Methylation of DNA in early development: 5-methyl cytosine content of DNA in sea urchin sperm and embryos

Elevated temperature triggers increase in global DNA methylation, 5-methylcytosine expression levels, apoptosis and NOx levels in the gonads of Atlantic sea urchin

Global warming is one of the greatest threats to living organisms. Among them, marine invertebrates are severely impacted on reproductive fitness by rising seawater surface temperatures due to climate change (e.g., massive heat waves). In this study, we used highly sensitive radioimmunoassay, immunohistochemistry, enzyme-linked immunosorbent assay (ELISA), in situ TUNEL assay, luminescence assay, and colorimetric assay techniques to investigate the impacts of high temperatures on global DNA methylation, cellular apoptosis, and nitrative stress in gonads of Atlantic sea urchin (Arbacia punctulata, a commercially important species). Young adult sea urchins were exposed to 24, 28, and 32 °C for one week in a controlled laboratory setting. High temperatures (28 and 32 °C) markedly increased global DNA methylation (around 1.1-1.5-fold in testes and ~ 1.7-fold in ovaries) and 5-methylcytosine (5-mC) levels in gonads (around 2.7- to ~5.1-fold in ovaries and ~ 3.5- to ~6.2-fold in testes) compared with controls (24 °C). The number of apoptotic nuclei in gonads was much higher in high-temperature groups. The caspase activity also increased significantly (P < 0.05) in gonads in high-temperature groups. Nitrate/nitrites (NOx, a biomarker of reactive nitrogen species) levels were increased around 2.6- to ~5.2-fold in testes and ~ 1.9- to ~3.8-fold in ovaries in high-temperature groups. Collectively, these outcomes indicate that high temperatures drastically induce global DNA methylation, 5-mC expression levels, cellular apoptosis, and NOx levels in the gonads of Atlantic sea urchin.

DNA methylation and body temperature in fishes

Previous investigations from our laboratory [Jabbari, K., Cacciò, S., Pais de Barros, J.P., Desgres, J., Bernardi G., 1997. Evolutionary changes in CpG and methylation levels in the genome of vertebrates. Gene 205, 109-118.] led to the discovery of two different methylation levels in the genomes of vertebrates, a higher one exhibited by fishes and amphibians and a lower one shown by mammals and birds. It was also noted that data from the literature indicated a higher CpG level in fishes and amphibians compared to mammals and birds. Such observations led to suggesting the existence of two equilibria and to speculate that the transitions between the two equilibria in DNA methylation and CpG levels were due to a higher deamination rate in warm-blooded vertebrates related to their higher body temperature. Here we used Reverse-Phase High-Performance Liquid Chromatography (RP-HPLC) analysis to study methylation levels in a number of fish genomes living at different temperatures. We found that polar fishes exhibit DNA methylation levels that are higher than those of tropical and temperate fishes, the latter being in turn higher than the methylation levels of warm-blooded vertebrates, as expected from previous work. A closer analysis of the data revealed that, among Antarctic fishes, the Channichthyidae (the icefishes, deprived of haemoglobin) had the highest methylation level, and that, among temperate and tropical fishes the latter showed the lowest methylation level. These results confirm the existence of an inverse relationship between DNA methylation and body temperature, when the latter is maintained over evolutionary times.

Evolutionary changes in CpG and methylation levels in the genome of vertebrates

We have analysed the levels of 5-methylcytosine (5mC) in DNAs from 42 vertebrates, and compiled, including data from literature, a table of genomic 5mC and GC levels (as well as the available c-values, i.e., the haploid genome sizes) of 87 species from all vertebrate classes. An analysis of the data indicates that (i) two positive correlations hold between the 5mC and GC levels of the genomes of fishes/amphibians and mammals/birds, respectively; (ii) the genomes of fishes and amphibians are, on average, about twice as methylated as those of mammals, birds and reptiles, this difference being unrelated to the amounts of repetitive DNA sequences; (iii) the 5mC and CpG observed/expected values show no overlap between the two groups of vertebrates and suggest the existence of two equilibria. The transition separating the two equilibria appears to have taken place at the time of appearance of reptiles. Its possible cause(s) and its implications are discussed.

