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PubMed1982

Nucleotide sequence analysis of the long terminal repeat of avian myeloblastosis virus and adjacent host sequences.

The nucleotide sequence of the integrated avian myeloblastosis virus long terminal repeat has been determined. The sequence is 385 base pairs long and is present at both ends of the viral DNA. The cell-virus junctions at each end consist of a 6-base-pair direct repeat of cell DNA next to the inverted repeat of viral DNA. The long terminal repeat also contains promoter-like sequences, an mRNA capping site, and polyadenylation signals. Several features of this long terminal repeat suggest a structural and functional similarity with sequences of transposable and other genetic elements. Comparison of these sequences with long terminal repeats of other avian retroviruses indicates that there is a great variation in the 3' unique sequence (U3), whereas the 5' specific sequences (U5) and the R region are highly conserved.

Avian Leukosis Virus↗
PubMed1985

Differential transformation of C3H10T1/2 cells by v-mos: sequential expression of transformation parameters.

Extremely small quantities of the product of the transforming gene v-mos of Moloney murine sarcoma virus are able to efficiently transform cells. Recent data indicate the existence of a threshold level for v-mos transformation of NIH3T3 cells. Using mouse mammary tumor virus long terminal repeat sequences or hybrid promoters consisting of mouse mammary tumor virus and Moloney murine sarcoma virus long terminal repeat elements to express v-mos in C3H10T1/2 cells, we established cell lines representing different stages of morphological transformation in vitro. The threshold level for v-mos transformation was considerably lower than that for NIH3T3 cells, because no treatment with dexamethasone or primary selection other than transformation was necessary during standard transfection procedures. Using the cell lines mentioned we established an association of the level of v-mos expression with the transformation parameters examined, but not with p53 levels. Furthermore, the characterization of the different promoters showed (i) that the distal binding site confers hormone responsiveness to Moloney murine sarcoma virus promoter elements and (ii) that artifactual transcription initiation sites can be detected in mouse mammary tumor virus-Moloney murine sarcoma virus hybrid promoters which are, however, not regulated by the hormone.

Animals↗
PubMed1992

Epstein-Barr virus induced lymphoproliferative tumors in severe combined immunodeficient mice are oligoclonal.

Severe combined immunodeficient (SCID) mice reconstituted with lymphocytes from Epstein-Barr virus (EBV) negative human donors develop aggressive tumors after the chimeric mice are infected with EBV. The tumors were composed of human B cells that expressed EBV encoded antigens (latent membrane protein and EBV nuclear antigen2). Southern blot analysis of DNA from 16 SCID/hu tumors with human Ig gene probes showed that each tumor contained multiple heavy and light chain gene rearrangements. Ig kappa gene rearrangements were frequent, while clonal lambda gene rearrangements were infrequent. Analysis of EBV terminal repeat sequences indicated two or more fused termini in each tumor, consistent with a multiclonal origin. Linear terminal repeat segments and viral antigens (EA-D and EA-R) associated with EBV replication were not detected in the tumors. High levels of human Igs in the SCID/hu serum were oligoclonal and primarily contained kappa light chains. Before the appearance of overt tumors, circulating cells with human and EBV DNA could be detected in the SCID/hu mice by the polymerase chain reaction. We conclude that EBV infection in SCID/hu chimeric mice produces a limited number of transformation events, which give rise to oligoclonal tumors resembling EBV-associated lymphoproliferative disorders in some immune-deficient patients.

Animals↗
PubMed1984

Sequences in the long terminal repeats of the Moloney murine sarcoma virus-124 genome which control transforming gene function.

The role of long terminal repeat (LTR) sequences in the efficient expression of Moloney murine sarcoma virus (MSV-124) transforming gene function was investigated. Recombinant plasmids containing a single LTR positioned 3' of v-mos were subjected to sequential deletions, and the relative transforming efficiency of these recombinants was analyzed in the NIH/3T3 transfection assay. Recombinants lacking CAAT, TATA, and poly(A) signals within the LTR were able to transform with an efficiency comparable to that of the wild-type MSV-124 genome. Deletion of one of the two 74-bp tandem repeat units within the LTR did not abolish v-mos gene function, whereas removal of both 74-bp repeat units completely eliminated transforming activity. The addition of a fragment containing only a single 74-bp unit and 29-bp downstream sequences derived from the LTR to a position 3' of v-mos led to efficient activation of v-mos transforming function. Residual potentiating activity for v-mos expression was retained even when the distance between v-mos and the 3' LTR was increased by several kilobase pairs. All these findings are consistent with the concept that the potentiating action of the LTR in its 3' position is due to activator/enhancer sequences localized to one of its 74-bp repeats. A permuted MSV-124 molecule, whose single LTR was localized 5' of v-mos, was very inefficient at transformation. However, its transforming activity could be increased by approximately 1000-fold by tandemization of the molecule.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1983

AKR thymic lymphomas involving mink cell focus-inducing murine leukemia viruses have a common region of provirus integration.

