Chromatin structure of endogenous retroviral genes and activation by an inhibitor of DNA methylation

Endogenous avian retroviruses contain deficient promoter and leader sequences

A sensitive and quantitative biological assay has been utilized to measure the ability of the exogenous and endogenous avian retroviral long terminal repeats (LTR) to promote gene expression in avian cells. This assay has revealed that the exogenous virus RAV-2 LTR is approximately equal to 10-fold more active than the LTRs of endogenous viruses RAV-0, ev-1, and ev-2. The endogenous viral LTRs show approximately equal activity. Upstream flanking cellular or viral sequences have no significant modulating effect on gene expression in our assay. Unexpectedly, we have detected and localized an additional defect outside of the LTR in the 5' noncoding leader sequence of ev-1 that further decreases gene expression relative to RAV-0 by approximately equal to 10-fold.

Transcriptional activation of endogenous rat retrovirus with and without hypomethylation of proviral DNA

Induction of latent, endogenous retrovirus from normal vertebrate cells has been reported following exposure in-vitro to the thymidine analog 5-bromodeoxyuridine (BrdU), as well as to the cytidine analog 5-azacytidine (azaC). Although the mode of action of BrdU is still unclear, azaC is known to cause the hypomethylation of DNA in replicating cells. This work was performed in order to determine whether a common molecular mechanism existed. Although both drugs were equally effective in the induction of the same proviral DNA in normal rat embryo cells, only azaC-treated sequences demonstrated extensive hypomethylation of proviral genes. In contrast, viral-specific sequences from BrdU-treated DNA were indistinguishable from untreated samples with respect to digestion with Hpa II and Msp I. It is likely, therefore, that the drugs effect viral induction by different mechanisms, and that hypomethylation of structural genes may not be a requisite for transcriptional activation in general of proviral DNA.

Genomes of endogenous and exogenous avian retroviruses

The endogenous viruses of chickens are closely related to the exogenous avian leukosis viruses (ALV) yet as a group differ from these viruses in their host range, growth rate, and oncogenicity. The present study was undertaken to determine the patterns of relationship among the genomes of endogenous and exogenous ALVs. Complete or partial T1 oligonucleotide maps were prepared from the genomes of endogenous viruses that reside at eight distinct loci in chickens. Selected endogenous viruses and recombinants of endogenous or endogenous and exogenous viruses were characterized for host range and growth rate. From these data we could infer the following: (1) Endogenous viruses form a distinct lineage of ALVs with the most distinctive differences occurring in the portion of env that encodes host range and the U3 portion of the long terminal repeat; (2) The U3 sequences of endogenous ALVs determine the low growth rates of these viruses; and (3) Endogenous ALVs have distinctive oligonucleotide markers that allow them to be subclassified into distinct lineages. Our results suggest that endogenous viruses are derived from one another and not from exogenous field strains of ALV. This phenomenon may be related to the unique env encoded host range of endogenous ALVs, their unique U3 encoded growth rates, or perhaps their unique access, as residents of germ line DNA, to germ line cells.

Regulation of viral and cellular oncogene expression by cytosine methylation

Mink cells morphologically transformed by either Snyder-Theilen feline sarcoma virus (ST-FeSV) or Abelson murine leukemia virus (Abelson-MuLV) exhibit relatively high rates of reversion to the nontransformed phenotype. The proviral DNAs are conserved within the revertant lines and have not undergone changes in integration sites due to translocations or other genomic rearrangements. In contrast, expression of well-defined viral-encoded transforming proteins is blocked and elevated levels of phosphotyrosine characteristic of the parental transformed cells are reduced to control levels. Loss of the transformed phenotype is associated with increased cytosine methylation of proviral DNA sequences while levels of methylation resume control levels upon spontaneous retransformation of revertant clones. Following molecular cloning, and transfection to Rat-2 cells, ST-FeSV proviral DNAs from revertant and transformed cells induced similar numbers of transformed foci. Cytosine methylation sites involved in regulation of expression of the major ST-FeSV encoded transforming protein have been localized within the proviral DNA itself rather than in adjacent cellular flanking sequences. In contrast to the v-fes proviral DNA, c-fes, the cellular homolog of the ST-FeSV acquired transforming sequences, is highly methylated in cytosine residues in both transformed and revertant clones. These findings demonstrate regulation of viral oncogene-mediated transformation by cytosine methylation and suggest that expression of cellular homologs of viral oncogenes, such as c-fes, are also subject to regulation at this level.

