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

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

ORGANISM(S): Mus musculus

PROVIDER: GSE95635 | GEO | 2018/05/08

REPOSITORIES: GEO

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

Project description:Class switch recombination (CSR) at the immunoglobulin heavy-chain (IgH) locus is associated with the formation of R-loop structures over switch (S) regions. While these often occur co-transcriptionally between nascent RNA and template DNA, we now show that they also form as part of a post-transcriptional mechanism targeting AID to IgH S-regions. This depends on the RNA helicase DDX1 that is also required for CSR in vivo. DDX1 binds to G-quadruplex (G4) structures present in intronic switch transcripts and converts them into S-region R-loops. This in turn targets the cytidine deaminase enzyme AID to S-regions so promoting CSR. Notably R-loop levels over S-regions are diminished by chemical stabilization of G4 RNA or by the expression of a DDX1 ATPase-deficient mutant that acts as a dominant-negative protein to reduce CSR efficiency. In effect, we provide evidence for how S-region transcripts interconvert between G4 and R-loop structures to promote CSR in the IgH locus.

| S-EPMC5971202 | biostudies-literature

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.

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

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DDX1 regulates alternative splicing and insulin secretion in pancreatic β cells

Project description:DEAD-box helicase 1 (DDX1) is a multifunction protein involved in diverse cellular processes including transcription, viral replication, mRNA/miRNA processing, and tRNA splicing. Here, we report a novel function of DDX1 in mRNA alternative splicing in pancreatic β cells. By performing integrated data analysis of high-throughput RNA sequencing (RNA-Seq), and cross-linking and immunoprecipitation coupled with deep sequencing (CLIP-Seq), we identify hundreds of alternative splicing genes that are targeted by DDX1. These DDX1-targeted alternative splicing genes are mainly associated with calcium ion binding, high voltage-gated calcium channel, and transmembrane transporter. Functionally, silencing DDX1 impairs calcium influx and insulin secretion in the pancreatic β cells. These results reveal an important role for DDX1 in the regulation of gene alternative splicing and insulin secretion in pancreatic β cells.

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

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

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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]

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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]

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RNA binding protein DDX1 is responsible for fatty acid mediated repression of insulin translation

Project description:Previous studies have focused on the combined glucolipoxicity that is presence of high glucose and free fatty acid levels effect on insulin gene expression, but the effect of high FFA and normal glucose level on insulin expression is unkown. Here we observed that palmitate can inhibit insulin translation. And we identified a novel insulin mrna binding protein DDX1 that is responsible for fatty acid mediated insulin translation inhibition. Palmitate treatment causes phosphorylation of DDX1 at S295 and dissociation from insulin mRNA, which decreases insulin translation.

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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.

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Polymerase η Recruits DHX9 Helicase to Promote Replication across Guanine Quadruplex Structures.

Project description:DNA polymerase η (Pol η) catalyzes accurate bypass of ultraviolet light-induced cyclobutane pyrimidine dimers, and it also functions in several other related processes, including bypassing DNA with unusual structures. Here, we performed unbiased proteome-wide profiling of Pol η-interacting proteins by using two independent approaches, i.e., proximity labeling and affinity pull-down followed by LC-MS/MS analysis. We identified several helicases, including DHX9, as novel Pol η-interacting proteins. Additionally, ChIP-Seq analysis showed that Pol η is enriched at guanine quadruplex (G4) structure sites in chromatin. Moreover, Pol η promotes the recruitment of DHX9 to G4 structure loci in chromatin and facilitates DHX9-mediated unwinding of G4 structures. Deficiency in Pol η or DHX9 leads to attenuated replication across G4 regions in genomic DNA. Together, we unveiled the interaction between Pol η and DHX9 and demonstrated that the interaction promotes the replicative bypass of G4 structures in chromatin.

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