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Journal of Virology Oct 2015It has been known for a number of years that integration sites of human immunodeficiency virus type 1 (HIV-1) DNA show a preference for actively expressed chromosomal... (Review)
Review
It has been known for a number of years that integration sites of human immunodeficiency virus type 1 (HIV-1) DNA show a preference for actively expressed chromosomal locations. A number of viral and cellular proteins are implicated in this process, but the underlying mechanism is not clear. Two recent breakthrough publications advance our understanding of HIV integration site selection by focusing on the localization of the preferred target genes of integration. These studies reveal that knockdown of certain nucleoporins and components of nucleocytoplasmic trafficking alter integration site preference, not by altering the trafficking of the viral genome but by altering the chromatin subtype localization relative to the structure of the nucleus. Here, we describe the link between the nuclear basket nucleoporins (Tpr and Nup153) and chromatin organization and how altering the host environment by manipulating nuclear structure may have important implications for the preferential integration of HIV into actively transcribed genes, facilitating efficient viral replication.
Topics: Cell Nucleus; Chromatin; HIV Infections; HIV-1; HeLa Cells; Humans; Microscopy, Electron; Nuclear Pore Complex Proteins; Virus Attachment; Virus Integration
PubMed: 26136574
DOI: 10.1128/JVI.01669-15 -
Proceedings of the National Academy of... Jul 2013The selection of chromosomal targets for retroviral integration varies markedly, tracking with the genus of the retrovirus, suggestive of targeting by binding to...
The selection of chromosomal targets for retroviral integration varies markedly, tracking with the genus of the retrovirus, suggestive of targeting by binding to cellular factors. γ-Retroviral murine leukemia virus (MLV) DNA integration into the host genome is favored at transcription start sites, but the underlying mechanism for this preference is unknown. Here, we have identified bromodomain and extraterminal domain (BET) proteins (Brd2, -3, -4) as cellular-binding partners of MLV integrase. We show that purified recombinant Brd4(1-720) binds with high affinity to MLV integrase and stimulates correct concerted integration in vitro. JQ-1, a small molecule that selectively inhibits interactions of BET proteins with modified histone sites impaired MLV but not HIV-1 integration in infected cells. Comparison of the distribution of BET protein-binding sites analyzed using ChIP-Seq data and MLV-integration sites revealed significant positive correlations. Antagonism of BET proteins, via JQ-1 treatment or RNA interference, reduced MLV-integration frequencies at transcription start sites. These findings elucidate the importance of BET proteins for MLV integration efficiency and targeting and provide a route to developing safer MLV-based vectors for human gene therapy.
Topics: Animals; Azepines; Cell Cycle Proteins; Cell Line, Tumor; Chromatin Immunoprecipitation; HEK293 Cells; High-Throughput Nucleotide Sequencing; Host-Pathogen Interactions; Humans; Integrases; Leukemia Virus, Murine; Mass Spectrometry; Mice; NIH 3T3 Cells; Nuclear Proteins; Proteomics; RNA Interference; Recombinant Proteins; Transcription Factors; Transcription Initiation Site; Triazoles; Virus Integration
PubMed: 23818621
DOI: 10.1073/pnas.1307157110 -
Nature Structural & Molecular Biology Jan 2017
Topics: DNA, Viral; HIV Infections; HIV-1; Humans; Virus Integration
PubMed: 28054568
DOI: 10.1038/nsmb.3358 -
PLoS Pathogens Nov 2017Avian 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...
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.
