Transformation of Tetrahymena with hypermethylated ribosomal RNA genes.
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Animals↗
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Results for “DNA Modification Methylases”
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Chlorella viruses code for restriction and modification enzymes.
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Chlorella↗
Construction of a temperature-sensitive mutation for the direct identification of plasmids encoding DNA methyltransferases.
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Bacterial Proteins↗
The effect of site-specific DNA methylation on restriction endonucleases and DNA modification methyltransferases--a review.
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Bacterial Proteins↗
DNA methylation in Neisseria gonorrhoeae and other Neisseriae.
It has been reported in the literature that Neisseria gonorrhoeae DNA is modified by the methyltransferases (MTases) M.NgoI, M.NgoII, and M.NgoIII, as well as three other cytosine MTases and one adenine MTase, even if the corresponding restriction endonucleases are not present. We envisioned the possibility of cloning one of the N. gonorrhoeae MTase-encoding genes for use as a species-specific DNA probe. We therefore undertook a survey of methylation patterns of several clinical isolates of N. gonorrhoeae and N. meningitidis as well as ATCC strains of other Neisseriae. We found, from digestion patterns with isoschizomers, one N. gonorrhoeae strain that lacked M.NgoII and two that lacked M.NgoIII. All N. meningitidis strains (save one) were resistant to digestion with NlaIV thus possessing an MTase like NgoV, and one was resistant to SstII, thus having an NgoIII-like MTase. None were resistant to isoschizomers of NgoI, NgoIII and NgoIV. Some other Neisseriae had an MTase with NlaIV (NgoV) specificity, but none had NgoI, II, III or IV specificity, except for the Branhamella-like N. caviae-ovis group and N. lactamica where these specificities were present in at least one strain of this group. Therefore, among the Neisseriae other than N. caviae only M.NgoI is N. gonorrhoeae-specific.
DNA Modification Methylases↗
Specificity of restriction endonucleases and DNA modification methyltransferases a review (Edition 3).
The properties and sources of all known class-I, class-II and class-III restriction endonucleases (ENases) and DNA modification methyltransferases (MTases) are listed and newly subclassified according to their sequence specificity. In addition, the enzymes are distinguished in a novel manner according to sequence specificity, cleavage position and methylation sensitivity. Furthermore, new nomenclature rules are proposed for unambiguously defined enzyme names. In the various Tables, the enzymes are cross-indexed alphabetically according to their names (Table I), classified according to their recognition sequence homologies (Table II), and characterized within Table II by the cleavage and methylation positions, the number of recognition sites on the DNA of the bacteriophages lambda, phi X174, and M13mp7, the viruses Ad2 and SV40, the plasmids pBR322 and pBR328, and the microorganisms from which they originate. Other tabulated properties of the ENases include relaxed specificities (integrated within Table II), the structure of the generated fragment ends (Table III), interconversion of restriction sites (Table IV) and the sensitivity to different kinds of DNA methylation (Table V). Table VI shows the influence of class-II MTases on the activity of class-II ENases with at least partially overlapping recognition sequences. Table VII lists all class-II restriction endonucleases and MTases which are commercially available. The information given in Table V focuses on the influence of methylation of the recognition sequences on the activity of ENases. This information might be useful for the design of cloning experiments especially in Escherichia coli containing M.EcodamI and M.EcodcmI [H16, M21, U3] or for studying the level and distribution of site-specific methylation in cellular DNA, e.g., 5'- (M)CpG-3' in mammals, 5'-(M)CpNpG-3' in plants or 5'-GpA(M)pTpC-3' in enterobacteria [B29, E4, M30, V4, V13, W24]. In Table IV a cross index for the interconversion of two- and four-nt 5'-protruding ends into new recognition sequences is complied. This was obtained by the fill-in reaction with the Klenow (large) fragment of the E. coli DNA polymerase I (PolIk), or additional nuclease S1 treatment followed by ligation of the modified fragment termini [P3]. Interconversion of restriction sites generates novel cloning sites without the need of linkers. This should improve the flexibility of genetic engineering experiments [K56, P3].(ABSTRACT TRUNCATED AT 400 WORDS)
Animals↗
Cloning the BstVI restriction-modification system in Escherichia coli.
A standard DNA modification methyltransferase (MTase) selection protocol was followed to clone the BstVI restriction and modification system from Bacillus stearothermophilus in Escherichia coli. Both genes were contained in a 4.4-kb EcoRI fragment from B. stearothermophilus V chromosomal DNA. The heterologous expression of these genes did not depend on their orientation in the vector, suggesting that the genes are expressed in E. coli under the control of promoters located on the cloned fragment. Subcloning experiments demonstrated that the bstVIR gene was expressed in the absence of its cognate MTase.
