Light-Regulated Transcription of Genes Encoding Peridinin Chlorophyll a Proteins and the Major Intrinsic Light-Harvesting Complex Proteins in the Dinoflagellate Amphidinium carterae Hulburt (Dinophycae)1 : Changes in Cytosine Methylation Accompany Photoadaptation

In the dinoflagellate Amphidinium carterae, photoadaptation involves changes in the transcription of genes encoding both of the major classes of light-harvesting proteins, the peridinin chlorophyll a proteins (PCPs) and the major a/c-containing intrinsic light-harvesting proteins (LHCs). PCP and LHC transcript levels were increased up to 86- and 6-fold higher, respectively, under low-light conditions relative to cells grown at high illumination. These increases in transcript abundance were accompanied by decreases in the extent of methylation of CpG and CpNpG motifs within or near PCP- and LHC-coding regions. Cytosine methylation levels in A. carterae are therefore nonstatic and may vary with environmental conditions in a manner suggestive of involvement in the regulation of gene expression. However, chemically induced undermethylation was insufficient in activating transcription, because treatment with two methylation inhibitors had no effect on PCP mRNA or protein levels. Regulation of gene activity through changes in DNA methylation has traditionally been assumed to be restricted to higher eukaryotes (deuterostomes and green plants); however, the atypically large genomes of dinoflagellates may have generated the requirement for systems of this type in a relatively “primitive” organism. Dinoflagellates may therefore provide a unique perspective on the evolution of eukaryotic DNA-methylation systems.

Switch from monoallelic to biallelic human IGF2 promoter methylation during aging and carcinogenesis.

We have previously linked aging, carcinogenesis, and de novo methylation within the promoter of the estrogen receptor (ER) gene in human colon. We now examine the dynamics of this process for the imprinted gene for insulin-like growth factor II (IGF2). In young individuals, the P2-4 promoters of IGF2 are methylated exclusively on the silenced maternal allele. During aging, this promoter methylation becomes more extensive and involves the originally unmethylated allele. Most adult human tumors, including colon, breast, lung, and leukemias, exhibit increased methylation at the P2-4 IGF2 promoters, suggesting further spreading during the neoplastic process. In tumors, this methylation is associated with diminished or absent IGF2 expression from the methylated P3 promoter but maintained expression from P1, an upstream promoter that is not contained within the IGF2 CpG island. Our results demonstrate a remarkable evolution of methylation patterns in the imprinted promoter of the IGF2 gene during aging and carcinogenesis, and provide further evidence for a potential link between aberrant methylation and diseases of aging.

Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands.

Precise mapping of DNA methylation patterns in CpG islands has become essential for understanding diverse biological processes such as the regulation of imprinted genes, X chromosome inactivation, and tumor suppressor gene silencing in human cancer. We describe a new method, MSP (methylation-specific PCR), which can rapidly assess the methylation status of virtually any group of CpG sites within a CpG island, independent of the use of methylation-sensitive restriction enzymes. This assay entails initial modification of DNA by sodium bisulfite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA. MSP requires only small quantities of DNA, is sensitive to 0.1% methylated alleles of a given CpG island locus, and can be performed on DNA extracted from paraffin-embedded samples. MSP eliminates the false positive results inherent to previous PCR-based approaches which relied on differential restriction enzyme cleavage to distinguish methylated from unmethylated DNA. In this study, we demonstrate the use of MSP to identify promoter region hypermethylation changes associated with transcriptional inactivation in four important tumor suppressor genes (p16, p15, E-cadherin, and von Hippel-Lindau) in human cancer.

Methylation of coding region alone inhibits gene expression in plant protoplasts.

Derivatives of the cauliflower mosaic virus 35S promoter lacking CG and CNG methylation targets were constructed and used to direct transcription of reporter gene constructs in transiently transformed protoplasts. Such methylation-target-free (MTF) promoters, although weaker than the 35S promoter, retain significant activity despite mutation of the as-1 element. The effect of methylation on gene expression in MTF- and 35S-promoter driven constructs was examined. Even when the promoter region was free of methylation targets, reporter gene expression was markedly reduced when cytosine residues in CG dinucleotides were methylated in vitro prior to transformation. Mosaic methylation experiments, in which only specific parts of the plasmids were methylated, revealed that methylation of the coding region alone has a negative effect on reporter gene expression. Methylation nearer the 5' end of the coding region was more inhibitory, consistent with inhibition of transcription elongation.

Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development.

Arabidopsis plants transformed with an antisense construct of an Arabidopsis methyltransferase cDNA (METI) have reduced cytosine methylation in CG dinucleotides. Methylation levels in progeny of five independent transformants ranged from 10% to 100% of the wild type. Removal of the antisense construct by segregation in sexual crosses did not fully restore methylation patterns in the progeny, indicating that methylation patterns are subject to meiotic inheritance in Arabidopsis. Plants with decreased methylation displayed a number of phenotypic and developmental abnormalities, including reduced apical dominance, smaller plant size, altered leaf size and shape, decreased fertility, and altered flowering time. Floral organs showed homeotic transformations that were associated with ectopic expression of the floral homeotic genes AGAMOUS and APETALA3 in leaf tissue. These observations suggest that DNA methylation plays an important role in regulating many developmental pathways in plants and that the developmental abnormalities seen in the methyltransferase antisense plants may be due to dysregulation of gene expression.

Dynamic methylation adjustment and counting as part of imprinting mechanisms.

Monoallelic expression in diploid mammalian cells appears to be a widespread phenomenon, with the most studied examples being X-chromosome inactivation in eutherian female cells and genomic imprinting in the mouse and human. Silencing and methylation of certain sites on one of the two alleles in somatic cells is specific with respect to parental source for imprinted genes and random for X-linked genes. We report here evidence indicating that: (i) differential methylation patterns of imprinted genes are not simply copied from the gametes, but rather established gradually after fertilization; (ii) very similar methylation patterns are observed for diploid, tetraploid, parthenogenic, and androgenic preimplantation mouse embryos, as well as parthenogenic and androgenic mouse embryonic stem cells; (iii) haploid parthenogenic embryos do not show methylation adjustment as seen in diploid or tetraploid embryos, but rather retain the maternal pattern. These observations suggest that differential methylation in imprinted genes is achieved by a dynamic process that senses gene dosage and adjusts methylation similar to X-chromosome inactivation.

5-Methyl-2'-deoxycytidine in single-stranded DNA can act in cis to signal de novo DNA methylation.

Methylation of cytosine residues in DNA plays an important role in regulating gene expression during vertebrate embryonic development. Conversely, disruption of normal patterns of methylation is common in tumors and occurs early in progression of some human cancers. In vertebrates, it appears that the same DNA methyltransferase maintains preexisting patterns of methylation during DNA replication and carries out de novo methylation to create new methylation patterns. There are several indications that inherent signals in DNA structure can act in vivo to initiate or block de novo methylation in adjacent DNA regions. To identify sequences capable of enhancing de novo methylation of DNA in vitro, we designed a series of oligodeoxyribonucleotide substrates with substrate cytosine residues in different sequence contexts. We obtained evidence that some 5-methylcytosine residues in these single-stranded DNAs can stimulate de novo methylation of adjacent sites by murine DNA 5-cytosine methyltransferase as effectively as 5-methylcytosine residues in double-stranded DNA stimulate maintenance methylation. This suggests that double-stranded DNA may not be the primary natural substrate for de novo methylation and that looped single-stranded structures formed during the normal course of DNA replication or repair serve as "nucleation" sites for de novo methylation of adjacent DNA regions.

Silencing of the E-cadherin invasion-suppressor gene by CpG methylation in human carcinomas.

E-Cadherin, a cell adhesion molecule, which plays a key role in maintaining the epithelial phenotype, is regarded as an invasion-suppressor gene in light of accumulating evidence from in vitro experiments and clinical observations. In an attempt to clarify the mechanism responsible for inactivation of this gene in carcinomas, we investigated the methylation state around the promoter region by digestion of DNA with the methylation-sensitive restriction enzyme Hpa II, as CpG methylation of the promoter has been postulated to be a mechanism of transcriptional inactivation of some genes. We found that E-cadherin expression-negative carcinoma cell lines were accompanied by the hypermethylation state, whereas E-cadherin-positive cell lines were not. Furthermore, treatment of E-cadherin-negative carcinoma cells with the demethylating agent 5-azacytidine resulted in reexpression of the gene and reversion of scattered spindle-shaped cells to cells with epithelial morphology. These results suggest that hypermethylation around the promoter may be a mechanism of E-cadherin inactivation in human carcinomas and that treatment of E-cadherin-inactivated cells with a demethylating agent may cause gene expression reversion leading to epithelial morphogenesis with acquisition of the homophilic cell-cell adhesive property.

