Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

G-quadruplex roles in transcription deciphered by comparative transcriptomic analyses

ABSTRACT: G-quadruplex roles in transcription deciphered by comparative transcriptomic analyses

PROVIDER: PRJNA551432 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR9606710_1.fastq.gz	Fastqsanger.gz
	SRR9606710_2.fastq.gz	Fastqsanger.gz
	SRR9606720_1.fastq.gz	Fastqsanger.gz
	SRR9606720_2.fastq.gz	Fastqsanger.gz
	SRR9606711_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 36

Similar Datasets

G-quadruplex roles in transcription deciphered by comparative transcriptomic analyses

Project description:G-quadruplexes (G4) are non-canonical nucleic acid structures that can form at certain DNA or RNA guanine-rich sequences. G4 motifs are dispersed throughout the genome and considerably enriched at promoters, where they flank the transcription start site (TSS) and cluster at the 5’ end of the first intron, which suggests potential regulatory roles of quadruplexes in transcription. To improve our understanding of these roles, we have associated gene expression with the frequency of canonical G4 motifs near gene promoters and characterized perturbations caused by treatment with three G-quadruplex ligands, Pyridostatin and the two bisquinolinium compounds PhenDC3 and PhenDC6. We show that enrichment of G4 motifs characterizes the most actively transcribed genes, challenging the notion that quadruplexes chiefly exert negative regulation by blocking progress of RNA polymerase. G4 ligand-treatment altered splicing of transcripts at genes enriched for G4 motifs at the 5’-end of intron 1, suggesting that G-quadruplexes in the pre-mRNA can regulate splicing. Furthermore, our analysis also revealed some of the effects of G4 ligand treatment that likely reflect quadruplex-dependent replication stress leading to the induction of transcriptional signatures compatible with impaired cell cycle progression. Collectively, our results support the view that G-quadruplexes typically function as positive regulators of transcription, suggesting that quadruplexes may stabilize promoter architecture to enable efficient transcription. This analysis provides strong support for function of quadruplexes near the promoter as regulators of transcription and splicing.

2020-11-02 | GSE133419 | 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

G4 Quadruplex Binding Proteins

Project description:In this study we discover proteins that bind to G4 quadruplex DNA structure. We use modified c-myc quadruplex as a bait, and compare it to the control bait - T15 oligo. We use spectral counts and G-test to determine significant binders. T15 and G4 datafiles are uploaded

2016-07-07 | PXD003501 | Pride

Genome-wide analyses reveal widespread roles for Spt5 in sense and antisense transcription

Project description:Genome-wide analyses reveal widespread roles for Spt5 in sense and antisense transcription

| PRJNA336474 | ENA

Comparative transcriptome analyses of the Drosophila pupal eye

Project description:Comparative transcriptome analyses of the Drosophila pupal eye

| PRJNA673208 | ENA

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

2013-05-08 | GSE45241 | GEO

Bisquinolinium Compounds Induce Quadruplex-Specific Transcriptome Changes in HeLa S3 Cell Line

Project description:The effect of bisquinolinium compounds PhenDC3 and 360A genome wide gene expression changes modulated via promoter based G-quadruplex (G4) motifs. The total RNA was extracted after treating HeLa S3 cells with 10 ÂµM of no molecule (DMSO), 8979A (control molecule), PhenDC3 (G4 specific molecule) or 360A (G4 specific molecule) for 48 hrs in triplicate.

2012-05-29 | E-GEOD-32170 | biostudies-arrayexpress

Non-canonical RNA-binding of the histone lysine demethylase KDM5 through interactions with G-quadruplex sequences

Project description:RNA-binding proteins are important regulators of RNA biogenesis and function, and recent work shows that chromatin- and RNA-binding proteins can have regulatory roles in transcription. Several approaches have been developed to predict RNA-binding proteins and to identify them experimentally at large scale, including binding to structural elements as G-quadruplexes. Here, we show that the histone lysine demethylase protein KDM5 can bind to RNA through interaction with G-quadruplexes with high affinity despite neither being categorized as an RNA-binding protein nor identified as a G-quadruplex binding protein across numerous experimental large-scale and computational studies. In addition to characterizing the KDM5 G-quadruplex interaction we show that RNA is directly involved in the formation of KDM5-containing protein complexes. Computational predictions and comparison to other ARID domain containing proteins suggest that the ARID domain is directly interacting with both DNA and RNA across several proteins. Our work highlights that non-canonical aspects of RNA-binding proteins are present, and that G-quadruplex RNA-binding could provide a regulatory mechanism for chromatin-binding proteins with impact on transcription through linking protein complexes within the cell.

2024-04-11 | PXD050767 | Pride

Comparative transcriptomics analyses of fruiting body development in Fusarium species

Project description:Comparative transcriptomics analyses of fruiting body development in Fusarium species

| PRJNA512482 | ENA

Comparative analyses of human saliva and plasma IgG antibody reactivities

Project description:Comparative analyses of human saliva and plasma IgG antibody reactivities

| PRJNA481267 | ENA