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PubMed2000

Transcriptional repression of BRCA1 by aberrant cytosine methylation, histone hypoacetylation and chromatin condensation of the BRCA1 promoter.

BRCA1 expression is repressed by aberrant cytosine methylation in sporadic breast cancer. We hypothesized that aberrant cytosine methylation of the BRCA1 promoter was associated with the transcriptionally repressive effects of histone hypoacetylation and chromatin condensation. To address this question, we developed an in vitro model of study using normal cells and sporadic breast cancer cells with known levels of BRCA1 transcript to produce a 1.4 kb 5-methylcytosine map of the BRCA1 5' CpG island. While all cell types were densely methylated upstream of -728 relative to BRCA1 transcription start, all normal and BRCA1 expressing cells were non-methylated downstream of -728 suggesting that this region contains the functional BRCA1 5' regulatory region. In contrast, the non-BRCA1 expressing UACC3199 cells were completely methylated at all 75 CpGs. Chromatin immunoprecipitations showed that the UACC3199 cells were hypoacetylated at both histones H3 and H4 in the BRCA1 promoter compared to non-methylated BRCA1 expressing cells. The chromatin of the methylated UACC3199 BRCA1 promoter was inaccessible to DNA-protein interactions. These data indicate that the epigenetic effects of aberrant cytosine methylation, histone hypoacetylation and chromatin condensation act together in a discrete region of the BRCA1 5' CpG island to repress BRCA1 transcription in sporadic breast cancer.

5-Methylcytosine↗
PubMed1978

Methylation of DNA in early development: 5-methyl cytosine content of DNA in sea urchin sperm and embryos.

By separating formic acid hydrolysates with high pressure chromatography on an Aminex-10 column, we determined the ratio of 5-methyl cytosine to cytosine and other bases of DNA from sea urchin sperm and nuclei of embryos from early cleavage through pluteus stages. Contrary to several previous reports, we could not find any measurable changes in the methylation levels of embryonic nuclear DNAs at different stages of development. We also found no consistent differences between the methylation levels of sea urchin sperm and embryonic nuclei or the 5-methyl cytosine content of fish (Mugil cephalus) sperm and liver nuclei. While these measurements would not have detected subtle variations associated with differentiation, they would have indicated the gross changes previously reported for embryos or between sperm and somatic nuclei had those changes been present.

Animals↗
PubMed1979

Determination of the recognition sites of cytosine DNA-methylases from Escherichia coli SK.

Two different cytosine DNA-methylases, NI and GII, are present in Escherichia coli SK. The GII methylase recognizes the five-member symmetric sequence: 5'...NpCpCpApGpGpN...3'. This sequence is identical with the recognition site of the hsp II type determined by RII plasmid but, in contrast to RII methylase, the GII enzyme methylates cytosine located on the 5' side of the site. By analogy with the isoshizomery of the restricting endonucleases, RII and GII DNA methylaeses may be called isomethymers which recognize the same site but methylate different bases. Since the phage of the SK and hsp II phenotypes is effectively restricted in respective cells it may be assumed that the isomethymeric modification does not provide any protection against the corresponding restrictases. NI methylase recognizes the five-member symmetric site which represents an inverted sequence of the GII site: 5'...NpGpGpApCpCpN...3'. In this case cytosine at the 3'-end of the recognition site is methylated.

Base Sequence↗
PubMed1980

Transfer RNA structure by carbon NMR: C2 of adenine, uracil and cytosine.

Fourier transform 13C NMR spectra of E. coli tRNA enriched on 13C in either position 2 of adenine (60 atom % 13C) or in position 2 of uracil (82%) and cytosine (63%) were taken at 25.16 MHz over the temperature range 10 degrees - 76 degrees. For C2 of adenine the peak as initially 5 ppm wide, but narrowed to 0.5 ppm as the molecule unfolded. C2 of uracil displayed behavior similar to that of adenine while the cytosine peak, initially relatively narrow at low temperature, sharpened less dramatically. Comparison of spectra at 26.16 MHz and 67.9 MHz showed that the peak widths for folded tRNA were determined largely by chemical shift non-equivalence. T2 T2 measurements suggested that intrinsic line widths of most cytosine C2 peaks were 4 Hz and 2-3 Hz for uracil. Adenine C2 with a directly bonded proton had resonances of about 40 Hz line width. T1 values were measured for C2 of adenine and the ribose carbons of tRNA. Consideration of dipolar relaxation and chemical shift anisotrophy led to a calculated rotational correlation time of 1.6 +/- 0.4 x 10(-8) sec for the adenines and 1.3 +/- 0.3 x 10(-8) sec for the ribose carbons.

