Integration of viral DNA sequences in cells transformed by adenovirus 2 or SV40

1980 ◽  
Vol 210 (1180) ◽  
pp. 423-435 ◽  
Keyword(s):  
Cell Lines ◽  
Dna Sequences ◽  
Viral Genome ◽  
Viral Dna ◽  
Viral Genomes ◽  
Viral Dnas ◽  
Cellular Dna ◽  
Viral Insertion ◽  
Viral Sequences ◽  
Heteroduplex Formation

We have cloned and propagated in prokaryotic vectors the viral DNA sequences that are integrated in a variety of cells transformed by adenovirus 2 or SV40. Analysis of the clones reveals that the viral DNA sequences sometimes are arranged in a simple fashion, collinear with the viral genome; in other cell lines there are complex arrangements of viral sequences in which tracts of the viral genome are inverted with respect to each other. In several cases the nucleotide sequences at the joints between cell and viral sequences have been determined: usually there is a sharp transition between cellular and viral DNAs. The viral sequences are integrated at different locations within the genomes of different cell lines; likewise there is no specific site on the viral genomes at which integration occurs. Sometimes the viral sequences are integrated within repetitive cellular DNA, and sometimes within unique sequences. In some cases there is evidence that the viral sequences along with the flanking cell DNA have been amplified after integration. The sequences that flank the viral insertion in the line of SV40-transformed rat cells known as 14B have been used as probes to isolate, from untransformed rat cells, clones that carry the region of the chromosome in which integration occurred. Analysis of the structure of these clones by restriction endonuclease digestion and heteroduplex formation shows that a rearrangement of cellular sequences has occurred, presumably as a consequence of integration.

scholarly journals PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Maria Artesi ◽  
Vincent Hahaut ◽  
Basiel Cole ◽  
Laurens Lambrechts ◽  
Fereshteh Ashrafi ◽  
...  
Keyword(s):  
Viral Genome ◽  
Clonal Expansion ◽  
Endogenous Retroviruses ◽  
Viral Genomes ◽  
Short Read Sequencing ◽  
Long Reads ◽  
Infected Cells ◽  
Insertion Sites ◽  
Viral Insertion ◽  
Hiv 1

AbstractThe integration of a viral genome into the host genome has a major impact on the trajectory of the infected cell. Integration location and variation within the associated viral genome can influence both clonal expansion and persistence of infected cells. Methods based on short-read sequencing can identify viral insertion sites, but the sequence of the viral genomes within remains unobserved. We develop PCIP-seq, a method that leverages long reads to identify insertion sites and sequence their associated viral genome. We apply the technique to exogenous retroviruses HTLV-1, BLV, and HIV-1, endogenous retroviruses, and human papillomavirus.

Inheritance of Chromosomally Integrated Human Herpesvirus 6 DNA

Blood ◽  
1999 ◽  
Vol 94 (5) ◽  
pp. 1545-1549 ◽  
Author(s):  
Masanori Daibata ◽  
Takahiro Taguchi ◽  
Yuiko Nemoto ◽  
Hirokuni Taguchi ◽  
Isao Miyoshi
Keyword(s):  
Dna Sequences ◽  
Viral Genome ◽  
Family Members ◽  
Human Herpesvirus ◽  
Single Step ◽  
Human Herpesvirus 6 ◽  
Viral Genomes ◽  
Herpesvirus 6

Abstract Human herpesvirus 6 (HHV-6) genome has been detected in several human lymphoproliferative disorders with no signs of active viral infection, and found to be integrated into chromosomes in some cases. We previously reported a woman with HHV-6–infected Burkitt’s lymphoma. Fluorescence in situ hybridization showed that the viral genome was integrated into the long arm of chromosome 22 (22q13). The patient’s asymptomatic husband also carried HHV-6 DNA integrated at chromosome locus 1q44. To assess the possibility of chromosomal transmission of HHV-6 DNA, we looked for HHV-6 DNA in the peripheral blood of their daughter. She had HHV-6 DNA on both chromosomes 22q13 and 1q44, identical to the site of viral integration of her mother and father, respectively. The findings suggested that her viral genomes were inherited chromosomally from both parents. The 3 family members were all seropositive for HHV-6, but showed no serological signs of active infection. To confirm the presence of HHV-6 DNA sequences, we performed polymerase chain reaction (PCR) with 7 distinct primer pairs that target different regions of HHV-6. The viral sequences were consistently detected by single-step PCR in all 3 family members. We propose a novel latent form for HHV-6, in which integrated viral genome can be chromosomally transmitted. The possible role of the chromosomally integrated HHV-6 in the pathogenesis of lymphoproliferative diseases remains to be explained.

