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PubMed1990

Methylation of mouse adenine phosphoribosyltransferase gene is altered upon cellular differentiation and loss of phenotypic expression.

Morphologically differentiated cell lines were previously isolated from a mouse teratocarcinoma stem cell line exhibiting an unstable heterozygous deficiency for adenine phosphoribosyltransferase (APRT) expression. In this study, the methylation sensitive and insensitive isoschizomer restriction endonucleases HpaII and MspI, respectively, were used to demonstrate that the aprt gene in the heterozygous deficient stem cell line was hypomethylated. Loss of APRT activity in this stem cell line was not associated with DNA methylation change. However, differentiation of this stem cell line was associated with hypermethylation of three consecutive HpaII/MspI sites that were located in the second intron and the third exon of the aprt gene. A total of 15 independent APRT homozygous deficient cell lines were isolated from three differentiated heterozygous deficient cell lines, and in all 15 cell lines this differentiation-related methylation pattern was altered. Two classes of alterations were noted: (1) hypomethylation of a site located in the second intron or (2) the apparent spreading of methylation to downstream methylation sites. The CpG-rich promoter region remained hypomethylated in the APRT homozygous deficient differentiated cell lines and a methylation change affecting a specific CpG site upstream of the promoter region was noted in only two of the 15 homozygous deficient cell lines. It is proposed that methylation of the mouse aprt gene may be involved in controlling phenotypic expression in the differentiated cell lines, but not in the stem cell line they were derived from.

Adenine Phosphoribosyltransferase↗
PubMed2003

Methylation dynamics of repetitive DNA elements in the mouse germ cell lineage.

Repetitive DNA elements account for a substantial fraction of the mammalian genome. Many are subject to DNA methylation, which is known to undergo dynamic change during mouse germ cell development. We found that repeat sequences of three different classes retain high levels of methylation at E12.5, when methylation is erased from many single-copy genes. Maximal demethylation of repeats was seen later in development and at different times in male and female germ cells. At none of the time points examined (E12.5, E15.5, and E17.5) did we see complete demethylation, suggesting that methylation patterns on repeats may be passed on from one generation to the next. In male germ cells, we observed a de novo methylation event resulting in complete methylation of all the repeats in the interval between E15.5 and E17.5, which was not seen in females. These results suggest that repeat sequences undergo coordinate changes in methylation during germ cell development and give further insights into germ cell reprogramming in mice.

Animals↗
PubMed1990

Synthesis and evaluation of N-substituted cis-N-methyl-2-(1-pyrrolidinyl)cyclohexylamines as high affinity sigma receptor ligands. Identification of a new class of highly potent and selective sigma receptor probes.

Certain benzeneacetamides [(-)- and (+)-cis-3,4-dichloro-N-methyl-N-[2-(1-pyrrolidinyl) cyclohexyl]benzeneacetamide] were recently reported to be potent sigma receptor ligands. In order to determine whether efficacy for the sigma receptor could be improved, a series of compounds related to the benzeneacetamides, N-substituted cis-2-(1-pyrrolidinyl)-N-methylcyclohexylamines, were synthesized and their structure-activity requirements were determined. The compounds were synthesized by starting with the previously reported (+/-)-, 1S,2R-(+)-, and 1R,2S-(-)-cis-2-(1-pyrrolidinyl)-N-methylcyclohexylamines. Analysis of sigma ([3H](+)-3-PPP), kappa ([3H]bremazocine and [3H]U69,593), dopamine-d2 ([3H](-)-sulpiride), and phencyclidine (PCP) ([3H]TCP) receptor binding in guinea pig brain revealed a number of highly potent and selective sigma receptor ligands. Notably, 1S,2R-cis-(-)-N-methyl-N-[2-(1-pyrrolidinyl)cyclohexyl]-(2-naphthyl) acetamide [(-)-29] (Ki = 8.66 +/- 0.35 nM), (+/-)-cis-2-amino-4,5-dichloro-N-methyl-N-[2-(1-pyrrolidinyl)cyclohexyl] benzeneacetamide [(+/-)-17] (Ki = 11 +/- 3 nM), 1S,2R-(-)-cis-N-methyl-N-[2-(3,4-dichlorophenyl)ethyl]-2-(1-pyrrolidinyl ) cyclohexylamine [(-)-44] (Ki = 1.3 +/- 0.3 nM), and 1R,2S-(+)-cis-N-methyl-N-[2-(3,4-dichlorophenyl)ethyl]-2-(1-pyrrolidinyl ) cyclohexylamine. [(+)-44] (Ki = 6 +/- 3 nM) exhibited very high affinity at sigma receptors, by displacement of [3H]-(+)-3-(3-hydroxyphenyl)-N-(1-propyl)piperidine [( 3H]-(+)-3-PPP). These compounds showed insignificant affinity for kappa, dopamine, or PCP receptors, making them valuable tools for the study of sigma receptors. Furthermore, these compounds also exhibited enantioselectivity ranging from 5-fold for (+)- and (-)-44 to 160-fold for (+)- and (-)-29. Several other compounds showed equivalent selectivity but displayed lower sigma receptor affinity.

