The changes in proviral chromatin that accompany morphological variation in avian sarcoma virus-infected rat cells

Molecular biology of cell nonpermissiveness to retroviruses. Has the time come?

The problem of host cell nonpermissiveness to retrovirus infection is characterized and illustrated on several retroviral models, including the role of viral receptors, cell fusion, and endogenous retroviral genomes as modifiers of the outcome of retroviral infection. Special attention is paid to different barriers against the infection of mammalian cells with avian leukosis/sarcoma viruses (ALV/ASV). Even when avian retroviruses become integrated in mammalian cells, several blocks at the level of provirus expression, processing of viral RNAs, and posttranslational modification prevent virus production in such virogenic cells. The significance of these blocks and new strategies making it possible to overcome some of them are discussed in relation to the development of ALV/ASV-based vectors suitable for gene therapy in mammals.

Suppression of transformed phenotype in hybrids of v-fgr and v-raf transformed rat-1 cells with rat embryonic fibroblasts is due to transcriptional inactivation of viral oncogenes

Rat-1 cells that had been transformed to tumorigenicity by transfection with the retroviral oncogenes v-raf from 3611-murine sarcoma virus, or v-fgr from Gardner-Rasheed feline sarcoma virus were fused with rat embryonic fibroblasts at an early passage. In both fusion experiments hybrid cells were isolated that exhibited normal morphology, anchorage requirement for proliferation, and either no tumorigenicity (v-fgr) or extended latency periods for tumor growth (v-raf) in nude mice. Transcription of viral oncogenes is drastically reduced in hybrid cells (at least 30-fold compared to their transformed parental cells), while the half-life of the corresponding transcripts is not effected. In the chromatin of hybrid cells the integrated retroviral oncogenes are as sensitive to degradation with pancreatic DNase I as the endogenous actin gene. Thus the observed down regulation of proviral transcript levels does not correlate with changes in chromatin structure. We conclude that in hybrids of (v-fgr)- and (v-raf)-transformed Rat-1 cells with embryonic fibroblasts, transcription of the retroviral oncogenes appears to be repressed by trans-acting factors of the normal parental cell.

Dissection of the mouse N-ras gene upstream regulatory sequences and identification of the promoter and a negative regulatory element

The 5' flanking region of the mouse N-ras gene was investigated to determine the elements governing transcriptional activity of the gene. The promoter did not contain typical TATA or CCAAT boxes, and according to primer extension and RNase protection analyses, transcription started at several sites. These assays also confirmed the short nucleotide distance interposed between the N-ras transcription unit and the previously described upstream unr gene. Chromatin studies performed by digestion of nuclei with DNase I revealed the presence of four hypersensitive sites: a, b, c, and d. Deletion mutagenesis of the 5' flanking region revealed sequences responsible for both promotion and inhibition of transcription. These sequences resided within 230 bp upstream of the transcription initiation site. Hypersensitive site b colocalized with the 76-bp segment with promoter activity. The negative regulatory element at position -180 colocalized with hypersensitive site a, was active on the N-ras promoter in stable as well as transient assays, and down-regulated the heterologous herpes simplex virus thymidine kinase promoter. Footprint analysis and in vivo transfection-competition experiments indicated that a trans-acting factor is responsible for the negative effect on transcription. The interaction between the cis-acting negative regulatory element and the promoter region may play a role in the tissue- and developmental-stage-specific patterns of expression of the N-ras gene.

