Gene reactivation: a tool for the isolation of mammalian DNA methylation mutants

Bacteria-related changes in host DNA methylation and the risk for CRC

Colorectal cancer (CRC) is the second most common cause of cancer deaths in men and women combined. Colon-tumor growth is multistage and the result of the accumulation of spontaneous mutations and epigenetic events that silence tumor-suppressor genes and activate oncogenes. Environmental factors are primary contributors to these somatic gene alterations, which account for the increase in incidence of CRC in western countries. In recent decades, gut microbiota and their metabolites have been recognized as essential contributing factors to CRC, and now serve as biomarkers for the diagnosis and prognosis of CRC. In the present review, we highlight holistic approaches to understanding how gut microbiota contributes to CRC. We particularly focus herein on bacteria-related changes in host DNA methylation and the risk for CRC.

Strategies for DNA methylation analysis in developmental studies

Developmental processes in eukaryotes are highly dependent on DNA methylation. 5-methylcytosine (m(5) C) is the most prevalent and best understood DNA modification implicated in maintenance of genomic integrity and function across species. Although m(5) C occurs almost exclusively in symmetrical CpG context in vertebrates, additional asymmetrical distribution in CpHpG and CpHpH sites has been observed in plants and embryonic stem cells. To this end, accurate and reproducible methodology for full analysis of the DNA methylome is highly demanded. Fortunately, a variety of methods enable quantitative DNA methylation mapping at a single-base resolution and in a large scale. Here, we provide a critical overview of methods applied primarily to m(5) C detection with particular emphasis on technical improvements of the classical bisulfite-conversion protocol. We further describe strategies in combination with emerging technologies that allow acquisition of highly reliable data for developmental studies.

Process development for a recombinant Chinese hamster ovary (CHO) cell line utilizing a metal induced and amplified metallothionein expression system

The suspension Chinese Hamster Ovary cell line, 13-10-302, utilizing the metallothionein (MT) expression system producing recombinant human growth hormone (hGH) was studied in a serum-free and cadmium-free medium at different fermentation scales and modes of operation. Initial experiments were carried out to optimize the concentration of metal addition to induce the MT promoter. Subsequently, the cultivation of the 13-10-302 cell line was scaled up from spinner flasks into bioreactors, and the cultivation duration was extended with fed-batch and perfusion strategies utilizing 180 microM zinc to induce the promoter controlling expression of recombinant hGH. It was shown that a fed-batch process could increase the maximum cell numbers twofold, from 3.3 to 6.3 x 10(6) cell/mL, over those obtained in normal batch fermentations, and this coupled with extended fermentation times resulted in a fourfold increase in final hGH titer, from 135 +/- 15 to 670 +/- 70 mg/L at a specific productivity q(hGH) value of 12 pg cell(-1)d(-1). The addition of sodium butyrate increased the specific productivity of hGH in cells to a value of approximately 48 pg cell(-1)d(-1), resulting in a final hGH titer of over a gram per liter during fed-batch runs. A BioSep acoustic cell recycler was used to retain the cells in the bioreactor during perfusion operation. It was necessary to maintain the specific feeding rates (SFR) above a value of 0.2 vvd/(10(6) cell/mL) to maintain the viability and productivity of the 13-10-302 cells; under these conditions the viable cell number increased to over 10(7) cell/mL and resulted in a volumetric productivity of over 120 mg(hGH) L(-1)d(-1). Process development described in this work demonstrates cultivation at various scales and sustained high levels of productivity under cadmium free condition in a CHO cell line utilizing an inducible metallothionein expression system.

High-throughput clonal selection of recombinant CHO cells using a dominant selectable and amplifiable metallothionein-GFP fusion protein

Transfected mammalian cells can be used for the production of fully processed recombinant proteins for medical and industrial purposes. However, the isolation of high-producing clones is traditionally time-consuming. Therefore, we developed a high-throughput screening method to reduce the time and effort required to isolate high-producing cells. This involved the construction of an expression vector containing the amplifiable gene metallothionein (MT), fused in-frame to green fluorescent protein (GFP). The fusion gene (MTGFP) confers metal resistance similar to that of the wild-type metallothionein and expression can be monitored using either flow cytometry or a fluorometer to measure green fluorescence. Expression of MTGFP acted as a dominant selectable marker allowing rapid and more efficient selection of clones at defined metal concentrations than with the antibiotic G418. Cells harboring MTGFP responded to increasing metal concentrations with a corresponding increase in fluorescence. There was also a corresponding increase in recombinant protein production, indicating that MTGFP could be used as a selectable and amplifiable gene for the coexpression of foreign genes. Using our expression vector encoding MTGFP, we demonstrate a high-throughput clonal selection protocol for the rapid isolation of high-producing clones from transfected CHO cells. We were able to isolate cell lines reaching specific productivities of >10 microg hGH/10(6) cells/day within 4 weeks of transfection. The advantage of this method is that it can be easily adapted for automated procedures using robotic handling systems.