Animals↗
PubMed1996

Validation studies of SNRPN methylation as a diagnostic test for Prader-Willi syndrome.

Prader-Willi syndrome (PWS) is caused by absence of a paternal contribution of the chromosome region 15q11-q13, resulting from paternal deletions, maternal uniparental disomy, or rare imprinting mutations. Laboratory diagnosis is currently performed using fluorescence in situ hybridization (FISH), DNA polymorphism (microsatellite) analysis, or DNA methylation analysis at locus PW71 (D15S63). We examined another parent-of-origin-specific DNA methylation assay at exon alpha of the small nuclear ribonucleoprotein-associated polypeptide N gene (SNRPN) in patients referred with clinical suspicion of PWS or Angelman syndrome (AS). These included 30 PWS and 17 AS patients with known deletion or uniparental disomy status, and a larger cohort of patients (n = 512) suspected of PWS who had been analyzed previously for their methylation status at the PW71 locus. Results of SNRPN methylation were consistent with known deletion or uniparental disomy (UPD) status as determined by other molecular methods in all 47 cases of PWS and AS. In the larger cohort of possible PWS patients, SNRPN results were consistent with clinical diagnosis by examination and with PW71 methylation results in all cases. These data provide support for the use of SNRPN methylation as a diagnostic method. Because methylation analysis can detect all three major classes of genetic defects associated with PWS (deletion, UPD, or imprinting mutations), methylation analysis with either PW71 or SNRPN is an efficient primary screening test to rule out a diagnosis of PWS. Only patients with an abnormal methylation result require further diagnostic investigation by FISH or DNA polymorphism analysis to distinguish among the three classes for accurate genetic counseling and recurrence-risk assessment.

Autoantigens↗
PubMed2003

Polymerase chain reaction-based methods of DNA methylation analysis.

DNA methylation is the main epigenetic modification in humans, and changes in methylation patterns play an important role in tumorigenesis. Hypermethylation of normally unmethylated CpG islands in the promoter regions often occurs in important tumor suppressor genes, DNA repair genes, and metastasis inhibitor genes. The changes of methylation status of various gene promoters seem to be a common feature of malignant cells and these changes can occur early in the progression process. Therefore detection of aberrant promoter hypermethylation of cancer-related genes may be useful for cancer diagnosis or detection of cancer recurrence. The purpose of this review is to provide a summary of the most commonly used techniques for the study of DNA methylation. Current scientific literature involving methylation detection methods was reviewed with an emphasis on polymerase chain reaction (PCR)-based detection methods. The current methodologies may be broadly classed into PCR-based methylation assays and non-PCR-based methylation assays. The problems and advantages of the different methods for detecting aberrant methylation are discussed. As the number of genes known to be hypermethylated in cancer is growing, the detection of aberrant promoter region methylation will be a promising approach for using DNA-based markers for the early detection of human cancers. Many techniques, especially PCR-based methylation assay techniques, make it practical to use these new methylation biomarkers in early cancer diagnosis.

