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Widespread transmission of DNA supercoiling and selective topoisomerase utilization regulates torsional stress within the neuronal genome [RNA-Seq]

GSE231690 Mus musculus (mouse) RNA-seq (gene expression) 3 samples Submitted 2026/07/14 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 3 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
3 samples: 3 × RNA-seq_in_Control WTGroups 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)
DNA supercoiling has the potential to alter gene transcription and chromatin topology, yet how its distribution is regulated on a genome-wide level is poorly understood. Here we utilized psoralen crosslinking and sequencing (TMP-seq) to assess the distribution of underwound DNA at high resolution in postmitotic neurons.
Read the full summary ↓
We report that supercoiling propagates widely (> 200 kb) from the sites of active RNAPII and that its distribution is constrained by chromosome compartments and by specific nucleosome configurations, including H3K27me3-rich regions and broad distributions of active promoter-related chromatin marks. Underwound DNA does not accrue upstream of expressed genes in postmitotic neurons, which could shield them from cumulative torsional stress. Inhibiting either transcription or TOP1 affect underwound DNA levels genome-wide; however, supercoiling at the boundaries of expressed genes is minimally perturbed, indicating that dynamic supercoiling is not locally confined to sites of RNAPII activity at expressed genes. Surprisingly, TOP1 inhibition elevates supercoiling but stimulates nascent transcription at most genes and other sites of transcription, including enhancers, suggesting that torsional stress generally favors transcription, and that topoisomerase activity is not essential for transcription at most genes. We show that the induction of cryptic transcription within gene bodies, and not supercoiling buildup, could underlie the vulnerability of long neuronal genes to topoisomerase inhibition. These observations illuminate how chromatin organization governs the distribution of torsional stress within the genome and how the interplay of supercoiling and topoisomerases regulates transcription.
This dataset
Open GSE231690 in finder → Find more mouse 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 GSE231690_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA967310 and SRA study SRP435966. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
3 × RNA-seq_in_Control WT

Supports a between-group comparison across 3 samples.

How we read this: 1 replicated groups read from 3 sample titles; they account for 3 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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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.