Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Virus Integration”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 271 records · Page 15Linked to original sources
PubMed1991

DNase I-hypersensitive sites are associated with both long terminal repeats and with the intragenic enhancer of integrated human immunodeficiency virus type 1.

After reverse transcription and integration of the genome of human immunodeficiency virus (HIV) in a target cell, the viral DNA becomes packaged into chromatin. Regions of chromatin associated with regulatory functions in eukaryotes can generally be distinguished from the bulk of chromatin by an increased accessibility of the DNA to nucleases (nuclease-hypersensitive sites). In this report, the chromatin structure of the complete HIV-1 genome has been analyzed in three chronically infected cell lines of monocyte/macrophage and lymphoid origins. Digestion of purified nuclei from these cells with DNase I followed by restriction digestion and Southern blotting identified several DNase I-hypersensitive regions throughout the viral genome. Two constitutive sites were associated with the U3 region of the 5' long terminal repeat (LTR) in which the viral promoter and enhancer are located. An additional site in the R region of the 5' LTR was present only after activation of viral transcription by phorbol ester or tumor necrosis factor alpha. A fourth site was identified in all cell lines downstream of the 5' LTR (nucleotides [nt] 656 to 720), and the band corresponding to this site decreased in intensity upon activation of transcription. In the 3' LTR, a constitutive hypersensitive site was identified in all cell lines (nt 9322 to 9489). A major site (nt 4534 to 4733) was present only in a cell line of macrophage/monocyte origin in a region of the genome in which an intragenic enhancer was recently identified (E. Verdin, N. Becker, F. Bex, L. Droogmans, and A. Burny, Proc. Natl. Acad. Sci. USA 87:4874-4878, 1990). This study defines regions of the HIV genome associated with an open chromatin configuration and points to the potential regulatory role of these elements in the HIV life cycle.

Base Sequence↗
PubMed1989

Features of two hepatitis B virus (HBV) DNA integrations suggest mechanisms of HBV integration.

Two integrated hepatitis B virus (HBV) DNA molecules were cloned from two primary hepatocellular carcinomas each containing only a single integration. One integration (C3) contained a single linear segment of HBV DNA, and the other integration (C4) contained a large inverted duplication of viral DNA at the site of a chromosome translocation (O. Hino, T.B. Shows, and C.E. Rogler, Proc. Natl. Acad. Sci. USA 83:8338-8342, 1986). Sequence analysis of the virus-cell junctions of C3 placed the left virus-cell junction at nucleotide 1824, which is at the 5' end of the directly repeated DR1 sequence and is 6 base pairs from the 3' end of the long (L) negative strand. The right virus-cell junction was at nucleotide 1762 in a region of viral DNA (within the cohesive overlap) which shared 5-base-pair homology with cellular DNA. Sequence analysis of the normal cellular DNA across the integration site showed that 11 base pairs of cellular DNA were deleted at the site of integration. On the basis of this analysis, we suggest a mechanism for integration of the viral DNA molecule which involves strand invasion of the 3' end of the L negative strand of an open circular or linear HBV DNA molecule (at the DR1 sequence) and base pairing of the opposite end of the molecule with cellular DNA, accompanied by the deletion of 11 base pairs of cellular DNA during the double recombination event. Sequencing across the inverted duplication of HBV DNA in clone C4 located one side of the inversion at nucleotide 1820, which is 2 base pairs from the 3' end of the L negative strand. Both this sequence and the left virus-cell junction of C3 are within the 9-nucleotide terminally redundant region of the HBV L negative strand DNA. We suggest that the terminal redundancy is a preferred topoisomerase I nicking region because of both its base sequence and forked structure. Such nicking would lead to integration and rearrangement of HBV molecules within the terminal redundancy, as we have observed in both our clones.

Base Sequence↗
PubMed1997

A rapid RT-PCR based method to isolate complementary DNA fragments flanking retrovirus integration sites.