Role of de novo DNA methylation in the glucocorticoid resistance of a T-lymphoid cell line

A correlation has been shown between changes in the methylation pattern of cytosine residues in DNA and the expression of specific genes in differentiated tissues. The pattern of DNA methylation is conserved, through cell division, by a maintenance methylase but the mechanism by which a given pattern of methylation is established is unknown. De novo methylation of foreign DNA molecules has been shown to occur in several systems, and may serve as a signal to arrest gene expression. Conversely, treatment of cultured cell lines with 5-azacytidine results in DNA hypomethylation and leads to transcriptional activation of previously unexpressed genes. The results described here demonstrate spontaneous de novo methylation of DNA in a T-lymphoid cell line previously treated with 5-azacytidine to generate glucocorticoid sensitivity. This de novo methylation is accompanied by the acquisition of the glucocorticoid-resistant phenotype.

Independent mechanisms involved in suppression of the Moloney leukemia virus genome during differentiation of murine teratocarcinoma cells

Expression and DNA methylation of the Moloney murine leukemia virus (M-MuLV) genome were investigated in murine teratocarcinoma cells after virus infection. The newly acquired viral genome was devoid of methylation, yet its expression was repressed. The integrated viral genome in undifferentiated teratocarcinoma cells was methylated within 15 days after infection. Although 5-azacytidine decreased the level of DNA methylation, it did not activate M-MuLV in undifferentiated cells. Activation by 5-azacytidine occurred only in differentiated teratocarcinoma cells. Thus two independent mechanisms seem to regulate gene expression during the course of differentiation. The first mechanism operates in undifferentiated cells to block expression of M-MuLV and other exogeneously acquired viral genes, such as SV40 and polyoma virus, and does not depend on DNA methylation. The second mechanism relates only to differentiated cells and represses expression of genes in which DNA is methylated.

Methylation of the chicken vitellogenin gene: influence of estradiol administration

The degree of methylation of the chicken vitellogenin gene has been investigated. Upon induction by administration of estradiol to a rooster, methyl groups at specific sites near the 5'-end of the gene are eliminated. The process of demethylation is slower than the activation of the gene. Demethylation is therefore probably not a prerequisite to gene transcription. At least two other sites in the coding region of the gene are methylated in the liver of estrogenized roosters, but not in the liver of a laying hen, where the gene is naturally active.

Composition and synthesis during G1 and S phase of a high mobility group-E/G component from Chinese hamster ovary cells

A perchloric acid soluble protein from the sedimented chromatin of blended Chinese hamster ovary (line CHO) cells has been isolated by guanidine hydrochloride gradient chromatography on Bio . Rex-70 ion exchange resin. The amino acid composition of the protein (designated as CHO HMG-E/G) is similar to that of mouse HMG-E, but it differs from that of bovine HMG-14 and HMG-17 or any possible mixture of the two. CHO HMG-E/G incorporates [32P]phosphate like HMG-14 and HMG-17 class proteins from other species, but all resolvable molecular species incorporate phosphate, and the more highly-phosphorylated band migrates faster, rather than slower, than the other in acid-urea gel systems. Incorporation of [3H]lysine into HMG-E/G following release from isoleucine deprivation G1 block indicates that the protein is extensively synthesized during both the G1 and S phases of the cell cycle.

In vitro methylation of specific regions of the cloned Moloney sarcoma virus genome inhibits its transforming activity

The transforming activity of cloned Moloney sarcoma virus (MSV) proviral DNA was inhibited by in vitro methylation of the DNA at cytosine residues, using HpaII and HhaI methylases before transfection into NIH 3T3 cells. The inhibition of transforming activity due to HpaII methylation was reversed by treatment of the transfected cells with 5-azacytidine, a specific inhibitor of methylation. Analysis of the genomic DNA from the transformed cells which resulted from the transfection of methylated MSV DNA revealed that the integrated MSV proviral DNA was sensitive to HpaII digestion in all cell lines examined, suggesting that loss of methyl groups was necessary for transformation. When cells were infected with Moloney murine leukemia virus at various times after transfection with methylated MSV DNA, the amount of transforming virus produced indicated that the loss of methyl groups occurred within 24 h. Methylation of MSV DNA at HhaI sites was as inhibitory to transforming activity as methylation at HpaII sites. In addition, methylation at both HpaII and HhaI sites did not further reduce the transforming activity of the DNA. These results suggested that; whereas methylation of specific sites on the provirus may not be essential for inhibiting the transforming activity of MSV DNA, methylation of specific regions may be necessary. Thus, by cotransfection of plasmids containing only specific regions of the MSV provirus, it was determined that methylation of the v-mos gene was more inhibitory to transformation than methylation of the viral long terminal repeat.

