DNA demethylase is a processive enzyme

Modeling DNA methylation by analyzing the individual configurations of single molecules

DNA methylation is often analyzed by reporting the average methylation degree of each cytosine. In this study, we used a single molecule methylation analysis in order to look at the methylation conformation of individual molecules. Using D-aspartate oxidase as a model gene, we performed an in-depth methylation analysis through the developmental stages of 3 different mouse tissues (brain, lung, and gut), where this gene undergoes opposite methylation destiny. This approach allowed us to track both methylation and demethylation processes at high resolution. The complexity of these dynamics was markedly simplified by introducing the concept of methylation classes (MCs), defined as the number of methylated cytosines per molecule, irrespective of their position. The MC concept smooths the stochasticity of the system, allowing a more deterministic description. In this framework, we also propose a mathematical model based on the Markov chain. This model aims to identify the transition probability of a molecule from one MC to another during methylation and demethylation processes. The results of our model suggest that: 1) both processes are ruled by a dominant class of phenomena, namely, the gain or loss of one methyl group at a time; and 2) the probability of a single CpG site becoming methylated or demethylated depends on the methylation status of the whole molecule at that time.

Epigenetic function of activation-induced cytidine deaminase and its link to lymphomagenesis

Activation-induced cytidine deaminase (AID) is essential for somatic hypermutation and class switch recombination of immunoglobulin (Ig) genes during B cell maturation and immune response. Expression of AID is tightly regulated due to its mutagenic and recombinogenic potential, which is known to target not only Ig genes, but also non-Ig genes, contributing to lymphomagenesis. In recent years, a new epigenetic function of AID and its link to DNA demethylation came to light in several developmental systems. In this review, we summarize existing evidence linking deamination of unmodified and modified cytidine by AID to base-excision repair and mismatch repair machinery resulting in passive or active removal of DNA methylation mark, with the focus on B cell biology. We also discuss potential contribution of AID-dependent DNA hypomethylation to lymphomagenesis.

Hypomethylation of serum blood clot DNA, but not plasma EDTA-blood cell pellet DNA, from vitamin B12-deficient subjects

Vitamin B12, a co-factor in methyl-group transfer, is important in maintaining DNA (deoxycytidine) methylation. Using two independent assays we examined the effect of vitamin B12-deficiency (plasma vitamin B12<148 pmol/L) on DNA methylation in women of childbearing age. Coagulated blood clot DNA from vitamin B12-deficient women had significantly (p<0.001) lower percentage deoxycytidine methylation (3.23±0.66%; n = 248) and greater [3 H]methyl-acceptance (42,859±9,699 cpm; n = 17) than DNA from B12-replete women (4.44±0.18%; n = 128 and 26,049±2,814 cpm; n = 11) [correlation between assays: r = -0.8538; p<0.001; n = 28]. In contrast, uncoagulated EDTA-blood cell pellet DNA from vitamin B12-deficient and B12-replete women exhibited similar percentage methylation (4.45±0.15%; n = 77 vs. 4.47±0.15%; n = 47) and [3 H]methyl-acceptance (27,378±4,094 cpm; n = 17 vs. 26,610±2,292 cpm; n = 11). Therefore, in simultaneously collected paired blood samples, vitamin B12-deficiency was associated with decreased DNA methylation only in coagulated samples. These findings highlight the importance of sample collection methods in epigenetic studies, and the potential impact biological processes can have on DNA methylation during collection.

5-Aza-2'-deoxycytidine stress response and apoptosis in prostate cancer

While studying on epigenetic regulatory mechanisms (DNA methylation at C-5 of -CpG- cytosine and demethylation of methylated DNA) of certain genes (FAS, CLU, E-cadh, CD44, and Cav-1) associated with prostate cancer development and its better management, we noticed that the used in vivo dose of 5-aza-2'-deoxycytidine (5.0 to 10.0 nM, sufficient to inhibit DNA methyltransferase activity in vitro) helped in the transcription of various genes with known (steroid receptors, AR and ER; ER variants, CD44, CDH1, BRCA1, TGFβR1, MMP3, MMP9, and UPA) and unknown (DAZ and Y-chromosome specific) proteins and the respective cells remained healthy in culture. At a moderate dose (20 to 200 nM) of the inhibitor, cells remain growth arrested. Upon subsequent challenge with increased dose (0.5 to 5.0 μM) of the inhibitor, we observed that the cellular morphology was changing and led to death of the cells with progress of time. Analyses of DNA and anti-, pro-, and apoptotic factors of the affected cells revealed that the molecular events that went on are characteristics of programmed cell death (apoptosis).