Proto-oncogenes in retrovirally induced myeloid mouse leukemias are frequently activated following retroviral insertion. The identification of common virus integration sites (VISs) and isolation of the transforming oncogene is laborious and time consuming. We established a rapid and simple PCR based procedure which facilitates the identification of VISs and novel proto-oncogenes. Complementary DNA fragments adjacent to retrovirus integration sites were selectively isolated by applying a reverse transcriptase (RT) reaction using an oligo(dT)-adaptor primer, followed by PCR using the adaptor sequence and a retrovirus long terminal repeat (LTR) specific primer. Multiple chimeric cDNA fragments suitable for Southern and northern blot analysis were isolated.

Animals↗
PubMed2001

Lymphoma-type adult T-cell leukaemia-lymphoma with a bulky cutaneous tumour showing multiple human T-lymphotropic virus-1 DNA integration.

Human T-lymphotropic virus-1 (HTLV-1) is considered to be the cause of adult T-cell leukaemia-lymphoma (ATL). Monoclonal integration of HTLV-1 proviral DNA, as is analysed by Southern blotting, has been demonstrated in ATL patients. Unusual integration patterns of HTLV-1 proviral DNA have occasionally been described, and it is suggested that the patterns have clinical implications for ATL pathophysiology. Multiple, complete and defective types of integration patterns, in that order, are apparently associated with prognoses from good to poor. We report a 73-year-old Japanese woman with lymphoma-type ATL and a bulky cutaneous tumour on the left thigh. Four bands of slightly differing intensity were seen after EcoRI digestion of skin and lymph node samples on Southern blot analysis of HTLV-1 proviral DNA. Analysis for T-cell receptor-beta gene revealed five novel bands after restriction enzyme digestion with HindIII, indicating that the patient has four separate tumour cell clones, each of which carries one copy of the provirus. She was treated with chemotherapy and radiation and remains under reasonable control despite some relapsing cutaneous nodules. The indolent course in this present case could be related to the multiple integration pattern of HTLV-1 proviral DNA detected.

Aged↗
PubMed1979

Influenza virus-specific T cell-mediated cytotoxicity: integration of the virus antigen into the target cell membrane is essential for target cell formation.

This study deals with the requirements for target cell recognition by influenza A virus-specific cytotoxic T lymphocytes (CTL). H-2-identical cells were incubated with infectious or UV light-inactivated influenza A virus expressing either cleaved or uncleaved hemagglutinin (HA). Thereafter, the treated cells were tested in a 4-h 51Cr assay for susceptibility to CTL-mediated cytolysis. Regardless whether the influenza virus was infectious, virions expressing cleaved HA were efficient in target cell formation. In contrast, cells incubated with either active or UV-inactivated virions expressing uncleaved HA were not lysed by virus-specific CTL. Yet, after mere trypsin-mediated cleavage of the HA of cell-absorbed viroins, strong cytolysis could be observed. On the other hand, solubilization of the envelope lipid bilayer by ethylether abolished the capacity of the remaining HA to induce target cell formation. The results clearly suggest that mere absorption of virions to the membrane of cells, which is performed by virus with uncleaved HA, is insufficient for target cell formation. For this, both cleaved HA and an intact envelope appear to be crucial. We conclude that fusion of the virion into the cell membrane is essential for target cell formation.

Antigens, Surface↗
PubMed2004

Cell cycle regulation of human immunodeficiency virus type 1 integration in T cells: antagonistic effects of nuclear envelope breakdown and chromatin condensation.

We examined the influence of mitosis on the kinetics of human immunodeficiency virus type 1 integration in T cells. Single-round infection of cells arrested in G1b or allowed to synchronously proceed through division showed that mitosis delays virus integration until 18-24 h postinfection, whereas integration reaches maximum levels by 15 h in G1b-arrested cells. Subcellular fractionation of metaphase-arrested cells indicated that, while nuclear envelope disassembly facilitates docking of viral DNA to chromatin, chromosome condensation directly antagonizes and therefore delays integration. As a result of the balance between the two effects, virus integration efficiency is eventually up to threefold greater in dividing cells. At the single-cell level, using a green fluorescent protein-expressing reporter virus, we found that passage through mitosis leads to prominent asymmetric segregation of the viral genome in daughter cells without interfering with provirus expression.

