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RNA transcripts regulate G-quadruplex landscapes through G-loop formation (G4 and R-loop CUT&Tag)

GSE269082 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 28 samples Submitted 2025/04/02 Platform GPL30172
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 28 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
28 samples: 12 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
RNA transcripts regulate G-quadruplex landscapes through G-loop formationScience (New York, N.Y.) · 2025
Summary (written by the submitters)
G-quadruplexes (G4s) are prevalent DNA structures that regulate transcription but also threaten genome stability. How G4 dynamics is controlled remains poorly understood. Here, we report that RNA transcripts govern G4 landscapes through coordinated ‘G-loop’ assembly and disassembly. G-loop assembly involves activation of the ATM and ATR kinases followed by homology-directed invasion of RNA opposite the G4 strand mediated by BRCA2 and RAD51.
Read the full summary ↓
Disassembly of the G-loop resolves the G4 structure via DHX36-FANCJ-mediated G4 unwinding that triggers nucleolytic incision and subsequent hybrid strand renewal by DNA synthesis. Inhibition of G-loop disassembly causes global G4 and R-loop accumulation, leading to transcriptome dysregulation, replication stress, and genome instability. These findings establish an intricate G-loop assembly-disassembly mechanism that controls G4 landscapes and is essential for cellular homeostasis and survival.
Published in
RNA transcripts regulate G-quadruplex landscapes through G-loop formation
Sato K, Lyu J, van den Berg J et al. · Science (New York, N.Y.) 2025 · PMID 40504899 · doi:10.1126/science.adr0493
This dataset
Open GSE269082 in finder → Find more mouse 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 GSE269082_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 PRJNA1120075 and SRA study SRP511761. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40504899) ↗
Study design
12 conditions, mostly in duplicate
G4 (BG4) CUT&Tag WT mESC ×3 G4 (BG4) CUT&Tag DHX36 knockout mESC ×3 G4 (BG4) CUT&Tag FANCJ knockout mESC ×3 G4 (BG4) CUT&Tag DHX36/FANCJ double knockout … ×3 Rloop (S9.6) CUT&Tag WT mESC ×2 Rloop (S9.6) CUT&Tag DHX36 knockout mESC ×2 Rloop (S9.6) CUT&Tag FANCJ knockout mESC ×2 Rloop (S9.6) CUT&Tag DHX36/FANCJ double knock… ×2 +4 more

Supports a case/control comparison: 15 samples read as cases, 9 as controls.

How we read this: 12 replicated groups read from 28 sample titles; they account for 28 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
Datasets on a similar topic

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