1
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Walsh D. Primal FEAR protects against infection. Nat Microbiol 2024; 9:886-888. [PMID: 38538831 DOI: 10.1038/s41564-024-01649-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Affiliation(s)
- Derek Walsh
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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2
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Miklík D, Grim J, Elleder D, Hejnar J. Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models. Genome Res 2023; 33:1395-1408. [PMID: 37463751 PMCID: PMC10547254 DOI: 10.1101/gr.277694.123] [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: 01/13/2023] [Accepted: 07/12/2023] [Indexed: 07/20/2023]
Abstract
A weak palindromic nucleotide motif is the hallmark of retroviral integration site alignments. Given that the majority of target sequences are not palindromic, the current model explains the symmetry by an overlap of the nonpalindromic motif present on one of the half-sites of the sequences. Here, we show that the implementation of multicomponent mixture models allows for different interpretations consistent with the existence of both palindromic and nonpalindromic submotifs in the sets of integration site sequences. We further show that the weak palindromic motifs result from freely combined site-specific submotifs restricted to only a few positions proximal to the site of integration. The submotifs are formed by either palindrome-forming nucleotide preference or nucleotide exclusion. Using the mixture models, we also identify HIV-1-favored palindromic sequences in Alu repeats serving as local hotspots for integration. The application of the novel statistical approach provides deeper insight into the selection of retroviral integration sites and may prove to be a valuable tool in the analysis of any type of DNA motifs.
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Affiliation(s)
- Dalibor Miklík
- Laboratory of Viral and Cellular Genetics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague 4, 142 20, Czech Republic
| | - Jiří Grim
- Pattern Recognition Department, Institute of Information Theory and Automation of the Czech Academy of Sciences, Prague 8, 182 08, Czech Republic
| | - Daniel Elleder
- Laboratory of Viral and Cellular Genetics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague 4, 142 20, Czech Republic
| | - Jiří Hejnar
- Laboratory of Viral and Cellular Genetics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague 4, 142 20, Czech Republic;
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3
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Pellaers E, Bhat A, Christ F, Debyser Z. Determinants of Retroviral Integration and Implications for Gene Therapeutic MLV-Based Vectors and for a Cure for HIV-1 Infection. Viruses 2022; 15:32. [PMID: 36680071 PMCID: PMC9861059 DOI: 10.3390/v15010032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
To complete their replication cycle, retroviruses need to integrate a DNA copy of their RNA genome into a host chromosome. Integration site selection is not random and is driven by multiple viral and cellular host factors specific to different classes of retroviruses. Today, overwhelming evidence from cell culture, animal experiments and clinical data suggests that integration sites are important for retroviral replication, oncogenesis and/or latency. In this review, we will summarize the increasing knowledge of the mechanisms underlying the integration site selection of the gammaretrovirus MLV and the lentivirus HIV-1. We will discuss how host factors of the integration site selection of retroviruses may steer the development of safer viral vectors for gene therapy. Next, we will discuss how altering the integration site preference of HIV-1 using small molecules could lead to a cure for HIV-1 infection.
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Affiliation(s)
| | | | | | - Zeger Debyser
- Molecular Virology and Gene Therapy, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
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4
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Abstract
A hallmark of retroviral replication is establishment of the proviral state, wherein a DNA copy of the viral RNA genome is stably incorporated into a host cell chromosome. Integrase is the viral enzyme responsible for the catalytic steps involved in this process, and integrase strand transfer inhibitors are widely used to treat people living with HIV. Over the past decade, a series of X-ray crystallography and cryogenic electron microscopy studies have revealed the structural basis of retroviral DNA integration. A variable number of integrase molecules congregate on viral DNA ends to assemble a conserved intasome core machine that facilitates integration. The structures additionally informed on the modes of integrase inhibitor action and the means by which HIV acquires drug resistance. Recent years have witnessed the development of allosteric integrase inhibitors, a highly promising class of small molecules that antagonize viral morphogenesis. In this Review, we explore recent insights into the organization and mechanism of the retroviral integration machinery and highlight open questions as well as new directions in the field.
