Alteration of c-myc chromatin structure by avian leukosis virus integration

Identification of a transcriptional enhancer element upstream from the proto-oncogene fos

Sequences upstream from the proto-oncogene fos were shown to be essential for its transcription. Transient expression of the chloramphenicol acetyl-transferase (CAT) gene linked to upstream sequences of the fos gene including its promoter reveals that sequences located 64 to 404 base pairs 5' to the fos cap site contain a typical transcriptional enhancer. Moreover, these enhancer sequences, which are strikingly conserved between mouse and human fos genes, coincide with a deoxyribonuclease I-hypersensitive site in the chromatin. The expression of the fos-CAT fusion genes was stimulated only two to three times by the fos inducer 12-0-tetradecanoyl phorbol-13-acetate. The fos enhancer does not appear to be tissue-specific.

Enhanced transcription of c-myc in bursal lymphoma cells requires continuous protein synthesis

In several bursal lymphoma cell lines in which c-myc transcription is regulated by avian leukosis virus (ALV) long terminal repeat (LTR) sequences, protein synthesis inhibition decreases the transcriptional activity of c-myc as well as other LTR driven viral genes. This decrease in transcription is associated with a change in the chromatin structure of c-myc, as measured by deoxyribonuclease I (DNase I) hypersensitivity, and a shift of transcription from the LTR to the normal c-myc promoter. In contrast, cycloheximide had little or no effect on the transcription of LTR driven genes in infected chicken embryo fibroblasts treated with the drug. These results suggest that a labile, cell type-specific protein may interact with the retroviral LTR and regulate transcription of genes under LTR control. Further, the results demonstrate that the increase in intracellular concentration of c-myc RNA induced by cycloheximide treatment of normal cells is the result of stabilization of this message.

Sequences outside of the long terminal repeat determine the lymphomogenic potential of Rous-associated virus type 1

Recombinant avian leukosis viruses have been constructed from the molecularly cloned DNAs of Rous-associated virus type 1 (RAV-1) and Rous-associated virus type 0(RAV-0). Virus encoded by the cloned RAV-1 DNA induced a high incidence of B-cell lymphoma and a moderate incidence of a variety of other neoplasms. Virus encoded by the cloned RAV-0 DNA did not cause disease. Virus recovered from DNA constructions that encoded the gag, pol, and 5' env sequences of RAV-0 and the 3' env and long terminal repeat sequences of RAV-1 did not cause a high incidence of lymphoma. Rather, these constructed viruses induced a low incidence of a variety of neoplasms. Virus recovered from reconstructed pRAV-1 DNA had the same disease potential as did virus recovered from the parental pRAV-1 DNA. These results indicate that the long terminal repeat sequences of RAV-1 do not confer the potential to induce a high incidence of B-cell lymphoma.

Chromosomal position and specific demethylation in enhancer sequences of germ line-transmitted retroviral genomes during mouse development

The methylation pattern of the germ line-transmitted Moloney leukemia proviral genome was analyzed in DNA of sperm, of day-12 and day-17 embryos, and of adult mice from six different Mov substrains. At day 12 of gestation, all 50 testable CpG sites in the individual viral genomes as well as sites in flanking host sequences were highly methylated. Some sites were unmethylated in sperm, indicating de novo methylation of unique DNA sequences during normal mouse development. At subsequent stages of development, specific CpG sites which were localized exclusively in the 5' and 3' enhancer regions of the long terminal repeat became progressively demethylated in all six proviruses. The extent of enhancer demethylation, however, was tissue specific and strongly affected by the chromosomal position of the respective proviral genome. This position-dependent demethylation of enhancer sequences was not accompanied by a similar change within the flanking host sequences, which remained virtually unchanged. Our results indicate that viral enhancer sequences, but not other sequences in the M-MuLV genome, may have an intrinsic ability to interact with cellular proteins, which can perturb the interaction of the methylase with DNA. Demethylation of enhancer sequences is not sufficient for gene expression but may be a necessary event which enables the enhancer to respond to developmental signals which ultimately lead to gene activation.

Active T-cell receptor genes have intron deoxyribonuclease hypersensitive sites

The T-cell receptor beta-chain gene has a nuclease hypersensitive site in several kinds of T cells, which does not appear in B cells expressing immunoglobulins. Conversely, the kappa immunoglobulin gene shows a known hypersensitive site at its enhancer element in B cells, as expected, but this site is absent in T cells. As is the case with immunoglobulin genes, the T-cell receptor site lies within the gene, in the intron separating joining and constant region segments. These nuclease hypersensitive DNA configurations in the introns of active T-cell receptor and immunoglobulin genes may arise from control elements that share ancestry but have diverged to the extent that each normally acts only in lymphoid cells which use the proximal gene product.