Activation of nonexpressed endogenous ecotropic murine leukemia virus by transfection of genomic DNA into embryo cells

We studied the infectivity of endogenous ecotropic murine leukemia virus genomes contained in high-molecular-weight DNA prepared from virus-free cells of the AKR-2B line, and from RF, BALB/c, B6, and (BALB/c x B6)F(1) mouse embryo cells. When DNA prepared from virus-free AKR-2B cells was transfected into NIH-3T3 cells, no virus-positive cultures were observed, a result consistent with previous reports. However, when DNAs from virus-free AKR-2B cells or virus-free cells containing the RF/J or BALB/c ecotropic proviruses were transfected into chicken embryo cells that were then cocultivated with SC-1 (mouse) cells, virus-positive cultures were recovered. The specific infectivities of the AKR provirus(es) contained in virus-free cells and the molecularly cloned Akv-1 provirus were similar when chicken embryo cells were used as primary recipients. Virus-positive cultures were also observed when secondary mouse embryo cells were used as recipients for DNA from virus-free AKR-2B and RF/J cells. The transfected chicken embryo-SC-1 cultures produced XC-positive murine leukemia virus that is N-tropic. Virus-positive recipient cultures were observed 10- to 100-fold more frequently when AKR-2B DNA was used than when BALB/c DNA was used as the donor DNA. Our studies indicate that some nonexpressed ecotropic murine leukemia virus proviruses are activated upon transfection into chicken embryo cells. Such studies suggest that there are different factors governing the expression of murine leukemia virus after transfection into established cell lines (NIH-3T3) and into nonestablished secondary cultures (chicken and mouse).

Hypomethylation of ras oncogenes in primary human cancers

We have examined the methylation status of two cellular oncogenes, c-Ha-ras and c-Ki-ras, in primary human carcinomas and the adjacent analogous normal tissues from which the tumors derived. The c-Ha-ras gene was hypomethylated in six of eight carcinomas, including five colonic adenocarcinomas and one small cell lung carcinoma, when compared to adjacent normal tissues. The c-Ki-ras gene was hypomethylated to a lesser extent in two colonic adenocarcinomas. This is the first demonstration of alterations in methylation of cellular oncogenes in human cancer.

Patterns of expression of erythroblast non-globin mRNAs

Three classes of erythroblast non-globin mRNAs have been identified using cDNA recombinants isolated from a mouse foetal liver cDNA library. One erythroid cell-specific 12S mRNA coding for a 16-19,000 dalton protein has been identified using two independent cDNA recombinants (pFC5 and pFA6). The gene encoding this mRNA is unique in the genome and its organisation seems to be the same in both erythroid and non erythroid cell genomic DNA as judged by digestion with restriction enzymes and Southern blotting. Another erythroblast mRNA of size 16S represented by recombinant pFD12 is expressed in brain cells as well as a variety of haemopoietic cell types, but not in adult liver or fibroblasts. Two other erythroblast mRNAs of size 8S and 12S represented by recombinants pD6 and pA4 are expressed in many differentiated cell types with the exception of non-dividing cells such as reticulocytes, peripheral white blood cells, adult liver and brain cells. These mRNAs are, therefore, presumed to be involved ubiquitously in cell proliferation or general cell metabolism.

Nucleotide sequence of the long terminal repeat and flanking cellular sequences of avian endogenous retrovirus ev-2: variation in Rous-associated virus-0 expression cannot be explained by differences in primary sequence

A fragment of chicken DNA containing the left long terminal repeat of endogenous retrovirus ev-2 and flanking cellular sequences has been molecularly cloned and analyzed. Comparison with sequence data from the analogous regions of ev-1 and Rous-associated virus-0 viral DNA reveals similarities among flanking regions of the integrated proviruses and among all three long terminal repeats. From the latter finding, we conclude that the difference in level of expression of ev-2 and its progeny Rous-associated virus-0 provirus cannot be due to sequence differences in their upstream long terminal repeats.