Dissection of the mouse N-ras gene upstream regulatory sequences and identification of the promoter and a negative regulatory element

The 5' flanking region of the mouse N-ras gene was investigated to determine the elements governing transcriptional activity of the gene. The promoter did not contain typical TATA or CCAAT boxes, and according to primer extension and RNase protection analyses, transcription started at several sites. These assays also confirmed the short nucleotide distance interposed between the N-ras transcription unit and the previously described upstream unr gene. Chromatin studies performed by digestion of nuclei with DNase I revealed the presence of four hypersensitive sites: a, b, c, and d. Deletion mutagenesis of the 5' flanking region revealed sequences responsible for both promotion and inhibition of transcription. These sequences resided within 230 bp upstream of the transcription initiation site. Hypersensitive site b colocalized with the 76-bp segment with promoter activity. The negative regulatory element at position -180 colocalized with hypersensitive site a, was active on the N-ras promoter in stable as well as transient assays, and down-regulated the heterologous herpes simplex virus thymidine kinase promoter. Footprint analysis and in vivo transfection-competition experiments indicated that a trans-acting factor is responsible for the negative effect on transcription. The interaction between the cis-acting negative regulatory element and the promoter region may play a role in the tissue- and developmental-stage-specific patterns of expression of the N-ras gene.

Fusion of Rous-sarcoma-virus-transformed rat cells to morphologically normal human or rat cells results in transcriptional suppression of the provirus that depends on its chromosomal integration site

The fusion of a Rous sarcoma virus (RSV)-transformed rat fibroblast clone to at least 2 different human cell types reproducibly produces phenotypically normal hybrids. Analysis of such hybrids reveals that proviral silence is the result of transcriptional down-regulation, presumably by a trans-acting human molecule. Furthermore, this phenomenon seems to be strongly influenced by the proviral chromosomal integration site and its imposition may entail a mechanism that is required only transiently.

Specific nuclear proteins interact with the Rous sarcoma virus internal enhancer and share a common element with the enhancer located in the long terminal repeat of the virus

We have documented that the Rous sarcoma virus (RSV) internal enhancer functions in the nontransformed Baby Hamster Kidney (BHK) cell line. The sequences within this region were assayed for their ability to bind to specific factors present in BHK nuclear extracts using the gel retardation assay and DNAse I footprinting. At least two sequences within the internal enhancer which can specifically bind nuclear factors in vitro have been identified. These regions are located between nucleotides 813-850 and 856-877. These sites map within the overall region of the internal enhancer which has been shown to be essential for enhancer activity and within the specific region which can function as an orientation independent enhancer. Using the DNase I footprinting and binding data to design an oligonucleotide, we have demonstrated that an oligonucleotide extending from nucleotides 804-877 will substitute efficiently as an enhancer. We also demonstrate that the SV40 enhancer does not compete for the factors which bind to the RSV internal enhancer, whereas an oligonucleotide to the binding site for EFII in the LTR can compete for factor binding to the internal enhancer.

Efficient transformation by Prague A Rous sarcoma virus plasmid DNA requires the presence of cis-acting regions within the gag gene

A region in addition to and outside the long terminal repeats (LTRs) in the gag gene of the Prague A strain of Rous sarcoma virus was found to be essential in cis for efficient cell transformation by cloned viral DNA. Transformation in chicken embryo fibroblasts, which requires infectious virus production and reinfection, was facilitated in cis by sequences between nucleotides 630 and 1659. Efficient transformation of NIH 3T3 cells in which secondary spread of virus is not necessary (as it is in chicken embryo fibroblasts) required sequences between nucleotides 630 and 1149. A src cDNA clone which also lacks this region demonstrated low transformation efficiency, indicating that the role of the cis element cannot be attributed to interference with RNA splicing. The gag gene segment required in cis for transformation, between nucleotides 630 and 1149, could substitute for the simian virus 40 enhancer in either orientation, and cells transfected with Rous sarcoma virus LTR-driven plasmids containing the gag cis element had a two- to threefold increase in steady-state viral RNA levels compared with plasmids lacking this region. Thus, additional cis-acting regulatory elements located outside the viral LTRs may modulate viral gene expression and contribute to the efficiency of cell transformation.

