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PubMed2006

A type IV modification dependent restriction nuclease that targets glucosylated hydroxymethyl cytosine modified DNAs.

The Escherichia coli CT596 prophage exclusion genes gmrS and gmrD were found to encode a novel type IV modification-dependent restriction nuclease that targets and digests glucosylated (glc)-hydroxymethylcytosine (HMC) DNAs. The protein products GmrS (36 kDa) and GmrD (27 kDa) were purified and found to be inactive separately, but together degraded several different glc-HMC modified DNAs (T4, T2 and T6). The GMR enzyme is able to degrade both alpha-glucosy-HMC T4 DNA and beta-glucosyl-HMC T4 DNA, whereas no activity was observed against non-modified DNAs including unmodified T4 cytosine (C) DNA or non-glucosylated T4 HMC DNA. Enzyme activity requires NTP, favors UTP, is stimulated by calcium, and initially produces 4 kb DNA fragments that are further degraded to low molecular mass products. The enzyme is inhibited by the T4 phage internal protein I* (IPI*) to which it was found to bind. Overall activities of the purified GmrSD enzyme are in good agreement with the properties of the cloned gmr genes in vivo and suggest a restriction enzyme specific for sugar modified HMC DNAs. IPI* thus represents a third generation bacteriophage defense against restriction nucleases of the Gmr type.

5-Methylcytosine↗
PubMed2004

Androgen receptor gene cytosine, adenine, and guanine trinucleotide repeats in patients with endometriosis.

OBJECTIVE: A genetic variation in the androgen receptor (AR) has been associated with the risk of developing endometriosis. The AR gene is located on the X chromosome and contains a highly polymorphic trinucleotide repeat (cytosine, adenine, and guanine: CAG) in its first exon, whose length and methylation pattern affect both AR expression and function. Thus, we sought to further investigate the potential association between endometriosis and the AR-CAG polymorphism. METHODS: Genomic DNA was obtained from a consecutive series of 197 white Italian women of reproductive age who underwent laparoscopy for benign gynecologic pathologies. Molecular analysis of AR-CAG repeats was performed by polymerase chain reaction amplification and Genescan evaluation. The pattern of CAG repeat distribution was compared between subjects with and without endometriosis. RESULTS: Endometriosis was documented in 105 women (stage I-II in 33 women and stage III-IV in 72 women). We found no difference in the number of AR-CAG repeats between women with endometriosis and controls. The CAG repeat length ranged from eight to 27 (mean +/- standard deviation, 17.4 +/- 1.9) for endometriosis patients and from 11 to 27 (mean +/- standard deviation, 17.4 +/- 2) for controls. Moreover, no association was found between AR gene polymorphisms and the various clinical manifestations of the disease. CONCLUSION: We conclude that AR-CAG repeat length does not constitute an important factor for the genetic predisposition to endometriosis.

Adenine↗
PubMed2005

Short hairpin RNA-directed cytosine (CpG) methylation of the RASSF1A gene promoter in HeLa cells.

Methylation of cytosines in CpG motifs is an important mechanism for epigenetic regulation of gene expression in mammalian cells. The initiating event(s) for de novo methylation in mammalian cells, particularly in cancer, is unknown. In plants, short RNAs homologous to DNA sequences are known to initiate de novo methylation. To investigate whether short hairpin RNAs (shRNAs) may also serve as initiators for de novo methylation in human cells we have expressed short hairpin RNAs complementary to the CpG island including the promoter and early transcribed regions of the human RASSF1A gene. RASSF1A encodes a putative tumor suppressor that is hypermethylated in a variety of human cancers, whereas in some human cell lines, such as HeLa, RASSF1A is unmethylated and transcriptionally active. We demonstrate that shRNAs complementary to the RASSF1A promoter or early transcribed regions can direct low levels of de novo DNA methylation and partial gene silencing in HeLa cells. In contrast, an shRNA harboring four central mismatches with the target cannot direct such methylation. The results presented suggest provocative potential mechanisms for transcriptional gene silencing via DNA methylation in cancer cells.

Base Sequence↗
PubMed2005

Nonviral jet-injection gene transfer for efficient in vivo cytosine deaminase suicide gene therapy of colon carcinoma.

