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DNA G-quadruplex structures act as functional elements in α- and β-globin enhancers

GSE267666 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 238 samples Submitted 2025/05/13 Platform GPL18573Platform GPL30173
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 238 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
238 samples: 78 conditions, mostly in duplicateGroups 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
DNA G-quadruplex structures act as functional elements in α- and β-globin enhancersGenome biology · 2025
Summary (written by the submitters)
Enhancer elements interact with target genes at a distance to modulate their expression, but the molecular details of enhancer-promoter interaction are incompletely understood. G-quadruplex DNA secondary structures (G4s) have recently been shown to co-occur with 3D chromatin interactions, however, the functional importance of G4s within enhancers remains unclear.
Read the full summary ↓
Results: In this study we identify novel G4 structures within two locus control regions at the human α- and β- globin loci. We find that mutating G4 motifs by genome editing prevents their folding into G4 structures in cells and disrupts 3D enhancer-promoter interactions and target gene expression in a manner comparable to whole enhancer deletion. Furthermore, restoration of G4 structure formation using a dissimilar G4-forming primary sequence recovers specific enhancer-gene interactions and gene expression. Through proteomic, biophysical, and genomic profiling, we find that enhancer G4s are tightly linked to the maintenance of an active chromatin state and RNA polymerase II recruitment to regulate target gene expression.
Published in
DNA G-quadruplex structures act as functional elements in α- and β-globin enhancers
Doyle C, Herka K, Flynn SM et al. · Genome biology 2025 · PMID 40468392 · doi:10.1186/s13059-025-03627-1
This dataset
Open GSE267666 in finder → Find more human RNA-seq 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 GSE267666_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 PRJNA1112375 and SRA study SRP508181. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40468392) ↗
Study design
78 conditions, mostly in duplicate
RNAseq_aRes1_B ×8 RNAseq_aRes2_B ×8 RNAseq_aWT_B ×8 RNAseq_aMut1_B ×7 RNAPII_5SP_aMut1_B ×4 RNAPII_5SP_aRes_B ×4 RNAPII_5SP_aWT_B ×4 RNAseq_aMut2_B ×4 +82 more

Supports a between-group comparison across 226 samples.

How we read this: 78 replicated groups read from 238 sample titles; they account for 226 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

+ 198 more — browse all 238 samples with per-sample file links →

Datasets on a similar topic

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