Relationship between differentially expressed genes and epigenetic modification during the early stage of esophageal carcinoma induced by nitrosamine

AIM: To detect the differentially expressed genes in the process of esophageal carcinoma induced by nitrosamine, and analyze the property of gene expression at different stages, especially the relationship between differentially expressed genes and DNA methylation.

METHODS: One hundred and ten mice were randomly divided into group A (n = 40) and B (n = 70). The mice in group A were fed with distilled water, while those in group B were fed with carcinoma-inducing mixture containing 20 g/L sodium nitrite and 200 g/L N, N-dimethyl benzyl amine. At the 4, 8, and 20 wk of induction stages, the total RNA from esophageal tissues was isolated and reversely transcripted, and then hybridization with gene-chip was performed. The differentially expressed genes of the two groups were analyzed.

RESULTS: During the process of induction, the number of up-regulated oncogenes increased in a step-by-step fashion in group B as compared with that in group A, and the phase-specificity of oncogenes was observed. But most antioncogenes did not change remarkably. Most genes of DNA methylation did not change at 4 wk, but were up-regulated at 8 and 20 wk. The DNA demethylation gene Mdb2b was up-regulated from the 8 wk, but Gadd45a was up-regulated from the 4 wk and maintained a high level at 8 and 20 wk. Genes of histone acetylation, which were changed obviously, were not found.

CONCLUSION: During the process of nitrosamine-induced esophageal carcinoma, up-regulation of numerous genes may associate with the demethylation of genomic DNA at the early stage. Gadd45a may be involved in the demethylation during the early weeks.

Chromatin-remodelling mechanisms in cancer

Chromatin-remodelling mechanisms include DNA methylation, histone-tail acetylation, poly-ADP-ribosylation, and ATP-dependent chromatin-remodelling processes. Some epigenetic modifications among others have been observed in cancer cells, namely (1) local DNA hypermethylation and global hypomethylation, (2) alteration in histone acetylation/deacetylation balance, (3) increased or decreased poly-ADP-ribosylation, and (4) failures in ATP-dependent chromatin-remodelling mechanisms. Moreover, these alterations can influence the response to classical anti-tumour treatments. Drugs targeting epigenetic alterations are under development. Currently, DNA methylation and histone deacetylase inhibitors are in use in cancer therapy, and poly-ADP-ribosylation inhibitors are undergoing clinical trials. Epigenetic therapy is gaining in importance in pharmacology as a new tool to improve anti-cancer therapies.

Evaluation in mammalian oocytes of gene transcripts linked to epigenetic reprogramming

The mature mammalian metaphase II (MII) oocyte has a unique ability to reprogram sperm chromatin and support early embryonic development. This feature even extends to the epigenetic reprogramming of a terminally differentiated cell nucleus as observed in connection with somatic cell nuclear transfer. Epigenetic nuclear reprogramming is highly linked to chromatin structure and includes covalent modifications of DNA and core histone proteins as well as reorganization of higher-order chromatin structure. A group of conserved enzymes mediating DNA methylation, methyl-CpG-binding protein (MeCP), histone acetylation and methylation, and chromatin remodeling are extensively involved in epigenetic reprogramming in mammalian cells. Using the oligonucleotide microarray technique, the present study compared the expression levels of 86 genes associated with epigenetic reprogramming in murinein vivomatured MII oocytes with that of germinal vesicle oocytes. Correlation between biological replicates was high. A total of 57 genes with potential reprogramming effect were detected. In MII oocytes, four genes were significant up-regulated, whereas 18 were down-regulated and 35 unchanged. The significantly regulated genes were validated by real-time quantitative RT-PCR. For example, MII oocytes showed a significant down-regulation of oocyte-specific maintenance DNA methyltransferase, Dnmt1o, and up-regulation of MeCP transcript, methyl-CpG binding domain protein 2. Furthermore, histone acetyltransferases were proportionally overrepresented when compared with histone deacetylases. These data elucidate for the first time some of the mechanisms that the oocyte may employ to reprogram a foreign genome either in form of a spermatozoa or a somatic nucleus and may thus be of importance for advancing the fields of stem cell research and regenerative medicine.