Animals↗
PubMed1980

Integration of Moloney leukaemia virus into the germ line of mice: correlation between site of integration and virus activation.

Endogenous avian and murine C-type viruses are genetic elements which are transmitted at several distinct chromosomal loci. Different patterns of virus activation have been observed in a variety of different mouse strains. However, because there are multiple copies of closely related endogenous viruses in every mouse strain, the genetic basis of the differential expression of these genes is poorly understood. A new substrain of mice, BALB/Mo, was derived previously carrying the exogenous Moloney leukaemia virus (M-MuLV) genome on chromosome 6 (ref. 14). Virus activation occurs in lymphatic tissues of all BALB/Mo mice soon after birth. We report here the derivation of three new substrains of mice each carrying a single M-MuLV genome on different chromosomal integration sites. Each locus was associated with a distinct phenotype of virus expression. Evidence is presented that apparently identical viral genomes show differences in spontaneous virus activation and that defective viral genomes can be carried in the germ line of mice.

Animals↗
PubMed2003

Demethylation of host-cell DNA at the site of avian retrovirus integration.

The transcriptional activity of an integrated retroviral copy strongly depends on the adjacent host-cell DNA at the site of integration. Transcribed DNA loci as well as cis-acting sequences like enhancers or CpG islands usually permit expression of nearby integrated proviruses. In contrast, proviruses residing close to cellular silencers tend to transcriptional silencing and CpG methylation. Little is known, however, about the influence of provirus integration on the target sequence in the host genome. Here, we report interesting features of a simplified Rous sarcoma virus integrated into a non-transcribed hypermethylated DNA sequence in the Syrian hamster genome. After integration, CpG methylation of this sequence has been lost almost completely and hypomethylated DNA permits proviral transcription and hamster cell transformation by the proviral v-src oncogene. This, however, is not a stable state, and non-transformed revertants bearing transcriptionally silenced proviruses segregate with a high rate. The provirus silencing is followed by DNA methylation of both provirus regulatory regions and adjacent cellular sequences. This CpG methylation is very dense and resistant to the demethylation effects of 5-aza-2(')-deoxycytidine and/or trichostatin A. Our description exemplifies the capacity of retroviruses/retroviral vectors to overcome, at least transiently, negative position effects of DNA methylation at the site of integration.

Agar↗
PubMed1995

Epstein-Barr virus induction of recombinase-activating genes RAG1 and RAG2.

In experimental B-cell infections, Epstein-Barr virus induced sustained expression of V(D)J recombinase-activating genes RAG1 and RAG2, whose aberrant activity has been implicated in chromosomal translocations in B-cell neoplasms. In cell lines in which RAG1 and RAG2 were detected, virus integrated into cellular DNA rather than assumed the configuration of extrachromosomal episomes. Expression of the Epstein-Barr virus nuclear antigen 1 in transient transfection assays was sufficient to induce both recombinase-activating genes.

Antigens, Viral↗
PubMed1990

A trans-activator function is generated by integration of hepatitis B virus preS/S sequences in human hepatocellular carcinoma DNA.

The X gene of wild-type hepatitis B virus or integrated DNA has recently been shown to stimulate transcription of a variety of enhancers and promoters. To further delineate the viral sequences responsible for trans-activation in hepatomas, we cloned the single hepatitis B virus insert from human hepatocellular carcinoma DNA M1. The plasmid pM1 contains 2004 base pairs of hepatitis B virus DNA subtype adr, including truncated preS/S sequences and the enhancer element. The X promoter and 422 nucleotides of the X coding region are present. The entire preC/C gene is deleted. In transient cotransfection assays using Chang liver cells (CCL 13), pM1 DNA exerts a 6- to 10-fold trans-activating effect on the expression of the pSV2CAT reporter plasmid. The trans-activation occurs by stimulation of transcription and is dependent on the simian virus 40 enhancer in the reporter plasmid. Deletion analysis of pM1 subclones reveals that the trans-activator is encoded by preS/S and not by X sequences. A frameshift mutation within the preS2 open reading frame shows that this portion is indispensable for the trans-activating function. Initiation of transcription has been mapped to the S1 promoter. A comparable trans-activating effect is also observed with cloned wild-type hepatitis B virus sequences similarly truncated. These results show that a transcriptional trans-activator function not present in the intact gene is generated by 3' truncation of integrated hepatitis B virus DNA preS/S sequences.

