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DNA methylation analysis by RRBS in germ cells of mice exposed to Vinclozolin

ABSTRACT: We provide quantitative maps of cytosine methylation at single base resolution by RRBS in E13.5 primordial germ cells and adult sperm purified from mice exposed to Vinclozolin.

ORGANISM(S): Mus musculus

PROVIDER: GSE65784 | GEO | 2015/06/22

SECONDARY ACCESSION(S): PRJNA275009

REPOSITORIES: GEO

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DNA methylation analysis by RRBS in germ cells of mice exposed to Vinclozolin

Project description:We provide quantitative maps of cytosine methylation at single base resolution by RRBS in E13.5 primordial germ cells and adult sperm purified from mice exposed to Vinclozolin. Pregnant F0 female mice were exposed to two doses (a low dose VD1=1 mg/kg bw/d and a high dose VD2=100mg/kg bw/d) of Vinclozolin in the drinking water during pregnancy. We isolated primordial germ cells at E13.5 and mature sperm from adult F1 males obtained from control and exposed mothers. For PGCs, we sequenced RRBS libraries prepared from one pool isolated from F1 embryos exposed to the low dose, one pool isolated from F1 embryos exposed to the high dose, and two control pools isolated from unexposed embryos. For sperm, we sequenced three RRBS libraries prepared from a pool of sperm isolated from F1 males exposed to the high dose, and five RRBS libraries prepared from control pools isolated from unexposed animals.

2015-06-22 | E-GEOD-65784 | biostudies-arrayexpress

Primordial Germ Cell Transgenerational Sperm DNA Methylation Epimutations Following Ancestral Vinclozolin Exposure

2020-07-29 | GSE151458 | GEO

Primordial Germ Cell Transgenerational Sperm DNA Methylation Epimutations Following Ancestral Vinclozolin Exposure

Project description:Primordial Germ Cell Transgenerational Sperm DNA Methylation Epimutations Following Ancestral Vinclozolin Exposure

| PRJNA635897 | ENA

Developmental Origins of Transgenerational Sperm DNA Methylation Epimutations Following Ancestral Vinclozolin Exposure

Project description:Previously the agricultural fungicide vinclozolin was found to promote the transgenerational inheritance of sperm differential DNA methylation regions (DMRs) termed epimutations that help mediate this epigenetic inheritance. The current study was designed to investigate the developmental origins of the transgenerational DMRs during gametogenesis. Male control and vinclozolin lineage F3 generation rats were used as a source of embryonic day 16 (E16) prospermatogonia, postnatal day 10 (P10) spermatogonia, and adult pachytene spermatocytes, round spermatids, caput epididymal sperm, and caudal sperm. The DMRs between the control versus vinclozolin lineage samples were determined for each developmental stage. The top 100 statistically significant DMRs for each stage were compared and the developmental origins of the caudal epididymal sperm DMRs were assessed.

2018-11-01 | GSE117995 | GEO

Alterations in sperm DNA Methylation, Non-Coding RNA expression, and histone retention mediate Vinclozolin induced epigenetic transgenerational inheritance of disease

Project description:Environmental factors have been shown to induce the epigenetic transgenerational inheritance of disease through the germline. This study was designed to investigate vinclozolin induced concurrent alterations of a number of different epigenetic processes including DNA methylation and histone retention in sperm. Gestating female rats were exposed transiently to vinclozolin during fetal gonadal development and then F1, F2 and F3 generation sperm were analyzed.

2018-06-05 | GSE111441 | GEO

Reduced representation bisulfite sequencing (RRBS) for primordial germ cells and somatic cells during zebrafish early embryogenesis

Project description:Zebrafish Primordial Germ Cells (PGCs) and somatic cells were isolated via FACS from Buc-GFP fish strain. Reduced representation bisulfite sequencing (RRBS) was performed on PGCs and somatic cells at high(6000-7000 cells per replicate), dome (7500 cells per replicate)and prim-5 stages(4500-5000 cells per replicate). Two replicates were collected for each cell type and stage.

