5-methylcytosine Content Of DNA Research Articles

Genome-wide investigation of DNA methylation dynamics reveals a critical role of DNA demethylation during the early somatic embryogenesis of Dimocarpus longan Lour.

DNA methylation plays essential roles in gene regulation, chromatin structure stability, gene imprinting, X chromosome inactivation and embryonic development. However, the dynamics and functions of DNA methylation during the early stage of longan (Dimocarpus longan) somatic embryogenesis (SE) are still unclear. In this study, we carried out whole genome bisulphite sequencing and transcriptome sequencing analyses for embryogenic callus (EC), incomplete compact pro-embryogenic cultures (ICpEC) and globular embryos (GE) in an early SE system. At a global level, the DNA 5-methylcytosine content in EC, ICpEC and GE was 24.59, 19.65 and 19.74%, respectively, suggesting a global decrease in DNA methylation from EC to ICpEC and then a slight increase from ICpEC to GE. Differentially methylated region (DMR) analysis showed that hypomethylation mainly occurred in CHH contexts. Gene ontology and Kyoto encyclopedia of genes and genomes analysis of hypomethylated-CHH-DMR-associated genes revealed that zein biosynthesis, fatty acid biosynthesis, circadian rhythm and mitophagy pathways were involved in longan early SE. Expression patterns of DNA methyltransferase and demethylase genes during longan early SE suggested that the decrease in DNA methylation was probably regulated by DNA methyltransferase genes and the DNA demethylase gene REPRESSOR OF SILENCING 1 (ROS1). The correlation between DNA hypomethylation and gene expression revealed that decreased DNA methylation did not cause extensive changes in gene expression during early longan SE and that gene expression may be affected by methylation changes in gene and downstream regions. Inhibiting DNA methylation with 5-azacytidine treatment in EC promoted the formation of GE and enhanced the capability of longan SE. Our results suggest that DNA demethylation has important roles in longan SE development.

Estimation of global content of 5-methylcytosine in DNA during allantoic and pulmonary respiration in the chicken embryo.

DNA methylation is an epigenetic modification that plays an important role in the proper development and functioning of an organism. The DNA methylation level is species-, tissue- and organelle-specific, and the methylation pattern is determined during embryogenesis. A correlation between methylation and age is also observed. Epigenetic phenomena are an enormously interesting research subject, not only from the perspective of pure science, but also due to their possible applications in medicine. The aim of this study was to determine the global DNA methylation level in relation to the developmental stage of the embryo. The global level of 5-methylcytosine in the DNA during pulmonary respiration was found to be higher than during allantoic respiration. The analysis shows a clear dependence between the stage of individual development and the global DNA level of 5-methylcytosine. In the future, methylation level may be a determinant of age and perhaps even a tool for predicting life expectancy. Abnormalities in the methylation process result in premature ageing at the cellular and individual level.

The relationship between 8-oxo-7,8-dihydro-2′-deoxyguanosine level and extent of cytosine methylation in leukocytes DNA of healthy subjects and in patients with colon adenomas and carcinomas

It has been known for a long time that DNA hypomethylation occurs in many human cancers and precancerous conditions. However, the mechanisms of hypomethylation are largely unknown. It is possible that endogenous 8-oxo-7,8-dihydroguanine (8-oxoGua) level may be linked to aberrant DNA methylation of adjacent cytosine and in this way influences carcinogenesis. Therefore, the aim of the present study was to assess a possible link between 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodG) background level and 5-methylcytosine content in DNA from human leukocytes of healthy subjects (n=105) as well as in patients with colon adenomas (n=39) and carcinomas (n=50).Our results demonstrated statistically significant negative correlation between background level of 8-oxodG and 5-methylcytosine content in DNA isolated from leukocytes of healthy donors (r=−0.3436, p=0.0003). The mean content of 5-methylcytosine was significantly lower, while 8-oxodG level was significantly higher in leukocytes DNA of patients with colon adenomas and carcinomas in comparison with healthy subjects. The mean values for 5-methylcytosine were: 3.59±0.173% (healthy subjects), 3.38±0.128% (patients with adenomas), 3.40±0.208% (colon cancer patients). The mean values of 8-oxodG in DNA were, respectively: 4.67±1.276, 5.72±1.787, 5.76±1.884 8-oxodG per 106 dG molecules. DNA from affected tissue (colon) suffered from significant, about 10% reduction in cytosine methylation in comparison with leukocytes of the paired subjects.Our work provides the first in vivo evidence suggesting that increased levels of 8-oxodG in DNA may lead to carcinogenesis not only via mispair/mutagenic potential of the modified base but also through its ability to influence gene expression by affecting DNA methylation.

