Genome-wide DNA methylation reprogramming in porcine primordial germ cells
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB39278 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR4326650.fastq.gz | Fastqsanger.gz | |||
| ERR4326660.fastq.gz | Fastqsanger.gz | |||
| ERR4326651.fastq.gz | Fastqsanger.gz | |||
| ERR4326661.fastq.gz | Fastqsanger.gz | |||
| ERR4326652.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 16 |
Similar Datasets
Project description:DNA methylation reprogramming of primordial germ cells (PGCs) is an essential step that affects the activation and inactivation of certain genes, therefore having a direct impact on the transcriptome of an individual. In this study, we have described the methylome landscape of porcine PGCs, characterizing the genomic elements that resist methylation erasure.
2021-02-04 | E-MTAB-9326 | biostudies-arrayexpress
Project description:A number of environmental factors (e.g. toxicants) have been shown to promote the epigenetic transgenerational inheritance of disease and phenotypic variation. Transgenerational inheritance requires the germline transmission of altered epigenetic information between generations in the absence of direct environmental exposures. The primary periods for epigenetic programming of the germline is associated with primordial germ cell development and during fetal gonadal sex determination. The current study examined the actions of an agricultural fungicide vinclozolin on gestating female (F0 generation) progeny in regards to the primordial germ cell (PGC) epigenetic reprogramming of the F3 generation (i.e. great-grandchildren). The F3 generation primordial germ cell transcriptome and epigenome (DNA methylation) was altered transgenerationally. Interestingly, the differential DNA methylation regions (DMR) and altered transcriptomes were distinct between the onset of gonadal sex determination at embryonic day 13 (E13) and after cord formation in the testis at embryonic day 16 (E16). A larger number of DMR and transcriptional alterations were observed in the E13 PGC than E16 germ cells. Observations demonstrate an altered transgenerational epigenetic reprogramming and function of the primordial germ cells and subsequent male germline is a component of vinclozolin induced epigenetic transgenerational inheritance of disease. Insights into the molecular control of germline transmitted epigenetic inheritance are provided. The combined observations demonstrate ancestral exposure of a gestating female during fetal gonadal sex determination can promote transgenerational alterations in the primordial germ cell and subsequent male germline epigenetic and transcriptional programming. This altered germline programming leads to the epigenetic transgenerational inheritance of disease and phenotypic variation. Observations support the role of the primordial germ cell programming in the molecular mechanism involved and provides insights into the molecular mechanisms that control the epigenetic transgenerational inheritance phenomena. Results suggest a cascade of epigenetic and transcriptional events during germ cell development is needed to obtain the mature germline epigenome that is then transmitted transgenerationally. RNA samples from PGC of 2 F3-control lineage groups were compared to PGC of 2 F3-vinclozolin lineage groups for two embryonic age E13 and E16
2013-01-17 | E-GEOD-43559 | biostudies-arrayexpress
Project description:The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells
| PRJEB3376 | ENA
Project description:A number of environmental factors (e.g. toxicants) have been shown to promote the epigenetic transgenerational inheritance of disease and phenotypic variation. Transgenerational inheritance requires the germline transmission of altered epigenetic information between generations in the absence of direct environmental exposures. The primary periods for epigenetic programming of the germline is associated with primordial germ cell development and during fetal gonadal sex determination. The current study examined the actions of an agricultural fungicide vinclozolin on gestating female (F0 generation) progeny in regards to the primordial germ cell (PGC) epigenetic reprogramming of the F3 generation (i.e. great-grandchildren). The F3 generation primordial germ cell transcriptome and epigenome (DNA methylation) was altered transgenerationally. Interestingly, the differential DNA methylation regions (DMR) and altered transcriptomes were distinct between the onset of gonadal sex determination at embryonic day 13 (E13) and after cord formation in the testis at embryonic day 16 (E16). A larger number of DMR and transcriptional alterations were observed in the E13 PGC than E16 germ cells. Observations demonstrate an altered transgenerational epigenetic reprogramming and function of the primordial germ cells and subsequent male germline is a component of vinclozolin induced epigenetic transgenerational inheritance of disease. Insights into the molecular control of germline transmitted epigenetic inheritance are provided. The combined observations demonstrate ancestral exposure of a gestating female during fetal gonadal sex determination can promote transgenerational alterations in the primordial germ cell and subsequent male germline epigenetic and transcriptional programming. This altered germline programming leads to the epigenetic transgenerational inheritance of disease and phenotypic variation. Observations support the role of the primordial germ cell programming in the molecular mechanism involved and provides insights into the molecular mechanisms that control the epigenetic transgenerational inheritance phenomena. Results suggest a cascade of epigenetic and transcriptional events during germ cell development is needed to obtain the mature germline epigenome that is then transmitted transgenerationally.
2013-01-17 | GSE43559 | GEO
Project description:Epigenetic reprogramming enables the primordial germ cell-to-gonocyte transition
| PRJNA309236 | ENA
Project description:A number of environmental factors (e.g. toxicants) have been shown to promote the epigenetic transgenerational inheritance of disease and phenotypic variation. Transgenerational inheritance requires the germline transmission of altered epigenetic information between generations in the absence of direct environmental exposures. The primary periods for epigenetic programming of the germ line are those associated with primordial germ cell development and subsequent fetal germline development. The current study examined the actions of an agricultural fungicide vinclozolin on gestating female (F0 generation) progeny in regards to the primordial germ cell (PGC) epigenetic reprogramming of the F3 generation (i.e. great-grandchildren). The F3 generation germline transcriptome and epigenome (DNA methylation) were altered transgenerationally. Interestingly, disruptions in DNA methylation patterns and altered transcriptomes were distinct between germ cells at the onset of gonadal sex determination at embryonic day 13 (E13) and after cord formation in the testis at embryonic day 16 (E16). A larger number of DNA methylation abnormalities (epimutations) and transcriptional alterations were observed in the E13 germ cells than in the E16 germ cells. These observations indicate that altered transgenerational epigenetic reprogramming and function of the male germline is a component of vinclozolin induced epigenetic transgenerational inheritance of disease. Insights into the molecular control of germline transmitted epigenetic inheritance are provided.
