j.gpb.2017.08.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 07/18/2017] [Accepted: 08/08/2017] [Indexed: 11/23/2022]
Abstract
Deciphering important genes and pathways from incomplete gene expression data could facilitate a better understanding of cancer. Different imputation methods can be applied to estimate the missing values. In our study, we evaluated various imputation methods for their performance in preserving significant genes and pathways. In the first step, 5% genes are considered in random for two types of ignorable and non-ignorable missingness mechanisms with various missing rates. Next, 10 well-known imputation methods were applied to the complete datasets. The significance analysis of microarrays (SAM) method was applied to detect the significant genes in rectal and lung cancers to showcase the utility of imputation approaches in preserving significant genes. To determine the impact of different imputation methods on the identification of important genes, the chi-squared test was used to compare the proportions of overlaps between significant genes detected from original data and those detected from the imputed datasets. Additionally, the significant genes are tested for their enrichment in important pathways, using the ConsensusPathDB. Our results showed that almost all the significant genes and pathways of the original dataset can be detected in all imputed datasets, indicating that there is no significant difference in the performance of various imputation methods tested. The source code and selected datasets are available on http://profiles.bs.ipm.ir/softwares/imputation_methods/.
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Affiliation(s)
- Rosa Aghdam
- School of Biological Science, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5746, Iran.
| | - Taban Baghfalaki
- Department of Statistics, Faculty of Mathematical Sciences, Tarbiat Modares University, Tehran 14115-111, Iran
| | - Pegah Khosravi
- School of Biological Science, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5746, Iran; Department of Physiology and Biophysics, Institute for Computational Biomedicine and Institute for Precision Medicine, Weill Cornell Medical College, New York, NY 10021, USA
| | - Elnaz Saberi Ansari
- School of Biological Science, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5746, Iran; Institut Cochin, Inserm U1016, CNRS UMR 8104, Universit Paris Descartes UMR-S1016, F-75014 Paris, France.
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28
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Kipandula W, Smith TK, MacNeill SA. Tandem affinity purification of exosome and replication factor C complexes from the non-human infectious kinetoplastid parasite Crithidia fasciculata. Mol Biochem Parasitol 2017; 217:19-22. [PMID: 28844893 DOI: 10.1016/j.molbiopara.2017.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 08/16/2017] [Accepted: 08/18/2017] [Indexed: 11/17/2022]
Abstract
Kinetoplastid parasites are responsible for a range of diseases with significant global impact. Trypanosoma brucei and Trypanosoma cruzi cause human African trypanosomiasis and Chagas disease, respectively, while various Leishmania species are responsible for cutaneous, mucocutaneous and visceral leishmaniasis. Understanding the biology of these organisms is key for effective diagnosis, prophylaxis and treatment. The insect parasite Crithidia fasciculata offers a safe and low-cost alternative for studies of kinetoplastid biology. C. fasciculata does not infect humans, can be cultured to high yields in inexpensive serum-free medium in a standard laboratory, and has a completely sequenced publically available genome. Taking advantage of these features, however, requires the adaptation of existing methods of analysis to C. fasciculata. Tandem affinity purification is a widely used method that allows for the rapid purification of intact protein complexes under native conditions. Here we report the application of tandem affinity purification to C. fasciculata for the first time, demonstrating the effectiveness of the technique by purifying both the intact exosome and replication factor C complexes. Adding tandem affinity purification to the C. fasciculata toolbox significantly enhances the utility of this excellent model system.
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Affiliation(s)
- Wakisa Kipandula
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK; Department of Biomedical Sciences, College of Medicine, University of Malawi, Private Bag 360, Chichiri, Blantyre 3, Malawi
| | - Terry K Smith
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Stuart A MacNeill
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK.
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29
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Steluti J, Carvalho AM, Carioca AAF, Miranda A, Gattás GJF, Fisberg RM, Marchioni DM. Genetic Variants Involved in One-Carbon Metabolism: Polymorphism Frequencies and Differences in Homocysteine Concentrations in the Folic Acid Fortification Era. Nutrients 2017; 9:E539. [PMID: 28587068 PMCID: PMC5490518 DOI: 10.3390/nu9060539] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 04/28/2017] [Accepted: 05/18/2017] [Indexed: 12/13/2022] Open
Abstract
Folate and other B vitamins are essential co-factors of one-carbon metabolism, and genetic variants, such as polymorphisms, can alter the metabolism. Furthermore, the adoption of food fortification with folic acid showed a decrease of homocysteine concentration. The aim of this study was to investigate the frequencies of the polymorphisms of enzymes and carrier proteins involved in one-carbon metabolism, and to evaluate homocysteine concentrations in the presence of these genetic variants in a population exposed to mandatory food fortification with folic acid. Using data from a population-based cross-sectional study in São Paulo, Brazil, the study population comprised 750 participants above 12 years of age of both genders. A linear regression model was used to evaluate the homocysteine concentrations according to genetic variants and folate level. The results showed that the minor allelic frequencies were 0.33 for MTHFR (rs1801133), 0.24 for MTHFR (rs1801131), 0.19 for MTR (rs1805087), 0.42 for MTRR (rs1801394), 0.46 for RFC1 (rs1051266), and 0.47 for DHFR (19-bp deletion). The genetic variants of MTHFR 677C>T, MTRR 66A>G and RFC-1 80G>A were different according to race. The homocysteine concentrations increased in the CT and TT compared to CC genotypes of polymorphism MTHFR 677C>T in all populations, and differences between the homocysteine concentrations according to the genotypes of MTHFR 677C>T were observed regardless of folate level.
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Affiliation(s)
- Josiane Steluti
- Department of Nutrition, School of Public Health, Sao Paulo University, Avenida Doutor Arnaldo, 715-Cerqueira César, São Paulo-SP, São Paulo 01246-904, Brazil.
| | - Aline M Carvalho
- Department of Nutrition, School of Public Health, Sao Paulo University, Avenida Doutor Arnaldo, 715-Cerqueira César, São Paulo-SP, São Paulo 01246-904, Brazil.
| | - Antonio A F Carioca
- Department of Nutrition, School of Public Health, Sao Paulo University, Avenida Doutor Arnaldo, 715-Cerqueira César, São Paulo-SP, São Paulo 01246-904, Brazil.
| | - Andreia Miranda
- Department of Nutrition, School of Public Health, Sao Paulo University, Avenida Doutor Arnaldo, 715-Cerqueira César, São Paulo-SP, São Paulo 01246-904, Brazil.
| | - Gilka J F Gattás
- Department of Legal Medicine, Bioethics and Occupational Health, School of Medicine, University of São Paulo, Avenida Doutor Arnaldo, 455-Cerqueira César, São Paulo-SP, São Paulo 01246-903, Brazil.
| | - Regina M Fisberg
- Department of Nutrition, School of Public Health, Sao Paulo University, Avenida Doutor Arnaldo, 715-Cerqueira César, São Paulo-SP, São Paulo 01246-904, Brazil.
| | - Dirce M Marchioni
- Department of Nutrition, School of Public Health, Sao Paulo University, Avenida Doutor Arnaldo, 715-Cerqueira César, São Paulo-SP, São Paulo 01246-904, Brazil.