Epigenetic dedifferentiation of somatic cells into pluripotency: cellular alchemy in the age of regenerative medicine?

Ever since the derivation of the first human embryonic stem cell line, hopes have persisted for the treatment of a wide range of cellular degenerative diseases. However, significant immuno-incompatibility between donor cells and recipient patients remains an unsolved challenge. Currently, three main strategies are investigated in humans to create autologous pluripotent stem cells: somatic cell nuclear transfer, cell fusion and cell extract incubation. All methods exploit the fact that a somatic genome is amenable to epigenetic dedifferentiation into a more plastic state, presumably through direct exposure to and manipulation by heterologous transcriptional factors. Epigenetic reprogramming includes profound modifications of chromatin structure, but the responsible mechanisms that work in toti- and pluripotent cells remain largely unknown. This review presents a brief introduction to stem cell terminology and epigenetics, followed by a critical examination of the predominant methodologies involved. Finally, the search for specific reprogramming factors is discussed, and obstacles for the clinical implementation of reprogrammed cells are addressed.

Epigenetic programming of the rRNA promoter by MBD3

Within the human genome there are hundreds of copies of the rRNA gene, but only a fraction of these genes are active. Silencing through epigenetics has been extensively studied; however, it is essential to understand how active rRNA genes are maintained. Here, we propose a role for the methyl-CpG binding domain protein MBD3 in epigenetically maintaining active rRNA promoters. We show that MBD3 is localized to the nucleolus, colocalizes with upstream binding factor, and binds to unmethylated rRNA promoters. Knockdown of MBD3 by small interfering RNA results in increased methylation of the rRNA promoter coupled with a decrease in RNA polymerase I binding and pre-rRNA transcription. Conversely, overexpression of MBD3 results in decreased methylation of the rRNA promoter. Additionally, overexpression of MBD3 induces demethylation of nonreplicating plasmids containing the rRNA promoter. We demonstrate that this demethylation occurs following the overexpression of MBD3 and its increased interaction with the methylated rRNA promoter. This is the first demonstration that MBD3 is involved in inducing and maintaining the demethylated state of a specific promoter.

Epigenetic tête-à-tête: the bilateral relationship between chromatin modifications and DNA methylation

The epigenome, which comprises chromatin, associated proteins, and the pattern of covalent modification of DNA by methylation, sets up and maintains gene expression programs. It was originally believed that DNA methylation was the dominant reaction in determining the chromatin structure. However, emerging data suggest that chromatin can affect DNA methylation in both directions, triggering either de novo DNA methylation or demethylation. These events are particularly important for the understanding of cellular transformation, which requires a coordinated change in gene expression profiles. While genetic alterations can explain some of the changes, the important role of epigenetic reprogramming is becoming more and more evident. Cancer cells exhibit a paradoxical coexistence of global loss of DNA methylation with regional hypermethylation.

Epigenetics and its implications for plant biology. 1. The epigenetic network in plants

BACKGROUND

Epigenetics has rapidly evolved in the past decade to form an exciting new branch of biology. In modern terms, 'epigenetics' studies molecular pathways regulating how the genes are packaged in the chromosome and expressed, with effects that are heritable between cell divisions and even across generations.

CONTEXT

Epigenetic mechanisms often conflict with Mendelian models of genetics, and many components of the epigenetic systems in plants appeared anomalous. However, it is now clear that these systems govern how the entire genome operates and evolves.

SCOPE

In the first part of a two-part review, how epigenetic systems in plants were elucidated is addressed. Also there is a discussion on how the different components of the epigenetic system--regulating DNA methylation, histones and their post-translational modification, and pathways recognizing aberrant transcripts--may work together.

