Cytosine methylation and the unequal developmental potentials of the oocyte and sperm genomes.
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Animals↗
Biomedical subjects
T H Bestor
Publications and source records attributed to T H Bestor.
A candidate mammalian DNA methyltransferase related to pmt1p of fission yeast.
Trace levels of 5-methylcytosine persist in the DNA of mouse embryonic stem cells that are homozygous for null mutations in Dnmt1 , the gene for the one previously recognized metazoan DNA methyltransferase. This residual 5-methylcytosine may be the product of a candidate second DNA methyltransferase, Dnmt2, that has now been identified in human and mouse. Dnmt2 contains all the sequence motifs diagnostic of DNA (cytosine-5)-methyltransferases but appears to lack the large N-terminal regulatory domain common to other eukaryotic methyltransferases. Dnmt2 is more similar to a putative DNA methyltransferase of the fission yeast Schizosaccharomyces pombe than to Dnmt1. Dnmt2 produces multiple mRNA species that are present at low levels in all tissues of human and mouse and is not restricted to those cell types known to be active in de novo methylation. The human DNMT2 gene was mapped to chromosome 10p12-10p14 in a panel of radiation hybrids. Dnmt2 is a candidate for the activity that methylates newly integrated retroviral DNA and maintains trace levels of 5-methylcytosine in the DNA of embryonic stem cells homozygous for null mutations in Dnmt1.
5-Methylcytosine↗
Sex-specific exons control DNA methyltransferase in mammalian germ cells.
The spermatozoon and oocyte genomes bear sex-specific methylation patterns that are established during gametogenesis and are required for the allele-specific expression of imprinted genes in somatic tissues. The mRNA for Dnmt1, the predominant maintenance and de novo DNA (cytosine-5)-methyl transferase in mammals, is present at high levels in postmitotic murine germ cells but undergoes alternative splicing of sex-specific 5' exons, which controls the production and localization of enzyme during specific stages of gametogenesis. An oocyte-specific 5' exon is associated with the production of very large amounts of active Dnmt1 protein, which is truncated at the N terminus and sequestered in the cytoplasm during the later stages of oocyte growth, while a spermatocyte-specific 5' exon interferes with translation and prevents production of Dnmt1 during the prolonged crossing-over stage of male meiosis. During the course of postnatal oogenesis, Dnmt1 is present at high levels in nuclei only in growing dictyate oocytes, a stage during which gynogenetic developmental potential is lost and biparental developmental potential is gained.
Alternative Splicing↗
DNA (cytosine-5)-methyltransferases in mouse cells and tissues. Studies with a mechanism-based probe.
The mechanisms that establish and maintain methylation patterns in the mammalian genome are very poorly understood, even though perturbations of methylation patterns lead to a loss of genomic imprinting, ectopic X chromosome inactivation, and death of mammalian embryos. A family of sequence-specific DNA methyltransferases has been proposed to be responsible for the wave of de novo methylation that occurs in the early embryo, although no such enzyme has been identified. A universal mechanism-based probe for DNA (cytosine-5)-methyltransferases was used to screen tissues and cell types known to be active in de novo methylation for new species of DNA methyltransferase. All identifiable de novo methyltransferase activity was found to reside in Dnmt1. As this enzyme is the predominant de novo methyltransferase at all developmental stages inspected, it does not fit the definition of maintenance methyltransferase or hemimethylase. Recent genetic data indicate that de novo methylation of retroviral DNA in embryonic stem cells is likely to involve one or more additional DNA methyltransferases. Such enzymes were not detected and are either present in very small amounts or are very different from Dnmt1. A new method was developed and used to determine the sequence specificity of intact Dnmt1 in whole-cell lysates. Specificity was found to be confined to the sequence 5'-CpG-3'; there was little dependence on sequence context or density of CpG dinucleotides. These data suggest that any sequence-specific de novo methylation mediated by Dnmt1 is either under the control of regulatory factors that interact with Dnmt1, or is cued by alternative secondary structures in DNA.
