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Frappier L. EBNA1. Curr Top Microbiol Immunol 2025. [PMID: 40399573 DOI: 10.1007/82_2025_299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2025]
Abstract
EBNA1 plays multiple important roles in EBV latent infection and has also been shown to impact EBV lytic infection. EBNA1 is required for the stable persistence of the EBV genomes in latent infection and activates the expression of other EBV latency genes through interactions with specific DNA sequences in the viral episomes. EBNA1 also interacts with several cellular proteins and cellular DNA sites to modulate multiple cellular pathways important for viral persistence and cell survival. These cellular effects are also implicated in oncogenesis, suggesting a direct role of EBNA1 in the development of EBV-associated tumours.
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Affiliation(s)
- Lori Frappier
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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2
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Ummarino S, Poluben L, Ebralidze AK, Autiero I, Zhang Y, Paniza T, Deshpande M, Rinaldi L, Lee JD, Bassal MA, Trinh BQ, Balk SP, Flaumenhaft R, Gerhardt J, Mirkin SM, Tenen DG, Di Ruscio A. RNAs anchoring replication complex control initiation and firing of DNA replication. RESEARCH SQUARE 2025:rs.3.rs-5723221. [PMID: 39975922 PMCID: PMC11838740 DOI: 10.21203/rs.3.rs-5723221/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
Coordinated initiation of DNA replication is essential to ensure efficient and timely DNA synthesis. Yet, molecular mechanism describing how replication initiation is coordinated in eukaryotic cells is not completely understood. Herein, we present data demonstrating a novel feature of RNAs transcribed in the proximity of actively replicating gene loci. We show that RNAs aNChoring ORC1 (ANCORs) to the histone variant H2A.Z are licensors of the DNA replication process. This ANCOR-H2A.Z interaction is essential for cells to initiate duplication of their genetic material. Widespread and locus-specific perturbations of these transcripts correlate with anomalous replication patterns and a notable loss of the H2A.Z replicative marker at the origin site. Collectively, we present a previously undescribed RNA-mediated mechanism that is associated with the generation of active replication origins in eukaryotic cells. Our findings delineate a strategy to modulate the origins of replication in human cells at a local and global level, with potentially broad biomedical implications.
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Affiliation(s)
- Simone Ummarino
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, 330 Brookline Avenue Boston, MA 02215, USA
- Beth Israel Deaconess Medical Center, Department of Medicine, Division of Hematology-Oncology, Boston, MA, 02115, USA
| | - Larysa Poluben
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA, 02115, USA
- These two authors equally contributed to the work
| | - Alex K. Ebralidze
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, 330 Brookline Avenue Boston, MA 02215, USA
- Beth Israel Deaconess Medical Center, Department of Medicine, Division of Hematology-Oncology, Boston, MA, 02115, USA
- These two authors equally contributed to the work
| | - Ida Autiero
- Institute of Biostructures and Bioimaging, CNR, Naples, 80100, Italy
| | - Yanzhou Zhang
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, 330 Brookline Avenue Boston, MA 02215, USA
- Beth Israel Deaconess Medical Center, Department of Medicine, Division of Hematology-Oncology, Boston, MA, 02115, USA
| | - Theodore Paniza
- Center for Reproductive Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Madhura Deshpande
- Center for Reproductive Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Lucrezia Rinaldi
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, 330 Brookline Avenue Boston, MA 02215, USA
- Beth Israel Deaconess Medical Center, Department of Medicine, Division of Hematology-Oncology, Boston, MA, 02115, USA
| | - Johnathan D. Lee
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, 330 Brookline Avenue Boston, MA 02215, USA
| | - Mahmoud A. Bassal
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, 330 Brookline Avenue Boston, MA 02215, USA
- Beth Israel Deaconess Medical Center, Department of Medicine, Division of Hematology-Oncology, Boston, MA, 02115, USA
- Cancer Science Institute of Singapore, National University of Singapore, 117456, Singapore
| | | | - Steven P. Balk
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Robert Flaumenhaft
- Beth Israel Deaconess Medical Center, Division of Hemostasis and Thrombosis, Harvard Medical School, Boston, MA, 02115, USA
| | - Jeannine Gerhardt
- Center for Reproductive Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | | | - Daniel G. Tenen
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA
- These two authors equally contributed to the work
| | - Annalisa Di Ruscio
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, 330 Brookline Avenue Boston, MA 02215, USA
- Beth Israel Deaconess Medical Center, Department of Medicine, Division of Hematology-Oncology, Boston, MA, 02115, USA
- University of Eastern Piedmont, Department of Translational Medicine, Novara, 28100, Italy
- These two authors equally contributed to the work
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3
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Graesser C, Nord R, Flaswinkel H, Kremmer E, Meese E, Caban KM, Fröhlich T, Grässer FA, Hart M. Use of antibodies against Epstein-Barr virus nuclear antigen 1 for detection of cellular proteins with monomethylated arginine residues that are potentially involved in viral transformation. Arch Virol 2024; 169:241. [PMID: 39514105 PMCID: PMC11549202 DOI: 10.1007/s00705-024-06172-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 09/30/2024] [Indexed: 11/16/2024]
Abstract
Epstein-Barr virus nuclear antigen 1 (EBNA1) contains two arginine-glycine (RG) repeats that contain symmetric/asymmetric dimethylarginine (SDMA/ADMA) and monomethylarginine (MMA) residues. We generated mouse monoclonal antibodies directed against a monomethylated GRGRGG-containing repeat located between amino acids 328 and 377 of EBNA1. In addition to detecting MMA-modified EBNA1, we also had the goal of identifying cellular proteins that bind to MMA-modified EBNA1 in EBV-positive Raji cells. Furthermore, we hypothesized that antibodies against MMA-modified EBNA1 might also recognize cell factors that use an MMA-modified surface structure similar to that of EBNA1 to bind to their common targets. Using a combination of immunoprecipitation and mass spectrometry, we identified a number of such cellular proteins, including SNRPD1-3, ALY/REF, RPS15, DIDO1, LSM12, LSM14A, DAP3, and CPSF1. An NACA complex protein that was shown previously to bind to the glycine-alanine repeat of EBNA1 was also identified. The proteins identified in this study are involved in splicing, tumorigenesis, transcriptional activation, DNA stability, and RNA processing or export.
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Affiliation(s)
- Christian Graesser
- Institute of Virology, Saarland University Medical School, Kirrbergerstraße, Haus 47, D-66421, Homburg/Saar, Germany
| | - Ruth Nord
- Institute of Virology, Saarland University Medical School, Kirrbergerstraße, Haus 47, D-66421, Homburg/Saar, Germany
| | - Heinrich Flaswinkel
- Department of Biology II, Ludwigs-Maximilians-Unversität (LMU) Munich, Butenandtstraße 1, 81377, Munich, Germany
| | - Elisabeth Kremmer
- Department of Biology II, Ludwigs-Maximilians-Unversität (LMU) Munich, Butenandtstraße 1, 81377, Munich, Germany
| | - Eckart Meese
- Institute of Human Genetics, Saarland University (USAAR), Kirrbergerstraße, Haus 60, 66421, Homburg/Saar, Germany
| | - Karolina Magdalena Caban
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Straße 25, 81377, Munich, Germany
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Straße 25, 81377, Munich, Germany
| | - Friedrich A Grässer
- Institute of Virology, Saarland University Medical School, Kirrbergerstraße, Haus 47, D-66421, Homburg/Saar, Germany
| | - Martin Hart
- Center of Human and Molecular Biology (ZHMB), Institute of Human Genetics, Saarland University (USAAR), Kirrbergerstraße, Haus 60, Building 60, D-66421, Homburg/Saar, Germany.
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4
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Battista S, Fedele M, Secco L, Ingo AMD, Sgarra R, Manfioletti G. Binding to the Other Side: The AT-Hook DNA-Binding Domain Allows Nuclear Factors to Exploit the DNA Minor Groove. Int J Mol Sci 2024; 25:8863. [PMID: 39201549 PMCID: PMC11354804 DOI: 10.3390/ijms25168863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 08/08/2024] [Accepted: 08/10/2024] [Indexed: 09/02/2024] Open
Abstract
The "AT-hook" is a peculiar DNA-binding domain that interacts with DNA in the minor groove in correspondence to AT-rich sequences. This domain has been first described in the HMGA protein family of architectural factors and later in various transcription factors and chromatin proteins, often in association with major groove DNA-binding domains. In this review, using a literature search, we identified about one hundred AT-hook-containing proteins, mainly chromatin proteins and transcription factors. After considering the prototypes of AT-hook-containing proteins, the HMGA family, we review those that have been studied in more detail and that have been involved in various pathologies with a particular focus on cancer. This review shows that the AT-hook is a domain that gives proteins not only the ability to interact with DNA but also with RNA and proteins. This domain can have enzymatic activity and can influence the activity of the major groove DNA-binding domain and chromatin docking modules when present, and its activity can be modulated by post-translational modifications. Future research on the function of AT-hook-containing proteins will allow us to better decipher their function and contribution to the different pathologies and to eventually uncover their mutual influences.
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Affiliation(s)
- Sabrina Battista
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” (IEOS), National Research Council (CNR), 80131 Naples, Italy; (S.B.); (M.F.)
| | - Monica Fedele
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” (IEOS), National Research Council (CNR), 80131 Naples, Italy; (S.B.); (M.F.)
| | - Luca Secco
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (L.S.); (A.M.D.I.)
| | | | - Riccardo Sgarra
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (L.S.); (A.M.D.I.)
| | - Guidalberto Manfioletti
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (L.S.); (A.M.D.I.)
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5
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Adiji OA, McConnell BS, Parker MW. The origin recognition complex requires chromatin tethering by a hypervariable intrinsically disordered region that is functionally conserved from sponge to man. Nucleic Acids Res 2024; 52:4344-4360. [PMID: 38381902 PMCID: PMC11077064 DOI: 10.1093/nar/gkae122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 01/26/2024] [Accepted: 02/08/2024] [Indexed: 02/23/2024] Open
Abstract
The first step toward eukaryotic genome duplication is loading of the replicative helicase onto chromatin. This 'licensing' step initiates with the recruitment of the origin recognition complex (ORC) to chromatin, which is thought to occur via ORC's ATP-dependent DNA binding and encirclement activity. However, we have previously shown that ATP binding is dispensable for the chromatin recruitment of fly ORC, raising the question of how metazoan ORC binds chromosomes. We show here that the intrinsically disordered region (IDR) of fly Orc1 is both necessary and sufficient for recruitment of ORC to chromosomes in vivo and demonstrate that this is regulated by IDR phosphorylation. Consistently, we find that the IDR confers the ORC holocomplex with ATP-independent DNA binding activity in vitro. Using phylogenetic analysis, we make the surprising observation that metazoan Orc1 IDRs have diverged so markedly that they are unrecognizable as orthologs and yet we find that these compositionally homologous sequences are functionally conserved. Altogether, these data suggest that chromatin is recalcitrant to ORC's ATP-dependent DNA binding activity, necessitating IDR-dependent chromatin tethering, which we propose poises ORC to opportunistically encircle nucleosome-free regions as they become available.