Changes in Composition of Acid Soluble Proteins and DNA in Chromatin of Rat Liver and Brain Bound and Not Bound to Nuclear Envelope as a Function of Age and under the Influence of Antioxidant Ionol

In two-day rat pups, the histone H1 content in the brain chromatin was higher than in the liver chromatin, as compared to histone of the nucleosome core. The H1 content in the brain chromatin decreased with the age, while in the liver chromatin it increased. At the same time, in the adult brain chromatin bound to the nuclear envelope, a high level of H1 characteristic of chromatin of the newborn rats was preserved, while in a similar chromatin of the adult liver, the H1 content increased, but still remained less than in the chromatin not bound to the nuclear envelope. In both organs, the composition and quantitation of H1 subfractions were different in chromatins bound and not bound to the nuclear envelope. The chromatin from the liver and brain bound to the nuclear envelope differed also in the composition and quantitation of minor acid soluble proteins. In the presence of the antioxidant ionol, the 5-methylcytosine content in DNA of chromatin of the rat liver bound to the nuclear envelope increased while in the chromatin not bound to the nuclear envelope, it remained unchanged. Thus the chromatins bound and not bound to the nuclear envelope differ in the composition and mount of acid soluble proteins, including histone H1, the contents of these proteins in bound and not bound chromatin are different and change with the age in different ways. The antioxidant ionol affects differently the methylation of bound and not bound chromatin.

Effect of dibromoacetic acid on DNA methylation, glycogen accumulation, and peroxisome proliferation in mouse and rat liver.

Dibromoacetic acid (DBA) is a drinking water disinfection by-product. Its analogs, dichloroacetic acid (DCA) and trichloroacetic acid (TCA), are liver carcinogens in rodents. We evaluated the ability of DBA to cause DNA hypomethylation, glycogen accumulation, and peroxisome proliferation that are activities previously reported for the two other haloacetic acids. Female B6C3F1 mice and male Fischer 344 rats were administered 0, 1,000, and 2,000 mg/l DBA in drinking water. The animals were euthanized after 2, 4, 7, and 28 days of exposure. Dibromoacetic acid caused a dose-dependent and time-dependent decrease of 20%-46% in the 5-methylcytosine content of DNA. Hypomethylation of the c-myc gene was observed in mice after 7 days of DBA exposure. Methylation of 24 CpG sites in the insulin-like growth factor 2 (IGF-II) gene was reduced from 80.2% +/- 9.2% to 18.8% +/- 12.9% by 2,000 mg/l DBA for 28 days. mRNA expression of the c-myc and IGF-II genes in mouse liver was increased by DBA. A dose-dependent increase in the mRNA expression of the c-myc gene was also observed in rats. In both mice and rats, DBA caused dose-dependent accumulation of glycogen and an increase of peroxisomal lauroyl-CoA oxidase activity. Hence, DBA, like DCA and TCA, induced hypomethylation of DNA and of the c-myc and IGF-II genes, increased mRNA expression of both genes, and caused peroxisome proliferation. Again like DCA, DBA also induced glycogen accumulation. These results indicate that DBA shares biochemical and molecular activities in common with DCA and/or TCA, suggesting that it might also be a liver carcinogen.

