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G-quadruplex DNA suppresses transcription during DNA replication

GSE287896 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 80 samples Submitted 2025/01/29 Platform GPL29480Platform GPL24676Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 80 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
80 samples: 60 distinct titles, 18 of them repeatedGroups 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.
Summary (written by the submitters)
In eukaryotic cells, although the B-form double helix is the predominant structure of DNA, various non-B-form DNA structures, including G-quadruplex DNA (G4-DNA), are also widely present. For a long time, G4-DNA has been thought to impede DNA replication due to its unique spatial conformation. However, this study demonstrates that S phase G4-DNA accumulation, far from being a passive byproduct, actively functions as a critical safeguard for genomic stability.
Read the full summary ↓
Contrary to the traditional view of G4-DNA as a replication barrier, its physiological increase during Early S phase minimizes impact on replication itself. Instead, S phase G4-DNA specifically suppresses transcription by stabilizing the negative elongation factor (NELF) complex, thereby preventing transcription-replication conflicts (TRCs) by spatiotemporally segregating transcription and replication. Replication Factor C3 (RFC3), a component of the replication machinery, directly binds and stabilizes G4-DNA to promote its S phase accumulation. Disruption of RFC3 function or G4-DNA unwinding during S phase releases transcriptional suppression, exacerbating TRCs.
This dataset
Open GSE287896 in finder → Find more 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 GSE287896_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 PRJNA1214877 and SRA study SRP559531. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
60 distinct titles, 18 of them repeated
RNA-SEQ for shCtrl cells ×3 RNA-SEQ for shRFC3 cells ×3 CUT&Tag of G4-DNA in G1/S cells ×2 CUT&Tag of G4-DNA in Early_S cells ×2 CUT&Tag of G4-DNA in Late_S cells ×2 CUT&Tag of RNAPII S2P in G1/S cells ×2 CUT&Tag of RNAPII S2P in Early_S cells ×2 CUT&Tag of RNAPII S2P in Late_S cells ×2 +10 more

Supports a case/control comparison: 1 samples read as cases, 27 as controls.

How we read this: Read from 80 sample titles: 60 distinct titles with little repetition. 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

+ 40 more — browse all 80 samples with per-sample file links →

Datasets on a similar topic

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