Jet-injection technology has developed into an efficient gene delivery system for nonviral in vivo gene transfer. In this study the jet-injector system was used for the intratumoral gene transfer of small volumes of naked DNA encoding the Escherichia coli cytosine deaminase (CD) suicide gene. In our in vivo studies human colon carcinoma (patient-derived tumor model Colo5734 and SW480 colon carcinoma)-bearing NMRI-nu/nu male mice received four jet injections (10 microl per injection) of the CD-gene-carrying plasmid, representing 40 microg plasmid DNA per animal. Forty-eight hours after jet-injection, treatment of tumors with 5-fluorocytosine (5-FC; 500 mg/kg ip) was started and during treatment tumor volumes were measured. Starting from day 5 of 5-FC treatment inhibition of tumor growth was seen in the CD-gene-transduced tumors compared to the respective control groups, which lasted for the entire observation time. Expression analysis at the mRNA and protein levels revealed efficient expression of the CD gene in the jet-injected tumors. Therefore, in this in vivo study jet-injection gene transfer of 40 microg CD-expressing naked plasmid DNA leads to a significant tumor growth inhibition. This study demonstrates the applicability of the jet-injection technology for in vivo gene transfer into tumors to achieve efficient tumor gene therapy.

Animals↗
PubMed2003

Methods for the design and analysis of oligodeoxynucleotide-based DNA (cytosine-5) methyltransferase inhibitors.

Several second-generation inhibitors of DNA (cytosine-5) methyltransferases based on studies of modified synthetic oligodeoxynucleoides have been described. As an aid to studies of these inhibitors, we present an electronic structure-based algorithm that can be used as a method for predicting the nature of the expected inhibition by any noncytosine nucleotide target. Targeting by the major human enzyme (hDnmt1) is governed by the presence of a three-nucleotide motif. In hemimethylated DNA, this motif consists of a 5-methylcytosine targeting signal that causes the enzyme to probe the opposite strand for a normally paired guanosine or inosine residue and attempt to methylate the residue 5' to that site. As a demonstration of the method, we apply these rules to the design and characterization of a novel oligodeoxynucleotide inhibitor of hDnmt1. This inhibitor takes advantage of the three-nucleotide recognition motif characteristic of hDnmt1 and shows that the enzyme is inhibited in vitro by non-CG methylation which targets the enzyme to normally basepaired but unproductive nucleotides such as dG, dA, and dT. Kinetic analysis at constant S-adenosyl-L-methionine concentration shows that representative inhibitory oligodeoxynucleotides are best viewed as weakly productive components of systems containing two DNA substrates. This model suggests that the most effective inhibitors are those with very low apparent Vmax and very low Km values. Oligodeoxynucleotides containing mispaired and unproductive targets such as dG, dA, dT, and dU are also inhibitory as secondary substrates for the human enzyme. Biologically, fail-safe mechanisms identified by the ab initio approach appear to be active in preventing potentially mutagenic deamination of dihydrocytosine and enzymatic methylation of dU.

Base Sequence↗
PubMed1999

Characterization of a new variant DNA (cytosine-5)-methyltransferase unable to methylate double stranded DNA isolated from the marine annelid worm Chaetopterus variopedatus.

The enzyme S-adenosylmethionine-DNA (cytosine-5)-methyltransferase has been identified, first time for invertebrates, in embryos of the marine polychaete annelid worm Chaetopterus variopedatus. The molecule has been isolated from embryos at 15 h of development. It is a single peptide of about 200 kDa molecular weight, cross-reacting with antibodies against sea urchin DNA methyltransferase. The enzymatic properties of the molecule are similar to those of Dnmt1 methyltransferases isolated from other organisms, but with the peculiarity to be unable to make 'de novo' methylation on double stranded DNA.

Animals↗
PubMed1977

Separation of alkylated guanines, adenines, uracils and cytosines by thin-layer chromatography.

A one-dimensional thin-layer chromatographic (TLC) method using a mixture of two solvents and commercially available silica gel plates to separate mixtures of alkylated guanines, adenines, uracils and cytosines is presented. RF values for the bases and the solvent systems used are listed. The addition of approximately 1 ml of ammonium hydroxide to the solvent has been found to prevent streaking and results in non-distorted developed spots. A mixture of 19 adenine and uracil bases was resolved on silica gel plates employing two-dimensional TLC. Chloroform-methanol (90:10) was used for the first dimension and chloroform-propanol (90:30) for the second.

Adenine↗
PubMed1989

Measurement of deoxyguanosine/thymidine ratios in complex mixtures by high-performance liquid chromatography for determination of the mole percentage guanine + cytosine of DNA.