Kinetics of expression of infectious ecotropic, xenotropic, and mink cell focus-forming murine leukemia virus after 5-iododeoxyuridine induction of cells from high- and low-leukemia mouse strains

Endogenous murine leukemia virus (MuLV) was induced with 5-iododeoxyuridine (IdUrd) from the high-leukemia mouse strain AKR and from two low-leukemia strains, C3H/He and BALB/c. A virus-free cell line from strain AKR readily gave rise to infectious, XC-positive MuLV upon treatment with IdUrd, whereas cells from strains C3H/He and BALB/c produced replication-deficient, XC-negative MuLV. IdUrd-induced cells also produced xenotropic and mink cell focus-forming MuLV. Xenotropic virus emerged at a higher titer from both AKR and BALB/c cells during two discrete time intervals, first at day 3 after induction and a second time during spread of the induced ecotropic MuLV. Xenotropic and mink cell focus-forming MuLVs were also produced by IdUrd-induced C3H/He cells but required another round of infection in Sc-1 cells for detection. The in vitro infectivity of endogenous ecotropic MuLV isolated by IdUrd induction from C3H/He cells correlated with pathogenicity in the Fv-1-compatible, leukemia-negative mouse strain NFS/N. Thus, the virulence of endogenous ecotropic MuLV may be an important factor in determining the leukemia incidence in these inbred strains of mice.

Effect of several inhibitors of enzymatic DNA methylation on the in vivo methylation of different classes of DNA sequences in a cultured human cell line

We have previously demonstrated that, while most enzymatic formation of 5-methylcytosine in the DNA of mammalian cells occurs very shortly after strand synthesis, there is also a minor fraction of methylation which occurs in some DNA sequences up to at least several hours after strand synthesis. Using a human cell line, we have examined the effects on these two classes of enzymatic DNA methylation of several compounds which have been reported to be inhibitors of methylation reactions. We have found that cycloleucine, ethionine, and 5'-deoxy-5'-methylthioadenosine (MTA) are all effective as inhibitors of enzymatic DNA methylation, but that there is no differential effect between the delayed and non-delayed methylation reactions. Tubericidin (7-deaza-adenosine) plus homocysteine inhibited delayed DNA methylation much more than non-delayed methylation (by up to 4 times). By contrast, 5-azacytidine produced a higher level of inhibition of DNA methylation at sites in the DNA in which the methylation occurred very shortly after strand synthesis. Also 5-azacytidine was by far the most potent inhibitor of DNA methylation of the compounds tested. S-Adenosyl-homocysteine and caffeine were found to have no effect on DNA methylation. These results are discussed in relation to the number and specificity of DNA methylases in these cells and to the cellular functions of those DNA sequences in which methylation is delayed for some hours after strand synthesis.

DNA methylation patterns in the 5S DNAs of Xenopus laevis

The frequency of cytosine methylation at specific sites in the somatic 5S DNA (X1s) and trace oocyte 5S DNA (X1t) of X. laevis has been determined using restriction enzymes that are inhibited by the presence of 5-methylcytosine (5mC) within their cleavage sequences. 5S DNA methylation patterns were determined in genomic DNA from mature red blood cells, which express neither type of 5S gene, and from liver, which expresses only X1s. All the sites examined in X1t are greater than 95% methylated in red cells and liver. In the X1s of red cells all the sites examined are methylated in greater than 95% of repeats, while in liver some sites are modified in only 90% of repeats. Repeats containing unmethylated sites are randomly distributed throughout the tandem arrays in both red cells and liver. The high levels of methylation for X1s are in marked contrast to the situation with other Xenopus genes which do have sites of significant undermethylation in tissues where they are active. Thus, undermethylation in active genetic regions may not be a general feature for all classes of eukaryotic genes.

Methylation of the T-DNA in Agrobacterium tumefaciens and in several crown gall tumors

Methylation of the T-DNA in Agrobacterium tumefaciens and in four octopine-type (A6S/2, E9, 15955/1, 15955/01) and one nopaline-type (HT37#15) crown gall tumors was investigated using the isoschizomeric restriction endonucleases Msp I and Hpa II. T-DNA in the octopine-type Ti-plasmid pTiB6(806) was not methylated at the sequence 5'CCGG3' in Agrobacterium. With two possible exceptions, neither was the T-DNA of the nopaline-type Ti-plasmid pTiT37 methylated in the bacterium. In all tumor lines investigated, at least one copy of the T-DNA was not methylated. DNA methylation was not detected in the lines A6S/2, 15955/1, HT37#15, and the TL region of E9. DNA methylation of some copies of TR in the E9 tumor line, and possibly in the 15955/01 line, was detected. The methylation of some copies of TR in the E9 line may indicate that not all copies of TR are transcribed in this tumor.

