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Erasure of methylation imprinting of Igf2r during mouse primordial germ-cell development.

During germ cell differentiation in mice, the genome undergoes specific epigenetic modifications. These include demethylation of imprinted genes and subsequent establishment of parental allele-specific methylation. The mouse Igf2r gene is an imprinted gene that shows maternal-specific expression. Maternal-specific methylation of differentially methylated region 2 (DMR2) of this gene may be necessary for its maternal-specific expression. Before the allele-specific methylation is established, DMR2 is demethylated in both male and female primordial germ cells (PGCs) by 13.5 days post coitum (dpc), indicating that the demethylation of this region occurs earlier in PGC development. The timing of the demethylation has been, however, unknown. In this study, we attempted to determine the timing of methylation erasure of Igf2r DMR2 in developing PGCs, using transgenic mice expressing green fluorescent protein specifically in the germ line. We purified migrating PGCs from the transgenic mice and examined the methylation status of DMR2. The results show that some CpG sites within DMR2 start demethylation at 9.5 dpc in some migrating PGCs, before the cells colonize genital ridges, and the progression of demethylation is rapid after colonization of the genital ridges. To examine whether the gonadal environment is involved in demethylation, we analyzed the methylation of DMR2 after culturing migrating PGCs in the absence of a gonadal environment. These culture experiments support the idea that a gonadal environment is not required for demethylation of the region in at least a fraction of PGCs.

Animals↗

Spatially restricted imprinting of mouse chromosome 7.

Three of the four known imprinted genes (Igf-2, H19, and Snrpn) map to mouse chromosome 7. We used mRNA phenotyping to examine the tissue-specific transcription of Igf-1r, H-ras-1, and Gabrb3, which map to chromosome 7 between Snrpn and the Igf-2/H19 domain, and Myod-1, which maps proximal to Snrpn. We found that all of these genes were expressed by both parental alleles in tissues from day 1 neonates. The fact that imprinted genes can flank or map closely to genes that escape such epigenetic modification suggests that autosomal imprinting is not manifested globally along imprinted chromosomes but rather is spatially restricted, perhaps even defined by specific DNA consensus sequences or an "imprint box" associated with imprintable genes.

Alleles↗

Regulation of histone acetylation during meiotic maturation in mouse oocytes.

Histone acetylation is an important epigenetic modification implicated in the regulation of chromatin structure and, subsequently, gene expression. Global histone deacetylation was reported in mouse oocytes during meiosis but not mitosis. The regulation of this meiosis-specific deacetylation has not been elucidated. Here, we demonstrate that p34(cdc2) kinase activity and protein synthesis are responsible for the activation of histone deacetylases and the inhibition of histone acetyltransferases (HATs), respectively, resulting in deacetylation of histone H4 at lysine-12 (H4K12) during mouse oocyte meiosis. Temporal changes in the acetylation state of H4K12 were examined immunocytochemically during meiotic maturation using an antibody specific for acetylated H4K12. H4K12 was deacetylated during the first meiosis, temporarily acetylated around the time of the first polar body (PB1) extrusion, and then deacetylated again during the second meiosis. Because these changes coincided with the known oscillation pattern of p34(cdc2) kinase activity, we investigated the involvement of the kinase in H4K12 deacetylation. Roscovitine, an inhibitor of cyclin-dependent kinase activity, prevented H4K12 deacetylation during both the first and second meiosis, suggesting that p34(cdc2) kinase activity is required for deacetylation during meiosis. In addition, cycloheximide, a protein synthesis inhibitor, also prevented deacetylation. After PB1 extrusion, at which time H4K12 had been deacetylated, H4K12 was re-acetylated in the condensed chromosomes by treatment with cycloheximide but not with roscovitine. These results demonstrate that HATs are present but inactivated by newly synthesized protein(s) that is (are) not involved in p34(cdc2) kinase activity. Our results suggest that p34(cdc2) kinase activity induces the deacetylation of H4K12 and that the deacetylated state is maintained by newly synthesized protein(s) that inhibits HAT activity during meiosis.

Acetylation↗

Pronuclear stage porcine embryos do not possess a strict asymmetric distribution of lysine 9 dimethylation of histone H3 based solely on parental origin.