Newly acquired proviruses related to a mink cell focus-inducing murine leukemia virus were detected in low copy number in restriction endonuclease-digested DNAs from thymic lymphomas of AKR/J mice. These extra proviruses were not present in DNAs of either normal thymus or leukemic brain tissues. Extra tumor-specific DNA fragments generated by restriction endonucleases either were identical in size or fell into similar size classes, suggesting a common site(s) of provirus integration. Characterization of extra EcoRI DNA fragments for mink cell focus-inducing viral sequences revealed that all of them contained large terminal repeat sequences and that a significant number represented proviruses with deletions.

AKR murine leukemia virus↗
PubMed1999

R region sequences in the long terminal repeat of a murine retrovirus specifically increase expression of unspliced RNAs.

A stem-loop structure at the 5' end of the R region of the long terminal repeat (LTR) of the murine leukemia virus SL3 and other type C mammalian retroviruses is important for maximum levels of expression of a reporter gene under the control of the viral LTR. This element, termed the R region stem-loop (RSL), has a small effect on transcriptional initiation and no effect on RNA polymerase processivity. Its major effect is on posttranscriptional processing of LTR-driven transcripts. Here we tested whether the RSL affected the production of RNAs from a full-length SL3 genome. Mutation of the RSL in the 5' LTR of SL3 reduced the cytoplasmic levels of full-length viral transcripts but not those of spliced, env mRNA transcripts. Thus, the RSL specifically affected the cytoplasmic levels of the unspliced viral RNA. To test further whether the effect was specific for unspliced transcripts, a system was devised in which the expression of a reporter gene under the control of the viral LTR was tested in the presence or absence of an intron. Mutation of the RSL resulted in only about a twofold decline in the level of reporter gene expression when the transcripts contained an intron. However, when the intron was removed, mutation of the RSL reduced expression of the reporter gene about 10- to 60-fold in various cell lines. The secondary structure of the RSL was essential for its activity on the intronless transcript. Thus, the RSL appears to be important for the cytoplasmic accumulation of unspliced viral RNA and unspliced RNA from chimeric transcription units under the control of the viral LTR.

Animals↗
PubMed1984

Cellular targets and host genes in multistage carcinogenesis.

Recent studies indicate that although cellular DNA is the critical target in the action of initiating carcinogens, specific membrane-associated receptors mediate the actions of certain tumor promoters. A stereochemical model is presented to explain how three different types of tumor promoters (phorbol esters, indole alkaloids, and polyacetates) can interact with the same class of cellular receptors. Multistage chemical carcinogenesis might involve progressive alterations in the expression of cellular DNA sequences homologous to oncogenes and regulatory sequences in certain retroviruses. We found that the oncogene c-mos is not rearranged or expressed in a series of carcinogen-transformed murine C3H 10T112 cells. These cells do express, however, a unique set of poly(A)+ RNAs that contain sequences homologous to the Moloney leukemia virus long terminal repeat sequence. Studies are in progress to determine the significance of this finding with respect to the carcinogenic process.

Animals↗
PubMed1989

Adenoviruses with nonidentical terminal sequences are viable.