Base Sequence↗
PubMed2005

Natural history of S-adenosylmethionine-binding proteins.

BACKGROUND: S-adenosylmethionine is a source of diverse chemical groups used in biosynthesis and modification of virtually every class of biomolecules. The most notable reaction requiring S-adenosylmethionine, transfer of methyl group, is performed by a large class of enzymes, S-adenosylmethionine-dependent methyltransferases, which have been the focus of considerable structure-function studies. Evolutionary trajectories of these enzymes, and especially of other classes of S-adenosylmethionine-binding proteins, nevertheless, remain poorly understood. We addressed this issue by computational comparison of sequences and structures of various S-adenosylmethionine-binding proteins. RESULTS: Two widespread folds, Rossmann fold and TIM barrel, have been repeatedly used in evolution for diverse types of S-adenosylmethionine conversion. There were also cases of recruitment of other relatively common folds for S-adenosylmethionine binding. Several classes of proteins have unique unrelated folds, specialized for just one type of chemistry and unified by the theme of internal domain duplications. In several cases, functional divergence is evident, when evolutionarily related enzymes have changed the mode of binding and the type of chemical transformation of S-adenosylmethionine. There are also instances of functional convergence, when biochemically similar processes are performed by drastically different classes of S-adenosylmethionine-binding proteins. Comparison of remote sequence similarities and analysis of phyletic patterns suggests that the last universal common ancestor of cellular life had between 10 and 20 S-adenosylmethionine-binding proteins from at least 5 fold classes, providing for S-adenosylmethionine formation, polyamine biosynthesis, and methylation of several substrates, including nucleic acids and peptide chain release factor. CONCLUSION: We have observed several novel relationships between families that were not known to be related before, and defined 15 large superfamilies of SAM-binding proteins, at least 5 of which may have been represented in the last common ancestor.

Amino Acid Sequence↗
PubMed1991

Blockade of both NMDA and non-NMDA receptors is required for optimal protection against ischemic neuronal degeneration in the in vivo adult mammalian retina.

Under ischemic conditions, the excitatory amino acids (EAA), glutamate and aspartate, accumulate in the extracellular compartment of brain and, by excessive stimulation of EAA receptors, trigger excitotoxic degeneration of CNS neurons. Since glutamate and aspartate exert excitotoxic activity through both of the generally recognized classes of EAA receptors [N-methyl-D-aspartate (NMDA) and non-NMDA], it follows that both receptor classes may play a role in ischemic neuronal degeneration. Although several laboratories have reported that NMDA receptor antagonists confer protection in vivo against ischemic neuronal degeneration, very little is known about the ability of non-NMDA antagonists to confer such protection, a major reason being that non-NMDA antagonists that penetrate blood-brain barriers have not been available. In the present study, we examined the ability of NMDA or non-NMDA antagonists, either individually or in combination, to prevent neuronal degeneration in vivo in the adult rat retina rendered ischemic by dye/photothrombotic occlusion of retinal blood vessels. In this model, delivery of drugs to the ischemic tissue is assured by intravitreal administration. Intravitreal administration of the NMDA antagonist, MK-801, reduced the severity of ischemic damage approximately 50% (a ceiling effect that could not be increased by administering higher doses). The predominantly non-NMDA antagonist, CNQX, when administered in the highest dose permitted by its solubility limitations, provided equivocal (statistically nonsignificant) protection, but the two drugs combined provided greater than 80% protection.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1999

Modulation of the intracellular calcium concentration in photoreceptor terminals by a presynaptic metabotropic glutamate receptor.

