Aspects Of DNA Methylation Research Articles

Comprehensive review and updated analysis of DNA methylation in hepatocellular carcinoma: From basic research to clinical application.

Hepatocellular carcinoma (HCC) is a primary malignant tumour, ranking second in global mortality rates and posing significant health threats. Epigenetic alterations, particularly DNA methylation, have emerged as pivotal factors associated with HCC diagnosis, therapy, prognosis and malignant progression. However, a comprehensive analysis of the DNA methylation mechanism driving HCC progression and its potential as a therapeutic biomarker remains lacking. This review attempts to comprehensively summarise various aspects of DNA methylation, such as its mechanism, detection methods and biomarkers aiding in HCC diagnosis, treatment and prognostic assessment of HCC. It also explores the role of DNA methylation in regulating HCC's malignant progression and sorafenib resistance, alongside elaborating the therapeutic effects of DNA methyltransferase inhibitors on HCC. A detailed examination of these aspects underscores the significant research on DNA methylation in tumour cells to elucidate malignant progression mechanisms, identify diagnostic markers and develop new tumour-specific inhibitors for HCC. KEY POINTS: A comprehensive summary of various aspects of DNA methylation, such as its mechanism, detection methods and biomarkers aiding in diagnosis and treatment. The role of DNA methylation in regulating hepatocellular carcinoma's (HCC) malignant progression and sorafenib resistance, alongside elaborating therapeutic effects of DNA methyltransferase inhibitors. Deep research on DNA methylation is critical for discovering novel tumour-specific inhibitors for HCC.

High-throughput Sequencing Technology and Its Application in Epigenetics Studies

DNA sequencing technology is one of the important tools in modern life science research, and with the development of science and technology, sequencing technology is constantly changing. High-throughput sequencing technology is known as the second generation sequencing technology. Compared with Sanger sequencing technology, high-throughput sequencing technology has the characteristics of high throughput, fast speed and low cost. In this paper, the researcher briefly introduced the emergence and development of DNA sequencing technology, and expounded the application of high-throughput sequencing in epigenetic research from the aspects of DNA methylation and histone modification.

MethySource: Data Sources of Methylation Researcher

DNA methylation was reported to play a surprising role in regulatory, evolutionary processes and diseases in eukaryotes. The emergence of DNA methylation chip data, to some extent, showed us the characteristics of the promoter DNA methylation among the genome. While the introduction of whole-genome bisulfite sequencing had highly enabled the study of DNA methylation at a single-base resolution, revealing many new aspects of DNA methylation and highlighting the usefulness of methylome data in understanding a variety of genomic phenomena. And hundreds of methylome from well-studied organisms had been stored in different database or project platform. Here, we reviewed the most common used public databases, big projects and analyzing tools of DNA methylation.

210 DNA METHYLATION AND HYDROXYMETHYLATION ANALYSIS IN A MODEL OF OOCYTE DIFFERENTIAL DEVELOPMENTAL COMPETENCE IN SHEEP

DNA methylation is an important epigenetic mark that plays a role in gene regulation by the addition of a methyl group to CpG islands in the DNA. Despite being relatively stable in somatic cells, DNA methylation is subject to reprogramming during embryo development and gametogenesis. The aim of this work was to evaluate different aspects of DNA methylation in relation to oocyte quality in the ovine species. A model of differential developmental competence consisting in ovine oocytes and in vitro produced (IVP) blastocysts derived from adult (AD) and prepubertal (PR) donors, was used. The methylation was analysed in terms of: expression of a panel of genes involved in DNA methylation [DNA methyltransferases (DNMTs)] and demethylation [ten-eleven translocation dioxygenases (TET)] in oocytes and blastocysts; global methylation and hydroxymethylation by direct immunofluorescence; locus-specific methylation of 2 imprinted genes by pyrosequencing. Gene relative quantification was performed by RNA reverse transcription followed by real-time PCR. Pools of 10 immature (GV) and in vitro-matured (MII) oocytes and (IVP) blastocysts derived from AD and PR donors (4 replicates per class) were analysed. Lower expression of TET1, TET2, and TET3 was observed in PR GV oocytes (ANOVA; P < 0.05), while no significant differences were found for the enzymes involved in methylation (DNMT1, DNMT3A, DNMT3B; ANOVA; P > 0.05). The levels of all the genes studied showed no significant differences in embryos at blastocyst stage (ANOVA; P > 0.05). Methylation and hydroxymethylation immunostaining were performed in GV and MII oocytes using anti-5-methylcytosine mouse mAb and 5-hydroxymethylcytosine rabbit pAB. High levels of DNA methylation were observed in both AD and PR GV and MII oocytes, while hydroxymethylation immunopositivity was scattered evident throughout the gamete chromatin. Pyrosequencing of bisulfite converted DNA was used to determine the methylation status within differentially methylated regions (DMR) of maternally imprinted H19 (CTCF binding site IV; 11 CpG sites) and paternally imprinted IGF2R (17CpG sites within intron 2). No differences were observed between classes of oocytes for each gene (pools of 40 oocytes per replicate, 3 replicates per class; ANOVA; P > 0.05). Our work shows no differences in the expression of the enzymes involved in methylation, in accordance with the results of global and locus specific methylation analysis. Conversely, we observed lower expression of the TET genes in PR GV oocytes (ANOVA; P > 0.05). TET1, TET2, and TET3, whose expression has never been studied in ovine, generate 5-hydroxymethlcytosine (5hmC) by oxidation of 5-methylcytosine (5mC), and are involved in active DNA demethylation during early embryo development. Our observation of lower expression of the TET genes in lower competence PR GV oocytes suggests that epigenetic mechanisms may affect oocyte quality and paves the way to better understand methylation dynamics during sheep pre-implantation development.