Carcinoma, Hepatocellular↗
PubMed2003

Svi3: A provirus common integration site in c-myc in SL/Kh pre-B lymphomas.

Spontaneous pre-B lymphomas in SL/Kh mice occur by somatic acquisition of a provirus genome of endogenous murine leukemia virus (MuLV). Inverse PCR amplification and sequence analyses of a provirus and its host flanking fragment revealed a proviral insertion into c-myc in 3 out of 60 SL/Kh pre-B lymphomas, named Svi3 lymphomas (SL/Kh virus integration site-3). Southern blot analysis revealed that two lymphomas had clonal integration in c-myc exon 1 and the other, in the promoter region. In 2 out of 3 Svi3 lymphomas, a fusion transcript of provirus 3' long terminal repeat and c-myc and a normal full-length c-myc transcript were obtained, but in one Svi3 lymphoma, only the normal transcript was obtained. All three Svi3 lymphomas had increased c-myc expression, producing normal 67-kDa c-Myc protein. Svi3 lymphomas had more mature phenotypes in the steps of early B-cell differentiation than Svi1 lymphomas, in which c-myc expression was indirectly up-regulated by provirus integration into Stat5a.

3' Untranslated Regions↗
PubMed2005

HPV in situ hybridization: impact of different protocols on the detection of integrated HPV.

Although there is consensus that HPV integration is common in invasive cervical carcinomas and uncommon or absent in low-grade uterine cervical intraepithelial neoplasia (CIN I), estimates for HPV integration in CIN II/III range from 5 to 100% using different PCR-based and in situ hybridization (ISH) approaches. It has been suggested that HPV integration can be identified using ISH by scoring of punctate signals. The increased sensitivity of fluorescence ISH (FISH) methods, allowing the detection of single copies of HPV, complicates the distinction between integrated and episomal HPV. Recently it has been suggested that, in such assays, the signals originating from integrated virus can be hidden in a background of episomal HPV. We therefore compared 2 different FISH protocols for the detection of integrated HPV in a series of CIN II/III lesions: 1) a mild protocol in which episomal HPV and RNA is retained and 2) a harsh protocol that extensively extracts proteins and RNA, and which promotes the partial loss of episomal HPV but not integrated HPV. A series of 28 HPV 16/18 positive CIN II/III lesions (17 solitary lesions and 11 lesions adjacent to microinvasive carcinoma) were studied. A punctate signal pattern was identified in 7 of these lesions with both protocols. Punctate signal was also present in control samples from lesions that are known to be associated with HPV integration (invasive squamous cell carcinoma (n = 3), adenocarcinoma in situ (n = 3), and invasive adenocarcinoma (n = 1). HPV RNA contributed significantly to the intensity of punctate FISH signal, especially when applying the mild protocol, as shown by omitting DNA denaturation, including RNase pretreatment steps and measuring the fluorescence signal intensity. Also, HPV RNA was frequently detected in addition to episomal/integrated HPV DNA in the majority of the other 21 CIN II/III lesions; this resulted in intense granular/diffuse FISH signals throughout the epithelium. However, in 7 of these lesions, the harsh protocol gave a more consistent punctate pattern in cells throughout the full thickness of the epithelium. This supports the hypothesis that the harsh protocol unmasks integrated HPV more efficiently by extracting RNA and episomal HPV. Overall, with this harsh protocol, a clonally expanded population of cells containing punctate HPV signals was found in 5 of 17 (29%) solitary CIN II/III lesions and in 9 of 11 (88%) CIN II/III lesions associated with microinvasive carcinoma. Combining these data with the results from our previous study, with the harsh protocol in 7 of 40 (18%) solitary CIN II/III lesions and 19/21 (90%) CIN II/III lesions associated with microinvasive carcinoma (p < 0.001), this pattern was found. This indicates that, when robustly defined, a punctate HPV pattern in CIN II/III lesions is associated with the presence of an invasive carcinoma.

