Tissue specificity and organisation of CpG methylation in calf satellite DNA I.

Examination of bovine satellite DNA I methylation within CpG dinucleotides has been made by restriction analysis. It is shown that variations in the methylation patterns occur between different tissues (brain, liver, thymus and sperm) . Some of the 8 Hpa II sites present per repeat are clearly undermethylated in sperm as compared to other tissues. Methylation is considered therefore, as a highly specific event. It is also shown that there is a spatial specificity in the methylation pattern of the 3 Hha I sites in all tissues. These results are discussed in the light of methylation and satellite DNA functions.     

Effect of CpG methylation on gene expression in transfected plant protoplasts

Activity of the cat gene driven by the cauliflower mosaic virus 35S promoter has been assayed by transfecting petunia protoplasts with the pUC8CaMVCAT plasmid. In vitro methylation of this plasmid with M.HpaII (methylates C in CCGG sites) and M.HhaI (methylates GCGC sites) did not affect bacterial chloramphenicol acetyltransferase (CAT) activity. It should be noted, however, that no HpaII or HhaI sites are present in the promoter sequence. In contrast, in vitro methylation of the plasmid with the spiroplasma methylase M.SssI, which methylates all CpG sites, resulted in complete inhibition of CAT activity. The promoter sequence contains 16 CpG sites and 13 CpNpG sites that are known to be methylation sites in plant DNA. In the light of this fact, and considering the results of the experiments presented here, we conclude that methylation at all CpG sites leaving CpNpG sites unmethylated is sufficient to block gene activity in a plant cell. Methylation of CpNpG sites in plant cells may, therefore, play a role other than gene silencing.     

Effect of CpG methylation on isotype and magnitude of antibody responses to influenza hemagglutinin-expressing plasmid.

We previously showed that intramuscular saline DNA immunizations favor the development of an IgG2a-dominant Th1 immune response, whereas gene gun DNA immunizations stimulate the production of an IgG1-dominant Th2 immune response. Several studies have implicated immunostimulatory CpG sequences as the causative factor in the development of Th1 immune responses to saline DNA immunization. To determine whether the Th1 cytokine-inducing properties of CpG sequences in plasmid DNA (pDNA) were responsible for the induction of a Th1 immune response, in vitro methylated and untreated (nonmethylated) hemagglutinin-expressing pDNA were compared for immunogenicity. Methylation abrogated the immunostimulatory activity of pDNA for cultured splenocytes and significantly reduced antigen expression. However, methylation of pDNA was not associated with a change from the induction of IgG2a to IgG1. After immunization with the methylated plasmid, the magnitude of the immune response was reduced. However, the decline in the total antibody response matched the decline in antigen expression. The dose of DNA or the presence of lipopolysaccharide in pDNA likewise did not affect the preferential development of an IgG2a antibody response. Our findings reveal that high levels of CpG sequences are not required for raising IgG2a-predominant, Thl-biased immune responses to intramuscular injections of hemagglutinin-expressing DNA.     

DNA methylation and CpG suppression

Cytosine methylation in vertebrate genomes occurs predominantly at the dinucleotide CpG. This dinucleotide is deficient in vertebrate DNA, an observation which has hitherto been explained by passive deamination of S-methylcytosine to thymidine. Since the frequency and distribution of CpG may prove to be a useful indirect means to study the function of DNA methylation, it is of interest that the observed 'CpG suppression' is less apparent within and around coding sequences. A variety of different mechanisms now appear to be responsible for maintaining a relatively high CpG level in these regions despite the apparent attendant disadvantage of mutation.     

Tissue-specific methylation of a CpG island in transgenic mice.

Clustering of CpG dinucleotides in CpG-rich islands is a characteristic feature of mammalian genomes. Such CpG islands are frequently associated with genes and usually hypomethylated, regardless of the gene activity. This is the case for the CpG island of the murine Thy-1 gene. A transgenic line containing multiple copies of a truncated, concatemeric CpG island from the Thy-1.1 allele (Thy-1.2 background) showed that a stable fraction (approx. 0.20) became fully methylated in somatic tissues of homozygous mice with respect to testable restriction sites, while the remaining copies were methylation-free, i.e., this methylation appears to be an 'all-or-none' phenomenon. DNA from extraembryonic tissues (placenta and yolk sac) and epididymal sperm showed, however, an even higher degree of methylation in two distinct patterns. In the extraembryonic tissue, partial methylation of each copy was seen, whereas in sperm a high degree of 'all-or-none' methylation (greater than 0.35) was observed.     