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5
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Passos DO, Li M, Craigie R, Lyumkis D. Retroviral integrase: Structure, mechanism, and inhibition. Enzymes 2021; 50:249-300. [PMID: 34861940 DOI: 10.1016/bs.enz.2021.06.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The retroviral protein Integrase (IN) catalyzes concerted integration of viral DNA into host chromatin to establish a permanent infection in the target cell. We learned a great deal about the mechanism of catalytic integration through structure/function studies over the previous four decades of IN research. As one of three essential retroviral enzymes, IN has also been targeted by antiretroviral drugs to treat HIV-infected individuals. Inhibitors blocking the catalytic integration reaction are now state-of-the-art drugs within the antiretroviral therapy toolkit. HIV-1 IN also performs intriguing non-catalytic functions that are relevant to the late stages of the viral replication cycle, yet this aspect remains poorly understood. There are also novel allosteric inhibitors targeting non-enzymatic functions of IN that induce a block in the late stages of the viral replication cycle. In this chapter, we will discuss the function, structure, and inhibition of retroviral IN proteins, highlighting remaining challenges and outstanding questions.
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Affiliation(s)
| | - Min Li
- National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, United States
| | - Robert Craigie
- National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, United States
| | - Dmitry Lyumkis
- The Salk Institute for Biological Studies, La Jolla, CA, United States; The Scripps Research Institute, La Jolla, CA, United States.
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6
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Yoder KE, Rabe AJ, Fishel R, Larue RC. Strategies for Targeting Retroviral Integration for Safer Gene Therapy: Advances and Challenges. Front Mol Biosci 2021; 8:662331. [PMID: 34055882 PMCID: PMC8149907 DOI: 10.3389/fmolb.2021.662331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/29/2021] [Indexed: 12/11/2022] Open
Abstract
Retroviruses are obligate intracellular parasites that must integrate a copy of the viral genome into the host DNA. The integration reaction is performed by the viral enzyme integrase in complex with the two ends of the viral cDNA genome and yields an integrated provirus. Retroviral vector particles are attractive gene therapy delivery tools due to their stable integration. However, some retroviral integration events may dysregulate host oncogenes leading to cancer in gene therapy patients. Multiple strategies to target retroviral integration, particularly to genetic safe harbors, have been tested with limited success. Attempts to target integration may be limited by the multimerization of integrase or the presence of host co-factors for integration. Several retroviral integration complexes have evolved a mechanism of tethering to chromatin via a host protein. Integration host co-factors bind chromatin, anchoring the complex and allowing integration. The tethering factor allows for both close proximity to the target DNA and specificity of targeting. Each retrovirus appears to have distinct preferences for DNA sequence and chromatin features at the integration site. Tethering factors determine the preference for chromatin features, but do not affect the subtle sequence preference at the integration site. The sequence preference is likely intrinsic to the integrase protein. New developments may uncouple the requirement for a tethering factor and increase the ability to redirect retroviral integration.