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30
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Qiu Q, Huang J, Lin Y, Shu X, Fan H, Tu Z, Zhou Y, Xiao C. Polymorphisms and pharmacogenomics for the toxicity of methotrexate monotherapy in patients with rheumatoid arthritis: A systematic review and meta-analysis. Medicine (Baltimore) 2017; 96:e6337. [PMID: 28296761 PMCID: PMC5369916 DOI: 10.1097/md.0000000000006337] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Methotrexate (MTX) is widely used and considered a first-line disease modifying antirheumatic drug (DMARD) for the treatment of rheumatoid arthritis (RA). However, 10% to 30% of patients discontinue therapy within a year of starting the treatment, usually because of undesirable side effects. Many of the relevant genes have been investigated to estimate the association between gene polymorphisms and MTX toxicity in RA patients, although inconsistent results have been reported. METHODS We searched EMBASE and PubMed in February 2016 for polymorphisms and pharmacogenomics study of the toxicity of MTX monotherapy in RA patients. The meta-analysis was stratified by whether genetic variants associated with MTX toxicity. RESULTS A total of 42 publications that included 28 genes with 88 gene SNPs associated with the transporters, enzymes, and metabolites of MTX or the progression of RA were included in the SR, and 31 studies were included in 7 meta-analyses. The meta-analysis showed a significant association between the toxicity of MTX and the RFC-1 80G > A (rs1051266) polymorphism in the European RA patients. CONCLUSION RFC-1 80G > A (rs1051266) polymorphism was associated with MTX toxicity, and larger and more stringent study designs may provide more accurate results for the effect of these SNPs on the MTX toxicity.
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Affiliation(s)
- Qi Qiu
- Institute of Clinical Pharmacology, Beijing Anzhen Hospital, Capital Medical University
| | - Jing Huang
- Institute of Clinical Medicine, China-Japan Friendship Hospital
- Beijing University of Chinese Medicine
| | - Yang Lin
- Institute of Clinical Pharmacology, Beijing Anzhen Hospital, Capital Medical University
| | - Xiaoming Shu
- Department of Rheumatology, China-Japan Friendship Hospital, Beijing
| | - Huizheng Fan
- Department of Gastroenterology, People's Hospital of Yichun, Jiangxi Yichun
| | - Zhihua Tu
- Department of Rheumatology, Yili Kazak Autonomous Prefecture Hospital of Traditional Chinese Medicine, Xinjiang Yining, China
| | - Youwen Zhou
- Department of Dermatology and Skin Science, University of British Columbia
- Molecular Medicine Lab and Chieng Genomics Center, Vancouver Coastal Health Research Institute, Vancouver, BC, Canada
| | - Cheng Xiao
- Institute of Clinical Medicine, China-Japan Friendship Hospital
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31
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Johnson C, Gali VK, Takahashi TS, Kubota T. PCNA Retention on DNA into G2/M Phase Causes Genome Instability in Cells Lacking Elg1. Cell Rep 2016; 16:684-95. [PMID: 27373149 PMCID: PMC4956615 DOI: 10.1016/j.celrep.2016.06.030] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/28/2016] [Accepted: 06/03/2016] [Indexed: 12/05/2022] Open
Abstract
Loss of the genome maintenance factor Elg1 causes serious genome instability that leads to cancer, but the underlying mechanism is unknown. Elg1 forms the major subunit of a replication factor C-like complex, Elg1-RLC, which unloads the ring-shaped polymerase clamp PCNA from DNA during replication. Here, we show that prolonged retention of PCNA on DNA into G2/M phase is the major cause of genome instability in elg1Δ yeast. Overexpression-induced accumulation of PCNA on DNA causes genome instability. Conversely, disassembly-prone PCNA mutants that relieve PCNA accumulation rescue the genome instability of elg1Δ cells. Covalent modifications to the retained PCNA make only a minor contribution to elg1Δ genome instability. By engineering cell-cycle-regulated ELG1 alleles, we show that abnormal accumulation of PCNA on DNA during S phase causes moderate genome instability and its retention through G2/M phase exacerbates genome instability. Our results reveal that PCNA unloading by Elg1-RLC is critical for genome maintenance.
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Affiliation(s)
- Catherine Johnson
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Vamsi K Gali
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Tatsuro S Takahashi
- Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Takashi Kubota
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK.
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32
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Shen H, Xu J, Zhao S, Shi H, Yao S, Jiang N. ShRNA-mediated silencing of the RFC3 gene suppress ovarian tumor cells proliferation. Int J Clin Exp Pathol 2015; 8:8968-8975. [PMID: 26464638 PMCID: PMC4583870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 07/27/2015] [Indexed: 06/05/2023]
Abstract
Ovarian carcinoma is one of the most common and lethal malignancies in the world. Replication factor C (RFC) plays an important role in DNA replication, DNA damage repair, and checkpoint control during cell cycle progression in all eukaryotes. Our previous study found that one unit of RFC complex, RFC3, is over-expressed in ovarian tumor tissues. However, its role in the development of ovarian carcinoma remains unclear. Western blot and real-time RT-PCR analysis were used to measure the expression of RFC3 in ovarian cancer cells. Lentivirus-mediated RFC3-specific shRNA was used to knock down RFC3 expression in ovarian cancer cells. Furthermore, the effect of RFC3 on tumor cellular proliferation and growth were examined, respectively. The expression level of RFC3 was remarkably up-regulated in ovarian cancer OVCAR-3 cells. With MTS and cell growth assays, the viability and proliferation of RFC3 knocking-down OVCAR-3 cell line were shown to be effectively restrained. Down-regulation of RFC3 expression arrested the cell cycle of OVCAR-3 cell in the S-phase and induced apoptosis. This study suggests that RFC3 may play an important role in the the process of ovarian carcinoma, and that it may be a potential biological treatment target in the future.