The association of human c-Ha-ras sequences with chromatin and nuclear proteins

As a step towards the understanding of possible relationship between chromatin organization and regulation of the oncogene expression, we have investigated the chromatin structure of one of the more frequently activated oncogenes, c-Ha-ras, in HeLa-S3 cells. This was accomplished by isolation of the chromatin fractions (soluble and insoluble) after micrococcal nuclease digestion of purified nuclei and probing for the distribution of ras sequences. The polynucleosomal fraction was further resolved by sucrose gradient sedimentation. Southern-blot hybridization of the DNA isolated from various fractions yielded following results: (1) c-Ha-ras sequences segregated predominantly in the lysate fraction. (2) Unlike the B-globin (transcriptionally inactive) sequences, ras-H associated chromatin lacked typical nucleosomal packaging. Furthermore, since post-translational modifications of nuclear proteins have been suggested to modulate the nucleosome structure during DNA transcription and replication, ras sequences, in polynucleosomes immunofractionated on anti-poly (ADP-Ribose) Sepharose were also examined. The data suggested that the major class of this oncogene sequence exists in chromatin more distal to the sites of this particular chromatin modification.

Clusters of CpG dinucleotides implicated by nuclease hypersensitivity as control elements of housekeeping genes

DNA sequences of the X-chromosome-linked hypoxanthine phosphoribosyltransferase (HPRT) and glucose 6-phosphate dehydrogenase (G6PD) genes have revealed the presence of clusters of CpG dinucleotides, raising the possibility that such clusters are involved in the control of expression of these genes, which are expressed in all tissues. Although CpG clusters are not exclusive features of the X chromosome, the analysis of X-linked genes provides the means to determine whether CpG clusters are control elements; one of the two homologous X loci in female mammals is not expressed, so that active and inactive versions of the gene can be compared. In fact, it has been shown that these CpG clusters are undermethylated when the gene is active and extensively methylated when the gene is inactive. In addition to hypomethylation, chromatin hypersensitivity to endonuclease digestion is a known hallmark of regulatory sequences in eukaryotic genes. We report here that the CpG clusters of the active hprt and g6pd genes are not only undermethylated, but also hypersensitive to MspI, DNase I and S1 nuclease, further supporting the suggestion that they are involved in the control of expression of these genes.

c-myc oncogene protein synthesis is independent of the cell cycle in human and avian cells

Several lines of evidence suggest a role for the myc oncogene in cell proliferation. Most recently, mitogenic stimulation of quiescent lymphoid, fibroblast and epithelial cells has been demonstrated to lead to a sharp increase in c-myc RNA levels. To determine how c-myc expression is linked to the cell proliferative cycle, we have used centrifugal elutriation to enrich for populations of avian and human cells at different stages of the cell cycle. Centrifugal elutriation is a counterflow centrifugation method that separates cells on the basis of volume, a parameter correlating well with progression through the cell cycle. Using myc-specific anti-peptide antibodies, we show here that the synthesis, half-life and modification of c-myc proteins are constant throughout the cell cycle of normal and transformed cells.

Levels of c-myc oncogene mRNA are invariant throughout the cell cycle

The steady-state messenger RNA levels of several genes increase when cells are stimulated to proliferate. The transcripts from one such gene, the proto-oncogene c-myc, increase approximately 20-fold shortly after cells are stimulated to proliferate and then decline before the onset of DNA synthesis. It has been inferred from these data that expression of c-myc may be specific to the G1 portion of the cell cycle. Alternatively, this transient increase in c-myc mRNA following the stimulation of quiescent cells could be the result of an activational event that renders the cells competent to enter the cell cycle. To distinguish between these possibilities, we performed experiments to determine whether the amount of c-myc mRNA fluctuates during the cell cycle in cells that are under constant stimulation to proliferate. Although c-myc mRNA does undergo a transient increase within 2 h of serum stimulation of quiescent serum-deprived cells, our results show that the level of c-myc mRNA is constant throughout the cell cycle and does not diminish in density-arrested cells maintained in the presence of serum growth factors. In contrast to c-myc, the mRNA levels of two other genes whose expression has been associated with cellular proliferation do show consistent variations within the cell cycle. Both thymidine kinase (TK) and histone 2b (H2b) mRNA levels increase during S phase in continuously growing cells and decrease when cell replication ceases in density-arrested cultures. Therefore, the transient increase in c-myc transcription following the activation of quiescent cells is not due to the type of cell cycle-dependent regulation characteristic of the TK and H2b genes.