Fast excitatory neurotransmission in the central nervous system is mediated through glutamate acting on ionotropic glutamate receptors. However, glutamate acting on metabotropic glutamate receptors (mGluRs) can also exert an inhibitory action. Here, we report by immunocytochemistry and physiology, to our knowledge, the first glutamate receptor to be found in terminals of photoreceptors in the mammalian retina-the group III metabotropic glutamate receptor mGluR8. Glutamate is the transmitter of photoreceptors, and thus mGluR8 functions as an autoreceptor. Activation of mGluR8 by the group III mGluR agonists L-2-amino-4-phosphonobutyrate and L-serine-O-phosphate, or by glutamate itself, evokes a decrease in the intracellular calcium ion concentration ([Ca(2+)](i)) in isolated photoreceptors. This effect is blocked by the group III mGluR antagonists (RS)-alpha-methyl-4-phosphonophenylglycine and (RS)-alpha-methylserine-O-phosphate. Agonists for other classes of glutamate receptors-N-methyl-D-aspartic acid, quisqualic acid, kainic acid, or (RS)-alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid-have no effect on the [Ca(2+)](i) in isolated photoreceptors. The down-regulation of the [Ca(2+)](i) in photoreceptors by mGluR8 provides evidence for an inhibitory feedback loop at the photoreceptor synapse in the mammalian retina. This negative feedback may be a mechanism for the fine adjustment of the light-regulated release of glutamate from photoreceptors and may serve as a safety device against excitotoxic levels of release at this tonic synapse. Such a mechanism may provide a model for feedback inhibition in other parts of the central nervous system.

Amino Acid Sequence↗
PubMed2003

Cutting edge: the G-U mismatch glycosylase methyl-CpG binding domain 4 is dispensable for somatic hypermutation and class switch recombination.

Affinity maturation of the humoral response is accomplished by somatic hypermutation and class switch recombination (CSR) of Ig genes. Activation-induced cytidine deaminase likely initiates these processes by deamination of cytidines in the V and switch regions of Ig genes. This activity is expected to produce G-U mismatches that can be substrates for MutS homolog 2/MutS homolog 6 heterodimers and for uracil DNA glycosylase. However, G-T and G-U mismatches are also substrates of the methyl-CpG binding domain 4 (Mbd4) glycosylase. To determine whether Mbd4 functions downstream of activation-induced cytidine deaminase activity, we examined somatic hypermutation and CSR in Mbd4(-/-) mice. In this study, we report that CSR, as analyzed by an in vitro switch assay and by in vivo immunizations, is unaffected in Mbd4(-/-) mice. In addition, the hypermutated JH2 to JH4 region in Peyer's patch B cells showed no effects as a result of Mbd4 deficiency. These data indicate that the Mbd4 glycosylase does not significantly contribute to mechanisms of Ab diversification.

Animals↗
PubMed1995

[(Alkylamino)methyl]acrylophenones: potent and selective inhibitors of the epidermal growth factor receptor protein tyrosine kinase.

[(Alkylamino)methyl]acrylophenones and (alkylamino)propiophenones, bearing a spacer moiety such as the benzyloxy or (benzoylsulfonyl)oxy group in the 4-position, represent a novel class of inhibitors of the epidermal growth factor (EGF) receptor protein tyrosine kinase with a high degree of selectivity versus other tyrosine and serine/threonine kinases. The most active compounds inhibited the EGF receptor protein tyrosine kinase from A431 cell membranes with IC50 values of < 0.5 microM. Derivatives with a benzyloxy substituent in the 4-position of the aromatic ring inhibited both the EGF receptor kinase and the proliferation of an EGF-dependent mouse epidermal keratinocyte cell line (BALB/MK) but were only marginally active in the inhibition of the cellular EGF-dependent tyrosine phosphorylation. Compound 18 inhibited ligand-induced tyrosine phosphorylation and BALB/MK cell proliferation with IC50 values of approximately 100 and 1.21 microM, respectively, and showed antitumor activity in vivo in a nude mouse model. However, the discrepancy between the IC50 values for antiproliferative activity and cellular tyrosine phosphorylation as well as the relatively low tolerability in animals suggests a second site of action of this class of inhibitors. Nevertheless, [(alkylamino)methyl]acrylophenones and (alkylamino)propiophenones may prove to be interesting tools for studying the action of tyrosine kinases.