Adenine↗
PubMed2004

Accelerated bisulfite-deamination of cytosine in the genomic sequencing procedure for DNA methylation analysis.

Understanding the biological consequences of DNA methylation is a current focus of intensive studies. A standard method for analyzing the methylation at position 5 of cytosines in genomic DNA involves chemical modification of the DNA with bisulfite, followed by PCR amplification and sequencing. Bisulfite deaminates cytosine, but it deaminates 5-methylcytosine only very slowly, thereby allowing determination of the methylated sites. The determination is usually performed using sodium bisulfite solutions of 3-5 M concentration with an incubation period of 12-16 hr at 50 degrees C. We demonstrate here that this deamination can be speeded up significantly by increasing the bisulfite concentration and the temperature with which the reaction is performed. In an experiment, in which denatured DNA was treated with 9 M bisulfite for 10 min at pH 5.4 and 90 degrees C, deamination of cytosines occurred to an extent of 99.6%, while 5-methylcytosine residues in the DNA were deaminated at less than 10%. Using a plasmid DNA fragment, we observed that the DNA can serve as a template for PCR amplification after the bisulfite treatment. This new procedure is expected to offer an improved genomic sequencing method, leading to the promotion of research on understanding the biological and medical significance of DNA methylation.

Animals↗
PubMed2004

Promoter selection for the cytosine deaminase suicide gene constructs in gastric cancer.

OBJECTIVE: Carcinomas of the digestive tract represent the second most abundant type of carcinomas in the Western world. During the past two decades, studies of genetic alterations in oncogenes, tumor-suppressor genes, and further cancer-related genes led to growing understanding of molecular mechanisms of gastrointestinal cancer resulting in a genetic progression model. Nevertheless, with a few exceptions, our knowledge of participating genes has not been exploited for gene therapy approaches. Therefore, we monitored promoter activity of a variety of genes shown to be significantly expressed in gastric tumor cells to select optimally active promoters for therapeutical recombinant DNA constructs. When driving a suicide gene these genetic elements can exert cytotoxic effects. METHODS: Using promoter-reporter gene (luciferase) constructs we compared the activities of KRT19, TFF1, SEL1L, MUC4, MUC1, CEL and hTERT by transfecting them into the gastrointestinal cell lines MKN45 and DAN-G for transient expression. After choosing strong promoters we tested the expression of the prokaryotic cytosine deaminase and its cytotoxic effect on the cell cultures. RESULTS: The promoters of SEL1L, MUC1 and KRT19 displayed the highest activity levels in reporter gene assays while other genes reported as upregulated in gastric cancer were moderately expressed. When driving cytosine deaminase in MKN45 cells, the SEL1L promoter induced a 66% cytotoxic effect and the TP1 promoter reached 82%. CONCLUSIONS: From a selection of nine promoter constructs three proved to upregulate the reporter gene well above the level of average activity. They also appear highly capable to drive a suicide gene construct, here tested using prokaryotic cytosine deaminase.

Cell Death↗
PubMed2006

An orphan DNA (cytosine-5-)-methyltransferase in Vibrio cholerae.

5-Methyl cytosine (m5C) was detected in genomic DNA of the enteric pathogen Vibrio cholerae by HPLC analysis and immunoblotting with m5C-specific antibody. Although cleavage with the restriction endonuclease EcoRII revealed the absence of a Dcm homologue in V. cholerae, analysis of the genome sequence indicated the presence of a gene, designated in this study as vchM, which encodes a DNA (cytosine-5-)-methyltransferase (m5C-MTase) designated M.Vch. M.Vch is not associated with a restriction endonuclease or a mismatch very short patch repair (Vsr)-like endonuclease and is hence an 'orphan' or solitary MTase, although analysis of a phylogenetic tree indicated that related cytosine MTases are all components of restriction-modification systems. M.Vch recognizes and methylates the first 5' C in the degenerate sequence 5'-RCCGGY-3'. RT-PCR analysis suggested that vchM gene expression is increased during the stationary phase of growth. During stationary phase, the spontaneous mutation frequency in the V. cholerae wild-type strain was significantly higher than in the corresponding vchM mutant strain, suggesting that the presence of M.Vch and the absence of a very short patch (VSP) repair-like system imposes upon V. cholerae a mutator phenotype.