Interactions in glycine and methionine uptake, conversion and incorporation into proteins in the preimplantation mouse embryo

Glycine is the most concentrated amino acid in the female genital tract. In this study, we report its conversion and incorporation into proteins in the presence or absence of methionine, in both 1-cell and blastocyst mouse embryos. The uptake, incorporation and conversion of radiolabelled glycine were studied in the presence or absence of unlabelled methionine. For control purposes, the reciprocal experiment was performed with labelled methionine in the presence or absence of unlabelled glycine. At the 1-cell stage neither glycine uptake nor its incorporation into proteins is inhibited by methionine. Glycine is, however, highly used as an oxidisable energy substrate, via glycolate. At the blastocyst stage, glycine conversion into other amino acids is high and mainly utilised in the formation of glutamic acid. Glycine is highly incorporated into proteins, resulting in a poor exchange of glycine from the preloaded embryos. Methionine competes for glycine uptake and consequently reduces its overall incorporation into proteins. For methionine, neither its uptake nor its incorporation into proteins is reduced in the presence of glycine for the two embryonic stages tested here. The embryo has different mechanisms for incorporation and utilisation of methionine and glycine. Glycine, which has an important function in the embryo, has an inefficient transport system compared with methionine. We were unable to demonstrate the presence of methylglycine since SAM-glycine-methyltransferase (EC 2.1.1.20) was not detected. The same results were obtained when exogenous methionine was added. We therefore concluded that glycine does not compete in transmethylation within the embryo.

Mechanisms of genomic imprinting in mammals

This chapter can be summarized by the following main points: Genomic imprinting results in the functional nonequivalence of the maternal and paternal genomes, thereby preventing the development of viable parthenogenotes and androgenotes in eutherian mammals. Imprinting may have arisen as a result of the specialized evolutionary requirements of the parental genomes or may have been an obligatory step in the development of placentation. A substantial proportion of transgenes and a smaller number of endogenous genes demonstrate imprinted pattern of expression in mice and humans. An analysis of DNA methylation in somatic tissues and germ cells during embryonic and postnatal development reveals dynamic changes, particularly during gametogenesis and early embryogenesis. The nature and timing of these changes suggest that DNA methylation may be involved in genomic imprinting. Imprinted genes display complex methylation patterns. Many aspects of these patterns are consistent with a role for methylation in the imprinted phenotype, although it is currently unclear whether methylation functions in the establishment of imprinting or plays a secondary role in the maintenance of the imprinted pattern of expression. Studies underway to identify new imprinted genes may help elucidate both the function and mechanism of genomic imprinting.

Abnormal chromosome behavior in Neurospora mutants defective in DNA methylation

The function and regulation of DNA methylation in eukaryotes remain unclear. Genes affecting methylation were identified in the fungus Neurospora crassa. A mutation in one gene, dim-2, resulted in the loss of all detectable DNA methylation. Abnormal segregation of the methylation defects in crosses led to the discovery that the methylation mutants frequently generate strains with extra chromosomes or chromosomal parts. Starvation for S-adenosylmethionine, the presumed methyl group donor for DNA methylation, also produced aneuploidy. These results suggest that DNA methylation plays a role in the normal control of chromosome behavior.

