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The three-dimensional genome structure shapes the recombination landscape of chromatin features during female germline stem cell development [RNA-Seq]

ABSTRACT: We use in situ Hi-C to report the most comprehensive survey to date of chromatin organization during FGSC development

ORGANISM(S): Mus musculus

PROVIDER: GSE199583 | GEO | 2025/03/28

REPOSITORIES: GEO

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Three-dimensional genome structure shapes the recombination landscape of chromatin features during female germline stem cell development.

Project description:BackgroundDuring meiosis of mammalian cells, chromatin undergoes drastic reorganization. However, the dynamics of the three-dimensional (3D) chromatin structure during the development of female germline stem cells (FGSCs) are poorly understood.MethodsThe high-throughput chromosome conformation capture technique was used to probe the 3D structure of chromatin in mouse germ cells at each stage of FGSC development.ResultsThe global 3D genome was dramatically reorganized during FGSC development. In topologically associating domains, the chromatin structure was weakened in germinal vesicle stage oocytes and still present in meiosis I stage oocytes but had vanished in meiosis II oocytes. This switch between topologically associating domains was related to the biological process of FGSC development. Moreover, we constructed a landscape of chromosome X organization, which showed that the X chromosome occupied a smaller proportion of the active (A) compartment than the autosome during FGSC development. By comparing the high-order chromatin structure between female and male germline development, we found that 3D genome organization was remodelled by two different potential mechanisms during gamete development, in which interchromosomal interactions, compartments, and topologically associating domain were decreased during FGSC development but reorganized and recovered during spermatogenesis. Finally, we identified conserved chromatin structures between FGSC development and early embryonic development.ConclusionsThese results provide a valuable resource to characterize chromatin organization and for further studies of FGSC development.

| S-EPMC9214757 | biostudies-literature

The three-dimensional genome structure shapes the recombination landscape of chromatin features during female germline stem cell development [RNA-Seq]

Project description:The three-dimensional genome structure shapes the recombination landscape of chromatin features during female germline stem cell development [RNA-Seq]

| PRJNA820756 | ENA

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 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 [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 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

2024-11-01 | GSE195970 | GEO

Genome-wide profiling of Alternative polyadenylation sites in mouse female germline stem cells

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.

2015-11-20 | E-MTAB-4038 | biostudies-arrayexpress

Stella regulates the development of female germline stem cells by modulating chromatin structure and DNA methylation [ChIP-Seq]

Project description:We use ChIP-seq to report the most comprehensive survey to date of chromatin organization in female germline stem cells

2022-05-25 | GSE188660 | GEO

Stella regulates the development of female germline stem cells by modulating chromatin structure and DNA methylation [Hi-C]

Project description:We use in situ Hi-C to report the most comprehensive survey to date of chromatin organization in female germline stem cells

2022-05-25 | GSE188661 | GEO

Stella regulates the development of female germline stem cells by modulating chromatin structure and DNA methylation [Hi-C_2]

Project description:We use in situ Hi-C to report the most comprehensive survey to date of chromatin organization in female germline stem cells

2022-05-25 | GSE199075 | GEO