Adenovirus genomes consist of linear DNA molecules containing inverted terminal repeat sequences (ITRs) of 100 to 200 base pairs. The importance of identical termini for viability of adenoviruses was investigated. The viral strains used in this study were wild-type adenovirus type 5 (Ad5) and a variant Ad2 strain with termini which were distinct from those of all other human adenoviruses sequenced to date. A hybrid virus (sub54), obtained by recombination between Ad2 and Ad5, derived the left 42 to 52% of its genome from Ad2 and the right 58 to 48% from Ad5. Southern blotting analysis with labeled oligodeoxynucleotides indicated that both Ad2 and Ad5 ITRs were present in sub54 viral DNA preparations, and successive plaque purifications of sub54 demonstrated that viruses with nonidentical terminal sequences were viable but were rapidly converted to viruses with identical ends. Cloning of the sub54 genome as a bacterial plasmid supported the observations made by analysis of sub54 virion DNA. A plasmid, pFG154, was isolated which contained the entire adenovirus genome with an Ad2 ITR at the left terminus covalently linked to an Ad5 ITR at the right terminus. Upon transfection of mammalian cells with pFG154, viral progeny were obtained which had all possible combinations of termini, thus confirming that molecules with nonidentical termini are viable. Pure populations of viruses with nonidentical termini could not be isolated, suggesting efficient repair of one end with the opposite terminus used as a template. A model for this process is proposed involving strand displacement replication and emphasizing the importance of panhandle formation (annealing of terminal sequences) as a replicative intermediate.

Adenoviruses, Human↗
PubMed1987

Cotransfection with adenovirus DNA enhances transcription from linear DNA containing eucaryotic promoters.

Linear DNAs, containing a copy of the adenovirus serotype 2 (Ad2) inverted terminal repeat sequence at each end, replicate in 293 cells when cotransfected with Ad2 DNA (Hay et al., J. Mol. Biol. 175:493-510, 1984). We have linked either the Ad2 IVa2 promoter (IVa2) or major late promoter (MLP) to the chloramphenicol acetyltransferase gene and inserted this DNA into such a plasmid (pARKR) between its two inverted terminal repeats. These recombinant plasmids were linearized and then used to transfect 293 cells in the presence or absence of Ad2 helper DNA. Synthesis of IVa2 and MLP RNAs, and production of chloramphenicol acetyltransferase was increased dramatically when the Ad2 DNA was included. However, unlike the patterns of temporal regulation which are seen during a cycle of virus replication when these genes are contained within the virion, there was no obvious difference in the timing of RNA synthesis from plasmid IVa2 or MLP after cotransfection. When linearized plasmids containing IVa2 and MLP sequences but lacking inverted terminal repeats at their ends (replication deficient plasmids) were used for transfection, an increase in RNA synthesis from IVa2 or MLP was also observed and similarly required cotransfection with Ad2 DNA. When HeLa cells, which do not constitutively express the adenovirus E1a gene, were cotransfected with linearized plasmids and adenovirus DNA that lacks the E1a region (H5dl312), a stimulation of transcription was also observed, although it was less than the level observed with wild-type DNA. The results of the present study demonstrate that an early gene product(s) besides E1a functions in trans to regulate transcription.

Adenoviruses, Human↗
PubMed2001

The HIV-1 repeated sequence R as a robust hot-spot for copy-choice recombination.

Template switching during reverse transcription is crucial for retroviral replication. While strand transfer on the terminal repeated sequence R is essential to achieve reverse transcription, template switching from internal regions of the genome (copy choice) leads to genetic recombination. We have developed an experimental system to study copy-choice recombination in vitro along the HIV-1 genome. We identify here several genomic regions, including the R sequence, where copy choice occurred at high rates. The frequency of copy choice occurring in a given region of template was strongly influenced by the surrounding sequences, an observation that suggests a pivotal role of the folding of template RNA in the process. The sequence R, instead, constituted an exception to this rule since it was a strong hot-spot for copy choice in the different sequence contexts tested. We suggest therefore that the structure of this region has been optimised during viral evolution to ensure efficient template switching independently from the sequences that might surround it.

Genome, Viral↗
PubMed1980

Biological activity of cloned Moloney sarcoma virus DNA: Terminally redundant sequences may enhance transformation efficiency.

We have measured the ability of cloned restriction fragments containing the whole and partial genomes of two strains of Moloney murine sarcoma virus to induce cell transformation in DNA transfection assays. The cloned intact ml and HTl murine sarcoma virus proviruses transform with an efficiency of approximately 40,000-50,000 focus-forming units/pmol of proviral DNA, and the majority of these transformed cells contain a rescuable viral genome. A cloned 2.1-kilobase-pair internal fragment of the murine sarcoma virus containing 1.2 kilobase pairs of sarcoma virus-specific sequences (src) and approximately 900 base pairs of leukemia virus-derived sequences adjacent to the 5' end of src transforms with approximately 1/10,000th the efficiency of the intact genome. When leukemia virus-deprived sequences containing a single copy of the 600-base-pair direct terminal repeated sequences are present at either the 5' or 3' end of this src-containing fragment, the transforming activity is stimulated 1000-fold. Cotransfection with a mixture of cloned fragments, one containing the internal 2.1-kilobase-pair src fragment and the other containing a single copy of the terminally redundant sequence, results in a 300-fold increase in transformation efficiency.

