PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “DNA Modification Methylases”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 703 records · Page 39Linked to original sources
PubMed2005

Phase II study of low-dose decitabine in patients with chronic myelogenous leukemia resistant to imatinib mesylate.

PURPOSE: To determine the activity of decitabine, a DNA methylation inhibitor, in imatinib-refractory or intolerant chronic myelogenous leukemia. MATERIALS AND METHODS: Thirty-five patients were enrolled in this phase II study (12 in chronic phase, 17 in accelerated phase, and six in blastic phase). Decitabine was administered at 15 mg/m2 intravenously over 1 hour daily, 5 days a week for 2 weeks. DNA methylation was measured using a LINE1 bisulfite/pyrosequencing assay. RESULTS: Complete hematologic responses were seen in 12 patients (34%) and partial hematologic responses in seven patients (20%), for an overall hematologic response rate of 54% (83% in chronic phase, 41% in accelerated phase, and 34% in blastic phase). Major cytogenetic responses were observed in six patients (17%), and minor cytogenetic responses were seen in 10 patients (29%) for an overall cytogenetic response rate of 46%. Median response duration was 3.5 months (range, 2 to 13+ months). Myelosuppression was the major adverse effect, with neutropenic fever in 28 (23%) of 124 courses of therapy. LINE1 methylation decreased from 71.3% +/- 1.4% (mean +/- standard error of the mean) to 60.7% +/- 1.4% after 1 week, 50.9% +/- 2.4% after 2 weeks, and returned to 66.5% +/- 2.7% at recovery of counts (median, 46 days). LINE1 methylation at the end of week 1 did not correlate with subsequent responses. However, at day 12, the absolute decrease in methylation was 14.5% +/- 3.0% versus 26.8% +/- 2.7% in responders versus nonresponders (P = .007). CONCLUSION: Decitabine induces hypomethylation and has clinical activity in imatinib refractory chronic myelogenous leukemia. We hypothesize that the inverse correlation between hypomethylation 2 weeks after therapy and response is due to a cell death mechanism of response, whereby resistant cells can withstand more hypomethylation.

Adult↗
PubMed1998

Tissue-specific imprinting of the mouse insulin-like growth factor II receptor gene correlates with differential allele-specific DNA methylation.

Imprinted genes may be expressed uniparentally in a tissue- and development-specific manner. The insulin-like growth factor II receptor gene (Igf2r), one of the first imprinted genes to be identified, is an attractive candidate for studying the molecular mechanism of genomic imprinting because it is transcribed monoallelically in the mouse but biallelically in humans. To identify the factors that control genomic imprinting, we examined allelic expression of Igf2r at different ages in interspecific mice. We found that Igf2r is not always monoallelically expressed. Paternal imprinting of Igf2r is maintained in peripheral tissues, including liver, kidney, heart, spleen, intestine, bladder, skin, bone, and skeletal muscle. However, in central nervous system (CNS), Igf2r is expressed from both parental alleles. Southern analysis of the Igf2r promoter (region 1) revealed that, outside of the CNS where Igf2r is monoallelically expressed, the suppressed paternal allele is fully methylated while the expressed maternal allele is completely unmethylated. In CNS, however, both parental alleles are unmethylated in region 1. The importance of DNA methylation in the maintenance of the genomic imprint was also confirmed by the finding that Igf2r imprinting was relaxed by 5-azacytidine treatment. The correlation between genomic imprinting and allelic Igf2r methylation in CNS and other tissues thus suggests that the epigenetic modification in the promoter region may function as one of the major factors in maintaining the monoallelic expression of Igf2r.

Alleles↗
PubMed1995

The mechanism of nuclear transport of natural or artificial transport substrates in digitonin-permeabilized cells.

