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

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

ORGANISM(S): Mus musculus

PROVIDER: GSE195970 | GEO | 2024/11/01

REPOSITORIES: GEO

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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

Retinoic acid induced meiosis initiation in female germline stem cells by remodelling three-dimensional chromatin structure.

Project description:ObjectivesThis study aimed to clarify the regulation and mechanism of meiotic initiation in FGSC development.Materials and methodsFGSCs were induced to differentiate into meiosis in differentiation medium. RNA sequencing was performed to analysis the difference of transcription level. High-through chromosome conformation capture sequencing (Hi-C) was performed to analysis changes of three-dimensional chromatin structure. Chromosome conformation capture further confirmed a spatial chromatin loop. ChIP-qPCR and dual luciferase reporter were used to test the interaction between Stimulated by retinoic acid gene 8 (STRA8) protein and Trip13 promoter.ResultsCompared with FGSCs, the average diameter of STRA8-positive germ cells increased from 13 μm to 16.8 μm. Furthermore, there were 4788 differentially expressed genes between the two cell stages; Meiosis and chromatin structure-associated terms were significantly enriched. Additionally, Hi-C results showed that FGSCs underwent A/B compartment switching (switch rate was 29.81%), the number of topologically associating domains (TADs) increasing, the average size of TADs decreasing, and chromatin loop changes at genome region of Trip13 from undifferentiated stage to meiosis-initiation stage. Furthermore, we validated that Trip13 promoter contacted distal enhancer to form spatial chromatin loop and STRA8 could bind Trip13 promoter to promote gene expression.ConclusionFGSCs underwent chromatin structure remodelling from undifferentiated stage to meiosis-initiation stage, which facilitated STRA8 binding to Trip13 promoter and promoting its expression.

| S-EPMC9251051 | biostudies-literature

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

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-11-01 | GSE195971 | GEO

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

Project description:Retinoic acid induced meiosis initiation of female germline stem cells by remodeling three-dimensional chromatin structure

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

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

| PRJNA802818 | ENA

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

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

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

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

2022-01-20 | GSE175730 | GEO

Roles of Stra8 and Tcerg1l in retinoic acid induced spermatogonial differentiation in mouse.

Project description:Retinoic acid (RA) induces spermatogonial differentiation, but the mechanism by which it operates remains largely unknown. We developed a germ cell culture assay system to study genes involved in spermatogonial differentiation triggered by RA. Stimulated by Retinoic Acid 8 (Stra8), an RA-inducible gene, is indispensable for meiosis initiation, and its deletion results in a complete block of spermatogenesis at the pre-leptotene/zygotene stage due to failure to complete pre-meiotic DNA replication. To interrogate the role of Stra8 in RA mediated differentiation of spermatogonia, we derived germ cell cultures from the neonatal testis of both wild type and Stra8 knock-out mice. We provide the first evidence that Stra8 plays a crucial role in modulating the responsiveness of undifferentiated spermatogonia to RA and facilitates transition to a differentiated state. Stra8-mediated differentiation is achieved through downregulation of a large portfolio of genes and pathways, most notably including genes involved in the spermatogonial stem cell self-renewal process. We also report here for the first time the role of Transcription Elongation Regulator-1 Like (Tcerg1l) as a downstream effector of RA-induced spermatogonial differentiation.

2021-05-05 | GSE173873 | GEO

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.

2024-08-15 | PXD054663 | Pride

Three-dimensional EM structure of an intact activator-dependent transcription initiation complex.

Project description:We present the experimentally determined 3D structure of an intact activator-dependent transcription initiation complex comprising the Escherichia coli catabolite activator protein (CAP), RNA polymerase holoenzyme (RNAP), and a DNA fragment containing positions -78 to +20 of a Class I CAP-dependent promoter with a CAP site at position -61.5 and a premelted transcription bubble. A 20-A electron microscopy reconstruction was obtained by iterative projection-based matching of single particles visualized in carbon-sandwich negative stain and was fitted using atomic coordinate sets for CAP, RNAP, and DNA. The structure defines the organization of a Class I CAP-RNAP-promoter complex and supports previously proposed interactions of CAP with RNAP alpha subunit C-terminal domain (alphaCTD), interactions of alphaCTD with sigma(70) region 4, interactions of CAP and RNAP with promoter DNA, and phased-DNA-bend-dependent partial wrapping of DNA around the complex. The structure also reveals the positions and shapes of species-specific domains within the RNAP beta', beta, and sigma(70) subunits.

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