Effect of in vitro shoot multiplication and somatic embryogenesis on 5-methylcytosine content in DNA of Myrtus communis L.

Reversed-phase HPLC analysis of 2′-deoxynucleosides was performedto study the amount of 5-methylcytosine in genornic DNA of Myrtuscommunis L. About 11% cytosines were found to be methylated inDNA of field growing shoots. This amount showed no variation after theestablishment of shoots in vitro or their subsequentrooting and acclimatisation to ex vitro conditions.Therefore, adult elite plants can be micropropagated and transferred to thefield without global DNA methylation changes. Likewise, no trend in5-methylcytosine content was introduced by increasing the number of subculturesin either adult- or seedling-originated shoot stocks. On the other hand, nodifference was found in DNA methylation after plant regeneration fromembryogenic calli. The significance of a tissue culture model system with noglobal hypo- or hypermethylation is discussed.

Liquid chromatographic determination of 5-methylcytosine in DNA with fluorescence detection

A novel method to determine the content of 5-methylcytosine in DNA precisely, sensitively and simply has been developed using liquid chromatography (LC) with fluorescence detection. DNA was mildly digested by cooperation of nuclease P1 and DNase I, then the generated 2′-deoxynucleoside 5′-monophosphates (dNmp) were specifically derivatized fluorometrically at the position of the phosphoric acid moiety with 5-dimethylaminonaphthalene-1-[ N-(2-aminoethyl)]sulfonamide (dansylEDA), followed by the separation of fluorescent dansylEDA derivatives of dNmp on the reversed-phase partition column. The method was more than 10 times as sensitive as the conventional ultraviolet detection method.

Alterations of DNA methylation by glutathione depletion

One of the most consistent findings in cancer cells is an overall decrease of 5-methylcytosine content in DNA. The causes that lead to this alteration are not known. We have shown in a recent study that the methyl-donor, methionine (Met), can easily be depleted and that O- and S-methylation can be impaired in response to glutathione (GSH) depletion. This is because mammalian cells are capable of resynthesizing GSH after GSH is depleted, and GSH turnover occurs at the expense of Met. An extensive utilization of Met for the resynthesis of GSH causes Met depletion and impairment in methylation. In the present study we now demonstrate that GSH depletion has a significant impact on DNA methylation. An i.p. dose of a model GSH-depleting hepatotoxin, bromobenzene (BB), caused a progressive impairment in genomic DNA methylation in the Syrian hamster. The administration of a single i.p. dose of Met labeled with [ 14CH 3]Met to BB-treated hamsters at either 1, 3, 5.5 or 9 h after BB resulted in an increase of methyl-group incorporation into liver genomic DNA at 24 h after BB. With respect to the time points chosen for Met administration, methyl-group incorporation found in the BB+Met groups were 1-, 2-, 4- and 12-fold of the controls that received only Met. We further employed an in vitro methylation assay using specific bacterial SssI CpG methylase as the catalyzing enzyme to demonstrate that BB caused a progressive increase of unmethylated CpG sites in genomic DNA. Interestingly, the time response curve of global DNA methylation in vitro showed an identical pattern to that observed in the in vivo experiment. The results provide strong evidence that GSH-depleting agents significantly impair cytosine methylation. Thus, alterations in gene expression could result from a high dose and/or prolonged exposure to GSH-depleting agents, e.g. medications, chemotherapeutic agents and environmental toxins.

Hypermethylation of calcitonin gene regulatory sequences in human breast cancer as revealed by genomic sequencing.