Topics: Animals; Avian Leukosis Virus; Carcinogenesis; Chickens; Clone Cells; Lymphoma, B-Cell; Promoter Regions, Genetic; Proviruses; Virus Integration
PubMed: 29099869
DOI: 10.1371/journal.ppat.1006708 -
Annual Review of Genetics 1992Today the retroviral integration reaction is probably understood, both in terms of its genetics and chemistry, in as much detail as any eukaryotic recombination process.... (Review)
Review
Today the retroviral integration reaction is probably understood, both in terms of its genetics and chemistry, in as much detail as any eukaryotic recombination process. That understanding is in part due to its high efficiency (for it can be induced to occur synchronously in every cell of a culture); to its simplicity (for there is only one major protein player); to its accessibility (for the viral genome has provided all the cis- and trans-acting players); and to its willingness to perform well in vitro, ultimately with purified components. The process has thus made the classic transition from a phenomenon to be studied genetically to a reaction that can also be studied biochemically. The next advances in our understanding of the process of retroviral integration are likely to center on chemical issues. Some basic enzymological issues need to be addressed: we need to determine the oligomeric state of the native IN protein; its state when bound to linear viral DNA; the residues at the active site; the residues involved in sequence-specific recognition of DNA; and the points of contact between IN monomers. Much of this information will follow from detailed mutagenesis of expressed IN genes. A crucial step will be the determination of the structure of the IN protein at atomic resolution through X-ray diffraction analysis of protein crystals, a project underway in several laboratories. That structure may immediately suggest how the enzyme contacts and joins two DNA molecules, and will enormously facilitate the design and interpretation of mutational studies. It seems plausible that we can understand the IN protein as a machine as well as any nuclease or recombinase. A significant number of larger biological questions about integration remain unanswered and will require genetic approaches. What is the true structure of the preintegration complex in the cytoplasm? How does the complex enter the nucleus, and obtain access to the host DNA? Why, at least for most viruses in most cells, does integration depend on cell division? Why does efficient expression of the viral DNA to form progeny viral RNA and proteins depend on integration? How are target sites for integration on the host genome selected, and why are there "hot spots" for insertion? Are there host proteins that facilitate or participate in the integration reaction itself, and what are those proteins? Are any of those proteins involved in site selection?(ABSTRACT TRUNCATED AT 400 WORDS)
Topics: DNA Mutational Analysis; DNA, Viral; Genes, Viral; Retroviridae; Virus Integration
PubMed: 1482125
DOI: 10.1146/annurev.ge.26.120192.002523 -
International Journal of Oncology Apr 1998Adeno-associated virus (AAV), a defective parvovirus, is considered a promising vector for the delivery of therapeutic genes to cells. Both wild-type and recombinant AAV...
Adeno-associated virus (AAV), a defective parvovirus, is considered a promising vector for the delivery of therapeutic genes to cells. Both wild-type and recombinant AAV display a wide tropism and integrate into the host genome, in the absence of helper virus, establishing a latent infection. A unique characteristic of wild-type AAV and a potential advantage for use as a delivery system for gene therapy is the site-specific integration of wild-type virus within a small region of chromosome 19, 19q13.3-qter (AAVS1), in up to 85% of cell lines infected with the virus. Although recombinant AAVs, containing only the inverted terminal repeats of wild-type virus, can integrate efficiently into the host genome, specificity for the AAVS1 site appears to be lost. To address this question, the integration characteristics of two recombinant AAVs lacking the rep and cap genes in HeLa cells were examined. Analysis of Southern blots indicated that none of twenty-six cell clones generated after infection with either one of the recombinant AAVs demonstrated integration within the AAVS1 locus on chromo-some 19. Analysis of five of the cell lines by fluorescent chromosome in situ hybridization confirmed the loss of chromosome 19 specificity. Each integration site mapped near a known fragile site and/or location of a proto-oncogene or growth regulatory gene. Retention of site-specific integration of wild-type AAV will require the inclusion of additional AAV-specific sequences within the recombinant vectors.
Topics: Dependovirus; HeLa Cells; Humans; Proto-Oncogene Mas; Recombination, Genetic; Virus Integration
PubMed: 9499439
DOI: 10.3892/ijo.12.4.805 -
Current Biology : CB Apr 1995The newly discovered Ini1 cellular protein binds HIV-1 integrase and is part of a protein complex thought to alter nucleosomal structure; such alterations may influence... (Review)
Review
The newly discovered Ini1 cellular protein binds HIV-1 integrase and is part of a protein complex thought to alter nucleosomal structure; such alterations may influence the selection of sites for HIV-1 DNA integration.