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Affiliation(s)
- Kristine E Yoder
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Anthony J Rabe
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Richard Fishel
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Ross C Larue
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, United States
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7
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Kotlar RM, Jones ND, Senavirathne G, Gardner AM, Messer RK, Tan YY, Rabe AJ, Fishel R, Yoder KE. Retroviral prototype foamy virus intasome binding to a nucleosome target does not determine integration efficiency. J Biol Chem 2021; 296:100550. [PMID: 33744295 PMCID: PMC8050864 DOI: 10.1016/j.jbc.2021.100550] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 01/15/2023] Open
Abstract
Retroviral integrases must navigate host DNA packaged as chromatin during integration of the viral genome. Prototype foamy virus (PFV) integrase (IN) forms a tetramer bound to two viral DNA (vDNA) ends in a complex termed an intasome. PFV IN consists of four domains: the amino terminal extension domain (NED), amino terminal domain (NTD), catalytic core domain (CCD), and carboxyl terminal domain (CTD). The domains of the two inner IN protomers have been visualized, as well as the CCDs of the two outer IN protomers. However, the roles of the amino and carboxyl terminal domains of the PFV intasome outer subunits during integration to a nucleosome target substrate are not clear. We used the well-characterized 601 nucleosome to assay integration activity as well as intasome binding. PFV intasome integration to 601 nucleosomes occurs in clusters at four independent sites. We find that the outer protomer NED and NTD domains have no significant effects on integration efficiency, site selection, or binding. The CTDs of the outer PFV intasome subunits dramatically affect nucleosome binding but have little effect on total integration efficiency. The outer PFV IN CTDs did significantly alter the integration efficiency at one site. Histone tails also significantly affect intasome binding, but have little impact on PFV integration efficiency or site selection. These results indicate that binding to nucleosomes does not correlate with integration efficiency and suggests most intasome-binding events are unproductive.
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Affiliation(s)
- Randi M Kotlar
- Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Nathan D Jones
- Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio, USA; The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Gayan Senavirathne
- Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio, USA; The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Anne M Gardner
- Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio, USA; The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Ryan K Messer
- Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio, USA; The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Yow Yong Tan
- Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio, USA; The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Anthony J Rabe
- Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio, USA; The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Richard Fishel
- Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio, USA; The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Kristine E Yoder
- Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio, USA; The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA.
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8
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Mauro E, Lesbats P, Lapaillerie D, Chaignepain S, Maillot B, Oladosu O, Robert X, Fiorini F, Kieffer B, Bouaziz S, Gouet P, Ruff M, Parissi V. Human H4 tail stimulates HIV-1 integration through binding to the carboxy-terminal domain of integrase. Nucleic Acids Res 2019; 47:3607-3618. [PMID: 30767014 PMCID: PMC6468294 DOI: 10.1093/nar/gkz091] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 01/28/2019] [Accepted: 02/04/2019] [Indexed: 12/22/2022] Open
Abstract
The integration of the retroviral genome into the chromatin of the infected cell is catalysed by the integrase (IN)•viral DNA complex (intasome). This process requires functional association between the integration complex and the nucleosomes. Direct intasome/histone contacts have been reported to modulate the interaction between the integration complex and the target DNA (tDNA). Both prototype foamy virus (PFV) and HIV-1 integrases can directly bind histone amino-terminal tails. We have further investigated this final association by studying the effect of isolated histone tails on HIV-1 integration. We show here that the binding of HIV-1 IN to a peptide derived from the H4 tail strongly stimulates integration catalysis in vitro. This stimulation was not observed with peptide tails from other variants or with alpha-retroviral (RAV) and spuma-retroviral PFV integrases. Biochemical analyses show that the peptide tail induces both an increase in the IN oligomerization state and affinity for the target DNA, which are associated with substantial structural rearrangements in the IN carboxy-terminal domain (CTD) observed by NMR. Our data indicate that the H4 peptide tail promotes the formation of active strand transfer complexes (STCs) and support an activation step of the incoming intasome at the contact of the histone tail.
