Dissecting the epigenomic dynamics of human fetal germ cell development at single-cell resolution
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PROVIDER: PRJNA421287 | ENA |
REPOSITORIES: ENA
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Project description:The proper development of fetal germ cells (FGCs) is vital for genetic and epigenetic information transmission in generations. We have depicted the transcriptional landscape of distinct phases FGCs and the interaction between FGCs and gonadal niche cells. However, the epigenetic dynamics of sequential phases FGCs still remains in dimness. Here applied with single cell sequencing techniques (scBS-seq and scCOO-seq), we analyzed the genome-wide DNA methylation and chromatin accessibility map of female mitosis, meiotic prophase, and oogenesis FGCs, as well as male mitosis and mitotic-arrest FGCs.
2020-10-27 | GSE107714 | GEO
Project description:The limited number of in vivo germ cells poses an impediment to genome-wide studies. Here, we applied a small-scale ChIP-Seq method on purified mouse fetal germ cells to generate genome-wide maps of four histone modifications (H3K4me3, H3K27me3, H3K27ac and H2BK20ac), facilitating the identification of active and repressed cis-regulatory elements in germ cells in vivo. Comparison of active chromatin state between somatic, embryonic stem cells (ESC) and germ cells revealed promoters and enhancers needed for stem cell maintenance and germ cell development. The nuclear receptor Nr5a2 motif is enriched at a subset of cis-regulatory regions and we confirm its role in germ cell differentiation. Interestingly, germ cells have comparatively more H3K27me3-marked sites that are absent in ESC and other somatic cell types. These repressed regions are enriched for retrotransposons and MHC genes and this indicates that these loci are specifically silenced in germ cells. Together, our study provides the first genome-wide histone modification maps of in vivo germ cells and revealed the molecular chromatin signatures unique to germ cells. Germ cells were FACS-purified from gonadal single cell suspension based on Pou5f1-GFP expression. ChIP-seq of Histone modification was done for two timepoints in this study: E11.5 (male/female), E13.5 (male). For E13.5 timepoint, two biological replicates were analyzed. In order to validate small scale ChIP-seq method limited number of ES cells were used to check consistency of ChIP-seq data.
2013-01-25 | E-GEOD-38164 | biostudies-arrayexpress
Project description:The limited number of in vivo germ cells poses an impediment to genome-wide studies. Here, we applied a small-scale ChIP-Seq method on purified mouse fetal germ cells to generate genome-wide maps of four histone modifications (H3K4me3, H3K27me3, H3K27ac and H2BK20ac), facilitating the identification of active and repressed cis-regulatory elements in germ cells in vivo. Comparison of active chromatin state between somatic, embryonic stem cells (ESC) and germ cells revealed promoters and enhancers needed for stem cell maintenance and germ cell development. The nuclear receptor Nr5a2 motif is enriched at a subset of cis-regulatory regions and we confirm its role in germ cell differentiation. Interestingly, germ cells have comparatively more H3K27me3-marked sites that are absent in ESC and other somatic cell types. These repressed regions are enriched for retrotransposons and MHC genes and this indicates that these loci are specifically silenced in germ cells. Together, our study provides the first genome-wide histone modification maps of in vivo germ cells and revealed the molecular chromatin signatures unique to germ cells.
2013-01-25 | GSE38164 | GEO
Project description:transcriptional landscape of Germ cell differentiation at single cell resolution
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Project description:Sex-specific metabolic characteristics emerge in the mouse germline after reaching the genital ridges around embryonic day 10.5, coinciding with the initiation of sexual differentiation. However, the impact of such metabolic characteristics on the development of male and female germ cells remains unclear. In this study, we observed the specific upregulation in male fetal germ cells of D-3-phosphoglycerate dehydrogenase (PHGDH), the primary enzyme in the serine-glycine–one-carbon (SGOC) metabolic pathway. A concurrent increase was observed in a downstream metabolite, S-adenosylmethionine (SAM), a crucial substrate for protein and nucleic acid methylation. Inhibiting PHGDH in fetal testes resulted in reduced SAM levels in germ cells, accompanied by increases in the number of germ cells and the undifferentiated spermatogonia ratio. Furthermore, PHGDH inhibition led to a decrease in the methylation of histone H3 and DNA, resulting in aberrations in gene expression profiles. In summary, our findings underscore the significant role of certain metabolic mechanisms in the development of male germ cells.
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Project description:We used microarrays to profile global gene expression changes of Pou5f1-GFP-positive germ cells between E11.5 to E15.5. Germ cells were FACS-purified from gonadal single cell suspension based on Pou5f1-GFP expression. Three timepoints were included in this study: E11.5 (male/female), E13.5 (male) and E15.5 (male). For each timepoint, three biological replicates were analyzed. The Pou5f1-GFP-negative (non-germ cell) fraction of E13.5 (male) gonads was also included as a control.
2013-01-25 | E-GEOD-38126 | biostudies-arrayexpress