Correlation between synthesis and methylation of DNA in HeLa cells

Aging as an Epigenetic Phenomenon

INTRODUCTION

Hypermethylation of genes associated with promoter CpG islands, and hypomethylation of CpG poor genes, repeat sequences, transposable elements and intergenic genome sections occur during aging in mammals. Methylation levels of certain CpG sites display strict correlation to age and could be used as "epigenetic clock" to predict biological age. Multi-substrate deacetylases SIRT1 and SIRT6 affect aging via locus-specific modulations of chromatin structure and activity of multiple regulatory proteins involved in aging. Random errors in DNA methylation and other epigenetic marks during aging increase the transcriptional noise, and thus lead to enhanced phenotypic variation between cells of the same tissue. Such variation could cause progressive organ dysfunction observed in aged individuals. Multiple experimental data show that induction of NF-κB regulated gene sets occurs in various tissues of aged mammals. Upregulation of multiple miRNAs occurs at mid age leading to downregulation of enzymes and regulatory proteins involved in basic cellular functions, such as DNA repair, oxidative phosphorylation, intermediate metabolism, and others.

CONCLUSION

Strong evidence shows that all epigenetic systems contribute to the lifespan control in various organisms. Similar to other cell systems, epigenome is prone to gradual degradation due to the genome damage, stressful agents, and other aging factors. But unlike mutations and other kinds of the genome damage, age-related epigenetic changes could be fully or partially reversed to a "young" state.

Epimutagenesis: A prospective mechanism to remediate arsenic-induced toxicity

Arsenic toxicity is a global issue, addressed by the World Health Organization as one of the major natural calamities faced by humans. More than 137 million individuals in 70 nations are affected by arsenic mainly through drinking water and also through diet. Chronic arsenic exposure leads to various types of patho-physiological end points in humans including cancers. Arsenic, a xenobiotic substance, is biotransformed in the body to its methylated species by using the physiological S-adenosyl methionine (SAM). SAM dictates methylation status of the genome and arsenic metabolism leads to depletion of SAM leading to an epigenetic disequilibrium. Since epigenetics is one of the major phenomenon at the interface between the environment and human health impact, its disequilibrium by arsenic inflicts upon the chromatin compaction, gene expression, genomic stability and a host of biomolecular interactions, the interactome within the cell. Since arsenic is not mutagenic but is carcinogenic in nature, arsenic induced epimutagenesis has come to the forefront since it determines the transcriptional and genomic integrity of the cell. Arsenic toxicity brings forth several pathophysiological manifestations like dermatological non-cancerous, pre-cancerous and cancerous lesions, peripheral neuropathy, DNA damage, respiratory disorders and cancers of several internal organs. Recently, several diseases of similar manifestations have been explained with the relevant epigenetic perspectives regarding the possible molecular mechanism for their onset. Hence, in the current review, we comprehensively try to intercalate the information on arsenic-induced epigenetic alterations of DNA, histones and microRNA so as to understand whether the arsenic-induced toxic manifestations are brought about by the epigenetic changes. We highlight the need to understand the aspect of epimutagenesis and subsequent alterations in the cellular interactome due to arsenic-induced molecular changes, which may be utilized to develop putative therapeutic strategies targeting both oxidative potential and epimutagenesis in humans.