Cloning, Molecular↗
Cloning, sequence and characterization of m5C-methyltransferase-encoding gene, hgiDIIM (GTCGAC), from Herpetosiphon giganteus strain Hpa2.
We have cloned the gene (hgiDIIM) encoding the methyltransferase (MTase) of the SalI isoschizomeric restriction-modification (R-M) system, HgiDII (GTCGAC), into Escherichia coli. The hgiDIIM gene has been isolated from the same plasmid library of Herpetosiphon giganteus strain Hpa2, as was the previously cloned R-M system, HgiDI [AcyI/GRCGYC; Düsterhöft et al., Nucleic Acids Res. 19 (1991) 1049-1056]. Sequencing and functional localization of hgiDIIM revealed an open reading frame (ORF) of 354 codons (39786 Da) with significant homologies to the group of m5C-, rather than the m4C-/m6A-, MTases. Subsequent cloning and analysis of adjacent chromosomal segments led to the identification of two additional ORFs upstream (ORF15, 139 codons) and downstream (ORF68, 611 codons) from hgiDIIM with the same transcriptional orientation as the hgiDIIM gene. However, the expected restriction enzyme function was not found in either of these ORFs.
Amino Acid Sequence↗
Cloning and analysis of translational control for genes encoding the Cfr9I restriction-modification system.
The complete type-II Cfr9I restriction-modification (R-M) system of Citrobacter freundii strain RFL9, recognizing the DNA sequence CCCGGG, has been cloned and expressed, and functionally active enzymes have been produced in Escherichia coli. Both the methyltransferase (MTase; M.Cfr9I) and restriction endonuclease (ENase; R.Cfr9I) were found to be encoded on a 2.3-kb cloned fragment in the same transcriptional orientation, but differing in translational phases. The last codon (underlined) (ATGA) of the MTase-encoding gene (Cfr9IM) overlaps with the start codon for the ENase-encoding gene (overlined) (cfr9IR). A nucleotide sequence complementary to a predicted Shine-Dalgarno sequence preceding cfr9IR is within this gene. Predicted free energy (delta G) for formation of the mRNA secondary structure involving these complementary sequences was found to be -16.1 kcal/mol. Amino-acid sequence homology of 80% was found between R.Cfr9I and R.XcyI.
Amino Acid Sequence↗
The restriction-modification system of Pasteurella haemolytica is a member of a new family of type I enzymes.
Genes encoding the type I restriction-modification (R-M) system of the bovine pathogen, Pasteurella haemolytica, have been identified immediately downstream of a locus that encodes a transcriptional activator of P. haemolytica leukotoxin expression. Type I enzymes are encoded by three genes called hsdM, hsdS and hsdR, and have fallen into three groups, called Ia, Ib and Ic. HsdS provides a sequence recognition function which in concert with HsdM forms an active methyltransferase (MTase). Inclusion of the HsdR subunit in the complex creates an active restriction endonuclease (ENase) capable of cleaving unmethylated target DNA. The P. haemolytica hsdMSR genes were mapped using transposon Tn10d-Cam insertions, and bacteriophage restriction and modification assays in Escherichia coli. We determined the nucleotide sequences of hsdM, hsdS and hsdR, and observed that the deduced amino acid (aa) sequences were very similar to predicted R-M subunits in the respiratory pathogen, Haemophilus influenzae. Phylogenetic comparisons of all known Hsd aa sequences placed the P. haemolytica and H. influenzae proteins into a new group which we labeled the Type Id R-M family. Expression of the P. haemolytica R-M genes in E. coli was inefficient and is likely to be a consequence of the unusual codon usage in P. haemolytica genes.
Amino Acid Sequence↗
Roles of transcription and repair in alkylation mutagenesis.
