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

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

PROVIDER: PRJNA572588 | ENA |

REPOSITORIES: ENA

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

Project description:We use in situ Hi-C to report the female germline cell development

2022-01-20 | GSE137771 | GEO

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

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

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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

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The variation of 3D Chromosome Structure were tested during germline stem cell differentiation [HiC]

Project description:During in vitro spermatogenesis and transdifferentiation of female germline stem cells into haploid spermatid-like cells , the variation of chromatin organization by using in situ Hi-C were tested

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The variation of 3D Chromosome Structure were tested during germline stem cell differentiation [HiC]

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3D Chromosome Structure of SSCs, iGSCs and FGSCs

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

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RNA surveillance controls 3D genome structure via stable cohesin chromosome interaction

Project description:The 3D architecture that the genome is folded into is regulated by CTCF, which determines domain borders, and cohesin, which generates interactions within domains. However, organisms lacking CTCF have been reported to still have cohesin-mediated 3D structures with strong borders. How this can be achieved and precisely regulated are yet unknown. Using in situ Hi-C, we found that 3’-end RNA processing factors coupled with proper transcription termination are a cis-acting determinant that regulates the localization and dynamics of cohesin on the chromosome arms. Loss of RNA processing factors, including nuclear exosome and Pfs2, destabilizes cohesin from the 3'-ends of convergent genes and results in decreased cohesin-mediated domain boundaries. We observed the co-localization between Rad21 and a wide range of 3'end RNA processing/termination factors. Further, deletion of Rrp6 leads to cohesin redistribution to facultative heterochromatin, resulting in improper domain boundaries. Importantly, we observed that knockdown of Rrp6Exosc10 caused a defect in cohesin binding and loss of local topologically associating domains (TADs) interactions in mouse embryonic stem cells. Based on these findings, we propose a novel function of the RNA surveillance pathway in 3D genome organization via cohesin complex, which provides the molecular basis underlying the dynamics of cohesin function.

2022-12-01 | GSE85147 | GEO