Amino Acid Sequence↗
Interference with DNA methyltransferase activity and genome methylation during F9 teratocarcinoma stem cell differentiation induced by polyamine depletion.
When ornithine decarboxylase, the initial and highly regulated enzyme in polyamine biosynthesis, is irreversibly inactivated by alpha-difluoromethylornithine, F9 teratocarcinoma stem cells are depleted of putrescine and spermidine and as a result differentiate into a cell type which phenotypically resembles the parietal endoderm cells of the early mouse embryo. Simultaneously the level of decarboxylated S-adenosylmethionine (dcAdoMet), the aminopropyl group donor in spermidine and spermine synthesis, increases dramatically, as the aminopropyl group acceptor molecules (putrescine and spermidine) become limiting. When this excessive accumulation of dcAdoMet is prevented by specific inhibition of the AdoMet decarboxylase activity, the differentiative effect is counteracted, despite the fact that the extent of polyamine depletion remains almost identical. Therefore, it may be concluded that dcAdoMet plays an important role in the induction of differentiation. Moreover, this key metabolite acts as a competitive inhibitor of DNA methyltransferase and is therefore capable of interfering with the maintenance methylation of newly replicated DNA. During the course of F9 cell differentiation, the highly methylated genome is gradually demethylated, and its pattern of gene expression is changed. Our present findings, that the DNA remains highly methylated and that the differentiative process is counteracted when the build-up of dcAdoMet is prevented, provide strong evidence for a causative relation between the level of dcAdoMet and the state of DNA methylation as well as cell differentiation.
Adenosylmethionine Decarboxylase↗
Cytosine methylation and the ecology of intragenomic parasites.
Most of the 5-methylcytosine in mammalian DNA resides in transposons, which are specialized intragenomic parasites that represent at least 35% of the genome. Transposon promoters are inactive when methylated and, over time, C-->T transition mutations at methylated sites destroy many transposons. Apart from that subset of genes subject to X inactivation and genomic imprinting, no cellular gene in a non-expressing tissue has been proven to be methylated in a pattern that prevents transcription. It has become increasingly difficult to hold that reversible promoter methylation is commonly involved in developmental gene control; instead, suppression of parasitic sequence elements appears to be the primary function of cytosine methylation, with crucial secondary roles in allele-specific gene expression as seen in X inactivation and genomic imprinting.
Animals↗
Formation of methylation patterns in the mammalian genome.
Cytosine methylation in mammals is an epigenetic modification required for viability of the developing embryo. It has been suggested that DNA methylation plays important roles in X-chromosome inactivation, imprinting, protection of the genome from invasive DNA sequences, and compartmentalization of the genome into active and condensed regions. Despite the significance of DNA methylation in mammalian cells, the mechanisms used to establish methylation patterns during development are not understood. This review will summarize the current state of knowledge about potential roles for cis- and trans-acting factors in the formation of methylation patterns in the mammalian genome.
Animals↗
Cytosine methylation targetted to pre-determined sequences.
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5-Methylcytosine↗
New 5' regions of the murine and human genes for DNA (cytosine-5)-methyltransferase.
DNA (cytosine-5)-methyltransferases (EC 2.1.1.37) maintain patterns of methylated cytosine residues in the mammalian genome; faithful maintenance of methylation patterns is required for normal development of mice, and aberrant methylation patterns are associated with certain human tumors and developmental abnormalities. The organization of coding sequences at the 5'-end of the murine and human DNA methyltransferase genes was investigated, and the DNA methyltransferase open reading frame was found to be longer than previously suspected. Expression of the complete open reading frame by in vitro transcription-translation and by transfection of expression constructs into COS7 cells resulted in the production of an active DNA methyltransferase of the same apparent mass as the endogenous protein, while translation from the second in-frame ATG codon produced a slightly smaller but fully active protein. Characterization of mRNA 5' sequences and the intron-exon structure of the 5' region of the murine and human genes indicated that a previously described promoter element (Rouleau, J., Tanigawa, G., and Szyf, M. (1992) J. Biol. Chem. 267, 7368-7377) actually lies in an intron that is more than 5 kilobases downstream of the transcription start sites.