The language of methylation in genomics of eukaryotes

Background studies have shown that 6-methylaminopurine (m6A) and 5-methylcytosine (m5C), detected in DNA, are products of its post-synthetic modification. At variance with bacterial genomes exhibiting both, eukaryotic genomes essentially carry only m5C in m5CpG doublets. This served to establish that, although a slight extra-S phase asymmetric methylation occurs de novo on 5'-CpC-3'/3'GpG-5', 5'-CpT-3'/3'-GpA-5', and 5'-CpA-3'/3'-GpT-5' dinucleotide pairs, a heavy methylation during S involves Okazaki fragments and thus semiconservatively newly made chains to guarantee genetic maintenance of -CH3 patterns in symmetrically dimethylated 5'-m5CpG-3'/3'-Gpm5C-5' dinucleotide pairs. On the other hand, whilst inverse correlation was observed between bulk DNA methylation, in S, and bulk RNA transcription, in G1 and G2, probes of methylated DNA helped to discover the presence of coding (exon) and uncoding (intron) sequences in the eukaryotic gene. These achievements led to the search for a language that genes regulated by methylation should have in common. Such a deciphering, initially providing restriction minimaps of hypermethylatable promoters and introns vs. hypomethylable exons, became feasible when bisulfite methodology allowed the direct sequencing of m5C. It emerged that, while in lymphocytes, where the transglutaminase gene (hTGc) is inactive, the promoter shows two fully methylated CpG-rich domains at 5 and one fully unmethylated CpG-rich domain at 3' (including the site +1 and a 5'-UTR), in HUVEC cells, where hTGc is active, in the first CpG-rich domain of its promoter four CpGs lack -CH3: a result suggesting new hypotheses on the mechanism of transcription, particularly in connection with radio-induced DNA demethylation.

Specific methylation of the CpG-rich domains in the promoter of the human tissue transglutaminase gene

The activity of tissue transglutaminase is present in many cells and tissues but almost absent in leucocytes and lymphocytes. The present work describes the distribution of 5-methylcytosine along the bisulphite-converted promoter of the human tissue transglutaminase gene as being in an essentially repressed state. In this promoter, the chain-specific sequencing revealed the location of three CpG-rich domains whose methylation responds to an 'all or nothing' signal. While the CpGs of domain 1, at the 5'-end, and 2, in the mid-promoter, were fully methylated, those of domain 3, at the 3'-end, were fully unmethylated. Before the 5'-UTR sequence, from site+1 to site+67, also unmethylated, there was thus a striking contrast in the post-synthetic modification between the sequence, from -1594 to -436, containing domains 1 and 2, and the sequence, from -435 to -1, containing domain 3 with the core promoter.

5-Methylcytosine in genes with methylation-dependent regulation

An asymmetric distribution of deoxy-5-methylcytidylic acid-inhibiting restriction sites (dcm-sites) takes place in ten human genes regulated by 5-methylcytosine. These genes are dcm-site enriched upstream and dcm-site poor downstream. Along them, there is a scattering of hypermethylatable introns and hypomethylatable exons with a common code: the 5mCpG dinucleotides characterize promoters; Gp5mCs characterize introns; Tp5mCs and Cp5mCs are in small concentrations in exons. Housekeeping genes contain more dcm-sites when compared with tissue-specific genes. This depends on the higher number of dcm-sites in their promoters and introns. In exons, the relatively lower number of dcm-sites is almost the same in both housekeeping and tissue-specific genes. Going from 5' to 3', the average frequency of occurrence of these sites per nucleotide units decreases in introns and increases in exons. This difference is highly discriminated for tissue-specific and less discriminated for housekeeping genes.

Repair-modification and evolution of the eukaryotic genome organization

For a complete reconstruction of the damaged unmethylated islands, in theory, the conventional excision-repair is sufficient. For a complete reconstruction of the damaged methylated domains, a coupling has to take place involving the excision-repair (able to reestablish their ATGC-language) plus the DNA-methylase (able to reestablish their modified ATGC5mC-language). This coupling, defined as "repair-modification," is essentially functioning during the S-phase, because the DNA-polymerase beta (pol beta) is active during the whole cell cycle, whereas the DNA-methylase (met) is active in S and appears to be repressed or inactive during the major part of G1 and during the phases G2 and M. Consequently, after damage, some silent genes might become expressed during these phases, if it is true that DNA methylation is inversely proportional to transcription. Repair-modification should, therefore, exert a continuous differential pressure on evolution of given parts of the genome, when they are methylated to a different extent. According to Darwinian concepts, repair-modification would lead to a high variability, especially of uncoding DNA sequences (if hypermethylated), whereas on the basis of this variability, selection might favor transposition of specific regulatory elements into given transcriptional units. In these, the conservative nature of the coding elements (if unmethylated) would obviously be ensured by the conventional excision-repair.