Adenocarcinoma↗
PubMed1998

The peripheral cannabinoid receptor, Cb2, in retrovirally-induced leukemic transformation and normal hematopoiesis.

Following retroviral insertional mutagenesis we recently identified the gene encoding the peripheral cannabinoid receptor (Cb2) near a common virus integration site (VIS), Evi11. In 13 out of 105 Cas-Br-M murine leukemia virus (MuLV) induced leukemias retroviral integrations occured either in the 5' or 3' part of the Cb2 gene. The Cb2 receptor protein is 44% homologous to the central cannabinoid receptor Cb1, which belongs to the superfamily of seven transmembrane (7TM) receptors. Cb1 is mainly expressed in brain, whereas Cb2 encodes the hematopoietic form. Besides the natural cannabinoids, delta9-tetrahydrocannabinol (delta9-THC) and cannabinol, and the many synthetic agonists that have been generated, e.g CP55,940 or WIN55,212-2, several endogenous ligands have recently been identified. These include the arachidonic acid derivatives anandamide and 2-arachidonylglycerol as well as the fatty acid palmitoylethanolamide. Although in the past many studies described growth inhibitory effects of cannabinoid agonists on the in vitro proliferation of hematopoietic cells, recent studies demonstrated that activation of Cb2 may have growth stimulatory effects on blood precursor cells. We demonstrated that many murine hematopoietic growth factor (HGF) dependent cell lines also require the presence of anandamide for optimal growth in serum free culture. Thus, the Cb2 receptor may be an important regulator of normal hematopoietic growth and development. These results strengthen our finding that Cb2 is a proto-oncogene and may implicate a growth advantage for leukemia cells that aberrantly express Cb2. Here we briefly review the mechanisms and application of retroviral insertional mutagenesis in leukemic transformation in mice and discuss the role of the peripheral cannabinoid receptor in leukemia development and normal hematopoiesis.

Animals↗
PubMed1987

Transformation of NIH/3T3 cells by DNA from a human hepatoma cell line with integrated hepatitis B virus DNA.

We have studied by means of DNA-mediated gene transfer the transforming activity of the DNA of the human hepatoma cell line HCC-M, which contains genomes of hepatitis B virus (HBV) in integrated form. DNA from HCC-M induced transformed foci on transfection of NIH/3T3 cells. DNAs from primary transformants were capable of inducing secondary transformants. Most of the DNAs of these transformants were demonstrated to contain both human repetitive sequences and HBV DNA, indicating that the transformants had incorporated exogenous human DNA and HBV DNA as well. These results suggest that transformation occurs as the result of the transfer of oncogene which might be closely associated with HBV genome.

Carcinoma, Hepatocellular↗
PubMed1984

Retrovirus-induced lethal mutation in collagen I gene of mice is associated with an altered chromatin structure.

The chromatin structure of the collagen alpha 1(I) gene, which has been mutated by retrovirus insertion in Mov13 mice, was compared with that of the wildtype allele. Limited digestions with DNAase I revealed the presence of two hypersensitive sites in all normal cells analyzed, while a third site at 100 to 200 bp 5' of the transcription start was detected only in cells synthesizing collagen alpha 1(I) mRNA. This transcription-associated site was not present in chromatin of the mutant allele, while the two other hypersensitive sites, one of which is located close to the provirus, were not changed by the virus integration. Our results suggest that the virus insertion in Mov13 mice may prevent the developmentally regulated appearance of a transcription-associated hypersensitive site, thereby interfering with proper activation of the gene during embryonic development.