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Affiliation(s)
- Eric Mauro
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France
| | - Paul Lesbats
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France
| | - Delphine Lapaillerie
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France
| | - Stephane Chaignepain
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France.,Université de Bordeaux, UMR CNRS 5248 CBMN (Chimie Biologie des Membranes et Nanoobjets), 33076 Bordeaux, France
| | - Benoit Maillot
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Département de Biologie Structurale Intégrative, UDS, U596 INSERM, UMR7104 CNRS, Strasbourg, France
| | - Oyindamola Oladosu
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Département de Biologie Structurale Intégrative, UDS, U596 INSERM, UMR7104 CNRS, Strasbourg, France
| | - Xavier Robert
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France.,MMSB-Institute of the Biology and Chemistry of Proteins, UMR 5086 CNRS-Lyon 1 University, Lyon, France
| | - Francesca Fiorini
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France.,MMSB-Institute of the Biology and Chemistry of Proteins, UMR 5086 CNRS-Lyon 1 University, Lyon, France
| | - Bruno Kieffer
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Département de Biologie Structurale Intégrative, UDS, U596 INSERM, UMR7104 CNRS, Strasbourg, France
| | - Serge Bouaziz
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France.,CiTCoM, CNRS, UMR 8038, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Patrice Gouet
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France.,MMSB-Institute of the Biology and Chemistry of Proteins, UMR 5086 CNRS-Lyon 1 University, Lyon, France
| | - Marc Ruff
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France.,IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Département de Biologie Structurale Intégrative, UDS, U596 INSERM, UMR7104 CNRS, Strasbourg, France
| | - Vincent Parissi
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed. Bordeaux, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France
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9
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Gallay K, Blot G, Chahpazoff M, Yajjou-Hamalian H, Confort MP, De Boisséson C, Leroux A, Luengo C, Fiorini F, Lavigne M, Chebloune Y, Gouet P, Moreau K, Blanchard Y, Ronfort C. In vitro, in cellulo and structural characterizations of the interaction between the integrase of Porcine Endogenous Retrovirus A/C and proteins of the BET family. Virology 2019; 532:69-81. [DOI: 10.1016/j.virol.2019.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 03/30/2019] [Accepted: 04/09/2019] [Indexed: 01/17/2023]
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10
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Prototype foamy virus intasome aggregation is mediated by outer protein domains and prevented by protocatechuic acid. Sci Rep 2019; 9:132. [PMID: 30644416 PMCID: PMC6333793 DOI: 10.1038/s41598-018-36725-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/23/2018] [Indexed: 12/01/2022] Open
Abstract
The integrase (IN) enzyme of retrovirus prototype foamy virus (PFV) consists of four domains: amino terminal extension (NED), amino terminus (NTD), catalytic core (CCD), and carboxyl terminus domains (CTD). A tetramer of PFV IN with two viral DNA ends forms the functional intasome. Two inner monomers are catalytically active while the CCDs of the two outer monomers appear to play only structural roles. The NED, NTD, and CTD of the outer monomers are disordered in intasome structures. Truncation mutants reveal that integration to a supercoiled plasmid increases without the outer monomer CTDs present. Deletion of the outer CTDs enhances the lifetime of the intasome compared to full length (FL) IN or deletion of the outer monomer NTDs. High ionic strength buffer or several additives, particularly protocatechuic acid (PCA), enhance the integration of FL intasomes by preventing aggregation. These data confirm previous studies suggesting the disordered outer domains of PFV intasomes are not required for intasome assembly or integration. Instead, the outer CTDs contribute to aggregation of PFV intasomes which may be inhibited by high ionic strength buffer or the small molecule PCA.
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11
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Mackler RM, Lopez MA, Osterhage MJ, Yoder KE. Prototype foamy virus integrase is promiscuous for target choice. Biochem Biophys Res Commun 2018; 503:1241-1246. [PMID: 30017200 PMCID: PMC6119477 DOI: 10.1016/j.bbrc.2018.07.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 07/06/2018] [Indexed: 12/11/2022]
Abstract
Retroviruses have two essential activities: reverse transcription and integration. The viral protein integrase (IN) covalently joins the viral cDNA genome to the host DNA. Prototype foamy virus (PFV) IN has become a model of retroviral intasome structure. However, this retroviral IN has not been well-characterized biochemically. Here we compare PFV IN to previously reported HIV-1 IN activities and discover significant differences. PFV IN is able to utilize the divalent cation calcium during strand transfer while HIV-1 IN is not. HIV-1 IN was shown to completely commit to a target DNA within 1 min, while PFV IN is not fully committed after 60 min. These results suggest that PFV IN is more promiscuous compared to HIV-1 IN in terms of divalent cation and target commitment.
