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Transcriptional memory is conferred by combined heritable maintenance and local removal of selective chromatin modifications

GSE249136 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 102 samples Submitted 2025/01/20 Platform GPL18573
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 102 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
Homo sapiens (human)
Samples
102 samples: 40 conditions, mostly in triplicateGroups 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
Heritable maintenance of chromatin modifications confers transcriptional memory of interferon-γ signalingNature structural & molecular biology · 2025
Summary (written by the submitters)
Interferon-γ (IFNγ) transiently activates genes involved in inflammation and innate immunity. A subset of targets maintain a mitotically heritable memory of prior IFNγ exposure resulting in hyperactivation upon reexposure. Here we discovered that the active chromatin marks H3K4me1, H3K14Ac and H4K16Ac are established during IFNγ priming and selectively maintained on a cluster of GBP genes for at least 7 days in dividing cells in the absence of transcription.
Read the full summary ↓
The histone acetyltransferase KAT7 is required for the accelerated GBP reactivation upon reexposure to IFNγ. In naïve cells, we find the GBP cluster is maintained in low-level repressive chromatin marked by H3K27me3 limiting priming in a PRC2-dependent manner. Unexpectedly, IFNγ results in transient accumulation of this repressive mark but is then selectively depleted from primed GBP genes during the memory phase facilitating hyperactivation of primed cells. Furthermore, we identified a cis-regulatory element that makes transient, long-range contacts across the GBP cluster and acts as a repressor, primarily to curb the hyperactivation of previously IFNγ-primed cells. Combined our results identify the putative chromatin basis for long-term transcriptional memory of interferon signalling that may contribute to enhanced innate immunity.
Published in
Heritable maintenance of chromatin modifications confers transcriptional memory of interferon-γ signaling
Mikulski P, Tehrani SSH, Kogan A et al. · Nature structural & molecular biology 2025 · PMID 40186025 · doi:10.1038/s41594-025-01522-8
This dataset
Open GSE249136 in finder → Find more human 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 GSE249136_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 PRJNA1047536 and SRA study SRP475316. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40186025) ↗
Study design
40 conditions, mostly in triplicate
Hela, Naive, H3K4me3, ×3 Hela, Primed7d, H3K4me3, ×3 Hela, Naive, H3K4me1, ×3 Hela, Priming, H3K4me1, ×3 Hela, Primed2d, H3K4me1, ×3 Hela, Naive, H3K14ac, ×3 Hela, Priming, H3K14ac, ×3 Hela, Primed2d, H3K14ac, ×3 +32 more

Supports a between-group comparison across 102 samples.

How we read this: 40 replicated groups read from 102 sample titles; they account for 102 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

+ 62 more — browse all 102 samples with per-sample file links →

Datasets on a similar topic

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