Significance of DNase I-hypersensitive sites in the long terminal repeats of a Moloney murine leukemia virus vector

A Moloney murine leukemia virus-derived retroviral vector (N4) carrying the bacterial neomycin resistance gene (neo) was used to study the chromatin configuration of integrated proviral DNA in NIH 3T3-derived cell lines containing one copy of the vector DNA per cell. Three independently obtained cell lines were examined. In two of these cell lines, the vector was introduced by viral infection, while in the third the construct was introduced by DNA transfection. Such transfected cell lines (including the one examined) usually express 10- to 50-fold less virus-specific RNA than do cell lines obtained by viral infection. All three cell lines exhibited similar patterns of DNase I-hypersensitive (HS) sites. Two strong DNase I HS sites were detected in the 5' long terminal repeat, which contains signals required for proper and efficient initiation of viral transcription. One of these sites was found to overlap the viral enhancer sequences, while the other site mapped very close to the start site for viral transcription. A third HS site was detected in nearby internal viral sequences. Only one HS site was found in the 3' long terminal repeat, which contains the signal(s) required for proper addition of a poly(A) tail to viral transcripts. This HS site was located in the region of the viral enhancer. Several weak DNase I HS sites were also found in the cellular sequences adjacent to the integration sites, at different locations in each cell line analyzed. No common pattern of cellular DNase I HS sites was found. These observations suggest that the 5' and 3' long terminal repeats of integrated retroviral proviruses exhibit different chromatin conformations, possibly reflecting the different functions encoded by the otherwise identical sequences, and the DNase I HS sites detected in these studies reflect only a potential for transcription and are not a reflection of the high transcriptional activity characteristic of retroviruses.

Chromatin structure of the promoter region of the human c-K-ras gene

The chromatin structure of the human c-K-ras gene has been investigated in various cultured normal and tumor human cells and in a rat cell line transformed with the human oncogene. The promoter region is hypersensitive to DNAse I, micrococcal nuclease, endogenous nucleases and to S1 nuclease in supercoiled plasmids. This hypersensitive region is present in the different cell types analyzed and both normal and mutant alleles exhibit similar general sensitivity to DNAse I digestion in the same tumor cells. However, the 5' more distal DNAse I hypersensitive site, which is coincident with a region of the gene containing sequence homologies with known enhancers, exhibits variable sensitivity which appears to be higher in the tumor than in the normal and in the human than in the rat cells which we have analyzed. These data suggest the presence of specific factors interacting with the promoter sequences and delimits the transcription unit of the c-K-ras locus.

Control of expression of an integrated Rous sarcoma provirus in rat cells: role of 5' genomic duplications reveals unexpected patterns of gene transcription and its regulation

Rat cells transformed by Rous sarcoma virus frequently contain duplications of viral (and sometimes cellular) DNA 5' to the integrated provirus, suggesting that such rearrangements favor provirus expression. In one cell line, A11, the duplication includes the viral src gene and proviral sequences that flank it. We examined three possible roles for this structure. Since the proviral v-src gene transformed recipient cells upon DNA transfer and was the major template for v-src transcription in A11 cells, the presence of v-src in the duplication is presumably not necessary for transformation. Since the size and structure of transcripts from the proviral v-src gene in A11 cells were conventional, the duplication does not facilitate transformation by providing a novel transcriptional strategy. Thus, we favor the concept that the duplication either attenuates a negative effect of flanking elements at the host chromosome integration site or augments the positive regulation of conventional provirus expression or both. Gene transfer and transcription analyses with both genomic and cloned DNA showed that the mechanisms of such regulatory phenomena are complex. Identical sequences in the provirus and the 5' duplication displayed different patterns of expression in A11 cells that could be disrupted in segments of cloned DNA. Among the elements that influenced such expression were sequences from the gag-pol region of the provirus.