DNA methylases separated through the HeLa cell cycle methodology show allosteric properties

Two DNA methylases (DNAmets) can be separated through the cell cycle. The first appears as a minor peak in G1, the second as a major peak in S. Both enzymes protect from HpaII a plasmid (H31), constructed with the pBR322 vector (4.3 kbp) and the inverted A gamma fragment of the human globin gene (3.5 kbp), inserted at its HindIII site (the vector carries several HpaII sites, the insert only one HpaII site). DNAmets G1 and S show distinct Km values and different kinetics vs the ionic strength of the medium, while their Michaelis-Menten and Lineweaver-Burk plots are sigmoidal and hyperbolical curves, respectively. This is the first suggestion about the allosteric nature of the eukaryotic DNAmet system.

Effect of 5-azacytidine (5-azaC) on the induction of chromatid aberrations (CA) and sister-chromatid exchanges (SCE)

Experiments were carried out using human lymphocytes from a male donor in order to test the action of 5-azaC treatment on the induction of SCE and chromatid aberrations. The 5-azaC was found to increase the frequency of both baseline and MMC-induced SCEs. Using the same 5-azaC treatment conditions it was found that the frequency of X-ray-induced CA did not increase.

Hypomethylation of repair patches in HeLa cells

In HeLa cells, under conditions where normal semiconservative synthesis is suppressed by hydroxyurea, the excision repair process after irradiation by UV results in a small amount of incorporation of nucleotides into nonreplicated DNA. By labelling the cytosine moieties of these repair patches, and measuring the ratio between cytosine and 5-methylcytosine, we have found that the level of methylation of cytosine in repair patches five hours after UV-irradiation of the cells is about half of that observed in normal semiconservatively synthesized DNA.

Differential regulation of polyamine synthesis and transmethylation reactions in methylthioadenosine phosphorylase deficient mammalian cells

The consumption of S-adenosylmethionine during polyamine synthesis and transmethylation reactions yields stoichiometric amounts of 5'-deoxy-5'-methylthioadenosine and S-adenosylhomocysteine, respectively. Information concerning the regulation of the two routes of S-adenosylmethionine metabolism in viable cells under changing growth conditions is limited. The present experiments have measured the time-dependent accumulation of 5'-deoxy-5'-methylthioadenosine and L-homocysteine in the medium of four malignant human and murine cell lines deficient in 5'-deoxy-5'-methylthioadenosine phosphorylase (5'-methylthioadenosine: orthophosphate methylthioribosyltransferase). Included in this group were anchorage-independent and anchorage-dependent cells. The enzyme-deficient cells did not detectably cleave 5'-deoxy-5'-methylthioadenosine, and did not appreciably metabolize homocysteine. A comparison of 5'-deoxy-5'-methylthioadenosine and homocysteine excretion therefore provided a noninvasive method for estimating the relative rates of polyamine synthesis and transmethylation. Early after the release of human CEM lymphoblasts from density dependent growth arrest, 5'-deoxy-5'-methylthioadenosine production increased, and exceeded homocysteine synthesis. 5'-Deoxy-5'-methylthioadenosine formation reached a maximum of 0.9 nmol/12 h per 10(6) cells prior to the onset of exponential growth. The kinetics of homocysteine synthesis were different. Homocysteine accumulation was proportional to the specific growth rate, and achieved a peak of 3.1 nmol/12 h per 10(6) cells during mid-exponential phase, at which time 5'-deoxy-5'-methylthioadenosine production was falling. Similar patterns of 5'-deoxy-5'-methylthioadenosine and homocysteine excretion were observed in other 5'-deoxy-5'-methylthioadenosine phosphorylase deficient cell lines. These data show that polyamine synthesis and transmethylation are differentially regulated during the growth cycle of mammalian cells.