scholarly journals The Essential Human Cytomegalovirus Gene UL52 Is Required for Cleavage-Packaging of the Viral Genome

2007 ◽  
Vol 82 (5) ◽  
pp. 2065-2078 ◽  
Author(s):  
Eva Maria Borst ◽  
Karen Wagner ◽  
Anne Binz ◽  
Beate Sodeik ◽  
Martin Messerle
Keyword(s):  
Human Cytomegalovirus ◽  
Viral Genome ◽  
Essential Role ◽  
Unit Length ◽  
Viral Dna ◽  
Subnuclear Localization ◽  
Viral Genomes ◽  
Nuclear Egress ◽  
C Terminus ◽  
Infected Cells

ABSTRACT Replication of human cytomegalovirus (HCMV) produces large DNA concatemers of head-to-tail-linked viral genomes that upon packaging into capsids are cut into unit-length genomes. The mechanisms underlying cleavage-packaging and the subsequent steps prior to nuclear egress of DNA-filled capsids are incompletely understood. The hitherto uncharacterized product of the essential HCMV UL52 gene was proposed to participate in these processes. To investigate the function of pUL52, we constructed a ΔUL52 mutant as well as a complementing cell line. We found that replication of viral DNA was not impaired in noncomplementing cells infected with the ΔUL52 virus, but viral concatemers remained uncleaved. Since the subnuclear localization of the known cleavage-packaging proteins pUL56, pUL89, and pUL104 was unchanged in ΔUL52-infected fibroblasts, pUL52 does not seem to act via these proteins. Electron microscopy studies revealed only B capsids in the nuclei of ΔUL52-infected cells, indicating that the mutant virus has a defect in encapsidation of viral DNA. Generation of recombinant HCMV genomes encoding epitope-tagged pUL52 versions showed that only the N-terminally tagged pUL52 supported viral growth, suggesting that the C terminus is crucial for its function. pUL52 was expressed as a 75-kDa protein with true late kinetics. It localized preferentially to the nuclei of infected cells and was found to enclose the replication compartments. Taken together, our results demonstrate an essential role for pUL52 in cleavage-packaging of HCMV DNA. Given its unique subnuclear localization, the function of pUL52 might be distinct from that of other cleavage-packaging proteins.

scholarly journals B-lymphocytic hairy cells contain no HTLV-II DNA sequences

Blood ◽  
1988 ◽  
Vol 72 (4) ◽  
pp. 1428-1430
Author(s):  
T Lion ◽  
N Razvi ◽  
HM Golomb ◽  
RH Brownstein
Keyword(s):  
T Cell ◽  
B Cell ◽  
Dna Sequences ◽  
Viral Genome ◽  
Mononuclear Cells ◽  
Hairy Cell ◽  
Cell Leukemia ◽  
Cell Form ◽  
Hairy Cells ◽  
Viral Sequences

HTLV-II has been found in some cases of the rare T-cell form of hairy- cell leukemia (HCL) and in a leukopenic chronic T-cell leukemia mimicking HCL. We asked whether the virus is implicated in the more frequent B-cell form of HCL. DNA extracted from the mononuclear cells derived from spleen (eight cases) or peripheral blood (eight cases) of 16 patients with the B-cell form of HCL was probed. No viral sequences were detected at levels of sensitivity as low as one viral genome in five cells. Therefore HTLV-II may not be involved in the B-cell form of HCL.

Inheritance of Chromosomally Integrated Human Herpesvirus 6 DNA

Blood ◽  
1999 ◽  
Vol 94 (5) ◽  
pp. 1545-1549 ◽  
Author(s):  
Masanori Daibata ◽  
Takahiro Taguchi ◽  
Yuiko Nemoto ◽  
Hirokuni Taguchi ◽  
Isao Miyoshi
Keyword(s):  
Dna Sequences ◽  
Viral Genome ◽  
Family Members ◽  
Human Herpesvirus ◽  
Single Step ◽  
Human Herpesvirus 6 ◽  
Viral Genomes ◽  
Herpesvirus 6

Human herpesvirus 6 (HHV-6) genome has been detected in several human lymphoproliferative disorders with no signs of active viral infection, and found to be integrated into chromosomes in some cases. We previously reported a woman with HHV-6–infected Burkitt’s lymphoma. Fluorescence in situ hybridization showed that the viral genome was integrated into the long arm of chromosome 22 (22q13). The patient’s asymptomatic husband also carried HHV-6 DNA integrated at chromosome locus 1q44. To assess the possibility of chromosomal transmission of HHV-6 DNA, we looked for HHV-6 DNA in the peripheral blood of their daughter. She had HHV-6 DNA on both chromosomes 22q13 and 1q44, identical to the site of viral integration of her mother and father, respectively. The findings suggested that her viral genomes were inherited chromosomally from both parents. The 3 family members were all seropositive for HHV-6, but showed no serological signs of active infection. To confirm the presence of HHV-6 DNA sequences, we performed polymerase chain reaction (PCR) with 7 distinct primer pairs that target different regions of HHV-6. The viral sequences were consistently detected by single-step PCR in all 3 family members. We propose a novel latent form for HHV-6, in which integrated viral genome can be chromosomally transmitted. The possible role of the chromosomally integrated HHV-6 in the pathogenesis of lymphoproliferative diseases remains to be explained.

scholarly journals Characterization of polyoma viral DNA sequences in polyoma-induced hamster tumor cell lines.

