← BioTransfer GEO Dataset Finder
GEO series

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

GSE270033 Homo sapiens Genome binding/occupancy profiling by high throughput sequencing 6 samples Submitted 2024/06/20 Platform GPL34281Platform GPL24676
Summary
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.
Published in
DNA 5mC methylation inhibits the formation of G-quadruplex structures in the genome
Niu K, Xiang L, Zhang X et al. · Genome biology 2025 · PMID 40646558 · doi:10.1186/s13059-025-03678-4
This dataset
Download

Direct links to NCBI, no account and no request form: the whole study as GSE270033_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 6 samples. Raw sequencing reads are also available from ENA.

Also filed as BioProject PRJNA1124893 and SRA study SRP514325. Searching any of these in the dataset finder brings you back here.

Samples in this study

The sample list for this study is not cached yet. Press Sort into groups and it will be fetched from NCBI.

+ 6 more — browse all 6 samples with per-sample file links →

Similar datasets

Search all human ChIP / ATAC / CUT&Tag datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.