The ratio of deoxyguanosine and thymidine can be determined in a complex mixture containing the major ribonucleosides and deoxynucleosides, the minor deoxynucleosides, and the nucleotide monophosphates by high-performance liquid chromatography. The isocratic procedure utilizes a C18 column and a solvent of methanol-triethylamine phosphate (pH 5.1). A single analysis requires 15 min. Within the range of 0.5-1.5 micrograms of total deoxynucleosides per sample, the determination is very precise and the relative standard deviation is about 0.1%. From the deoxyguanosine/thymidine ratio, a precise determination of the mole percentage guanine + cytosine of double-stranded DNA is calculated.

Archaea↗
PubMed2002

Structural effects of cytosine methylation on DNA sugar pucker studied by FTIR.

This FTIR investigation concerns structural consequences of 5-methylation of cytosine in a DNA decamer in solution. Methylation of DNA is an important functional signal in transcription, but its effect on DNA structure is variable and not fully understood. Here, single and multiple 5-methylcytosine substitutions are introduced into the self-complementary sequence d(CCGGCGCCGG)(2). No major structural effect of methylation on the DNA duplex in solution is seen in the IR spectra: The overall B-form character of the backbone and S-type of sugar puckering are maintained in all the studied sequences, in agreement with previous literature. However, certain significant effects are detected in the IR regions sensitive to sugar pucker and glycosidic torsional angle. A single or multiple 5-methylcytosine substitution in d(CCGGCGCCGG)(2) leads to a doublet splitting of the S-type 840-820 cm(-1) sugar conformational band. The results suggest the coexistence of two different major sugar puckers within the S-conformational family, with an increased relative contribution of the C2'-endo type of sugar in the methylated sequences. In addition, a partial or full downshift of the guanosine/anti marker band at 1,375 cm(-1) in the methylated sequences reflects a change in the value of the dihedral angle chi of guanosine upon methylation. The IR spectra are interpreted in terms of localized transitions between the BI and BII subconformational states of the B-DNA backbone caused by the methylation. An increased amount of the BII subconformer in the methylated sequences should give rise to a structurally more rigid conformation, in agreement with earlier observations on DNA backbone dynamics and bending flexibility in methylated DNA.

Base Sequence↗
PubMed1999

Expression of size-polymorphic androgen receptor (AR) gene in ovarian endometriosis according to the number of cytosine, adenine, and guanine (CAG) repeats in AR alleles.

An increase in androgen receptor (AR) caused by estrogen is recognized as one of the biological phenomena related to estrogen-induced growth in uterine endometrium. The A/B region of AR gene in X chromosome involves the cytosine, adenine, and guanine (CAG) repeats. Random X chromosome inactivation with AR alleles in individual cells occurs in females. Therefore, approximately either paternal or maternal single dominant polymorphic AR mRNA must be expressed in neoplastic tissue originated from monoclone. This prompted us to determine deviated number of CAG repeats in AR mRNA to understand clonality in ovarian endometriosis. In all cases of heterozygous AR alleles, although paternal and maternal AR mRNAs from normal eutopic uterine endometrium were consistently expressed as AR alleles, either paternal or maternal single dominant AR mRNA expression was found in an individual ovarian endometrioma. Therefore, an individual ovarian endometrioma might be formed from an independent monoclonal ovarian endometriotic endometrial cell after inactivation of either AR allele in X chromosome.

Adenine↗
PubMed2000

Interaction of Ia and IIa group cations with the guanine site in cytosine-guanine nucleic acid base pair: an ab initio Hartree Fock study in the absence of basis set superposition error.

Structures and energetics of complexes between guanine...cytosine Watson Crick (GCWC) DNA base pair and various metal cations were investigated by an ab initio Hartree Fock (HF) study in the absence of basis set superposition error. Cations were allowed to interact with N7 and O6 sites of guanine. The BSSE free gradient geometry optimisation were performed in the framework of the SCF-MI (self consistent field for molecular interactions) theory. In particular, the structure of the complex with the mono and bivalent cations, like H+, Na+, K+, Mg++, Ca++ were analysed showing that the coordination to the N7 and O6 sites of the GCWC pair can generate non-WC hydrogen bonding patterns. The results demonstrate that the a priori elimination of the BSSE allows to study molecular clusters of biological interest by employing small basis sets.

Base Pair Mismatch↗
PubMed1997

(S)-1-(3-hydroxy-2-phosphonylmethoxypropyl)cytosine (HPMPC) inhibits HIV-1 replication in epithelial cells, but not T-lymphocytes.