A role for poly(ADP-ribosyl)ation in DNA methylation

The aberrant DNA methylation of promoter regions of housekeeping genes leads to gene silencing. Additional epigenetic events, such as histone methylation and acetylation, also play a very important role in the definitive repression of gene expression by DNA methylation. If the aberrant DNA methylation of promoter regions is the starting or the secondary event leading to the gene silencing is still debated. Mechanisms controlling DNA methylation patterns do exist although they have not been ultimately proven. Our data suggest that poly(ADP-ribosyl)ation might be part of this control mechanism. Thus an additional epigenetic modification seems to be involved in maintaining tissue and cell-type methylation patterns that when formed during embryo development, have to be rigorously conserved in adult organisms.

DNA methyltransferase and demethylase in human prostate cancer

Recent studies have shown that cytosine-5 methylation at CpG islands in the regulatory sequence of a gene is one of the key mechanisms of inactivation. The enzymes responsible for CpG methylation are DNA methyltransferase (DNMT) 1, DNMT3a, and DNMT3b, and the enzyme responsible for demethylation is DNA demethylase (MBD2). Studies on methylation-demethylation enzymes are lacking in human prostate cancer. We hypothesize that MBD2 enzyme activity is repressed and that DNMT1 enzyme activity is elevated in human prostate cancer. To test this hypothesis, we analyzed enzyme activities, mRNA, and protein levels of MBD2 and DNMT1, DNMT3a, and DNMT3b in human prostate cancer cell lines and tissues. The enzyme activities of DNMTs and MBD2 were analyzed by biochemical assay. The mRNA expression was analyzed by reverse transcriptase-polymerase chain reaction and by Northern blotting. The protein expression was measured by immunohistochemistry with specific antibodies. The results of these experiments demonstrated that (1) the activity of DNMTs was twofold to threefold higher in cancer cell lines and cancer tissues, as compared with a benign prostate epithelium cell line (BPH-1) and benign prostatic hyperplasia (BPH) tissues; (2) MBD2 activity was lacking in prostate cancer cell lines but present in BPH-1 cells; (3) immunohistochemical analyses exhibited higher expression of DNMT1 in all prostate cancer cell lines and cancer tissues, as compared with BPH-1 cell lines and BPH tissues; (4) MBD2 protein expression was significantly higher in BPH-1 cells and lacking in prostate cancer cell lines and, in BPH tissues, MBD2 protein expression was poorly observed, as compared with no expression in prostate cancer tissues; and (5) mRNA expression for DNMT1 was upregulated in prostate cancer, as compared with BPH-1, and mRNA expression for MBD2 was found to be significantly expressed in all cases. The results of these studies clearly demonstrate that DNMT1 activity is upregulated, whereas MBD2 is repressed at the level of translation in human prostate cancer. These results may demonstrate molecular mechanisms of CpG hypermethylation of various genes in prostate cancer.

The battle of the sexes after fertilization: behaviour of paternal and maternal chromosomes in the early mammalian embryo

In the early diploid mammalian embryo, a father's chromosomes don't mix with the mother's until some time after fertilization. This topological genome separation is preserved up to the four-cell embryo stage and then gradually disappears. Unlike maternal DNA, sperm DNA arrives in an almost crystalline structure, heavily modified with methylcytosines (MeCs), which keep genes inactive. Compartmentalization of the nucleus according to parental origin may make it easier for the cellular machinery of the fertilized egg to revive the paternal chromosomes and to control paternal gene expression. Active zygotic demethylation of the paternal genome by a putative demethylase in the egg is a striking example for the battle of the sexes at the genomic level and beyond the single-gene level. It has important implications for genomic imprinting, and the establishment of genetic totipotency in fertilized eggs and in somatic cells during mammalian cloning.

Demethylase activity is directed by histone acetylation

Mammalian genomes are compartmentalized into dense inactive chromatin that is hypermethylated and active open chromatin that is hypomethylated. It is generally accepted that this bimodal pattern of methylation is established during development and is then faithfully inherited through subsequent cell divisions by a maintenance DNA methyltransferase (DNMT1). The pattern of methylation is believed to direct local histone acetylation states. In contrast to this well accepted consensus, we show here using a transient transfection model that an active demethylase is involved in shaping patterns of methylation in somatic cells. Demethylase activity is directed by the state of histone acetylation, and therefore, the resulting methylation pattern is determined by local histone acetylation states contrary to the accepted model. Our data support a new model suggesting that the pattern of methylation is maintained by a dynamic balance of methylation and demethylation activities and the local state of histone acetylation. This provides a simple mechanism for explaining why active genes are not methylated.