DNA methyltransferases in normal and avian sarcoma virus-transformed rat cells. Quantitation of 5-methyldeoxycytidine in DNA and enzyme kinetics study

In rat kidney cells transformed by avian sarcoma virus (B77 strain) DNA is hypomethylated (2.61 +/- 0.07%) when compared to DNA extracted from normal cells (3.33 +/- 0.11%) as revealed by high-performance liquid chromatography analysis. Kinetics studies showed that no significant differences could be detected between DNA methyltransferase activities from normal and transformed cells with regard to apparent Vmax, apparent Km for S-adenosylmethionine (2.32 X 10(-6) M and 6.64 X 10(-6) M respectively) and apparent Ki for S-adenosylhomocysteine (9.2 X 10(-7) M and 7.8 X 10(-7) M respectively), when unmethylated duplex DNA was used as second substrate. Equivalent ratios of S-adenosylmethionine over S-adenosylhomocysteine were measured in each cell type and DNA methyltransferase activities from both sources were found to be strictly additive. These results show that the hypomethylation of DNA detected in transformed cells is related neither to alterations of enzymatic activities extracted from nuclei nor to unbalanced S-adenosylmethionine/S-adenosylhomocysteine ratios.

The effect of salt extraction on the structure of transcriptionally active genes; evidence for a DNAseI-sensitive structure which could be dependent on chromatin structure at levels higher than the 30 nm fibre

The procedure developed by Lawson and Cole (Biochemistry, 1979, 18 2161-2166) for removing lysine-rich histones from nuclei at low pH also quantitatively extracts proteins HMG14 and 17. The effect of this low pH extraction on the DNAseI-sensitive structures of active genes in avian red blood cells has been investigated. No major perturbation of a developmentally regulated DNAseI hypersensitive site in the beta-globin domain and at the 5' end of the alpha D gene was seen. The overall DNAseI-sensitive conformation of the beta A-globin gene (relative to the ovalbumin gene) is minimally affected by pH3 salt extraction, but there is some loss of sensitivity of the alpha D gene. Removal of HMG proteins at neutral pH had no effect on the sensitivity of active genes in erythroid or fibroblast nuclei. These results, together with those carried out on DNAseI sensitivity and HMG binding to monomer nucleosomes, indicate that there is a major structural feature of active genes responsible for DNAseI-sensitivity which is independent of HMG proteins or nucleosome core particle structure but may be dependent on higher order chromatin structures.

Rearrangements of viral and cellular DNA are often associated with expression of Rous sarcoma virus in rat cells

Rous sarcoma virus (RSV) proviruses integrated within the DNA of transformed rat cells frequently display duplications of variable segments of proviral DNA upstream of an intact provirus. The rearrangement in the A11 clone of transformed rat cells consists of a partial duplication of both viral and cellular DNA segments whose origin is a region of approximately 4 kb encompassing the 3' virus-cell junction. Transposition of this DNA appears to have occurred at or after virus integration by a mechanism involving at least two recombination events. In every case examined, including A11, the transcriptional organization of the original provirus has been conserved and viral RNA expression appears to occur normally. The frequency of such rearranged proviruses in the DNA of transformed rat cells suggests that upstream rearrangements may influence provirus expression.

Mapping of DNase I-hypersensitive sites in the 5' and 3' long terminal repeats of integrated moloney murine leukemia virus proviral DNA