Animals↗
PubMed1992

Demethylation of the constant region genes of immunoglobulins reflects the differentiation state of the B cell.

Previous results showed a developmentally regulated, strong linkage between demethylation and transcriptional activity for the light chain kappa locus in the mouse (Kelley et al., Molec. cell. Biol. 8, 930-937, 1988). These results indicate the existence of a stage of development of the B cell in which permanent expression (which may be enhancer independent) of a gene is associated with its demethylation. According to this result, demethylation could mirror terminal differentiation of a cell. We tested this hypothesis by analyzing the methylation status of immunoglobulin (Ig) genes in normal B cells before and after their activation with lipopolysaccharide (LPS) to induce IgM secretion and an immunoglobulin class switch. This pattern of methylation has been compared with that of Ig genes in nonlymphoid tissues and in transformed cell lines. In general, transformed cells are terminally differentiated cells. Our results show, that in normal splenic B cells only regions proximal to the heavy chain enhancer are demethylated. The coding regions of the c mu, c delta and the c gamma 1 genes remain methylated regardless of transcription. Demethylation of the coding regions is only detectable in transformed cell lines. Hence demethylation of immunoglobulin genes may reflect a stage of terminal differentiation in which the transcription pattern of the cell is fixed. Methylation of the genes before terminal differentiation may be necessary to allow controlled expression of genes on the transcriptional level, such as by splicing and differential termination.

Animals↗
PubMed2006

Direct interaction of post-synaptic density-95/Dlg/ZO-1 domain-containing synaptic molecule Shank3 with GluR1 alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptor.

A class of scaffolding protein containing the post-synaptic density-95/Dlg/ZO-1 (PDZ) domain is thought to be involved in synaptic trafficking of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptors during development. To clarify the molecular mechanism of AMPA receptor trafficking, we performed a yeast two-hybrid screening system using the cytoplasmic tail of the GluR1 subunit of AMPA receptor as a bait and identified a synaptic molecule, Shank3/ProSAP2, as a GluR1 subunit-interacting molecule. Shank3 is a PDZ domain-containing multidomain protein and is predominantly expressed in developing neurons. Using the glutathione S-transferase pull-down assay and immunoprecipitation technique we demonstrated that the GluR1 subunit directly binds to the PDZ domain of Shank3 via its carboxyl terminal PDZ-binding motif. We raised anti-Shank3 antibody to investigate the expression of Shank3 in cortical neurons. The pattern of Shank3 immunoreactivity was strikingly punctate, mainly observed in the spines, and closely matched the pattern of post-synaptic density-95 immunoreactivity, indicating that Shank3 is colocalized with post-synaptic density-95 in the same spines. When Shank3 and the GluR1 subunit were overexpressed in primary cortical neurons, they were also colocalized in the spines. Taken together with the biochemical interaction of Shank3 with the GluR1 subunit, these results suggest that Shank3 is an important molecule that interacts with GluR1 AMPA receptor at synaptic sites of developing neurons.

Animals↗
PubMed2003

Methyl-CpG-binding protein 2 is localized in the postsynaptic compartment: an immunochemical study of subcellular fractions.