Demethylation and expression of murine mammary tumor proviruses in mouse thymoma cell lines

Murine mammary tumor virus (MMTV) expression is analyzed in a T-lymphoid cell line (T1M1) sensitive to the killing effect of glucocorticoids and in two of its variants, one resistant (T1M1r) and one supersensitive (T1M1ss) to glucocorticoid-induced lymphocytolysis. In the T1M1 line, MMTV is expressed and induced approximately 10-fold by short treatment with dexamethasone. Southern blot analyses of restriction enzyme digests of DNA from T1M1 cells reveal three proviruses similar to those of normal C57BL mouse tissue. In the T1M1ss line, which has retained functional glucocorticoid receptors, MMTV mRNA is inducible by glucocorticoids, while induction is reduced in the T1M1r line defective in glucocorticoid receptors. Moreover, the T1M1r line expresses a strikingly elevated basal level of MMTV mRNA in the absence of hormone. No rearrangements or superinfection have occurred in the variants, but all the regions containing 5'-long terminal repeats are demethylated in the T1M1r variant although other sites of the provirus remain methylated. Because this variant was selected by prolonged treatment with dexamethasone, these observations raise the possibility that the continuous transcription of MMTV that occurred during this selection can result in glucocorticoid-induced demethylation of long-terminal-repeat sequences.

Inhibition of DNA methylation by 5-azacytidine

The nucleoside analog z5C induced marked changes in the differentiated state of mouse embryo cells and inhibited the methylation of newly synthesized DNA. Other analogs of cytidine containing modifications in the 5 position (5-aza-2'-deoxycytidine, 5-fluoro-2'-deoxycytidine, and pseudoisocytidine) also induced the formation of striated muscle cells in treated cultures and inhibited DNA methylation. Together the data suggests a causative role for the methylation of specific cytosine residues in the control of gene expression. Hemimethylated duplex DNA was extracted from cultures treated with z5C and was an efficient acceptor of methyl groups from S-adenosyl-methionine in the presence of a mouse spleen methyltransferase. The ability of this hemimethylated DNA to accept methyl groups was markedly impaired if it was pretreated with several different ultimate chemical carcinogens.

Can DNA methylation regulate gene expression?

The E2a region of the Ad2 genome encodes the Ad2-specific DBP. An inverse correlation between the level of DNA methylation at the 5'-CC*GG-3' sites of the E2a region and the extent of expression of DBP has been demonstrated in Ad2-transformed hamster cell lines (Vardimon et al. 1980). Four different leaders are used in the transcription of the E2a region in cells productively infected with Ad2. The leader located at coordinate 75 on the viral genome is used early after infection and the other three leaders are used late after infection (Chow et al. 1979). The analysis of the integration patterns of the viral DNA in the Ad2-transformed cell lines has revealed that the early leader is deleted in the cell lines which do not express the DBP (Vardimon and Doerfler 1981). The late leader located at coordinate 72 on the viral genome is present. The region encoding that late leader has been subcloned, and the cytoplasmic RNA from the cell line which expresses the DBP has been analyzed. It has been shown that the late leader is used in transformed cells. Hence the absence of the early leader cannot be the immediate reason for the lack of expression of the DBP. Correlations between DNA methylation and the absence of gene expression may indicate that methylation regulates gene expression or that methylation is the consequence of lacking gene expression. In order to decide between these alternatives an in vitro system has been employed. The HindIII A fragment of the Ad2 DNA which encodes the DBP has been methylated in vitro by the HpaII DNA methyltransferase. Methylated or unmethylated HindIII A fragment has been microinjected into the nuclei of Xenopus laevis oocytes. Unmethylated HindIII A fragment has been found to be expressed as specific viral RNA, whereas no viral RNA can be found in oocytes microinjected with methylated HindIII A fragment. The possibility of a nonspecific inhibitory factor in the methylated DNA preparation has been ruled out by the simultaneous microinjection of sea urchin histone gene DNA together with the methylated HindIII A fragment. Histone genes are expressed, while the expression of the methylated viral gene is blocked. By using the single-strand-specific endonuclease S1 we have shown that in Xenopus laevis oocytes initiation of transcription of the E2a region starts exactly at the same site as in Ad2 productively infected cells. These results provide direct evidence for the notion that DNA methylation at specific sites is involved in the regulation of gene expression.