The chromatin state of integrated Moloney murine leukemia virus (M-MuLV) proviral DNA was investigated. Nuclei from M-MuLV-infected mouse NIH 3T3 cells were digested with limited amounts of DNase I, and hypersensitive (HS) sites were mapped by the indirect end labeling technique. Particular emphasis was placed on the 5' long terminal repeat (LTR), since viral transcription initiates there. M-MuLV proviral DNA showed two strong DNase I-HS sites in the 5' LTR, one coincident with the transcription initiation (cap) site and the other with the transcriptional enhancers. Two weaker DNase I-HS sites were also detected in internal proviral DNA. The 3' LTR also showed a strong HS site in the region of the enhancers, but an HS site at the cap site of the 3' LTR was not detected. Thus, the chromatin configurations of the 5' and 3' LTRs of integrated M-MuLV proviruses appear to be different. The chromatin configuration of M-MuLV proviruses which contain LTR insertions of polyomavirus enhancer sequences was also studied. The 5' LTR of M-MuLV proviruses containing polyoma enhancer sequences substituted for the M-MuLV enhancers showed two strong HS sites, one in the polyoma sequences and one at the cap site. The 5' LTR of M-MuLV proviruses containing polyoma enhancer sequences inserted into the wild-type M-MuLV LTR between the cap site and the M-MuLV enhancers showed three HS sites. Two HS sites corresponded to those of the wild-type M-MuLV LTR, whereas the third mapped to the inserted polyoma sequences. The HS site associated with the inserted polyoma sequences was considerably stronger than the M-MuLV-associated HS sites.

The chromatin structure of Rous sarcoma proviruses is changed by factors that act in trans in cell hybrids

In several lines of Rous sarcoma virus (RSV)-transformed rat cells the proviruses are in a configuration typical of active eukaryotic genes. They are sensitive to pancreatic DNase I, with sites hypersensitive to nuclease near the 5' end of the genome, they are close to the nuclear 'cage' and they show a low level of cytosine methylation in CpG doublets. In contrast, in phenotypically untransformed hybrids between these cells and uninfected rat or mouse cells, RSV inactivity is associated with hypermethylation of the provirus, reduced DNase I sensitivity (in two out of three examples) and, where examined, relative remoteness from the nuclear cage. These changes in proviral configuration, which occur rarely in spontaneous reversion of transformed cells, can thus be induced at high frequency and stability in cell hybrids by trans-acting influences of the uninfected parents.

Analysis of the variations in proviral cytosine methylation that accompany transformation and morphological reversion in a line of Rous sarcoma virus-infected Rat-1 cells

Cells of the A11 lineage of Rat-1 contain a single complete Rous sarcoma provirus. Variation in the activity of this provirus accompanies fluctuations in the lineage between normal and transformed phenotypes. Increased proviral cytosine methylation of the doublet CpG in the tetranucleotide CCGG correlates with transcriptional inactivity and this pattern of cytosine hypermethylation is stable, even when the cells are transformed by another virus. However, transformation can also be induced by 5-azacytidine (but not by other mutagens) and in these transformants reduced proviral cytosine methylation is accompanied by increased proviral transcription. Differences in CCGG methylation between normal and transformed cells are found mainly in the 3' half of the provirus; sites near and within the src gene are heavily methylated only when the provirus is transcriptionally inactive. On the other hand, both transformed and normal A11 derivatives show little, if any, cytosine methylation of CCGG sequences in and flanking the 5' portion of the provirus.

Revertants and partial transformants of rat fibroblasts infected with Fujinami sarcoma virus

Fifteen revertants were isolated from three independent clones of rat fibroblasts transformed by Fujinami sarcoma virus (FSV). Three revertant clones resulted from the deletion of the one copy of the FSV provirus, and one encoded an enzymatically inactive, transformation-defective protein. The remaining revertant clones were characterized by a transcriptional block of the provirus. Digestion of chromosomal DNA with MspI and HpaII revealed that the FSV provirus was hypermethylated in these revertants, whereas proviral DNA of their spontaneous retransformants was hypomethylated. Furthermore, the revertants had lost DNase I-hypersensitive sites in and around the FSV provirus. The effect of transcriptional regulation of the FSV provirus was further analyzed in clones showing various degrees of phenotypic transformation. We quantitated v-fps mRNA levels in these cells by liquid hybridization and found that increasing levels of viral RNA correlated with a more pronounced transformed phenotype. These results suggest that transcription of FSV proviral DNA is under both viral and cellular control and that transformation by FSV is a function of the dosage of v-fps mRNA.

