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Results for “DNA Modification Methylases”

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PubMed2003

Purification and characterisation of a novel DNA methyltransferase, M.AhdI.

We have cloned the M and S genes of the restriction-modification (R-M) system AhdI and have purified the resulting methyltransferase to homogeneity. M.AhdI is found to form a 170 kDa tetrameric enzyme having a subunit stoichiometry M2S2 (where the M and S subunits are responsible for methylation and DNA sequence specificity, respectively). Sedimentation equilibrium experiments show that the tetrameric enzyme dissociates to form a heterodimer at low concentration, with K(d) approximately 2 microM. The intact (tetrameric) enzyme binds specifically to a 30 bp DNA duplex containing the AhdI recognition sequence GACN5GTC with high affinity (K(d) approximately 50 nM), but at low enzyme concentration the DNA binding activity is governed by the dissociation of the tetramer into dimers, leading to a sigmoidal DNA binding curve. In contrast, only non-specific binding is observed if the duplex lacks the recognition sequence. Methylation activity of the purified enzyme was assessed by its ability to prevent restriction by the cognate endonuclease. The subunit structure of the M.AhdI methyltransferase resembles that of type I MTases, in contrast to the R.AhdI endonuclease which is typical of type II systems. AhdI appears to be a novel R-M system with properties intermediate between simple type II systems and more complex type I systems, and may represent an intermediate in the evolution of R-M systems.

Amino Acid Sequence↗

PubMed2005

Subunit assembly modulates the activities of the Type III restriction-modification enzyme PstII in vitro.

We demonstrate that, like other Type III restriction endonuclease, PstII does not turnover such that a DNA substrate is only fully cleaved at a Res2Mod2-to-site ratio of approximately 1:1. However, unlike other Type III enzymes, the cleavage rate profiles varied with protein concentration: using 5 nM DNA and 25 nM PstII, approximately half of the DNA was cut at a fast rate while the remainder was cut 24 times more slowly; in comparison, with 100 nM PstII cleavage occurs at a single fast rate. The inclusion of the methyl donor S-adenosyl methionine does not alter the rates with 100 nM PstII but with 25 nM PstII the reaction stopped after completion of the initial fast cleavage phase owing to methylation. Concentration-dependent rates were also observed in methylation assays: at 100 nM PstII, a single slow rate was measured while at lower PstII concentrations both fast and slow rates were measured. We propose a model in which the intact Res2Mod2 complex favoured at high PstII concentrations is a fast endonuclease/slow methyltransferase while the various subassemblies which coexist at lower concentrations are fast methyltransferases. A potential role for disassembly in control of restriction activity in vivo is discussed.

Bacterial Proteins↗

PubMed2006

High allelic diversity in the methyltransferase gene of a phase variable type III restriction-modification system has implications for the fitness of Haemophilus influenzae.

Phase variable restriction-modification (R-M) systems are widespread in Eubacteria. Haemophilus influenzae encodes a phase variable homolog of Type III R-M systems. Sequence analysis of this system in 22 non-typeable H.influenzae isolates revealed a hypervariable region in the central portion of the mod gene whereas the res gene was conserved. Maximum likelihood (ML) analysis indicated that most sites outside this hypervariable region experienced strong negative selection but evidence of positive selection for a few sites in adjacent regions. A phylogenetic analysis of 61 Type III mod genes revealed clustering of these H.influenzae mod alleles with mod genes from pathogenic Neisseriae and, based on sequence analysis, horizontal transfer of the mod-res complex between these species. Neisserial mod alleles also contained a hypervariable region and all mod alleles exhibited variability in the repeat tract. We propose that this hypervariable region encodes the target recognition domain (TRD) of the Mod protein and that variability results in alterations to the recognition sequence of this R-M system. We argue that the high allelic diversity and phase variable nature of this R-M system have arisen due to selective pressures exerted by diversity in bacteriophage populations but also have implications for other fitness attributes of these bacterial species.

Alleles↗

PubMed2004

Covalent DNA display as a novel tool for directed evolution of proteins in vitro.

We present a novel method for the directed evolution of polypeptides, which combines in vitro compartmentalization and covalent DNA display. A library of linear DNA fragments is co-packaged with an in vitro transcription/translation mixture in the compartments of a water-in-oil emulsion. Experimental conditions are adjusted so that, in most cases, one compartment contains one DNA molecule. The DNA fragments encode fusion proteins containing a DNA-methyltransferase (M.Hae III), which can form a covalent bond with a 5-fluorodeoxycytidine base at the extremity of the DNA fragment. The resulting library of DNA-protein fusions is extracted from the emulsion and DNA molecules displaying a protein with desired binding properties are selected from the pool of DNA-protein fusions by affinity panning on target antigens. We applied this methodology in model selection experiments, using specific ligands for the capture of peptides and globular proteins bound to DNA. We observed enrichment factors >1000-fold for selections performed in separate emulsions and up to 150-fold for selections performed using mixtures of DNA molecules. M.Hae III could be fused to small globular proteins (such as calmodulin and fibronectin domains), which are ideally suited for the generation of combinatorial libraries and for the isolation of novel binding specificities.