Methyl-CpG-binding protein 2 is a characteristic member of the methyl-CpG-binding protein family of transcription regulators. In conjunction with Sin3, MeCP2 recruits class I histone deacetylases to methyl-CpG regions to suppress transcription. Rett syndrome, a disorder characterized by mental retardation and autistic features, is associated in a majority of cases with mutations within the coding region of the MeCP2 gene. Considering that defective MeCP2 has mainly been related to Rett syndrome and other neurologic manifestations, we examined methyl-CpG-binding protein 2 cellular and subcellular compartmentalization in normal brain by immunochemical methods. Methyl-CpG-binding protein 2 immunoreactivity is present mainly in neurons; while the few immunostained glia show label confined to nuclei, many neurons also show slight perikaryal staining. Using well-characterized tissue fractions, we found that methyl-CpG-binding protein 2 but not Sin3 is found in both nuclear and postsynaptic compartments. This novel extranuclear localization is not unique to methyl-CpG-binding protein 2, since it has been previously reported for other transcription regulators such as c-Fos. These findings support the concept that methyl-CpG-binding protein 2 may link synaptic activity and transcriptional regulation in neurons.

Brain Chemistry↗
PubMed1975

Methylation of a membrane protein involved in bacterial chemotaxis.

A protein methylation reaction involved in chemotaxis of Escherichia coli has been identified. The involvement of this reaction in chemotaxis in indicated by four lines of evidence. (a) The methylation reaction is altered in several classes of generally nonchemotactic mutants and is coreverted with the chemotaxis defects. (b) The methylation level of the protein is affected by chemotactic stimuli. (c) The transferred methyl group is derived from methionine and is labile, in accord with the known fact that chemotaxis requires a continuous supply of methionine. (d) Methylation is abnormal in various mutants having defective or missing flagella.

Bacterial Proteins↗
PubMed1994

Importance of peptide amino and carboxyl termini to the stability of MHC class I molecules.

An influenza virus matrix peptide in which either the charged amino or carboxyl terminus was substituted by methyl groups promoted folding of the class I human histocompatibility antigen (HLA-A2). A peptide modified at both termini did not promote stable folding. The thermal stability of HLA-A2 complexed with peptides that did not have either terminus was approximately 22 degrees C lower than that of the control peptide, whereas matrix peptide in which both anchor positions were substituted by alanines had its stability decreased by only 5.5 degrees C. Thus, the conserved major histocompatibility complex class I residues at both ends of the peptide binding site form energetically important sites for binding the termini of short peptides.

Amino Acid Sequence↗
PubMed2005

Direct methylation from mouse plasma and from liver and brain homogenates.

The analysis of fatty acid composition of plasma and tissue is important as a method for studying lipid nutrition. We investigated the possibility of direct methylation of fatty acids by BF(3)-methanol from plasma and from liver and brain homogenates without lipid extraction. There were no ghost peaks in the chromatogram produced by the direct methylation method. The 18:0 percentages were significantly higher in the direct methylation method than in the lipid extraction method. There were not remarkable differences in fatty acid composition in the direct methylation and methylation after lyophilization methods. Furthermore, the recovery ratio of the internal standard in the direct methylation method was higher than that in the lipid extraction method. The difference of fatty acid composition with lipid extraction may be caused by the change of lipid class extraction. Therefore, the direct methylation method without lipid extraction is the most suitable for determining fatty acid composition in plasma and tissue.

Animals↗
PubMed1985

IS10 transposition is regulated by DNA adenine methylation.

We show that dam- mutants are a major class of E. coli mutants with increased IS10 activity. IS10 has two dam methylation sites, one within the transposase promoter and one within the inner terminus where transposase presumably binds. Absence of methylation results in increased activity of both promoter and terminus, and completely accounts for increased transposition in dam- strains. Transposition of Tn903 and Tn5 are also increased in dam- strains, probably for analogous reasons. Transposition is also increased when IS10 is hemimethylated. One hemimethylated species is much more active than the other and is estimated to be at least 1000 times more active than a fully methylated element. Evidence is presented that the promoter and inner terminus of IS10 are coordinately activated in a dam-dependent fashion, presumably because they are hemimethylated at the same time. Thus, in dam+ strains, IS10 will transpose preferentially when DNA is hemimethylated. We suggest specifically that IS10 transposition may preferentially occur immediately after passage of a chromosomal replication fork.

Adenine↗