Methylation of simian virus 40 Hpa II site affects late, but not early, viral gene expression

Expression of the chloramphenicol acetyltransferase gene in mammalian cells under the control of adenovirus type 12 promoters: effect of promoter methylation on gene expression

The effect of DNA methylation at specific promoter sites on gene expression was tested by using a sensitive and quantitative assay system. The plasmid pSVO CAT contains the prokaryotic gene chloramphenicol acetyltransferase (CAT) and a HindIII site in front of it for experimental promoter insertion. Upon insertion into pSVO CAT, the E1a and protein IX gene promoters from adenovirus type 12 (Ad12) DNA were capable of mediating CAT expression upon transfection in mouse cells. In many viral and nonviral eukaryotic genes, DNA methylation at highly specific sites in the promoter region can attain a regulatory function in gene expression. One of the important sites is the 5' C-C-G-G 3' sequence. The CAT-promoting activity of the early simian virus 40 promoter in plasmid pSV2 CAT is refractory to methylation by the Hpa II or Hha I DNA methyltransferase at 5' C-C-G-G 3' or 5' G-C-G-C 3' sequences, respectively, because this promoter lacks such sites. The CAT coding sequence of this plasmid carries four Hpa II and no Hha I sites. Methylation of the Hpa II sites in the coding region does not affect expression. The E1a promoter of Ad12 DNA comprising the leftmost 525 base pairs of the viral genome carries two 5' C-C-G-G 3' and three 5' G-C-G-C 3' sites upstream from the leftmost "TATA" signal. Methylation of the Hpa II or Hha I sites incapacitates this promoter. The promoter of protein IX gene of Ad12 DNA contains one 5' C-C-G-G 3' and one 5' G-C-G-C 3' site downstream and two 5' G-C-G-C 3' sites greater than 300 base pairs upstream from the TATA motif and probably outside the promoter. The protein IX promoter is not inactivated by methylation of these sites. These data demonstrate that critical 5' methylations in the promoter region decrease or eliminate transcription; methylations of sites too far upstream or probably any sites downstream from the TATA site do not affect expression.

Methylation of unique sequence DNA during spermatogenesis in mice

In order to study whether changes in methylation of unique sequence DNA were related to meiosis, DNA was purified from F9 embryonal carcinoma (a "primordial germ cell" equivalent), germ cells from immature testes (containing germ cells up to early spermatocytes), sperm, and appropriate somatic tissues. Restriction was performed with the isoschizomers Msp I and Hpa II, and Eco RI as a control. Electrophoresis and Southern transfers were followed by hybridization to a mouse major beta-globin clone (f7), a mouse pancreatic amylase clone (pMPa21), a type I, histocompatibility-2 clone (pH-2D-4), and a spermatid cDNA clone (pPM 459). The variably methylated sites were all hypomethylated in the embryonal carcinoma DNA and hypermethylated in DNA from immature testes and sperm, irrespective of the transcription state of the gene. The pattern in control tissues generally conformed to an inverse correlation of methylation with transcription. These results suggest that hypermethylation of sperm DNA persists from hypermethylation of these sequences early in testicular development, independent of gene expression.

Transcription in oocytes of highly methylated rDNA from Xenopus laevis sperm

The genes for ribosomal RNA exist as multiple copies in the genome. Each repeated unit comprises a region that codes for the 40S rRNA precursor, and a spacer region of uncertain function (Fig. 1a). In Xenopus laevis there are about 1,000 copies of the dinucleotide sequence C-G in each repeat unit, and of these about 250 can be tested for the presence of 5-methylcytosine using restriction endonucleases. Most of the detectable C-Gs are heavily methylated, but in somatic cells unmethylated C-Gs occur in a 60 base pair (bp) sequence (NTS-60) that is repeated in the spacer. In contrast, the spacer of sperm rDNA is heavily methylated at these and all other testable C-Gs. Loss of methylation at NTS-60 takes place during the first day of embryonic development, near the time when rDNA transcription begins. In an attempt to assess the significance of this developmental change in methylation, we have isolated sperm rDNA and investigated whether it can be transcribed in oocytes. We have found that sperm rDNA is transcribed as efficiently as cloned rDNA, although no loss of methylation was detectable. Direct sequencing of sperm rDNA showed that all 19 C-GS in the promoter are highly methylated. Thus, in the case of rDNA injected into oocytes, loss of methylation is unnecessary for effective transcription.

