Improved method for determination of 5-methylcytosine by ion-pair reversed-phase high-performance liquid chromatography

Specific Method for the Determination of Genomic DNA Methylation by Liquid Chromatography-Electrospray Ionization Tandem Mass Spectrometry

Herein we report a novel method for determining genomic DNA methylation that utilizes liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) to measure 5-methyl-2'-deoxycytidine levels following enzymatic hydrolysis of genomic DNA. LC separation of 5-methyl-2'-deoxycytidine from the four deoxyribonucleosides, the four ribonucleosides, and 5-methyl-2'-cytidine, a RNA methylation product, has been achieved within 15 min. In combination with ESI-MS/MS detection, the reported method is highly specific and extremely sensitive with a limit of detection (LOD) of 0.2 fmol and a quantification linearity range from 1 fmol to 20 pmol. Genomic DNA methylation was expressed as the ratio of 5-methyl-2'-deoxycytidine to 2'-deoxyguanosine and was determined directly using 2'-deoxyguanosine as the internal standard. Because deoxycytidine methylation typically ranges from 2 to 6% in mammalian genomes, and pharmacological or genetic manipulations have not achieved levels lower than 0.1%, we validated the assay for methylation levels ranging from 0.05 to 10%. Importantly, both RNA contamination and incomplete DNA hydrolysis had no appreciable effect on 5-methyl-2'-deoxycytidine quantification. LOD studies indicate that only 4 ng of DNA is required for this assay. This LOD should permit the use of this method for applications having limiting amounts of DNA that were not previously candidates for global genomic DNA methylation analysis, e.g., clinical trial samples, or cells collected by laser capture microdissection.

Quantitation of 5-methylcytosine by one-dimensional high-performance thin-layer chromatography

A method for the quantitative analysis of DNA 5-methylcytosine by one-dimensional high-performance thin-layer chromatography using alkylamino modified silica (HPTLC-NH2) plates is described. The preparative method is simple, involving enzymatic digestion of DNA with micrococcal nuclease and phosphodiesterase II to 3'-monophosphate nucleosides, conversion by T4 polynucleotide kinase to 32P-labeled 3',5'-bisphosphate nucleosides, and chromatographic separation of nuclease P1-cleaved 5'-monophosphate nucleosides. The weak, basic anion exchanger property of the HPTLC-NH2 plate enables separation of multiple samples in one dimension, whereas traditional polyethyleneimine cellulose plates require development of individual samples in two dimensions for analysis of 5'-methylcytosine.

Employment of hydrolytic enzymes in the study of the level of DNA methylation

A new method for the determination of the level of DNA methylation was established. The method involves enzymatic hydrolysis of DNA by nuclease P1 and bacterial alkaline phosphatase, and separation of the resulting deoxyribonucleosides by HPLC. By this method, DNA was hydrolysed completely to the five deoxyribonucleosides and the complete base composition was determined. Pairing bases were shown to occur in similar amounts, and analysis could be performed on as little as 1 microgram of DNA with a high degree of reproducibility. Among other enzymes hitherto used in order to hydrolyze DNA, micrococcal nuclease, phosphodiesterase II and nuclease P1 have been shown to cause deamination of deoxyadenosine, while deoxyribonuclease I, phosphodiesterase I and bacterial alkaline phosphatase have been shown to be sensitive to contamination by RNA, and to release 5-methyldeoxycytidine at a slower rate than the other four deoxyribonucleosides. Neither of these effects was seen with the new method.

DNA methylation of embryogenic carrot cell cultures and its variations as caused by mutation, differentiation, hormones and hypomethylating drugs

The level of auxin - both natural and synthetic - in the medium has a strong effect on the level of 5-methyl-cytosine in the DNA of carrot cells in culture. This level may vary from approximately 15% to 70% of total cytosine without apparent effects on growth rate and cell morphology. No effect was seen with cytokinin. During somatic embryogenesis, in the absence of hormones, variations were seen in the level of methylation according to a characteristic pattern. If hypomethylation is induced with drugs such as azacytidine, ethionine or ethoxy-carbonyl-pyrimidine, embryogenesis is immediately blocked. A mutant was isolated which is resistant to the action of hypomethylating drugs. It shows variations in the methylation pattern and variations in indole-acetic acid metabolism. In addition its regeneration is often associated with the production of tumors.

5-azacytidine-induced tumorous transformation and DNA hypomethylation in Nicotiana tissue cultures

The phenomenon of habituation is considered in plant tissue cultures to be a real process of chemical tumorogenesis; the cultures acquire the capacity of autonomous growth in a hormone-free medium under the influence of a variety of chemical and physical agents. Treatments with 5-azacytidine (AzaC) of in vitro cultured cells of the Nicotiana glauca x N. langsdorffii nontumorous hybrid (NNT) during the culture cycle led to the induction of a habituated phenotype. The repetitive DNA sequences showed a significant lower level of endogenous methylation in the treated cells in comparison with the normal ones. It is worth noting that it was impossible until now to habituate this strain by conventional methods and that the treatments were effective only in the first 5 days of subculturing; various evidence (cytological and biochemical) pointed out a phenomenon of DNA amplification, occurring in the same period. Moreover, analysis of DNA from control and treated cells shows the induction of variations in the endogenous methylation pattern by AzaC in a critical period of cell culture. These results suggest that demethylation can act as a switch from hormone-dependent to autonomous proliferation by activation of genes coding for or regulating the synthesis of growth factors.