Genome methylation of the marine annelid worm Chaetopterus variopedatus: methylation of a CpG in an expressed H1 histone gene

Hydrolysis by methylation-dependent restriction enzymes shows that the genomic DNA of the polychaete annelid worm Chaetopterus variopedatus is methylated. Electrophoretic analyses of the digestion products indicate that the degree of methylation is lower in adult tissues than in sperm and embryonic DNA. 5-Methylcytosine was identified by HPLC, absorption spectroscopy and mass spectrometry analyses of free bases obtained by acid hydrolysis of the DNA. An average value of 1.6% methylated cytosines was determined in sperm DNA. Partial methylation was also found in an actively expressed H1 histone gene. This is the first time that genomic DNA methylation is demonstrated to occur in a worm.

Molecular characterization of the Spirometra mansonoides genome: renaturation kinetics, methylation, and hybridization to human cDNA probes

High molecular weight DNA from pleroceroid larvae of the tapeworm Spirometra mansonoides was purified from isolated nuclei by conventional techniques. The DNA so isolated has a melting temperature (Tm) of 87 degrees C and a guanine plus cytosine (G/C) content of 44%. 5-Methyl cytosine could not be detected in plerocercoid DNA by HPLC analysis of DNA hydrolysates, by radiolabeling 5'-termini of MspI digests with polynucleotide kinase, or by comparing restriction patterns generated by MspI and HpaII. Renaturation kinetics demonstrated that the genome of S. mansonoides contains repetitive as well as single copy sequences and has a genome size estimated at approx. 1.6 X 10(9) bp. Hybridization was carried out between plerocercoid DNA and cDNAs for human beta-actin, alpha-tubulin and growth hormone (hGH). Rationale for this analysis was based on known homologies among actin and tubulin genes in numerous species and on apparent similarities between hGH and a plerocercoid growth factor that may be reflected in similar DNA sequence. Scanning densitometry of dot blots demonstrated that the hGH probe annealed to the same extent at low stringency (1 M NaCl, 55 degrees C) to DNA from plerocercoids, rat liver and chicken erythrocytes; but this interaction was less than to DNA from human lymphocytes, calf thymus and mouse skin. Similar results were obtained when restriction endonuclease digests of these DNAs were analyzed by Southern transfer. Little or no hybridization of the growth hormone probe to plerocercoid DNA was evident at higher stringency (1 M NaCl, 65 degrees C). In contrast, human tubulin and actin probes showed extensive hybridization to pleroceroid restriction fragments under the high stringency conditions.

Separation of naturally occurring or induced methylated nucleobases of DNA by reversed-phase high-performance liquid chromatography

Separation of the major bases of DNA along with seven minor methylated ones was obtained by reversed-phase high-performance liquid chromatography using an isocratic elution system. Application of this procedure to DNA treated in vitro by N-methyl-N-nitrosourea has allowed identification of two induced minor bases; a third one was resolved using a slightly modified mobile phase. Baseline resolution of 3-methyl- and 5-methylcytosine, detected in Euglena DNA hydrolyzates, was also achieved.

Absence of detectable 5-methylcytosine in DNA of embryos of the brine shrimp, Artemia

DNA from three developmental stages of the brine shrimp, Artemia was found to be undermethylated compared to DNA from calf thymus and salmon sperm. Using high-performance liquid chromatography we found that DNA hydrolysates from both dormant cysts and prefeeding nauplii contain less than 1 residue of 5-methylcytosine per 59 kilobases, placing Artemia DNA in the "insect type" category. The absence of detectable 5-methylcytosine in DNA of developing Artemia supports the view that methylation status alone cannot account for regulation of transcription in protostomes, and that DNA methylation may be more common among deuterostomes.

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 of satellite DNA

The lower amount of 5 methylcytosine in DNA from bull sperm relative to DNA of other bovine tissues is a result of the absence of this minor base from several of the satellite DNAs in sperm. This applies particularly to the 1.715, 1.711b and 1.709 satellites and less so to the 1.706 and 1.711a satellites. Mouse sperm DNA is also partially undermethylated.