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Affiliation(s)
- Huimin Shen
- The First Affiliated Hospital, Sun Yat-Sen University Guangzhou, China
| | - Juan Xu
- The First Affiliated Hospital, Sun Yat-Sen University Guangzhou, China
| | - Shanshan Zhao
- The First Affiliated Hospital, Sun Yat-Sen University Guangzhou, China
| | - Haijuan Shi
- The First Affiliated Hospital, Sun Yat-Sen University Guangzhou, China
| | - Shuzhong Yao
- The First Affiliated Hospital, Sun Yat-Sen University Guangzhou, China
| | - Nan Jiang
- The First Affiliated Hospital, Sun Yat-Sen University Guangzhou, China
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33
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Chae HD, Mitton B, Lacayo NJ, Sakamoto KM. Replication factor C3 is a CREB target gene that regulates cell cycle progression through the modulation of chromatin loading of PCNA. Leukemia 2015; 29:1379-89. [PMID: 25541153 PMCID: PMC4456282 DOI: 10.1038/leu.2014.350] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 10/04/2014] [Accepted: 11/11/2014] [Indexed: 11/09/2022]
Abstract
CREB (cyclic AMP response element-binding protein) is a transcription factor overexpressed in normal and neoplastic myelopoiesis and regulates cell cycle progression, although its oncogenic mechanism has not been well characterized. Replication factor C3 (RFC3) is required for chromatin loading of proliferating cell nuclear antigen (PCNA) which is a sliding clamp platform for recruiting numerous proteins in the DNA metabolism. CREB1 expression, which was activated by E2F, was coupled with RFC3 expression during the G1/S progression in the KG-1 acute myeloid leukemia (AML) cell line. There was also a direct correlation between the expression of RFC3 and CREB1 in human AML cell lines as well as in the AML cells from the patients. CREB interacted directly with the CRE site in RFC3 promoter region. CREB-knockdown inhibited primarily G1/S cell cycle transition by decreasing the expression of RFC3 as well as PCNA loading onto the chromatin. Exogenous expression of RFC3 was sufficient to rescue the impaired G1/S progression and PCNA chromatin loading caused by CREB knockdown. These studies suggest that RFC3 may have a role in neoplastic myelopoiesis by promoting the G1/S progression and its expression is regulated by CREB.
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MESH Headings
- Blotting, Western
- Cell Cycle/physiology
- Cell Proliferation
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Chromatin/genetics
- Chromatin Immunoprecipitation
- Cyclic AMP Response Element-Binding Protein/genetics
- Cyclic AMP Response Element-Binding Protein/metabolism
- Flow Cytometry
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Proliferating Cell Nuclear Antigen/genetics
- Proliferating Cell Nuclear Antigen/metabolism
- Promoter Regions, Genetic/genetics
- RNA, Messenger/genetics
- Real-Time Polymerase Chain Reaction
- Replication Protein C/genetics
- Replication Protein C/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Tumor Cells, Cultured
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Affiliation(s)
- Hee-Don Chae
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305
| | - Bryan Mitton
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305
| | - Norman J. Lacayo
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305
| | - Kathleen M. Sakamoto
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305
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Vasianovich Y, Harrington LA, Makovets S. Break-induced replication requires DNA damage-induced phosphorylation of Pif1 and leads to telomere lengthening. PLoS Genet 2014; 10:e1004679. [PMID: 25329304 PMCID: PMC4199488 DOI: 10.1371/journal.pgen.1004679] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 08/18/2014] [Indexed: 11/18/2022] Open
Abstract
Broken replication forks result in DNA breaks that are normally repaired via homologous recombination or break induced replication (BIR). Mild insufficiency in the replicative ligase Cdc9 in budding yeast Saccharomyces cerevisiae resulted in a population of cells with persistent DNA damage, most likely due to broken replication forks, constitutive activation of the DNA damage checkpoint and longer telomeres. This telomere lengthening required functional telomerase, the core DNA damage signaling cascade Mec1-Rad9-Rad53, and the components of the BIR repair pathway - Rad51, Rad52, Pol32, and Pif1. The Mec1-Rad53 induced phosphorylation of Pif1, previously found necessary for inhibition of telomerase at double strand breaks, was also important for the role of Pif1 in BIR and telomere elongation in cdc9-1 cells. Two other mutants with impaired DNA replication, cdc44-5 and rrm3Δ, were similar to cdc9-1: their long telomere phenotype was dependent on the Pif1 phosphorylation locus. We propose a model whereby the passage of BIR forks through telomeres promotes telomerase activity and leads to telomere lengthening.
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Affiliation(s)
- Yulia Vasianovich
- Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Lea A. Harrington
- Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
- Institut de Recherche en Immunologie et en Cancérologie, Université de Montréal, Montréal, Québec, Canada
| | - Svetlana Makovets
- Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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35
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Zhang T, Lou J, Zhong R, Wu J, Zou L, Sun Y, Lu X, Liu L, Miao X, Xiong G. Genetic variants in the folate pathway and the risk of neural tube defects: a meta-analysis of the published literature. PLoS One 2013; 8:e59570. [PMID: 23593147 PMCID: PMC3617174 DOI: 10.1371/journal.pone.0059570] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 02/18/2013] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Neural Tube Defects (NTDs) are among the most prevalent and most severe congenital malformations worldwide. Polymorphisms in key genes involving the folate pathway have been reported to be associated with the risk of NTDs. However, the results from these published studies are conflicting. We surveyed the literature (1996-2011) and performed a comprehensive meta-analysis to provide empirical evidence on the association. METHODS AND FINDINGS We investigated the effects of 5 genetic variants from 47 study populations, for a total of 85 case-control comparisons MTHFR C677T (42 studies; 4374 cases, 7232 controls), MTHFR A1298C (22 studies; 2602 cases, 4070 controls), MTR A2756G (9 studies; 843 cases, 1006 controls), MTRR A66G (8 studies; 703 cases, 1572 controls), and RFC-1 A80G (4 studies; 1107 cases, 1585 controls). We found a convincing evidence of dominant effects of MTHFR C677T (OR 1.23; 95%CI 1.07-1.42) and suggestive evidence of RFC-1 A80G (OR 1.55; 95%CI 1.24-1.92). However, we found no significant effects of MTHFR A1298C, MTR A2756G, MTRR A66G in risk of NTDs in dominant, recessive or in allelic models. CONCLUSIONS Our meta-analysis strongly suggested a significant association of the variant MTHFR C677T and a suggestive association of RFC-1 A80G with increased risk of NTDs. However, other variants involved in folate pathway do not demonstrate any evidence for a significant marginal association on susceptibility to NTDs.