The 5''-cytosine in CCGG1 is methylated in two eukaryotic DNAs and Msp I is sensitive to methylation at this site.

Novikoff rat hepatoma and bovine liver DNAs were digested with Msp I or Hpa II. Restriction fragments were end-labeled using [alpha-32P]-dCTP and the Klenow fragment of E. coli DNA polymerase I and then digested to 2'-deoxyribonucleoside-3'-monophosphates using micrococcal nuclease and spleen phosphodiesterase. Mononucleotides were separated by two-dimensional thin layer chromatography, localized by radioautography, and the [32P]-label quantitated by scintillation spectrometry. This method, based on known specificities of Msp I and Hpa II, shows that CCGG, CMGG, and MCGG (M refers to 5-methylcytosine) occur at frequencies of 89.6%, 1.4%, and 9.0%, respectively, in the rat DNA and at 41.6%, 48.3%, and 10.0%, respectively, in the bovine DNA. [32P] recovery in 3'-5-MedCMP from end-labeled Msp I digests was negligible compared to recovery from Hpa II digests. Hence, Msp I is sensitive to methylation at the 5' cytosine in the sequence CCGG.     

DNA methylation and the frequency of CpG in animal DNA.

An analysis of nearest neighbour dinucleotide frequencies and the level of DNA methylation in animals strongly supports the suggestion that 5-methylcytosine (5mC) tends to mutate abnormally frequently to T. This tendency is the likely cause of the CpG deficiency in heavily methylated genomes.     

Effect of various factors on the methylation of DNAse I

The effects of NaCl, EDTA and tRNA on methylation and enzymatic properties of deoxyribonuclease I (DNase I) were investigated. The methylation was carried out by S-methylmethionine (vitamin U) in the phosphate-citric buffer pH 4.0. It was found that 0.5 M NaCl decreases by about 30% the incorporation of CH3-groups into the DNase, whereas 1.5 M NaCl-by 47%. A similar, although a less pronounced effect, was exerted by tRNA within the concentration range of 1.36-34.7 microM. On the contrast, EDTA (0.01-0.05 M) stimulated the incorporation of CH3-groups by 15 and 30%, respectively. The functional properties of methylated DNase I in the presence of EDTA remained unaffected. The enzyme methylation in the presence of NaCl or tRNA caused deceleration of the 3H-DNA hydrolysis (by 15-30%) only within the first 20 min of the reaction.     

CpG methylation controls reactivation of HIV from latency

What are the purposes of prizes and recognitions? Are they lagging indicators of past achievements or leading indicators of things to come?     

The dynamic impact of CpG methylation in DNA

Solid-state deuterium NMR is used to investigate perturbations of the local, internal dynamics in the EcoRI restriction binding site, -GAATTC- induced by cytidine methylation. Methylation of the cytidine base in this sequence is known to suppress hydrolysis by the EcoRI restriction enzyme. Previous solid-state deuterium NMR studies have detected large amplitude motions of the phosphate-sugar backbone at the AT-CG junction of the unmethylated DNA sequence. This study shows that methylation of the cytidine base in a CpG dinucleotide reduces the amplitudes of motions of the phosphate-sugar backbone. These observations suggest a direct link between suppression of the amplitudes of localized, internal motions of the sugar-phosphate backbone of the DNA and inhibition of restriction enzyme cleavage.     

CpG island methylation in precursors of gastrointestinal malignancies

Gastrointestinal malignancies account for about 20% of all cancers worldwide. It is widely accepted that cancer evolves through several stepwise morphological stages such as the adenoma-carcinoma and hyperplastic polyp-serrated adenoma-carcinoma sequences in colorectal cancers, and the metaplasia-dysplasia-carcinoma sequences in esophageal and gastric cancers. The morphological progression is associated with the accumulation of multiple genetic and epigenetic events. It is now recognized that epigenetic silencing of gene expression by CpG island methylation is an important alternative mechanism of inactivating tumor suppressor genes. Inflammatory conditions of the gastrointestinal and pancreaticobiliary tracts and liver such as Barrett esophagus, Helicobacter pylori gastritis, inflammatory bowel disease and viral hepatitis, are associated with increased frequency of malignancies and CpG methylation. In addition, CpG methylation is present in aberrant crypt foci and pancreatic intraepithelial neoplasia that are considered putative precursors of colon and pancreatic carcinomas, respectively. Understanding of these early genetic and epigenetic changes allows for the discoveries of potential screening, monitoring and therapeutic strategies. Targeting of the epigenetic changes that occur before the development of frank malignancy offers a potential chemopreventive strategy.