A Reference Methylome Database and Analysis Pipeline to Facilitate Integrative and Comparative Epigenomics

DNA methylation is implicated in a surprising diversity of regulatory, evolutionary processes and diseases in eukaryotes. The introduction of whole-genome bisulfite sequencing has enabled the study of DNA methylation at a single-base resolution, revealing many new aspects of DNA methylation and highlighting the usefulness of methylome data in understanding a variety of genomic phenomena. As the number of publicly available whole-genome bisulfite sequencing studies reaches into the hundreds, reliable and convenient tools for comparing and analyzing methylomes become increasingly important. We present MethPipe, a pipeline for both low and high-level methylome analysis, and MethBase, an accompanying database of annotated methylomes from the public domain. Together these resources enable researchers to extract interesting features from methylomes and compare them with those identified in public methylomes in our database.

DNA Methylation in Plants: Relationship to Small RNAs and Histone Modifications, and Functions in Transposon Inactivation

DNA methylation is a type of epigenetic marking that strongly influences chromatin structure and gene expression in plants and mammals. Over the past decade, DNA methylation has been intensively investigated in order to elucidate its control mechanisms. These studies have shown that small RNAs are involved in the induction of DNA methylation, that there is a relationship between DNA methylation and histone methylation, and that the base excision repair pathway has an important role in DNA demethylation. Some aspects of DNA methylation have also been shown to be shared with mammals, suggesting that the regulatory pathways are, in part at least, evolutionarily conserved. Considerable progress has been made in elucidating the mechanisms that control DNA methylation; however, many aspects of the mechanisms that read the information encoded by DNA methylation and mediate this into downstream regulation remain uncertain, although some candidate proteins have been identified. DNA methylation has a vital role in the inactivation of transposons, suggesting that DNA methylation is a key factor in the evolution and adaptation of plants.

DNA methylation with a sting: An active DNA methylation system in the honeybee

The existence of DNA methylation in insects has been a controversial subject over a long period of time. The recently completed genome sequence of the honeybee Apis mellifera has revealed the first insect with a full complement of DNA methyltransferases. A parallel study demonstrated that these enzymes are catalytically active and that Apis genes can be methylated in specific patterns. These findings establish bees as a model to analyze the function of DNA methylation systems in invertebrate organisms and might also be important to understand evolutionary aspects of DNA methylation in higher eukaryotes.

The effects of cladribine and fludarabine on DNA methylation in K562 cells

The effects of the antileukemic adenosine analogues, 2-chloro-2′-deoxyadenosine (cladribine) and 9-β- d-arabinosyl-2-fluoroadenine (fludarabine), on DNA methylation were studied in a cell line K562. It was previously found that both drugs inactivated SAH hydrolase, an enzyme which participates in the “active methyl” cycle. The study examined the effects of these drugs on three aspects of DNA methylation: (i) activity of endogenous C-5 DNA methyltransferase; (ii) capacity of genomic DNA (gDNA) to accept methyl groups, transferred from S-adenosylmethionine by the bacterial methyltransferase, SssI; (iii) estimation of changes of methylated cytosine levels in gDNA, using methylation-dependent restriction analysis. Cladribine and fludarabine inhibited C-5 DNA methyltransferase, with ed 50 values of 3.5 and 47.0 μM, respectively, after 24 hr cell growth in the presence of the drugs. After 48 hr growth of cells with cladribine (0.1 μM) or fludarabine (3 μM), the capacity of DNA to accept methyl groups, in the presence of exogenous bacterial SssI methylase, increased by approximately 1.8 and 1.6 times, respectively, compared to control DNA. Digestion of gDNA with endonucleases HpaII and BssHII followed by SssI DNA methylation, indicated that cladribine (0.1 μM) reduced the level of methylated cytosines in both CpG islands and CCGG sequences, sensitive to HpaII restriction enzyme. Inhibition of DNA methylation by fludarabine was observed mainly in CpG dinucleotide located within sequences sensitive to HpaII. The perturbation of DNA methylation was considered as a complex process. Our findings for cladribine and fludarabine should be regarded as an extra element of their antileukemic efficacy.