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Affiliation(s)
- Ti Zhang
- Department of Epidemiology and Biostatistics and MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiao Lou
- Department of Epidemiology and Biostatistics and MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rong Zhong
- Department of Epidemiology and Biostatistics and MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Wu
- Department of Epidemiology and Biostatistics and MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Li Zou
- Department of Epidemiology and Biostatistics and MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Sun
- Department of Epidemiology and Biostatistics and MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuzai Lu
- Department of Epidemiology and Biostatistics and MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Li Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics and MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guanglian Xiong
- Department of Epidemiology and Biostatistics and MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Foltman M, Evrin C, De Piccoli G, Jones RC, Edmondson RD, Katou Y, Nakato R, Shirahige K, Labib K. Eukaryotic replisome components cooperate to process histones during chromosome replication. Cell Rep 2013; 3:892-904. [PMID: 23499444 DOI: 10.1016/j.celrep.2013.02.028] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 12/30/2012] [Accepted: 02/28/2013] [Indexed: 11/30/2022] Open
Abstract
DNA unwinding at eukaryotic replication forks displaces parental histones, which must be redeposited onto nascent DNA in order to preserve chromatin structure. By screening systematically for replisome components that pick up histones released from chromatin into a yeast cell extract, we found that the Mcm2 helicase subunit binds histones cooperatively with the FACT (facilitiates chromatin transcription) complex, which helps to re-establish chromatin during transcription. FACT does not associate with the Mcm2-7 helicase at replication origins during G1 phase but is subsequently incorporated into the replisome progression complex independently of histone binding and uniquely among histone chaperones. The amino terminal tail of Mcm2 binds histones via a conserved motif that is dispensable for DNA synthesis per se but helps preserve subtelomeric chromatin, retain the 2 micron minichromosome, and support growth in the absence of Ctf18-RFC. Our data indicate that the eukaryotic replication and transcription machineries use analogous assemblies of multiple chaperones to preserve chromatin integrity.
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Affiliation(s)
- Magdalena Foltman
- Paterson Institute for Cancer Research, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
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Wang Y, Cheng Z, Huang J, Shi Q, Hong Y, Copenhaver GP, Gong Z, Ma H. The DNA replication factor RFC1 is required for interference-sensitive meiotic crossovers in Arabidopsis thaliana. PLoS Genet 2012; 8:e1003039. [PMID: 23144629 PMCID: PMC3493451 DOI: 10.1371/journal.pgen.1003039] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Accepted: 09/05/2012] [Indexed: 11/18/2022] Open
Abstract
During meiotic recombination, induced double-strand breaks (DSBs) are processed into crossovers (COs) and non-COs (NCO); the former are required for proper chromosome segregation and fertility. DNA synthesis is essential in current models of meiotic recombination pathways and includes only leading strand DNA synthesis, but few genes crucial for DNA synthesis have been tested genetically for their functions in meiosis. Furthermore, lagging strand synthesis has been assumed to be unnecessary. Here we show that the Arabidopsis thaliana DNA REPLICATION FACTOR C1 (RFC1) important for lagging strand synthesis is necessary for fertility, meiotic bivalent formation, and homolog segregation. Loss of meiotic RFC1 function caused abnormal meiotic chromosome association and other cytological defects; genetic analyses with other meiotic mutations indicate that RFC1 acts in the MSH4-dependent interference-sensitive pathway for CO formation. In a rfc1 mutant, residual pollen viability is MUS81-dependent and COs exhibit essentially no interference, indicating that these COs form via the MUS81-dependent interference-insensitive pathway. We hypothesize that lagging strand DNA synthesis is important for the formation of double Holliday junctions, but not alternative recombination intermediates. That RFC1 is found in divergent eukaryotes suggests a previously unrecognized and highly conserved role for DNA synthesis in discriminating between recombination pathways. Meiotic recombination is important for pairing and sustained association of homologous chromosomes (homologs), thereby ensuring proper homolog segregation and normal fertility. DNA synthesis is thought to be required for meiotic recombination, but few genes coding for DNA synthesis factors have been studied for possible meiotic functions because their essential roles in the mitotic cell cycle make it difficult to study their meiotic functions due to the lethality of corresponding null mutations. Current models for meiotic recombination only include leading strand DNA synthesis. We found that the Arabidopsis gene encoding the DNA REPLICATION FACTOR C1 (RFC1) important for lagging strand synthesis promotes meiotic recombination via a specific pathway for crossovers (COs) that involves the formation of double Holliday Junction (dHJ) intermediates. Therefore, lagging strand DNA synthesis is likely important for meiotic recombination. Because DNA synthesis is a highly conserved process and meiotic recombination is highly similar among budding yeast, mammals, and flowering plants, the proposed function of lagging strand synthesis for meiotic recombination might be a general feature of meiosis.
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Affiliation(s)
- Yingxiang Wang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhihao Cheng
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jiyue Huang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Qian Shi
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yue Hong
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Gregory P. Copenhaver
- Department of Biology and the Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Hong Ma
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- * E-mail:
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Gellon L, Razidlo DF, Gleeson O, Verra L, Schulz D, Lahue RS, Freudenreich CH. New functions of Ctf18-RFC in preserving genome stability outside its role in sister chromatid cohesion. PLoS Genet 2011; 7:e1001298. [PMID: 21347277 PMCID: PMC3037408 DOI: 10.1371/journal.pgen.1001298] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 01/07/2011] [Indexed: 12/30/2022] Open
Abstract
Expansion of DNA trinucleotide repeats causes at least 15 hereditary neurological diseases, and these repeats also undergo contraction and fragility. Current models to explain this genetic instability invoke erroneous DNA repair or aberrant replication. Here we show that CAG/CTG tracts are stabilized in Saccharomyces cerevisiae by the alternative clamp loader/unloader Ctf18-Dcc1-Ctf8-RFC complex (Ctf18-RFC). Mutants in Ctf18-RFC increased all three forms of triplet repeat instability--expansions, contractions, and fragility--with effect over a wide range of allele lengths from 20-155 repeats. Ctf18-RFC predominated among the three alternative clamp loaders, with mutants in Elg1-RFC or Rad24-RFC having less effect on trinucleotide repeats. Surprisingly, chl1, scc1-73, or scc2-4 mutants defective in sister chromatid cohesion (SCC) did not increase instability, suggesting that Ctf18-RFC protects triplet repeats independently of SCC. Instead, three results suggest novel roles for Ctf18-RFC in facilitating genomic stability. First, genetic instability in mutants of Ctf18-RFC was exacerbated by simultaneous deletion of the fork stabilizer Mrc1, but suppressed by deletion of the repair protein Rad52. Second, single-cell analysis showed that mutants in Ctf18-RFC had a slowed S phase and a striking G2/M accumulation, often with an abnormal multi-budded morphology. Third, ctf18 cells exhibit increased Rad52 foci in S phase, often persisting into G2, indicative of high levels of DNA damage. The presence of a repeat tract greatly magnified the ctf18 phenotypes. Together these results indicate that Ctf18-RFC has additional important functions in preserving genome stability, besides its role in SCC, which we propose include lesion bypass by replication forks and post-replication repair.