Characterization of DNA methylation in the rat

In the rat, differentiation and cell proliferation both affect DNA methylation. We studied 5-methylcytosine at the inner cytosine of the sequence C-C-G-G, a common methylation site, using endonuclease MspI (which cleaves C-C-G-G- and C-mC-G-G), and its isoschizomer HpaII (which cleaves only C-C-G-G). DNA from all tissues and cell lines studied was methylated at C-C-G-G, at levels ranging from 45 to 80%, but the methylation sites were not distributed uniformly. Our analysis suggests a model in which cells contain variable amounts of three DNA methylation states, averaging 30-40, 70-80 and 95-100% methylation, respectively. One biological parameter that alters methylation is the proliferative state of the cell. We observed that NRK, a non-transformed cell line, increased its DNA methylation from 45 to 67% when monolayer cultures became confluent and non-dividing. We also observed that a class of repetitive DNA was completely methylated in DNA from all sources except a transformed cell line.

DNase I hypersensitive regions correlate with a site-specific endogenous nuclease activity on the r-chromatin of Tetrahymena

A novel nuclease activity have been detected at three specific sites in the chromatin of the spacer region flanking the 5'-end of the ribosomal RNA gene from Tetrahymena. The endogenous nuclease does not function catalytically in vitro, but is in analogy with the DNA topoisomerases activated by strong denaturants to cleave DNA at specific sites. The endogenous cleavages have been mapped at positions +50, -650 and -1100 relative to the 5'-end of the pre-35S rRNA. The endogenous cleavage sites are associated with micrococcal nuclease hypersensitive sites and DNase I hypersensitive regions. Thus, a single well-defined micrococcal nuclease hypersensitive site is found approximately 130 bp upstream from each of the endogenous cleavages. Clusters of defined sites, the majority of which fall within the 130 bp regions defined by vicinal micrococcal nuclease and endogenous cleavages, constitute the DNase I hypersensitive regions.

5-azacytidine selectively increases gamma-globin synthesis in a patient with beta+ thalassemia

5-Azacytidine is a cytidine analogue that is capable of activating repressed genes in tissue-culture cells and has been shown to increase hemoglobin-F production in anemic baboons. This drug was administered to a patient with severe beta-thalassemia in an attempt to stimulate hemoglobin-F production. After seven days of 5-azacytidine treatment, gamma-globin synthesis increased approximately sevenfold, temporarily normalizing the patient's unbalanced globin synthesis. Erythropoiesis became more effective, leading to a temporary increase in the absolute reticulocyte count (from 5000 to 22,000 per cubic millimeter) and in hemoglobin concentration (from 8.0 to 10.8 g per deciliter). Hypomethylation of bone-marrow DNA near both the gamma-globin and epsilon-globin genes was directly demonstrated. At the time of peak drug effect, about 7000 gamma-globin messenger RNA molecules were present per erythroid bone-marrow cell, in contrast to 10 to 15 epsilon-globin messenger RNA molecules per cell. 5-Azacytidine selectivity increases gamma-globin synthesis and therefore provides a new approach to the treatment of severe beta-thalassemia. Further studies will be required to evaluate the efficacy, risks, and long-term toxicity of 5-azacytidine (or related compounds) before this approach can be used as a therapy for patients with disorders of hemoglobin synthesis.

Methylation state and DNase I sensitivity of chromatin containing Moloney murine leukemia virus DNA in exogenously infected mouse cells

The nature of Moloney murine leukemia virus (M-MuLV)-specific proviral DNA in exogenously infected mouse cells was studied. M-MuLV clone A9 cells, NIH-3T3 fibroblasts productively infected with M-MuLV, were used. These cells contain 10 to 15 copies of M-MuLV proviral DNA. The state of methylation of M-MuLV proviral DNA was examined by cleaving A9 cell DNA with restriction endonucleases which have the dinucleotide CpG in their cleavage sequences. Analysis with such enzymes, which recognized nine different sites in M-MuLV DNA, indicated that most if not all of the M-MuLV proviruses in A9 cells were completely unmethylated. An individual proviral integration was examined, using as probe adjacent single-copy cellular sequences. These sequences were obtained from a lambda phage recombinant clone containing an M-MuLV provirus from the A9 cells. This individual integration also showed no detectable methylation. In contrast, endogenous MuLV-related sequences present in NIH-3T3 cells before infection were largely methylated. The configuration chromatin containing M-MuLV proviruses was also investigated by digesting A9 nuclei with DNase I, followed by restriction analysis of the remaining DNA. Endogenous MuLV-related DNA was in chromatin relatively resistant to DNase I digestion, whereas the majority of M-MuLV-specific proviruses were in domains of intermediate DNase I sensitivity. Two proviral copies hypersensitive to DNase I digestion were identified. Analogy to the DNase I sensitivity of expressed and nonexpressed globin genes suggested that the proviral copies containing DNase I-hypersensitive sites were transcribed.