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Affiliation(s)
- Olubu A Adiji
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Brendan S McConnell
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Matthew W Parker
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
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6
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Dinh VT, Loaëc N, Quillévéré A, Le Sénéchal R, Keruzoré M, Martins RP, Granzhan A, Blondel M. The hide-and-seek game of the oncogenic Epstein-Barr virus-encoded EBNA1 protein with the immune system: An RNA G-quadruplex tale. Biochimie 2023; 214:57-68. [PMID: 37473831 DOI: 10.1016/j.biochi.2023.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/11/2023] [Accepted: 07/13/2023] [Indexed: 07/22/2023]
Abstract
The Epstein-Barr virus (EBV) is the first oncogenic virus described in human. EBV infects more than 90% of the human population worldwide, but most EBV infections are asymptomatic. After the primary infection, the virus persists lifelong in the memory B cells of the infected individuals. Under certain conditions the virus can cause several human cancers, that include lymphoproliferative disorders such as Burkitt and Hodgkin lymphomas and non-lymphoid malignancies such as 100% of nasopharyngeal carcinoma and 10% of gastric cancers. Each year, about 200,000 EBV-related cancers emerge, hence accounting for at least 1% of worldwide cancers. Like all gammaherpesviruses, EBV has evolved a strategy to escape the host immune system. This strategy is mainly based on the tight control of the expression of its Epstein-Barr nuclear antigen-1 (EBNA1) protein, the EBV-encoded genome maintenance protein. Indeed, EBNA1 is essential for viral genome replication and maintenance but, at the same time, is also highly antigenic and T cells raised against EBNA1 exist in infected individuals. For this reason, EBNA1 is considered as the Achilles heel of EBV and the virus has seemingly evolved a strategy that employs the binding of nucleolin, a host cell factor, to RNA G-quadruplex (rG4) within EBNA1 mRNA to limit its expression to the minimal level required for function while minimizing immune recognition. This review recapitulates in a historical way the knowledge accumulated on EBNA1 immune evasion and discusses how this rG4-dependent mechanism can be exploited as an intervention point to unveil EBV-related cancers to the immune system.
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Affiliation(s)
- Van-Trang Dinh
- Univ Brest; Inserm UMR1078; Etablissement Français Du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 Avenue Camille Desmoulins, F-29200 Brest, France.
| | - Nadège Loaëc
- Univ Brest; Inserm UMR1078; Etablissement Français Du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 Avenue Camille Desmoulins, F-29200 Brest, France
| | - Alicia Quillévéré
- Univ Brest; Inserm UMR1078; Etablissement Français Du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 Avenue Camille Desmoulins, F-29200 Brest, France
| | - Ronan Le Sénéchal
- Univ Brest; Inserm UMR1078; Etablissement Français Du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 Avenue Camille Desmoulins, F-29200 Brest, France
| | - Marc Keruzoré
- Univ Brest; Inserm UMR1078; Etablissement Français Du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 Avenue Camille Desmoulins, F-29200 Brest, France
| | | | - Anton Granzhan
- Chemistry and Modelling for the Biology of Cancer (CMBC), CNRS UMR9187, Inserm U1196, Institut Curie, Université Paris Saclay, F-91405 Orsay, France
| | - Marc Blondel
- Univ Brest; Inserm UMR1078; Etablissement Français Du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 Avenue Camille Desmoulins, F-29200 Brest, France.
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7
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Torma G, Tombácz D, Csabai Z, Almsarrhad IAA, Nagy GÁ, Kakuk B, Gulyás G, Spires LM, Gupta I, Fülöp Á, Dörmő Á, Prazsák I, Mizik M, Dani VÉ, Csányi V, Harangozó Á, Zádori Z, Toth Z, Boldogkői Z. Identification of herpesvirus transcripts from genomic regions around the replication origins. Sci Rep 2023; 13:16395. [PMID: 37773348 PMCID: PMC10541914 DOI: 10.1038/s41598-023-43344-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/22/2023] [Indexed: 10/01/2023] Open
Abstract
Long-read sequencing (LRS) techniques enable the identification of full-length RNA molecules in a single run eliminating the need for additional assembly steps. LRS research has exposed unanticipated transcriptomic complexity in various organisms, including viruses. Herpesviruses are known to produce a range of transcripts, either close to or overlapping replication origins (Oris) and neighboring genes related to transcription or replication, which possess confirmed or potential regulatory roles. In our research, we employed both new and previously published LRS and short-read sequencing datasets to uncover additional Ori-proximal transcripts in nine herpesviruses from all three subfamilies (alpha, beta and gamma). We discovered novel long non-coding RNAs, as well as splice and length isoforms of mRNAs. Moreover, our analysis uncovered an intricate network of transcriptional overlaps within the examined genomic regions. We demonstrated that herpesviruses display distinct patterns of transcriptional overlaps in the vicinity of or at the Oris. Our findings suggest the existence of a 'super regulatory center' in the genome of alphaherpesviruses that governs the initiation of both DNA replication and global transcription through multilayered interactions among the molecular machineries.
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Affiliation(s)
- Gábor Torma
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Dóra Tombácz
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
- MTA -SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary
| | - Zsolt Csabai
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
- MTA -SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary
| | - Islam A A Almsarrhad
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Gergely Ármin Nagy
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Balázs Kakuk
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
- MTA -SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary
| | - Gábor Gulyás
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
- MTA -SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary
| | - Lauren McKenzie Spires
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, FL, USA
| | - Ishaan Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi, India
| | - Ádám Fülöp
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Ákos Dörmő
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
- MTA -SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary
| | - István Prazsák
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
- MTA -SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary
| | - Máté Mizik
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Virág Éva Dani
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Viktor Csányi
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Ákos Harangozó
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Zoltán Zádori
- HUN-REN Veterinary Medical Research Institute HU, Budapest, Hungary
| | - Zsolt Toth
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, FL, USA
| | - Zsolt Boldogkői
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary.
- MTA -SZTE Lendület GeMiNI Research Group, University of Szeged, Szeged, Hungary.
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8
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Mas AM, Goñi E, Ruiz de Los Mozos I, Arcas A, Statello L, González J, Blázquez L, Lee WTC, Gupta D, Sejas Á, Hoshina S, Armaos A, Tartaglia GG, Waga S, Ule J, Rothenberg E, Gómez M, Huarte M. ORC1 binds to cis-transcribed RNAs for efficient activation of replication origins. Nat Commun 2023; 14:4447. [PMID: 37488096 PMCID: PMC10366126 DOI: 10.1038/s41467-023-40105-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/11/2023] [Indexed: 07/26/2023] Open
Abstract
Cells must coordinate the activation of thousands of replication origins dispersed throughout their genome. Active transcription is known to favor the formation of mammalian origins, although the role that RNA plays in this process remains unclear. We show that the ORC1 subunit of the human Origin Recognition Complex interacts with RNAs transcribed from genes with origins in their transcription start sites (TSSs), displaying a positive correlation between RNA binding and origin activity. RNA depletion, or the use of ORC1 RNA-binding mutant, result in inefficient activation of proximal origins, linked to impaired ORC1 chromatin release. ORC1 RNA binding activity resides in its intrinsically disordered region, involved in intra- and inter-molecular interactions, regulation by phosphorylation, and phase-separation. We show that RNA binding favors ORC1 chromatin release, by regulating its phosphorylation and subsequent degradation. Our results unveil a non-coding function of RNA as a dynamic component of the chromatin, orchestrating the activation of replication origins.
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Affiliation(s)
- Aina Maria Mas
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 31008, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Enrique Goñi
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 31008, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Igor Ruiz de Los Mozos
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 31008, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Aida Arcas
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 31008, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Luisa Statello
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 31008, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Jovanna González
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 31008, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Lorea Blázquez
- RNA Networks Lab, The Francis Crick Institute, NW11BF, London, UK
- Neurosciences Area, Biodonostia Health Research Institute, 20014, San Sebastian, Spain
- Ikerbasque, Basque Foundation for Science, 48009, Bilbao, Spain
| | - Wei Ting Chelsea Lee
- Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - Dipika Gupta
- Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - Álvaro Sejas
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 31008, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain
| | - Shoko Hoshina
- Department of Chemical and Biological Sciences, Japan Women's University, Tokyo, 112-8681, Japan
| | - Alexandros Armaos
- Center for Human Technologies, Istituto Italiano di Tecnologia, Genova, Italy
| | - Gian Gaetano Tartaglia
- Center for Human Technologies, Istituto Italiano di Tecnologia, Genova, Italy
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Department of Biology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Shou Waga
- Department of Chemical and Biological Sciences, Japan Women's University, Tokyo, 112-8681, Japan
| | - Jernej Ule
- RNA Networks Lab, The Francis Crick Institute, NW11BF, London, UK
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - María Gómez
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Nicolás Cabrera 1, 28049, Madrid, Spain
| | - Maite Huarte
- Center for Applied Medical Research, University of Navarra, Pio XII 55 Ave, 31008, Pamplona, Spain.
- Institute of Health Research of Navarra (IdiSNA), Cancer Center Clínica Universidad de Navarra (CCUN), Pamplona, Spain.
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9
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Hu Y, Stillman B. Origins of DNA replication in eukaryotes. Mol Cell 2023; 83:352-372. [PMID: 36640769 PMCID: PMC9898300 DOI: 10.1016/j.molcel.2022.12.024] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 01/15/2023]
Abstract
Errors occurring during DNA replication can result in inaccurate replication, incomplete replication, or re-replication, resulting in genome instability that can lead to diseases such as cancer or disorders such as autism. A great deal of progress has been made toward understanding the entire process of DNA replication in eukaryotes, including the mechanism of initiation and its control. This review focuses on the current understanding of how the origin recognition complex (ORC) contributes to determining the location of replication initiation in the multiple chromosomes within eukaryotic cells, as well as methods for mapping the location and temporal patterning of DNA replication. Origin specification and configuration vary substantially between eukaryotic species and in some cases co-evolved with gene-silencing mechanisms. We discuss the possibility that centromeres and origins of DNA replication were originally derived from a common element and later separated during evolution.
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Affiliation(s)
- Yixin Hu
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA; Program in Molecular and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Bruce Stillman
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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10
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Li YT, Liu CJ, Kao JH, Lin LF, Tu HC, Wang CC, Huang PH, Cheng HR, Chen PJ, Chen DS, Wu HL. Metastatic tumor antigen 1 contributes to hepatocarcinogenesis posttranscriptionally through RNA-binding function. Hepatology 2023; 77:379-394. [PMID: 35073601 DOI: 10.1002/hep.32356] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 01/07/2022] [Accepted: 01/12/2022] [Indexed: 01/28/2023]
Abstract
BACKGROUND AND AIMS Both nuclear and cytoplasmic overexpression of metastatic tumor antigen 1 (MTA1) contributes to tumorigenesis of HCC. Most studies have focused on nuclear MTA1 whose function is mainly a chromatin modifier regulating the expression of various cancer-promoting genes. By contrast, the molecular mechanisms of cytoplasmic MTA1 in carcinogenesis remain elusive. Here, we reveal a role of MTA1 in posttranscriptional gene regulation. APPROACH AND RESULTS We conducted the in vitro and in vivo RNA-protein interaction assays indicating that MTA1 could bind directly to the 3'-untranslated region of MYC RNA. Mutation at the first glycine of the conserved GXXG loop within a K-homology II domain-like structure in MTA1 (G78D) resulted in the loss of RNA-binding activity. We used gain- and loss-of-function strategy showing that MTA1, but not the G78D mutant, extended the half-life of MYC and protected it from the lethal -7-mediated degradation. The G78D mutant exhibited lower activity in promoting tumorigenesis than wild-type in vitro and in vivo. Furthermore, RNA-immunoprecipitation sequencing analysis demonstrated that MTA1 binds various oncogenesis-related mRNAs besides MYC . The clinical relevance of cytoplasmic MTA1 and its interaction with MYC were investigated using HBV-HCC cohorts with or without early recurrence. The results showed that higher cytoplasmic MTA1 level and MTA1- MYC interaction were associated with early recurrence. CONCLUSIONS MTA1 is a generic RNA-binding protein. Cytoplasmic MTA1 and its binding to MYC is associated with early recurrence in patients with HBV-HCC. This function enables it to regulate gene expression posttranscriptionally and contributes to hepatocarcinogenesis.