1980 ◽  
Vol 255 (8) ◽  
pp. 3798-3805
Author(s):  
M.A. Israel ◽  
D.F. Vanderryn ◽  
M.L. Meltzer ◽  
M.A. Martin
Keyword(s):  
Tumor Cell ◽  
Cell Lines ◽  
Dna Sequences ◽  
Tumor Cell Lines ◽  
Viral Dna

scholarly journals Reads Binning Improves the Assembly of Viral Genome Sequences From Metagenomic Samples

2021 ◽  
Vol 12 ◽  
Author(s):  
Kai Song
Keyword(s):  
Dna Sequences ◽  
Viral Genome ◽  
Metagenomic Data ◽  
Viral Sequence ◽  
Genome Sequences ◽  
Sequence Identification ◽  
Viral Genes ◽  
Eukaryotic Dna ◽  
Viral Sequences

Metagenomes can be considered as mixtures of viral, bacterial, and other eukaryotic DNA sequences. Mining viral sequences from metagenomes could shed insight into virus–host relationships and expand viral databases. Current alignment-based methods are unsuitable for identifying viral sequences from metagenome sequences because most assembled metagenomic contigs are short and possess few or no predicted genes, and most metagenomic viral genes are dissimilar to known viral genes. In this study, I developed a Markov model-based method, VirMC, to identify viral sequences from metagenomic data. VirMC uses Markov chains to model sequence signatures and construct a scoring model using a likelihood test to distinguish viral and bacterial sequences. Compared with the other two state-of-the-art viral sequence-prediction methods, VirFinder and PPR-Meta, my proposed method outperformed VirFinder and had similar performance with PPR-Meta for short contigs with length less than 400 bp. VirMC outperformed VirFinder and PPR-Meta for identifying viral sequences in contaminated metagenomic samples with eukaryotic sequences. VirMC showed better performance in assembling viral-genome sequences from metagenomic data (based on filtering potential bacterial reads). Applying VirMC to human gut metagenomes from healthy subjects and patients with type-2 diabetes (T2D) revealed that viral contigs could help classify healthy and diseased statuses. This alignment-free method complements gene-based alignment approaches and will significantly improve the precision of viral sequence identification.

scholarly journals Functional cloning of mouse chromosomal loci specifically active in embryonal carcinoma stem cells.

1988 ◽  
Vol 8 (8) ◽  
pp. 3251-3259 ◽  
Author(s):  
K Bhat ◽  
M W McBurney ◽  
H Hamada
Keyword(s):  
Stem Cells ◽  
Cell Lines ◽  
Dna Sequences ◽  
Embryonal Carcinoma ◽  
Regulatory Elements ◽  
Embryonal Carcinoma Cell ◽  
P19 Cells ◽  
Embryonal Carcinoma Cell Line ◽  
Cellular Dna ◽  
Chromosomal Loci

Chromosomal loci that are specifically active in embryonal carcinoma stem cells were cloned from the mouse genome by functional selection. P19 cells, a pluripotent embryonal carcinoma cell line, were transfected with an enhancer trap (a plasmid containing an enhancerless inactive neo gene), and NEO+ transformants were isolated. All of the NEO+ cell lines retained pluripotency and expressed the neo gene. When the cells were induced to differentiate, most of the cell lines continued to express the neo gene, while the neo gene in some cell lines became repressed. From the latter group of cell lines, we have cloned the integrated neo gene plus the flanking cellular DNA sequences. Three of the six cloned DNAs possessed a high NEO+-transforming activity in undifferentiated P19 cells. Among these three, two (015 and 052) were inactive in differentiated P19 cells and NIH 3T3 cells, while the remaining one was active in these differentiated cells. Deletion analysis suggested that both 015 and 052 contain two regulatory elements (promoter and enhancer) of cellular DNA origin. The putative enhancer and promoter are separated by at least 6 kilobases in 015 and 1 kilobase in 052. Therefore, 015 and 052 cloned fragments contain regulatory DNA elements that are specifically active in the embryonal carcinoma stem cells.

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