DNA Adducts↗

PubMed2003

Epigenetic characteristics and development of embryos cloned from donor cells treated by trichostatin A or 5-aza-2'-deoxycytidine.

Development to blastocyst following nuclear transfer is dependent on the donor cell's ability to reprogram its genome to that of a zygote. This reprogramming step is inefficient and may be dependent on a number of factors, including chromatin organization. Trichostatin A (TSA; 0-5 microM), a histone deacetylase inhibitor, was used to increase histone acetylation and 5-aza-2'-deoxycytidine (5-aza-dC; 0-5 microM), a DNA methyl-transferase inhibitor, was used to decrease methylation of chromatin in donor cells in an attempt to improve their reprogrammability. Adult fibroblast cells treated with 1.25 or 5 microM TSA had elevated histone H3 acetylation compared to untreated controls. Cells treated with 0.3 microM 5-aza-dC had decreased methylation compared to untreated controls. Both drugs at 0.08 microM caused morphological changes of the donor cells. Development to blastocysts by embryos cloned from donor cells after 0.08 or 0.3 microM 5-aza-dC treatments was lower than in embryos cloned from untreated control cells (9.7% and 4.2%, respectively, vs. 25.1%), whereas 0.08 microM TSA treatment of donor cells increased blastocyst development compared to controls (35.1% vs. 25.1%). These results indicate that partial erasure of preexisting epigenetic marks of donor cells improves subsequent in vitro development of cloned embryos.

Acetylation↗

PubMed1994

Developmental expression of DNA methyltransferase messenger ribonucleic acid, protein, and enzyme activity in the mouse testis.

Sex- and sequence-specific patterns of methylation of mammalian DNA are established during gametogenesis and are believed to be important for genomic imprinting and developmental gene regulation. DNA methylation in mammalian cells is performed predominantly by the enzyme DNA (cytosine-5)-methyltransferase (DNA MTase). For a better understanding of how DNA methylation events are regulated during spermatogenesis, a developmental study comparing the expression of DNA MTase mRNA, protein, and enzyme activity was performed. Northern and Western blotting and enzyme activity assays were carried out on testes and purified populations of cells from the testes of mice aged 6-70 days. The 5.2-kb DNA MTase transcript was most abundant in testes of mice aged 6-10 days (2-3-fold the 70-day values); it had decreased in abundance by 40% by Day 20 and reached steady adult levels by 63 days. On Western blot analysis, developmental changes in the relative abundance of DNA MTase protein paralleled the changes seen in mRNA concentrations. DNA MTase enzyme activity in the testis was highest at 6 days of age (10-fold the 70-day values); it had decreased by more than 65% by 20 days and reached steady adult levels at 35 days. Analysis of purified germ cells from the adult testis revealed high levels of expression of both DNA MTase mRNA and protein in haploid round spermatids. In conclusion, DNA MTase is clearly developmentally regulated during spermatogenesis at the level of mRNA, protein, and enzyme activity. These results argue for an important role for this DNA-methylating enzyme during spermatogenesis.

Aging↗

PubMed1995

Regulated synthesis and localization of DNA methyltransferase during spermatogenesis.

Differences in the methylation patterns of male and female gamete DNA are likely to be involved in genomic imprinting. However, little is known of the mechanisms that regulate de novo methylation and demethylation during gametogenesis. We report here that the well-characterized M(r) 190,000 form of DNA methyltransferase (the only known form) is present in isolated mitotic, meiotic, and postmeiotic male germ cells, with the exception of meiotic pachytene spermatocytes, where the protein is undetectable by immunoblot analysis and a novel 6.2-kb DNA methyltransferase transcript is present. Whereas replication and methylation are coupled in somatic cells, the presence of DNA methyltransferase in postreplicative male germ cells is consistent with previously observed de novo methylation events in these cells. Immunofluorescence experiments revealed that DNA methyltransferase is localized to the nuclei of male germ cells, with a subset of spermatogonia and postreplicative leptotene/zygotene spermatocytes displaying prominent nuclear foci that are strongly enriched in DNA methyltransferase. The data suggest that down-regulation of DNA methyltransferase expression during the pachytene stage of meiosis utilizes an mechanism that is associated with the production of a larger mRNA, and that de novo methylation in leptotene/zygotene spermatocytes may take place in spatially restricted nuclear domains that are enriched in DNA methyltransferase.

