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DNA 5-methylcytosine regulates genome-wide formation of G-quadruplex structures [CUT&Tag]

ABSTRACT: DNA 5-methylcytosine regulates genome-wide formation of G-quadruplex structures [CUT&Tag]

PROVIDER: PRJNA1124891 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29433400_1.fastq.gz	Fastqsanger.gz
	SRR29433400_2.fastq.gz	Fastqsanger.gz
	SRR29433401_1.fastq.gz	Fastqsanger.gz
	SRR29433401_2.fastq.gz	Fastqsanger.gz

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DNA 5-methylcytosine regulates genome-wide formation of G-quadruplex structures [CUT&TAG]

Project description:DNA 5-methylcytosine regulates genome-wide formation of G-quadruplex structures [CUT&TAG]

| PRJNA914300 | ENA

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

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

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

| PRJNA723824 | ENA

DNA 5-methylcytosine regulates genome-wide formation of G-quadruplex structures

Project description:DNA 5-methylcytosine regulates genome-wide formation of G-quadruplex structures

| PRJNA914298 | ENA

DNA 5-methylcytosine regulates genome-wide formation of G-quadruplex structures [CUT&Tag]

Project description:G-quadruplex structures (G4s) have been identified in genomes of multiple organisms and proven to play important epigenetic regulatory roles in various cellular functions. However, the G4 formation mechanism remains largely unknown. Here, we found a negative correlation between DNA 5mC methylation and G4 abundance. The abundance of genomic G4s significantly increased when the whole-genome methylation level was reduced in DNMT1-knockout cells. This increase was then suppressed by DNMT1 over-expression. And more G4s were detected in the hypomethylated cancer cell line HepG2 and rectal cancer tissues. Besides, 5mC modification significantly inhibited G4 formation of the potential G-quadruplex sequences (PQSs). The transcription of genes with 5mC modification sites in their promoter PQSs was affected after treatment with G4 stabilizer pyridostatin or methylation inhibitor 5-aza-dC. The global reduction of genomic methylation elevates gene transcription levels through increased G4s. Taken together, DNA 5mC methylation prevents PQSs from folding into G4s in genomes.

2024-06-20 | GSE270035 | GEO

DNA 5-methylcytosine regulates genome-wide formation of G-quadruplex structures [CUT&TAG]

2022-12-20 | GSE221436 | GEO

DNA 5-methylcytosine regulates genome-wide formation of G-quadruplex structures [WGBS]

Project description:DNA 5-methylcytosine regulates genome-wide formation of G-quadruplex structures [WGBS]

| PRJNA1124892 | ENA

DNA 5-methylcytosine regulates genome-wide formation of G-quadruplex structures [ATAC-seq]

Project description:DNA 5-methylcytosine regulates genome-wide formation of G-quadruplex structures [ATAC-seq]

| PRJNA1124893 | ENA

DNA 5-methylcytosine regulates genome-wide formation of G-quadruplex structures [RNA-seq]

Project description:DNA 5-methylcytosine regulates genome-wide formation of G-quadruplex structures [RNA-seq]

| PRJNA914301 | ENA

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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