Regulation of the DNA methylation machinery and its role in cellular transformation

DNA methylation, a covalent modification of the genome, is emerging as an important player in the regulation of gene expression. This review discusses the different components of the DNA methylation machinery responsible for replicating the DNA methylation pattern. Recent data have changed our basic understanding of the DNA methylation machinery. A number of DNA methyltransferases (DNMT) have been identified and a demethylase has recently been reported. Because the DNA methylation pattern is critical for gene expression programs, the cell possesses a number of mechanisms to coordinate DNA replication and methylation. DNMT1 levels are regulated with the cell cycle and are induced upon entry into the S phase of the cell cycle. DNMT1 also regulates expression of cell-cycle proteins by its other regulatory functions and not through its DNA methylation activity. Once the mechanisms that coordinate DNMT1 and the cell cycle are disrupted, DNMT1 exerts an oncogenic activity. Tumor suppressor genes are frequently methylated in cancer but the mechanisms responsible are unclear. Overexpression of DNMT1 is probably not responsible for the aberrant methylation of tumor suppressor genes. Unraveling how the different components of the DNA methylation machinery interact to replicate the DNA methylation pattern, and how they are disrupted in cancer, is critical for understanding the molecular mechanisms of cancer.

MMTV promoter hypomethylation is linked to spontaneous and MNU associated c-neu expression and mammary carcinogenesis in MMTV c-neu transgenic mice

The erbB family of receptor tyrosine kinases is frequently implicated in neoplasia. Amplification and overexpression of erbB2/neu has been found in 20 to 40% of human breast cancers. Previous studies using MMTV/c-neu transgenic mice have linked rat neu overexpression to mammary tumor development. In this study, we provide evidence that rat neu overexpression in mammary tumors of MMTV/c-neu transgenic mice is always associated with demethylation of the MMTV promoter, whereas the normal mammary glands of these transgenic mice always contain specific methylated regions of the MMTV promoter. In addition, after exposure to N-methyl-N-nitrosourea (MNU), the latency of mammary tumor development is significantly reduced and again is also associated with MMTV promoter demethylation. Thus, the transition from methylation to hypomethylation of the MMTV promoter induces high-level expression of c-neu and appears to be a prerequisite for transformation from normal to malignant mammary epithelium, either spontaneously or after carcinogen exposure. Expression of transgenic c-neu from the demethylated MMTV promoter appears to be an early event that allows outgrowth of mammary epithelium predisposed to malignant transformation.

DNA demethylase is expressed in ovarian cancers and the expression correlates with demethylation of CpG sites in the promoter region of c-erbB-2 and survivin genes

The objectives of this study were to examine DNA demethylase (dMTase) expression in ovarian cancers and evaluate methylation of CpG sites in the promoter of the c-erbB-2 gene and survivin gene exon 1. Forty-three epithelial ovarian cancers and 43 non-cancerous ovarian tissues were studied for dMTase expression by RT-PCR. Genomic DNA was extracted and digested with HindIII and then HpaII. CpG site-sensitive primers were constructed to amplify the promoter of the c-erbB-2 gene and survivin gene exon 1. Immunohistochemical evaluation of ErbB-2 protein and RT-PCR for survivin were also performed. dMTase was positive in 88.4% of ovarian cancers but only in 9.3% of non-cancerous ovaries (P<0.001, Fisher's exact test). The expression was similarly observed in both early stage (stage I+II: 17/19) and advanced stage (stage III+IV: 21/24) groups of ovarian malignancy. It was found that 78.9% of dMTase-positive cancers had both c-erbB-2 promoter and survivin gene exon 1 unmethylated, whereas 40% of dMTase-negative cancers had both sites methylated. In non-cancerous ovaries, these sites were mostly methylated (90.6%) and the difference from cancer cases was highly significant (P<0.001). Immunohistochemical evaluation of ErbB-2 showed significant correlation of unmethylated c-erbB-2 promoter and ErbB-2 expression. The RT-PCR for survivin expression showed that 86% of cancers were positive and six cases were negative. Exon 1 was methylated in 83% of the survivin-negative cases. This is the first report of dMTase expression in ovarian cancers. The correlation of dMTase expression with unmethylation of c-erbB-2 promoter and survivin gene exon 1 suggests that these sites may be targets for demethylation by the enzyme. The up-regulation of oncogenes may be the consequence of epigenetic control of gene expression by the dMTase.