Transcription of three c-myc exons is enhanced in chicken bursal lymphoma cell lines

The chicken c-myc gene, as defined by its homology to the v-myc gene of MC29 virus, is comprised of two exons. Using the techniques of runoff transcription, primer extension, and S1 nuclease protection, we demonstrate that there is a third c-myc exon of approximately equal to 345 base pairs (bp) located 0.7 kbp upstream of the 5' end of the v-myc homology. This first exon is transcribed and present in myc mRNA in normal chicken cells. We also examined RNA from five cell lines derived from avian leukosis virus-induced bursal lymphomas. In all these lines, the level of transcription of the 2.2- to 2.5-kbp myc mRNA is increased 30- to 60-fold over normal cells. The myc mRNA in four of these lines also contains increased levels of the first noncoding exon, and evidence is presented that the long terminal repeat (LTR) in the vicinity of c-myc is functioning as an enhancer of c-myc transcription rather than as a promoter in several of these cell lines. In two cell lines in which the viral LTR has integrated between the first and second exons in the proper orientation for downstream promotion of myc, the LTR does not exhibit promoter function. The pattern of c-myc transcription observed by others in a vast majority of avian leukosis virus-induced neoplasms is not observed in any of the five cell lines examined.

Chromatin structure at the 44D larval cuticle gene locus in Drosophila: the effect of a transposable element insertion

The chromatin structure of the larval cuticle gene cluster at 44D was characterized in embryos from wild-type (Oregon R) and a variant line (2/3) of Drosophila melanogaster. A major DNase I hypersensitive (DH) site was found between genes II and III in the chromatin, in a position 5' to the transcriptional start of the genes in the cluster. The introduction of a 7.3 kilobase transposable element into the cluster in the 2/3 variant enhanced the sensitivity of the major site in 2/3 chromatin but had no other effect upon the pattern of DH sites associated with the wild-type sequences. The wild-type sequences were packaged into an ordered nucleosome-like array in embryos, as revealed by digestion with the chemical cleavage reagent (methidiumpropyl-EDTA) iron (II) [MPE . Fe(II)]. Nucleolytic cleavage within the transposable element chromatin shows it to be organized in an ordered array punctuated by several DH sites. While the patterns of DNase I hypersensitivity are similar in the vicinity of the direct terminal repeats, the patterns revealed by micrococcal nuclease and MPE . Fe(II) are not, indicating a different chromatin organization of these two identical sequences.

Viral integration near c-myc in 10-20% of mcf 247-induced AKR lymphomas

We induced AKR thymomas by injecting retrovirus MCF 247 that we had tagged with a fragment of phage lambda in its U3 region. About 10-20% of the 26 primary tumors studied showed both rearranged and germline c-myc bands in Southern blots. The rearranged c-myc genes were cloned from two of the tumors and studied by Southern analysis in two others. In all four cases, rearrangement was due to integration of MCF 247 proviruses about 2 kilobases (kb) 5' of the three c-myc exons and in the opposite transcriptional orientation. Thus, viral integrations were clustered within a 1-kb range in the tumors that revealed c-myc rearrangements. Three of the four proviruses appeared to be intact, whereas the fourth had an internal deletion of about 3 kb.

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.

Nucleotide sequence 5' of the chicken c-myc coding region: localization of a noncoding exon that is absent from myc transcripts in most avian leukosis virus-induced lymphomas

We have determined the nucleotide sequence of the 2.2-kilobase-pair region upstream of the chicken c-myc coding exons. Using RNA blot analysis, we have localized a noncoding exon to a region that is separated from the c-myc coding sequences by an intron of 700-800 base pairs. In most avian leukosis virus-induced lymphomas proviral integration has occurred within, or downstream of, the first exon, thus presumably displacing the regulatory sequences that normally control c-myc expression. More than 70% of the integration sites were clustered in a 250-base-pair region in the first intron, immediately preceding the coding sequences. Sequences from the upstream noncoding exon were absent from the myc transcripts in these lymphomas; RNA transcripts from the normal c-myc allele were not expressed at detectable levels.