2014-07-17 | GSE59510 | GEO
Project description:Porcine embryonic germ cells (EGC) are cultured pluripotent cells derived from primordial germ cells (PGC). This study explored the possibilities to establish porcine EGC lines in the domestic breed pig more efficiently and from earlier embryonic stages than reported to date. In vitro culture of PGC from both pooled and individual embryos at days 17-24 of gestation resulted in the successful derivation of putative EGC lines from days 20-24 with high efficiency, while no lines could be established from days 17-18. The EGC-like colonies had characteristic morphology and electron microscopy revealed tight junctions and presence of primary cilia on the cell surfaces. The cells formed simple embryoid bodies in suspension culture and further differentiated into epithelial-like, mesenchymal-like, and neuronal-like cells. Our results show that putative porcine EGC can be derived from migrating PGC with high efficiency using individual embryos from different genetic backgrounds. RNA-Seq profiling of 2 different in vitro cultures of pig embryonic cells. The cells, both the pig Embryonic Germ cells (pEGCs) and the pig Fetal Fibroblasts (pFF) show properties of pluripotency and self renewal.
2011-03-24 | E-GEOD-24220 | biostudies-arrayexpress
Project description:Temporal and spatial regulation of trimethylation of histone H3 lysine27 (H3K27me3) is crucial for cell lineage commitment and development. Resetting the ground state of H3K27me3 is important for establishing a proper development program of primordial germ cells (PGCs). The mechanisms that regulate global erasure of epigenetic information in the germ line are not well understood. Here we show that HP1γ suppresses the demethylation activity of Utx through direct interaction in vitro and in vivo. Down-regulation of mammalian heterochromatin protein 1 gamma (HP1γ) coincides with transient loss of H3K27me3 in PGCs on Embryonic Day 10.5 (E10.5). Furthermore, transient abolishment of HP1γ promotes the induction of embryonic stem cells into putative PGCs in vitro. These data reveal a cross-talk between HP1γ and Utx in controlling histone H3K27 methylation status, thereby define HP1γ as a molecular regulator of germ cell epigenetic reprogramming.
2017-01-24 | GSE93924 | GEO
Project description:A number of environmental factors (e.g. toxicants) have been shown to promote the epigenetic transgenerational inheritance of disease and phenotypic variation. Transgenerational inheritance requires the germline transmission of altered epigenetic information between generations in the absence of direct environmental exposures. The primary periods for epigenetic programming of the germ line are those associated with primordial germ cell development and subsequent fetal germline development. The current study examined the actions of an agricultural fungicide vinclozolin on gestating female (F0 generation) progeny in regards to the primordial germ cell (PGC) epigenetic reprogramming of the F3 generation (i.e. great-grandchildren). The F3 generation germline transcriptome and epigenome (DNA methylation) were altered transgenerationally. Interestingly, disruptions in DNA methylation patterns and altered transcriptomes were distinct between germ cells at the onset of gonadal sex determination at embryonic day 13 (E13) and after cord formation in the testis at embryonic day 16 (E16). A larger number of DNA methylation abnormalities (epimutations) and transcriptional alterations were observed in the E13 germ cells than in the E16 germ cells. These observations indicate that altered transgenerational epigenetic reprogramming and function of the male germline is a component of vinclozolin induced epigenetic transgenerational inheritance of disease. Insights into the molecular control of germline transmitted epigenetic inheritance are provided. The F0 generation females were exposed to a vehicle (dimethylsulfoxide DMSO) as control or to vinclozolin, as described in the Methods. The F1 generation offspring were bred to generate the F2 generation and the F2 generation offspring were bred to generate the F3 generation offspring. The timed pregnant F2 generation females were used to isolate the F3 generation control and vinclozolin lineage fetal gonads at the E13 and E16 time points. The F3 generation E13 PGC and E16 prospermatogonia were isolated. DNA was isolated from the freshly isolated cells to examine DNA methylation by methylated DNA immunoprecipitation (MeDIP) followed by analysis on a genome-wide promoter tiling array (Chip) using a comparative hybridization MeDIP-Chip analysis between control and vinclozolin lineage samples as described in Methods. This allowed a comparison of the epigenome alterations in F3 vinclozolin lineage germ cells at E13 and E16. Three separate experimental comparisons of control and vinclozolin-lineage animals involving different germ cell isolations were analyzed with three different MeDIP-Chip analyses at each time point.
2014-07-17 | E-GEOD-59510 | biostudies-arrayexpress
Project description:Porcine embryonic germ cells (EGC) are cultured pluripotent cells derived from primordial germ cells (PGC). This study explored the possibilities to establish porcine EGC lines in the domestic breed pig more efficiently and from earlier embryonic stages than reported to date. In vitro culture of PGC from both pooled and individual embryos at days 17-24 of gestation resulted in the successful derivation of putative EGC lines from days 20-24 with high efficiency, while no lines could be established from days 17-18. The EGC-like colonies had characteristic morphology and electron microscopy revealed tight junctions and presence of primary cilia on the cell surfaces. The cells formed simple embryoid bodies in suspension culture and further differentiated into epithelial-like, mesenchymal-like, and neuronal-like cells. Our results show that putative porcine EGC can be derived from migrating PGC with high efficiency using individual embryos from different genetic backgrounds.
2011-03-24 | GSE24220 | GEO