Animals↗
PubMed2000

Sequence analysis of porcine adenovirus type 3 E1 region, pIX and pIVa2 genes, and two novel open reading frames.

The porcine adenovirus type 3 (PAd3) genome between map units 0 and 13.7 was sequenced and compared with similar regions of other adenoviruses. This region consists of the left inverted terminal repeat sequences involved in DNA packaging, the entire early region 1 (E1) and the protein IX (pIX) transcription unit. The lower strand contains the C-terminal end of IVa2 of the E2A transcriptional unit and two novel open reading frames (ORFs). The E1 transcription unit consists of ORFs for proteins homologous to the E1A, E1B-17k and E1B-55k of both human adenovirus type 5 (HAd5) and bovine adenovirus type 3 (BAd3). The predicted PAd3 pIX demonstrated homology with the N-terminal portion of the pIXs of HAd5 and BAd3. On the lower strand, immediately after the putative IVa2 ORF, there are two unique ORFs of 208 and 203 amino acid residues that showed homology with Epstein-Barr virus nuclear antigens and other cellular transcription factors.

Adenovirus E1A Proteins↗
PubMed1989

Identification of nuclear proteins that specifically interact with adeno-associated virus type 2 inverted terminal repeat hairpin DNA.

A palindromic hairpin duplex containing the inverted terminal repeat sequence of adeno-associated virus type 2 (AAV) DNA was used as a substrate in gel retardation assays to detect putative proteins that specifically interact with the AAV hairpin DNA structures. Nuclear proteins were detected in extracts prepared from human KB cells coinfected with AAV and adenovirus type 2 that interacted with the hairpin duplex but not in nuclear extracts prepared from uninfected, AAV-infected, or adenovirus type 2-infected KB cells. The binding was specific for the hairpin duplex, since no binding occurred with a double-stranded DNA duplex with the identical nucleotide sequence. Furthermore, in competition experiments, the binding could be reduced with increasing concentrations of the hairpin duplex but not with the double-stranded duplex DNA with the identical nucleotide sequence. S1 nuclease assays revealed that the binding was sensitive to digestion with the enzyme, whereas the protein-bound hairpin duplex was resistant to digestion with S1 nuclease. The nucleotide sequence involved in the protein binding was localized within the inverted terminal repeat of the AAV genome by methylation interference assays. These nuclear proteins may be likely candidates for the pivotal enzyme nickase required for replication or resolution (or both) of single-stranded palindromic hairpin termini of the AAV genome.

Base Sequence↗
PubMed1990

Tumour-induced host stromal-cell transformation: induction of mouse spindle-cell fibrosarcoma not mediated by gene transfer.

Tumour-induced host-cell transformation has been addressed by examining human tumours in situ and following xenograft to nude mice. We have found evidence for the transformation of host stromal fibroblasts both in vivo and following the introduction of the tumours to in vitro culture. The in vitro culture of one such xenograft--derived from a human prostatic adenocarcinoma--resulted in the outgrowth of a transformed aneuploid mouse cell line. This transformed line was tumourigenic both in BALB/c nu/nu (nude) mice and in heterozygous nu/+mice, with the morphology of a spindle-cell sarcoma. The cell line did not express human isozymes or human histocompatibility antigens, nor were human chromosomes present. Moreover, human DNA sequences were not detected by human Alu repeat sequence element probing in the transformed cell line grown either in vitro or in vivo. The line contained retroviral long terminal repeat sequences but there was no evidence of proviral activation. These findings indicate that tumour cells may cause transformation of neighbouring stromal cells; that this transformation may proceed in the absence of DNA transfer or activation of endogenous proviruses; and that the means of this observed transformation may involve humoral factors elaborated by the tumour cells.

Adenocarcinoma↗
PubMed1988

Differences between normal and transformed murine fibroblasts in the expression of various promoter/enhancer-chloramphenicol acetyltransferase constructs.