Alteration of enzymatic DNA methylation by chemical carcinogens

It is generally accepted that the DNA methylation pattern in a particular cell type is stable over the cell generations and is clonally inherited by a semiconservative mechanism in which the methylation of the progeny strand is determined by the 5-methylcytosine residue present in the parental strand. In our experiments, we have been able to show that the chemical carcinogens MNU, MNNG, and L-ethionine affect the methylation process either by modification of the DNA substrate or by interference at the cofactor level. The changes introduced into the cellular methylation pattern persist and are inherited in the progeny cells regardless of whether the carcinogens or their adducts in the DNA persist in the cell or not. The carcinogen-induced hypomethylation correlates with the increased transcriptional complexity of the nRNA of treated cells, indicating the initiation of transcription at sites previously inactive. This means that chemical carcinogens can cause, by interference with the process of DNA methylation, stable changes in the program of genetic expression; the possibility that such changes are related to the process of initiation of carcinogenesis should not be overlooked.

Cytochrome P1-450 structural gene in mouse, rat, and rabbit: differences in DNA methylation and developmental expression of mRNA

Clone 46 previously was shown to represent an 1100-bp cDNA clone of the mouse cytochrome P1-450 structural gene. Clone 46 [32P]DNA was hybridized to DNA and mRNA from mouse, rat, and rabbit of different ages. In Hpa II digests of DNA, two hybridizable fragments of less than 0.5 kb exist in adult "Ah-responsive" C57BL/6N mouse liver but not in C57BL/6N sperm or embryo or in adult "Ah-nonresponsive" DBA/2N mouse liver. The reason for this hypomethylation of adult C57BL/6N liver DNA is not known but might be related to the high degree of expressivity of this gene in adult C57BL/6N liver, compared with adult DBA/2N liver. No differences in Hpa II- or Msp I-digested DNA are seen in C57BL/6N or DBA/2N inbred strains treated with the P1-450 inducer, 3-methylcholanthrene (3-MC), versus untreated controls. The ontogenetic expression of 3-MC-induced P1-450 mRNA (23S) from mouse or rat liver corresponds well to previous developmental studies from this laboratory involving 3-MC-inducible aryl hydrocarbon (benzo[a]pyrene) hydroxylase (AHH) (EC 1.14.14.1) activity. P1-450 mRNA--induced transplacentally by 3-MC given to the mother--is readily detectable by clone 46 as early as gestational day 15. The cloned cDNA probe hybridizes to rat and rabbit DNA fragments of different sizes, and with less intensity, when compared with hybridization to mouse DNA. No hybridization of this DNA is observed with rabbit mRNA of all ages ranging from neonate to adult. These data suggest that sequence homology exists among the mouse, rat, and rabbit P1-450 structural genes and between mouse and rat P1-450 mRNA. The mouse cDNA probe is believed to hybridize to a segment of the rabbit P1-450 gene that is not transcribed.

DNA methylation in eukaryotes

The DNA of higher eukaryotes contains one minor base, namely 5-methylcytosine. The distribution of this minor base between different species and different DNA fractions will be considered together with the actual sequences methylated. The properties of the enzyme responsible for DNA modification will be reviewed, particular note being paid to the efficiency of methylation of different DNA substrates. Various possible functions of the 5-methylcytosine in DNA will be considered and particular attention will be paid to the finding that specific modified bases present in DNA not undergoing transcription are absent in the same genes when these are being actively transcribed.

DNA methylase during Xenopus laevis development

The DNA methylase activity present in embryos and cultured cells of Xenopus laevis resembles DNA methylase from mammalian tissues. Little or no activity is found in mature germinal vesicles, though nuclear activity rises rapidly after fertilization. This rise may result in part from a relocation of cytoplasmic enzyme.

Distribution of 5-methylcytosine in the DNA of somatic and germline cells from bovine tissues

Genomic DNA of calf thymus contains 1.5 times as much 5-methylcytosine as similar sperm DNA, but the major EcoRI repeat fragment from satellite I of thymus contains ten times as much 5-methylcytosine as the corresponding fragment from sperm DNA. Restriction enzyme analyses of the total DNA and the satellite I fragment show that three HpaII sites in the fragment are completely unmethylated in sperm but fully methylated in thymus DNA. Under-methylation of many sites in the satellite DNAs can probably account for the lower level of methylation of sperm DNA rather than hemimethylation as previously suggested. These results are also discussed in relation to maintenance and de novo (initiation-type) methylases.

