Piroska E Szabó

Piroska E Szabó
Van Andel Research Institute · Center for Epigenetics

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115
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Publications

Publications (115)
Article
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To understand what dictates the emerging patterns of de novo DNA methylation in the male germline, we mapped DNA methylation, chromatin, and transcription changes in purified fetal mouse germ cells by using methylated CpG island recovery assay (MIRA)-chip, chromatin immunoprecipitation (ChIP)-chip, and strand-specific RNA deep sequencing, respectiv...
Article
Full-text available
Genome-wide erasure of DNA cytosine-5 methylation has been reported to occur along the paternal pronucleus in fertilized oocytes in an apparently replication-independent manner, but the mechanism of this reprogramming process has remained enigmatic. Recently, considerable amounts of 5-hydroxymethylcytosine (5hmC), most likely derived from enzymatic...
Article
Full-text available
Genomic imprints-parental allele-specific DNA methylation marks at the differentially methylated regions (DMRs) of imprinted genes-are erased and reestablished in germ cells according to the individual's sex. Imprint establishment at paternally methylated germ line DMRs occurs in fetal male germ cells. In prospermatogonia, the two unmethylated alle...
Article
Parent-of-origin-specific expression of the mouse insulin-like growth factor 2 (Igf2) gene and the closely linked H19 gene are regulated by an intervening 2 kb imprinting control region (ICR), which displays parentspecific differential DNA methylation [1] [2]. Four 21 bp repeats are embedded within the ICR and are conserved in the putative ICR of h...
Article
Oxidative DNA damage has been linked to inflammation, cancer, and aging. Here, we have mapped two types of oxidative DNA damage, oxidized guanines produced by hydrogen peroxide and oxidized thymines created by potassium permanganate, at a single-base resolution. 8-Oxo-guanine occurs strictly dependent on the G/C sequence context and shows a pronoun...
Preprint
We have developed a mouse Infinium DNA methylation array that contains 297,415 probes to capture the diversity of mouse DNA methylation biology. We present a mouse DNA methylation atlas as a rich reference resource of 1,239 DNA samples encompassing distinct tissues, strains, age, sex, and pathologies. We describe applications for comparative epigen...
Article
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EHMT2 is the main euchromatic H3K9 methyltransferase. Embryos with zygotic, or maternal mutation in the Ehmt2 gene exhibit variable developmental delay. To understand how EHMT2 prevents variable developmental delay we performed RNA sequencing of mutant and somite stage-matched normal embryos at 8.5–9.5 days of gestation. Using four-way comparisons...
Article
Aim: Paternal allele-specific expression of noncanonical imprinted genes in the extraembryonic lineages depends on an H3K27me3-based imprint in the oocyte, which is not a lasting mark. We hypothesized that EHMT2, the main euchromatic H3K9 dimethyltransferase, also has a role in controlling noncanonical imprinting. Methods: We carried out allele-spe...
Preprint
Full-text available
Unlike regular imprinted genes, non-canonical imprinted genes are known to not depend on gamete-specific DNA methylation difference. Instead, the paternal allele-specific expression of these genes in the extra-embryonic lineages depends on an H3K27me3-based imprint in the oocyte, but this marking is not maintained beyond pre-implantation developmen...
Preprint
Full-text available
Embryos that carry zygotic or parental mutations in Ehmt2, the gene encoding the main euchromatic histone H3K9 methyltransferase, EHMT2, exhibit variable developmental delay. We asked the question whether the delayed embryo is different transcriptionally from the normally developing embryo when they reach the same developmental stage. We collected...
Article
Full-text available
Beckwith-Wiedemann syndrome (BWS) and Silver-Russell syndrome (SRS) are imprinting disorders manifesting as aberrant fetal growth and severe postnatal-growth-related complications. Based on the insulator model, one-third of BWS cases and two-thirds of SRS cases are consistent with misexpression of insulin-like growth factor 2 (IGF2), an important f...
Chapter
DNA methylation undergoes dynamic changes at the genome-wide scale during the early steps of mammalian embryo development. Immunochemical detection of 5-methylcytosine (5mC) in the zygote has led to the discovery that a global loss of DNA methylation takes place soon after fertilization, occurring rapidly in the paternal pronucleus. Using the same...
Chapter
DNA cytosine modification is an important epigenetic mechanism that serves critical functions in a variety of biological processes in development and disease. 5-Methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are the two most common epigenetic marks found in the mammalian genome. 5hmC is generated from 5mC by the ten-eleven translocation (T...
Article
Full-text available
A battery of chromatin modifying enzymes play essential roles in remodeling the epigenome in the zygote and cleavage stage embryos, when the maternal genome is the sole contributor. Here we identify an exemption. DOT1L methylates lysine 79 in the globular domain of histone H3 (H3K79). Dot1l is an essential gene, as homozygous null mutant mouse embr...