Amino Acid Sequence↗
DNA methyltransferase in normal and Dnmtn/Dnmtn mouse embryos.
The mouse genome experiences a large decrease in net 5-methylcytosine between fertilization and implantation; de novo methylation brings 5-methylcytosine to adult somatic cell levels between implantation and gastrulation. Very little is known of the regulation of demethylation or de novo methylation. Levels of the one known form of DNA methyltransferase are very high in early embryos, but the enzyme is localized to the cytoplasm during most of preimplantation development. We show here that DNA methyltransferase is found exclusively in nuclei of the conceptus after implantation, and that nuclei of proximal decidual cells are free of detectable DNA methyltransferase. High levels of DNA methyltransferase were seen in all tissues, including the developing nervous system, of 9.5- to 12.5-day embryos. The large maternal stores of DNA methyltransferase become limiting prior to embryonic day 9.5, as shown by barely detectable immunostaining in 9.5-day embryos homozygous for a loss-of-function mutation (Dnmtn) in the DNA methyltransferase gene. These mutant embryos failed to develop past the 25-somite stage and showed evidence of developmental delay and some developmental asynchrony. Normal embryonic and extraembryonic tissues contained similar levels of DNA methyltransferase, even though severely reduced methylation levels and a loss of imprinting have previously been observed in extraembryonic tissues. These findings suggest that methylation patterns are not a simple function of the concentration of DNA methyltransferase, and that unidentified factors must be involved in the regulation of de novo methylation during early development of the mouse.
5-Methylcytosine↗
Base eversion and shuffling by DNA methyltransferases.
The structures of two DNA cytosine methyltransferases reveal two novel methods of gaining access to the substrate cytosine residue, both of which involve eversion of the cytosine in a process that may require DNA bending. In one instance there is also widespread base shuffling and distortion of the DNA.
DNA Modification Methylases↗
Creation of genomic methylation patterns.
There are two biological properties of genomic methylation patterns that can be regarded as established. First, methylation of 5'-CpG-3' dinucleotides within promoters represses transcription, often to undetectable levels. Second, in most cases methylation patterns are subject to clonal inheritance. These properties suit methylation patterns for a number of biological roles, although none of the current hypotheses can be regarded as proved or disproved. One hypothesis suggests that the activity of parasitic sequence elements is repressed by selective methylation. Features of invasive sequences that might allow their identification and inactivation are discussed in terms of the genome defense hypothesis. Identification of the cues that direct de novo methylation may reveal the biological role (or roles) of genomic methylation patterns.
Alleles↗
Genetic analysis of genomic methylation patterns in plants and mammals.
While it is now accepted that methylation of cytosine residues plays a role in various epigenetic phenomena in mammals and flowering plants, the involvement of methylation patterns in the regulation of normal development has remained a controversial and essentially untested issue in the 20 years since such a role was first proposed. Antisense suppression of a DNA methyltransferase in Arabidopsis and characterization of methylation-defective mutants of Arabidopsis have shown that perturbations of methylation patterns disrupt the development of plants, and targeted mutation of the murine gene that encodes the one known from of DNA methyltransferase has shown that methylation is required for cellular differentiation, genomic imprinting, and X chromosome inactivation in mammals. Ectopic expression of homeotic genes and homeotic transformations of floral organs in methylation-defective plants suggest that (in plants and perhaps mammals) heritable methylation patterns reinforce and may have supplanted heritable gene control mediated by chromosomal proteins of the Polycomb and trithorax groups. It is also possible that the developmental abnormalities are the result of ectopic gene expression caused by activation of transcription from nearby parasitic sequence elements that are normally repressed by methylation. Application of modern methods of genetic analysis promises to give definite answers to long-standing questions as to the roles and significance of genomic methylation patterns in normal development and genome defense.