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Affiliation(s)
- Yung-Tsung Li
- Hepatitis Research Center , National Taiwan University Hospital , Taipei , Taiwan
- Department of Internal Medicine , National Taiwan University Hospital , Taipei , Taiwan
- Graduate Institute of Clinical Medicine , National Taiwan University College of Medicine , Taipei , Taiwan
| | - Chun-Jen Liu
- Hepatitis Research Center , National Taiwan University Hospital , Taipei , Taiwan
- Department of Internal Medicine , National Taiwan University Hospital , Taipei , Taiwan
- Graduate Institute of Clinical Medicine , National Taiwan University College of Medicine , Taipei , Taiwan
| | - Jia-Horng Kao
- Hepatitis Research Center , National Taiwan University Hospital , Taipei , Taiwan
- Department of Internal Medicine , National Taiwan University Hospital , Taipei , Taiwan
- Graduate Institute of Clinical Medicine , National Taiwan University College of Medicine , Taipei , Taiwan
| | - Li-Feng Lin
- Hepatitis Research Center , National Taiwan University Hospital , Taipei , Taiwan
| | - Hui-Chu Tu
- Hepatitis Research Center , National Taiwan University Hospital , Taipei , Taiwan
| | - Chih-Chiang Wang
- Graduate Institute of Clinical Medicine , National Taiwan University College of Medicine , Taipei , Taiwan
| | - Po-Hsi Huang
- Hepatitis Research Center , National Taiwan University Hospital , Taipei , Taiwan
| | - Huei-Ru Cheng
- Graduate Institute of Clinical Medicine , National Taiwan University College of Medicine , Taipei , Taiwan
| | - Pei-Jer Chen
- Hepatitis Research Center , National Taiwan University Hospital , Taipei , Taiwan
- Department of Internal Medicine , National Taiwan University Hospital , Taipei , Taiwan
- Graduate Institute of Clinical Medicine , National Taiwan University College of Medicine , Taipei , Taiwan
| | - Ding-Shinn Chen
- Hepatitis Research Center , National Taiwan University Hospital , Taipei , Taiwan
- Department of Internal Medicine , National Taiwan University Hospital , Taipei , Taiwan
- Graduate Institute of Clinical Medicine , National Taiwan University College of Medicine , Taipei , Taiwan
- Genomics Research Center , Academia Sinica , Taipei , Taiwan
| | - Hui-Lin Wu
- Hepatitis Research Center , National Taiwan University Hospital , Taipei , Taiwan
- Graduate Institute of Clinical Medicine , National Taiwan University College of Medicine , Taipei , Taiwan
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11
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Episomes and Transposases-Utilities to Maintain Transgene Expression from Nonviral Vectors. Genes (Basel) 2022; 13:genes13101872. [PMID: 36292757 PMCID: PMC9601623 DOI: 10.3390/genes13101872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/07/2022] [Accepted: 10/14/2022] [Indexed: 11/04/2022] Open
Abstract
The efficient delivery and stable transgene expression are critical for applications in gene therapy. While carefully selected and engineered viral vectors allowed for remarkable clinical successes, they still bear significant safety risks. Thus, nonviral vectors are a sound alternative and avoid genotoxicity and adverse immunological reactions. Nonviral vector systems have been extensively studied and refined during the last decades. Emerging knowledge of the epigenetic regulation of replication and spatial chromatin organisation, as well as new technologies, such as Crispr/Cas, were employed to enhance the performance of different nonviral vector systems. Thus, nonviral vectors are in focus and hold some promising perspectives for future applications in gene therapy. This review addresses three prominent nonviral vector systems: the Sleeping Beauty transposase, S/MAR-based episomes, and viral plasmid replicon-based EBV vectors. Exemplarily, we review different utilities, modifications, and new concepts that were pursued to overcome limitations regarding stable transgene expression and mitotic stability. New insights into the nuclear localisation of nonviral vector molecules and the potential consequences thereof are highlighted. Finally, we discuss the remaining limitations and provide an outlook on possible future developments in nonviral vector technology.
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12
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Hoggard T, Hollatz AJ, Cherney RE, Seman MR, Fox CA. The Fkh1 Forkhead associated domain promotes ORC binding to a subset of DNA replication origins in budding yeast. Nucleic Acids Res 2021; 49:10207-10220. [PMID: 34095951 PMCID: PMC8501964 DOI: 10.1093/nar/gkab450] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/03/2021] [Accepted: 06/02/2021] [Indexed: 12/14/2022] Open
Abstract
The pioneer event in eukaryotic DNA replication is binding of chromosomal DNA by the origin recognitioncomplex (ORC). The ORC-DNA complex directs the formation of origins, the specific chromosomal regions where DNA synthesis initiates. In all eukaryotes, incompletely understood features of chromatin promote ORC-DNA binding. Here, we uncover a role for the Fkh1 (Forkhead homolog) protein and its forkhead associated (FHA) domain in promoting ORC-origin binding and origin activity at a subset of origins in Saccharomyces cerevisiae. Several of the FHA-dependent origins examined required a distinct Fkh1 binding site located 5′ of and proximal to their ORC sites (5′-FKH-T site). Genetic and molecular experiments provided evidence that the Fkh1-FHA domain promoted origin activity directly through Fkh1 binding to this 5′ FKH-T site. Nucleotide substitutions within two relevant origins that enhanced their ORC-DNA affinity bypassed the requirement for their 5′ FKH-T sites and for the Fkh1-FHA domain. Significantly, assessment of ORC-origin binding by ChIPSeq provided evidence that this mechanism was relevant at ∼25% of yeast origins. Thus, the FHA domain of the conserved cell-cycle transcription factor Fkh1 enhanced origin selection in yeast at the level of ORC-origin binding.
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Affiliation(s)
- Timothy Hoggard
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA
| | - Allison J Hollatz
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA.,Integrated Program in Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Rachel E Cherney
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA
| | - Melissa R Seman
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA
| | - Catherine A Fox
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA.,Integrated Program in Biochemistry, University of Wisconsin, Madison, WI 53706, USA
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13
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Liu Y, Hu Z, Zhang Y, Wang C. Long non-coding RNAs in Epstein-Barr virus-related cancer. Cancer Cell Int 2021; 21:278. [PMID: 34034760 PMCID: PMC8144696 DOI: 10.1186/s12935-021-01986-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 05/13/2021] [Indexed: 12/17/2022] Open
Abstract
Epstein Barr-virus (EBV) is related to several cancers. Long non-coding RNAs (lncRNAs) act by regulating target genes and are involved in tumourigenesis. However, the role of lncRNAs in EBV-associated cancers is rarely reported. Understanding the role and mechanism of lncRNAs in EBV-associated cancers may contribute to diagnosis, prognosis and clinical therapy in the future. EBV encodes not only miRNAs, but also BART lncRNAs during latency and the BHLF1 lncRNA during both the latent and lytic phases. These lncRNAs can be targeted regulate inflammation, invasion, and migration and thus tumourigenesis. The products of EBV also directly and indirectly regulate host lncRNAs, including LINC00312, NORAD CYTOR, SHNG8, SHNG5, MINCR, lncRNA-BC200, LINC00672, MALATI1, LINC00982, LINC02067, IGFBP7-AS1, LOC100505716, LOC100128494, NAG7 and RP4-794H19.1, to facilitate tumourigenesis using different mechanisms. Additionally, lncRNAs have been previously validated to interact with microRNAs (miRNAs), and lncRNAs and miRNAs mutually suppress each other. The EBV-miR-BART6-3p/LOC553103/STMN1 axis inhibits EBV-associated tumour cell proliferation. Additionally, H. pylori-EBV co-infection promotes inflammatory lesions and results in EMT. HPV-EBV co-infection inhibits the transition from latency to lytic replication. KSHV-EBV co-infection aggravates tumourigenesis in huNSG mice. COVID-19-EBV co-infection may activate the immune system to destroy a tumour, although this situation is rare and the mechanism requires further confirmation. Hopefully, this information will shed some light on tumour therapy strategies tumourigenesis. Additionally, this strategy benefits for infected patients by preventing latency to lytic replication. Understanding the role and expression of lnRNAs in these two phases of EBV is critical to control the transition from latency to the lytic replication phase. This review presents differential expressed lncRNAs in EBV-associated cancers and provides resources to aid in developing superior strategies for clinical therapy.
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Affiliation(s)
- Yitong Liu
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, 28 West Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China
| | - Zhizhong Hu
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, 28 West Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China
| | - Yang Zhang
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, 28 West Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China.
| | - Chengkun Wang
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, 28 West Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China.
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14
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Dheekollu J, Wiedmer A, Ayyanathan K, Deakyne JS, Messick TE, Lieberman PM. Cell-cycle-dependent EBNA1-DNA crosslinking promotes replication termination at oriP and viral episome maintenance. Cell 2021; 184:643-654.e13. [PMID: 33482082 DOI: 10.1016/j.cell.2020.12.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 10/17/2020] [Accepted: 12/15/2020] [Indexed: 02/08/2023]
Abstract
Epstein-Barr virus (EBV) is an oncogenic human herpesvirus that persists as a multicopy episome in proliferating host cells. Episome maintenance is strictly dependent on EBNA1, a sequence-specific DNA-binding protein with no known enzymatic activities. Here, we show that EBNA1 forms a cell cycle-dependent DNA crosslink with the EBV origin of plasmid replication oriP. EBNA1 tyrosine 518 (Y518) is essential for crosslinking to oriP and functionally required for episome maintenance and generation of EBV-transformed lymphoblastoid cell lines (LCLs). Mechanistically, Y518 is required for replication fork termination at oriP in vivo and for formation of SDS-resistant complexes in vitro. EBNA1-DNA crosslinking corresponds to single-strand endonuclease activity specific to DNA structures enriched at replication-termination sites, such as 4-way junctions. These findings reveal that EBNA1 forms tyrosine-dependent DNA-protein crosslinks and single-strand cleavage at oriP required for replication termination and viral episome maintenance.