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Affiliation(s)
- Lionel Gellon
- Department of Biology, Tufts University, Medford, Massachusetts, United States of America
| | - David F. Razidlo
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Olive Gleeson
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Lauren Verra
- Department of Biology, Tufts University, Medford, Massachusetts, United States of America
| | - Danae Schulz
- Department of Biology, Tufts University, Medford, Massachusetts, United States of America
| | - Robert S. Lahue
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
- * E-mail: (CHF); (RSL)
| | - Catherine H. Freudenreich
- Department of Biology, Tufts University, Medford, Massachusetts, United States of America
- * E-mail: (CHF); (RSL)
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Murakami T, Takano R, Takeo S, Taniguchi R, Ogawa K, Ohashi E, Tsurimoto T. Stable interaction between the human proliferating cell nuclear antigen loader complex Ctf18-replication factor C (RFC) and DNA polymerase {epsilon} is mediated by the cohesion-specific subunits, Ctf18, Dcc1, and Ctf8. J Biol Chem 2010; 285:34608-15. [PMID: 20826785 PMCID: PMC2966076 DOI: 10.1074/jbc.m110.166710] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Revised: 08/30/2010] [Indexed: 01/28/2023] Open
Abstract
One of the proliferating cell nuclear antigen loader complexes, Ctf18-replication factor C (RFC), is involved in sister chromatid cohesion. To examine its relationship with factors involved in DNA replication, we performed a proteomics analysis of Ctf18-interacting proteins. We found that Ctf18 interacts with a replicative DNA polymerase, DNA polymerase ε (pol ε). Co-immunoprecipitation with recombinant Ctf18-RFC and pol ε demonstrated that their binding is direct and mediated by two distinct interactions, one weak and one stable. Three subunits that are specifically required for cohesion in yeast, Ctf18, Dcc1, and Ctf8, formed a trimeric complex (18-1-8) and together enabled stable binding with pol ε. The C-terminal 23-amino acid stretch of Ctf18 was necessary for the trimeric association of 18-1-8 and was required for the stable interaction. The weak interaction was observed with alternative loader complexes including Ctf18-RFC(5), which lacks Dcc1 and Ctf8, suggesting that the common loader structures, including the RFC small subunits (RFC2-5), are responsible for the weak interaction. The two interaction modes, mediated through distinguishable structures of Ctf18-RFC, both occurred through the N-terminal half of pol ε, which includes the catalytic domain. The addition of Ctf18-RFC or Ctf18-RFC(5) to the DNA synthesis reaction caused partial inhibition and stimulation, respectively. Thus, Ctf18-RFC has multiple interactions with pol ε that promote polymorphic modulation of DNA synthesis. We propose that their interaction alters the DNA synthesis mode to enable the replication fork to cooperate with the establishment of cohesion.
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Affiliation(s)
- Takeshi Murakami
- From the Department of Biology, Faculty of Sciences, Kyushu University, 6-10-1 Hakozaki, Fukuoka 812-8581, Japan
| | - Ryuji Takano
- From the Department of Biology, Faculty of Sciences, Kyushu University, 6-10-1 Hakozaki, Fukuoka 812-8581, Japan
| | - Satoshi Takeo
- From the Department of Biology, Faculty of Sciences, Kyushu University, 6-10-1 Hakozaki, Fukuoka 812-8581, Japan
| | - Rina Taniguchi
- From the Department of Biology, Faculty of Sciences, Kyushu University, 6-10-1 Hakozaki, Fukuoka 812-8581, Japan
| | - Kaori Ogawa
- From the Department of Biology, Faculty of Sciences, Kyushu University, 6-10-1 Hakozaki, Fukuoka 812-8581, Japan
| | - Eiji Ohashi
- From the Department of Biology, Faculty of Sciences, Kyushu University, 6-10-1 Hakozaki, Fukuoka 812-8581, Japan
| | - Toshiki Tsurimoto
- From the Department of Biology, Faculty of Sciences, Kyushu University, 6-10-1 Hakozaki, Fukuoka 812-8581, Japan
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Abstract
Background The replication of DNA in Archaea and eukaryotes requires several ancillary complexes, including proliferating cell nuclear antigen (PCNA), replication factor C (RFC), and the minichromosome maintenance (MCM) complex. Bacterial DNA replication utilizes comparable proteins, but these are distantly related phylogenetically to their archaeal and eukaryotic counterparts at best. Methodology/Principal Findings While the structures of each of the complexes do not differ significantly between the archaeal and eukaryotic versions thereof, the evolutionary dynamic in the two cases does. The number of subunits in each complex is constant across all taxa. However, they vary subtly with regard to composition. In some taxa the subunits are all identical in sequence, while in others some are homologous rather than identical. In the case of eukaryotes, there is no phylogenetic variation in the makeup of each complex—all appear to derive from a common eukaryotic ancestor. This is not the case in Archaea, where the relationship between the subunits within each complex varies taxon-to-taxon. We have performed a detailed phylogenetic analysis of these relationships in order to better understand the gene duplications and divergences that gave rise to the homologous subunits in Archaea. Conclusion/Significance This domain level difference in evolution suggests that different forces have driven the evolution of DNA replication proteins in each of these two domains. In addition, the phylogenies of all three gene families support the distinctiveness of the proposed archaeal phylum Thaumarchaeota.
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Affiliation(s)
- Nicholas Chia
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
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Wang Y, Song X, Guo J, Zhu W. [Relationship between genetic polymorphisms of RFC1 A80G and nonsymdromic cleft lip with or without palate]. Wei Sheng Yan Jiu 2009; 38:276-279. [PMID: 19548564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
OBJECTIVE To explore the relationship between genetic polymorphisms of reduced folate carrier (RFC)1 A80G and nonsymdromic cleft lip with or without palate on Chinese population. METHODS There were 97 NSCL/P case-parent triads those were selected as case group. At the same period, 104 healthy subjects were selected together with their biological parents as control group. For all subjects the polymorphisms of RFC1 A80G were examined by PCR-RFLP method. RESULTS There was no statistical difference in genotype and gene frequencies for RFC1 A80G variants among family members between case group and control group in offsprings and fathers and mothers (P < 0.05). The odds ratio (OR), confidence interval (CI) and P value of offspring, father and mother genotype (AG) were 0.87 (0.44-1.70), 0.657; 1.09 (0.54-2.21), 0.788; 1.63 (0.79-3.36), 0.152 respectively. The OR, CI and P value of offspring, father and mother allele (GG) were 0.48 (0.19-1.23), 0.094; 0.93 (0.38-2.23), 0.850; 1.30 (0.46-3.67), 0.584 respectively. The OR, CI and P value of offspring, father and mother allele (G) were 1.22 (0.78-1.94), 0.386; 1.02 (0.64-1.61), 0.945; 0.91 (0.58-1.41), 0.660. The G allele could not increase the risk of NSCL/P. But in the transmission disequilibrium test (TDT) analysis, the transmission of the G allele was 40 times, the A allele was 71 times, the A allele was more likely to transmit to the sicken offspring (chi-2 = 8.658, P < 0.05). Results of haplotype-based haplotype relative risk (HHRR) analysis (chi-2 = 10.31, P < 0.05) and family-based association tests (FBAT) ( Z = 2.942, P < 0.05) were showed that there was an association between RFC1 A80G variant and the risk of NSCL/P. CONCLUSION The statistical analysis of nuclear family could evidence of linkage in the presence of disequilibrium, there was an association between RFC1 A80G variant and the risk of NSCL/P, and the A allele could have an association with the dominant high-risk of NSCL/P.
