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The RNA helicase DDX1 associates with the nuclear RNA exosome and modulates R-loops

ABSTRACT: The RNA helicase DDX1 associates with the nuclear RNA exosome and modulates R-loops

PROVIDER: PRJNA957682 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24225900_1.fastq.gz	Fastqsanger.gz
	SRR24225900_2.fastq.gz	Fastqsanger.gz
	SRR24226183_1.fastq.gz	Fastqsanger.gz
	SRR24226183_2.fastq.gz	Fastqsanger.gz
	SRR24226184_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

The RNA helicase DDX1 associates with the nuclear RNA exosome and modulates R-loops [RNA-seq]

Project description:The RNA exosome is a ten-subunit complex that mediates both RNA processing and degradation. This complex is evolutionarily conserved, ubiquitously expressed, and required for fundamental cellular functions, including rRNA processing. The RNA exosome plays many roles in regulating gene expression and protecting the genome, including modulating the accumulation of R-loops at sites of transcription. The RNA exosome interacts with specific target RNAs for decay or processing by interacting proteins termed cofactors. Attributing to the essential function of the RNA exosome for processes critical in all cells, such as production of mature rRNA, missense mutations in structural subunit genes of this complex cause neurological diseases. One possibility for why point mutations cause neurological diseases is that the RNA exosome partners with cell- or tissue-specific protein cofactors. Here, we employed a murine neuronal cell line (N2A) and performed immunoprecipitation of the RNA exosome subunit, EXOSC3, followed by mass spectrometry to obtain a snapshot of the RNA exosome interactome. We validated an interaction with DDX1, a putative RNA helicase. DDX1 plays roles in double-strand break repair, rRNA processing, and RNA metabolism. To explore shared functions of EXOSC3 and DDX1, we investigated the interaction after inducing DNA damage, and performed DNA/RNA immunoprecipitation followed by sequencing (DRIP-Seq) and RNA-seq on N2A cells depleted of either EXOSC3 or DDX1. These findings suggest that EXOSC3 and DDX1 function together in the absence of severe DNA damage to modulate spontaneous events such as RNA-DNA hybrid (R-loop) formation.

2024-02-12 | GSE230120 | GEO

The RNA helicase DDX1 associates with the nuclear RNA exosome and modulates R-loops [DRIP-seq]

2024-02-12 | GSE230115 | GEO

The RNA helicase DDX1 associates with the nuclear RNA exosome and modulates R-loops [RNA-seq]

Project description:The RNA helicase DDX1 associates with the nuclear RNA exosome and modulates R-loops [RNA-seq]

| PRJNA957691 | ENA

The RNA helicase DDX1 associates with the nuclear RNA exosome and modulates R-loops [DRIP-seq]

Project description:The RNA helicase DDX1 associates with the nuclear RNA exosome and modulates R-loops [DRIP-seq]

| PRJNA957690 | ENA

The putative RNA helicase DDX1 associates with the nuclear RNA exosome and modulates RNA/DNA hybrids (R-loops).

Project description: Not available

| S-EPMC10875230 | biostudies-literature

Targeting XPO1/DDX1-mediated nuclear export of R-loops in inflammaging [RIP-Seq]

Project description:R-loops are three-stranded nucleic acids containing DNA-RNA hybrid and a third displaced ssDNA and are widely distributed across the genome. Dysregulation in R-loop dynamics cause DNA damage and genome instability. Although its role has been extensively investigated in various pathological processes, whether R-loops are perturbed during senescence and tissue aging remains unclear. Here we observe a global decline in R-loop stalling across the genome during senescence. While R-loops in nucleus were dramatically decreased, we detected their significant accumulation in the cytoplasm in senescent cells. We identify their source as nuclear R-loops with a specific enrichment in alpha-satellites, a subset of repetitive elements. Notably, these cytoplasmic R-loops localize into cytoplasmic chromatin fragments (CCF) to induce cGAS-STING innate immune response, and this nucleocytoplasmic transport is dependent on exportin 1 (XPO1)/DEAD-Box helicase 1 (DDX1) complex. Targeting R-loop nuclear export by XPO1 inhibitor Selinexor (KPT-330) suppresses the inflammatory response in senescent cells and relieves inflammaging in aged mice. In summary, our findings linked aberrant accumulation of cytoplasmic R-loops to inflammaging, rendering their nucleocytoplasmic transport process an ideal target for suppressing inflammaging.

2026-04-30 | GSE296054 | GEO

Targeting XPO1/DDX1-mediated nuclear export of R-loops in inflammaging [cytoDRIP-seq]

2026-04-30 | GSE296055 | GEO

Targeting XPO1/DDX1-mediated nuclear export of R-loops in inflammaging [CUT&Run]

2026-04-30 | GSE296056 | GEO

The RNA helicase DDX1 associates with the nuclear RNA exosome and modulates R-loops

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

2024-02-12 | GSE230121 | GEO

RNA Helicase DDX1 Converts RNA G-Quadruplex Structures into R-Loops to Promote IgH Class Switch Recombination

Project description:We performed high-throughput sequencing of chromatin-associated RNA from CH12 cells depleted of Ddx1 and induced to undergo Class Switch Recombination (CSR).

2018-05-08 | GSE95635 | GEO

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