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Affiliation(s)
- R M Mackler
- Department of Cancer Biology and Genetics, Ohio State University College of Medicine, 460 West 12(th)Ave, Columbus, OH, 43210, USA
| | - M A Lopez
- Department of Cancer Biology and Genetics, Ohio State University College of Medicine, 460 West 12(th)Ave, Columbus, OH, 43210, USA
| | - M J Osterhage
- Department of Cancer Biology and Genetics, Ohio State University College of Medicine, 460 West 12(th)Ave, Columbus, OH, 43210, USA
| | - K E Yoder
- Department of Cancer Biology and Genetics, Ohio State University College of Medicine, 460 West 12(th)Ave, Columbus, OH, 43210, USA.
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12
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Proviruses with Long-Term Stable Expression Accumulate in Transcriptionally Active Chromatin Close to the Gene Regulatory Elements: Comparison of ASLV-, HIV- and MLV-Derived Vectors. Viruses 2018. [PMID: 29517993 PMCID: PMC5869509 DOI: 10.3390/v10030116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Individual groups of retroviruses and retroviral vectors differ in their integration site preference and interaction with the host genome. Hence, immediately after infection genome-wide distribution of integrated proviruses is non-random. During long-term in vitro or persistent in vivo infection, the genomic position and chromatin environment of the provirus affects its transcriptional activity. Thus, a selection of long-term stably expressed proviruses and elimination of proviruses, which have been gradually silenced by epigenetic mechanisms, helps in the identification of genomic compartments permissive for proviral transcription. We compare here the extent and time course of provirus silencing in single cell clones of the K562 human myeloid lymphoblastoma cell line that have been infected with retroviral reporter vectors derived from avian sarcoma/leukosis virus (ASLV), human immunodeficiency virus type 1 (HIV) and murine leukaemia virus (MLV). While MLV proviruses remain transcriptionally active, ASLV proviruses are prone to rapid silencing. The HIV provirus displays gradual silencing only after an extended time period in culture. The analysis of integration sites of long-term stably expressed proviruses shows a strong bias for some genomic features-especially integration close to the transcription start sites of active transcription units. Furthermore, complex analysis of histone modifications enriched at the site of integration points to the accumulation of proviruses of all three groups in gene regulatory segments, particularly close to the enhancer loci. We conclude that the proximity to active regulatory chromatin segments correlates with stable provirus expression in various retroviral species.
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13
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Šenigl F, Miklík D, Auxt M, Hejnar J. Accumulation of long-term transcriptionally active integrated retroviral vectors in active promoters and enhancers. Nucleic Acids Res 2018; 45:12752-12765. [PMID: 29244184 PMCID: PMC5727404 DOI: 10.1093/nar/gkx889] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 09/26/2017] [Indexed: 01/13/2023] Open
Abstract
Most retroviruses preferentially integrate into certain genomic locations and, as a result, their genome-wide integration patterns are non-random. We investigate the epigenetic landscape of integrated retroviral vectors and correlate it with the long-term stability of proviral transcription. Retroviral vectors derived from the avian sarcoma/leukosis virus expressing the GFP reporter were used to transduce the human myeloid lymphoblastoma cell line K562. Because of efficient silencing of avian retrovirus in mammalian cells, only ∼3% of established clones displayed stable proviral expression. We analyzed the vector integration sites in non-selected cells and in clones selected for the GFP expression. This selection led to overrepresentation of proviruses integrated in active transcription units, with particular accumulation in promoter-proximal areas. In parallel, we investigated the integration of vectors equipped with an anti-silencing CpG island core sequence. Such modification increased the frequency of stably expressing proviruses by one order. The modified vectors are also overrepresented in active transcription units, but stably expressed in distal parts of transcriptional units further away from promoters with marked accumulation in enhancers. These results suggest that integrated retroviruses subject to gradual epigenetic silencing during long-term cultivation. Among most genomic compartments, however, active promoters and enhancers protect the adjacent retroviruses from transcriptional silencing.