Determination of 5-methylcytosine from plant DNA by high-performance liquid chromatography

The relative amounts of the five nucleosides (deoxycytidine, 5-methyldeoxycytidine, deoxyadenosine, deoxyguanosine and thymidine) in the DNA of nine plant species, one plant satellite DNA, and one animal species were determined by high performance liquid chromatography. The method allows the clean separation of the nucleosides from 10 microgram samples with 15 min. The following values for the proportion of methylated cytosines among all cytosines were obtained: Lobularia maritima 18.5%, Nicotiana tabacum 32.6%, Pisum sativum 23.2%, Rhinanthus minor 29.2%, Sinapsis alba 12.2%, Vicia faba 30.5%, Viscum album 23.2%, Cymbidium pumilum 18.8%, Cymbidium pumilum AT-rich satellite DNA 15.8%, Triticum aestivum 22.4%. DNA of an animal, the gerbil, Meriones unguiculatus, had a methylation percentage of 3.1%. An estimate of the GC content based on the buoyant density of DNA tends to be lower than the actual value, an estimate based on the melting temperature tends to be higher. This supports the finding by other authors that DNA methylation decreases the buoyant density and may increase the melting temperature at high m5C concentration.

5-Methylcytosine in eukaryotic DNA

A small portion of the cytosine residues in the DNA of higher eukaryotes as well as in that of many lowe eukaryotes if methylated. The resulting 5-methylcytosine residues occur in specific in the DNA, usually adjacent to guanine residues on the 3' side. This methylation of eukaryotic DNA has been proposed to function in many ways, including control of transcription, maintenance of chromosome structure, repair of DNA, establishment of preferred sites for mutation, oncogenic transformation, and, in certain systems, protection of DNA against enzymatic degradation.

Sequence organisation in nuclear DNA from Physarum polycephalum: methylation of repetitive sequences

Nuclear DNA from the slime mould Physarum polycephalum is digested by the restriction endonuclease HpaII to generate a high molecular weight and a low molecular weight component. These are referred to as the M+ and the M- compartment, respectively. Sequences that are present in the M+ compartment are cleaved by MspI, the restriction enzyme isoschizomer of HpaII, thus showing that the recognition sequences for these enzymes in M+ DNA contain methylated CpG doublets. The distribution of repetitive sequences in the M+ and M- DNA compartments was investigated by comparison of the 'fingerprint' patterns of total Physarum DNA and isolated M+ DNA after digestion using different restriction endonucleases, and by probing for the presence of specific repetitive sequences in Southern blots of M+ and M- DNA by the use of cloned DNA segments. Both types of experiment indicate that many repetitive sequences are shared by both compartments, though some repetitive sequences appear to be considerably enriched, or are present exclusively, either in M+ DNA or in M- DNA.

Amplified ribosomal RNA genes in a rat hepatoma cell line are enriched in 5-methylcytosine

In a rat hepatoma cell line, H4-IIE-C3, a 10-fold excess of 18S and 28S rRNA genes has been found in amplified chromosome regions. Antibodies to 5-methylcytidine bound extensively to the DNA of these regions, indicating a high level of DNA methylation. Most of the amplified rRNA genes were transcriptionally inactive, as shown by their failure to stain with silver. DNAs from the tumor cells and control rat hepatocytes grown with L-[methyl-14C]methionine were digested with restriction endonuclease EcoRI; the DNA fragments were separated by agarose gel electrophoresis, denatured, transferred to nitrocellulose filters, and hybridized to 32P-labeled rRNA or cDNA. Fragments containing the 18S or 28S rRNA coding sequences occurred in three major size classes; all three were rich in 5-methylcytosine. Analysis of EcoRI fragments of DNA from the tumor and control cells after digestion with Hpa II or Msp I endonuclease indicated that the 5'-C-C-G-G-3' sequences in most of the amplified rRNA genes were methylated. Analysis of the fragments produced by digestion with Hha I endonuclease indicated a high degree of methylation within its recognition sequence in the amplified rRNA genes as well. The association of hypermethylation with restricted transcriptional activity suggests that DNA methylation may regulate the activity of the rRNA genes.

DNA methylation and gene function

In most higher organisms, DNA is modified after synthesis by the enzymatic conversion of many cytosine residues to 5-methylcytosine. For several years, control of gene activity by DNA methylation has been recognized as a logically attractive possibility, but experimental support has proved elusive. However, there is now reason to believe, from recent studies, that DNA methylation is a key element in the hierarchy of control mechanisms that govern vertebrate gene function and differentiation.