Clonal origins of human breast cancer

Tumours are usually considered as the clonal progeny of single transformed cells. An X-chromosome inactivation assay has been applied to exploring clonal relationships in human breast cancer. Analysis of X-inactivation in DNA extracted from microdissected in situ and invasive breast carcinoma by Hpa II restriction and polymerase chain reaction (PCR) of the androgen receptor exon I CAG polymorphism confirmed monoclonality in 105/133 samples of carcinoma cells from 31/32 informative breast cancers. Clonality was identical in seven cases between in situ and invasive carcinoma. Unexpectedly, 4 of 12 cancers (33%) with two or more monoclonal samples available were mosaic (polyclonal) in respect of X-chromosome inactivation between separate morphologically homogeneous tumour cell samples. Concordant clonality supports a common clonal origin of in situ and invasive breast cancers, but frequent apparently mosaic X-inactivation in breast cancer cannot be explained by non-tumour cell contamination. It is concluded that these carcinomas may be genuinely multiclonal. Possible mechanisms of multiclonality include simultaneous transformation of cell groups straddling X-chromosome inactivation patch boundaries, tumour-initiating mutations prior to X-inactivation, or recruitment of bystander stem cells by DNA transfer from necrotic or apoptotic tumour cells. Collision of independent cancers appears implausible at this frequency. Further studies using independent analytical techniques are required to test the important possibility that a significant proportion of mammary carcinomas are not monoclonal.

Methylation matters

DNA methylation is not just for basic scientists any more. There is a growing awareness in the medical field that having the correct pattern of genomic methylation is essential for healthy cells and organs. If methylation patterns are not properly established or maintained, disorders as diverse as mental retardation, immune deficiency, and sporadic or inherited cancers may follow. Through inappropriate silencing of growth regulating genes and simultaneous destabilisation of whole chromosomes, methylation defects help create a chaotic state from which cancer cells evolve. Methylation defects are present in cells before the onset of obvious malignancy and therefore cannot be explained simply as a consequence of a deregulated cancer cell. Researchers are now able to detect with exquisite sensitivity the cells harbouring methylation defects, sometimes months or years before the time when cancer is clinically detectable. Furthermore, aberrant methylation of specific genes has been directly linked with the tumour response to chemotherapy and patient survival. Advances in our ability to observe the methylation status of the entire cancer cell genome have led us to the unmistakable conclusion that methylation abnormalities are far more prevalent than expected. This methylomics approach permits the integration of an ever growing repertoire of methylation defects with the genetic alterations catalogued from tumours over the past two decades. Here we discuss the current knowledge of DNA methylation in normal cells and disease states, and how this relates directly to our current understanding of the mechanisms by which tumours arise.

DNA demethylase expression correlates with lung resistance protein expression in common epithelial ovarian cancers

We examined DNA demethylase (dMTase) expression, a common feature of ovarian cancer, to establish if there is any relationship between gene expression and disease stage, histopathology and survival. We also sought evidence of concurrent dMTase and lung resistance protein (LRP) expression. In 43 epithelial ovarian cancers studied we found that the relative strength of gene expression correlated with disease stage, histology and survival. dMTase expression was positive in 38/43 cases studied (88.4%). We also identified a significant correlation between dMTase and LRP expression. In 80% of cases where dMTase was not expressed, LRP was not found. Conversely, 70% of cases where dMTase expression was positive were also LRP-positive. We also identified a weak trend indicating that dMTase expression may occur more frequently in cases of endometrioid and serous adenocarcinoma. The expression of dMTase is a common feature of ovarian cancer and there is a correlation between dMTase and LRP expression, suggesting that there may be an epigenetic upregulation of the gene.