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Affiliation(s)
- Filip Šenigl
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, CZ-14220 Prague 4, Czech Republic
| | - Dalibor Miklík
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, CZ-14220 Prague 4, Czech Republic
| | - Miroslav Auxt
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, CZ-14220 Prague 4, Czech Republic
| | - Jirí Hejnar
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, CZ-14220 Prague 4, Czech Republic
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14
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Abstract
Integration of the reverse-transcribed viral cDNA into the host's genome is a critical step in the lifecycle of all retroviruses. Retrovirus integration is carried out by integrase (IN), a virus-encoded enzyme that forms an oligomeric 'intasome' complex with both ends of the linear viral DNA to catalyze their concerted insertions into the backbones of the host's DNA. IN also forms a complex with host proteins, which guides the intasome to the host's chromosome. Recent structural studies have revealed remarkable diversity as well as conserved features among the architectures of the intasome assembly from different genera of retroviruses. This chapter will review how IN oligomerizes to achieve its function, with particular focus on alpharetrovirus including the avian retrovirus Rous sarcoma virus. Another chapter (Craigie) will focus on the structure and function of IN from HIV-1.
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Affiliation(s)
- Duane P Grandgenett
- Saint Louis University Health Sciences Center, Department of Microbiology and Immunology, Institute for Molecular Virology, Doisy Research Center, St. Louis, MO, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.
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15
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Malhotra S, Winans S, Lam G, Justice J, Morgan R, Beemon K. Selection for avian leukosis virus integration sites determines the clonal progression of B-cell lymphomas. PLoS Pathog 2017; 13:e1006708. [PMID: 29099869 PMCID: PMC5687753 DOI: 10.1371/journal.ppat.1006708] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 11/15/2017] [Accepted: 10/23/2017] [Indexed: 12/19/2022] Open
Abstract
Avian leukosis virus (ALV) is a simple retrovirus that causes a wide range of tumors in chickens, the most common of which are B-cell lymphomas. The viral genome integrates into the host genome and uses its strong promoter and enhancer sequences to alter the expression of nearby genes, frequently inducing tumors. In this study, we compare the preferences for ALV integration sites in cultured cells and in tumors, by analysis of over 87,000 unique integration sites. In tissue culture we observed integration was relatively random with slight preferences for genes, transcription start sites and CpG islands. We also observed a preference for integrations in or near expressed and spliced genes. The integration pattern in cultured cells changed over the course of selection for oncogenic characteristics in tumors. In comparison to tissue culture, ALV integrations are more highly selected for proximity to transcription start sites in tumors. There is also a significant selection of ALV integrations away from CpG islands in the highly clonally expanded cells in tumors. Additionally, we utilized a high throughput method to quantify the magnitude of clonality in different stages of tumorigenesis. An ALV-induced tumor carries between 700 and 3000 unique integrations, with an average of 2.3 to 4 copies of proviral DNA per infected cell. We observed increasing tumor clonality during progression of B-cell lymphomas and identified gene players (especially TERT and MYB) and biological processes involved in tumor progression. The Avian Leukosis Virus (ALV) is a simple retrovirus that causes cancer in chickens. The virus integrates its genome into the host genome and induces changes in expression of nearby genes. Here, we determine the sites of viral integrations and their role in the progression of tumors. We report pathways and novel gene players that might cooperate and play a role in the progression of B-cell lymphomas. Our study provides new insights into the changes during lymphoma initiation, progression, and metastasis, as a result of selection for specific ALV integration sites.