Animals↗

PubMed2005

Effects of epigenetic modulation on reporter gene expression: implications for stem cell imaging.

Tracking stem cell localization, survival, differentiation, and proliferation after transplantation in living subjects is essential for understanding stem cell biology and physiology. In this study, we investigated the long-term stability of reporter gene expression in an embryonic rat cardiomyoblast cell line and the role of epigenetic modulation on reversing reporter gene silencing. Cells were stably transfected with plasmids carrying cytomegalovirus promoter driving firefly luciferase reporter gene (CMV-Fluc) and passaged repeatedly for 3-8 months. Within the highest expressor clone, the firefly luciferase activity decreased progressively from passage 1 (843+/-28) to passage 20 (250+/-10) to passage 40 (44+/-3) to passage 60 (3+/-1 RLU/microg; P<0.05 vs. passage 1). Firefly luciferase activity was maximally rescued by treatment with 5-azacytidine (DNA methyltransferase inhibitor) compared with trichostatin A (histone deacetylase inhibitor) and retinoic acid (transcriptional activator; P<0.05). Increasing dosages of 5-azacytidine treatment led to higher levels of firefly luciferase mRNA (RT-PCR) and protein (Western blots) and inversely lower levels of methylation in the CMV promoter (DNA nucleotide sequence). These in vitro results were extended to in vivo bioluminescence imaging (BLI) of cell transplant in living animals. Cells treated with 5-azacytidine were monitored for 2 wk compared with 1 wk for untreated cells (P<0.05). These findings should have important implications for reporter gene-based imaging of stem cell transplantation.

Animals↗

PubMed1996

Circadian variation in O6-methylguanine-DNA methyltransferase activity in mouse liver.

Bifunctional chloroethylating cytostatic agents produce lethal DNA lesions, as a result of the formation of O6-alkylguanines. These lesions can be repaired by O6-methylguanine-DNA methyltransferase (MGMT). This ubiquitous nuclear and cytosolic enzyme removes the alkyl group by accepting it to the cysteine residue of its active site, thus preventing the formation of DNA interstrand cross-links. The role of the circadian organization in cellular protection against such DNA insults was examined in male B6D2F1 mice, synchronized with an alternation of 12 h of light and 12 h of darkness (LD12:12). MGMT activity was determined in liver of mice obtained at eight different circadian times, located 3 h apart. MGMT activity varied 5-fold along the 24 h time-scale, from 7 +/- 1 pmol/g of tissue at 7 h after light onset (HALO), during the rest span, up to 32 +/- 9 pmol/g at 19 HALO (second mid to late activity span). This large amplitude circadian rhythm in MGMT activity may be an important determinant of the susceptibility rhythms to alkylating agents. The greatest DNA repair activity occurred at night when mice were active, eat and drink, and thus are at a higher risk of being exposed to chemical insults.

Animals↗

PubMed1992

Properties and localization of DNA methyltransferase in preimplantation mouse embryos: implications for genomic imprinting.

Preimplantation mouse embryos contain very high levels of DNA methyltransferase activity. We show here that the form of DNA methyltransferase (DNA MTase) in early embryos differs from the form found in other cells and tissues by a slightly higher mobility on gel electrophoresis. Levels of DNA MTase were found to be very high throughout preimplantation development even though levels of 5-methylcytosine (m5C) in nuclear DNA are known to undergo a substantial decline in the same period. Confocal laser scanning microscopy of mouse embryos stained with DNA MTase-specific antibodies showed striking developmentally regulated changes in the distribution of DNA MTase. From the oocyte stage to the four-cell-stage, most DNA MTase was concentrated in peripheral cytoplasm, and nuclei did not contain detectable DNA MTase. In four- and eight-cell embryos, DNA MTase was seen in cytoplasmic granules; and in eight-cell embryos, DNA MTase was also present in large amounts in nuclei. Nuclei of blastocysts stained only faintly, whereas the cytoplasmic granules remained prominent. Paradoxically, DNA MTase was found to be at its highest levels in nuclei at a developmental stage where levels of m5C in DNA are decreasing most rapidly. Changes in methylation patterns in preimplantation embryos are therefore proposed to be under the control of unidentified regulatory factors rather than DNA MTase itself; these regulatory factors could be members of the group that contains the products of the Ssm-1 and Imp-1 genes, which are involved in the regulation of genomic imprinting.