Epigenetic modification of core histone proteins plays an important role in gene transcription and chromatin structure. It is known that the methylation status of the lysine 9 residue of histone H3 (H3K9) is closely linked with repression of transcription and heterochromatin formation. It has been reported that a strict asymmetric distribution of the dimethylated form of H3K9 exists between the two parental genomes in murine embryos. The aim of this study was to characterize the H3K9 dimethylation pattern in cleavage stage porcine embryos. Indirect immunocytochemical analysis showed that this modification is present throughout the nuclei of pronuclear, 2-cell, 4-cell and blastocyst stage porcine embryos. However, at the pronuclear stage the pronuclei within in vitro-fertilized porcine embryos possessed an asymmetric distribution of the dimethylated form of H3K9; this distribution was not based solely on the parent-of-origin. These results show that dimethylation of H3K9 is differentially regulated in pronuclear stage porcine embryos.

Androgens↗

Sex-specific windows for high mRNA expression of DNA methyltransferases 1 and 3A and methyl-CpG-binding domain proteins 2 and 4 in human fetal gonads.

DNA methyltransferases (DNMTs) and 5-methyl-CpG-binding domain proteins (MBDs) are involved in the acquisition of parent-specific epigenetic modifications in human male and female germ cells. Reverse Northern blot analyses demonstrated sex-specific differences in mRNA expression for the maintenance DNMT1 and the de novo DNMT3A in developing testis and ovary. In fetal testis DNMT1 and DNMT3A expression peaked in mitotically arrested spermatogonia around 21 weeks gestation. In fetal ovary transcriptional upregulation of DNMT1 and DNMT3A occurred during a very brief period at 16 weeks gestation, when the oocytes proceeded through meiotic prophase. Fetal gonads showed several fold higher DNMT3A expression levels than fetal brain and adult tissues. The most abundant DNMT3A isoform in fetal testis and ovary was DNMT3A2, whereas in all other analyzed tissues DNMT3A1 predominated. The catalytically inactive DNMT3A3 isoform was also present at relatively high levels in developing gonads and may perform a regulatory function(s). In both male and female fetal gonads expression of genes for MBD2 and MBD4, which may be implicated in chromatin remodeling of methylated genomic DNA sequences, was tightly linked to DNMT expression. We propose that the sex-specific time windows for concomitant upregulation of DNMT1, DNMT3A, MBD2, and MBD4 are associated with prenatal remethylation of the human male and female germ line.

DNA (Cytosine-5-)-Methyltransferase 1↗

MeCP2 and other methyl-CpG binding proteins.

DNA methylation is an epigenetic modification that is implicated in transcriptional silencing. Recently, it has become increasingly clear that both correct levels and proper interpretation of methylation are important factors for normal development and function of the human organism. One example is the neurological disorder Rett syndrome (RTT), which affects approximately one in 10,000 girls. RTT is caused by mutations in MeCP2, a protein that was identified by its ability to bind specifically to CpG-methylated DNA. Furthermore, MeCP2 represses transcription in a methylation-dependent manner, and it is the founding member of the family of methyl-CpG binding domain (MBD) proteins.

Animals↗

MGMT promoter methylation correlates with survival benefit and sensitivity to temozolomide in pediatric glioblastoma.

BACKGROUND: Methylation of the DNA-repair gene O6-methylguanine-DNA methyltransferase (MGMT) causes gene silencing. This epigenetic modification has been associated with a favorable prognosis in adult patients with glioblastoma (GBM) who receive temozolomide and other alkylating agents. We explored MGMT promoter methylation in pediatric GBM and its relationship to survival and temozolomide sensitivity. PROCEDURE: We performed a retrospective study of MGMT promoter methylation in 10 pediatric GBM. The methylation status of the MGMT was determined using a 2-stage methylation specific PCR analysis on DNA extracted from tumor specimens which had been snap frozen at surgery. The relationships between MGMT promoter methylation and patient outcome and response to temozolomide were evaluated. RESULTS: Four of our 10 pediatric patients with GBM were found to have methylation of the MGMT gene promoter. Methylation of the MGMT promoter was shown to correlate (P = 0.0005) with survival. The average survival time for patients with methyltated MGMT was 13.7 months as compared to 2.5 months for the 6 patients with unmethylated MGMT promoter. Of the seven patients that received temozolomide, those patients that had the methylated MGMT gene promoter responded better to treatment (P = 0.007). CONCLUSIONS: As in adults, pediatric GBM patients with methylated MGMT promoter benefited from temozolomide. However, a stronger correlation with overall survival, regardless of treatment, was observed in this group of patients. These data suggest that MGMT methylation may be a prognostic factor for survival in pediatric GBM, as well as a marker for temozolomide sensitivity.

