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Results for “DNA Modification Methylases”

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PubMed2005

Increased heparanase expression is caused by promoter hypomethylation and up-regulation of transcriptional factor early growth response-1 in human prostate cancer.

PURPOSE: Heparanase degrades heparan sulfate and has been implicated in tumor invasion and metastasis. The transcription factor, early growth response 1 (EGR1), is associated with the inducible transcription of the heparanase gene. We hypothesize that CpG hypomethylation in the heparanase promoter coupled with up-regulation of EGR1 levels may induce heparanase expression in human prostate cancer. EXPERIMENTAL DESIGN: Cultured prostate cancer cell lines (Du145, DuPro, LNCaP, and PC-3) with and without 5'-aza-2-deoxycytidine treatment, 177 prostate cancer samples, and 69 benign prostatic hyperplasia (BPH) samples were used. The frequency and level of heparanase promoter methylation were analyzed by methylation-specific primers which covered the core binding motif of EGR1 (GGCG) or SP1 (GGGCGG) or both. RESULTS: In cultured Du145, DuPro, LNCaP, and PC-3 cell lines, mRNA transcripts of heparanase were significantly increased after 5'-aza-2-deoxycytidine treatment, suggesting that promoter methylation was involved in the regulation of heparanase mRNA transcript. Significantly higher methylation was found in BPH samples than in prostate cancer samples (P < 0.0001), whereas mRNA transcripts of the heparanase gene were inversely lower in BPH samples than in prostate cancer samples (P < 0.01). EGR1 expression in prostate cancer tissues was significantly higher than in BPH tissues (P < 0.001) and correlated with heparanase expression (P < 0.0001). Moreover, multiple regression analysis revealed that up-regulation of EGR1 contributed significantly more to heparanase expression than did promoter CpG hypomethylation in prostate cancer samples (P < 0.0001). CONCLUSIONS: To our knowledge this is the first comprehensive study demonstrating that increased heparanase expression in prostate cancer tissues is due to promoter hypomethylation and up-regulation of transcription factor EGR1.

Aged↗
PubMed1988

Do tightly-bound chromatin proteins play a role in DNA methylation?

When chromatin matrix, "stripped" from its loosely-bound components by extraction with 3 M NaCl, is extensively digested with DNAase I, a fraction is obtained, which carries no endogenous DNA methyltransferase activity but which is a good substrate for externally added enzyme. Under the same conditions, protein-free DNA isolated from this fraction can instead hardly be methylated, this different behaviour pointing to a role of DNA-tightly-bound proteins in favoring or promoting the catalytic action of the enzyme. A similar stimulation of enzymatic methylation could also be shown when, in the presence of this same fraction, single stranded Micrococcus luteus DNA was incubated with placental methyltransferase, using S-adenosylmethionine as a methyl donor. This finding can be correlated to the existence, in chromatin loops, of small regions which resist digestion by DNAase I also after high-salt removal of their loosely-bound components (presumably because of the presence of tightly-bound proteins) and whose DNA is characterized by high methylation levels and, at the same time, by high relative content of thymine.

Binding Sites↗
PubMed2003

Interaction of 5-aza-2'-deoxycytidine and depsipeptide on antineoplastic activity and activation of 14-3-3sigma, E-cadherin and tissue inhibitor of metalloproteinase 3 expression in human breast carcinoma cells.

