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Transcriptome-wide identification of transient RNA G-quadruplexes in human cells

ABSTRACT: Transcriptome-wide identification of transient RNA G-quadruplexes in human cells

PROVIDER: PRJNA449395 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6973960_1.fastq.gz	Fastqsanger.gz
	SRR6973960_2.fastq.gz	Fastqsanger.gz
	SRR6973961_1.fastq.gz	Fastqsanger.gz
	SRR6973961_2.fastq.gz	Fastqsanger.gz
	SRR6973962_1.fastq.gz	Fastqsanger.gz

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Transcriptome-wide identification of transient RNA G-quadruplexes in human cells

Project description:We report here on G4RP-seq, which comprises of a cross-linking step, followed by chemical-affinity capture with the G4-specific small-molecule, BioTASQ and target identification using sequencing. This allows for capturing global snapshots of relative average levels of transiently folded G4-RNAs. We observed widespread G4-RNA targets indicative of transient G4 formation in several RNA entities in living human cells. G4RP-seq has also demonstrated that G4-stabilizing ligands (BRACO-19 and RHPS4) can change the G4 transcriptomic landscape, most notably in long non-coding RNAs. G4RP-seq thus provides a proof-of-principle for studying the G4-RNA landscape, as well as new ways of considering the mechanisms underlying G4-RNA formation and the activity of G4-stabilizing ligands.

2018-11-09 | GSE112898 | GEO

Transcriptome-wide identification of transient RNA G-quadruplexes in human cells.

Project description:Guanine-rich RNA sequences can fold into four-stranded structures, termed G-quadruplexes (G4-RNAs), whose biological roles are poorly understood, and in vivo existence is debated. To profile biologically relevant G4-RNA in the human transcriptome, we report here on G4RP-seq, which combines G4-RNA-specific precipitation (G4RP) with sequencing. This protocol comprises a chemical crosslinking step, followed by affinity capture with the G4-specific small-molecule ligand/probe BioTASQ, and target identification by sequencing, allowing for capturing global snapshots of transiently folded G4-RNAs. We detect widespread G4-RNA targets within the transcriptome, indicative of transient G4 formation in living human cells. Using G4RP-seq, we also demonstrate that G4-stabilizing ligands (BRACO-19 and RHPS4) can change the G4 transcriptomic landscape, most notably in long non-coding RNAs. G4RP-seq thus provides a method for studying the G4-RNA landscape, as well as ways of considering the mechanisms underlying G4-RNA formation, and the activity of G4-stabilizing ligands.

| S-EPMC6226477 | biostudies-literature

Identification of endogenous G-quadruplexes (G4s) in human, mouse, and pig

Project description:Identification of endogenous G-quadruplexes (G4s) in human, mouse, and pig

| PRJNA912748 | ENA

Genome-wide profiling of DNA G-quadruplexes in living neurons

Project description:We report a genome-wide mapping of DNA G-quadruplexes and histone modifications in living neurons. We used primary cultured neurons from the fetus mouse cortex. Cultured cells were treated with 2 µM Ara-C at DIV3 to prevent the proliferation of mitotic cells and were harvested at DIV10. For iG4 CUT&Tag, a BG4-expressing plasmid was transfected by electroporation at DIV0.

2021-12-19 | GSE191063 | GEO

Whole genome mapping of DNA G-quadruplexes in multiple species by G4-seq

Project description:The identification of DNA G-quadruplexes (G4s) in the genome is important to study different biological processes in which these structures play a role, such as genome rearrangement, transcriptional regulation and DNA replication. G4-seq allowed the high-throughput experimental mapping of G-quadruplexes in the human genome. We developed here an improved version of this method, named G4-seq2, which we applied to generate G-quadruplexes genomic maps for 12 species, selected as important models organism to study development or as pathogens of clinical relevance. Those multi-species maps, publicly available for the community, will allow to further understand the design principle of G-quadruplex formation in genomic context, to study G-quadruplex biology in those model organisms, to predict ligand targeting for therapeutic usage and to design G-quadruplex computational predictors based on genome-wide experimental measurements.

2018-08-01 | GSE110582 | GEO

Identification of endogenous G-quadruplexes (G4s) in human, mouse, and pig (CUT&Tag)

Project description:G-quadruplexes (G4s) are non-canonical four-stranded structures and emerge as novel genetic regulatory elements. Endogenous G4s (eG4s) can form quadruplex structures and induce double strand breaking during DNA replication, and thus contributing to genomic instability and genome evolution. Besides, eG4s are closely associated with gene expression regulation, and both their stimulative and repressive roles in the genome have been elucidated. Although functions of several specific G4s have been reported, a systematical identification and characterization of eG4s is still unconducted. Here we applied Cleavage Under Targets and Tagmentation (CUT&Tag) for mapping eG4s across human, mouse, and pig at high resolution and low background. We analyzed their genomics distribution, evolutionary conservation, dynamics, regulation, and impacts on gene expression in a single framework. CUT&Tag using G4-specific antibody, BG4

2025-08-06 | GSE217860 | GEO

Genome-wide profiling of DNA G-quadruplexes in living neurons

Project description:Genome-wide profiling of DNA G-quadruplexes in living neurons

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Identification of endogenous G-quadruplexes (G4s) in human, mouse, and pig (CUT&Tag)

Project description:Identification of endogenous G-quadruplexes (G4s) in human, mouse, and pig (CUT&Tag)

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Identification of endogenous G-quadruplexes (G4s) in human, mouse, and pig (ATAC-Seq)

Project description:Identification of endogenous G-quadruplexes (G4s) in human, mouse, and pig (ATAC-Seq)

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Native G-quadruplexes Stabilization Impairs Transcription Initiation

Project description:G-quadruplexes (G4s) are noncanonical DNA secondary structures formed through the self-association of guanines. They are distributed genome-widely and participate in multiple biological processes including gene transcription, and quadruplex-targeted ligands serve as potential therapeutic agents for DNA-targeted therapies. However, the roles of G-quadruplexes in transcriptional regulation remains elusive. Here, we establish a sensitive G4-CUT&Tag method for genome-wide profiling of native G-quadruplexes with high resolution and specificity. We find that native G-quadruplex signals are cell-type specific and are associated with transcriptional regulatory elements with active epigenetic modifications. Promoter-proximal RNA polymerase II pausing promotes native G-quadruplex formation, oppositely, G-quadruplex stabilization by quadruplex-targeted ligands globally reduces RNA polymerase II occupancy at gene promoters as well as nascent RNA synthesis. Moreover, G-quadruplex stabilization modulates chromatin states and impedes transcription initiation via inhibiting the loading of general transcription factors to promoters.Together, these studies reveal a reciprocal regulation between native G-quadruplex dynamics and gene transcription in the genome, which will deepen our knowledge of G-quadruplex biology towards considering therapeutically targeting G-quadruplexes in human diseases.

2021-07-19 | GSE178668 | GEO

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