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15
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Hau PM, Lung HL, Wu M, Tsang CM, Wong KL, Mak NK, Lo KW. Targeting Epstein-Barr Virus in Nasopharyngeal Carcinoma. Front Oncol 2020; 10:600. [PMID: 32528868 PMCID: PMC7247807 DOI: 10.3389/fonc.2020.00600] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 04/01/2020] [Indexed: 12/11/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) is consistently associated with Epstein-Barr virus (EBV) infection in regions in which it is endemic, including Southern China and Southeast Asia. The high mortality rates of NPC patients with advanced and recurrent disease highlight the urgent need for effective treatments. While recent genomic studies have revealed few druggable targets, the unique interaction between the EBV infection and host cells in NPC strongly implies that targeting EBV may be an efficient approach to cure this virus-associated cancer. Key features of EBV-associated NPC are the persistence of an episomal EBV genome and the requirement for multiple viral latent gene products to enable malignant transformation. Many translational studies have been conducted to exploit these unique features to develop pharmaceutical agents and therapeutic strategies that target EBV latent proteins and induce lytic reactivation in NPC. In particular, inhibitors of the EBV latent protein EBNA1 have been intensively explored, because of this protein's essential roles in maintaining EBV latency and viral genome replication in NPC cells. In addition, recent advances in chemical bioengineering are driving the development of therapeutic agents targeting the critical functional regions of EBNA1. Promising therapeutic effects of the resulting EBNA1-specific inhibitors have been shown in EBV-positive NPC tumors. The efficacy of multiple classes of EBV lytic inducers for NPC cytolytic therapy has also been long investigated. However, the lytic-induction efficiency of these compounds varies among different EBV-positive NPC models in a cell-context-dependent manner. In each tumor, NPC cells can evolve and acquire somatic changes to maintain EBV latency during cancer progression. Unfortunately, the poor understanding of the cellular mechanisms regulating EBV latency-to-lytic switching in NPC cells limits the clinical application of EBV cytolytic treatment. In this review, we discuss the potential approaches for improvement of the above-mentioned EBV-targeting strategies.
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Affiliation(s)
- Pok Man Hau
- Department of Anatomical & Cellular Pathology and State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - Hong Lok Lung
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Man Wu
- Department of Anatomical & Cellular Pathology and State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - Chi Man Tsang
- Department of Anatomical & Cellular Pathology and State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ka-Leung Wong
- Department of Chemistry, Hong Kong Baptist University, Hong Kong, China
| | - Nai Ki Mak
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Kwok Wai Lo
- Department of Anatomical & Cellular Pathology and State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China
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16
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Wang Z, Zhu T, Ma W, Fan E, Lu N, Ouyang F, Wang N, Yang G, Kong L, Qu G, Zhang S, Wang J. Potential function of CbuSPL and gene encoding its interacting protein during flowering in Catalpa bungei. BMC PLANT BIOLOGY 2020; 20:105. [PMID: 32143577 PMCID: PMC7060540 DOI: 10.1186/s12870-020-2303-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 02/24/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND "Bairihua", a variety of the Catalpa bungei, has a large amount of flowers and a long flowering period which make it an excellent material for flowering researches in trees. SPL is one of the hub genes that regulate both flowering transition and development. RESULTS SPL homologues CbuSPL9 was cloned using degenerate primers with RACE. Expression studies during flowering transition in "Bairihua" and ectopic expression in Arabidopsis showed that CbuSPL9 was functional similarly with its Arabidopsis homologues. In the next step, we used Y2H to identify the proteins that could interact with CbuSPL9. HMGA, an architectural transcriptional factor, was identified and cloned for further research. BiFC and BLI showed that CbuSPL9 could form a heterodimer with CbuHMGA in the nucleus. The expression analysis showed that CbuHMGA had a similar expression trend to that of CbuSPL9 during flowering in "Bairihua". Intriguingly, ectopic expression of CbuHMGA in Arabidopsis would lead to aberrant flowers, but did not effect flowering time. CONCLUSIONS Our results implied a novel pathway that CbuSPL9 regulated flowering development, but not flowering transition, with the participation of CbuHMGA. Further investments need to be done to verify the details of this pathway.
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Affiliation(s)
- Zhi Wang
- Present address: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Tianqing Zhu
- Present address: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Wenjun Ma
- Present address: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Erqin Fan
- Present address: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
- Present address: State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040 People’s Republic of China
| | - Nan Lu
- Present address: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Fangqun Ouyang
- Present address: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Nan Wang
- Present address: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Guijuan Yang
- Present address: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Lisheng Kong
- Present address: Department of Biology Centre for Forest Biology, University of Victoria, Victoria 11, BC Canada
| | - Guanzheng Qu
- Present address: State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040 People’s Republic of China
| | - Shougong Zhang
- Present address: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
| | - Junhui Wang
- Present address: State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 People’s Republic of China
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17
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Kim KD, Tanizawa H, De Leo A, Vladimirova O, Kossenkov A, Lu F, Showe LC, Noma KI, Lieberman PM. Epigenetic specifications of host chromosome docking sites for latent Epstein-Barr virus. Nat Commun 2020; 11:877. [PMID: 32054837 PMCID: PMC7018943 DOI: 10.1038/s41467-019-14152-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 12/07/2019] [Indexed: 12/12/2022] Open
Abstract
Epstein-Barr virus (EBV) genomes persist in latently infected cells as extrachromosomal episomes that attach to host chromosomes through the tethering functions of EBNA1, a viral encoded sequence-specific DNA binding protein. Here we employ circular chromosome conformation capture (4C) analysis to identify genome-wide associations between EBV episomes and host chromosomes. We find that EBV episomes in Burkitt's lymphoma cells preferentially associate with cellular genomic sites containing EBNA1 binding sites enriched with B-cell factors EBF1 and RBP-jK, the repressive histone mark H3K9me3, and AT-rich flanking sequence. These attachment sites correspond to transcriptionally silenced genes with GO enrichment for neuronal function and protein kinase A pathways. Depletion of EBNA1 leads to a transcriptional de-repression of silenced genes and reduction in H3K9me3. EBV attachment sites in lymphoblastoid cells with different latency type show different correlations, suggesting that host chromosome attachment sites are functionally linked to latency type gene expression programs.
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MESH Headings
- Attachment Sites, Microbiological/genetics
- Attachment Sites, Microbiological/physiology
- Burkitt Lymphoma/genetics
- Burkitt Lymphoma/virology
- Cell Line, Tumor
- Chromosomes, Human/genetics
- Chromosomes, Human/virology
- Epigenesis, Genetic
- Epstein-Barr Virus Nuclear Antigens/physiology
- Herpesvirus 4, Human/genetics
- Herpesvirus 4, Human/pathogenicity
- Herpesvirus 4, Human/physiology
- Host Microbial Interactions/genetics
- Host Microbial Interactions/physiology
- Humans
- Models, Biological
- Plasmids/genetics
- Virus Latency/genetics
- Virus Latency/physiology
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Affiliation(s)
- Kyoung-Dong Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Korea
| | - Hideki Tanizawa
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403, USA
| | - Alessandra De Leo
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19146, USA
| | - Olga Vladimirova
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19146, USA
| | - Andrew Kossenkov
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19146, USA
| | - Fang Lu
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19146, USA
| | - Louise C Showe
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19146, USA
| | - Ken-Ichi Noma
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403, USA
| | - Paul M Lieberman
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19146, USA.
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18
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Abstract
Persistent viral infections require a host cell reservoir that maintains functional copies of the viral genome. To this end, several DNA viruses maintain their genomes as extrachromosomal DNA minichromosomes in actively dividing cells. These viruses typically encode a viral protein that binds specifically to viral DNA genomes and tethers them to host mitotic chromosomes, thus enabling the viral genomes to hitchhike or piggyback into daughter cells. Viruses that use this tethering mechanism include papillomaviruses and the gammaherpesviruses Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus. This review describes the advantages and consequences of persistent extrachromosomal viral genome replication.
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Affiliation(s)
- Tami L Coursey
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA;
| | - Alison A McBride
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA;
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19
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Boldogkői Z, Balázs Z, Moldován N, Prazsák I, Tombácz D. Novel classes of replication-associated transcripts discovered in viruses. RNA Biol 2019; 16:166-175. [PMID: 30608222 PMCID: PMC6380287 DOI: 10.1080/15476286.2018.1564468] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The role of RNA molecules in the priming of DNA replication and in providing a template for telomerase extension has been known for decades. Since then, several transcripts have been discovered, which play diverse roles in governing replication, including regulation of RNA primer formation, the recruitment of replication origin (Ori) recognition complex, and the assembly of replication fork. Recent studies on viral transcriptomes have revealed novel classes of replication-associated (ra)RNAs, which are expressed from the genomic locations in close vicinity to the Ori. Many of them overlap the Ori, whereas others are terminated close to the replication origin. These novel transcripts can be both protein-coding and non-coding RNAs. The Ori-overlapping part of the mRNAs is generally either the 5ʹ-untranslated regions (UTRs), or the 3ʹ-UTRs of the longer isoforms. Several raRNAs have been identified in various viral families using primarily third-generation long-read sequencing. Hyper-editing of these transcripts has also been described.
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Affiliation(s)
- Zsolt Boldogkői
- a Department of Medical Biology, Faculty of Medicine , University of Szeged , Szeged , Hungary
| | - Zsolt Balázs
- a Department of Medical Biology, Faculty of Medicine , University of Szeged , Szeged , Hungary
| | - Norbert Moldován
- a Department of Medical Biology, Faculty of Medicine , University of Szeged , Szeged , Hungary
| | - István Prazsák
- a Department of Medical Biology, Faculty of Medicine , University of Szeged , Szeged , Hungary
| | - Dóra Tombácz
- a Department of Medical Biology, Faculty of Medicine , University of Szeged , Szeged , Hungary
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EBNA1: Oncogenic Activity, Immune Evasion and Biochemical Functions Provide Targets for Novel Therapeutic Strategies against Epstein-Barr Virus- Associated Cancers. Cancers (Basel) 2018; 10:cancers10040109. [PMID: 29642420 PMCID: PMC5923364 DOI: 10.3390/cancers10040109] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 03/26/2018] [Accepted: 03/29/2018] [Indexed: 12/12/2022] Open
Abstract
The presence of the Epstein-Barr virus (EBV)-encoded nuclear antigen-1 (EBNA1) protein in all EBV-carrying tumours constitutes a marker that distinguishes the virus-associated cancer cells from normal cells and thereby offers opportunities for targeted therapeutic intervention. EBNA1 is essential for viral genome maintenance and also for controlling viral gene expression and without EBNA1, the virus cannot persist. EBNA1 itself has been linked to cell transformation but the underlying mechanism of its oncogenic activity has been unclear. However, recent data are starting to shed light on its growth-promoting pathways, suggesting that targeting EBNA1 can have a direct growth suppressing effect. In order to carry out its tasks, EBNA1 interacts with cellular factors and these interactions are potential therapeutic targets, where the aim would be to cripple the virus and thereby rid the tumour cells of any oncogenic activity related to the virus. Another strategy to target EBNA1 is to interfere with its expression. Controlling the rate of EBNA1 synthesis is critical for the virus to maintain a sufficient level to support viral functions, while at the same time, restricting expression is equally important to prevent the immune system from detecting and destroying EBNA1-positive cells. To achieve this balance EBNA1 has evolved a unique repeat sequence of glycines and alanines that controls its own rate of mRNA translation. As the underlying molecular mechanisms for how this repeat suppresses its own rate of synthesis in cis are starting to be better understood, new therapeutic strategies are emerging that aim to modulate the translation of the EBNA1 mRNA. If translation is induced, it could increase the amount of EBNA1-derived antigenic peptides that are presented to the major histocompatibility (MHC) class I pathway and thus, make EBV-carrying cancers better targets for the immune system. If translation is further suppressed, this would provide another means to cripple the virus.