Genes that suppress tumorigenesis can be silenced by epigenetic events, such as aberrant DNA methylation and modification of chromatin structure. Inhibitors of DNA methylase and histone deacetylase (HDAC) can potentially reverse these events. The aim of this study was to determine the in vitro antineoplastic activity of 5-aza-2'-deoxycytidine (5-AZA-CdR), a potent inhibitor of DNA methylase, in combination with depsipeptide (depsi), an inhibitor of HDAC, on human breast carcinoma cells. We observed a synergistic antineoplastic interaction between 5-AZA-CdR and depsi in their capacity to inhibit colony formation of Hs578T and MCF-7 breast carcinoma cells. In order to understand the molecular mechanism of this interaction, we investigated the effect of these drugs on the activation of the 14-3-3sigma, E-cadherin and tissue inhibitor of metalloproteinase 3 (TIMP3) cancer-related genes, which were reported to be silenced by aberrant methylation in many breast tumor cell lines. 14-3-3sigma was reported to produce G cell cycle arrest following DNA damage. E-cadherin and TIMP3 function as suppressors of tumor metastasis. Semi-quantitative RT-PCR was used to determine the effect of the co-administration of 5-AZA-CdR and depsi on four breast carcinoma cell lines for the reactivation of these genes. We observed a synergistic activation of E-cadherin by the combination in Hs578T, MDA-MB-231 and MDA-MB-435 tumor cells. For 14-3-3sigma, we demonstrated an additive to synergistic activation by the combination for Hs578T and MDA-MB-435 tumor cells, respectively. In the MCF-7 tumor cells, the drug combination produced a synergistic activation of TIMP3. The association between the synergistic antineoplastic activity and the synergistic activation of the target genes in this study suggests that the mechanism of anticancer activity of 5-AZA-CdR, in combination with depsi, is probably related to their enhanced activation of different types of tumor suppressor genes that have been silenced by epigenetic events.(2)

14-3-3 Proteins↗
PubMed1989

The FokI restriction-modification system. II. Presence of two domains in FokI methylase responsible for modification of different DNA strands.

Based on the previous findings that the FokI methylase (MFokI) consists of 647 amino acid residues and contains two copies of the segment specific for adenine methylase, Asp-Pro-Pro-Tyr, at amino acid positions 218-221 and 548-551, the role of these copies in the methylation reaction was investigated by introduction of a mutation into each segment. The MFokI gene was inserted into M13 vectors, and the Asp residues in the two segments were converted to Gly and Ala by oligonucleotide-directed mutagenesis. The wild-type and mutant genes were recloned into an expression vector, from which gene products were purified. A short DNA fragment carrying the FokI recognition site was treated with each of these enzymes, and after separation of the two strands by duplex formation with M13 viral DNAs carrying the respective strands, the presence or absence of modification was judged from susceptibility to FokI endonuclease. The results of analysis showed that different strands were modified in an asymmetric way by the introduction of mutations into one of the two segments, and that the segments at the N-terminal and C-terminal moieties participated in modification of the strands carrying 5'-GGATG-3' and 3'-CCTAC-5', respectively. We concluded that MFokI contained two functional domains each of which was responsible for modification of different strands in the target DNA.

Deoxyribonucleases, Type II Site-Specific↗
PubMed1992

Cloning and characterization of genes for the PvuI restriction and modification system.

The genes encoding the endonuclease and the methylase of the PvuI restriction and modification system were cloned in E.coli and characterized. The genes were adjacent in tandem orientation spanning a distance of 2200 bases. The PvuI endonuclease was a single polypeptide with a calculated molecular weight of 27,950 daltons. The endonuclease was easily detectable when the gene was expressed from its endogenous promotor and present on a low copy plasmid, but expression was considerably enhanced when the endonuclease gene was placed under the control of a strong promoter on a high copy plasmid. The methylase did not completely protect plasmid DNA from R.PvuI digestion until the methylase gene was placed under lac promotor control in a multicopy plasmid. In the absence of the M.PvuI methylase, expression of the R.PvuI endonuclease from the lac promotor on a multicopy plasmid was not lethal to wild type E.coli, but was lethal in a temperature-sensitive ligase mutant at the non-permissive temperature. Moreover, induction of the R.PvuI endonuclease under lambda pL promotor control resulted in complete digestion of the E.coli chromosome by R.PvuI.

Base Sequence↗
PubMed2025

A MGMT Enhancer Variant is Associated with Glioma Susceptibility and Progression.