Mutations and epimutations in mammalian cells

Early studies on heritable variation in cultured mammalian cells suggested that both mutation and epigenetic events might be involved. The importance of mutations has subsequently been fully documented, but only recently has an alternative form of inheritance been uncovered. This is based on the post-synthetic methylation of cytosine in regulatory regions of genes. The pattern of methylation is heritable, and in almost all cases studied, methylation of a region is associated with lack of gene expression. Such silent genes can be reactivated by the powerful demethylating agent 5-azacytidine (5-aza-CR). Changes in heritable DNA methylation which alter phenotype are referred to as epimutations. It now seems very likely that the well known 'functional hemizygosity' in CHO cells and other near diploid cell lines is due to the existence of one active and one silent gene at many autosomal loci. It is clear that permanent cell lines inactivate genes by de novo methylation, whereas normal diploid cells do not have this activity. This has important implications for our understanding of cellular transformation, tumor progression, and the increase in chromosome number frequently associated with these cellular changes. It is likely that both mutations and epimutations are important in the emergence of fully transformed tumorigenic cells. Agents which increase or reduce DNA methylation in cells can be regarded as epimutagens, although in many cases the mechanisms of inducing hypo- or hyper-methylation are not understood. Two exceptions are 5-aza-CR which inhibits the normal DNA maintenance methylase activity, and 5-methyldeoxycytidine triphosphate which is incorporated into cellular DNA following electroporation and has been shown to silence genes.

Regulation of O6-methylguanine-DNA methyltransferase expression in the Burkitt's lymphoma cell line Raji

We have investigated the expression of the DNA-repair enzyme O6-methylguanine-DNA methyltransferase in the Burkitt's lymphoma cell line Raji. An existing mutant Raji cell line which lacks thymidine kinase activity had previously been shown to be Mex- and to no longer express O6-methylguanine-DNA methyltransferase. We report here that in addition to the methyltransferase and thymidine kinase, a third enzyme with an unrelated function, galactokinase, is also not expressed in Raji cells. The control of thymidine kinase expression is post-transcriptional and it is possible that galactokinase and methyltransferase can share a common post-transcriptional regulation with thymidine kinase.

High levels of de novo methylation and altered chromatin structure at CpG islands in cell lines

CpG islands are normally methylation free in cells of the animal, even when the associated gene is transcriptionally silent. In mouse NIH 3T3 and L cells, however, over half of the islands are heavily methylated. Near identity of the methylated subset in the two cell lines suggested that methylation is confined to genes that are nonessential in culture. In agreement with this, islands at several tissue-specific genes, but not at housekeeping genes, have become methylated in many human and mouse cell lines. At the chromatin level, methylated islands are Mspl resistant compared with their nonmethylated counterparts. We suggest that mutation-like gene inactivation due to CpG island methylation is widespread in many cell lines and could explain the loss of cell type-specific functions in culture.

DNA methylation and epigenetic inheritance

Classical genetics has revealed the mechanisms for the transmission of genes from generation to generation, but the strategy of the genes in unfolding the developmental programme remains obscure. Epigenetics comprises the study of the mechanisms that impart temporal and spatial control on the activities of all those genes required for the development of a complex organism from the zygote to the adult. Epigenetic changes in gene activity can be studied in relation to DNA methylation in cultured mammalian cells and it is also possible to isolate and characterize mutants with altered DNA methylase activity. Although this experimental system is quite far removed from the epigenetic controls acting during development it does provide the means to clarify the rules governing the silencing of genes by specific DNA methylation and their reactivation by demethylation. This in turn will facilitate studies on the control of gene expression in somatic cells of the developing organism or the adult. The general principles of epigenetic mechanisms can be defined. There are extreme contrasts between instability or switches in gene expression, such as those in stem-line cells, and the stable heritability of a specialized pattern of gene activities. In some situations cell lineages are known to be important, whereas in others coordinated changes in groups of cells have been demonstrated. Control of numbers of cell divisions and the size of organisms, or parts of organisms, is also essential. The epigenetic determination of gene expression can be reversed or reprogrammed in the germ line. The extent to which methylation or demethylation of specific DNA sequences can help explain these basic epigenetic mechanisms is briefly reviewed.

Reversion in thymidine kinase deficient variants of mouse lymphoma P388

The ability of 5 independently isolated thymidine kinase-deficient clones of mouse lymphoma P388 to revert has been examined. We were unable to detect spontaneous revertants in any of the 5 clones. Treatment with the hypomethylating agent 5-azacytidine induced reversion in 4 of the clones, but the frequency of revertants was very low (less than 10(-6). The response was not dose-dependent. The mutagen EMS was capable of inducing reversion in 3 of the clones with a variable level of response. The activity of thymidine kinase in 16 revertants was determined. In half of these the level of enzyme activity was considerably greater than the original P388 cell line. The high frequency loss of thymidine kinase that occurs in these cells may represent a stable inactivation of gene activity rather than an alteration in the DNA base sequence.

