Methylation of CpG sequences in eukaryotic DNA.
Explore the source record for details and available documents.
Animals↗
Biomedical subjects
H Cedar
Publications and source records attributed to H Cedar.
Active gene sequences are undermethylated.
The degree of methylation of active regions of the chromosome has been investigated by several techniques. DNase I (deoxyribonuclease I, EC 3.1.21.1) was used to introduce nicks in the active regions of the nucleus and thereby specifically label these areas. By using the methylation-specific restriction enzymes Hpa II and Hha I it could be shown that active genes are more sensitive to these probes than are other parts of the genome. In order to measure the amount of methylation at all CpG residues, DNA was nick-translated in the presence of [alpha-32P]dGTP as the sole nucleotide source and the methylated cytosine was detected by the standard nearest-neighbor analysis. Using this assay, we found that about 70% of all CpG sequences in animal cell DNA are methylated. In active nuclear regions that are sensitive to DNase I, only 30-40% of the CpG residues are methylated. This method was also employed to study the gene sequences that are complementary to cellular RNA. By this criterion expressed gene sequences are only 20-30% methylated. These data suggest that undermethylation is a general phenomenon in all actively transcribed genes.
Animals↗
Methylation of adenovirus genes in transformed cells and in vitro: influence on the regulation of gene expression?
An inverse correlation has been described between the levels of DNA methylation in specific segments of adenovirus DNA integrated into the genomes of transformed and tumor cells and the extent to which these segments are expressed as messenger RNA. In the adenovirus type 2 (Ad2)-transformed hamster cell lines HE2 and HE3, the virus-specific DNA binding protein (DBP) is not expressed, and the DNA in the DBP gene is completely methylated in all 5'-CCGG-3' sites. At least part of the late promoter/leader sequence of the DBP gene is present in cell lines HE2 and HE3. In line HE1, on the other hand, the DBP is expressed, and the DNA in the DBP gene is unmethylated at the 5'-CCGG-3' (HpaII) sites. The late promotor/leader sequence of the DBP gene is expressed in cytoplasmic RNA isolated from line HE1. The effect of DNA methylation has also been tested in vitro in a microinjection system using Xenopus laevis oocytes. Unmethylated DNA fragments of Ad2 (E2a region) have been found to serve as active templates. When the same fragments are methylated at the 5'-CCGG-3' sites by the HpaII DNA-methyltransferase, viral RNA synthesis is inhibited upon microinjection into oocyte nuclei. These results provide direct evidence for the notion that DNA methylated at highly specific sites is somehow involved in the regulation of gene expression.
5-Methylcytosine↗
Nuclease sensitivity of active chromatin.
The active regions of chicken erythrocyte nuclei were labeled using the standard DNase I directed nick translation reaction. These nuclei were then used to study the characteristics and, in particular, the nuclease sensitivity of active genes. Although DNase I specifically attacks active genes, micrococcal nuclease solubilizes these regions to about the same degree as the total DNA. On the other hand micrococcal nuclease does selectively cut the internucleosomal regions of active genes resulting in the appearance of mononucleosomal fraction which is enriched in active gene DNA. A small percentage of the active chromatin is also released from the nucleus by low speed centrifugation following micrococcal nuclease treatment. The factors which make active genes sensitive to DNase I were shown to reside on individual nucleosomes from these regions. This was established by showing that isolated active mononucleosomes were preferentially sensitive to DNase I digestion. Although the high mobility group proteins are essential for the maintenance of DNase I sensitivity in active regions, these proteins are not necessary for the formation of the conformation which makes these genes preferentially accessible to micrococcal nuclease. The techniques employed in this paper enable one to study the chromatin structure of the entire population of actively expressed genes. Previous studies have elucidated the structure of a few special highly prevalent genes such as ovalbumin and hemoglobin. The results of this paper show that this special conformation is a general feature of all active genes irregardless of the extent of expression.
Animals↗
Hybridization analysis of the methylated bases of Escherichia coli DNA.
The 5-methylcytosine residues of Escherichia coli DNA are randomly dispersed along the genome. Hybridization data indicate that these methyl moieties are transcribed at the same frequency as the total DNA. These results suggest that DNA methylation probably does not play a role in gene expression in bacteria.
5-Methylcytosine↗
Methylation of foreign DNA sequences in eukaryotic cells.
