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G-quadruplexes are promoter elements controlling nucleosome exclusion and RNA polymerase II pausing

GSE159276 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 63 samples Submitted 2025/04/15 Platform GPL24247Platform GPL11154Platform GPL24676Platform GPL10999
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 63 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
Mus musculus (mouse)
Samples
63 samples: 24 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
G-quadruplexes are promoter elements controlling nucleosome exclusion and RNA polymerase II pausingNature genetics · 2025
Summary (written by the submitters)
Despite their central role in transcription, it has been difficult to define universal sequences associated with eukaryotic promoters. Within the chromatin context, recruitment of transcriptional machinery requires promoter opening, but how DNA elements contribute to this process is unclear. Here we show that G-quadruplex (G4) secondary DNA structures are highly enriched at mammalian promoters.
Read the full summary ↓
G4s are located at the deepest point of nucleosome exclusion at promoters and correlate with maximum promoter activity. We found that experimental G4s exclude nucleosomes in vivo and in vitro while favouring strong positioning. At model promoters, impairing G4s affected both transcriptional activity and chromatin opening. G4 destabilization also resulted in an inactive promoter state and affected the transition to effective RNA production. Finally, G4 stabilization resulted in global reduction of proximal promoter pausing. Altogether, our data introduce G4s as bona fide promoter elements allowing nucleosome exclusion and facilitating pause-release by RNA polymerase II.
Published in
G-quadruplexes are promoter elements controlling nucleosome exclusion and RNA polymerase II pausing
Esnault C, Zine El Aabidine A, Robert MC et al. · Nature genetics 2025 · PMID 40696173 · doi:10.1038/s41588-025-02263-6
This dataset
Open GSE159276 in finder → Find more 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 GSE159276_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 PRJNA668189 and SRA study SRP286816. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40696173) ↗
Study design
24 conditions, mostly in duplicate
Raji_chrRNA-seq_T0_PDS_rep1 ×4 Raji_chrRNA-seq_T0_PDS_rep2 ×4 Raji_chrRNA-seq_T10_PDS_rep1 ×4 Raji_chrRNA-seq_T10_PDS_rep2 ×4 NIH3T3_G4access_Starved ×3 NIH3T3_G4access_FCS_15min ×3 NIH3T3_chrRNA-seq_Starved ×3 NIH3T3_chrRNA-seq_FCS_15min ×3 +19 more

Supports a between-group comparison across 60 samples.

How we read this: 24 replicated groups read from 63 sample titles; they account for 60 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

+ 23 more — browse all 63 samples with per-sample file links →

Datasets on a similar topic

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