Animals↗

PubMed2003

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of HP1352, a putative DNA methyltransferase in Helicobacter pylori.

The putative methyltransferase gene HP1352 from Helicobacter pylori strain 26695 was heterologously expressed in Escherichia coli. The 359-amino-acid gene product was purified and crystallized. The crystals belong to space group I2(1)2(1)2(1) and show diffraction to at least 2.5 A resolution. The unit-cell parameters are a = 69.6, b = 86.6, c = 140.0 A. A greater than 90% complete native data set has been collected and structure determination using the molecular-replacement method is ongoing.

Cloning, Molecular↗

PubMed2004

Reproductive epigenetics.

Epigenetics refers to covalent modifications of DNA and core histones that regulate gene activity without altering DNA sequence. To date, the best-characterized DNA modification associated with the modulation of gene activity is methylation of cytosine residues within CpG dinucleotides. Human disorders associated with epigenetic abnormalities include rare imprinting diseases, molar pregnancies, and childhood cancers. Germ cell development and early embryo development are critical times when epigenetic patterns are initiated or maintained. This review focuses on the epigenetic modification DNA methylation and discusses recent progress that has been made in understanding when and how epigenetic patterns are differentially established in the male and female germlines, the mouse, and human disorders associated with abnormalities in epigenetic programming in germ cells and early embryos, as well as genetic and other modulators (e.g. nutrition and drugs) of reproductive epigenetic events.

Animals↗

PubMed1996

Induction of MAGE genes in lymphoid cells by the demethylating agent 5-aza-2'-deoxycytidine.

MAGE genes encoding tumor antigens recognized by cytotoxic T lymphocytes are appropriate target molecules for specific immunotherapy of cancer. We have investigated whether the demethylating agent 5-aza-2'-deoxycytidine (DAC) induces MAGE-1, -2, -3, and -6 in normal and malignant lymphoid cells. DAC induced these MAGE genes in both PHA/interleukin-2 (IL-2)-activated T cells from healthy donors and MAGE-negative T and B cell leukemias in most cases. It also induced MAGE-1 in IL-2-dependent T cell clones and all MAGE genes tested in Epstein-Barr virus-transformed B cell lines. Expression of MAGE-1 protein in the cells was confirmed by western blot analysis with anti-MAGE-1 polyclonal antibody. Therefore, demethylation is a potent stimulus to induce MAGE genes in both normal and malignant lymphoid cells.

Amino Acid Sequence↗

PubMed2000

Trans-regulated silencing and reactivation of TP53 tumor suppressor gene in malignant transformation and its reversion.

Despite growing interest in the methylation-mediated silencing of tumor suppressor genes in the neoplastic process, its signaling mechanism remains largely unknown. Here we show in a cultured murine cell line system that the silencing and reactivation of tumor suppressor gene TP53 were reversibly controlled by a trans-acting regulatory mechanism. The gene product p53, which was constitutively expressed and activated upon X-ray irradiation in non-malignant parental cell line, was undetectable in its X-ray-induced malignant transformants, while they retained a wild-type TP53. The silencing was cancelled by transferring a human chromosome 11 and the expression of p53 was restored. The non-malignant revertants thus obtained were again susceptible to transformation by X-irradiation, giving rise to re-transformants, in which p53 was again repressed while the human chromosome 11 retained the ability to turn on TP53 when it was transferred into other malignant clone. The silent TP53 could be reactivated by treatment with the demethylating agent 5-azadeoxycytidine. These observations indicate the presence of a trans-acting signaling mechanism in the methylation-mediated regulation of TP53 expression which is associated with the acquisition of malignancy.

Animals↗

PubMed2004

Methylation-associated silencing of the Wnt antagonist SFRP1 gene in human ovarian cancers.

The SFRP1 gene on chromosome 8p11.2 encodes a Wnt signaling antagonist, and was recently demonstrated to be a new tumor suppressor that is inactivated by promoter methylation in human colon cancers. Here, we analyzed promoter methylation of the SFRP1 gene in human ovarian cancers, in which loss of heterozygosity in 8p is frequently observed and involvement of the Wnt signaling pathway has been suggested. Methylation-specific PCR (MSP) analysis showed that four of 13 ovarian cancer cell lines and two of 17 primary ovarian cancers had methylated SFRP1, while an immortalized ovarian epithelial cell line, HOSE, and seven ovarian endometrial cyst samples did not. In the four ovarian cancer cell lines with the methylation, SFRP1 was not expressed at all as determined by quantitative RT-PCR analysis. A cell line with SFRP1 methylation, MCAS, was treated with a demethylating agent, 5-aza-2'-deoxycytidine, and demethylation of the promoter and re-expression of SFRP1 were observed. These results show that SFRP1 is inactivated by promoter methylation in human ovarian cancers, as well as colon cancers.