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Kaposi's Sarcoma-Associated Herpesvirus K8 Is an RNA Binding Protein That Regulates Viral DNA Replication in Coordination with a Noncoding RNA. J Virol 2018; 92:JVI.02177-17. [PMID: 29321307 DOI: 10.1128/jvi.02177-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 01/03/2018] [Indexed: 12/16/2022] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) lytic replication and constant primary infection of fresh cells are crucial for viral tumorigenicity. The virus-encoded bZIP family protein K8 plays an important role in viral DNA replication in both viral reactivation and de novo infection. The mechanism underlying the functional role of K8 in the viral life cycle is elusive. Here, we report that K8 is an RNA binding protein that also associates with many other proteins, including other RNA binding proteins. Many protein-protein interactions involving K8 are mediated by RNA. Using a UV cross-linking and immunoprecipitation (CLIP) procedure combined with high-throughput sequencing, RNAs that are associated with K8 in BCBL-1 cells were identified, including both viral (PAN, T1.4, T0.7, etc.) and cellular (MALAT-1, MRP, 7SK, etc.) RNAs. An RNA binding motif in K8 was defined, and mutation of the motif abolished the ability of K8 to bind to many noncoding RNAs, as well as viral DNA replication during de novo infection, suggesting that the K8 functions in viral replication are carried out through RNA association. The functions of K8 and associated T1.4 RNA were investigated in detail, and the results showed that T1.4 mediates the binding of K8 to ori-Lyt DNA. The T1.4-K8 complex physically bound to KSHV ori-Lyt DNA and recruited other proteins and cofactors to assemble a replication complex. Depletion of T1.4 abolished DNA replication in primary infection. These findings provide mechanistic insights into the role of K8 in coordination with T1.4 RNA in regulating KSHV DNA replication during de novo infection.IMPORTANCE Genomewide analyses of the mammalian transcriptome revealed that a large proportion of sequence previously annotated as noncoding regions is actually transcribed and gives rise to stable RNAs. The emergence of a large number of noncoding RNAs suggests that functional RNA-protein complexes, e.g., ribosomes or spliceosomes, are not ancient relics of the last ribo-organism but would be well adapted to a regulatory role in biology. K8 has been puzzling because of its unique characteristics, such as multiple regulatory roles in gene expression and DNA replication without DNA binding capability. This study reveals the mechanism underlying its regulatory role by demonstrating that K8 is an RNA binding protein that binds to DNA and initiates DNA replication in coordination with a noncoding RNA. It is suggested that many K8 functions, if not all, are carried out through its associated RNAs.
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Popova VV, Brechalov AV, Georgieva SG, Kopytova DV. Nonreplicative functions of the origin recognition complex. Nucleus 2018; 9:460-473. [PMID: 30196754 PMCID: PMC6244734 DOI: 10.1080/19491034.2018.1516484] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 08/04/2018] [Accepted: 08/16/2018] [Indexed: 12/14/2022] Open
Abstract
Origin recognition complex (ORC), a heteromeric six-subunit complex, is the central component of the eukaryotic pre-replication complex. Recent data from yeast, frogs, flies and mammals present compelling evidence that ORC and its individual subunits have nonreplicative functions as well. The majority of these functions, such as heterochromatin formation, chromosome condensation, and segregation are dependent on ORC-DNA interactions. Furthermore, ORC is involved in the control of cell division via its participation in centrosome duplication and cytokinesis. Recent findings have also demonstrated a direct interaction between ORC and mRNPs and highlighted an essential role of ORC in mRNA nuclear export. Along with the growth of evolutionary complexity of organisms, ORC complex functions become more elaborate and new functions of the ORC sub-complexes and individual subunits have emerged.
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Affiliation(s)
- Varvara V. Popova
- Department of Transcription Regulation and Chromatin Dynamics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander V. Brechalov
- Department of Transcription Regulation and Chromatin Dynamics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sofia G. Georgieva
- Department of Transcription Regulation and Chromatin Dynamics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Daria V. Kopytova
- Department of Transcription Regulation and Chromatin Dynamics, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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Cheung CHY, Hsu CL, Chen KP, Chong ST, Wu CH, Huang HC, Juan HF. MCM2-regulated functional networks in lung cancer by multi-dimensional proteomic approach. Sci Rep 2017; 7:13302. [PMID: 29038488 PMCID: PMC5643318 DOI: 10.1038/s41598-017-13440-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 09/25/2017] [Indexed: 12/17/2022] Open
Abstract
DNA replication control is vital for maintaining genome stability and the cell cycle, perhaps most notably during cell division. Malignancies often exhibit defective minichromosome maintenance protein 2 (MCM2), a cancer proliferation biomarker that serves as a licensing factor in the initiation of DNA replication. MCM2 is also known to be one of the ATPase active sites that facilitates conformational changes and drives DNA unwinding at the origin of DNA replication. However, the biological networks of MCM2 in lung cancer cells via protein phosphorylation remain unmapped. The RNA-seq datasets from The Cancer Genome Atlas (TCGA) revealed that MCM2 overexpression is correlated with poor survival rate in lung cancer patients. To uncover MCM2-regulated functional networks in lung cancer, we performed multi-dimensional proteomic approach by integrating analysis of the phosphoproteome and proteome, and identified a total of 2361 phosphorylation sites on 753 phosphoproteins, and 4672 proteins. We found that the deregulation of MCM2 is involved in lung cancer cell proliferation, the cell cycle, and migration. Furthermore, HMGA1S99 phosphorylation was found to be differentially expressed under MCM2 perturbation in opposite directions, and plays an important role in regulating lung cancer cell proliferation. This study therefore enhances our capacity to therapeutically target cancer-specific phosphoproteins.
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Affiliation(s)
- Chantal Hoi Yin Cheung
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Chia-Lang Hsu
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Kai-Pu Chen
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 10617, Taiwan
| | - Siao-Ting Chong
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Chang-Hsun Wu
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Hsuan-Cheng Huang
- Institute of Biomedical Informatics, Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei, 11221, Taiwan.
| | - Hsueh-Fen Juan
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, 10617, Taiwan. .,Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan. .,Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 10617, Taiwan.
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24
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Ayoubian H, Fröhlich T, Pogodski D, Flatley A, Kremmer E, Schepers A, Feederle R, Arnold GJ, Grässer FA. Antibodies against the mono-methylated arginine-glycine repeat (MMA-RG) of the Epstein-Barr virus nuclear antigen 2 (EBNA2) identify potential cellular proteins targeted in viral transformation. J Gen Virol 2017; 98:2128-2142. [PMID: 28758620 DOI: 10.1099/jgv.0.000870] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The Epstein-Barr virus is a human herpes virus with oncogenic potential. The virus-encoded nuclear antigen 2 (EBNA2) is a key mediator of viral tumorigenesis. EBNA2 features an arginine-glycine (RG) repeat at amino acids (aa)339-354 that is essential for the transformation of lymphocytes and contains symmetrically (SDMA) and asymmetrically (ADMA) di-methylated arginine residues. The SDMA-modified EBNA2 binds the survival motor neuron protein (SMN), thus mimicking SMD3, a cellular SDMA-containing protein that interacts with SMN. Accordingly, a monoclonal antibody (mAb) specific for the SDMA-modified RG repeat of EBNA2 also binds to SMD3. With the novel mAb 19D4 we now show that EBNA2 contains mono-methylated arginine (MMA) residues within the RG repeat. Using 19D4, we immune-precipitated and analysed by mass spectrometry cellular proteins in EBV-transformed B-cells that feature MMA motifs that are similar to the one in EBNA2. Among the cellular proteins identified, we confirmed by immunoprecipitation and/or Western blot analyses Aly/REF, Coilin, DDX5, FXR1, HNRNPK, LSM4, MRE11, NRIP, nucleolin, PRPF8, RBM26, SMD1 (SNRDP1) and THRAP3 proteins that are either known to contain MMA residues or feature RG repeat sequences that probably serve as methylation substrates. The identified proteins are involved in splicing, tumorigenesis, transcriptional activation, DNA stability and RNA processing or export. Furthermore, we found that several proteins involved in energy metabolism are associated with MMA-modified proteins. Interestingly, the viral EBNA1 protein that features methylated RG repeat motifs also reacted with the antibodies. Our results indicate that the region between aa 34-52 of EBNA1 contains ADMA or SDMA residues, while the region between aa 328-377 mainly contains MMA residues.
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Affiliation(s)
- Hiresh Ayoubian
- Institute of Virology, Saarland University Medical School, Kirrbergerstrasse, Haus 47, D-66421 Homburg/Saar, Germany
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Strasse 25, 81377, Munich, Germany
| | - Dagmar Pogodski
- Institute of Virology, Saarland University Medical School, Kirrbergerstrasse, Haus 47, D-66421 Homburg/Saar, Germany
| | - Andrew Flatley
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchioninistrasse 25, 81377 Munich, Germany
| | - Elisabeth Kremmer
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchioninistrasse 25, 81377 Munich, Germany
| | - Aloys Schepers
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchioninistrasse 25, 81377 Munich, Germany
| | - Regina Feederle
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchioninistrasse 25, 81377 Munich, Germany
| | - Georg J Arnold
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Strasse 25, 81377, Munich, Germany
| | - Friedrich A Grässer
- Institute of Virology, Saarland University Medical School, Kirrbergerstrasse, Haus 47, D-66421 Homburg/Saar, Germany
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Kheir E, Krude T. Non-coding Y RNAs associate with early replicating euchromatin in concordance with the origin recognition complex. J Cell Sci 2017; 130:1239-1250. [PMID: 28235841 DOI: 10.1242/jcs.197566] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 02/13/2017] [Indexed: 12/18/2022] Open
Abstract
Non-coding Y RNAs are essential for the initiation of chromosomal DNA replication in vertebrates, yet their association with chromatin during the cell cycle is not characterised. Here, we quantify human Y RNA levels in soluble and chromatin-associated intracellular fractions and investigate, topographically, their dynamic association with chromatin during the cell cycle. We find that, on average, about a million Y RNA molecules are present in the soluble fraction of a proliferating cell, and 5-10-fold less are in association with chromatin. These levels decrease substantially during quiescence. No significant differences are apparent between cancer and non-cancer cell lines. Y RNAs associate with euchromatin throughout the cell cycle. Their levels are 2-4-fold higher in S phase than in G1 phase or mitosis. Y RNAs are not detectable at active DNA replication foci, and re-associate with replicated euchromatin during mid and late S phase. The dynamics and sites of Y1 RNA association with chromatin are in concordance with those of the origin recognition complex (ORC). Our data therefore suggest a functional role of Y RNAs in a common pathway with ORC.
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Affiliation(s)
- Eyemen Kheir
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Torsten Krude
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
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26
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Ravoitytė B, Wellinger RE. Non-Canonical Replication Initiation: You're Fired! Genes (Basel) 2017; 8:genes8020054. [PMID: 28134821 PMCID: PMC5333043 DOI: 10.3390/genes8020054] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 01/19/2017] [Indexed: 12/25/2022] Open
Abstract
The division of prokaryotic and eukaryotic cells produces two cells that inherit a perfect copy of the genetic material originally derived from the mother cell. The initiation of canonical DNA replication must be coordinated to the cell cycle to ensure the accuracy of genome duplication. Controlled replication initiation depends on a complex interplay of cis-acting DNA sequences, the so-called origins of replication (ori), with trans-acting factors involved in the onset of DNA synthesis. The interplay of cis-acting elements and trans-acting factors ensures that cells initiate replication at sequence-specific sites only once, and in a timely order, to avoid chromosomal endoreplication. However, chromosome breakage and excessive RNA:DNA hybrid formation can cause break-induced (BIR) or transcription-initiated replication (TIR), respectively. These non-canonical replication events are expected to affect eukaryotic genome function and maintenance, and could be important for genome evolution and disease development. In this review, we describe the difference between canonical and non-canonical DNA replication, and focus on mechanistic differences and common features between BIR and TIR. Finally, we discuss open issues on the factors and molecular mechanisms involved in TIR.