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Affiliation(s)
- Yun Wang
- Department of Nutrition and Food Hygiene, School of Public Health, Peking University Health Science Centre, Beijing 100191, China.
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Kang BY, You H, Bandyopadhyay S, Agrawal N, Melchert RB, Basnakian AG, Liu Y, Hermonat PL. Cervical cancer isolate PT3, super-permissive for adeno-associated virus replication, over-expresses DNA polymerase delta, PCNA, RFC and RPA. BMC Microbiol 2009; 9:79. [PMID: 19389243 PMCID: PMC2685399 DOI: 10.1186/1471-2180-9-79] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Accepted: 04/23/2009] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Adeno-associated virus (AAV) type 2 is an important virus due to its use as a safe and effective human gene therapy vector and its negative association with certain malignancies. AAV, a dependo-parvovirus, autonomously replicates in stratified squamous epithelium. Such tissue occurs in the nasopharynx and anogenitals, from which AAV has been clinically isolated. Related autonomous parvoviruses also demonstrate cell tropism and preferentially replicate in oncogenically transformed cells. Combining these two attributes of parvovirus tropism, squamous and malignant, we assayed if AAV might replicate in squamous cervical carcinoma cell isolates. RESULTS Three primary isolates (PT1-3) and two established cervical cancer cell lines were compared to normal keratinocytes (NK) for their ability to replicate AAV. One isolate, PT3, allowed for high levels of AAV DNA replication and virion production compared to others. In research by others, four cellular components are known required for in vitro AAV DNA replication: replication protein A (RPA), replication factor C (RFC), proliferating cell nuclear antigen (PCNA), and DNA polymerase delta (POLD1). Thus, we examined PT3 cells for expression of these components by DNA microarray and real-time quantitative PCR. All four components were over-expressed in PT3 over two representative low-permissive cell isolates (NK and PT1). However, this super-permissiveness did not result in PT3 cell death by AAV infection. CONCLUSION These data, for the first time, provide evidence that these four cellular components are likely important for AAV in vivo DNA replication as well as in vitro. These data also suggest that PT3 will be a useful reagent for investigating the AAV-permissive transcriptome and AAV anti-cancer effect.
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Affiliation(s)
- Bum Yong Kang
- Obstetrics and Gynecology, University of Arkansas for Medical Sciences, 4301 West Markham St, Little Rock, AR 72205, USA
- Central Arkansas Veterans Healthcare System, John L McClellan Memorial Veterans Hospital, 4300 West 7th St., Little Rock, AR 72205, USA
| | - Hong You
- Department of Internal Medicine, Gene Therapy Program, University of Arkansas for Medical Sciences, 4301 West Markham St, Little Rock, AR 72205, USA
- Obstetrics and Gynecology, University of Arkansas for Medical Sciences, 4301 West Markham St, Little Rock, AR 72205, USA
| | - Sarmistha Bandyopadhyay
- Department of Internal Medicine, Gene Therapy Program, University of Arkansas for Medical Sciences, 4301 West Markham St, Little Rock, AR 72205, USA
| | - Nalini Agrawal
- Obstetrics and Gynecology, University of Arkansas for Medical Sciences, 4301 West Markham St, Little Rock, AR 72205, USA
| | - Russell B Melchert
- Pharmaceutical Sciences, University of Arkansas for Medical Sciences, 4301 West Markham St, Little Rock, AR 72205, USA
| | - Alexei G Basnakian
- Pharmacology and Toxicology, University of Arkansas for Medical Sciences, 4301 West Markham St, Little Rock, AR 72205, USA
- Central Arkansas Veterans Healthcare System, John L McClellan Memorial Veterans Hospital, 4300 West 7th St., Little Rock, AR 72205, USA
| | - Yong Liu
- Department of Internal Medicine, Gene Therapy Program, University of Arkansas for Medical Sciences, 4301 West Markham St, Little Rock, AR 72205, USA
- Obstetrics and Gynecology, University of Arkansas for Medical Sciences, 4301 West Markham St, Little Rock, AR 72205, USA
| | - Paul L Hermonat
- Department of Internal Medicine, Gene Therapy Program, University of Arkansas for Medical Sciences, 4301 West Markham St, Little Rock, AR 72205, USA
- Obstetrics and Gynecology, University of Arkansas for Medical Sciences, 4301 West Markham St, Little Rock, AR 72205, USA
- Central Arkansas Veterans Healthcare System, John L McClellan Memorial Veterans Hospital, 4300 West 7th St., Little Rock, AR 72205, USA
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Tsuchiya A, Inoue YH, Ida H, Kawase Y, Okudaira K, Ohno K, Yoshida H, Yamaguchi M. Transcriptional regulation of the Drosophila rfc1 gene by the DRE-DREF pathway. FEBS J 2007; 274:1818-32. [PMID: 17381512 DOI: 10.1111/j.1742-4658.2007.05730.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The DNA replication-related element (DRE) is a common 8-bp sequence (5'-TATCGATA) found in the promoters of many DNA replication-related genes, to which DRE-binding factor (DREF) specifically binds to activate transcription. Replication factor C (RFC) is an essential five-subunit complex in DNA replication, the largest subunit being RFC140. We first identified the gene (rfc1) encoding the Drosophila RFC140 (dRFC140) protein and then isolated a mutant. The phenotypes suggested that the gene is essential for cell-cycle progression, and immunocytochemical studies also indicated a relation between its expression and the cell cycle. The rfc1 gene contains three DRE-like sequences in its 5'-flanking region, one of them perfectly matching DRE and the other two demonstrating a match in seven of eight nucleotides. These sequences were named DRE1 (-63 to -69), DRE2 (-378 to -385), and DRE3 (-1127 to -1134), respectively. Immunostaining of polytene chromosomes in third-instar larvae using anti-DREF sera detected a specific band in 82E2 of 3R chromosome, containing the rfc1 gene region. Band-mobility shift assays using Drosophila Kc cell nuclear extracts revealed that DREF binds to DRE1, -2, and -3 in vitro, and chromatin immunoprecipitation using anti-DREF IgG confirmed that this occurs in vivo. Luciferase transient expression assays in S2 cells further suggested that DREs in the rfc1 promoter are involved in transcriptional regulation of the gene. Moreover, rfc1 promoter activity was reduced by 38% in DREF double-stranded RNA-treated S2 cells. These results indicate that DREF positively regulates the rfc1 promoter.