High levels of poly(A)+ RNAs homologous to certain endogenous retrovirus-related DNA sequences are frequently seen in carcinogen-transformed rodent cells. To explore the underlying mechanism, transient expression assays were done to determine whether carcinogen- or radiation-transformed C3H 10T 1/2 cell lines differ from normal 10T 1/2 cells in terms of their ability to express the chloramphenicol acetyltransferase (CAT) gene when it is linked to various promoter/enhancer sequences, including two independently isolated intracisternal A particle (IAP) long terminal repeat sequences designated prcm and pMIA6. We found that with several constructs, CAT activity was always 3- to 10-fold higher in the transformed 10T 1/2 cell lines than in the normal 10T 1/2 cells. The prcm-CAT construct displayed the highest CAT activity in both the normal and transformed C3H 10T 1/2 cells. Studies with 32P-labeled prcm-CAT DNA and Southern blot analyses indicated that the differences in CAT activity between normal and transformed cells were not due to greater uptake or retention of the transfected DNA by the transformed cells. Competition studies provided evidence that factors required for the expression of the prcm-CAT construct are present in limited amounts in normal 10T 1/2 cells and in excess amounts in transformed 10T 1/2 cells. These putative factors may play a role in the increased expression of endogenous retrovirus-related sequences in the transformed cells.

Animals↗
PubMed1983

A mouse dispersed repeat sequence showing remarkable similarities to the long terminal repeats of retroviruses.

A mouse 1.3-kb EcoRI dispersed repeat sequence that shows homology by hybridisation to the long terminal repeat of intracisternal A-particle genes has been partially sequenced. One of the established sequence regions shows three major features reminiscent of the long terminal repeats of retroviruses. Firstly, a TATA box precedes a putative capping site (G) by 23 bp. Secondly, the TATA box is itself preceded by the sequence CCTAT. Thirdly, following the capping site, the signal sequence AATAA precedes by 20 bp a possible polyadenylation site (CA). Such a retroviral-like sequence may have been responsible for the initial amplification and dispersion of the mouse repeat family.

Animals↗
PubMed1991

A transposon with an unusual LTR arrangement from Chlamydomonas reinhardtii contains an internal tandem array of 76 bp repeats.

TOC1, a transposable element from Chlamydomonas reinhardtii, is 5662 bases long. The 217 and 237 base long terminal repeat sequences of TOC1 are unusually arranged around the 4600 and 123 base unique regions: [217]-4600-[237] [217]-123-[237]. Although TOC1 contains long terminal repeats and most TOC1 elements are complete, features shared with virus-like retroposons, its unique 4600 base region is more similar to the structure of the L1 family of non-virus retroposons: first, 11 3/4 tandemly repeated copies of a 76 base repeat are found 813 bases from the left end of TOC1, and second using the universal genetic code large open reading frames were not found in TOC1. The relationship between TOC1, virus-like retroposons and the L1 family of non-virus retroposons is unclear and may be very distant since only poor similarity was found between the TOC1 encoded ORFs and retrovirus polypeptides. The length of the tandem array of 76 base repeat sequences was conserved in most TOC1 elements and solo 76 base repeat sequences were not found outside TOC1 elements in the C. reinhardtii genome. Nucleotide substitutions allow all copies of the 76 base repeat to be distinguished from one another.

Base Sequence↗
PubMed1990

Integration of human immunodeficiency virus types 1 and 2 DNA in vitro by cytoplasmic extracts of Moloney murine leukemia virus-infected mouse NIH 3T3 cells.

An essential step in the life cycle of the human immunodeficiency virus (HIV) is integration of a DNA copy of the viral RNA into the genome of the infected cell. We show here that this step can be faithfully accomplished in vitro by the enzymatic machinery of another retrovirus, Moloney murine leukemia virus (MoMLV). Mini-HIV substrates, which are linearized plasmids with long terminal repeat sequences at their ends, were incubated with cytoplasmic extracts of MoMLV-infected NIH 3T3 cells and target DNA. The MoMLV integration apparatus carried out integration of the mini-HIV substrates correctly; the terminal nucleotides of the viral substrate were removed, and a 4-base-pair duplication of the target DNA flanked the inserted viral DNA (C. Shoemaker, S. P. Goff, E. Gilboa, M. Paskind, S. W. Mitra, and D. Baltimore, Proc. Natl. Acad. Sci. USA 77:3932-3936, 1980). Our experiments show that the substrate sequence requirements for integration in vitro were limited to a few nucleotides, as the similarity between HIV and MoMLV long terminal repeat ends is minimal.

Animals↗