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Affiliation(s)
- Bazilė Ravoitytė
- Nature Research Centre, Akademijos g. 2, LT-08412 Vilnius, Lithuania.
| | - Ralf Erik Wellinger
- CABIMER-Universidad de Sevilla, Avd Americo Vespucio sn, 41092 Sevilla, Spain.
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27
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Uzcanga G, Lara E, Gutiérrez F, Beaty D, Beske T, Teran R, Navarro JC, Pasero P, Benítez W, Poveda A. Nuclear DNA replication and repair in parasites of the genus Leishmania: Exploiting differences to develop innovative therapeutic approaches. Crit Rev Microbiol 2016; 43:156-177. [PMID: 27960617 DOI: 10.1080/1040841x.2016.1188758] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Leishmaniasis is a common tropical disease that affects mainly poor people in underdeveloped and developing countries. This largely neglected infection is caused by Leishmania spp, a parasite from the Trypanosomatidae family. This parasitic disease has different clinical manifestations, ranging from localized cutaneous to more harmful visceral forms. The main limitations of the current treatments are their high cost, toxicity, lack of specificity, and long duration. Efforts to improve treatments are necessary to deal with this infectious disease. Many approved drugs to combat diseases as diverse as cancer, bacterial, or viral infections take advantage of specific features of the causing agent or of the disease. Recent evidence indicates that the specific characteristics of the Trypanosomatidae replication and repair machineries could be used as possible targets for the development of new treatments. Here, we review in detail the molecular mechanisms of DNA replication and repair regulation in trypanosomatids of the genus Leishmania and the drugs that could be useful against this disease.
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Affiliation(s)
- Graciela Uzcanga
- a Centro Internacional de Zoonosis, Facultad de Ciencias Químicas, Facultad de Medicina Veterinaria , Universidad Central del Ecuador , Quito , Ecuador.,b Programa Prometeo , SENESCYT, Whymper E7-37 y Alpallana, Quito , Ecuador.,c Facultad de Ciencias Naturales y Ambientales, Universidad Internacional SEK Calle Alberto Einstein sn y 5ta transversal , Quito , Ecuador.,d Fundación Instituto de Estudios Avanzados-IDEA , Caracas , Venezuela
| | - Eliana Lara
- a Centro Internacional de Zoonosis, Facultad de Ciencias Químicas, Facultad de Medicina Veterinaria , Universidad Central del Ecuador , Quito , Ecuador.,e Institute of Human Genetics , CNRS UPR 1142, 141 rue de la Cardonille, Equipe Labellisée Ligue Contre le Cancer , Montpellier cedex 5 , France
| | - Fernanda Gutiérrez
- a Centro Internacional de Zoonosis, Facultad de Ciencias Químicas, Facultad de Medicina Veterinaria , Universidad Central del Ecuador , Quito , Ecuador
| | - Doyle Beaty
- a Centro Internacional de Zoonosis, Facultad de Ciencias Químicas, Facultad de Medicina Veterinaria , Universidad Central del Ecuador , Quito , Ecuador
| | - Timo Beske
- a Centro Internacional de Zoonosis, Facultad de Ciencias Químicas, Facultad de Medicina Veterinaria , Universidad Central del Ecuador , Quito , Ecuador
| | - Rommy Teran
- a Centro Internacional de Zoonosis, Facultad de Ciencias Químicas, Facultad de Medicina Veterinaria , Universidad Central del Ecuador , Quito , Ecuador
| | - Juan-Carlos Navarro
- a Centro Internacional de Zoonosis, Facultad de Ciencias Químicas, Facultad de Medicina Veterinaria , Universidad Central del Ecuador , Quito , Ecuador.,f Universidad Central de Venezuela, Instituto de Zoología y Ecología Tropical , Caracas , Venezuela.,g Facultad de Ciencias Naturales y Ambientales, Universidad Internacional SEK, Calle Alberto Einstein sn y 5ta transversal , Quito , Ecuador
| | - Philippe Pasero
- e Institute of Human Genetics , CNRS UPR 1142, 141 rue de la Cardonille, Equipe Labellisée Ligue Contre le Cancer , Montpellier cedex 5 , France
| | - Washington Benítez
- a Centro Internacional de Zoonosis, Facultad de Ciencias Químicas, Facultad de Medicina Veterinaria , Universidad Central del Ecuador , Quito , Ecuador
| | - Ana Poveda
- a Centro Internacional de Zoonosis, Facultad de Ciencias Químicas, Facultad de Medicina Veterinaria , Universidad Central del Ecuador , Quito , Ecuador
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28
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HCF1 and OCT2 Cooperate with EBNA1 To Enhance OriP-Dependent Transcription and Episome Maintenance of Latent Epstein-Barr Virus. J Virol 2016; 90:5353-5367. [PMID: 27009953 PMCID: PMC4934754 DOI: 10.1128/jvi.00239-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/11/2016] [Indexed: 12/14/2022] Open
Abstract
Epstein-Barr virus (EBV) establishes latent infections as multicopy episomes with complex patterns of viral gene transcription and chromatin structure. The EBV origin of plasmid replication (OriP) has been implicated as a critical control element for viral transcription, as well as viral DNA replication and episome maintenance. Here, we examine cellular factors that bind OriP and regulate histone modification, transcription regulation, and episome maintenance. We found that OriP is enriched for histone H3 lysine 4 (H3K4) methylation in multiple cell types and latency types. Host cell factor 1 (HCF1), a component of the mixed-lineage leukemia (MLL) histone methyltransferase complex, and transcription factor OCT2 (octamer-binding transcription factor 2) bound cooperatively with EBNA1 (Epstein-Barr virus nuclear antigen 1) at OriP. Depletion of OCT2 or HCF1 deregulated latency transcription and histone modifications at OriP, as well as the OriP-regulated latency type-dependent C promoter (Cp) and Q promoter (Qp). HCF1 depletion led to a loss of histone H3K4me3 (trimethylation of histone H3 at lysine 4) and H3 acetylation at Cp in type III latency and Qp in type I latency, as well as an increase in heterochromatic H3K9me3 at these sites. HCF1 depletion resulted in the loss of EBV episomes from Burkitt's lymphoma cells with type I latency and reactivation from lymphoblastoid cells (LCLs) with type III latency. These findings indicate that HCF1 and OCT2 function at OriP to regulate viral transcription, histone modifications, and episome maintenance. As HCF1 is best known for its function in herpes simplex virus 1 (HSV-1) immediate early gene transcription, our findings suggest that EBV latency transcription shares unexpected features with HSV gene regulation. IMPORTANCE EBV latency is associated with several human cancers. Viral latent cycle gene expression is regulated by the epigenetic control of the OriP enhancer region. Here, we show that cellular factors OCT2 and HCF1 bind OriP in association with EBNA1 to maintain elevated histone H3K4me3 and transcriptional enhancer function. HCF1 is known as a transcriptional coactivator of herpes simplex virus (HSV) immediate early (IE) transcription, suggesting that OriP enhancer shares aspects of HSV IE transcription control.
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29
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Kopytova D, Popova V, Kurshakova M, Shidlovskii Y, Nabirochkina E, Brechalov A, Georgiev G, Georgieva S. ORC interacts with THSC/TREX-2 and its subunits promote Nxf1 association with mRNP and mRNA export in Drosophila. Nucleic Acids Res 2016; 44:4920-33. [PMID: 27016737 PMCID: PMC4889942 DOI: 10.1093/nar/gkw192] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 03/11/2016] [Indexed: 12/20/2022] Open
Abstract
The origin recognition complex (ORC) of eukaryotes associates with the replication origins and initiates the pre-replication complex assembly. In the literature, there are several reports of interaction of ORC with different RNAs. Here, we demonstrate for the first time a direct interaction of ORC with the THSC/TREX-2 mRNA nuclear export complex. The THSC/TREX-2 was purified from the Drosophila embryonic extract and found to bind with a fraction of the ORC. This interaction occurred via several subunits and was essential for Drosophila viability. Also, ORC was associated with mRNP, which was facilitated by TREX-2. ORC subunits interacted with the Nxf1 receptor mediating the bulk mRNA export. The knockdown of Orc5 led to a drop in the Nxf1 association with mRNP, while Orc3 knockdown increased the level of mRNP-bound Nxf1. The knockdown of Orc5, Orc3 and several other ORC subunits led to an accumulation of mRNA in the nucleus, suggesting that ORC participates in the regulation of the mRNP export.
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Affiliation(s)
- Daria Kopytova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Varvara Popova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Maria Kurshakova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Yulii Shidlovskii
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Elena Nabirochkina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Alexander Brechalov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Georgii Georgiev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Sofia Georgieva
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
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30
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Abstract
DNA replication begins with the assembly of pre-replication complexes (pre-RCs) at thousands of DNA replication origins during the G1 phase of the cell cycle. At the G1-S-phase transition, pre-RCs are converted into pre-initiation complexes, in which the replicative helicase is activated, leading to DNA unwinding and initiation of DNA synthesis. However, only a subset of origins are activated during any S phase. Recent insights into the mechanisms underlying this choice reveal how flexibility in origin usage and temporal activation are linked to chromosome structure and organization, cell growth and differentiation, and replication stress.
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31
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Chakravorty A, Sugden B. The AT-hook DNA binding ability of the Epstein Barr virus EBNA1 protein is necessary for the maintenance of viral genomes in latently infected cells. Virology 2015; 484:251-258. [PMID: 26122471 DOI: 10.1016/j.virol.2015.05.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 04/02/2015] [Accepted: 05/20/2015] [Indexed: 02/01/2023]
Abstract
Epstein Barr Virus (EBV) is a human tumor virus that is causally linked to malignancies such as Burkitt׳s lymphoma, and gastric and nasopharyngeal carcinomas. Tethering of EBV genomes to cellular chromosomes is required for the synthesis and persistence of viral plasmids in tumor cells. However, it is not established how EBV genomes are tethered to cellular chromosomes. We test the hypothesis that the viral protein EBNA1 tethers EBV genomes to chromosomes specifically through its N-terminal AT-hook DNA-binding domains by using a small molecule, netropsin, that has been shown to inhibit the AT-hook DNA-binding of EBNA1 in vitro. We show that netropsin forces the loss of EBV genomes from epithelial and lymphoid cells in an AT-hook dependent manner and that EBV-positive lymphoma cells are significantly more inhibited in their growth by netropsin than are corresponding EBV-negative cells.
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Affiliation(s)
- Adityarup Chakravorty
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, United States
| | - Bill Sugden
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, United States.