Chromosomal insertion of foreign (adenovirus type 12, plasmid, or bacteriophage lambda) DNA is associated with enhanced methylation of cellular DNA segments.

Insertion of foreign DNA into an established mammalian genome can extensively alter the patterns of cellular DNA methylation. Adenovirus type 12 (Ad12)-transformed hamster cells, Ad12-induced hamster tumor cells, or hamster cells carrying integrated DNA of bacteriophage lambda were used as model systems. DNA methylation levels were examined by cleaving cellular DNA with Hpa II, Msp I, or Hha I, followed by Southern blot hybridization with 32P-labeled, randomly selected cellular DNA probes. For several, but not all, cellular DNA segments investigated, extensive increases in DNA methylation were found in comparison with the methylation patterns in BHK21 or primary Syrian hamster cells. In eight different Ad12-induced hamster tumors, moderate increases in DNA methylation were seen. Increased methylation of cellular genes was also documented in two hamster cell lines with integrated Ad12 DNA without the Ad12-transformed phenotype, in one cloned BHK21 cell line with integrated plasmid DNA, and in at least three cloned BHK21 cell lines with integrated lambda DNA. By fluorescent in situ hybridization, the cellular hybridization probes were located to different hamster chromosomes. The endogenous intracisternal A particle genomes showed a striking distribution on many hamster chromosomes, frequently on their short arms. When BHK21 hamster cells were abortively infected with Ad12, increases in cellular DNA methylation were not seen. Thus, Ad12 early gene products were not directly involved in increasing cellular DNA methylation. We attribute the alterations in cellular DNA methylation, at least in part, to the insertion of foreign DNA. Can alterations in the methylation profiles of hamster cellular DNA contribute to the generation of the oncogenic phenotype?

Xce haplotypes show modified methylation in a region of the active X chromosome lying 3' to Xist.

During early mammalian embryogenesis, one of the two X chromosomes in somatic cells of the female becomes inactivated through a process that is thought to depend on a unique initiator region, the X-chromosome inactivation center (Xic). The recently characterized Xist sequence (X-inactive-specific transcript) is thought to be a possible candidate for Xic. In mice a further genetic element, the X chromosome-controlling element (Xce), is also known to influence the choice of which of the two X chromosomes is inactivated. We report that a region of the mouse X chromosome lying 15 kb distal to Xist contains several sites that show hypermethylation specifically associated with the active X chromosome. Analysis of this region in various Xce strains has revealed a correlation between the strength of the Xce allele carried and the methylation status of this region. We propose that such a region could be involved in the initial stages of the inactivation process and in particular in the choice of which of the two X chromosomes present in a female cell will be inactivated.

Key factors involved in stress-induced microspore embryogenesis in barley and rapeseed: DNA methylation, arabinogalactan proteins and auxin

La embriogénesis de microsporas es un proceso in vitro en el que la microspora o polen inmaduro, mediante la aplicación de un tratamiento de estrés se reprograma y abandona su ruta de desarrollo gametofítico para iniciar la ruta embriogénica, dando lugar a embriones y plantas haploides y doble-haploides. Este proceso es de gran interés básico y aplicado en biotecnología y mejora vegetal para la obtención rápida de nuevas variedades, sin embargo aún tiene importantes limitaciones en su explotación por su baja eficiencia en muchas especies de interés económico. La limitación en la aplicación de este proceso es debida a que los mecanismos de inducción y progresión de la embriogénesis de microsporas no están todavía completamente dilucidados. La monocotiledónea Hordeum vulgare (cebada) y la dicotiledónea Brassica napus (colza) son especies modelo para este proceso, en las cuales se induce embriogénesis directa en cultivos de microsporas aisladas en medio líquido, mediante tratamientos de estrés con diferentes temperaturas...

