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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE230121 | GEO | 2024/02/12

REPOSITORIES: GEO

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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

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

Project description: Not available

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Nuclear exosome

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

2016-08-12 | GSE75587 | GEO

Mpp6 Incorporation in the Nuclear Exosome Contributes to RNA Channeling through the Mtr4 Helicase.

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Helicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex.

Project description: Not available

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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

The MTR4 helicase recruits nuclear adaptors of the human RNA exosome using distinct arch-interacting motifs.

Project description: Not available

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