DNA methylation has been studied intensively during the past years in order to elucidate its role in the regulation of gene expression, gene imprinting and cancer progression. Earlier studies have shown that a general genomic under-methylation is associated with chronic lymphocytic leukemia and metastatic prostate cancer. Site-specific methylation changes, as revealed by the use of methylation-sensitive restriction enzymes, have been reported to occur in the promotor region of the calcitonin gene in chronic myeloid leukemia as it progresses from the chronic phase to blast crisis, in non-Hodgkin's lymphoid neoplasms and in non-lymphocytic leukemia. We have now explored possible methylation changes associated with benign and malignant breast tumors. Two approaches were employed: (i) chemical determination of general genomic methylation status and (ii) base-specific analysis of the methylation changes in the promoter of the calcitonin gene with the aid of genomic sequencing. The results did not reveal any changes of total DNA 5-methylcytosine content in ductal carcinoma of breast in comparison with benign tumors. There was a small, yet significant, increase in 5-methylcytosine content in lobular carcinoma. Genomic sequencing of the promoter region of the calcitonin gene, however, revealed a striking hypermethylation at or around the transcription start site of the gene in ductal carcinomas. In benign tumors and lobular carcinomas, this region was either entirely unmethylated or only slightly methylated. The latter changes may reflect a regional hypermethylation of the short arm of chromosome 11, which harbors, in addition to the calcitonin gene, a number of putative or established tumor-suppressor genes. Our results demonstrate that genomic sequencing in its present form can be used for a reliable and precise DNA methylation analysis of primary human tumors.

Life span prediction from the rate of age-related DNA demethylation in normal and cancer cell lines.

A method has been proposed for the Hayflick Limit prediction by the analysis of the 5-methylcytosine content in DNA at earlier and later cell passages. The following facts were used as the basis of the method: (i) the rate of m5C loss from DNA remains approximately constant during cell divisions and it does not depend on the cell donor age; (ii) this rate is inversely proportional to the Hayflick Limit as well as to the life span of cell donor species; (iii) the period corresponded to loss of all m5C residues from the genome coincides with or somewhat exceeds the Hayflick Limit of normal cells. The prognosis of the Hayflick Limit has usually been found in good agreement with the experimental evidences for various human, hamster, and mouse cell lines. The method proposed may be used for early detection of precrisis and cancer cells. The age-related m5C loss may result from accumulation of the m5C-->T+C transitions occurring with DNA methylation in every cell division.

Enzymic removal of 5-methylcytosine from DNA by a human DNA-glycosylase.

DNA 5-methylcytosine is a major factor in the silencing of mammalian genes; it is involved in gene expression, differentiation, embryogenesis and neoplastic transformation. A decrease in DNA 5-methylcytosine content is associated with activation of specific genes. There is much evidence indicating this to be an enzymic process, with replacement of 5-methylcytosine by cytosine. We demonstrate here enzymic release of 5-methylcytosines from DNA by a human 5-methylcytosine-DNA glycosylase activity, which affords a possible mechanism for such replacement. This activity generates promutagenic apyrimidinic sites, which can be related to the high frequency of mutations found at DNA 5-methylcytosine loci. The recovery of most released pyrimidines as thymines indicates subsequent deamination of free 5-methylcytosines by a 5-methylcytosine deaminase activity. This prevents possible recycling of 5-methylcytosine into replicative DNA synthesis via a possible 5-methyl-dCTP intermediate synthesized through the pyrimidine salvage pathway. Taken together, these findings indicate mechanisms for removal of 5-methylcytosines from DNA, hypermutability of DNA 5-methylcytosine sites, and exclusion of 5-methylcytosines from DNA during replication.

5-Methylcytosine content of DNA in blood, synovial mononuclear cells and synovial tissue from patients affected by autoimmune rheumatic diseases

