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

PROVIDER: PRJNA820756 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18505532_1.fastq.gz	Fastqsanger.gz
	SRR18505532_2.fastq.gz	Fastqsanger.gz
	SRR18505533_1.fastq.gz	Fastqsanger.gz
	SRR18505533_2.fastq.gz	Fastqsanger.gz
	SRR18505534_1.fastq.gz	Fastqsanger.gz

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

2025-03-28 | GSE199583 | GEO

Germline DNA replication timing shapes mammalian genome composition

Project description:Germline DNA replication timing shapes mammalian genome composition

| PRJNA432066 | ENA

Meiotic recombination mirrors patterns of germline replication in mice and humans

Project description:Genetic recombination generates novel trait combinations, and understanding how recombination is distributed across the genome is key to modern genetics. The PRDM9 protein defines recombination hotspots; however, megabase-scale recombination patterning is independent of PRDM9. The single round of DNA replication, which precedes recombination in meiosis, may establish these patterns; therefore, we devised an approach to study meiotic replication that includes robust and sensitive mapping of replication origins. We find that meiotic DNA replication is distinct; reduced origin firing slows replication in meiosis, and a distinctive replication pattern in human males underlies the subtelomeric increase in recombination. We detected a robust correlation between replication and both contemporary and historical recombination and found that replication origin density coupled with chromosome size determines the recombination potential of individual chromosomes. Our findings and methods have implications for understanding the mechanisms underlying DNA replication, genetic recombination, and the landscape of mammalian germline variation.

2021-07-02 | GSE148327 | GEO

Intra-Vk Cluster Recombination Shapes the Ig Kappa Locus Repertoire

Project description:Intra-Vk Cluster Recombination Shapes the Ig Kappa Locus Repertoire

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Intra-Vk Cluster Recombination Shapes the Ig Kappa Locus Repertoire [HTGTS]

Project description:Intra-Vk Cluster Recombination Shapes the Ig Kappa Locus Repertoire [HTGTS]

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Meiotic recombination mirrors patterns of germline replication in mice and humans

Project description:Meiotic recombination mirrors patterns of germline replication in mice and humans

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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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Intra-Vk Cluster Recombination Shapes the Ig Kappa Locus Repertoire [END-seq]

Project description:Intra-Vk Cluster Recombination Shapes the Ig Kappa Locus Repertoire [END-seq]

| PRJNA590463 | ENA

Intra-Vk Cluster Recombination Shapes the Ig Kappa Locus Repertoire [ChIP-seq]

Project description:Intra-Vk Cluster Recombination Shapes the Ig Kappa Locus Repertoire [ChIP-seq]

| PRJNA590470 | ENA

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