Effect of the intercalated cation-exchanged on the properties of nanocomposites prepared by 2-aminobenzene sulfonic acid with aniline and montmorillonite

Polymer/montmorillonite nanocomposites were prepared. Intercalation of 2-aminobenzene sulfonic acid with aniline monomers into montmorillonite modified by cation was followed by subsequent oxidative polymerization of monomers in the interlayer spacing. The clay was prepared by cation exchange process between sodium cation in (M–Na) and copper cation (M–Cu). XRD analyses show the manifestation of a basal spacing (d-spacing) for M–Cu changes depending on the inorganic cation and the polymer intercalated in the M–Cu structure. TGA analyses reveal that polymer/M–Cu composites is less stable than M–Cu. The conductivity of the composites is found to be 103 times higher than that for M–Cu. The microscopic examinations including TEM picture of the nanocomposite demonstrated an entirely different and more compatible morphology. Remarkable differences in the properties of the polymers have also been observed by UV–Vis and FTIR, suggesting that the polymer produced with presence of aniline has a higher degree of branching. The electrochemical behavior of the polymers extracted from the nanocomposites has been studied by cyclic voltammetry which indicates the electroactive effect of nanocomposite gradually increased with aniline in the polymer chain.

Adsorption and first stages of polymerization of aniline on platinum single crystal electrodes

The present communication studies the adsorption of aniline on platinum single crystal electrodes and the electrochemical properties of the first layers of polyaniline(PANI) grown on those platinum surfaces. The adsorption process was studied in aqueous acidic solution (0.1 M HClO4) and the electrochemical properties of thin films of PANI in both aqueous (1 M HClO4) and non-aqueous media (tetrabutyl ammonium hexafluorophosphate (TBAPF6) with additions of methanesulphonic acid in acetonitrile). First of all, it was found that the adsorption of aniline on platinum single crystal surfaces is a surface sensitive process, and even more important that the adsorption features found at low concentrations (5 × 10−5 M) can be directly correlated to the electrochemical properties of thin films of PANI in the very early stages of polymerization. The Pt(1 1 0) surface was found to be more suitable to obtain polymers with more reversible redox transitions when studied in aqueous media (1 M HClO4). This is in good agreement with the higher polymerization rates found on this surface compared to Pt(1 0 0) and Pt(1 1 1). Finally the differences in ionic exchange rate were greatly enhanced when they were studied in organic media. The AC 250 Hz response in the case of the thin films synthesized on Pt(1 1 0) is about twice greater than that obtained in the other basal planes using polymer layers with the same thickness.

Synthesis, Characterization and Conducting Properties of Nanocomposites of Intercalated 2-Aminophenol with Aniline in Sodium-Montmorillonite

A simple method was used to synthesize poly(2-aminophenol), poly(2-aminophenol-co-Aniline) and polyaniline nanocomposites with sodium-montmorillonite (Na-M) using in situ intercalative oxidative polymerization. Morphology and thermal properties of the synthesized nanocomposites were examined by transmission electron microscopy (TEM) and thermogravimetric analysis. The thermal analysis shows an improved thermal stability of the nanocomposites in comparison with the pure poly(2-aminophenol). The intercalation of polymers into the clay layers was confirmed by X-ray diffraction studies, TEM images and FTIR spectroscopy. In addition, the room temperature conductivity values of these nanocomposites varied between 8.21 × 10−5 and 6.76 × 10−4 S cm−1. The electrochemical behavior of the polymers extracted from the nanocomposites, has been analyzed by cyclic voltammetry. Good electrochemical response has been observed for polymer films; the observed redox processes indicate that the polymerization into Na-M produces electroactive polymers.

Characterization and electrochemical properties of conducting nanocomposites synthesized from p-anisidine and aniline with titanium carbide by chemical oxidative method

A novel polymer/TiC nanocomposites “PPA/TiC, poly(PA-co-ANI)/TiC and PANI/TiC” was successfully synthesized by chemical oxidation polymerization at room temperature using p-anisidine and/or aniline monomers and titanium carbide (TiC) in the presence of hydrochloric acid as a dopant with ammonium persulfate as oxidant. These nanocomposites obtained were characterized by Fourier transform infrared (FTIR) spectroscopy, X-ray diffraction (XRD), transmission electron microscopy (TEM), energy dispersive spectroscopy (EDS), and thermogravimetric analysis (TGA). XRD indicated the presence of interactions between polymers and TiC nanoparticle and the TGA revealed that the TiC nanoparticles improve the thermal stability of the polymers. The electrical conductivity of nanocomposites is in the range of 0.079–0.91 S cm−1. The electrochemical behavior of the polymers extracted from the nanocomposites has been analyzed by cyclic voltammetry. Good electrochemical response has been observed for polymer films; the observed redox processes indicate that the polymerisation on TiC nanoparticles produces electroactive polymers. These nanocomposite microspheres can potentially used in commercial applications as fillers for antistatic and anticorrosion coatings.