The O6-methylguanine-DNA methyltransferase (MGMT) plays a significant role in the pathogenesis and progression of glioma. Numerous enhancer variants, including those within the MGMT gene region and adjacent gene regions, have been found to be associated with cancer development and progression. We investigated the significance of enhancer variants located in the intergenic spacer far from the MGMT gene in relation to glioma susceptibility and progression. We recruited 402 glioma patients and 654 controls for this investigation using Sequenom MassARRAY genotyping. We identified a significantly elevated risk of glioma among carriers with the rs11016629 TG genotype compared to those with the GG genotype (OR&#x2009;=&#x2009;1.41, 95% CI 1.03-1.93; P&#x2009;=&#x2009;0.034). Subgroup analyses revealed that rs11016629 was significantly associated with glioma risk in subjects with WHO grade IV tumor (OR&#x2009;=&#x2009;1.59, 95% CI 1.07-2.38; P&#x2009;=&#x2009;0.023) and high-grade glioma (OR&#x2009;=&#x2009;1.57, 95% CI 1.11-2.21; P&#x2009;=&#x2009;0.011). Patients who underwent gross total resection with TG/TT genotypes exhibited a 2.66-fold higher risk of disease progression than GG carriers (HR&#x2009;=&#x2009;2.66, 95% CI 1.23-5.79; P&#x2009;=&#x2009;0.014). The study demonstrates that a MGMT enhancer variant rs11016629 contributes to both glioma susceptibility and progression.

Humans↗
PubMedDate not supplied

Genomic structure of the human DNA methyltransferase gene.

We determined the genomic structure of the gene encoding human DNA methyltransferase (DNA MTase). Six overlapping human genomic DNA clones which include all of the known cDNA sequence were isolated. Analysis of these clones demonstrates that the human DNA MTase gene consists of at least 40 exons and 39 introns spanning a distance of 60 kilobases. Elucidation of the chromosomal organization of the human DNA MTase gene provides the template for future structure-function analysis of the properties of mammalian DNA MTase.

Cloning, Molecular↗
PubMed1999

[The plasmid carrying the temperature-sensitive mutation in the DNa-methylase gene of the PStI system: effect on host cells at nonpermissive temperature].

Temperature-sensitive (ts) derivatives of plasmid pRMP1, the derivative of PBR322 containing restriction and modification (RM) genes of the PstI system, were obtained using hydroxylamine mutagenesis. One of the isolated plasmids responsible for the inhibition of Escherichia coli cell growth at 42 degrees C, pRMPts, was analyzed in this work. Cells of Rec+ strains carrying this plasmid were unable to divide at 42 degrees C and formed long non-septated filaments that died upon prolonged cultivation. Cells of the RecA- strains carrying pRMPts did not form filaments at 42 degrees C and rapidly disappeared. On agar media with or without ampicillin, Rec+ and RecA- strains with this plasmid formed colonies of temperature-resistant (tr) derivatives with frequencies ranging from 1.5 x 10(-4) to 4 x 10(-6) in independent clones. The structure of plasmids from cells of tr-derivatives of Rec+ and RecA- strains carrying plasmid pRMPts was analyzed by the set of restriction enzymes. Reversions to the temperature-resistant phenotype were shown to result from the following events: (1) the insertional inactivation of the PstI restriction enzyme gene in pRMPts (the insertion of the IS1 element); (2) deletions in plasmid DNA fragments that partially or completely cover the restriction enzyme gene; (3) point mutations; and (4) others. The effect of the chromosomal sulA mutation on the maintenance of the ts-plasmid in bacterial cells was studied at 42 degrees C. High efficiency loss of the plasmid was detected in pRMPts-carrying Rec+ cells with the sulA::Tn5 mutation grown in liquid and solid nutrient media at this temperature. Under similar conditions, plasmid loss was not detected in SulA+ cells. On the basis of the data obtained, it is concluded that the ts-mutation is located in the DNA-methylase gene of plasmid pRMPts. Mutant DNA methylase was unable to methylate all sites in the chromosomal DNA at 42 degrees C. Some of the unmethylated sites can be digested with the PstI enzyme, which leads to the induction of SOS response in Rec+ cells or to total mortality in cells with the recA phenotype.

Bacterial Proteins↗
PubMed2000

The DNA methyltransferases of mammals.