2020-12-24 | E-MTAB-9858 | biostudies-arrayexpress

Genetic and Epigenetic Variation, but Not Diet, Shape the Sperm Methylome

Project description:The diet consumed by fathers prior to procreation impacts metabolic phenotypes in their offspring, but the mechanisms underlying such intergenerational information transfer remain obscure. Here, we carried out extensive analysis of cytosine methylation patterns in murine sperm, generating whole genome methylation maps for 4 pools of sperm samples and for 12 individual sperm samples, as well as 61 genome-scale reduced-representation bisulfite sequencing (RRBS) methylation maps, using samples obtained from male mice consuming various diets. We found that epivariation, either stochastic or due to unknown demographic or environmental factors, was a far stronger contributor to the sperm methylome than was the diet consumed. Variation in cytosine methylation was particularly dramatic over tandem repeat families, including ribosomal DNA (rDNA) repeats, and rDNA methylation levels were heritable from one generation to the next. However, rDNA methylation was strongly correlated with genetic variation in rDNA copy number, and analysis of hundreds of sperm samples revealed no consistent effect of diet on rDNA copy number or methylation level in sperm, indicating that paternal diet exerts an rDNA methylation-independent effect on offspring gene expression. These results reveal loci of genetic and epigenetic lability in the mammalian genome, but strongly argue against a direct mechanistic role for sperm cytosine methylation in dietary reprogramming of offspring metabolism.

2015-12-17 | GSE75323 | GEO

Vinclozolin induced epigenetic transgenerational inheritance of pathologies and sperm epimutation biomarkers for specific diseases

Project description:F0 generation rats were exposed to vinclozolin, and the subsequent F1, F2 and transgenerational F3 generations are evaluated for diseases and pathologies. F3 generation rats showed transgenerational increases in testis, prostate, and kidney disease, changes in the age of puberty onset in males, and an increased obesity rate in females. Overall there was an increase in the rate of animals with disease, and in the incidence of animals with multiple disease. The methylation of the F3 vinclozolin lineage rat samples was determined using MeDIP-seq. Unique signatures of differential DNA methylation regions (DMRs) in sperm were found that associated with testis disease, prostate disease and kidney disease, however, these signatures were not statistically significant.

2018-07-25 | GSE113785 | GEO

DNA methylation analysis and expression profiling during murine embryogenesis and in embryos deficient for DNMT3A or DNMT3B

Project description:We quantified the targets and kinetics of DNA methylation acquisition in mouse embryos, and determined the contribution of the de novo methyltransferases DNMT3A and DNMT3B to this process. We provide single-base maps of cytosine methylation by RRBS from the blastocysts to post-implantation stages and in embryos lacking DNMT3A or DNMT3B activity, and performed RNA-Seq in embryos lacking DNMT3B activity. We sequenced RRBS libraries prepared from genomic DNA isolated from embryos at consecutive stages of development between E3.5 and E11.5,and adult differentiated cells (sperm, liver). We performed RRBS on blastocysts at E3.5/E4.5, dissected epiblasts at E5.5/E6.5/E7/5, whole embryos at E8.5/E10.5 and limbs at E11.5. RRBS experiments in Dnmt3a-/- and Dnmt3b-/- embryos were performed in biological duplicates on individual embryos. We sequenced RNA-Seq libraries prepared from total RNAs of three WT and Dnmt3b-/- littermate embryos collected at E8.5.

2014-11-14 | E-GEOD-60334 | biostudies-arrayexpress

Role of Tet1 in genomic imprinting erasure [RRBS-PGC]

Project description:Genomic imprinting is an allele-specific gene expression system important for mammalian development and function. The molecular basis of genomic imprinting is allele-specific DNA methylation 2. While it is well known that the de novo DNA methyltransferases Dnmt3a/b are responsible for the establishment of genomic imprinting, how the methylation mark is erased during primordial germ cell (PGC) reprogramming remains a mystery. Here we report that Tet1 plays a critical role in the erasure of genomic imprinting. We show that despite their identical genotype, progenies derived from mating between Tet1-KO males and wild-type females exhibit a number of variable phenotypes including placental, fetal and postnatal growth defects, and early embryonic lethality. These defects are, at least in part, caused by the dysregulation of imprinted genes, such as Peg10 and Peg3, which exhibit aberrant hypermethylation in the paternal allele of differential methylated regions (DMRs). RNA-seq reveals extensive dysregulation of imprinted genes in the next generation due to paternal functional loss of Tet1. Genome-wide DNA methylation analysis of E13.5 PGCs and sperm derived from Tet1-KO mice reveals hypermethylation of DMRs of imprinted genes in sperm, which can be traced back to PGCs. Dynamics of methylation change in Tet1-affected sites suggested that Tet1 swipes remaining methylation including imprinted genes at late reprogramming stage. We also revealed that Tet1play a role in paternal imprinting erasure in females germline. Thus, our study establishes a critical function for Tet1 in the erasure of genomic imprinting. Genome-wide DNA methylation analysis of E13.5 PGCs from control and Tet1-KO mice

2013-12-02 | E-GEOD-49762 | biostudies-arrayexpress

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