Antineoplastic Agents, Alkylating↗

Sonographic findings in Beckwith-Wiedemann syndrome related to H19 hypermethylation.

Beckwith-Wiedemann syndrome (BWS) is an overgrowth syndrome associated with congenital malformations and tumour predisposition. BWS results from variable mutations or epigenetic modifications of imprinted genes in the 11p15 chromosomal region. We present a fetus with mild general overgrowth and bilateral enlarged echogenic kidneys with loss of the corticomedullary differentiation in which prenatal diagnosis of BWS was suspected. The rest of the fetal anatomy and the amniotic fluid volume appeared normal. After termination of the pregnancy, molecular analysis confirmed the diagnosis of BWS by showing an isolated hypermethylation of the H19 gene.

Adult↗

Screening hypermethylated regions by methylation-sensitive single-strand conformational polymorphism.

DNA methylation is an important epigenetic modification that alters transcription in those genes containing CpG islands. In this report we demonstrate that the familiar technique single-strand conformation polymorphism (SSCP) can be easily applied to bisulfite-treated DNA to detect methylation differences over large ( approximately 250 bp) CG-enriched regions. In the methylation-sensitive SSCP (Ms-SSCP) technique, sodium bisulfite modification of DNA converts unmethylated cytosine to uracil under conditions in which 5-methylcytosine remains unaltered. Amplification of these regions to be tested is then performed using primers specific for bisulfite-treated DNA. The resulting products are then subjected to nondenaturing gel analysis. Based on differential band mobility, Ms-SSCP is able to sensitively detect alterations in methylation density and determine if unmethylated alleles are present in a sample. Ms-SSCP is a rapid and simple technique for screening multiple samples for methylation changes. It has several advantages over existing techniques, including the utilization of nanogram amounts of DNA, the avoidance of difficulties in sequencing CG-enriched regions, and the screening of multiple sites for methylation across large regions of DNA.

DNA↗

Differentiation of trophoblast lineage is associated with DNA methylation and demethylation.

Our previous study has shown that the placenta and kidney had different genomic methylation patterns regarding CpG island loci detected by restriction landmark genomic scanning (RLGS). To investigate whether differentiation involves changes in DNA methylation, we analyzed the rat Rcho-1 cell line, which retains trophoblast cell features and differentiates from stem cells into trophoblast giant cells in vitro. By RLGS, a total of 1,232 spots were identified in the Rcho-1 stem and differentiated giant cells. Four spots (0.3%) were detected only in giant cells, implying that the loci were originally methylated, but became demethylated during differentiation. Another four spots (0.3%) were detected only in stem cells, implying that these loci, originally unmethylated, became methylated during differentiation. DNAs from three loci that became methylated during differentiation were cloned and sequenced. All showed high homologies with expressed sequence tags (ESTs) or with genomic DNA of other species, suggesting that these loci are biologically important. Thus, the eight differentially methylated loci should be good tools to study epigenetic modification specific to differentiation of trophoblast giant cells.

Animals↗

Mouse parthenogenetic embryos with monoallelic H19 expression can develop to day 17.5 of gestation.