PMEA [9-(2-phosphonylmethoxyethyl)adenine] inhibited both HSV-1 and HIV-1 replication in MT-2 and HeLa-CD4 cells. (S)-1-[3-hydroxy-2-(phosphonylmethoxy)propyl]cytosine (HPMPC) inhibited both these viruses in the epithelioid HeLa-CD4 cells, but did not inhibit either virus in the T-lymphocytic MT-2 cells. PMEA and HPMPC are metabolized to their diphosphorylated forms within cells, which then inhibit viral polymerases. We therefore compared the metabolism of PMEA and HPMPC in MT-2 and HeLa CD4 cells. PMEApp formation was efficient in both the cell types, whereas HPMPCpp levels were approximately 3-10 fold lower in MT-2 cells, compared to HeLa-CD4 cells. These results indicate that HPMPC can inhibt HIV replication in the appropriate cell types, and show that differences in their metabolism cannot account entirely for the lack of antiviral efficacy of HPMPC in MT-2 cells.

Adenine↗
PubMed1997

Cytosine methylation and the ecology of intragenomic parasites.

Most of the 5-methylcytosine in mammalian DNA resides in transposons, which are specialized intragenomic parasites that represent at least 35% of the genome. Transposon promoters are inactive when methylated and, over time, C-->T transition mutations at methylated sites destroy many transposons. Apart from that subset of genes subject to X inactivation and genomic imprinting, no cellular gene in a non-expressing tissue has been proven to be methylated in a pattern that prevents transcription. It has become increasingly difficult to hold that reversible promoter methylation is commonly involved in developmental gene control; instead, suppression of parasitic sequence elements appears to be the primary function of cytosine methylation, with crucial secondary roles in allele-specific gene expression as seen in X inactivation and genomic imprinting.

Animals↗
PubMed1998

Selective in vivo radiosensitization by 5-fluorocytosine of human colorectal carcinoma cells transduced with the E. coli cytosine deaminase (CD) gene.

PURPOSE: The E. coli cytosine deaminase (CD) gene encodes an enzyme capable of converting the nontoxic prodrug 5-fluorocytosine (5-FC) to 5-fluorouracil (5-FU), a known radiosensitizer. Having previously shown that combined CD suicide gene therapy and radiation (RT) results in pronounced radiosensitization in vitro, we progressed to in vivo studies of combined therapy. METHODS AND MATERIALS: WiDr human colon cancer cells were transduced in vitro with the CD gene and cells expressing CD were selected for use as xenografts in a nude mouse model. After administration of 5-FC, tumors received 10-30 Gy local field radiation (RT) and tumor growth delay was compared to control animals receiving either 5-FU, 5-FC, or RT alone. RESULTS: Maximal growth delay was seen in mice treated with 5-FC for 6 consecutive days prior to RT. Combined treatment with 15 Gy radiation resulted in a dose-modifying factor (DMF) of 1.50, and a greater DMF was observed with higher doses of radiation. There was no appreciable toxicity using this new approach. In contrast, a similar treatment of combined 5-FU and radiation resulted in considerable toxicity and no appreciable radiosensitization. CONCLUSION: The present results show that combined suicide gene therapy and RT results in pronounced antitumor effect without any notable toxicity. This indicates that the CD gene may be useful in the development of novel treatment strategies combining radiation and gene therapy in the treatment of locally advanced cancers.

Animals↗
PubMed2000

Primary structure and expression of the xiphophorus DNA-(cytosine-5)-methyltransferase XDNMT-1.

Small aquarium fishes become increasingly important in the study of normal vertebrate development and disease. Differential DNA methylation might play a role in these processes. In the teleost Xiphophorus, a well-established animal model for melanoma formation, tumour-specific hypomethylation of the melanoma-inducing gene ONC-Xmrk has been observed. We have isolated a cDNA for the DNA-(cytosine-5)-methyltransferase XDNMT-1 from this organism, which encodes the first full-length protein from a fish species. Linkage analysis showed that Xdnmt-1 is different from the Xiphophorus tumour suppressor R, which is involved in the transcriptional repression of the ONC-Xmrk melanoma oncogene in healthy fish. As methylation has been implicated in the regulation of ONC-Xmrk expression, XDNMT-1 might play a role by acting up- or downstream of R. Expression analysis demonstrated that the Xdnmt-1 transcript is present in all adult tissues and cell lines tested. However, developing embryos show a spatially and temporally regulated expression pattern suggesting that the enzyme might play a role during development in fish.

Animals↗
PubMed2001

DNA (cytosine-5) methyltransferase turnover and cellular localization in developing Paracentrotus lividus sea urchin embryo.