The percentage of 5-methylcytosine (m5Cyt) has been determined in peripheral blood, synovial mononuclear cells and synovial tissue from patients affected by various rheumatic autoimmune diseases. The determination was performed by reversed-phase high-performance liquid chromatography. Fifteen controls were compared to twenty-one patients affected by rheumatoid arthritis and to nine patients affected by systemic lupus erythematosus. The mean percentage of m5Cyt in normal individuals was significantly higher than in the rheumatoid arthritis and systemic lupus erythematosus patients. In addition, patients with active disease showed lower values than patients in remission. This finding is in agreement with the hypothesis that DNA hypomethylation may play a role in the pathogenesis of the autoimmune diseases, resulting in altered oncogene expression. Therapy with cyclosporin A led to a decrease in the percentage of m5Cyt in three rheumatoid arthritis patients, but a rebound was observed when the cyclosporin A was suspended. The percentage of m5Cyt in the DNA of synovial tissue from four rheumatoid arthritis patients and five patients with osteoarthritis was similar; this observation confirms that, in addition to disease-specific and disease activity-specific variations, the percentage of m5Cyt may also show tissue-specific variations.

Transitory DNA hypomethylation during liver cell proliferation induced by a single dose of lead nitrate

In the present study we have examined the effect of a single dose of the mitogen lead nitrate (75 μmol/kg body wt) on the methylation status of hepatic DNA in male Wistar rats. It was found that extensive hypomethylation of hepatic DNA occurs in mitogen-treated rat liver. This effect could be seen as early as 12 h after metal treatment and parallels the changes in liver weight. Probing with the methylation-sensitive enzymes HpaII, MspI, and HaeIII confirmed HPLC analyses and showed that methylation at these sites was affected by lead treatment. DNA hypomethylation has already been found in regenerating rat liver and in hepatic (pre)malignant lesions when compared to normal nondividing liver. Thus the lowering of the DNA 5-methylcytosine content appears to be a property characteristic of cellular proliferation, regardless of whether it is caused by partial hepatectomy, carcinogen treatments, or mitogen administration.

Agarose-selected variants of two human tumor cell lines exhibit altered methionine auxotrophy.

Our aim was to determine if the selection of human tumor cells with enhanced anchorage-independent growth capacity was associated with alterations in methionine auxotrophy. Cells with an increased ability to form colonies on soft agarose were selected from human melanoma (MeWo) and neuroepithelioma (SK-N-MC) cell lines. In contrast to their respective parental lines, a high proportion of the agarose-selected variants were completely unable to proliferate in methionine-free medium containing its immediate precursor homocysteine. The variants exhibited no significant change in their total DNA 5-methylcytosine content and showed no stimulation of either RNA or DNA synthesis upon the addition of homocysteine when the cells were cultured in methionine-free medium. These variants were unable to synthesize [3H]S-adenosylmethionine from [3H]adenine and homocysteine. The failure to detect the accumulation of [3H]S-adenosylmethionine in these variant lines was not likely due to the enhanced turnover of S-adenosylmethionine but rather to a reduced ability to synthesize methionine from homocysteine and 5-methyltetrahydrofolic acid. These results support our hypothesis that alterations in the metabolism of methionine and/or intracellular transmethylating activities may contribute to, or be associated with, the autonomous growth of malignant human tumor cells.

DNA Methylation and Differentiation of Human Keratinocytes

DNA methylation is a postreplicative modification thought to play a role in gene transcription in eucaryotes. Differences in the amount of 5-methylcytosine as a function of age and differentiation state have been reported. DNA isolated from human skin keratinocytes was analyzed for its 5-methylcytosine content. The 5-methylcytosine in DNA from neonatal and adult human keratinocytes was found to vary as a function of differentiation state. Differentiation of keratinocytes in vitro was promoted using a simple method where keratinocytes were plated directly onto the plastic surface of a culture flask, grown to confluence, and placed on a rocking culture platform that cyclically exposed the cells to air 50% of the time. Terminal differentiation was evident after approximately three weeks in culture. The 5-methylcytosine content of the DNA from differentiated human keratinocytes was 1.4%, whereas that of undifferentiated human keratinocytes was 3.1%. No difference in the 5-methylcytosine content of DNA as a function of the age of the donor was found.

Age-related methylation changes in DNA may reflect the proliferative potential of organs.