Delayed methylation and the matrix bound DNA methylase

It is shown that the methylation of DNA that occurs in isolated nuclei is "delayed methylation". This methylation is not reduced in nuclei which have been pretreated with 0.2M NaCl to extract the soluble methylase suggesting that this methylation is the product of a firmly bound matrix associated DNA methylase. Evidence is provided that, like the methylase, the DNA substrate is associated with the nuclear matrix.

In vitro methylation of total and foldback DNAs in normal and virus-transformed cells

The levels of the in vitro methylation of total and palindromic DNAs in nuclei isolated from normal and virus-transformed cells are compared. The methylation rate of total DNA in normal rat kidney cells is much higher than that detected in normal mouse fibroblasts. However, for both cell species, while the maximal rate of DNA methylation is observed in the mid-logarithmic phase of the cell culture growth, palindromes are always found to be more heavily methylated than total DNA. The 5-methylcytosine content of DNA, especially of palindromes, is higher in virus-transformed cells than in untransformed cells.

Eukaryotic DNA methylation

Eukaryotic genomes contain 5-methylcytosine (5mC) as a rare base.5mC arises by postsynthetic modification of cytosine and occurs, at least in animals, predominantly in the dinucleotide CpG. The base is not distributed randomly in these genomes but conforms to a pattern. This pattern varies between taxa but appears to be inherited in a semi-conservative fashion. At the level of the genome, gross changes in the level of DNA methylation have been noted. This has encouraged speculation that the modification may play a role in cellular differentiation. Tissue-specific patterns of DNA methylation, predicted by various models of differentiation, have been found for most vertebrate genes so far examined. A correlation has emerged between the undermethylation of these regions and their transcription, but this is not always the case. While data for eukaryotic viral sequences are less equivocal, studies of this kind cannot in isolation distinguish between undermethylation being a cause or a consequence of gene activity. If it were a cause, it is probable that the demethylation of specific CpG sites would be a necessary yet not a sufficient condition for transcription to occur. The introduction of artificially methylated DNA sequences into individual eukaryotic cells by microinjection or transformation may provide the means to elucidate these questions in the future. In the meantime, the study of eukaryotic DNA methylation promises to contribute much to our understanding of the regulation of gene expression in these organisms.

DNA methylation in eukaryotes

The DNA of higher eukaryotes contains one minor base, namely 5-methylcytosine. The distribution of this minor base between different species and different DNA fractions will be considered together with the actual sequences methylated. The properties of the enzyme responsible for DNA modification will be reviewed, particular note being paid to the efficiency of methylation of different DNA substrates. Various possible functions of the 5-methylcytosine in DNA will be considered and particular attention will be paid to the finding that specific modified bases present in DNA not undergoing transcription are absent in the same genes when these are being actively transcribed.

Organization, replication and modification of the human genome: synthesis and methylation of palindromic, repeated and unique HeLa nDNA sequences during the S-phase

At least five supermethylated nDNA families have been found in HeLa cells. The concentration of 5-methylcytosine increases on palindromes from 1 to 5 hours during the nDNA duplicative phase, decreasing again at the 6th hour of S. The early S-phase involves the accumulation of 5-methylcytosines on the nDNA sequences reassociating near a Cot = 3 x 10(-1). Late S involves increment of this base on the sequences which reassociate near a Cot = 9 x 10(-1) and Cot = 7 x 10(1). The unique sequences show a moderate methylation from 3 to 6 hours of S. This information shows that genes are methylated with an order during the S-phase in a system in which nDNA organization, modification and replication appear to be severely subordinated one to another. The possible role of methylation of foldback nDNA in regulation of transcription during the eukaryotic cell life cycle is discussed.

