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Stress promotes RNA G-quadruplex folding in human cells

ABSTRACT: Stress promotes RNA G-quadruplex folding in human cells

PROVIDER: PRJNA826109 | ENA |

REPOSITORIES: ENA

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Stress promotes RNA G-quadruplex folding in human cells

Project description:Guanine (G)-rich nucleic acids can fold into G-quadruplex (G4) structures under permissive conditions. Although many RNAs contain sequences that fold into RNA G4s (rG4s) in vitro, their folding and functions in vivo are not well understood. Here, we showed that the folding of putative rG4s in human cells into rG4 structures was dynamically induced by stress. By using high-throughput dimethylsulfate probing, we identified hundreds of endogenous stress-induced rG4s. Our results demonstrated that stress-induced rG4s were enriched in mRNA 3′-untranslated regions and enhanced mRNA stability. Furthermore, stress-induced rG4 folding was readily reversible upon stress removal. In summary, our study revealed the dynamic regulation of rG4 folding in living human cells and suggests suggested that widespread rG4 motifs may have a global regulatory impact on mRNA stability and cellular stress response.

2022-12-15 | GSE200706 | GEO

Stress promotes RNA G-quadruplex folding in human cells.

Project description:Guanine (G)-rich nucleic acids can fold into G-quadruplex (G4) structures under permissive conditions. Although many RNAs contain sequences that fold into RNA G4s (rG4s) in vitro, their folding and functions in vivo are not well understood. In this report, we showed that the folding of putative rG4s in human cells into rG4 structures is dynamically regulated under stress. By using high-throughput dimethylsulfate (DMS) probing, we identified hundreds of endogenous stress-induced rG4s, and validated them by using an rG4 pull-down approach. Our results demonstrate that stress-induced rG4s are enriched in mRNA 3'-untranslated regions and enhance mRNA stability. Furthermore, stress-induced rG4 folding is readily reversible upon stress removal. In summary, our study revealed the dynamic regulation of rG4 folding in human cells and suggested that widespread rG4 motifs may have a global regulatory impact on mRNA stability and cellular stress response.

| S-EPMC9839774 | biostudies-literature

Epigenetic regulation by dynamic RNA G-quadruplex folding and unfolding (RNA-Seq)

Project description:Epigenetic regulation by dynamic RNA G-quadruplex folding and unfolding (RNA-Seq)

| PRJNA907003 | ENA

Epigenetic regulation by dynamic RNA G-quadruplex folding and unfolding (CHART-Seq)

Project description:Epigenetic regulation by dynamic RNA G-quadruplex folding and unfolding (CHART-Seq)

| PRJNA907001 | ENA

Epigenetic regulation by dynamic RNA G-quadruplex folding and unfolding (DMS-Seq)

Project description:Epigenetic regulation by dynamic RNA G-quadruplex folding and unfolding (DMS-Seq)

| PRJNA907004 | ENA

Epigenetic regulation by dynamic RNA G-quadruplex folding and unfolding (ChIP-Seq)

Project description:Epigenetic regulation by dynamic RNA G-quadruplex folding and unfolding (ChIP-Seq)

| PRJNA907002 | ENA

Promoter G-quadruplex folding precedes transcription and is controlled by chromatin

Project description:Promoter G-quadruplex folding precedes transcription and is controlled by chromatin

| PRJNA681342 | ENA

ATRX promotes heterochromatin formation to protect cells from G-quadruplex DNA-mediated stress

Project description:ATRX promotes heterochromatin formation to protect cells from G-quadruplex DNA-mediated stress

| PRJNA634521 | ENA

Promoter G-quadruplex folding precedes transcription and is controlled by chromatin

Project description:Four stranded DNA G-quadruplex (G4) structures are common features of the human genome that are primarily found in active promoters associated with elevated transcription. Here, we explore the relationship between the folding of G4s in promoters, transcription and chromatin state. Transcriptional inhibition by DRB or by triptolide reveals that promoter G4 formation, as assessed G4 ChIP-seq, is not reliant on transcriptional activity. Establishing a link between G4 formation and chromatin accessibility, we demonstrate that chromatin compaction leads to loss of promoter G4s accompanied by a corresponding loss of RNA polymerase II (Pol II). Furthermore, pre-treatment of cells with a G4-stabilising ligand can mitigate Pol II loss at promoters induced by chromatin compaction. Overall, our findings show that G4 formation is fostered in accessible chromatin and does not require active transcription. Furthermore, our findings suggest that G4s have a role to recruit Pol II to promote transcription.

2021-03-31 | GSE162299 | GEO

G-Quadruplex structures are stable and detectable in human genomic DNA.

Project description:The G-quadruplex is an alternative DNA structural motif that is considered to be functionally important in the mammalian genome. Herein, we address the hypothesis that G-quadruplex structures can exist within double-stranded genomic DNA using a G-quadruplex-specific probe. An engineered antibody is employed to enrich for DNA containing G-quadruplex structures, followed by deep sequencing to detect and map G-quadruplexes at high resolution in genomic DNA from human breast adenocarcinoma cells. Our high sensitivity structure-based pull-down strategy enables the isolation of genomic DNA fragments bearing a single as well as multiple G-quadruplex structures. Stable G-quadruplex structures are found in sub-telomeres, gene bodies and gene regulatory regions. For a sample of identified target genes, we show that G-quadruplex stabilizing ligands can modulate transcription. These results confirm the existence of G-quadruplex structures and their persistence in human genomic DNA. Four independent libraries have been enriched in DNA G-quadruplex structures using a G-quadruplex-specific probe. One genomic input library was sequenced as control. Deep-sequencing of these libraries allowed the mapping of G-quadruplexes on the genome.

2013-05-08 | E-GEOD-45241 | biostudies-arrayexpress

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