Complete DNA methylation does not prevent polyoma and simian virus 40 virus early gene expression

The effect of DNA methylation on polyoma virus and simian virus 40 gene expression was investigated. For this purpose, the cytosines of all C-G dinucleotides of the viral DNAs were methylated by the use of rat liver methylase and the completeness of methylation was verified by dinucleotide analysis and restriction endonuclease treatment. The biological activity of unmethylated and fully methylated DNAs was tested by microinjecting them into tissue culture cells. The functions analyzed included early and late viral gene expression, viral DNA replication, oncogenic transformation efficiency, and virus maturation. No difference in any of these biological functions was observed between methylated and unmethylated DNA. Early gene expression of methylated DNA is not the result of demethylation because viral DNA reextracted from the injected cells, under nonpermissive conditions, retained the methylation pattern of the input DNA. In contrast, viral DNA extracted from transformed cells or from intact virus particles was partially or completely demethylated.

Eukaryotic DNA methylation

Eukaryotic genomes contain 5-methylcytosine (5mC) as a rare base.5mC arises by postsynthetic modification of cytosine and occurs, at least in animals, predominantly in the dinucleotide CpG. The base is not distributed randomly in these genomes but conforms to a pattern. This pattern varies between taxa but appears to be inherited in a semi-conservative fashion. At the level of the genome, gross changes in the level of DNA methylation have been noted. This has encouraged speculation that the modification may play a role in cellular differentiation. Tissue-specific patterns of DNA methylation, predicted by various models of differentiation, have been found for most vertebrate genes so far examined. A correlation has emerged between the undermethylation of these regions and their transcription, but this is not always the case. While data for eukaryotic viral sequences are less equivocal, studies of this kind cannot in isolation distinguish between undermethylation being a cause or a consequence of gene activity. If it were a cause, it is probable that the demethylation of specific CpG sites would be a necessary yet not a sufficient condition for transcription to occur. The introduction of artificially methylated DNA sequences into individual eukaryotic cells by microinjection or transformation may provide the means to elucidate these questions in the future. In the meantime, the study of eukaryotic DNA methylation promises to contribute much to our understanding of the regulation of gene expression in these organisms.

Methylation status and DNase I sensitivity of immunoglobulin genes: changes associated with rearrangement

Immunoglobulin V kappa genes are transcriptionally silent in their germline context and become transcriptionally active upon fusion to the J kappa-C kappa region (kappa locus). To elucidate the role of chromosomal structure in this regulatory phenomenon we have investigated the DNase I sensitivity and methylation status of the kappa locus and selected V kappa genes in a variety of alleles exhibiting different rearrangement configurations and different levels of transcriptional activity. Our findings indicate that the kappa locus in either germline or rearranged contexts maintains a distinctive DNase I-sensitive, hypomethylated structure in plasmacytomas and hybridomas, irrespective of its level of transcriptional activity. In contrast, the germline V kappa genes are in less accessible regions of chromatin and more highly methylated regions of DNA. Upon fusion to the kappa locus, V kappa genes become DNase I-sensitive and hypomethylated. This effect extends several kilobases upstream of the transcriptional initiation site but does not extend to the adjacent V kappa gene or to the identical V kappa allele on the other chromosome, indicating that the structural alteration is a localized cis-acting phenomenon.

Pattern of methylation of two genes coding for housekeeping functions

The distribution of sites that can be methylated was analyzed in the Chinese hamster adenine phosphoribosyl-transferase (aprt) gene and the patterns of methylation of this gene and the mouse dihydrofolate reductase (dhfr) gene were studied by using CpG restriction enzymes. Both genes were found to be unmethylated completely at their 5'-end region and methylated heavily throughout the rest of the gene. Because the hamster aprt gene can be inhibited by DNA methylation in vivo, the results suggest that 5' undermethylation of this gene may be a necessary condition for its expression. The pattern of methylation of each of these two genes was similar in sperm and all other somatic tissue DNAs. This is in contrast to many tissue-specific genes that were found to be highly methylated in sperm DNA and undermethylated in the tissue in which they are expressed. This result is consistent with the fact that both aprt and dhfr are key enzymes in the biosynthesis of nucleotides and therefore expected to be synthesized in all cells.