Article
5-Methylcytosine (5mC), the major modified DNA base in mammalian cells, can be oxidized enzymatically to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) by the Ten-Eleven-Translocation (TET) family of proteins. Whereas 5fC and 5caC are recognized and removed by base excision repair proteins, the 5hmC base accum...
Article
Full-text available
Genome-wide DNA “demethylation” in the zygote involves global TET3-mediated oxidation of 5‐methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) in the paternal pronucleus. Asymmetrically enriched histone H3K9 methylation in the maternal pronucleus was suggested to protect the underlying DNA f...
Article
Full-text available
Impaired neuronal processes, including dopamine imbalance, are central to the pathogenesis of major psychosis, but the molecular origins are unclear. Here we perform a multi-omics study of neurons isolated from the prefrontal cortex in schizophrenia and bipolar disorder (n = 55 cases and 27 controls). DNA methylation, transcriptomic, and genetic-ep...
Article
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The DNA base 5-hydroxymethylcytosine (5hmC) strongly accumulates along transcribed sequences (gene bodies) of tissue-specific genes. We discuss the potential origin and function of 5hmC in gene bodies and describe how genomic 5hmC patterns may be useful in cancer diagnosis.
Preprint
Full-text available
Dopamine dysregulation is central to the pathogenesis of diseases with major psychosis, but its molecular origins are unclear. In an epigenome-wide investigation in neurons, individuals with schizophrenia and bipolar disorder showed reduced DNA modifications at an enhancer in IGF2 , which disrupted the regulation of the dopamine synthesis enzyme ty...
Article
Full-text available
In a recent paper, we described our efforts in search for evidence supporting epigenetic transgenerational inheritance caused by endocrine disrupter chemicals. One aspect of our study was to compare genome-wide DNA methylation changes in the vinclozolin-exposed fetal male germ cells (n = 3) to control samples (n = 3), their counterparts in the next...
Article
Full-text available
Abhay Sharma brings two arguments in favor of transgenerational epigenetic inheritance (TGEI) in mammals when criticizing our work. He uses probability calculations and finds that the probability of obtaining the number of common changes in the in utero-exposed prospermatogonia and the same cells in the next generation is significant in our study....
Article
Full-text available
We report that the mammalian 5-methylcytosine (5mC) oxidase Tet3 exists as three major isoforms and characterized the full-length isoform containing an N-terminal CXXC domain (Tet3FL). This CXXC domain binds to unmethylated CpGs, but, unexpectedly, its highest affinity is toward 5-carboxylcytosine (5caC). We determined the crystal structure of the...
Article
Full-text available
Exposure to environmental endocrine-disrupting chemicals during pregnancy reportedly causes transgenerationally inherited reproductive defects. We hypothesized that to affect the grandchild, endocrine-disrupting chemicals must alter the epigenome of the germ cells of the in utero-exposed G1 male fetus. Additionally, to affect the great-grandchild,...
Article
Full-text available
We thank Dr. Nadeau for his interest in our work. Dr. Nadeau has raised concerns about the experimental approach (mouse strains, route of administration, lack of phenotypic assessment) and about the validity of our conclusions. We will respond to each of these concerns point-by point. Please see related article: www.dx.doi.org/10.1186/s13059-015-07...
Article
Full-text available
Background Exposure to environmental endocrine-disrupting chemicals during pregnancy reportedly causes transgenerationally inherited reproductive defects. We hypothesized that to affect the grandchild, endocrine-disrupting chemicals must alter the epigenome of the germ cells of the in utero-exposed G1 male fetus. Additionally, to affect the great-g...
Article
Full-text available
The DNA base 5-hydroxymethylcytosine (5hmC) is produced by enzymatic oxidation of 5-methylcytosine (5mC) by 5mC oxidases (the Tet proteins). Since 5hmC is recognized poorly by DNA methyltransferases, DNA methylation may be lost at 5hmC sites during DNA replication. In addition, 5hmC can be oxidized further by Tet proteins and converted to 5-formylc...
Article
Full-text available
Mouse embryo fibroblasts (MEFs) are convenient sources for biochemical studies when cell number in mouse embryos is limiting. To derive the imprinting signature of MEFs and potentially detect novel imprinted genes we performed strand- and allele-specific RNA deep sequencing. We used sequenom allelotyping in embryo and adult organs to verify parenta...
Article
Full-text available
The POU5F1 transcription factor is the gatekeeper of the pluripotent state in mammals. It is essential for epigenetic reprogramming events and also for germ cell viability. Pou5f1 gene expression is tightly controlled during embryogenesis, but its regulatory regions are not fully deciphered. The GOF18ΔPE-EGFP transgene, harboring the enhanced green...
Article
Full-text available
CTCF (CCCTC-binding factor)-mediated insulation at the H19-Insulin-like growth factor 2 (Igf2) imprinted domain is a classic example for imprinted gene regulation. DNA methylation difference in the imprinting control region (ICR) is inherited from the gametes and subsequently determines parental allele-specific enhancer blocking and imprinted expre...
