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G-quadruplex structures regulate long-range transcriptional reprogramming to promote drug resistance in ovarian cancer [CUT&Tag]

ABSTRACT: G-quadruplex structures regulate long-range transcriptional reprogramming to promote drug resistance in ovarian cancer [CUT&Tag]

PROVIDER: PRJNA1173756 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR31018155_1.fastq.gz	Fastqsanger.gz
	SRR31018155_2.fastq.gz	Fastqsanger.gz
	SRR31018156_1.fastq.gz	Fastqsanger.gz
	SRR31018156_2.fastq.gz	Fastqsanger.gz
	SRR31018157_1.fastq.gz	Fastqsanger.gz

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G-quadruplex structures regulate long-range transcriptional reprogramming to promote drug resistance in ovarian cancer [CUT&Tag]

Project description:Enhancers are regulatory elements of the genome involved in transcriptional regulation and reprogramming. Similarly, we propose that secondary DNA structures termed G-quadruplexes could also be impacting transcription in an enhancer based way via long-range interactions to bring together regulatory elements of the genome. In this study, we map G-quadruplex structures and h3k27ac enhancer marks in a paired ovarian cancer cell line; PEO1 and PEO4. We endeavour to use these findings to help link the transcriptional function of G-quadruplexes with enchancer in chemotherapy sensitive (PEO1) and chemotherapy resistant (PEO4) ovarian cancer cells.

2025-06-06 | GSE279641 | GEO

G-quadruplex structures regulate long-range transcriptional reprogramming to promote drug resistance in ovarian cancer [ChIP-seq]

Project description:G-quadruplex ChIP-seq has been performed to establish genomic maps of G-quadruplex structures in chemotherapy sensitive (PEO1) and chemotherapy resistant (PEO4) ovarian cancer cell lines to uncover how the changes in G-quadruplex landscape may contribute to the development of chemotherapy resistance for the first time.

2025-06-06 | GSE279497 | GEO

G-quadruplex structures regulate long-range transcriptional reprogramming to promote drug resistance in ovarian cancer [RNA-seq]

Project description:G-quadruplexes are secondary DNA structures which have been shown to have an impact on gene transcription via a variety of mechanisms, In this study we generate RNA-seq data of wildtype chemotherpay sensitive (PEO1 A) and chemostherapy resistant (PEO4 A) ovarian cancer cells to intersect with G-quadruplex mapping data to assess how transcription is impacted by G-quadruplex formation. In another variation of the PEO1/4 cell line, in which the PEO1 B cell line has a reversion mutation to reinstate BRCA2, we used the G-quadruplex stabilising molecule pyridostatin (PDS) to treat PEO1 B and its counterpart PEO4 B for either 0, 2 or 6 hours to see how stabilising G-quadruplexes effects gene expression in a temporal manner.

2025-06-06 | GSE279501 | GEO

Genome-wide mapping of G-quadruplex structures with CUT&Tag

Project description:Single-stranded genomic DNA can fold into G-quadruplex (G4) structures or form DNA:RNA hybrids (R loops). Recent evidence suggests that such non-canonical DNA structures affect gene expression, DNA methylation, replication fork progression and genome stability. When and how G4 structures form and are resolved remains unclear. Here we report the use of Cleavage Under Targets and Tagmentation (CUT&Tag) for mapping native G4 in mammalian cell lines at high resolution and low background. Mild native conditions used for the procedure retain more G4 structures and provide a higher signal-to-noise ratio than ChIP-based methods. We determine the G4 landscape of mouse embryonic stem cells (mESC), discovering G4 formation at active and poised promoters and enhancers. We discover that the presence of G4 motifs and G4 structures distinguishes active and primed enhancers in mESCs. Further performing R-loop CUT&Tag, we demonstrate the widespread co-occurence of single-stranded DNA, G4s and R loops, suggesting an intricate interrelation of non-canonical DNA structures, transcription and the formation and turnover of G4s.

2021-04-27 | GSE173103 | 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

Genome-wide mapping of G-quadruplex structures with CUT&Tag

Project description:Genome-wide mapping of G-quadruplex structures with CUT&Tag

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G-quadruplex structures regulate long-range transcriptional reprogramming to promote drug resistance in ovarian cancer [ChIP-seq]

Project description:G-quadruplex structures regulate long-range transcriptional reprogramming to promote drug resistance in ovarian cancer [ChIP-seq]

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G-quadruplex structures regulate long-range transcriptional reprogramming to promote drug resistance in ovarian cancer [RNA-seq]

Project description:G-quadruplex structures regulate long-range transcriptional reprogramming to promote drug resistance in ovarian cancer [RNA-seq]

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G-quadruplex structures regulate long-range transcriptional reprogramming to promote drug resistance in ovarian cancer [ATAC-seq]

Project description:G-quadruplex structures regulate long-range transcriptional reprogramming to promote drug resistance in ovarian cancer [ATAC-seq]

| PRJNA1173148 | ENA

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

2013-05-08 | GSE45241 | GEO