The turnover and localization of the enzyme DNA (cytosine-5) methyltransferase (Dnmt1) were studied during Paracentrotus lividus sea urchin embryo development using antibody preparations against the NH(2) and COOH-terminal regions of the molecule. The antibodies reveal, by Western blots and whole-mount analyses, that the enzyme is differently required during embryonic development. The changeover point is at blastula stage, where a proteolytic mechanism hydrolyses the enzyme present in all embryonic cells by removing a peptide of about 45 kDa from the amino terminal region of the 190 kDa enzyme initially synthesized on maternal transcripts. The resulting 145 kDa enzyme shows modified catalytic properties, different antibody reactivity and is rapidly destroyed in the few hours before gastrulation. At more advanced stages of development the enzyme is newly synthesized but only in particular cell types, among which neurons. The data show that Dnmt1 is removed from embryonic cells before gastrulation to be synthesized again at different levels in different cell types, indicating that the concentration of Dnmt1 is critical for the various differentiated cells of the developing sea urchin embryo.

Animals↗
PubMed2002

Wide intra-genomic G+C heterogeneity in human and chicken is mainly due to strand-symmetric directional mutation pressures: dGTP-oxidation and symmetric cytosine-deamination hypotheses.

The intra-strand Parity Rule 2 of DNA (PR2) states that A=T and G=C within each strands. Useful corollaries of PR2 are G/(G+C)=A/(A+T)=0.5, G/(G+A)=C/(C+T)=G+C, G/(G+T)=C/(C+A)=G+C. Here. A, T, G, and C represent relative contents of the four nucleotide residues in a specific strand of DNA, so that A+T+G+C=1. Thus, deviations from the PR2 is a sign of strand-specific (or asymmetric) mutation and/or selection pressures. The present study delineates the symmetric and asymmetric effects of mutations on the intra-genomic heterogeneity of the G+C content in the human genome. The results of this study on the human genome are: (1) When both two- and four-codon amino acids were combined, only slight departures from the PR2 were observed in the total ranges of G+C content of the third-codon position. Thus, the G+C heterogeneity is likely to be caused by symmetric mutagenesis between the two strands. (2) The above result makes the deamination of cytosine due to double-strand breathing of DNA [Mol. Biol. Evol. 17 (2000) 1371] and/or incorporation of the oxidized guanine (8-oxo-guanine) opposite adenine during DNA replication (dGTP-oxidation hypothesis) as the most likely candidates for the major cause of the diversities of the G+C content. (3) Patterns of amino acid-specific PR2-biases detected by plotting PR2 corollaries against the G+C content of third codon position revealed that eight four-codon amino acids can be divided into three types by the second codon letter: (a) C(2)-type (Ala, Pro, Ser4, and Thr), (b) G(2)-type (Arg4 and Gly), and (c) T(2)-type (Leu4 and Val). (4) Most of the asymmetric plot patterns of the above three classes in PR2 biases can be explained by C(2)-->T(2) deamination of C(2)pG(3) of C(2)-type to T(2)pG(3) (T(2)-type) in both human and chicken. This explains the existence of some preferred codons in human and chicken. However, these biases (asymmetric) hardly contribute to the overall G+C content diversity of the third codon position.

Animals↗
PubMed1997

The Corynebacterium glutamicum cglIM gene encoding a 5-cytosine methyltransferase enzyme confers a specific DNA methylation pattern in an McrBC-deficient Escherichia coli strain.

The cglIM gene of the coryneform soil bacterium Corynebacterium glutamicum ATCC 13032 has been cloned and characterized. The coding region comprises 1092 nucleotides and specifies a protein of 363 amino acid residues with a deduced Mr of 40700. The amino acid sequence showed striking similarities to methyltransferase enzymes generating 5-methylcytosine residues, especially to M x NgoVII from Neisseria gonorrhoeae recognizing the sequence GCSGC. The cglIM gene is organized in an unusual operon which contains, in addition, two genes encoding stress-sensitive restriction enzymes. Using PCR techniques the entire gene including the promoter region was amplified from the wild-type chromosome and cloned in Escherichia coli. Expression of the cglIM gene in E. coli under the control of its own promoter conferred the C. glutamicum-specific methylation pattern to co-resident shuttle plasmids and led to a 260-fold increase in the transformation rate of C. glutamicum. In addition, the methylation pattern produced by this methyltransferase enzyme is responsible for the sensitivity of DNA from C. glutamicum to the modified cytosine restriction (Mcr) system of E. coli.

Amino Acid Sequence↗