Chromatography, High Pressure Liquid↗
PubMed1988

Static deformation densities for cytosine and adenine.

X-ray diffraction intensities for cytosine monohydrate have been measured at 97 K, to 2sin theta/lambda = 2.74 A-1, and used in a deformation refinement. Crystal data for cytosine monohydrate at 97 K: a = 7.728 (1), b = 9.817 (3), c = 7.520 (1), beta = 100.50 degrees, V = 560.94 A3, R = 0.0341 for 6456 unique reflections. The experimental static deformation density of cytosine compares very well with the corresponding theoretical 4-31G deformation density. Differences between theory and experiment occur at hydrogen-bonding sites. They are very similar to the corresponding differences between the theoretical deformation densities of formic acid monomer and cyclic dimer. The experimental static deformation density of 9-methyladenine was obtained in a deformation refinement against the low-temperature X-ray data of Craven & Benci [Acta Cryst. (1981), B37, 1584-1591]. It is similar to the maps presented by these authors. The comparison of the experimental deformation density of 9-methyladenine with the theoretical 4-31G deformation density of adenine shows qualitative agreement, which is improved when the 4-31G results are corrected for the absence of polarization functions in the basis set. Some of the remaining differences reflect the effects of substituting CH3 for H. The weak N...H hydrogen bonds have little influence on the deformation density in this structure.

Adenine↗
PubMed1977

The effect of modification of cytosines in Escherichia coli 16-S rRNA on reconstitution and function of 30-S ribosomes.

O-Methylhydroxylamine (methoxyamine) was used for selective modification of cytosine residues in Escherichia coli 16-S rRNA. It was shown that cytosines accessible for methoxyamination are randomly distributed along the 16-S rRNA chain. Preparations of methoxyaminated 16-S rRNA, containing 2--130 modified cytosines/chain, still retained the ability to bind 30-S proteins, but the physical assembly of reconstituted particles was incorrect. The protein compositions of the reconstituted and native particles did not differ qualitatively from each other. However, the amount of protein in reconstituted particles decreased with an increasing number of methoxyaminated cytosines in 16-S rRNA. The particles obtained sedimented slower than native 30-S subunits, lost their ability to associate with 50-S ribosomes and to bind native phage f2 RNA. In contrast, modification of 16-S rRNA did not affect binding of poly(U) by reconstituted particles.

Cytosine↗
PubMed1989

Ring-opening photoreactions of cytosine and 5-methylcytosine with aliphatic alcohols.

Several reports in the late 1950s and early 1960s indicated that ultraviolet irradiation of dilute solutions of cytosine or 5-methylcytosine in aliphatic alcohols, such as methanol or ethanol, leads to reaction mixtures containing products with an absorption maximum around 300 nm. The present work reports the isolation and characterization of the products responsible for this absorption in the photochemical reactions of cytosine and 5-methylcytosine with methanol, ethanol and 2-propanol at concentrations in the neighborhood of 200 microM. Under these conditions the reactions have been shown, in each nucleobase/alcohol system, to give almost exclusively a single type of primary photoproduct; each product shows an absorption maximum in the region of 300 nm. Structural analysis showed the products to be alcohol adducts with an ester linkage at C2 of the ring-opened base and an enamine structure at C6. For example, in the case of the reaction of cytosine with methanol, the product is N-carbomethoxy-3-aminoacrylamidine (IIIa). The occurrence of this type of photoreaction suggests a mode by which alcoholic functional groups on amino acid side chains could contribute to photoinduced DNA-protein cross-linking.

5-Methylcytosine↗
PubMed1993

In vivo repair of cytosine hydrates in DNA of cultured human lymphoblasts.

Ultraviolet irradiation of DNA in vitro results in the production of a wide variety of pyrimidine base alterations, including cytosine hydrates. Enzymes that initiate the repair of monomeric pyrimidine damage have been identified in both bacterial and mammalian systems; however, the in vivo formation and repair of cytosine photohydrates has not been demonstrated in cellular DNA. Using Escherichia coli endonuclease III as a damage-specific probe, we have shown that ring-saturated pyrimidines are formed in cultured human cells by irradiation with broad-spectrum UV light. In addition, these types of base damage are removed from the DNA of human lymphoblasts within 5 h following the irradiation. Analysis of the action spectrum for the formation of cytosine hydrates in DNA reveals that these photoproducts are formed most efficiently by irradiation in the range of 255-265 nm light, coinciding with the wavelengths that are maximally absorbed by the DNA bases.