Alleles↗
PubMed1993

Stable in vivo expression of the cystic fibrosis transmembrane conductance regulator with an adeno-associated virus vector.

Adeno-associated virus (AAV) vectors expressing the normal cystic fibrosis transmembrane conductance regulator (CFTR) cDNA complement the cystic fibrosis (CF) defect in vitro. Unlike other DNA virus vectors, AAV is a stably integrating virus, which could make possible long-term in vivo complementation of the CF defect in the airway epithelium. We report AAV-CFTR gene transfer and expression after infection of primary CF nasal polyp cells and after in vivo delivery of AAV-CFTR vector to one lobe of the rabbit lung through a fiberoptic bronchoscope. In the rabbit, vector DNA could be detected in the infected lobe up to 6 months after administration. A 26-amino acid polypeptide sequence unique to the recombinant AAV-CFTR protein was used to generate both oligonucleotide probes and a polyclonal antibody which allowed the unambiguous identification of vector RNA and CFTR protein expression. With these reagents, CFTR RNA and protein were detected in the airway epithelium of the infected lobe for up to 6 months after vector administration. AAV vectors do, therefore, efficiently promote in vivo gene transfer to the airway epithelium which is stable over several months. These findings indicate that AAV-CFTR vectors could potentially be very useful for gene therapy.

Amino Acid Sequence↗
PubMed1993

Transactivating function of integrated hepatitis B virus.

HBV DNAs are often found in integrated forms in human hepatocellular carcinoma (HCC). Discovery of a transactivation function coded by a limited region of the HBV genome has promoted us to survey our collection of HBV integrants with flanking cellular sequences, asking whether they might exhibit a transactivation function. In transient cotransfection assays using the HepG2 cell line, six out of the twelve integrants showed transactivation effects on the expression of cellular genes such as c-fos. These results strongly demonstrate that the transactivating effects of integrated HBV DNA are widely distributed, and some of these effects might be correlated to hepatocarcinogenesis.

Carcinoma, Hepatocellular↗
PubMed1982

Integration site of polyoma virus DNA in the inducible LPT line of polyoma-transformed rat cells.

The structure of the polyoma virus (Py) integration site in the inducible LPT line of Py-transformed rat cells was determined by biochemical methods of gene mapping. LPT cell DNA was digested with various restriction enzymes. The digestion products were electrophoresed in agarose gels and transferred onto nitrocellulose sheets by Southern blotting. Fragments containing viral or cell DNA sequences, or both, were identified by hybridization with Py DNA or with a cloned flanking cell DNA probe. Cleavage of LPT DNA with enzymes that restrict the Py genome once generated linear Py DNA molecules and two fragments containing both cell and viral DNA sequences. Cleavage of LPT DNA with enzymes which do not restrict Py DNA generated series of fragments whose lengths were found to differ by increments of a whole Py genome; the smallest fragment in each series was found to be longer than the viral genome. These data indicate that LPT cultures contain Py insertions of various lengths integrated into the same chromosomal site in all the cells. The length heterogeneity of the viral insertions is due to the presence of 0, 1, 2, 3. . . Py genomes arranged in a direct tandem repeat within invariable sequences of viral DNA. Double-digestion experiments were also carried out with the above enzymes and with enzymes that cleave the Py genome at multiple sites. The data obtained in these experiments were used to construct a physical map of the integration site. This map showed that the early region of the virus remained intact even in the smallest insertion (which contains no whole duplicated genomes), whereas the late region was partially duplicated and split during integration. The smallest insertion is colinear with the Py physical map over a region including the entire Py genome and at least a part of the duplicated segment. This structure could give rise to nondefective circular viral DNA molecules by single homologous recombination events. Similar recombination events may occur at a higher frequency in the longer insertions, which include longer regions of homology, and may yield many more free viral genomes. The presence of these insertions in LPT cells could thus be one of the factors which account for the high inducibility of the LPT line.

Animals↗