In mammals, both maternal and paternal genomes are required for a fetus to develop normally to term. This requirement is due to the epigenetic modification of genomes during gametogenesis, which leads to an unequivalent expression of imprinted genes between parental alleles. Parthenogenetic mouse embryos that contain genomes from nongrowing (ng) and fully grown (fg) oocytes can develop into 13.5-day-old fetuses, in which paternally and maternally expressed imprinted genes are expressed and repressed, respectively, from the ng oocyte allele. The H19 gene, however, is biallelically expressed with the silent status Igf2 in such parthenotes. In this study, we examined whether the regulation of H19 monoallelic expression enhances the survival of parthenogenetic embryos. The results clearly show that the ng(H19-KO)/fg(wt) parthenogenetic embryos carrying the ng-oocyte genome that had been deleted by the H19 transcription unit successfully developed as live fetuses for 17.5 gestation days. Control experiments revealed that this unique phenomenon occurs irrespective of the genetic background effect. Quantitative gene expression analysis showed that day 12.5 ng(H19-KO)/fg(wt) parthenogenetic fetuses expressed Igf2 and H19 genes at <2 and 82% of the levels in the controls. Histological analysis demonstrated that the placenta of ng(H19-KO)/fg(wt) parthenotes was afflicted with atrophia with severe necrosis and other anomalies. The present results suggest that the cessation of H19 gene expression from the ng-allele causes extended development of the fetus and that functional defects in the placenta could be fatal for the ontogeny.

Alleles↗

Maternal-specific methylation of the human IGF2R gene is not accompanied by allele-specific transcription.

The human insulin-like growth factor type 2 receptor gene (IGF2R) is biallelically expressed in a variety of fetal and adult tissues. In contrast, the imprinted mouse Igf2r gene is expressed exclusively from the maternally inherited chromosome. The mouse gene contains two CpG islands that are methylated in a parent-specific manner. Methylation of the CpG island in the promoter region occurs on the repressed paternal gene copy. Methylation of the CpG island in intron 2 is specific for the active maternal allele and may represent the primary imprint. Here, we have analyzed the human IGF2R gene to investigate whether these motifs and their parent-of-origin-specific epigenetic modification have been conserved. As in the mouse, the human IGF2R gene was found to contain two CpG islands, one encompassing the transcription start site (CpG 1) and the other in the second intron (CpG 2). CpG 2 is hypermethylated on the maternal IGF2R allele. In contrast to the situation in the mouse, however, the human CpG 1 is completely unmethylated on both parental chromosomes. The human and mouse intronic CpG islands lack significant sequence homology, which suggests that DNA conformation plays a role in allele-specific methylation.

Alleles↗

Strain-dependent developmental relaxation of imprinting of an endogenous mouse gene, Kvlqt1.

Genomic imprinting is an epigenetic modification of the gamete or zygote leading to parental origin-specific differential expression of the two alleles of a gene in somatic cells of the offspring. We previously reported that the human KVLQT1 gene is imprinted and disrupted in patients with germline balanced chromosomal rearrangements and Beckwith-Wiedemann syndrome. In human, the gene is imprinted in most fetal tissues except the heart, and KVLQT1 is part of a 1-Mb cluster of imprinted genes on human chromosome 11p15. 5. We sought to determine whether the mouse Kvlqt1 gene is imprinted, by performing interspecific crosses of 129/SvEv mice with CAST/Ei (Mus musculus castaneus). We identified a transcribed polymorphism that distinguishes the two parental alleles in F1 offspring. Examination of embryonic, neonatal, and postnatal tissues revealed that Kvlqt1 is imprinted in mouse early embryos, in both female 129 x male CS and female CS x male 129 offspring, with preferential expression of the maternal allele, like the human homologue. Surprisingly, imprinting was developmentally relaxed, and the developmental stage and tissue specificity of relaxation of imprinting was strain-dependent. To our knowledge, this is the first example of an endogenous gene that shows strain-dependent developmental relaxation of imprinting.

Alleles↗

Bisulfite genomic sequencing-derived methylation profile of the xist gene throughout early mouse development.

Differential epigenetic modification by methylation of CpG dinucleotides is a candidate mechanism that may identify the alleles of imprinted genes and result in monoallelic expression of either the maternal or the paternal allele. Determination of the allelic methylation status of imprinted genes in the gametes and during early development is constrained by the limiting quantities of genomic DNA available from these early developmental stages. To circumvent this problem we have used bisulfite genomic sequencing to determine the allelic methylation status of the minimal promoter and a 1-kb region within the Xist gene during preimplantation development. We find that the parental Xist alleles are not differentially methylated in these regions. Our findings are discussed in the context of previous conflicting data obtained using methylation-sensitive restriction enzyme digestion followed by PCR amplification to assay for methylation.