Characterization of nuclear protein transport in digitonin-permeabilized cells revealed that the number of the nuclear localization signal sequences (NLS) within the transport substrate basically influences the mechanism of the transport reaction. Phycoerythrine-NLS transport substrate carrying a maximum of 4-5 conjugated NLSs/subunit, or Bsp methyltransferase-NLS fusion protein were efficiently transported into the nuclei of digitonin-permeabilized cultured cells without any exogenously added cytosolic protein. All the characteristic properties of in vivo nuclear transport are faithfully reproduced with these transport substrates: (i) the transport requires a functional NLS in the transported protein, a transport-incompetent mutant NLS being ineffective; (ii) the transport is energy dependent; (iii) the wild type nuclear localization peptide efficiently competes for transport, while the transport-incompetent mutant peptide does not; and (iv) wheat germ agglutinin inhibits this transport reaction. Nuclear transport observed with these substrates was not due to any damage of the nuclear membrane or inefficient extraction of the cytosolic proteins during the permeabilization of the cells. The nuclear transport was proportional to the number of conjugated NLSs. Nuclear transport of phycoerythrine carrying 7-8 conjugated NLSs/subunit required the addition of exogenous cytosolic proteins. This transport also fulfilled all the characteristic properties of an authentic nuclear transport. Nuclear transport with different combinations of transport substrates further supported the assumption that distinct transport mechanisms operate for different substrates. From a mixture of PE-NLS7-8 and Bsp methyltransferase-NLS, the highly conjugated substrate was completely retained in the cytoplasm in the absence of exogenous cytosol, while Bsp methyltransferase-NLS was efficiently transported. Exogenous cytosol promoted the nuclear transport of the highly conjugated substrate.

Amino Acid Sequence↗
PubMed2002

The prospective role of abnormal methyl metabolism in cadmium toxicity.

Several lines of evidence point to the probable role of abnormal methylation processes in the toxicology of metals and other xenobiotics. The spectrum of toxic effects exhibited by such metals as Ni, As, and Cd, as well as by Zn deficiency, often resemble those seen in animals chronically fed methyl-deficient diets. These metal-associated pathologies include cancer, atherosclerosis, birth defects, neurological disturbances, and pancreatic lesions. In addition, each of the above agents has been shown to alter normal methyl group metabolism in vivo or in vitro. In the present studies, we compared the effects on the enzyme DNA methyltransferase (MTase) of two metal ions: the essential metal Zn and the carcinogen Cd. MTase extracts were obtained from the hepatic nuclei of rats fed a methyl-deficient diet (lacking choline and folate) for 7 and 24 weeks. Control animals were fed the same diet supplemented with each of these vitamins. Zn and Cd both inhibited MTase in the nuclear extracts from both the control and the methyl-deficient rats. The inhibitory activity of Cd was greater than that of Zn regardless of whether the nuclear extracts were from the control or the deficient animals. In addition, the kinetics of Cd inhibition of MTase activity were different in the nuclear extracts from the control and methyl-deficient rats. The results provide evidence that the carcinogenic effects of Cd may be mediated in part through abnormal DNA methylation.

Administration, Oral↗
PubMed2005

5-azacytidine and decitabine monotherapies of myelodysplastic disorders.

OBJECTIVE: To review and differentiate the pharmacology, toxicology, pharmacokinetics, and results of major clinical trials of 5-azacytidine (5-AzaC) and 5-aza-2'-deoxycytidine (decitabine) therapy of myelodysplastic disorders. DATA SOURCES: A PubMed/MEDLINE search was conducted (1966-October 2004) using the following terms: DNA methylation, myelodysplastic disorders, 5-azacytidine, and 5-aza-2'-deoxycytidine (decitabine). Additional data sources included bibliographies from identified articles and manufacturer information. STUDY SELECTION AND DATA EXTRACTION: Clinical trials for the treatment of various malignancies by hypomethylating agents were selected from data sources. All published, major clinical trials evaluating 5-AzaC or decitabine in myelodysplastic disorders and transformed myeloid leukemia treatment were included. DATA SYNTHESIS: Myelodysplastic disorders are a group of bone marrow stem cell hyperplasias and dysplasias that result in ineffective hematopoiesis. Myelodysplastic disorders and transformed leukemia have poor prognosis and minimal response to chemotherapy. DNA hypomethylating agents have been shown to improve overall response rates (increased neutrophil, leukocyte, and platelet counts), time to leukemic progression, and quality of life compared with supportive therapy. The incidence of the most common adverse effects (nausea, vomiting, myelosuppression) can be reduced by low-dose, continuous, or extended-interval infusion. CONCLUSIONS: Since appropriate dosing schedules of decitabine are being investigated, comparison of the clinical effectiveness of 5-AzaC and decitabine would be premature at this time. DNA hypomethylating agents show promise as monotherapies of myelodysplastic disorders and transformed leukemia and may be useful as a component of combination chemotherapy of various malignancies.