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32
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Kowalski MP, Baylis HA, Krude T. Non-coding stem-bulge RNAs are required for cell proliferation and embryonic development in C. elegans. J Cell Sci 2015; 128:2118-29. [PMID: 25908866 PMCID: PMC4450293 DOI: 10.1242/jcs.166744] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 04/06/2015] [Indexed: 12/21/2022] Open
Abstract
Stem bulge RNAs (sbRNAs) are a family of small non-coding stem-loop RNAs present in Caenorhabditis elegans and other nematodes, the function of which is unknown. Here, we report the first functional characterisation of nematode sbRNAs. We demonstrate that sbRNAs from a range of nematode species are able to reconstitute the initiation of chromosomal DNA replication in the presence of replication proteins in vitro, and that conserved nucleotide sequence motifs are essential for this function. By functionally inactivating sbRNAs with antisense morpholino oligonucleotides, we show that sbRNAs are required for S phase progression, early embryonic development and the viability of C. elegans in vivo. Thus, we demonstrate a new and essential role for sbRNAs during the early development of C. elegans. sbRNAs show limited nucleotide sequence similarity to vertebrate Y RNAs, which are also essential for the initiation of DNA replication. Our results therefore establish that the essential function of small non-coding stem-loop RNAs during DNA replication extends beyond vertebrates.
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Affiliation(s)
- Madzia P Kowalski
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Howard A Baylis
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Torsten Krude
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
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Lombraña R, Almeida R, Álvarez A, Gómez M. R-loops and initiation of DNA replication in human cells: a missing link? Front Genet 2015; 6:158. [PMID: 25972891 PMCID: PMC4412123 DOI: 10.3389/fgene.2015.00158] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 04/08/2015] [Indexed: 11/13/2022] Open
Abstract
The unanticipated widespread occurrence of stable hybrid DNA/RNA structures (R-loops) in human cells and the increasing evidence of their involvement in several human malignancies have invigorated the research on R-loop biology in recent years. Here we propose that physiological R-loop formation at CpG island promoters can contribute to DNA replication origin specification at these regions, the most efficient replication initiation sites in mammalian cells. Quite likely, this occurs by the strand-displacement reaction activating the formation of G-quadruplex structures that target the origin recognition complex (ORC) in the single-stranded conformation. In agreement with this, we found that R-loops co-localize with the ORC within the same CpG island region in a significant fraction of these efficient replication origins, precisely at the position displaying the highest density of G4 motifs. This scenario builds on the connection between transcription and replication in human cells and suggests that R-loop dysregulation at CpG island promoter-origins might contribute to the phenotype of DNA replication abnormalities and loss of genome integrity detected in cancer cells.
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Affiliation(s)
- Rodrigo Lombraña
- Functional Organization of the Genome Group, Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid , Madrid, Spain
| | - Ricardo Almeida
- Functional Organization of the Genome Group, Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid , Madrid, Spain
| | - Alba Álvarez
- Functional Organization of the Genome Group, Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid , Madrid, Spain
| | - María Gómez
- Functional Organization of the Genome Group, Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid , Madrid, Spain
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34
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Hyrien O. Peaks cloaked in the mist: the landscape of mammalian replication origins. J Cell Biol 2015; 208:147-60. [PMID: 25601401 PMCID: PMC4298691 DOI: 10.1083/jcb.201407004] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 12/16/2014] [Indexed: 12/23/2022] Open
Abstract
Replication of mammalian genomes starts at sites termed replication origins, which historically have been difficult to locate as a result of large genome sizes, limited power of genetic identification schemes, and rareness and fragility of initiation intermediates. However, origins are now mapped by the thousands using microarrays and sequencing techniques. Independent studies show modest concordance, suggesting that mammalian origins can form at any DNA sequence but are suppressed by read-through transcription or that they can overlap the 5' end or even the entire gene. These results require a critical reevaluation of whether origins form at specific DNA elements and/or epigenetic signals or require no such determinants.
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Affiliation(s)
- Olivier Hyrien
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique UMR8197 and Institut National de la Santé et de la Recherche Médicale U1024, 75005 Paris, France
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35
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Abstract
Epstein-Barr nuclear antigen 1 (EBNA1) plays multiple important roles in EBV latent infection and has also been shown to impact EBV lytic infection. EBNA1 is required for the stable persistence of the EBV genomes in latent infection and activates the expression of other EBV latency genes through interactions with specific DNA sequences in the viral episomes. EBNA1 also interacts with several cellular proteins to modulate the activities of multiple cellular pathways important for viral persistence and cell survival. These cellular effects are also implicated in oncogenesis, suggesting a direct role of EBNA1 in the development of EBV-associated tumors.
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Affiliation(s)
- Lori Frappier
- Department of Molecular Genetics, University of Toronto, 1 Kings College Circle, Toronto, ON, M5S 1A8, Canada.
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36
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Abstract
EBV latent infection is characterized by a highly restricted pattern of viral gene expression. EBV can establish latent infections in multiple different tissue types with remarkable variation and plasticity in viral transcription and replication. During latency, the viral genome persists as a multi-copy episome, a non-integrated-closed circular DNA with nucleosome structure similar to cellular chromosomes. Chromatin assembly and histone modifications contribute to the regulation of viral gene expression, DNA replication, and episome persistence during latency. This review focuses on how EBV latency is regulated by chromatin and its associated processes.
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37
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Duarte Junior FF, de Lima Neto QA, Rando FDS, de Freitas DVB, Pattaro Júnior JR, Polizelli LG, Munhoz REF, Seixas FAV, Fernandez MA. Identification and molecular structure analysis of a new noncoding RNA, a sbRNA homolog, in the silkworm Bombyx mori genome. MOLECULAR BIOSYSTEMS 2014; 11:801-8. [PMID: 25521575 DOI: 10.1039/c4mb00595c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The small noncoding group of RNAs called stem-bulge RNAs (sbRNAs), first reported in Caenorhabditis elegans, is described as molecules homologous to the Y RNAs, a specific class of noncoding RNAs that is present in vertebrates. This homology indicates the possibility of the existence of sbRNAs in other invertebrate organisms. In this work, we used bioinformatic tools and conserved sequences of sbRNAs from C. Elegans and Y RNAs to search for homologous sbRNA sequences in the Bombyx mori genome. This analysis led to the discovery of one noncoding gene, which was translated into RNA segments and comparatively analysed with segments from human and hamster Y RNAs and C. elegans sbRNAs in molecular dynamic simulations. This gene represents the first evidence for a new sbRNA-like noncoding RNA, the BmsbRNA gene, in this Lepidoptera genome.
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Affiliation(s)
- Francisco Ferreira Duarte Junior
- Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Av. Colombo, 5790, 87020-900, Maringá, Paraná, Brasil.
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38
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Ge XQ, Lin H. Noncoding RNAs in the regulation of DNA replication. Trends Biochem Sci 2014; 39:341-3. [PMID: 25027733 DOI: 10.1016/j.tibs.2014.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 06/10/2014] [Accepted: 06/12/2014] [Indexed: 12/15/2022]
Abstract
Noncoding RNAs (ncRNAs) have crucial roles in epigenetic, transcriptional, and post-transcriptional regulation. Recent studies have begun to reveal a role of ncRNAs in DNA replication. Here, we review the roles of ncRNAs in regulating different aspects of DNA replication in prokaryotic and eukaryotic systems. We speculate that ncRNAs might function to guide the origin recognition complex (ORC) to chromosomal DNA during replication initiation in higher eukaryotes.
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Affiliation(s)
- Xin Quan Ge
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Haifan Lin
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA.
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39
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Modelling the structure of full-length Epstein–Barr virus nuclear antigen 1. Virus Genes 2014; 49:358-72. [DOI: 10.1007/s11262-014-1101-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 06/27/2014] [Indexed: 12/27/2022]
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40
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Temporal and spatial regulation of eukaryotic DNA replication: From regulated initiation to genome-scale timing program. Semin Cell Dev Biol 2014; 30:110-20. [DOI: 10.1016/j.semcdb.2014.04.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Accepted: 04/04/2014] [Indexed: 11/23/2022]
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41
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Singh J. Role of DNA replication in establishment and propagation of epigenetic states of chromatin. Semin Cell Dev Biol 2014; 30:131-43. [PMID: 24794003 DOI: 10.1016/j.semcdb.2014.04.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 04/03/2014] [Indexed: 10/25/2022]
Abstract
DNA replication is the fundamental process of duplication of the genetic information that is vital for survival of all living cells. The basic mechanistic steps of replication initiation, elongation and termination are conserved among bacteria, lower eukaryotes, like yeast and metazoans. However, the details of the mechanisms are different. Furthermore, there is a close coordination between chromatin assembly pathways and various components of replication machinery whereby DNA replication is coupled to "chromatin replication" during cell cycle. Thereby, various epigenetic modifications associated with different states of gene expression in differentiated cells and the related chromatin structures are faithfully propagated during the cell division through tight coupling with the DNA replication machinery. Several examples are found in lower eukaryotes like budding yeast and fission yeast with close parallels in metazoans.
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Affiliation(s)
- Jagmohan Singh
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, India.
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42
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Telomeric transcripts stimulate telomere recombination to suppress senescence in cells lacking telomerase. Proc Natl Acad Sci U S A 2014; 111:3377-82. [PMID: 24550456 DOI: 10.1073/pnas.1307415111] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In human somatic cells or yeast cells lacking telomerase, telomeres are shortened upon each cell division. This gradual shortening of telomeres eventually leads to senescence. However, a small population of telomerase-deficient cells can survive by bypassing senescence through the activation of alternative recombination pathways to maintain their telomeres. Although genes involved in telomere recombination have been identified, mechanisms that trigger telomere recombination are less known. The THO (suppressor of the transcriptional defects of Hpr1 mutants by overexpression) complex is involved in transcription elongation and mRNA export. Here we demonstrate that mutations in THO complex components can stimulate early senescence and type II telomere recombination in cells lacking telomerase. The accumulation of telomere-associated noncoding telomere repeat-containing RNA (TERRA) is required for the observed telomere effects in THO complex mutants; reduced transcriptional efficiency, or overexpression of RNase H or C(1-3)A RNA can severely impair the type II telomere recombination. The results highlight a unique function for telomere-associated TERRA, in the formation of type II survivors. Moreover, because TERRA is a long noncoding RNA, these results reveal a function for long noncoding RNA in regulating recombination.
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43
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Global bidirectional transcription of the Epstein-Barr virus genome during reactivation. J Virol 2013; 88:1604-16. [PMID: 24257595 DOI: 10.1128/jvi.02989-13] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Epstein-Barr virus (EBV) reactivation involves the ordered induction of approximately 90 viral genes that participate in the generation of infectious virions. Using strand-specific RNA-seq to assess the EBV transcriptome during reactivation, we found extensive bidirectional transcription extending across nearly the entire genome. In contrast, only 4% of the EBV genome is currently bidirectionally annotated. Most of the newly identified transcribed regions show little evidence of coding potential, supporting noncoding roles for most of these RNAs. Based on previous cellular long noncoding RNA size calculations, we estimate that there are likely hundreds more EBV genes expressed during reactivation than was previously known. Limited 5' and 3' rapid amplification of cDNA ends (RACE) experiments and findings of novel splicing events by RNA-seq suggest that the complexity of the viral genome during reactivation may be even greater. Further analysis of antisense transcripts at some of the EBV latency gene loci showed that they are "late" genes, they are nuclear, and they tend to localize in areas of the nucleus where others find newly synthesized viral genomes. This raises the possibility that these transcripts perform functions such as new genome processing, stabilization, organization, etc. The finding of a significantly more complex EBV transcriptome during reactivation changes our view of the viral production process from one that is facilitated and regulated almost entirely by previously identified viral proteins to a process that also involves the contribution of a wide array of virus encoded noncoding RNAs. Epstein-Barr virus (EBV) is a herpesvirus that infects the majority of the world's population, in rare cases causing serious disease such as lymphoma and gastric carcinoma. Using strand-specific RNA-seq, we have studied viral gene expression during EBV reactivation and have discovered hundreds more viral transcripts than were previously known. The finding of alternative splicing and the prevalence of overlapping transcripts indicate additional complexity. Most newly identified transcribed regions do not encode proteins but instead likely function as noncoding RNA molecules which could participate in regulating gene expression, gene splicing or even activities such as viral genome processing. These findings broaden the scope of what we need to consider to understand the viral manufacturing process. As more detailed studies are undertaken they will likely change the way we view this process as a whole.