Article
Full-text available
Imprinted genes are marked by parental allele specific DNA methylation and histone modifications which regulate their monoallelic expression. Chromatin immunoprecipitation (ChIP) is the technique of choice to characterize the histones associated with either maternal or paternal chromosomes. To study allele-specific chromatin composition at imprinte...
Article
Full-text available
Epigenetic reprogramming of the parental genome occurs in fertilized oocytes and involves oxidation of 5-methylcytosines (5-mC) to 5-hydroxymethylcytosines (5-hmC) in the paternal pronucleus. Recent work has shown that the maternal genome is protected from this remodeling step by an interaction between a modified histone, H3K9me2, and the oocyte-de...
Article
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Sperm and eggs carry distinctive epigenetic modifications that are adjusted by reprogramming after fertilization. The paternal genome in a zygote undergoes active DNA demethylation before the first mitosis. The biological significance and mechanisms of this paternal epigenome remodelling have remained unclear. Here we report that, within mouse zygo...
Data
Full-text available
Reproducubility of the image quantitation method. Image quantification results obtained in two independent experiments by two investigators (A) MA and (B) ST are shown for two antibodies, H3K79me2 and H3K79me3, at 17.5 dpc. The experiments included fetal gonad collection, immunostaining, microscopy and quantification. Mean fluorescence intensity/ar...
Article
Full-text available
Mammalian germ cells undergo global reprogramming of DNA methylation during their development. Global DNA demethylation occurs around the time when the primordial germ cells colonize the embryonic gonads and this coincides with dynamic changes in chromatin composition. Global de novo DNA methylation takes place with remarkably different dynamics be...
Article
Full-text available
Environmental endocrine disruptors (EDs) are synthetic chemicals that resemble natural hormones and are known to cause epigenetic perturbations. EDs have profound effects on development and fertility. Imprinted genes had been identified as susceptible loci to environmental insults by EDs because they are functionally haploid, and because the imprin...
Article
Full-text available
5-methyl-C (5mC) and 5-hydroxymethyl-C (5hmC) are epigenetic marks with well known and putative roles in gene regulation, respectively. These two DNA covalent modifications cannot be distinguished by bisulfite sequencing or restriction digestion, the standard methods of 5mC detection. The methylated CpG island recovery assay (MIRA), however, specif...
Article
Full-text available
To reveal the extent of domain-wide epigenetic features at imprinted gene clusters, we performed a high-resolution allele-specific chromatin analysis of over 100 megabases along the maternally or paternally duplicated distal chromosome 7 (Chr7) and Chr15 in mouse embryo fibroblasts (MEFs). We found that reciprocal allele-specific features are limit...
Article
Full-text available
Genomic imprinting is an epigenetic inheritance system characterized by parental allele-specific gene expression. Allele-specific DNA methylation and chromatin composition are two epigenetic modification systems that control imprinted gene expression. To get a general assessment of histone lysine acetylation at imprinted genes we measured allele-sp...
Data
Full-text available
Validation of the ChIP-SNuPE assays for small numbers of cells. ChIP-SNuPE Sequenom assays are shown. (A) ChIP was performed using 100,000 MEF cells from the 129 X CS mouse cross. The ChIP-SNuPE assays specific for the ICR −4 kb and −3 kb regions (A and B) were used to quantitate the percent of the maternal (black) or paternal (grey) allele in the...
Data
Full-text available
H3K4me2 ChIP intensities in germ cell chromatin real-time PCR results are shown for two sets of experiments at two ICR regions (A and B) as indicated above each graph. The CS X OG2 and CTCFm X OG2 germ cell ChIP precipitation values with the H3K4me2-specific antibody at 13.5 dpc and 14.5 dpc are comparable to those obtained of the same number of 12...
Data
Verification of the purity of fetal germ cell population. Fetal ovaries and testes were dissected from the OG2 transgenic mouse line [43] and dissociated by trypsin digestion. Germ cells were separated from gonadal somatic cells using flow-cytometry. Germ cells can be distinguished by their GFP expression from the Pou5f1 promoter. Male (m) and fema...
Data
Full-text available
DNA methylation is absent at the ICR in the female germ line. Bisulfite sequencing results of primary oocytes from (A) CS X OG2 and (B) CTCFm X OG2 fetuses was analyzed. Other details are as in Figure 2. (0.58 MB PDF)
Data
Full-text available
Methylation dynamics of the CTCF site mutant paternally inherited ICR. Bisulfite sequencing was performed using prospermatogonia from OG2 X CTCFm fetuses. The paternally inherited allele is shown. Other details are as in Figure 2. (0.26 MB PDF)
Data
CTCF enrichment at the ICR in germ cell chromatin. Real-time PCR quantification of CTCF-bound H19/Igf2 ICR is shown at regions A (−4 kb) and B (−3 kb). Average precipitated copy numbers are plotted with standard deviations. The copy numbers were calculated based on known copy numbers of serial dilution of sheared genomic DNA run in parallel. 3 µl o...