Nucleic acids methylation of synchronized BHK 21 HS 5 fibroblasts during the mitotic phase

The methylation of nucleic acids has been investigated during the cell cycle of an asparagine dependent strain of transformed fibroblasts (BHK 21 HS 5). The synchrony was carried out by a partial asparagine starvation of cells for 24 hours. The amino acid supply induced all cells to enter synchronously the G1 phase. Methylation and DNA synthesis were respectively measured by pulsed [methyl-14C] methionine and [methyl-3H] thymidine incorporation. DNA methylation followed a biphasic pattern with maximal methyl incorporations during both S phase and mitosis. A partial desynchronisation induced the S phase of the second cycle to proceed before all the cells have achieved their division. Hydroxyurea was used in order to inhibit the DNA synthesis of cells entering the second cell cycle, which might interfer with the mitosis of the first one. The inhibitor was added either at the first beginning of cell division or during all the G1 phase. In both conditions it suppressed 3H thymidine incorporation of the second cycle. However, mitosis took place and methylations occurred as in previous experiments. The DNA methylation of the mitotic phase in the first cell cycle could thus be dissociated from the classical post-synthetic DNA maturation and did not correspond to any DNA methylation appearing in the course of the second cell cycle.

Organization, replication and modification of the human genome: temporal order of synthesis and methylation of two classes of HeLa nDNA separated in Ag+--Cs2-SO4 gradients

During the HeLa S-phase, DNA was methylated, at 1-hr intervals in isolated nuclei and fractionated in Ag+-Cs2SO4 gradients providing a heavy GC-rich peak and a main light AT-rich peak. Both size and specific methylation of these peaks changed during the nDNA duplicative phase. Replication of the heavy GC-rich nDNA fraction, which contains genes for ribosomal RNA, occurred in early S; in contrast, replication of the main AT-rich nDNA fraction was maximal in late S. Concomitantly, specific methylation of the GC-rich nDNA was maximal in the first part of S, while that of the AT-rich nDNA was maximal in the second part of S. This suggested that genes are replicated and methylated with order during the S-phase.

Organization, replication and modification of the human genome: differential methylation of two classes of HeLa nuclear DNA separated on Ag+--Cs2SO4 gradients

HeLa nuclear DNA sediments as a single peak, in neutral CsCl, while it is separated in a heavier and a lighter components, in alkaline Ag+--Cs2SO4. The heavy fraction, on the average, represents about 20% of the total DNA. CsCl analytical ultracentrifugation shows that heavy DNA bands at 1.715 g/cm3 and contains 53% GC (10% of the total GC), whereas light DNA bands at 1.703 g/cm3 and contains 40% GC (32% of the total GC). Coherently, Tm values in 0.1 x SSC are 82.5 degrees C, for heavy DNA, and 72.5 degrees C, for light DNA. After treatment with [3H-methyl-S-adenosyl-L-methionine in isolated nuclei, the concentration of labelled 5-methylcytosine was found to be highest in the more dense regions of the heavy peak and in the less dense regions of the light peak. Exposure to ultrasound modifies the quantitative relationship of the two peaks and improves the separation of supermethylated AT- and GC-rich DNAs. Four possible triplets as sites for DNA-methylase recognition are discussed.

The effect of S-adenosylhomocysteine on DNA methylation in isolated rat liver nuclei

DNA methylation was studied in vitro using whole nuclei from regenerating rat liver. Methyl incorporation from S-adenosyl-[Me-3H]methionine in nuclei from regenerating liver was four times higher than that of normal liver. The effect of S-adenosylhomocysteine on DNA methylation was examined, and it was found at equal molar concentrations of S-adenosylhomocysteine to to S-adenosylmethionine that DNA methylation was competitively inhibited 50%.

Differential gene activity and segregation of cell lines: an attempt at a molecular interpretation of the primary events of embryonic development

The study of differentiation is concerned with the analysis of the processes responsible for ‘the cellular changes in macromolecular synthesis and composition, patterned in time and space and resulting in specialized functions, forms and organization’ (Moscona, 1973).