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3D chromosome structure reveals unique signatures involved in mouse female germline stem cells and their development II

ABSTRACT: We use RNA-seq to report the gene expression of FGSCs and shCTCF FGSCs

ORGANISM(S): Mus musculus

PROVIDER: GSE175730 | GEO | 2022/01/20

REPOSITORIES: GEO

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3D chromosome structure reveals unique signatures involved in mouse female germline stem cells and their development

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3D chromosome structure reveals unique signatures involved in mouse female germline stem cells and their development

Project description:3D chromosome structure reveals unique signatures involved in mouse female germline stem cells and their development

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3D chromosome structure reveals unique signatures involved in mouse female germline stem cells and their development II

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3D Chromosome Structure of SSCs, iGSCs and FGSCs

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Retinoic acid induced meiosis initiation of female germline stem cells by remodeling three-dimensional chromatin structure [HiC]

Project description:We use Hi-C to report the three-dimensional chromatin organization between FGSCs with stra8-positive germ cells induced by retinoic acid

2024-11-01 | GSE195967 | GEO

Integrative epigenomic analysis reveals unique epigenetic signatures involved in unipotency of mouse female germline stem cells.

Project description:BackgroundGermline stem cells play an essential role in establishing the fertility of an organism. Although extensively characterized, the regulatory mechanisms that govern the fundamental properties of mammalian female germline stem cells remain poorly understood.ResultsWe generate genome-wide profiles of the histone modifications H3K4me1, H3K27ac, H3K4me3, and H3K27me3, DNA methylation, and RNA polymerase II occupancy and perform transcriptome analysis in mouse female germline stem cells. Comparison of enhancer regions between embryonic stem cells and female germline stem cells identifies the lineage-specific enhancers involved in germline stem cell features. Additionally, our results indicate that DNA methylation primarily contributes to female germline stem cell unipotency by suppressing the somatic program and is potentially involved in maintenance of sexual identity when compared with male germline stem cells. Moreover, we demonstrate down-regulation of Prmt5 triggers differentiation and thus uncover a role for Prmt5 in maintaining the undifferentiated status of female germline stem cells.ConclusionsThe genome-wide epigenetic signatures and the transcription regulators identified here provide an invaluable resource for understanding the fundamental features of mouse female germline stem cells.

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Retinoic acid induced meiosis initiation of female germline stem cells by remodeling three-dimensional chromatin structure [RNA-seq]

Project description:We use RNA-sequencing to report the transcriptomic differences between FGSCs with stra8-positive germ cells induced by retinoic acid

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Proteomics dataset of knockdown of AKT3 on protein expression and function in female germline stem cells

Project description:Female germline stem cells (FGSCs) are adult stem cells capable of self-renewal and differentiation into mature oocytes. AKT3, a member of the AKT kinase family, plays crucial roles in multiple cellular processes, such as proliferation, migration, and apoptosis. However, the mechanism by which AKT3 affects the development of FGSCs is poorly understood. We performed liquid chromatography (LC)-mass spectrometry (MS) on mouse FGSCs in which AKT3 was knocked down using a lentivirus and on control FGSCs to investigate how AKT affects the development of FGSCs. Based on the raw LC-MS data and database searches and data filtering, we identified 46,260 peptides, including 45,821 unique peptides, corresponding to 6849 identified proteins and 6697 comparable proteins. These identified proteins were functionally annotated using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Protein Domain, Clusters of Orthologous Genes (COG)/Eukaryotic Orthologous Groups (KOG), STRING database, Reactome, WikiPathways, HallMark, and transcription factor (TF) analyses. Fisher’s exact test was used to assess the significance of functional enrichment of the differentially abundant proteins. We identified 281 differentially abundant proteins between AKT3 knockdown and control FGSCs, comprising 229 upregulated and 52 downregulated proteins. We performed clustering analysis on these differentially abundant proteins based on functional enrichment using GO, Domain, KEGG, Reactome and WikiPathways platforms. A protein–protein interaction network was constructed to demonstrate interactions between proteins. These datasets will facilitate future investigations into the mechanisms governing FGSC self-renewal and differentiation and will provide a foundation for understanding diseases related to abnormal germ cell development.

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The mechanism of restoration ovarian function using female germline stem cell

Project description:Germ stem cells are the only stem cells which can produce gametes in vivo. Recently, accumulating evidence demonstrates the isolation and culture of female germline stem cells (FGSCs) from adult mice and humans. Here, we established FGSCs line from single EGFP transgenetic mouse, and traced their differentiation in vivo. Then we compared the follile development from transplanted FGSCs mice (F-TF) with that from wide type mice (F-WT) by RNA-Seq. qRT–PCR validation was performed using SYBR Green assays. Using Illumina HiSeq2500 sequencer, we generated 51.5 Gb of sequencing data from the 8 samples. On average, we detected expression of 20 966 transcripts. Under the criteria fold change > 2 or < 0.5, we obtained 7005 and 5764 differential expressed genes (DEGs) from F-TF or F-WT,respectively. Weighted correlation network analysis (WGCNA) analysis identified core genes and two potential networks during folliculogenesis which were mainly down-regulated after preantral follicle. This study was the first to analyze the development of transplanted FGSCs progressively and would provide the theoretical basis for clinical translational research of FGSCs.

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Project description:Alternative polyadenylation (APA) is an important post-transcriptional modification implicated in development. Female germline stem cell (FGSC) is unipotent and capable of giving rise to oocyte. However, whether alternative polyadenylation plays a role in self-renew and cell fate determination of FGSCs remain elusive. Here, we used 3T-Seq developed in our lab to profile genome-wide 3a termini of transcripts and delineate APA sites in mouse FGSCs and explored the biological significance of APA modulation in FGSC identity.

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