DNA methylation and epigenetic mechanisms

Genes are essential for the transmission of genetic information from generation to generation, and this mechanism of inheritance is fully understood. Genes are also essential for unfolding the genetic program for development, but the rules governing this process are obscure. Epigenetics comprises the study of the switching on and off of genes during development, the segregation of gene activities following somatic cell division, and the stable inheritance of a given spectrum of gene activities in specific cells. Some of these processes may be explained by DNA modification, particularly changes in the pattern of DNA methylation and the heritability of that pattern. There is strong evidence that DNA methylation plays an important role in the control of gene activity in cultured mammalian cells, and the properties of a CHO mutant strain affected in DNA methylation are described. Human diploid cells progressively lose cytosine methylation during serial subculture, and this may be related to their in vitro senescence. There is also evidence that DNA modifications can be inherited through the germ line. Classical genetics is based on the study of all types of change in DNA base sequence, but the rules governing the activity of genes by epigenetic mechanisms are necessarily different. Their elucidation will depend both on a theoretical framework for development and on experimental studies at the molecular, chromosomal, and cellular levels.

Possible organ and age-related epigenetic factors in Huntington's disease and colorectal carcinoma

It is hypothesized that the expression of Huntington's disease and the development of sporadic colorectal carcinomas may largely depend on age-related epigenetic defects in methylation pattern of DNA at the disease associated loci. In the former case the potential defects may be coupled with a DNA demethylation and activation in the brain of a silent growth factor-like gene that may induce an abnormal cell differentiation. In the development of colon carcinomas the age-related process may affect potential growth regulatory genes that may normally become demethylated and active in the colon as part of their differential expression. In such a state and possibly also due to their structure, they may be especially prone to the epigenetic defects that may lead in this case to gene point mutation and deletion.

Rapid induction of genomic demethylation and T-DNA gene expression in plant cells by 5-azacytosine derivatives

We have optimized conditions for demethylation of the genome and induction of a silent, hypermethylated T-DNA gene (ipt) by 5-azacytosine (5-azaCyt) derivatives in a suspension culture of tobacco cells. In this system, 5-azacytidine (5-azaC) is more effective in causing genomic demethylation and ipt gene induction than 5-azaCyt or 5-azadeoxycytidine (5-azadC). A single treatment with 2.5 μM 5-azaC resulted in a maximal level of ipt gene induction without inhibiting cell growth. However, we could not reduce the level of genomic methylation below approximately 2/3 of that found in untreated controls, even after extensive 5-azaC treatment. Furthermore, remethylation of the genome occurred after removal of 5-azaC. The use of 5-azaC as an inducer of silent plant genes is discussed, along with differences in the response of plant and animal genomes to demethylating agents.

Regulation of S-adenosyl methionine synthesis in the mouse embryo

In early embryos, methylation is involved in "gamete imprinting" and inactivation of artificially introduced foreign genes. We studied the biosynthesis of the universal methylation cofactor: S-Adenosyl methionine (SAM). In the mouse, SAM conversion from methionine is limited by saturation of the methionine endogenous pool. SAM is present at a practically unchanged level from the unfertilized oocyte to early morula. SAM synthesis is increased at the time of compaction. In blastocysts, although methionine uptake is increased, the conversion rate from methionine is lowered. We observed no differences between C57 Black and Swiss albino random bred strains. In few experiments with human unfertilized oocytes and spared embryos, we observed higher methionine incorporation, and higher conversion to SAM. Next, the effect of two methylation inhibitors was tested, on early mouse embryonic development, at the one-cell and the two-cell stage. We found that ethionine is very toxic, even at the lowest tested concentration of 25 microM. Homocysteine is more potent at the one-cell stage than at the 2-cell stage, and it only partially blocks blastocyst formation from the 2-cell stage even at a concentration of 500 microM. It clearly acts as a methylation inhibitor; it lowers the SAM pool and the methylation index, SAH/SAM ratio (SAH: S-Adenosyl Homocysteine). We also found that homocysteine is an unexpected competitor for methionine influx and efflux.

The inheritance of epigenetic defects

Evidence from many sources shows that the control of gene expression in higher organisms is related to the methylation of cytosine in DNA, and that the pattern of methylation is inherited. Loss of methylation, which can result from DNA damage, will lead to heritable abnormalities in gene expression, and these may be important in oncogenesis and aging. Transformed permanent lines often lose gene activity through de novo methylation. It is proposed that epigenetic defects in germline cells due to loss of methylation can be repaired by recombination at meiosis but that some are transmitted to offspring.