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Abstract
The human gammaherpesviruses Epstein-Barr virus (EBV) and Kaposi's sarcoma-associated herpesvirus (KSHV) establish long-term latent infections associated with diverse human cancers. Viral oncogenesis depends on the ability of the latent viral genome to persist in host nuclei as episomes that express a restricted yet dynamic pattern of viral genes. Multiple epigenetic events control viral episome generation and maintenance. This Review highlights some of the recent findings on the role of chromatin assembly, histone and DNA modifications, and higher-order chromosome structures that enable gammaherpesviruses to establish stable latent infections that mediate viral pathogenesis.
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45
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Efficient replication of Epstein-Barr virus-derived plasmids requires tethering by EBNA1 to host chromosomes. J Virol 2013; 87:13020-8. [PMID: 24067969 DOI: 10.1128/jvi.01606-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The EBNA1 protein of Epstein-Barr virus enables plasmids carrying oriP both to duplicate and to segregate efficiently in proliferating cells. EBNA1 recruits the origin recognition complex (ORC) to establish a replication origin at one element of oriP, DS (dyad symmetry); at another element, FR (family of repeats), EBNA1 binds to an array of sites from which it tethers plasmids to host chromosomes for mitotic stability. We report experiments leading to the conclusion that tethering by EBNA1 to host chromosomes is also needed within interphase nuclei in order for plasmids to be replicated efficiently from oriP. The DNA-binding domain of EBNA1, which lacks chromosome-binding ability, was found to support weak, DS-specific replication in HEK293 cells after transient transfection, being 17% as active as wild-type EBNA1. The low efficiency of replication was not due to the failure of the DNA-binding domain to retain plasmids within nuclei, because plasmids were recovered in similar amounts and entirely from the nuclear fraction of these transiently transfected cells. A derivative of EBNA1 with its chromosome-tethering domains replaced by a 22-amino-acid nucleosome-binding domain was fully active in supporting oriP functions. The implication is that EBNA1's DNA-binding domain is able to recruit ORC to DS, but either this step or subsequent replication is only efficient if the plasmid is tethered to a host chromosome. Finally, with some cell lines, DS can hardly support even transient plasmid replication without FR. A loss of plasmids lacking FR from nuclei cannot account for this requirement, suggesting that the stronger tethering to chromosomes by FR is needed for plasmid replication within the nuclei of such cells.
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46
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Hoshina S, Yura K, Teranishi H, Kiyasu N, Tominaga A, Kadoma H, Nakatsuka A, Kunichika T, Obuse C, Waga S. Human origin recognition complex binds preferentially to G-quadruplex-preferable RNA and single-stranded DNA. J Biol Chem 2013; 288:30161-30171. [PMID: 24003239 DOI: 10.1074/jbc.m113.492504] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Origin recognition complex (ORC), consisting of six subunits ORC1-6, is known to bind to replication origins and function in the initiation of DNA replication in eukaryotic cells. In contrast to the fact that Saccharomyces cerevisiae ORC recognizes the replication origin in a sequence-specific manner, metazoan ORC has not exhibited strict sequence-specificity for DNA binding. Here we report that human ORC binds preferentially to G-quadruplex (G4)-preferable G-rich RNA or single-stranded DNA (ssDNA). We mapped the G-rich RNA-binding domain in the ORC1 subunit, in a region adjacent to its ATPase domain. This domain itself has an ability to preferentially recognize G4-preferable sequences of ssDNA. Furthermore, we found, by structure modeling, that the G-rich RNA-binding domain is similar to the N-terminal portion of AdoMet_MTase domain of mammalian DNA methyltransferase 1. Therefore, in contrast with the binding to double-stranded DNA, human ORC has an apparent sequence preference with respect to its RNA/ssDNA binding. Interestingly, this specificity coincides with the common signature present in most of the human replication origins. We expect that our findings provide new insights into the regulations of function and chromatin binding of metazoan ORCs.
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Affiliation(s)
- Shoko Hoshina
- From the Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Tokyo 112-8681, Japan
| | - Kei Yura
- the Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo 112-8610, Japan
| | - Honami Teranishi
- From the Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Tokyo 112-8681, Japan
| | - Noriko Kiyasu
- From the Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Tokyo 112-8681, Japan
| | - Ayumi Tominaga
- From the Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Tokyo 112-8681, Japan
| | - Haruka Kadoma
- From the Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Tokyo 112-8681, Japan
| | - Ayaka Nakatsuka
- From the Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Tokyo 112-8681, Japan
| | - Tomoko Kunichika
- the Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan, and
| | - Chikashi Obuse
- the Division of Molecular Life Science, Graduate School of Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Shou Waga
- From the Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Tokyo 112-8681, Japan,.
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47
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McFadden K, Luftig MA. Interplay between DNA tumor viruses and the host DNA damage response. Curr Top Microbiol Immunol 2013; 371:229-57. [PMID: 23686238 DOI: 10.1007/978-3-642-37765-5_9] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Viruses encounter many challenges within host cells in order to replicate their nucleic acid. In the case of DNA viruses, one challenge that must be overcome is recognition of viral DNA structures by the host DNA damage response (DDR) machinery. This is accomplished in elegant and unique ways by different viruses as each has specific needs and sensitivities dependent on its life cycle. In this review, we focus on three DNA tumor viruses and their interactions with the DDR. The viruses Epstein-Barr virus (EBV), Kaposi's sarcoma-associated herpesvirus (KSHV), and human papillomavirus (HPV) account for nearly all of the virus-associated human cancers worldwide. These viruses have also been excellent models for the study of oncogenic virus-mediated cell transformation. In this review, we will discuss how each of these viruses engage and subvert aspects of the host DDR. The first level of DDR engagement is a result of the genetic linkage between the oncogenic potential of these viruses and their ability to replicate. Namely, the promotion of cells from quiescence into the cell cycle to facilitate virus replication can be sensed through aberrant cellular DNA replication structures which activate the DDR and hinder cell transformation. DNA tumor viruses subvert this growth-suppressive DDR through changes in viral oncoprotein expression which ultimately facilitate virus replication. An additional level of DDR engagement is through direct detection of replicating viral DNA. These interactions parallel those observed in other DNA virus systems in that the need to subvert these intrinsic sensors of aberrant DNA structure in order to replicate must be in place. DNA tumor viruses are no exception. This review will cover the molecular features of DNA tumor virus interactions with the host DDR and the consequences for virus replication.
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Affiliation(s)
- Karyn McFadden
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
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48
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Kanda T, Horikoshi N, Murata T, Kawashima D, Sugimoto A, Narita Y, Kurumizaka H, Tsurumi T. Interaction between basic residues of Epstein-Barr virus EBNA1 protein and cellular chromatin mediates viral plasmid maintenance. J Biol Chem 2013; 288:24189-99. [PMID: 23836915 DOI: 10.1074/jbc.m113.491167] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Epstein-Barr virus (EBV) genome is episomally maintained in latently infected cells. The viral protein EBNA1 is a bridging molecule that tethers EBV episomes to host mitotic chromosomes as well as to interphase chromatin. EBNA1 localizes to cellular chromosomes (chromatin) via its chromosome binding domains (CBDs), which are rich in glycine and arginine residues. However, the molecular mechanism by which the CBDs of EBNA1 attach to cellular chromatin is still under debate. Mutation analyses revealed that stepwise substitution of arginine residues within the CBD1 (amino acids 40-54) and CBD2 (amino acids 328-377) regions with alanines progressively impaired chromosome binding activity of EBNA1. The complete arginine-to-alanine substitutions within the CBD1 and -2 regions abolished the ability of EBNA1 to stably maintain EBV-derived oriP plasmids in dividing cells. Importantly, replacing the same arginines with lysines had minimal effect, if any, on chromosome binding of EBNA1 as well as on its ability to stably maintain oriP plasmids. Furthermore, a glycine-arginine-rich peptide derived from the CBD1 region bound to reconstituted nucleosome core particles in vitro, as did a glycine-lysine rich peptide, whereas a glycine-alanine rich peptide did not. These results support the idea that the chromosome binding of EBNA1 is mediated by electrostatic interactions between the basic amino acids within the CBDs and negatively charged cellular chromatin.
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Affiliation(s)
- Teru Kanda
- Division of Virology, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya 464-8681, Japan.
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Abstract
ORC (origin recognition complex) serves as the initiator for the assembly of the pre-RC (pre-replication complex) and the subsequent DNA replication. Together with many of its non-replication functions, ORC is a pivotal regulator of various cellular processes. Notably, a number of reports connect ORC to numerous human diseases, including MGS (Meier-Gorlin syndrome), EBV (Epstein-Barr virus)-infected diseases, American trypanosomiasis and African trypanosomiasis. However, much of the underlying molecular mechanism remains unclear. In those genetic diseases, mutations in ORC alter its function and lead to the dysregulated phenotypes; whereas in some pathogen-induced symptoms, host ORC and archaeal-like ORC are exploited by these organisms to maintain their own genomes. In this review, I provide detailed examples of ORC-related human diseases, and summarize the current findings on how ORC is involved and/or dysregulated. I further discuss how these discoveries can be generalized as model systems, which can then be applied to elucidating other related diseases and revealing potential targets for developing effective therapies.
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50
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Abstract
Epstein-Barr virus (EBV) is a paradigm for human tumor viruses: it is the first virus recognized to cause cancer in people; it causes both lymphomas and carcinomas; yet these tumors arise infrequently given that most people in the world are infected with the virus. EBV is maintained extrachromosomally in infected normal and tumor cells. Eighty-four percent of these viral plasmids replicate each S phase, are licensed, require a single viral protein for their synthesis, and can use two functionally distinct origins of DNA replication, oriP, and Raji ori. Eighty-eight percent of newly synthesized plasmids are segregated faithfully to the daughter cells. Infectious viral particles are not synthesized under these conditions of latent infection. This plasmid replication is consistent with survival of EBV's host cells. Rare cells in an infected population either spontaneously or following exogenous induction support EBV's lytic cycle, which is lethal for the cell. In this case, the viral DNA replicates 100-fold or more, uses a third kind of viral origin of DNA replication, oriLyt, and many viral proteins. Here we shall describe the three modes of EBV's replication as a function of the viral origins used and the viral and cellular proteins that mediate the DNA synthesis from these origins focusing, where practical, on recent advances in our understanding.
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Affiliation(s)
- Wolfgang Hammerschmidt
- Department of Gene Vectors, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchioninistr. 25, D-81377 Munich, Germany
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