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Dynamic regulation of murine RNA Polymerase III transcription during heat shock stress

GSE282678 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 28 samples Submitted 2025/03/04 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: 14 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
Dynamic regulation of murine RNA polymerase III transcription during heat shock stressGenetics · 2025
Summary (written by the submitters)
Cells respond to many different types of stresses by overhauling gene expression patterns, both at the transcriptional and translational level. Under heat stress, global transcription and translation are inhibited, while the expression of chaperone proteins are preferentially favored. As the direct link between mRNA transcription and protein translation, tRNA expression is intricately regulated during the stress response.
Read the full summary ↓
Despite extensive research into the heat shock response (HSR), the regulation of tRNA expression by RNA Polymerase III (Pol III) transcription has yet to be fully elucidated in mammalian cells. Here, we examine the regulation of Pol III transcription during different stages of heat shock stress in mouse embryonic stem cells (mESCs). We observe that global transcription of tRNAs is downregulated after 30 minutes of heat shock, followed by an overall increase in tRNA transcription after 60 minutes of heat shock. This effect is more evident in tRNAs, though other RNA Pol III gene targets are also similarly affected. Notably, we show that the down-regulation at 30 minutes of heat shock is independent of HSF1, the master transcription factor of the HSR, but that the subsequent increase in expression at 60 minutes requires HSF1. Taken together, these results demonstrate an adaptive RNA Pol III response to heat stress, and an intricate relationship between the canonical HSR and tRNA expression.
Published in
Dynamic regulation of murine RNA polymerase III transcription during heat shock stress
Nguyen TF, Kwan JZJ, Mitchell JE et al. · Genetics 2025 · PMID 40101151 · doi:10.1093/genetics/iyaf042
This dataset
Open GSE282678 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 GSE282678_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 PRJNA1189596 and SRA study SRP547089. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40101151) ↗
Study design
14 conditions, mostly in duplicate
Pol3 CUT&Tag, mESCs, WT, unCond, HS0, ×2 Pol3 CUT&Tag, mESCs, WT, unCond, HS30, ×2 Pol3 CUT&Tag, mESCs, WT, unCond, HS60, ×2 Pol3 CUT&Tag, mESCs, WT, preCond, HS0, ×2 Pol3 CUT&Tag, mESCs, WT, preCond, HS10, ×2 Pol3 CUT&Tag, mESCs, WT, preCond, HS30, ×2 Pol3 CUT&Tag, mESCs, WT, preCond, HS60, ×2 Pol3 CUT&Tag, mESCs, KO, unCond, HS0, ×2 +6 more

Supports a between-group comparison across 28 samples.

How we read this: 14 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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