Loss of type I procollagen gene expression in SV40-transformed human fibroblasts is accompanied by hypermethylation of these genes

Transformation of human lung fibroblasts (WI-38) by Simian Virus 40 (SV40) resulted in a decline of 25-30% in the amount of secreted collagen. The collagen produced by the transformed fibroblasts contained no type I collagen (i.e. alpha 1(I) and alpha 2 chains), which was the major collagen component produced by untransformed fibroblasts. Measurement of the procollagen mRNA levels by dot hybridization with nick-translated procollagen-cDNA clones showed that the absence of type I collagen was due to the absence of alpha 1(I) and alpha 2 procollagen mRNAs. This result was confirmed by hybridization of cDNA to total RNA with southern blots of the procollagen clones. To clarify the mechanism by which type I procollagen gene transcription is abolished in transformed cells, the methylation patterns of the alpha 1(I) and alpha 2 procollagen genes in normal and SV40-transformed fibroblasts were compared, using the chicken alpha 1(I) and alpha 2 procollagen-cDNA clones as probes. Methylated sites were detected by means of the restriction endonuclease isoschizomers HpaII and MspI. Methylation of the procollagen alpha 1(I) and alpha 2 genes was increased in the SV40-transformed fibroblasts, concurrently with the loss of type I collagen synthesis. DNA methylation may thus contribute to altered regulation of gene expression upon cell transformation.

Undermethylation at the 5' end of the albumin gene is necessary but not sufficient for albumin production by rat hepatoma cells in culture

We have measured methylation of the albumin gene in clones of rat hepatoma cells that vary quantitatively in their rates of synthesis of albumin and in variant and hybrid cells that produce no albumin. Although the albumin gene is undermethylated for its entire length in rat liver, only the 5' end is ever undermethylated in hepatoma cells. Moreover, undermethylation of the 5' end of the gene appears to be necessary for stable expression of the albumin gene in hepatoma cells. Since undermethylation of this region is found in some variant cells that fail to produce albumin, it is not a sufficient condition for albumin gene expression. Despite the excellent correlation between undermethylation of the 5' end of the albumin gene and its stable expression, the results argue against the possibility that the methylated state of such genes during development determines whether they will or will not be expressed.

Expression of transferred thymidine kinase genes is controlled by methylation

Plasmid pTKx-1, containing the herpes simplex virus gene for thymidine kinase (TK) inserted into the BamHI site of plasmid pBR322, was introduced into Ltk- cells by calcium phosphate precipitation in the absence of carrier DNA. Line 101 is a TK+ derivative of Ltk- that contains multiple copies of pTKx-1 in a multimeric structure. A derivative of 101 that retained but no longer expressed the herpes simplex TK genes (termed 101BU1) and derivatives of line 101BU1 that reexpressed the genes (termed 101H1, 101HC, and 101HG) were selected. The TK genes in 101BU1 were hypermethylated relative to those in the TK+ parent and derivatives. Growth of 101BU1 in the presence of the methylation inhibitor 5-azacytidine resulted in an average 13-fold increase in the number of TK+ reexpressors, DNA from 101BU1 was inactive in secondary gene transfer, whereas DNA from 101 and from TK+ reexpressors was active. These data support a causative relationship between DNA methylation and decreased gene expression. All TK+ reexpressors examined had DNA rearrangements involving TK DNA.

DNA methylation affecting the expression of murine leukemia proviruses

The endogenous, vertically transmitted proviral DNAs of the ecotropic murine leukemia virus in AKR embryo fibroblasts were found to be hypermethylated relative to exogenous AKR murine leukemia virus proviral DNAs acquired by infection of the same cells. The hypermethylated state of the endogenous AKR murine leukemia virus proviruses in these cells correlated with the failure to express AKR murine leukemia virus and the lack of infectivity of cellular DNA. Induction of the endogenous AKR murine leukemia virus proviruses with the methylation antagonist 5-azacytidine suggested a causal connection between DNA methylation and provirus expression. Also found to be relatively hypermethylated and noninfectious were three of six Moloney murine leukemia virus proviral DNAs in an unusual clone of infected rat cells. Recombinant DNA clones which derived from a methylated, noninfectious Moloney provirus of this cell line were found to be highly active upon transfection, suggesting that a potentially active proviral genome can be rendered inactive by cellular DNA methylation. In contrast, in vitro methylation with the bacterial methylases MHpaII and MHhaI only slightly reduced the infectivity of the biologically active cloned proviral DNA. Recombinant DNA clones which derived from a second Moloney provirus of this cell line were noninfectious. An in vitro recombination method was utilized in mapping studies to show that this lack of infectivity was governed by mechanisms other than methylation.