The dynamics of myogenin site-specific demethylation is strongly correlated with its expression and with muscle differentiation

The molecular mechanisms underlying the activation of tissue-specific genes have not yet been fully clarified. We analyzed the methylation status of specific CCGG sites in the 5'-flanking region and exon 1 of myogenin gene, a very important myogenic differentiation factor. We demonstrated a loss of methylation, at the onset of C2C12 muscle cell line differentiation, limited to the CCGG site of myogenin 5'-flanking region, which was strongly correlated with the transcriptional activation of this gene and with myogenic differentiation. The same CCGG site was also found to be hypomethylated, in vivo, in embryonic mouse muscle (a myogenin-expressing tissue), as opposed to nonmuscle (nonexpressing) tissues that had a fully methylated site. In a C2C12-derived clone with enhanced myogenic ability, demethylation occurred within 2 h of induction of differentiation, suggesting the involvement of some active demethylation mechanism(s) that occur in the absence of DNA replication. Exposure to drugs that inhibit DNA methylation by acting on the S-adenosylmethionine metabolism produced a further reduction, to a few minutes, in the duration of the demethylation dynamics. These effects suggest that the final site-specific DNA methylation pattern of tissue-specific genes is defined through a continuous, relatively fast interplay between active DNA demethylation and re-methylation mechanisms.

DNA methylation and chromosome instability in lymphoblastoid cell lines

In order to gain more insight into the relationships between DNA methylation and genome stability, chromosomal and molecular evolutions of four Epstein-Barr virus-transformed human lymphoblastoid cell lines were followed in culture for more than 2 yr. The four cell lines underwent early, strong overall demethylation of the genome. The classical satellite-rich, heterochromatic,juxtacentromeric regions of chromosomes 1, 9, and 16 and the distal part of the long arm of the Y chromosome displayed specific behavior with time in culture. In two cell lines, they underwent a strong demethylation, involving successively chromosomes Y, 9, 16, and 1, whereas in the two other cell lines, they remained heavily methylated. For classical satellite 2-rich heterochromatic regions of chromosomes 1 and 16, a direct relationship could be established between their demethylation, their undercondensation at metaphase, and their involvement in non-clonal rearrangements. Unstable sites distributed along the whole chromosomes were found only when the heterochromatic regions of chromosomes 1 and 16 were unstable. The classical satellite 3-rich heterochromatic region of chromosomes 9 and Y, despite their strong demethylation, remained condensed and stable. Genome demethylation and chromosome instability could not be related to variations in mRNA amounts of the DNA methyltransferases DNMT1, DNMT3A, and DNMT3B and DNA demethylase. These data suggest that the influence of DNA demethylation on chromosome stability is modulated by a sequence-specific chromatin structure.

Human DNA-demethylating activity: a glycosylase associated with RNA and PCNA

We have partially purified and characterized the 5-methylcytosine removing activity (5-meC-DNA Glycosylase) from HeLa cells with 700-fold enrichment. This activity cleaves DNA specifically at fully methylated CpG sites. The mechanism of 5-meC removal is base excision from fully methylated CpG loci on DNA, producing abasic sites. Hemi-methylated DNA is not a substrate. A prominent 52 KDa protein is present in all partially purified fractions. This activity is tightly associated with other nuclear factors and proteins, which resulted in differential fractionation of this activity on ion exchange columns. One nuclear factor associated with this activity is identified as RNA. Another nuclear protein, proliferating cell nuclear antigen (PCNA) is also associated with this enzyme. Glycosylic removal of 5-meC from DNA by this activity could be involved in the regulation of transcription, replication, differentiation, and development through resultant hypomethylation of DNA.

Dynamics of DNA methylation pattern

Methylation patterns are the result of de novo methylation, demethylation, and the maintenance of existing methylation. Although the existence and identity of an active demethylase remain in doubt, recent evidence suggests that protein binding can specify sites of demethylation through a replication-dependent pathway. By using a stable episomal system in human cells, plus the Drosophila system, and mouse embryonic stem cells, we are beginning to understand the function and targets of de novo methyltransferases in murine and human cells.

Epigenetic aspects of cellular senescence

The limited proliferative potential of normal cells in culture has been proposed as a model for cellular aging in vivo. It is clear that cellular aging has a genetic component but epigenetic processes could also be involved. Insight gained during years of intensive study suggests cellular aging is a multi-step process and that cells possess a counting mechanism that determines the number of doublings the cells can complete. In this paper, we review evidence suggesting a role for epigenetic processes in cell senescence and discuss the possible insights that might be provided by experiments designed to induce a premature senescent like state.