Antimetabolites, Antineoplastic↗
PubMed2006

Constitutive nucleosome depletion and ordered factor assembly at the GRP78 promoter revealed by single molecule footprinting.

Chromatin organization and transcriptional regulation are interrelated processes. A shortcoming of current experimental approaches to these complex events is the lack of methods that can capture the activation process on single promoters. We have recently described a method that combines methyltransferase M.SssI treatment of intact nuclei and bisulfite sequencing allowing the representation of replicas of single promoters in terms of protected and unprotected footprint modules. Here we combine this method with computational analysis to study single molecule dynamics of transcriptional activation in the stress inducible GRP78 promoter. We show that a 350-base pair region upstream of the transcription initiation site is constitutively depleted of nucleosomes, regardless of the induction state of the promoter, providing one of the first examples for such a promoter in mammals. The 350-base pair nucleosome-free region can be dissected into modules, identifying transcription factor binding sites and their combinatorial organization during endoplasmic reticulum stress. The interaction of the transcriptional machinery with the GRP78 core promoter is highly organized, represented by six major combinatorial states. We show that the TATA box is frequently occupied in the noninduced state, that stress induction results in sequential loading of the endoplasmic reticulum stress response elements, and that a substantial portion of these elements is no longer occupied following recruitment of factors to the transcription initiation site. Studying the positioning of nucleosomes and transcription factors at the single promoter level provides a powerful tool to gain novel insights into the transcriptional process in eukaryotes.

Base Pairing↗
PubMed2004

Methods of epigenetic analysis.

Epigenetics encompasses heritable changes in DNA or its associated proteins except mutations in gene sequence. Many investigators in the field of epigenetics focus on histone modifications and DNA methylation, two molecular mechanisms that are often linked and interdependent. A variety of methods are applied to the study of epigenetic processes, and the past decade has witnessed an exponential increase in novel approaches to elucidate the molecular mysteries of epigenetic inheritance. This chapter summarizes some of the most contemporary methods used to study epigenetics presented throughout the book.

Chromatin↗
PubMed2005

Dietary arsenic affects dimethylhydrazine-induced aberrant crypt formation and hepatic global DNA methylation and DNA methyltransferase activity in rats.

Cell culture studies have suggested that arsenic exposure results in decreased S-adenosylmethionine (SAM), causing DNA hypomethylation. Previously, we have shown that hepatic SAM is decreased and/or S-adenosylhomocysteine increased in arsenic-deprived rats; these rats tended to have hypomethylated DNA. To determine the effect of dietary arsenic on dimethylhydrazine (DMH)-induced aberrant crypt formation in the colon, Fisher 344 weanling male rats were fed diets containing 0, 0.5, or 50 microg As (as NaAsO2)/g. After 12 wk, dietary arsenic affected the number of aberrant crypts (p<0.02) and aberrant crypt foci (p<0.007) in the colon and the amount of global DNA methylation (p<0.04) and activity of DNA methyltransferase (DNMT) (p<0.003) in the liver. In each case, there were more aberrant crypts and aberrant crypt foci, a relative DNA hypomethylation, and increased activity of DNMT in the rats fed 50 microg As/g compared to those fed 0.5 microg As/g. The same phenomenon, an increased number of aberrant crypts and aberrant crypt foci, DNA hypomethylation, and increased DNMT tended to hold when comparing rats fed the diet containing no supplemental arsenic compared to rats fed 0.5 microg As/g. The data suggest that there is a threshold for As toxicity and that possibly too little dietary As could also be detrimental.

Animals↗
PubMed2002

Epigenetic cancer therapies: DNA methyltransferase inhibitors.

Human cancers frequently show altered patterns of DNA methylation, particularly at CpG islands. These CpG islands are sequences of DNA rich in CpG dinucleotides and are often found close to gene promoters. Methylation within islands has been shown to be associated with transcriptional repression of the linked gene. Genes involved in all facets of tumour development and progression can become methylated and epigenetically silenced. Re-expression of such silenced genes can lead to suppression of tumour growth or sensitisation to anticancer therapies. Agents that can reverse DNA methylation include nucleoside and non-nucleoside inhibitors of DNA methyltransferase. Such agents are now undergoing preclinical evaluation and clinical trials in cancer patients.