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Affiliation(s)
- Akihiro Tsuchiya
- Department of Applied Biology, Kyoto Institute of Technology, Japan
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McCulloch SD, Wood A, Garg P, Burgers PMJ, Kunkel TA. Effects of accessory proteins on the bypass of a cis-syn thymine-thymine dimer by Saccharomyces cerevisiae DNA polymerase eta. Biochemistry 2007; 46:8888-96. [PMID: 17608453 PMCID: PMC2288658 DOI: 10.1021/bi700234t] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Among several hypotheses to explain how translesion synthesis (TLS) by DNA polymerase eta (pol eta) suppresses ultraviolet light-induced mutagenesis in vivo despite the fact that pol eta copies DNA with low fidelity, here we test whether replication accessory proteins enhance the fidelity of TLS by pol eta. We first show that the single-stranded DNA binding protein RPA, the sliding clamp PCNA, and the clamp loader RFC slightly increase the processivity of yeast pol eta and its ability to recycle to new template primers. However, these increases are small, and they are similar when copying an undamaged template and a template containing a cis-syn TT dimer. Consequently, the accessory proteins do not strongly stimulate the already robust TT dimer bypass efficiency of pol eta. We then perform a comprehensive analysis of yeast pol eta fidelity. We show that it is much less accurate than other yeast DNA polymerases and that the accessory proteins have little effect on fidelity when copying undamaged templates or when bypassing a TT dimer. Thus, although accessory proteins clearly participate in pol eta functions in vivo, they do not appear to help suppress UV mutagenesis by improving pol eta bypass fidelity per se.
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Affiliation(s)
- Scott D McCulloch
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
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O'Driscoll M, Dobyns WB, van Hagen JM, Jeggo PA. Cellular and clinical impact of haploinsufficiency for genes involved in ATR signaling. Am J Hum Genet 2007; 81:77-86. [PMID: 17564965 PMCID: PMC1950915 DOI: 10.1086/518696] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2007] [Accepted: 04/05/2007] [Indexed: 02/03/2023] Open
Abstract
Ataxia telangiectasia and Rad3-related (ATR) protein, a kinase that regulates a DNA damage-response pathway, is mutated in ATR-Seckel syndrome (ATR-SS), a disorder characterized by severe microcephaly and growth delay. Impaired ATR signaling is also observed in cell lines from additional disorders characterized by microcephaly and growth delay, including non-ATR-SS, Nijmegen breakage syndrome, and MCPH1 (microcephaly, primary autosomal recessive, 1)-dependent primary microcephaly. Here, we examined ATR-pathway function in cell lines from three haploinsufficient contiguous gene-deletion disorders--a subset of blepharophimosis-ptosis-epicanthus inversus syndrome, Miller-Dieker lissencephaly syndrome, and Williams-Beuren syndrome--in which the deleted region encompasses ATR, RPA1, and RFC2, respectively. These three genes function in ATR signaling. Cell lines from these disorders displayed an impaired ATR-dependent DNA damage response. Thus, we describe ATR signaling as a pathway unusually sensitive to haploinsufficiency and identify three further human disorders displaying a defective ATR-dependent DNA damage response. The striking correlation of ATR-pathway dysfunction with the presence of microcephaly and growth delay strongly suggests a causal relationship.
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Affiliation(s)
- Mark O'Driscoll
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK.
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Xia ST, Xiao LT, Bi DL, Zhu ZH. Arabidopsis replication factor C subunit 1 plays an important role in embryogenesis. Zhi Wu Sheng Li Yu Fen Zi Sheng Wu Xue Xue Bao 2007; 33:179-87. [PMID: 17556804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Replication factor C (RFC), consisting of one large subunit and four small subunits, is an important factor involved in DNA replication and repair mechanisms as well as cell proliferation. The subunit 1 of Arabidopsis RFC (AtRFC1) is a homologue of p140, the large subunit of human RFC. Three T-DNA insertion mutant lines of AtRFC1, i.e. rfc1-1, rfc1-2 and rfc1-3, with insertion mutations located in exons 16 and 19, and the promoter region respectively were verified. These mutations caused defects in embryogenesis and led to embryo and seed abortion. Transformation of wild type AtRFC1 gene into rfc1 mutant alleles reverted the mutant phenotypes, suggesting that AtRFC1 plays an important role in embryo development in Arabidopsis thaliana.
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Affiliation(s)
- Shi-Tou Xia
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China
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47
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Hashiguchi K, Matsumoto Y, Yasui A. Recruitment of DNA repair synthesis machinery to sites of DNA damage/repair in living human cells. Nucleic Acids Res 2007; 35:2913-23. [PMID: 17439963 PMCID: PMC1888830 DOI: 10.1093/nar/gkm115] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The eukaryotic sliding DNA clamp, proliferating cell nuclear antigen (PCNA), is essential for DNA replication and repair synthesis. In order to load the ring-shaped, homotrimeric PCNA onto the DNA double helix, the ATPase activity of the replication factor C (RFC) clamp loader complex is required. Although the recruitment of PCNA by RFC to DNA replication sites has well been documented, our understanding of its recruitment during DNA repair synthesis is limited. In this study, we analyzed the accumulation of endogenous and fluorescent-tagged proteins for DNA repair synthesis at the sites of DNA damage produced locally by UVA-laser micro-irradiation in HeLa cells. Accumulation kinetics and in vitro pull-down assays of the large subunit of RFC (RFC140) revealed that there are two distinct modes of recruitment of RFC to DNA damage, a simultaneous accumulation of RFC140 and PCNA caused by interaction between PCNA and the extreme N-terminus of RFC140 and a much faster accumulation of RFC140 than PCNA at the damaged site. Furthermore, RFC140 knock-down experiments showed that PCNA can accumulate at DNA damage independently of RFC. These results suggest that immediate accumulation of RFC and PCNA at DNA damage is only partly interdependent.