The herpesvirus thymidine kinase gene has been used to introduce foreign DNA sequences into mouse L cells by DNA-mediated gene transfer. These inserted genes were then assayed for methylation at the specific sequence C-C-G-G by using the restriction enzyme isoschizomers Hpa II and Msp I. Despite the fact that 70% of the cellular C-C-G-G sites are methylated, herpesvirus sequences, plasmid DNA, and growth hormone gene DNA were found to remain unmethylated in 90% of the clones that contain these genes. DNA that had been methylated in vitro with Hpa II methylase was also inserted into L cells. The presence of this modification in the vector DNA did not, however, guarantee that these sequences remained methylated in the recipient clones. Only 10% of all transformed clones were found to contain methylated C-C-G-G sequences in the vector DNA, and these modifications were stable for 25-50 generations. Hha I and Mbo I were used to probe for methyl groups at these restriction sites, but none of the inserted sequences acquired these modifications. These results are discussed in relation to various models put forth to explain the process of methylation in eukaryotic cells.
DNA↗
Reconstitution of a deoxyribonuclease I-sensitive structure on active genes.
Chicken erythrocyte nuclei have been labeled in the active regions of the chromosome by using the nick translation reaction. In this procedure, accessible areas of the genome are preferentially nicked by the action of pancreatic DNase I and subsequently labeled by using DNA polymerase I from Escherichia coli. These nuclei were employed as a substrate for studying the factors responsible for maintaining the special chromatin conformation of the overall population of active genes. Treatment of nuclei with 0.35 M NaCl resulted in the loss of DNase I sensitivity in the active genes, but this sensitivity could be restored when nuclei were reconstituted with the NaCl eluate. Further purification of the released factors revealed that the HMG (high-mobility group) proteins HMG-14 and HMG-17 are involved in maintaining the conformation of the active regions. These factors are not tissue specific and seem to be involved in the chromosomal structure of most of the active genes.
Animals↗
Quantification of newly synthesized virus RNA in moloney murine leukaemia virus-infected cells.
A technique for the isolation and characterization of newly transcribed murine leukaemia virus RNA in chronically infected cells has been developed. Cellular RNA was pulse labelled with 3H-uridine and virus-specific sequences were annealed with an excess of mercurated complementary DNA. Based on the affinity between mercurated cDNA and sulphydryl-Sepharose, the hybrid was specifically selected by affinity column chromatography. The specificity of this method was dependent on the purity of the cDNA and it was necessary to remove non-viral sequences from the cDNA in order to isolate virus-specific RNA. Between 0.5 and 0.8% of the labelled RNA in Moloney MuLV-infected rat cells and 1.5% of the labelled RNA in Moloney MuLV-infected NIH Swiss mouse cells were virus-specific. Using this methodology, the effect of the cell cycle on the transcriptional activity of proviral genes was investigated. Cultures of Moloney MuLV-infected rat cells arrested in Go phase of the cell cycle released reduced quantities of virus, but continued to synthesize virus RNA. The pools of virus RNA and p30 antigen in the Go-arrested cells equalled the pools in actively dividing cells. These results suggested that post-transcriptional events controlled virus production in the Go-arrested cells.
Animals↗
Nick translation of active genes in intact nuclei.
Explore the source record for details and available documents.
Animals↗
Direct detection of methylated cytosine in DNA by use of the restriction enzyme MspI.
The extent of methylation of the internal C in the sequence CCGG in DNA from various eukaryotic sources has been determined using the restriction enzyme MspI known to be specific for this sequence. The methylation of the CCGG sequence is reflected in the restriction pattern obtained by DNA treated with MspI and its isoschizomer HpaII and analyzed by gel electrophoresis. A direct method for detection 5-methylcytosine in the sequence CCGG has been deviced. DNA fragments obtained with MspI were radioactively labeled at their 5' ends and subsequently degraded to the corresponding 5'-deoxyribonucleoside monophosphates. 5 methylcytidylic acid has been found in most of the 5' ends of MspI fragments of calf thymus DNA (about 90%) indicating heavy methylation of the sequence CCGG in calf thymus DNA. The results also reveal a symmetric methylation of both strands at this sequence in calf thymus DNA. In contrast, the CCGG sequence in other eukaryotic DNAs from organisms like Neurospora, Drosophila and Herpes virus proved to be undermethylated at this sequence.
Animals↗
Activation of the endogenous proviral genes in mouse cells is not followed by increased sensitivity to deoxyribonuclease I digestion.
The disposition of chromosome proteins about the endogenous proviral DNA of BALB-c mouse has been studied. The sensitivity of the endogenous proviral DNA sequences to deoxyribonuclease I (DNaseI) was analysed in BALB-c mouse tissues (liver and spleen) and in the cell line JLS-V9 which does not produce virus. On all of these preparations the endogenous proviral DNA was as sensitive to DNase I digestion as total chromatin. Since the proviral genes in JLS-V9 cells were silent, it was of interest to study possible changes in the chromatin structure following virus induction by iododeoxyuridine. We could not detect any increase in the sensitivity of the endogenous proviral DNA to DNase I digestion following induction. The induction was very efficient, however, since 60% of the cells responded to produce intracellular virus antigens.