Animals↗

Expression and imprinting of insulin-like growth factor II (IGF2) and H19 genes in uterine leiomyomas.

Genomic imprinting is defined as a gamete of origin-specific epigenetic modification of DNA leading to differential gene expression in the zygote. Several imprinted genes have been identified and some of them are associated with tumor development. We investigated the expression and the imprinting status of IGF2 and H19 genes in 47 uterine leiomyomas. Using allelic transcription assay, we detected the expression of the IGF2 gene in 10 of a total of 15 informative cases. No loss of imprinting, as determined by the finding of biallelic expression, was detected in any case. The expression of H19 gene was detected in 10 of 20 informative cases and the imprinting pattern was also maintained in all of them. Our data suggest that alterations in IGF2 and H19 genes expression by loss of imprinting do not occur in uterine leiomyomas.

Adult↗

Optimization of baculovirus-mediated expression and purification of hexahistidine-tagged murine DNA (cytosine-C5)-methyltransferase-1 in Spodoptera frugiperda 9 cells.

Enzymatic DNA methylation of carbon 5 of cytosines is an epigenetic modification that plays a role in regulating gene expression, differentiation, and tumorigenesis. DNA (cytosine-C5)-methyltransferase-1 is the enzyme responsible for maintaining established methylation patterns during replication in mammalian cells. It is composed of a large ( approximately 1100 amino acids (a.a.)) amino-terminal region containing many putative regulatory domains and a smaller ( approximately 500 a.a.) carboxy-terminal region containing conserved, catalytic domains. In this study, murine DNA (cytosine C5)-methyltransferase-1, fused to an amino-terminal hexahistidine tag, was expressed by infecting Spodoptera frugiperda cells for 46 h with a recombinant baculovirus carrying the DNA (cytosine-C5)-methyltransferase-1 cDNA. A total of 3 x 10(8) infected S. frugiperda cells yielded approximately 1 mg of full-length, hexahistidine-tagged DNA (cytosine-C5)-methyltransferase-1, which was purified approximately 450-fold from RNase-treated S. frugiperda cell extracts by nickel affinity chromatography. The characterization of hexahistidine-tagged DNA (cytosine-C5)-methyltransferase-1 through DNA methylation and inhibitor-binding assays indicated that the purified enzyme had at least a 30-fold higher catalytic efficiency with hemimethylated double-stranded oligodeoxyribonucleotide substrates than unmethylated substrates and was most active with small oligodeoxyribonucleotide substrates with a capacity for forming stem-loop structures. The expression and purification procedures reported here differ significantly from the original reports of baculovirus-mediated hexahistidine-tagged DNA (cytosine-C5)-methyltransferase-1 expression and purification by nickel affinity chromatography and provide a consistent yield of active enzyme.

Animals↗

Origin and roles of genomic methylation patterns in male germ cells.

The epigenetic modification of DNA by methylation at cytosine residues is initiated in the germ line and is required for normal embryonic development in mammals. Marked differences in genomic methylation between male and female gametes arise during gametogenesis and have been implicated in genomic imprinting. While DNA methylation patterns for different types of gene sequences are known to change during spermatogenesis, the precise role(s) of DNA methylation in the normal development of male germ cells is poorly understood. The expression of the one known active form of DNA methyltransferase is highly regulated during spermatogenesis and may provide insight into mechanisms underlying the establishment of methylation patterns in germ cells.

Animals↗

Genome-wide analysis of DNA methylation changes in human malignancies.

DNA methylation is an epigenetic modification of the DNA sequence and thus does not change the genetic code but affects chromosomal stability and gene expression. DNA methylation patterns are heritable and can be passed on to the daughter cell. In this review, we briefly summarize our current knowledge on normal DNA methylation patterns and move on to discuss the current state of the field with respect to altered DNA methylation in cancer. We make a special attempt to address current questions relating to genome-wide DNA methylation patterns. Since DNA methylation is used as a therapeutic target in clinical studies, it is of utmost importance to define potential target sequences that could be used as diagnostic or prognostic markers. We conclude the review by outlining possible scenarios that may explain tumor type-specific DNA methylation patterns described by assays evaluating genome-wide levels of DNA methylation.

CpG Islands↗