Animals↗
PubMed2004

DNA methylation affects meiotic trans-sensing, not meiotic silencing, in Neurospora.

During the early stages of meiosis in Neurospora, the symmetry of homologous chromosomal regions is carefully evaluated by actively trans-sensing their identity. If a DNA region cannot be detected on the opposite homologous chromosome, then this lack of "sensing" activates meiotic silencing, a post-transcriptional gene silencing-like mechanism that silences all genes in the genome with homology to the loop of unpaired DNA, whether they are paired or unpaired. In this work, we genetically dissected the meiotic trans-sensing step from meiotic silencing by demonstrating that DNA methylation affects sensing without interfering with silencing. We also determined that DNA sequence is an important parameter considered during meiotic trans-sensing. Altogether, these observations assign a previously undescribed role for DNA methylation in meiosis and, on the basis of studies in other systems, we speculate the existence of an intimate connection among meiotic trans-sensing, meiotic silencing, and meiotic recombination.

DNA Methylation↗
PubMedDate not supplied

Methylation of a CpG island within the uroplakin Ib promoter: a possible mechanism for loss of uroplakin Ib expression in bladder carcinoma.

Uroplakin Ib is a structural protein on the surface of urothelial cells. Expression of uroplakin Ib mRNA is reduced or absent in many transitional cell carcinomas (TCCs) but molecular mechanisms underlying loss of expression remain to be determined. Analysis of the uroplakin Ib promoter identified a weak CpG island spanning the proximal promoter, exon 1, and the beginning of intron 1. This study examined the hypothesis that methylation of this CpG island regulates uroplakin Ib expression. Uroplakin Ib mRNA levels were determined by reverse transcription polymerase chain reaction and CpG methylation was assessed by bisulfite modification of DNA, PCR, and sequencing. A correlation was demonstrated in 15 TCC lines between uroplakin Ib mRNA expression and lack of CpG methylation. In support of a regulatory role for methylation, incubating uroplakin Ib-negative lines with 5-aza-2'-deoxycytidine reactivated uroplakin Ib mRNA expression. A trend between uroplakin Ib mRNA expression and CpG methylation was also observed in normal urothelium and bladder carcinomas. In particular, loss of uroplakin Ib expression correlated with methylation of a putative Sp1/NFkappaB binding motif. The data are consistent with the hypothesis that methylation of specific sites within the uroplakin Ib promoter may be an important factor in the loss of uroplakin Ib expression in TCCs.

Azacitidine↗
PubMed2000

In vivo demethylation of a MoMuLV retroviral vector expressing the herpes simplex thymidine kinase suicide gene by 5' azacytidine.

We constructed a functional MoMuLV-based bicistronic retroviral vector encoding the herpes simplex virus type I thymidine kinase gene, which induces sensitivity to the prodrug ganciclovir (gcv), and the reporter beta-galactosidase gene (MFG-tk-IRES-lacZ). The U937 histiocytic cell line was transduced with this vector, and a clone (VB71) with high-level transgene expression was selected. Severe combined immunodeficient (SCID) mice were injected with VB71 cells to evaluate the role of long terminal repeat methylation in transgene silencing in vivo and to see whether 5-azacytidine (5' aza-C) demethylating agent prevented it. We found 5' aza-C maintained gene expression at high level in vitro. In vivo, time to tumor onset was significantly longer in SCID mice receiving the VB71 cells, 5' aza-C, and gcv compared with animals treated with either 5' aza-C or gcv alone. The number of injected tumor cells influences tumor onset time and the efficacy of 5' aza-C and gcv treatment. The standard gcv treatment schedule (10 mg/kg from d + 1 until the onset of tumor) controlled tumor onset better than short-term treatment with high doses. In conclusion, the results extend our previous findings that transgene methylation in vivo may be prevented with an appropriate schedule of 5' aza-C and gcv.

Animals↗
PubMed2006

Selection of neural differentiation-specific genes by comparing profiles of random differentiation.