DNA methylation as a target for drug design.

DNA methylation is essential for normal embryonic development. Distinctive genomic methylation patterns must be formed and maintained with high fidelity to ensure the inactivities of specific promoters during development. The mutagenic and epigenetic aspects of DNA methylation are especially interesting because they may lead to the inactivation of genes which are involved in human carcinogenesis. The mutagenicity of 5-Methylcytosine (5mC) and the role of promoter hypermethylation in gene silencing, particularly in cancer, suggest a clinical significance for the design of novel DNA methylation inhibitors which may be utilized to reverse the effects of DNA methylation.

Hypomethylation of DNA: a nongenotoxic mechanism involved in tumor promotion

There is an abundant amount of information on the mechanisms of action of genotoxic chemicals that act as carcinogens and the role that mutations play in carcinogenesis. However, carcinogenesis is more than mutagenesis and many carcinogens are not mutagens. Thus, there is a need to consider nongenotoxic mechanisms that may be involved in carcinogenesis. In this paper, we review our working hypothesis that hypomethylation of DNA is an epigenetic, nongenotoxic mechanism that plays a role in tumor promotion by facilitating aberrant gene expression. The utility of employing experimental models that focus on relevant comparisons between sensitive and resistant strains of mice is emphasized. Additionally, aspects of DNA methylation in rodents and humans are compared and contrasted. We discuss hypomethylation of DNA as a secondary mechanism, that is expected to be threshold-exhibiting, and conclude by describing how this information may facilitate a rational approach towards risk assessment when dealing with nongenotoxic compounds that are carcinogenic in a bioassay.

Coupled Demethylation of Sites in a Conserved Sequence of Xenopus Ribosomal DNA

Like many cellular macromolecules, DNA is subject tc'postsynthetic modification. In animals, the most common modif icat ion involves methylat ion of cytosine in the dinucleotide sequence CpG (Wyatt 1951; Doscocil and Sorm 1962; Grippo et al. 1968; Vanyushin et al. 1970). Current interest in CpG methylation arises from three lcinds of observations. First, the presence or absence of cytosine methylation determines the interaction of DNA with restriction endonucleases in bacteria (Meselson et al. 1972; Mann and Smith 1978), and this has encouraged speculation that protein-DNA interact ions are similarly control led in eukaryotes (Holl iday and Pugh 1975, Riggs 1975). Second, there is evidence that the pattern of DNA methylation in a cell can be inherited by i ts daughter cel ls (for review, see Wigler l98l). The idea of a heri table, but reversible, switch on the DNA has obvious attract ions. Final ly, t issuespecific alterations in the methylation pattern of several genes have been observed. [n general, the level of methylation at a gene is lower in cells transcribing the sequence than in nontranscribing cells (see, e.g., Kuo et al. 1979; Mandel and Chambon 1979; van der Ploeg and Flavel l 1980; Bird et a l . l98lb; Weintraub et a l . l98l ; for review, see Doerf ler 198 1 ; Ehrl ich and Wang 198 1). In some cases i t has been demonstrated direct ly that transcription is inhibited when the DNA to be tested is first methylated in vitro (Vardimon et al. 1982). Our recent research on the function of DNA methylat ion has concentrated on the genes for 28S and l8S ribosomal RNAs (rRNAs). In animals, the r ibosomal DNA (rDNA) is made up of uni ts compris ing a nontranscribed spacer, plus a transcribed region that codes for the rRNA precursor. Units are tandemly repeated at one or more sites in the genome (for review, see Lewin 1980). The reason for our interest in this system is that rDNA exemplifies both the intriguing and the perplexing aspects of DNA methylat ion. Thus, in dif ferent organisms, rDNA can be found unmethylated (e.g., invertebrates), heavily methylated (e.9., amphibia), or a combination of both (e.g., mouse)(Rae and Steele l9l9; Bird and Taggart 1980; Bird et al. 1981a). Any model for the function of DNA methylation must explain this variability. In spite of the range of methylation patterns, however, there is good correspondence between expression of the r ibosomal genes and general or local ized absence of methylation. For example, in BALB/c mice the unmethylated fraction of rDNA is preferentially sensit ive to DNase I in isolated l iver nuclei (Bird et al. l98la). This impl ies that the methylated fract ion of