Quantitative reversed-phase high performance liquid chromatographic determination of major and modified deoxyribonucleosides in DNA

We have developed a method to accurately determine (< 3% RSD) the complete major and modified base composition of a few micrograms of unlabeled DNA. The DNA samples were quantitatively hydrolyzed with DNase 1, Nuclease P1, and bacterial alkaline phosphatase. The resulting deoxyribonucleosides were directly separated in 70 min by reversed-phase high performance liquid chromatography with detection by ultraviolet absorption at 254 nm and 280 nm (RP-HPLC). The highly sensitive and selective dual wavelength quantitation greatly enhances the precision and accuracy of the chromatographic analysis. Contamination of DNA preparations with RNA does not interfere with the DNA analysis due to the high resolution of the chromatography. We have used this method for the quantitation of m5dCyd in 5 microgram of calf thymus and salmon sperm DNA in which the m5dCyd comprises only 1 to 2% of the total bases. This method should be a useful research tool in studies on various DNAs and DNA subfractions and should help to elucidate the functions of methylation of DNA.

Enzymatic hypermethylation of DNA in mouse-mouse somatic cell hybrids

Somatic cell hybrids between mouse L fibroblasts (A9 cells) and Ehrlich ascites tumour cells were constructed by use of poly(ethyleneglycol). The hybrids were selected in hypoxanthine/aminopterin/thymidine medium and morphologically different syncaryons were isolated by a micromanipulation. They were simultaneously analysed for their tumourogeneity, a release of certain proteins into the culture medium, the activity of pyrimidine salvage pathways, and the extent of enzymatic DNA methylation. None of these hybrids gave a rise of tumours if transplanted into DBA/2 mice. Two of the hybrids released a protein immunologically cross-reacting with antibody against C-peptide of human proinsulin. Activities of pyrimidine salvage pathways as measured by incorporation of [14C]deoxycytidine into DNA cytosine and thymine, respectively, are different in the analyzed cells. Enzymatic DNA methylation in somatic cell hybrids was significantly elevated as compared to the parental cell lines.

DNA methylation: organ specific variations in the methylation pattern within and around ovalbumin and other chicken genes

The restriction enzymes HhaI and HpaII, whose activity is inhibited by cytosine methylation within their recognition sites, have been utilised as probes to study methylation in the vicinity of the ovalbumin gene in DNA from various chicken tissues. This was complemented by a preliminary study of methylation in the regions of chicken ovotransferrin (conalbumin), ovomucoid and beta-globin genes. From our data we conclude that HaI or HpaII sites can be divided in 3 classes according to their pattern of methylation in different tissues. In the first class of sites (mV class) the extent of methylation varies in different tissues. The patterns obtained show that methylation at the sites located within and around the 3 genes which code for egg white proteins is in general lowest in oviduct of laying hen, where these genes are expressed. However some sites are not methylated (m- class) and others are 95 to 100% resistant (m+ class) to digestion by HhaI or HpaII in the DNAs of all the tissues which were tested. Our study has also revealed a remarkable number of allelic variants for the presence of HhaI or HpaII sites in the region of the ovalbumin gene.

Methylation of DNA in mouse early embryos, teratocarcinoma cells and adult tissues of mouse and rabbit

The distribution and amount of 5-methylcytosine (5-MeCyt) in DNA was measured for early embryos of mouse strain CF1 (2 to 4 cell stage to blastocyst) and mouse teratocarcinoma cells. In each case, the pattern of methylation was examined by use of the restriction enzymes Hha I and HPA II HPA II, which cut DNA at the sites 5'GCGC and 5'CCGG respectively, when the cytosines at these sites are not methylated. Mouse embryo DNA was found to have the same level of methylation as adult mouse tissues, and no changes in methylation were seen during differentiation of the teratocarcinoma cells. The ratio of 5-MeCyt/Cyt in DNA was measured by high performance liquid chromatography for the differentiating teratocarcinoma cells and for several adult mouse and rabbit tissues. The variation between tissues or between teratocarcinoma cells at different stages of differentiation was less than 10 percent. These results are discussed in view of proposals that 5-MeCyt plays a role in differentiation.