Mutations occurring in Escherichia coli cells exposed to alkylating agents have been analyzed using an assay for forward mutations in the E. coli rpsL gene cloned on a high copy number plasmid. N-Methyl-N'-nitro-N-nitrosoguanidine (MNNG)-induced mutations were recovered from wild-type and O6-methylguanine methyltransferase-deficient mutant (ada- ogt-) cells and their sequence alterations determined. We found that the mutations recovered from the wild-type strain were predominantly G:C to A:T transitions located at several hot spots in the rpsL sequence. A vast majority of the mutations were found at guanine residues preceded by thymine on the transcribed strand of the target gene. Although the methyltransferase mutant showed hypersensitivity to the alkylating reagent in terms of mutagenic effect and cell killing effects, the class and site distributions of the rpsL- mutations recovered from MNNG-treated ada- ogt- cells were similar to those observed with MNNG-treated wild-type cells. Therefore, the site preference of MNNG-induced rpsL- mutations seems to be due not to the specificity of methyl-transferring repair enzymes but probably to the distribution of the mutagenic lesions (O6-methylguanine) in the target sequence. Mutations induced by methyl methanesulfonate, an SN2 alkylating agent, showed similar class and site distributions in the rpsL system. The site preference of MNNG-induced mutations was significantly changed when the level of transcription of the rpsL gene was decreased to 120-fold lower than that promoted by the authentic rpsL promoter. Under these conditions, 78% of mutations were induced at the central guanine of 5'-GG(A or C)-3' and 2/3 of them were on the non-transcribed strand of the rpsL gene. These results suggested that the site preference of MNNG-induced mutations is determined by at least three factors: (i) a flanking-base effect on the chemical reactivity of a guanine residue, (ii) transcribed strand-specific repair, probably by the UvrABC system, and (iii) the effects of transcription of the target gene on the alkylation of DNA and the strand-specific repair.
Alkylation↗
Restriction enzymes in cells, not eppendorfs.
Restriction enzymes are essential reagents to molecular biologists, but their relevance to bacterial populations is less obvious. Most bacteria encode restriction and modification systems and these are commonly considered to be a barrier to phage infection. Current evidence also supports a more general role for them in genetic recombination.
Bacteria↗
Hypermethylation of the PTEN gene in ovarian cancer cell lines.
This study was performed to investigate the hypermethylation status of the PTEN gene in ovarian cancer. To this end, we incubated eight ovarian cancer cell lines with the demethylating agent 5-aza-2' deoxycytidine in three different concentrations for 5 days. Subsequently, the PTEN expression was quantified by both real time RT-PCR and quantitative western analyses. PTEN mRNA varied considerably in response to demethylation whereas PTEN protein concentrations remained constant in all cell lines except OAW42 cells (12.5%). The data suggest that PTEN is highly regulated at translational level. However, methylation of the PTEN gene plays a subordinate role in ovarian cancer.
Antimetabolites, Antineoplastic↗
Inhibition of DNA methyltransferase reverses cisplatin induced drug resistance in murine neuroblastoma cells.
BACKGROUND: Acquired drug resistance is a major obstacle to the successful treatment of neuroblastoma by chemotherapy. Recent studies from our laboratory have demonstrated that drug-induced alterations in DNA methylation play an important role in this process. METHODS: The reversal of resistance to cisplatin in murine neuroblastoma (MNB) was induced by inhibition of DNA methyltransferase activity. MNB cells overexpressing DNA methyltransferase activity (Dnmt3a or Dnmt3b) were established by stable co-transfection of wild type MNB cells with plasmids containing Dnmt3a or Dnmt3b cDNA. Cytotoxic response (IC50), total DNA methyltransferase activity and expression of Dnmt3a or Dnmt3b methyltransferase were determined in Dnmt3a or Dnmt3b transfected MNB cells, respectively. RESULTS: These data demonstrated that total DNA methyltransferase activity was increased to 3-fold above controls (P<0.001) in cisplatin resistant MNB cells, 3-fold in Dnmt3a and 4-fold in Dnmt3b transfected MNB cells. Western blot and RT-PCR data confirmed a corresponding increase in Dnmt3a and 3b expression in cisplatin resistant and transfected cells when compared with control MNB cells (P<0.001). MNB clones overexpressing Dnmt3a or Dnmt3b proteins were resistant to cisplatin treatment (10(-6) M). Incubation of cisplatin resistant, Dnmt3a or Dnmt3b overexpressing MNB cells with 5'-azacytidine (5'-azaC), a methylation inhibitor (2.5 microM) significantly decreased DNA methyltransferase activity, expression of Dnmt3a and Dnmt3b proteins and mRNA levels of cisplatin resistant, Dnmt3a and Dnmt3b transfected MNB cells. Cytotoxicity studies using the MTT assay demonstrated that the sensitivity of cisplatin resistant, Dnmt3a and Dnmt3b overexpressing MNB cells to cisplatin was increased 10-fold (P<0.001) following 5'-azaC treatment. CONCLUSIONS: These findings suggest that the overexpression of DNA methyltransferase is associated with a cisplatin resistant phenotype in MNB cells that may or may not be true in animal studies or in the clinical setup. Thus, DNA methylation plays a central role in onset of drug resistance in cisplatin resistant neuroblastoma cells in vitro.
Animals↗
Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis.