Active genes are sensitive to deoxyribonuclease I during metaphase

The active exogenous murine leukemia virus sequences of mouse cells growing in culture are preferentially digested by deoxyribonuclease I in metaphase chromosomes. As determined by nuclear nick translation, all of the gene sequences of these cells active during interphase are in a deoxyribonuclease I-sensitive conformation during metaphase. This method of nick translation can therefore be used to label chromosomes in situ in order to visualize the active regions of the genome.

Propagation of globin DNAase I-hypersensitive sites in absence of factors required for induction: a possible mechanism for determination

We tested whether DNAase I-hypersensitive sites, once induced, can be propagated to daughter cells in the absence of the original inducer. Chicken embryo fibroblasts infected with a temperature-sensitive Rous sarcoma virus at 41 degrees C and then shifted to 36 degrees C become transformed and begin to transcribe globin RNA. DNAase I-hypersensitive sites appear in the alpha- and beta-globin chromatin domains. Neither transcription nor hypersensitive sites are detected in cells infected and maintained at 41 degrees C. Activation of the globin hypersensitive sites occurs within 30 min of a temperature shift to 36 degrees C and does not require new protein synthesis. To test for the self-propagation of these hypersensitive structures, we inactivated the v-src gene product by a shift back up to 41 degrees C, and allowed the cells to divide 20 times at 41 degrees C. Although transcription of the globin genes was minimal after this treatment, the DNAase I-hypersensitive sites remained. The same sites can be induced by NaCl shock of cells. After the cells are returned to normal medium and allowed to grow for 20 doublings, the hypersensitive sites remain. This suggests that once formed, DNAase I-hypersensitive sites have the capacity to template their own structure independent of the initial "inductive" event. The single-stranded character of these DNAase I-hypersensitive sites could explain these results.

Interclonal variation in methylation patterns for expressed and non-expressed genes

A mass culture of human diploid fibroblasts, and eight clones isolated from that mass culture, were examined for methylation patterns in several regions of DNA. Plasmid-inserted cDNA sequences were used as probes for alpha-hCG, beta-globin, A gamma- and G gamma-globin, and beta- and gamma-actin gene regions. Each probe revealed a different clone-specific pattern of DNA methylation, indicating a striking degree of inter-clonal heterogeneity, for those gene regions which are not normally expressed in diploid fibroblasts (alpha-hCG, gamma-globin and beta-globin). Intra-clonal variation was also evident in many instances, implying that heterogeneity could arise de novo in pure cell clones during serial passage. Thus methylation patterns, in particular for repressed genes, appear to be unstably inherited in these cells, and this instability may lead to random derepression in some cell lineages during mitotic growth.

Transcriptional control signals of a eukaryotic protein-coding gene

Transcriptional control signals of a model eukaryotic protein-coding gene have been identified by a new procedure of in vitro mutagenesis. This method allows small clusters of nucleotide residues to be substituted in a site-directed manner without causing the addition or deletion of other sequences. Transcription assays of a systematic series of these clustered point mutants have led to the identification of three distinct control signals located within the 105-nucleotide residues immediately upstream from the point where transcription begins.

Deoxyribonuclease II as a probe to sequence-specific chromatin organization: preferential cleavage in the 72 bp modulator sequence of SV40 minichromosome

T prove sequence-specific chromatin structure of SV40 minichromosome, we further modified previously described hybridization mapping. Actually (i) the digestion patterns by two nucleases (micrococcal and DNAase II) were compared and (ii) the kinetics of nuclease digestion was analyzed from early time points when only a fraction of minichromosomes was cleaved once to longer digestions when oligo- and mononucleosomal bands appeared. DNAase II is shown to possess certain sequence specificity different from that of micrococcal nuclease. The major finding is that DNAase II preferentially cleaves the SV40 minichromosome at a distinct region of the genome known as 72 bp modulator element. Other hypersensitive sites are located near the replication origin and T-ag binding site II and also near BamHI site where termination of replication and "late" transcription occurs. Micrococcal nuclease splits the BglI-Hpaii region in a different manner.