Adult↗

PubMed2006

Methylation of neutral endopeptidase 24.11 promoter in rat hepatocellular carcinoma.

Neutral endopeptidase 24.11 (NEP), a cell-surface enzyme expressed by epithelial cells that cleaves and inactivates biologically active small peptides, is downregulated in various cancers. NEP is encoded by a gene that contains a CpG island in the promoter region, whose hypermethylation appears related to decreased expression. Altered expression of NEP has also been reported in human hepatocellular carcinoma (HCC), suggesting its possible role in hepatocarcinogenesis. To elucidate the status of NEP in HCC, methylation in the promoter region of the gene that encodes NEP in male Fischer 344 rats with HCC, induced by a choline-deficient, l-amino acid-defined diet, was investigated by methylation-specific polymerase chain reaction, combined bisulfite restriction analysis, and bisulfite genomic sequencing. These analyses together showed the promoter to be frequently methylated in HCC in contrast to its unmethylated status in normal liver, the degree of methylation being inversely related to the level of mRNA expression evaluated by reverse transcription-polymerase chain reaction (P = 0.031). In two rat liver cell lines, RLC-16 and RLC-27, the promoter was heavily methylated and NEP mRNA expression was negative. However, administration of 5-aza-2'-deoxycytidine caused NEP expression, suggesting that methylation of CpG is a factor regulating transcriptional expression. Together with the data from microarray analyses performed previously using the same animal model, the current results suggest that reduced expression of NEP or other ectopeptidases could impact on molecules involved in signal-transducing systems, including G-protein coupled receptors, via modified turnover of extracellularly active small peptides.

Animals↗

PubMed2006

Synergic antiproliferative effect of DNA methyltransferase inhibitor in combination with anticancer drugs in gastric carcinoma.

Epigenetic alterations of DNA methylation play an important role in the regulation of gene expression associated with chemosensitivity of gastric carcinomas. With the aim of improving the chemotherapeutic efficacy of gastric carcinoma, the effect of DNA methyltransferase inhibitor, 5-aza-CdR, on the chemosensitivity of five anticancer drugs was investigated. Human gastric cancer cell lines, OCUM-2M and MKN-74, and five anticancer drugs, 5-FU, PTX, OXA, SN38, and GEM, were used. In both gastric cancer cell lines, a synergistic antiproliferative effect by a combination of 5-aza-CdR at 5 microM was found in SN38 and GEM. 5-Aza-CdR at 5 microM increased apoptosis induced by SN38 and GEM in both cell lines. 5-Aza-CdR increases the expression of DAPK-2 and DAPK-3, RASSF1, and THBS1 genes in both OCUM-2M and MKN-74 cells, but not that of hMLH1, p16, MGMT, E-cadherin, and p53 genes. These findings suggest that 5-aza-CdR is a promising chemotherapeutical agent for gastric carcinomas, in combination with the anticancer drugs SN38 and GEM, in apoptosis signaling. The upregulation of DAPK-2 and DAPK-3, RASSF1, and THBS1 genes by 5-aza-CdR might be associated with the synergistic effect.

Antineoplastic Agents↗

PubMed2004

DNA hypo-methylating agents and sickle cell disease.

Fetal haemoglobin (HbF, alpha2) decreases polymerization of sickle haemoglobin (HbS) and high levels correlate with decreased morbidity and mortality in sickle cell disease (SSD). Therefore, a therapeutic goal in SSD is the pharmacologic reactivation of HbF. Silencing of the globin (HbF) gene is associated with DNA methylation. The cytosine analogues 5-azacytidine and 5-aza-2'-deoxycytidine (decitabine) hypomethylate DNA by inhibiting DNA methyl-transferase. In clinical trials, 5-azacytidine and decitabine have demonstrated the greatest efficacy in HbF reactivation. Clinical development of these drugs has been delayed by concerns regarding the carcinogenic potential of 5-azacytidine. Furthermore, controversy regarding DNA hypomethylation versus more generic cytotoxic effects as the mechanism of action suggested that other cytotoxic/cytostatic agents might be as effective. Additional preclinical data and clinical studies of decitabine have tempered many safety concerns and have confirmed that DNA hypomethylation is the mechanism of action. Pharmacologic reactivation of HbF through DNA hypomethylation holds promise as an effective disease modifying intervention for patients with SSD. Larger studies are required to confirm safety and effectiveness with chronic use.

Anemia, Sickle Cell↗