Cytosine methylation is important for transposon silencing and epigenetic regulation of endogenous genes, although the extent to which this DNA modification functions to regulate the genome is still unknown. Here we report the first comprehensive DNA methylation map of an entire genome, at 35 base pair resolution, using the flowering plant Arabidopsis thaliana as a model. We find that pericentromeric heterochromatin, repetitive sequences, and regions producing small interfering RNAs are heavily methylated. Unexpectedly, over one-third of expressed genes contain methylation within transcribed regions, whereas only approximately 5% of genes show methylation within promoter regions. Interestingly, genes methylated in transcribed regions are highly expressed and constitutively active, whereas promoter-methylated genes show a greater degree of tissue-specific expression. Whole-genome tiling-array transcriptional profiling of DNA methyltransferase null mutants identified hundreds of genes and intergenic noncoding RNAs with altered expression levels, many of which may be epigenetically controlled by DNA methylation.
Arabidopsis↗
Should concomitant and adjuvant treatment with temozolomide be used as standard therapy in patients with anaplastic glioma?
Malignant gliomas are devastating tumors associated with poor prognosis. Standard treatment has been surgery followed by radiotherapy while the role of chemotherapy has remained controversial. Concomitant and adjuvant treatment with temozolomide has recently been shown to improve survival in patients with glioblastoma. While it seems intuitive to apply this regimen to patients with anaplastic gliomas which have traditionally been considered more chemosensitive, chemotherapy has not been shown to prolong life in patients with anaplastic gliomas. Despite promising preclinical and early clinical results, there is currently not enough level 1 evidence to justify concomitant and adjuvant temozolomide as standard therapy for patients with newly diagnosed anaplastic gliomas. Further investigation is needed to better define the role of chemotherapy in patients with anaplastic gliomas. Trials evaluating chemoradiotherapy as well as targeted therapeutic agents are the subject of further research.
Antineoplastic Agents, Alkylating↗
Progesterone receptor gene inactivation and CpG island hypermethylation in human leukemia cancer cells.
Previous studies showed that progesterone receptor (PR), one of the hormone receptor superfamily, was only connected with the sex-correlated cancers such as breast cancer, endometrial cancer, prostate cancer, etc. This article deals with the PR gene in leukemia. We investigated the methylation status and the expression of the two different PR isoforms, PRA and PRB, in three leukemia cancer cell lines using methylation-specific polymerase chain reaction (MSP-PCR) and reverse transcription-PCR. The correlation of PR methylation and expression together with DNA methyltransferase (DNMT1) was further studied. We found that DNMT1 is required to maintain CpG methylation and aberrant gene silencing of PR gene in human leukemia cancer cells. The activity of 5-aza-2'-deoxycytidine in demethylation and gene reactivation may be through depleting cellular DNMT1 levels. In addition, extensive methylation of PRA and PRB was also observed in leukemia samples. Our results suggest that PR CpG island aberrant hypermethylation could be one molecular and genetic alteration in leukemia.
Azacitidine↗
Genomic hypomethylation is specific for preneoplastic liver in folate/methyl deficient rats and does not occur in non-target tissues.
Chronic dietary insufficiency of the lipotropic nutrients choline and methionine is hepatocarcinogenic in male rats and certain mouse strains. Despite the fact that DNA hypomethylation is a hallmark of most cancer genomes, the tissue-specific consequences of this alternation with respect to tumorigenesis remain to be determined. In the present study, the folate/methyl deficient model of multistage hepatocarcinogenesis was used to evaluate in vivo alterations in DNA methylation in the liver, the carcinogenesis target tissue, and in non-target tissues, including pancreas, spleen, kidney, and thymus, of male F344 rats. By utilizing the HpaII/MspI-based cytosine extension assay, we demonstrated that the percent of CpG sites that lost methyl groups on both strands progressively increased in liver tissue after 9, 18, and 36 weeks of folate/methyl deficiency. The endogenous activity of DNA methyltransferase in liver of rats fed with folate/methyl deficient diet for the 36-week period gradually increased with time. In contrast, non-target tissues displayed no changes in DNA methylation level or activity of DNA methyltransferase. The failure of DNA methyltransferase to restore and maintain DNA methylation patterns in preneoplastic liver tissue may lead to the establishment of tumor-specific DNA methylation and DNA methyltransferase profiles that are not expressed in normal liver. These results provide additional information about alterations in DNA methylation during early preneoplastic stages of carcinogenesis. They also demonstrate that DNA hypomethylation is localized to tissue that undergoes carcinogenesis, and is not altered in non-target tissues.
Animals↗