Animals↗
Organization of 5-methylcytosine in chromosomal DNA.
The 5-methylcytosine residues of L-cells have been labeled with [methyl-3H]-L-methionine and their chromatin localization studied using deoxyribonucleases. The kinetics of micrococcal nuclease digestion showed that the methylated cytosine residues are concentrated within regions resistant to nuclease digestion and preferentially missing from those regions between nucleosomes which are nuclease sensitive. Using DNA hybridization kinetic analysis, it is shown that 5-methylcytosine is abundant in highly repeated sequences but is also present in middle repetitive and unique sequence DNA.
Base Sequence↗
Intragenic DNA spacers interrupt the ovalbumin gene.
We have performed restriction endonuclease mapping to examine the linear organization of the ovalbumin gene in chromosomal DNA. Treatment of genomic DNA with restriction endonucleases that do not cleave the ovalbumin mRNA sequence results in the generation of multiple DNA fragments capable of annealing with ovalbumin-specific probes in molecular hybridization reactions. These data strongly suggest that the linear order of DNA sequences coding for ovalbumin is interrupted by at least two intragenic DNA spacers absent from the corresponding RNA. At least one of these spacer sequences interrupts the coding sequence; therefore the chromosomal ovalbumin gene is not colinear with its translational product. We can discern no difference in the sequence organization about this gene in producer and nonproducer somatic cells, suggesting that the presence of intragenic spacers does not reflect that transcriptional activity of this gene. Furthermore, profiles obtained for gametes are identical to those observed for somatic cells, indicating that significant translocation during development is not responsible for the generation of this split sequence. Divergence of the intragenic spacer, however, is observed between individual chickens; thus multiple alleles may exist for this gene that are identifiable by differences in the organization of spacer with no apparent phenotypic evidence for their presence.
Animals↗
Selective degradation of integrated murine leukemia proviral DNA by deoxyribonucleases.
Explore the source record for details and available documents.
Animals↗
Distribution of 5-methylcytosine in chromatin.
The content of 5-methylcytosine in eukaryotic DNA was measured by mass spectrometry. Almost equal amounts of methylated cytosine were found in the DNA of various tissues of the chicken. When chromatin or nuclei were digested with micrococcal nuclease, 50% of the DNA was found to be nuclease resistant. In contrast to this, over 75% of the 5-methylcytosine was protected from nuclease digestion by chromatin proteins. These results suggest that 5-methylcytosine is nonrandomly distributed with respect to the nucleoproteins.
Animals↗
Methylation of chromatin DNA.
E. coli DNA methylase has been used to methylate chromatin DNA in vitro. At saturation only 50% of the chromatin DNA becomes methylated. The methylated regions of chromatin correspond to that fraction of the chromatin which is sensitive to staphylococcal nuclease. Using in vitro methylated chromatin followed by nuclease digestion movement of chromatin proteins along the DNA can be detected. By this criterion, sonication of chromatin or precipitation with MnCl2 causes 10% of the previously uncovered methylated regions to become covered by protein. Reconstitution of methylated chromatin results in the randomization of the chromatin proteins. Using nuclei which were methylated in vitro we have demonstrated that a small degree of protein sliding does occur during the preparation of chromatin from nuclei. Finally, we have prepared open region DNA by polylysine titration. This procedure does not cause displacement of chromatin proteins.
Animals↗
Control of RNA synthesis by chromatin proteins.
The effect of chromatin proteins on template activity has been studied. Using both E. coli RNA polymerase and calf thymmus polymerase B we have measured the number of initiation sites on chromatin and various histone-DNA complexes. Chromatin can be reconstituted with histone proteins alone and this complex is still a restricted template for RNA synthesis. The removal of histone f1 causes a large increase in the template activity. Chromatin is then treated with Micrococcal nuclease and the DNA fragments protected from nuclease attack ("covered DNA") are isolated. Alternatively, the chromatin is titrated with poly-D-lysine, and by successive treatment with Pronase and nuclease, the DNA regions accessible to polylysine are isolated ("open DNA"). Both fractions were tested for template activity. It was found that RNA polymerase initiation sites are distributed equally in open and covered region DNA.
Animals↗
The kinetics of E. coli RNA polymerase.
Using an assay specific for chain elongation of E. coli RNA polymerase the kinetics of this propagation reaction have been studied. The kinetic behaviour is consistent woth the mathematical model formulated for this multisubstrate enzyme. The effect of increasing salt concentration on the kinetics of the reaction indicated that DNA unwinding is probably a necessary step in the propagation step, although this may not be the rate limiting step under all conditions.
Adenosine Triphosphate↗