Topics: Chromosomal Proteins, Non-Histone; DNA Nucleotidyltransferases; DNA, Viral; DNA-Binding Proteins; HIV-1; Humans; Integrases; Protein Binding; SMARCB1 Protein; Transcription Factors; Viral Proteins; Virus Integration
PubMed: 7627549
DOI: 10.1016/s0960-9822(95)00074-1 -
Molecular Therapy : the Journal of the... Dec 2021
Topics: Dependovirus; Genetic Vectors; HeLa Cells; Humans; Virus Integration
PubMed: 34758291
DOI: 10.1016/j.ymthe.2021.10.024 -
Viruses Apr 2013Here we review viral and cellular requirements for entry and intracellular trafficking of foamy viruses (FVs) resulting in integration of viral sequences into the host... (Review)
Review
Here we review viral and cellular requirements for entry and intracellular trafficking of foamy viruses (FVs) resulting in integration of viral sequences into the host cell genome. The virus encoded glycoprotein harbors all essential viral determinants, which are involved in absorption to the host membrane and triggering the uptake of virus particles. However, only recently light was shed on some details of FV's interaction with its host cell receptor(s). Latest studies indicate glycosaminoglycans of cellular proteoglycans, particularly heparan sulfate, to be of utmost importance. In a species-specific manner FVs encounter endogenous machineries of the target cell, which are in some cases exploited for fusion and further egress into the cytosol. Mostly triggered by pH-dependent endocytosis, viral and cellular membranes fuse and release naked FV capsids into the cytoplasm. Intact FV capsids are then shuttled along microtubules and are found to accumulate nearby the centrosome where they can remain in a latent state for extended time periods. Depending on the host cell cycle status, FV capsids finally disassemble and, by still poorly characterized mechanisms, the preintegration complex gets access to the host cell chromatin. Host cell mitosis finally allows for viral genome integration, ultimately starting a new round of viral replication.
Topics: Animals; Biological Transport; Host-Pathogen Interactions; Humans; Spumavirus; Virus Assembly; Virus Attachment; Virus Integration; Virus Internalization
PubMed: 23567621
DOI: 10.3390/v5041055 -
Gene Oct 1991Rous sarcoma virus (RSV) can cause tumors in hamsters, which harbor complete or partially deleted RSV sequences, in their genomes. Here we have studied the localization...
Rous sarcoma virus (RSV) can cause tumors in hamsters, which harbor complete or partially deleted RSV sequences, in their genomes. Here we have studied the localization of RSV sequences integrated into the genome of cell lines derived from six independent hamster tumors. We have found that integration occurred in the isochores richest in guanine + cytosine, of the host genome, as it had been previously observed for bovine leukemia and hepatitis B viral sequences. The integration of RSV proviral sequences is, therefore, 'isopycnic' (i.e., it takes place in host genome sequences which compositionally match the viral sequences) and compartmentalized (i.e., it occurs in a small compositional compartment of the host genome). The hamster genome compartment hosting RSV sequences precisely corresponds to a compartment of the human genome which is the most active in both transcription and recombination. The notion of a compartmentalized, isopycnic integration of RSV proviral sequences fits, therefore, with the viral integration into transcriptionally active and recombinogenic regions of the host genome observed by other authors, but is broader, in that it includes, in addition, the requirement for a compositional match between host genome sequences and expressed viral sequences.
Topics: Animals; Avian Sarcoma Viruses; Base Composition; Cell Transformation, Viral; Centrifugation, Isopycnic; Cricetinae; Genome; Nucleic Acid Hybridization; Proviruses; Recombination, Genetic; Sequence Homology, Nucleic Acid; Transcription, Genetic; Tumor Cells, Cultured; Virus Integration
PubMed: 1657723
DOI: 10.1016/0378-1119(91)90196-i