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G-quadruplexes regulate chromatin accessibility and gene expression in Bloom Syndrome [ATAC-seq]

GSE283477 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 20 samples Submitted 2026/04/10 Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 20 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Homo sapiens (human)
Samples
20 samples: 6 conditions, mostly in triplicateGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
G-quadruplexes regulate chromatin accessibility and gene expression in Bloom SyndromebioRxiv : the preprint server for biology · 2026
Summary (written by the submitters)
Bloom Syndrome (BS) is a recessive genetic disorder characterized by hyper-recombination and genome instability. It is caused by mutations in the conserved RecQ helicase gene, BLM, which is essential in maintaining genome integrity and unwinds various aberrant DNA structures. One such structure is DNA G-quadruplexes (G4s), which have broad regulatory functions.
Read the full summary ↓
Although putative G4-forming sequences have been previously implicated in BS, it remains unclear what (dys)regulatory role, if any, endogenous G4 structures may play in BS. Here, we profiled chromatin accessibility and gene expression via ATAC-seq and RNA-seq and mapped endogenous G4 via ChIP-seq in wild-type (WT) vs. BS cell lines. We observed that in BS, differential G4 formation positively correlated with both chromatin accessibility and gene expression. Stabilizing G4 in WT cells with pyridostatin partially phenocopied BS. Additionally, data from a BS family showed that regions with increased chromatin accessibility in BS individuals were also enriched for G4-forming sequences. Our data showed that G4 formation is associated with higher chromatin accessibility and gene expression; likely in BS, unresolved G4 increases focal chromatin accessibility, thereby upregulating gene expression. In summary, our results revealed a central role of G4 in the molecular etiology of BS and provide a new perspective on BLM’s regulatory function through G4s.
Published in
G-quadruplexes regulate chromatin accessibility and gene expression in Bloom Syndrome
Su D, Altmannova V, Soltys V et al. · bioRxiv : the preprint server for biology 2026 · PMID 41867784 · doi:10.64898/2026.03.03.709275
This dataset
Open GSE283477 in finder → Find more human ChIP / ATAC / CUT&Tag datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE283477_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1194031 and SRA study SRP549338. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41867784) ↗
Study design
6 conditions, mostly in triplicate
GM16375, BLM-/-, none, ATACseq ×3 AG14980, Wildtype, none, ATACseq ×3 AG14980, Wildtype, 0.4%DMSO for 24h, ATACseq ×3 AG14980, Wildtype, 10 µM PDS for 24h, ATACseq ×3 GM00637, Wildtype, 0.4%DMSO for 24h, ATACseq ×3 GM00637, Wildtype, 10 µM PDS for 24h, ATACseq ×3 GM16375, BLM-/-, none, ATACseq control, genom… ×1 AG14980, Wildtype, none,ATACseq control, geno… ×1

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 20 sample titles; they account for 18 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
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