Differentiation of embryonic stem cells (ESCs) into neurons requires a high level of transcriptional regulation. To further understand the transcriptional regulation of neural differentiation of ESCs, we used oligonucleotide microarray to examine the gene expressions of the guided differentiation (GD) model for dopaminergic (DA) neurons from mouse ESCs. We also determined the gene expression profiles of the random differentiation (RD) model of mouse ESCs into embryoid bodies. From K-means clustering analysis using the expression patterns of the two models, most of the genes (1,282 of 1,884 genes [68.0%]) overlapped in their expression patterns. Six hundred twenty-two differentially expressed genes (DEGs) from the GD model by random variance F-test were classified by their critical molecular functions in neurogenesis and DNA replication (Gene Ontology analysis). However, 400 genes among GD-DEGs (64.3%) showed a high correlation with RD in Spearman's correlation analysis (Spearman's coefficient p(s) >or= .6). The genes showing marginal correlation (-.4 < p(s) < .6) were present in the early stages of differentiation of both GD and RD, which were non-specific to brain development. Finally, we distinguished 66 GD-specific genes based on p(s) <or= -.4, the molecular functions of which were related mainly to vesicle formation, neurogenesis, and transcription factors. From among these GD-specific genes, we confirmed the expression of Serpini1 and Rab33a in P19 differentiation models and adult brains. From these results, we identified the specific genes required for neural differentiation by comparing gene expressions of GD with RD; these would potentially be the highly specific candidate genes necessary for differentiation of DA neurons.

Animals↗
PubMed2006

Epigenetic control using natural products and synthetic molecules.

The term "epigenetics" is defined as "heritable changes in gene expression that occur without changes in DNA sequence". Recently, it has been revealed that DNA methylation and histone modifications such as acetylation, methylation and phosphorylation are epigenetic mechanisms according to this definition. In other words, these posttranslational modifications are important factors in determining when and where a gene will be expressed. To date, several enzymes that catalyze DNA or histone modifications have been identified, such as DNA methyltransferases and histone deacetylases. Inhibitors and activators of enzymes controlling epigenetic modifications are considered useful not only as tools for the elucidation of cellular and biological phenomena, but also as therapeutic agents, since disruption of the balance of epigenetic networks is known to cause some disease states such as cancer. In this review, we present natural products and synthetic molecules that inhibit or activate enzymes catalyzing DNA methylation or histone modifications, and discuss the potential of epigenetic therapy.

Acetylation↗
PubMed2003

The interaction of histone deacetylase inhibitors and DNA methyltransferase inhibitors in the treatment of human cancer cells.

The potential anticancer activities of histone deacetylase (HDAC) inhibitors and DNA methyltransferase (DNMT) inhibitors have been extensively studied in recent years. HDAC inhibitors suppress the activities of multiple HDACs, leading to an increase in histone acetylation. This histone acetylation induces an enhancement of the expression of specific genes that elicit extensive cellular morphologic and metabolic changes, such as growth arrest, differentiation and apoptosis. DNMT inhibitors, such as 5-aza-cytidine (5-aza-CR) and 5-aza-2'-deoxycytidine (5-aza-CdR) are also widely studied because DNA hypomethylation induces the re-activation of tumor suppressor genes that are silenced by methylation-mediated mechanisms. Recently, the combination of HDAC inhibitors or demethylating agents with other chemo-therapeutics has gained increasing interest as a possible molecularly targeted therapeutic strategy. In particular, the combination of HDAC inhibitors with demethylating agents has become attractive since histones are connected to DNA by both physical and functional interactions. To date, the accumulating evidence has confirmed the hypothesis that the combination of HDAC and DNMT inhibition is very effective (and synergistic) in inducing apoptosis, differentiation and/or cell growth arrest in human lung, breast, thoracic, leukemia and colon cancer cell lines. This review will discuss the in vitro effects of HDAC inhibitors, such as trichostatin A (TSA), sodium butyrate, depsipeptide (FR901228, FK228), valproic acid (VPA) and suberoylanilide hydroxamic acid (SAHA), and the demethylating agent, 5-aza-CdR used alone and in combination treatment of human cancer cells and the possible mechanisms involved.

Antineoplastic Agents↗