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LINE1 elements at Distal Junctions of rDNA repeats regulate nucleolar organization in human embryonic stem cells [RNA-seq]

ABSTRACT: In this study, we investigated whether RNA Pol II-mediated gene expression is affected by repression of DJ-LINE1. Guide RNAs targeting DJ-LINE1 or control genomic regions were transfected for 48h in CRISPRi naïve hESC.

ORGANISM(S): Homo sapiens

PROVIDER: GSE268669 | GEO | 2025/02/12

REPOSITORIES: GEO

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LINE1 elements at Distal Junctions of rDNA repeats regulate nucleolar organization in human embryonic stem cells [ATAC-seq]

Project description:In this study, we investigated the status of chromatin accessibility in naïve hES cells with DJ-LINE1 repression compared to control by Assay of Transposase Accessible Chromatin (ATAC)-seq.

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LINE1 elements at Distal Junctions of rDNA repeats regulate nucleolar organization in human embryonic stem cells [UMI-4C]

Project description:In this study, we constructed UMI-4C profiles of 5 different genomic loci (viewpoints) in two H9 human hES cell lines - naïve and primed - in order to study the 3D chromatin contact maps of these selected loci.

2025-02-12 | GSE268665 | GEO

LINE1 elements at Distal Junctions of rDNA repeats regulate nucleolar organization in human embryonic stem cells [UMI-4C]

Project description:LINE1 elements at Distal Junctions of rDNA repeats regulate nucleolar organization in human embryonic stem cells [UMI-4C]

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LINE1 elements at Distal Junctions of rDNA repeats regulate nucleolar organization in human embryonic stem cells [RNA-seq]

Project description:LINE1 elements at Distal Junctions of rDNA repeats regulate nucleolar organization in human embryonic stem cells [RNA-seq]

| PRJNA1118229 | ENA

LINE1 elements at Distal Junctions of rDNA repeats regulate nucleolar organization in human embryonic stem cells [ATAC-seq]

Project description:LINE1 elements at Distal Junctions of rDNA repeats regulate nucleolar organization in human embryonic stem cells [ATAC-seq]

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LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs [H3K27me3 ChIP-seq,RSeT+DT_L1KD]

Project description:In this study, we performed H3K27me3 ChIP-seq to compare LINE1 knockdown naive hES cells with the control.

2024-09-09 | GSE263290 | GEO

LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs [RNA-seq_PXGL H9_L1KD]

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Nucleolar release of rDNA repeats for repair involves SUMO-mediated untethering by the Cdc48/p97 segregase.

Project description:Ribosomal RNA genes (rDNA) are highly unstable and susceptible to rearrangement due to their repetitive nature and active transcriptional status. Sequestration of rDNA in the nucleolus suppresses uncontrolled recombination. However, broken repeats must be first released to the nucleoplasm to allow repair by homologous recombination. Nucleolar release of broken rDNA repeats is conserved from yeast to humans, but the underlying molecular mechanisms are currently unknown. Here we show that DNA damage induces phosphorylation of the CLIP-cohibin complex, releasing membrane-tethered rDNA from the nucleolus in Saccharomyces cerevisiae. Downstream of phosphorylation, SUMOylation of CLIP-cohibin is recognized by Ufd1 via its SUMO-interacting motif, which targets the complex for disassembly through the Cdc48/p97 chaperone. Consistent with a conserved mechanism, UFD1L depletion in human cells impairs rDNA release. The dynamic and regulated assembly and disassembly of the rDNA-tethering complex is therefore a key determinant of nucleolar rDNA release and genome integrity.

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LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs [ChIRP-seq,RSeT+DT H9]

Project description:In this study, we profiled for LINE1 binding loci in RSeT+DT naïve hES cells with the Chromatin Isolation by RNA Purification (ChIRP)-seq strategy. We followed a previously published ChIRP protocol described (Percharde et al. 2018; Lu et al. 2020).

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LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs [scRNA-seq]

Project description:In this study, we investigated LINE1 (L1), a major family of transposon elements (TEs) in the human genome, in naive hES cells for its roles in regulating 8-cell (8C) stage-specific totipotent genes. We performed single-cell RNA-seq (scRNA-seq) to assess if L1 knockdown in RSeT+DT naive hES cells induces 8-cell-like cells (8CLCs), and profile the transcriptome changes in the cells.

2024-09-07 | GSE232938 | GEO

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