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Affiliation(s)
- Sanandan Malhotra
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Shelby Winans
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Gary Lam
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - James Justice
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Robin Morgan
- Department of Biological Sciences, University of Delaware, Newark, Delaware, United States of America
| | - Karen Beemon
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
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Matysiak J, Lesbats P, Mauro E, Lapaillerie D, Dupuy JW, Lopez AP, Benleulmi MS, Calmels C, Andreola ML, Ruff M, Llano M, Delelis O, Lavigne M, Parissi V. Modulation of chromatin structure by the FACT histone chaperone complex regulates HIV-1 integration. Retrovirology 2017; 14:39. [PMID: 28754126 PMCID: PMC5534098 DOI: 10.1186/s12977-017-0363-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 07/24/2017] [Indexed: 01/23/2023] Open
Abstract
Background Insertion of retroviral genome DNA occurs in the chromatin of the host cell. This step is modulated by chromatin structure as nucleosomes compaction was shown to prevent HIV-1 integration and chromatin remodeling has been reported to affect integration efficiency. LEDGF/p75-mediated targeting of the integration complex toward RNA polymerase II (polII) transcribed regions ensures optimal access to dynamic regions that are suitable for integration. Consequently, we have investigated the involvement of polII-associated factors in the regulation of HIV-1 integration. Results Using a pull down approach coupled with mass spectrometry, we have selected the FACT (FAcilitates Chromatin Transcription) complex as a new potential cofactor of HIV-1 integration. FACT is a histone chaperone complex associated with the polII transcription machinery and recently shown to bind LEDGF/p75. We report here that a tripartite complex can be formed between HIV-1 integrase, LEDGF/p75 and FACT in vitro and in cells. Biochemical analyzes show that FACT-dependent nucleosome disassembly promotes HIV-1 integration into chromatinized templates, and generates highly favored nucleosomal structures in vitro. This effect was found to be amplified by LEDGF/p75. Promotion of this FACT-mediated chromatin remodeling in cells both increases chromatin accessibility and stimulates HIV-1 infectivity and integration. Conclusions Altogether, our data indicate that FACT regulates HIV-1 integration by inducing local nucleosomes dissociation that modulates the functional association between the incoming intasome and the targeted nucleosome. Electronic supplementary material The online version of this article (doi:10.1186/s12977-017-0363-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julien Matysiak
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS, University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, 33076, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France
| | - Paul Lesbats
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS, University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, 33076, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France
| | - Eric Mauro
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS, University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, 33076, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France
| | - Delphine Lapaillerie
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS, University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, 33076, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Paris, France
| | - Jean-William Dupuy
- Centre Génomique fonctionnelle Bordeaux, Plateforme Proteome, Université de Bordeaux, Bordeaux, France
| | - Angelica P Lopez
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
| | - Mohamed Salah Benleulmi
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS, University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, 33076, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Paris, France
| | - Christina Calmels
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS, University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, 33076, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Paris, France
| | - Marie-Line Andreola
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS, University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, 33076, Bordeaux Cedex, France.,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Paris, France
| | - Marc Ruff
- Département de Biologie Structurale Intégrative, UDS, U596 INSERM, UMR7104 CNRS, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Illkirch-Graffenstaden, France
| | - Manuel Llano
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
| | - Olivier Delelis
- LBPA, UMR8113, CNRS, ENS-Cachan, Cachan, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Paris, France
| | - Marc Lavigne
- Department of Virology, UMR 3569, CNRS, Institut Pasteur, Paris, France.,Institut Cochin-INSERM U1016-CNRS UMR8104, Université Paris Descartes, Paris, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Paris, France
| | - Vincent Parissi
- Fundamental Microbiology and Pathogenicity Laboratory, UMR 5234 CNRS, University of Bordeaux, SFR TransBioMed, 146 rue Léo Saignat, 33076, Bordeaux Cedex, France. .,International Associated Laboratory (LIA) of Microbiology and Immunology, CNRS/University de Bordeaux/Heinrich Pette Institute-Leibniz Institute for Experimental Virology, Bordeaux, France. .,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Paris, France.
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