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Affiliation(s)
- Kazunari Hashiguchi
- Department of Molecular Genetics, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575, Japan and Division of Medical Science, Fox Chase Cancer Center, PA 19111, USA
| | - Yoshihiro Matsumoto
- Department of Molecular Genetics, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575, Japan and Division of Medical Science, Fox Chase Cancer Center, PA 19111, USA
| | - Akira Yasui
- Department of Molecular Genetics, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575, Japan and Division of Medical Science, Fox Chase Cancer Center, PA 19111, USA
- *To whom correspondence should be addressed. +81-22-717-8465+81-22-717-8470 Correspondence may also be addressed to Kazunari Hashiguchi. +81-22-717-8469 +81-22-717-8470
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48
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Park M, Kong H, Kim H, Kim H, Kim J, Cheong J. Transcriptional repression of the gluconeogenic gene PEPCK by the orphan nuclear receptor SHP through inhibitory interaction with C/EBPalpha. Biochem J 2007; 402:567-74. [PMID: 17094771 PMCID: PMC1863575 DOI: 10.1042/bj20061549] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
SHP (short heterodimer partner) is an orphan nuclear receptor that plays an important role in regulating glucose and lipid metabolism. A variety of transcription factors are known to regulate transcription of the PEPCK (phosphoenolpyruvate carboxykinase) gene, which encodes a rate-determining enzyme in hepatic gluconeogenesis. Previous reports identified glucocorticoid receptor and Foxo1 as novel downstream targets regulating SHP inhibition [Borgius, Steffensen, Gustafsson and Treuter (2002) J. Biol. Chem. 277, 49761-49796; Yamagata, Daitoku, Shimamoto, Matsuzaki, Hirota, Ishida and Fukamizu (2004) J. Biol. Chem. 279, 23158-23165]. In the present paper, we show a new molecular mechanism of SHP-mediated inhibition of PEPCK transcription. We also show that the CRE1 (cAMP regulatory element 1; -99 to -76 bp relative to the transcription start site) of the PEPCK promoter is also required for the inhibitory regulation by SHP. SHP repressed C/EBPalpha (CCAAT/enhancer-binding protein alpha)-driven transcription of PEPCK through direct interaction with C/EBPalpha protein both in vitro and in vivo. The formation of an active transcriptional complex of C/EBPalpha and its binding to DNA was inhibited by SHP, resulting in the inhibition of PEPCK gene transcription. Taken together, these results suggest that SHP might regulate a level of hepatic gluconeogenesis driven by C/EBPalpha activation.
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Affiliation(s)
- Min Jung Park
- *Department of Molecular Biology, Pusan National University, Busan 609-735, Korea
| | - Hee Jeong Kong
- †Laboratory of Molecular Growth Regulation, National Institute of Child Health and Development, National Institutes of Health, Bethesda, Maryland 20892-2753, U.S.A
| | - Hye Young Kim
- *Department of Molecular Biology, Pusan National University, Busan 609-735, Korea
| | - Hyeong Hoe Kim
- ‡Department of Laboratory Medicine, College of Medicine, Pusan National University, Busan 602-739, Korea
| | - Joon Hong Kim
- §Department of Internal Medicine, College of Medicine, Pusan National University, Busan 602-739, Korea
| | - Jae Hun Cheong
- *Department of Molecular Biology, Pusan National University, Busan 609-735, Korea
- To whom correspondence should be addressed (email )
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49
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Hiraga SI, Robertson ED, Donaldson AD. The Ctf18 RFC-like complex positions yeast telomeres but does not specify their replication time. EMBO J 2006; 25:1505-14. [PMID: 16525505 PMCID: PMC1440320 DOI: 10.1038/sj.emboj.7601038] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2005] [Accepted: 02/15/2006] [Indexed: 11/09/2022] Open
Abstract
Chromosome ends in Saccharomyces cerevisiae are positioned in clusters at the nuclear rim. We report that Ctf18, Ctf8, and Dcc1, the subunits of a Replication Factor C (RFC)-like complex, are essential for the perinuclear positioning of telomeres. In both yeast and mammalian cells, peripheral nuclear positioning of chromatin during G1 phase correlates with late DNA replication. We find that the mislocalized telomeres of ctf18 cells still replicate late, showing that late DNA replication does not require peripheral positioning during G1. The Ku and Sir complexes have been shown to act through separate pathways to position telomeres, but in the absence of Ctf18 neither pathway can act fully to maintain telomere position. Surprisingly CTF18 is not required for Ku or Sir4-mediated peripheral tethering of a nontelomeric chromosome locus. Our results suggest that the Ctf18 RFC-like complex modifies telomeric chromatin to make it competent for normal localization to the nuclear periphery.
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Affiliation(s)
- Shin-ichiro Hiraga
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - E Douglas Robertson
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - Anne D Donaldson
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, UK
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK. Tel.: +44 1224 550975; Fax: +44 1224 555844; E-mail:
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50
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Gupte RS, Sampson V, Traganos F, Darzynkiewicz Z, Lee MYWT. Cyclic AMP regulates the expression and nuclear translocation of RFC40 in MCF7 cells. Exp Cell Res 2006; 312:796-806. [PMID: 16413017 DOI: 10.1016/j.yexcr.2005.11.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2005] [Revised: 11/29/2005] [Accepted: 11/30/2005] [Indexed: 11/30/2022]
Abstract
We have previously shown that the regulatory subunit of PKA, RIalpha, functions as a nuclear transport protein for the second subunit of the replication factor C complex, RFC40, and that this transport appears to be crucial for cell cycle progression from G1 to S phase. In this study, we found that N(6)-monobutyryl cAMP significantly up-regulates the expression of RFC40 mRNA by 1.8-fold and its endogenous protein by 2.3-fold with a subsequent increase in the RIalpha-RFC40 complex formation by 3.2-fold. Additionally, the nuclear to cytoplasmic ratio of RFC40 increased by 26% followed by a parallel increase in the percentage of S phase cells by 33%. However, there was reduction in the percentage of G1 cells by 16% and G2/M cells by 43% with a concurrent accumulation of cells in S phase. Interestingly, the higher percentage of S phase cells did not correlate with a parallel increase in DNA replication. Moreover, although cAMP did not affect the expression of the other RFC subunits, there was a significant decrease in the RFC40-37 complex formation by 81.3%, substantiating the decrease in DNA replication rate. Taken together, these findings suggest that cAMP functions as an upstream modulator that regulates the expression and nuclear translocation of RFC40.
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Affiliation(s)
- Rakhee S Gupte
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA
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