Animals↗
Proteins that glow in green and blue.
An intrinsically fluorescent protein from a Pacific jellyfish promises to become an important power tool in experimental biology. Mutant forms of this green fluorescent protein with altered spectral characteristics have recently been constructed. It is now possible to envision a range of derivatives optimized for specific applications.
Aequorin↗
Regulated synthesis and localization of DNA methyltransferase during spermatogenesis.
Differences in the methylation patterns of male and female gamete DNA are likely to be involved in genomic imprinting. However, little is known of the mechanisms that regulate de novo methylation and demethylation during gametogenesis. We report here that the well-characterized M(r) 190,000 form of DNA methyltransferase (the only known form) is present in isolated mitotic, meiotic, and postmeiotic male germ cells, with the exception of meiotic pachytene spermatocytes, where the protein is undetectable by immunoblot analysis and a novel 6.2-kb DNA methyltransferase transcript is present. Whereas replication and methylation are coupled in somatic cells, the presence of DNA methyltransferase in postreplicative male germ cells is consistent with previously observed de novo methylation events in these cells. Immunofluorescence experiments revealed that DNA methyltransferase is localized to the nuclei of male germ cells, with a subset of spermatogonia and postreplicative leptotene/zygotene spermatocytes displaying prominent nuclear foci that are strongly enriched in DNA methyltransferase. The data suggest that down-regulation of DNA methyltransferase expression during the pachytene stage of meiosis utilizes an mechanism that is associated with the production of a larger mRNA, and that de novo methylation in leptotene/zygotene spermatocytes may take place in spatially restricted nuclear domains that are enriched in DNA methyltransferase.
Animals↗
Epigenetic effects in eukaryotic gene expression.
In the broadest terms, epigenetic phenomena in eukaryotes depend on the interaction of alleles or repeated sequences or on the mitotic inheritance of chromatin states or methylation patterns. One of the most exciting aspects of the study of epigenetic phenomena is the insight that can be gained into the structure and assembly of higher-order chromatin structures, an important subject that has proved refractory to current biochemical methodologies. Rapid progress in the study of gene inactivation in fungi, plants, and invertebrates will provide new hypotheses to be tested in mammals.
Animals↗
DNA methyltransferases.
Mammals have long been known to tag their DNA by the addition of methyl groups to cytosine residues. Only quite recently, however, has the functional significance of DNA methylation established a firm footing. Evidence now indicates that DNA methylation is essential for development, and is involved in both programmed and ectopic gene inactivation. Recent structural and mechanistic work on bacterial cytosine-5-methyltransferases has provided much insight into the function of the carboxy-terminal catalytic domain of eukaryotic cytosine-5-methyltransferases; evidence is emerging that the amino-terminal domain targets the enzyme to the replication machinery and may be involved in sensing the pre-existing methylation state of the DNA.
Amino Acid Sequence↗
Expression of DNA methyltransferase gene in mature and immature neurons as well as proliferating cells in mice.
A major role of DNA-methyltransferase (MTase) is thought to be maintaining the DNA methylation profile through DNA replication. However, previous surveys of mRNA distribution in different tissues by Northern-blot analysis have shown unexpectedly high levels of expression of DNA-MTase mRNA in adult mouse brain, which consists mostly of slowly proliferating glial and nonproliferating neuronal cells. In order to identify cells expressing the gene in the brain, we performed an in situ hybridization analysis of mature brain as well as whole embryos of different ages. In addition to various embryonic tissues with active cell proliferation such as the ventricular neurogenic layer, hair follicle epithelia, thymus and epithelia of the base of intestinal villi, almost all mature neurons in brain of adult and even aged mice expressed DNA-MTase mRNA at substantial levels. No significant expression of the gene was detected in the white matter. These findings suggest some neuron-specific biological function of DNA methylation, unrelated to DNA replication.
Animals↗