The percentage of 5-methylcytosine in DNA was measured in brain, liver, heart and skeletal muscle of the rat at various ages. Age-related hypomethylation occurred rapidly shortly after birth and then declined to eventually stabilize in brain, heart and skeletal muscle. Hypomethylation in liver DNA continued throughout the period studied (6 months). Our hypothesis that the age-related decline of 5-methylcytosine content in DNA is related to the proliferative potential of organs is discussed.

Variable DNA methylation changes during differentiation of human melanoma cells

The DNA 5-methylcytosine content has been analyzed in the human melanoma cell line M21 at several time points after induction of differentiation by a variety of inducers. 5-Aza-2′-deoxycytidine reduces DNA methylation to about 50% of the control level and this demethylation occurs prior to the establishment of the differentiated phenotype. The DNA synthesis inhibitors cytosine arabinoside, aphidicolin, and hydroxyurea exert different effects on DNA methylation in these cells. Cytosine arabinoside induces an early DNA hypermethylation, which is however reversible and drops to the original level after 24 h. Hydroxyurea induces DNA hypermethylation after a lag period of more than 48 h and the DNA polymerase α inhibitor aphidicolin has no effect on the DNA methylation level. Treatment of cells with phorbol 12-myristate 13-acetate, another potent inducer of melanoma cell differentiation, does not result in a change of total DNA methylation over a period of 96 h. These results indicate that differentiation of human melanoma cells can be accompanied by variable changes of the DNA methylation pattern. These changes can be neither generally related to the differentiation process itself nor related to the effects of DNA synthesis inhibition on DNA methylation, but may more likely reflect a direct or indirect particular effect of the inducer on the DNA methylation process.

DNA methylating capacity in metastatic variants of a human melanoma cell line

Certain highly metastatic (in athymic immunosuppressed “nude” mice) variants of the poorly metastatic human melanoma cell line MeWo have been found to contain dramatically reduced levels of DNA 5-methylcytosine compared to the parental cell line. To identify the underlying biochemical defect which could be responsible for the reduced DNA methylation within these cells, the intracellular ratio of S-adenosylmethionine/ S-adenosylhomocysteine and level of extractable DNA-methyltransferase were examined. No significant difference in the ratio of S-adenosylmethionine/ S-adenosylhomocysteine or extractable DNA-methyltransferase activity were found between the highly malignant variants and the parental cell line. Thus, stable alterations in these cellular parameters are not likely responsible for the reduction in DNA 5-methylcytosine content which appears to occur during “progression” of the MeWo tumor line from a relatively benign to highly malignant state.

Determination of 5-methylcytosine by acid hydrolysis of DNA with hydrofluoric acid

Quantitation of 5-methylcytosine in DNA after acid hydrolysis has been inaccurate because deamination of cytosine and 5-methylcytosine occurs during the hydrolysis procedure. There is little information in the literature regarding the use of hydrofluoric acid (HF) for DNA hydrolysis and we have therefore undertaken a systematic study of this process. The deoxyribonucleotides of cytosine and 5-methylcytosine were shown not to undergo detectable levels of deamination during prolonged periods (up to 24 h) at 80°C in 48% HF. Kinetic studies show that the release of purine and pyrimidine bases was complete by 4 h under these conditions. Analysis of the 5-methylcytosine content of DNA from various tissues gave levels that were very close to the values reported in the literature. This method is ideally suited for the determination of the overall cytosine methylation levels in DNA.

Hypomethylation of DNA in meiotic and postmeiotic rooster testis cells.

To study whether changes in methylation of DNA are related to the structural and functional changes that chromatin undergoes throughout rooster spermatogenenis, we analyzed, by high-performance liquid chromatography, the 5-methylcytosine content of DNA purified from rooster testis cell nuclei at successive stages of the cell differentiation process. The DNA of meiotic and postmeiotic cells appears partially under-methylated, containing approximately 30% less methylcytosines than the DNA obtained from premeiotic and somatic cells.