Separation characteristics of alkylated guanines in high-performance liquid chromatography

The retention behavior of thirteen alkylated guanines on normal-phase silica gel and amino columns and on reversed-phase ODS and phenyl columns was studied. The larger the alkyl substituent at the same position of guanine the weaker was the retention in the normal-phase chromatographic system and the greater the retention during reversed-phase chromatography. O6-Derivatives possess the lowest polarity in each set of isomers. An amino column was found to be of highest efficiency in terms of separation of the set of ethylguanine isomers and of benzylguanines studied. A phenyl column provided the best resolution of methylated guanines.

DNA methylation and tissue-specific transcription of the storage protein genes of maize

We investigated the methylation state of a set of storage protein genes of maize, coding for zeins and glutelins, in different somatic tissues and in developing endosperms. These genes, present as multigene families in the maize genome and organized in clusters on different chromosomes, are coordinately and specifically transcribed only in endosperm cells. Southern blot analysis of DNA digested with methylation-sensitive restriction enzymes shows a specific and extensive undermethylation of zein and glutelin sequences in the endosperm, while a common methylated pattern is detected in the different somatic tissues and in the embryo. However, a constant fraction of endosperm DNA (∼35%) is methylated at all zein sequences, which are found to be heavily modified in pollen DNA as well. Undermethylation is extended along a zein cluster and cannot be explained by reduced levels of 5-methylcytosine in endosperm DNA with respect to other tissues. The undermethylated state of storage protein genes is already established at an early stage of endosperm development, when transcripts levels for both genes are almost undetectable.

High-performance liquid chromatographic profiling of nucleic acid components in physiological samples

The papers reviewed represent recent progress in HPLC profiling of nucleic acid components in physiological samples. Each method was designed for a particular application and possesses certain inherent advantages and/or disadvantages. Many methods are simply modifications of previous procedures. Although some methodologies appear to be superior to others, there is no "best" method for universal usage. The analyst must use the procedure which is best suited for the particular application at hand. This review is meant to be a starting point for the chromatographer who is comparing and evaluating HPLC methods for a given application.

Separation of naturally occurring or induced methylated nucleobases of DNA by reversed-phase high-performance liquid chromatography

Separation of the major bases of DNA along with seven minor methylated ones was obtained by reversed-phase high-performance liquid chromatography using an isocratic elution system. Application of this procedure to DNA treated in vitro by N-methyl-N-nitrosourea has allowed identification of two induced minor bases; a third one was resolved using a slightly modified mobile phase. Baseline resolution of 3-methyl- and 5-methylcytosine, detected in Euglena DNA hydrolyzates, was also achieved.

5'-Methyl-cytosine in the macronuclear DNA of Blepharisma japonicum

Brief report on the presence of 5'-methyl-cytosine as a minor base (0.56%) in the macronuclear DNA of the ciliate protozoan Blepharisma japonicum. The evidence comes from electrophoresis of macronuclear DNA digested by appropriate restriction endonucleases and high-performance liquid chromatography.

Quantitative reversed-phase high-performance liquid chromatography of major and modified nucleosides in DNA

Improved, highly accurate high-performance liquid chromatographic methods for the measurement of the major and modified nucleosides in enzymatic digests of DNA using a single column are described. Four high resolution separation protocols (isocratic, binary, ternary and high speed) with specifically improved selectivity for 5-methyldeoxycytidine (m5dCyd) from Ade, dIno and Guo are presented. From a detailed study of the various factors contributing to the precision and accuracy of the measurement, optimized conditions and quantitative protocols were established. The ternary buffer allows for the first time the determination of N6-methyldeoxyadenosine (m6dAdo) in the same chromatographic analysis with the other deoxyribonucleosides. The binary system allows quantitation of the absolute amounts of each ribo- and deoxyribonucleoside as well as the mole % of each as the second buffer elutes 5'dA and the internal standard 8-bromoguanosine. The isocratic system allows precise quantitation of the mole % of each ribo- and deoxyribonucleoside while eliminating the need for buffer change valves, buffer cycling and column re-equilibration. Also, a high-speed isocratic system is described which permits separation of the deoxyribonucleosides in 6 min. The quantitative, enzymatic hydrolysis of DNA was evaluated by comparing a 40-h, three-enzyme system with a 4-h, two-enzyme procedure. The latter protocol proved to be an excellent hydrolysis method. These high resolution liquid chromatography techniques provide the most precise, sensitive and accurate measurement of m5dCyd available, in a straightforward method using as little as 1 microgram of DNA, and have allowed us to demonstrate: the existence of tissue-specific differences in levels of m5dCyd in DNA of humans, monkeys, rats and mice; that m5dCyd levels in DNA change during fetal development; that genomic undermethylation of DNA is correlated with cancer and the presence of m6dAdo in DNA of thermophilic organisms.