Analysis of the pathogenicity of transformation defective partial deletion mutants of avian sarcoma virus: characterization of recovered viruses which encode novel src specific proteins

Several transformation defective (td) mutants of the Prague strain of Rous sarcoma virus, which had been previously shown to have deletions of varying sizes and positions within the src gene, were tested for their ability to induce disease in chickens. Several of the mutants induced sarcomas after long latency, in particular two mutants which had deletions spanning the presumed active site (i.e., the phosphotyrosine residue) of the RSV transforming protein, pp60src. Viruses recovered from these tumors, as well as the tumors themselves, were analyzed to study the mechanism of tumor induction. In some examples proviral DNA structurally similar to wild-type virus was found in tumors and virus recovered from these tumors was shown to transform chick cells in vitro. Transformation specific proteins of 55,000 Da immunoprecipitable with antisera against pp60src were encoded by the recovered viruses. These proteins displayed a protein kinase activity, appeared to have small deletions in the amino termini, and by phosphotryptic peptide mapping appeared to contain novel phosphotyrosine tryptic peptides, when compared to wild-type virus, which were presumably derived from endogenous c-src.

The nuclease sensitivity of active genes

Brief micrococcal nuclease digestion of chick embryonic red blood cells results in preferential excision and solubilization of monomer nucleosomes associated with beta-globin sequences and also 5'-sequences flanking the beta-globin gene. Both regions are DNAse-I sensitive in nuclei. Such salt-soluble nucleosomes are enriched in all four major HMG proteins but HMG1 and 2 are only weakly associated. These nucleosomes appear to have lost much of the DNAse-I sensitivity of active genes. The HMG14 and 17-containing salt-soluble nucleosomes separated by electrophoresis are not DNAse-I sensitive and contain inactive gene sequences as well as active sequences. Reconstitution of HMG proteins onto bulk nucleosomes or chromatin failed to reveal an HMG-dependent sensitivity of active genes as assayed by dot-blot hybridization and it was found that the DNAse-I sensitivity of ASV proviral sequences as assayed by dot-blot hybridization was not HMG-dependent. These results indicate that higher order chromatin structures might be responsible for nuclease sensitivity of active genes.

Restriction enzyme analysis of partially transformation-defective mutants of acute leukemia virus MC29

Restriction enzyme mapping and limited sequence analysis have been used to study the generation and genome structure of three partial-transformation mutants of avian acute leukemia virus MC29. The three mutants, td10A, td10C, and td10H, could be shown to have sustained overlapping deletions of 200, 400, and 600 base pairs, respectively, in their genomes. The precise location of the deletions was mapped within the v-myc gene of the mutants by limited sequence analysis of cloned MC29 DNA. The data obtained are discussed in terms of the effect of these deletions on the mechanism of transformation by MC29.

Recovery of myc-specific sequences by a partially transformation-defective mutant of avian myelocytomatosis virus, MC29, correlates with the restoration of transforming activity

Avian myelocytomatosis virus MC29 transforms fibroblasts and macrophages in vitro. Recently we isolated three deletion mutants of MC29 that have a decreased ability to transform macrophages while retaining their capacity to transform fibroblasts. One of these mutants, MC29 td10H, on passage through chicken embryo cultures gave rise to a recovered virus MC29 10H B1, which has regained the ability to transform macrophages efficiently. Immunoprecipitation analysis of MC29 10H B1-infected cells revealed a 108,000-dalton gag-myc polyprotein as opposed to the 90,000-dalton protein of MC29 td10H or the 110,000-dalton polyprotein of wtMC29. Tryptic peptide mapping studies demonstrated that the 108,000-dalton protein had acquired v-myc peptides that were lost from the td10H 90,000-dalton polyprotein and two novel peptides. Restriction enzyme analysis of the MC29 10H B1 proviral DNA also showed that myc sequences had been acquired. These results suggest that MC29 td10H has recombined with c-myc sequences to generate a recovered virus, MC29 10H B1.