Base Sequence↗
PubMed1997

Ultraviolet irradiation produces novel endonuclease III-sensitive cytosine photoproducts at dipyrimidine sites.

Ultraviolet light irradiation of DNA in vitro and in vivo induces cyclobutane dimers, (6-4) pyrimidine-pyrimidone photoproducts and a variety of minor products. Using a defined DNA fragment, we have identified two classes of sites that can be cleaved by Escherichia coli endonuclease III: single cytosines whose heat lability corresponds to that of cytosine hydrates and more heat-stable dipyrimidines containing cytosine. The dipyrimidine products are induced at sites suggestive of (6-4) photoproducts but are not recognized as (6-4) photoproducts by radioimmunoassay. Use of oligonucleotides containing a single cyclobutane thymine dimer, a (6-4) photoproduct or the Dewar photoisomer of the (6-4) photoproduct also indicated that these products are not substrates for endonuclease III. We have therefore identified a minor UV photoproduct that has the same sequence specificity as the two major dipyrimidine photoproducts; it may be a minor isomer, a unique derivative or an oxidative lesion confined to dipyrimidine sites. Its biological significance is not yet known but may be masked by the preponderance of major products at the same sites. Its occurrence at the particular site in dipyrimidine sequences involved in the mutagenic action of UV photoproducts suggests that it may play a role in generating C to T transitions that are common UV-induced mutations.

Animals↗
PubMed1968

Crystal structure of a complex of acridine, cytosine and water (1:1:1).

X-ray structural analysis of a crystalline complex between acridine C(13)H(9)N, cytosine C(4)H(5)N(3)O, and water (1:1:1) has been completed. The cytosine and water molecules form a sheet-like structure through a series of hydrogen bonds. The acridine molecules are bound to this layer through a hydrogen bridge from the water to the ring nitrogen. The acridine molecules stack in a parallel fashion normal to the cytosine-water sheets, with an average interplanar spacing of 3.5 angstroms.

Acridines↗
PubMed1994

Fenpropimorph affects uptake of uracil and cytosine in Saccharomyces cerevisiae.

Fenpropimorph was shown to inhibit the accumulation of the pyrimidine bases uracil and cytosine from the growth media in Saccharomyces cerevisiae. Uracil prototrophs of S. cerevisiae were more resistant to the growth-inhibitory effects of fenpropimorph than were uracil auxotrophs. High concentrations of uracil rescued fenpropimorph-treated uracil auxotrophs, and cytosine, which is accumulated by a separate mechanism, could also support growth of treated uracil auxotrophs. Fenpropimorph caused a significant decrease in the uptake of radiolabeled uracil, which was not due to accumulation of ergosta-8,14-dienol (ignosterol) in the treated cultures. Radiolabeled cytosine uptake was unaffected by drug treatment in a wild-type strain but was inhibited in a sterol mutant, in which ergosterol was absent from the cell. The role of fenpropimorph in causing membrane dysfunction through a mechanism other than altered sterol metabolism is discussed.

Culture Media↗
PubMed1975

Deoxyribonucleic acid-cytosine methylation by host- and plasmid-controlled enzymes.

Deoxyribonucleic acid (DNA)-cytosine methylation specified by the wild-type Escherichia coli K 12 mec+ gene and by the N-3 drug resistance (R) factor was studied in vivo and in vitro. Phage lambda and fd were propagated in the presence of L-[methyl-3H]methionine in various host bacteria. The in vivo labeled DNA was isolated from purified phage and depurinated by formic acid-diphenylamine treatment. The resulting pyrimidine oligonucleotide tracts were separated according to size and base composition by chromatography on diethylaminoethyl-cellulose in 7 M urea at pH 5.5 and 3.5, respectively. The distribution of labeled 5-methylcytosine in DNA pyrimidine tracts was identical for phage grown in mec+ and mec minus (N-3) cells. For phage lambda the major 5-methylcytosine containing tract was the tripyrimidine, C2T; for both fd-mec minus (N-3) DNA and fd-mec+DNA, C2T was the sole 5-methylcytosine-containing tract. When various lambda DNAs were methylated to saturation in vitro by crude extracts from mec+ and mec minus (N-3) cells, the extent of cytosine methylation was the same. This is in contrast to in vivo methylation where lambda-mec minus (N-3) DNA contains twice as many 5-methylcytosines per genome as lambda-mec+ DNA. Therefore, we suggest that the K12 met+ cytosine methylase and the N-3 plasmid modification methylase are capable of recognizing the same nucleotide sequences, but that the in vivo methylation rate is lower in mec+ cells.