The biological significance of 5-methylcytosine was in doubt for many years, but is no longer. Through targeted mutagenesis in mice it has been learnt that every protein shown by biochemical tests to be involved in the establishment, maintenance or interpretation of genomic methylation patterns is encoded by an essential gene. A human genetic disorder (ICF syndrome) has recently been shown to be caused by mutations in the DNA methyltransferase 3B (DNMT3B) gene. A second human disorder (Rett syndrome) has been found to result from mutations in the MECP2 gene, which encodes a protein that binds to methylated DNA. Global genome demethylation caused by targeted mutations in the DNA methyltransferase-1 (Dnmt1) gene has shown that cytosine methylation plays essential roles in X-inactivation, genomic imprinting and genome stabilization. The majority of genomic 5-methylcytosine is now known to enforce the transcriptional silence of the enormous burden of transposons and retroviruses that have accumulated in the mammalian genome. It has also become clear that programmed changes in methylation patterns are less important in the regulation of mammalian development than was previously believed. Although a number of outstanding questions have yet to be answered (one of these questions involves the nature of the cues that designate sites for methylation at particular stages of gametogenesis and early development), studies of DNA methyltransferases are likely to provide further insights into the biological functions of genomic methylation patterns.

Animals↗
PubMed2000

Biotin-avidin microplate assay for the quantitative analysis of enzymatic methylation of DNA by DNA methyltransferases.

An assay is described to measure methylation of biotinylated oligonucleotide substrates by DNA methyltransferases using [methyl-3H]-AdoMet. After the methylation reaction the oligonucleotides are immobilized on an avidin-coated microplate. The incorporation of [3H] into the DNA is quenched by addition of unlabeled AdoMet to the binding buffer. Unreacted AdoMet and enzyme are removed by washing. To release the radioactivity incorporated into the DNA, the wells are incubated with a non-specific endonuclease and the radioactivity determined by liquid scintillation counting. As an example, we have studied methylation of DNA by the EcoRV DNA methyltransferase. The reaction progress curves measured with this assay are linear with respect to time. Methylation rates linearly increase with enzyme concentration. The rates are comparable to results obtained with the same enzyme using a different assay. The biotin-avidin assay is inexpensive, convenient, quantitative, fast and well suited to process many samples in parallel. The accuracy of the assay is high, allowing to reproduce results within +/- 10%. The assay is very sensitive as demonstrated by the detection of incorporation of 0.8 fmol methyl groups into the DNA. Under the experimental conditions, this corresponds to methylation of only 0.03% of all target sites of the substrate. Using this assay, the DNA methylation activity of some M.EcoRV variants could be detected that was not visible by other in vitro methylation assays.

Avidin↗
PubMed1998

Novel procedure for the detection of 5-methylcytosine.

Bisulfite converts non-methylated cytosine in DNA to uracil leaving 5-methylcytosine unaltered. In this communication, we present a new approach omitting the conventional PCR amplification step. Bisulfite-converted methylated DNA is directly sequenced. The effectiveness of the new protocol is demonstrated by using it for the detection of 5-methylation of cytosine residues introduced by three different DNA methyltransferases (M.HaeIII, M.HpaII and M.HhaI). A simple experimental system useful to determine the sequence specificity of DNA methyltransferases is also presented.

5-Methylcytosine↗
PubMed2005

Genome analysis of the obligately lytic bacteriophage 4268 of Lactococcus lactis provides insight into its adaptable nature.

Analysis of the complete nucleotide sequence of the lactococcal phage 4268, which is lytic for the cheese starter Lactococcus lactis DPC4268, is presented. Phage 4268 has a linear genome of 36,596 bp, which is modularly organised and encompasses 49 open reading frames. Putative functions were assigned to approximately 45% of the predicted products of these open reading frames based on sequence similarity with known proteins, N-terminal sequence analysis and identification of conserved domains. Significantly, a segment of the genome has homology to the recently sequenced lysogenic module in lactococcal phage phi31 that contains a lytic switch but no phage integrase or attachment site. This suggests that it is derived from a prophage. A phage 4268-encoded and a host-encoded methylase were found to be highly similar, having only two nucleotide mismatches, suggesting that the phage acquired the methylase gene to protect it from a host endonuclease. Comparative genomic analysis revealed significant homology between phage 4268 and the lactococcal phage BK5-T. The comparative analysis also supported the classification of phage 4268 and other BK5-T-related phage as separate from the proposed P335 species of lactococcal phage.

Bacteriophages↗