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A histone hyperacetylation pulse induces cellular memory of gene expression and 3-dimensional genome folding

GSE280487 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 116 samples Submitted 2024/11/22 Platform GPL28457
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 116 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
116 samples: 52 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.
Summary (written by the submitters)
Epigenetic memory enables the stable propagation of gene expression patterns in response to transient developmental and environmental stimuli. Although 3-dimensional (3D) organisation is emerging as a key regulator of genome function due its role in gene expression control, it is unknown whether it contributes to cellular memory. Here, we establish that acute perturbation of the epigenome can induce cellular memory of gene expression in mouse embryonic stem cells (mESCs).
Read the full summary ↓
Specifically, we uncover how a pulse of histone deacetylase inhibition translates to changes in the histone acetylation and methylation landscape, as well as global and local genome folding. While most epigenomic and transcriptional changes are initially reversed once the perturbation is removed, architectural features are not fully reestablished. Upon a second transient pulse of hyperacetylation, hundreds of genes maintain their dysregulated state. Using ultra-deep Micro-C, we associate memory of gene expression with enhancer-promoter contacts and repressive chromatin topology mediated by Polycomb. These results uncover the complex interplay between different epigenetic regulatory layers and establish a novel link between genome folding and cellular memory.
This dataset
Open GSE280487 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 GSE280487_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 PRJNA1117356 and SRA study SRP510225. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
52 conditions, mostly in duplicate
H3K27ac ChIP-seq of mESC TSA-treated ×3 H3K27ac ChIP-seq mESC 24h recovery after TSA … ×3 ChIP input for 24h recovery ×3 H3K4me1 ChIP-seq of mESC DMSO control ×2 H3K4me1 ChIP-seq of mESC TSA-treated ×2 H3K4me1 ChIP-seq mESC 24h recovery after TSA … ×2 H3K4me3 ChIP-seq of mESC DMSO control ×2 H3K4me3 ChIP-seq of mESC TSA-treated ×2 +53 more

Supports a case/control comparison: 31 samples read as cases, 27 as controls.

How we read this: 52 replicated groups read from 116 sample titles; they account for 107 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

+ 76 more — browse all 116 samples with per-sample file links →

Datasets on a similar topic

Search all mouse ChIP / ATAC / CUT&Tag datasets in GEO →

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