Animals↗
PubMed1990

Cytosine methylation enhances Z-DNA formation in vivo.

The influence of cytosine methylation on the supercoil-stabilized B-Z equilibrium in Escherichia coli was analyzed by two independent assays. Both the M.EcoRI inhibition assay and the linking-number assay have been used previously to establish that dC-dG segments of sufficient lengths can exist as left-handed helices in vivo. A series of dC-dG plasmid inserts with Z-form potential, ranging in length from 14 to 74 base pairs, was investigated. Complete methylation of cytosine at all HhaI sites, including the inserts, was obtained by coexpression of the HhaI methyltransferase (M.HhaI) in cells also carrying a dC-dG-containing plasmid. Both assays showed that for all lengths of dC-dG inserts, the relative amounts of B and Z helices were shifted to more Z-DNA in the presence of M.HhaI than in the absence of M.HhaI. These results indicate that cytosine methylation enhances the formation of Z-DNA helices at the superhelix density present in E. coli. The B-Z equilibrium, in combination with site-specific base methylation, may constitute a concerted mechanism for the modulation of DNA topology and DNA-protein interactions.

Chloramphenicol↗
PubMed2003

Nitrogen regulation of the codBA (cytosine deaminase) operon from Escherichia coli by the nitrogen assimilation control protein, NAC.

Transcription of the cytosine deaminase (codBA) operon of Escherichia coli is regulated by nitrogen, with about three times more codBA expression in cells grown in nitrogen-limiting medium than in nitrogen-excess medium. Beta-galactosidase expression from codBp-lacZ operon fusions showed that the nitrogen assimilation control protein NAC was necessary for this regulation. In vitro transcription from the codBA promoter with purified RNA polymerase was stimulated by the addition of purified NAC, confirming that no other factors are required. Gel mobility shifts and DNase I footprints showed that NAC binds to a site centered at position -59 relative to the start site of transcription and that mutants that cannot bind NAC there cannot activate transcription. When a longer promoter region (positions -120 to +67) was used, a double footprint was seen with a second 26-bp footprint separated from the first by a hypersensitive site. When a shorter fragment was used (positions -83 to +67), only the primary footprint was seen. Nevertheless, both the shorter and longer fragments showed NAC-mediated regulation in vivo. Cytosine deaminase expression in Klebsiella pneumoniae was also regulated by nitrogen in a NAC-dependent manner. K. pneumoniae differs from E. coli in having two cytosine deaminase genes, an intervening open reading frame between the codB and codA orthologs, and a different response to hypoxanthine which increased cod expression in K. pneumoniae but decreased it in E. coli.

Bacterial Outer Membrane Proteins↗
PubMed1983

In vivo cleavage of cytosine-containing bacteriophage T4 DNA to genetically distinct, discretely sized fragments.

Mutants of bacteriophage T4D that are defective in genes 42 (dCMP hydroxymethylase), 46 (DNA exonuclease), and 56 (dCTPase) produce limited amounts of phage DNA in Escherichia coli B. In this DNA, glucoylated 5-hydroxymethylcytosine is completely replaced by cytosine. We found that this DNA rapidly becomes fragmented in vivo to at least 16 discrete bands as visualized on agarose gels subjected to electrophoresis. The sizes of the fragments ranged from more than 20 to less than 2 kilobase pairs. When DNAs from two of these bands were radioactively labeled in vitro by nick translation and hybridized to XbaI restriction fragments of cytosine-containing T4 DNA, evidence was obtained that the two bands are genetically distinct, i.e., they contain DNA from different parts of the T4 genome. Mutational inactivation of T4 endonuclease II (gene denA) prevented the fragmentation. Three different mutations in T4 endonuclease IV (gene denB) caused the same minor changes in the pattern of fragments. We conclude that T4 endonuclease II is required, and endonuclease IV is involved to a minor extent, in the in vivo production of these cytosine-containing T4 DNA fragments. We view these DNA fragments as "restriction fragments" since they represent degradation products of DNA "foreign" to T4, they are of discrete size, and they are genetically distinct. Thus, this report may represent the first, direct in vivo demonstration of discretely sized genetically distinct DNA restriction fragments.

Base Sequence↗