GEO series

Nucleosome dynamics render heterochromatin generally accessible in living human cells (qDA seq in MCF7 nuclei in buffer without spermidine)

GSE292648 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 10 samples Submitted 2025/05/01 Platform GPL30173

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 10 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: 10 samples: 5 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: Nucleosome dynamics render heterochromatin accessible in living human cellsNature communications · 2025

Summary (written by the submitters)

The eukaryotic genome is packaged into chromatin, which resembles beads on a string. Each bead consists of a nucleosome containing ~147 bp of DNA wrapped around a histone octamer. The nucleosomal filament undergoes additional folding to create a complex genomic organisation which is thought to restrict the access of gene-regulatory transcription factors to the genome.

Read the full summary ↓

Consequently, it is widely accepted that DNA accessibility, modulated by chromatin architecture, is pivotal in gene regulation. Here, we measure genome accessibility at all GATC sites in living human MCF7 and MCF10A cells, using an adenovirus vector to express the sequence-specific dam DNA adenine methyltransferase. We find that the human genome is globally accessible in living cells, unlike in isolated nuclei. Active promoters are methylated somewhat faster than gene bodies and inactive promoters. Remarkably, both constitutive and facultative heterochromatic sites are methylated only marginally more slowly than euchromatic sites. In contrast, sites in centromeric chromatin are methylated slowly and are partly inaccessible. We conclude that nucleosomes in euchromatin and heterochromatin are highly dynamic in living cells, whereas nucleosomes in centromeric asatellite chromatin are static. A dynamic chromatin architecture implies that simple occlusion of transcription factor binding sites is unlikely to be critical in gene regulation.

Published in

Nucleosome dynamics render heterochromatin accessible in living human cells

Prajapati HK, Xu Z, Eriksson PR et al. · Nature communications 2025 · PMID 40379692 · doi:10.1038/s41467-025-59994-7

This dataset

Open GSE292648 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 GSE292648_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 PRJNA1240587 and SRA study SRP572323. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40379692) ↗

Study design

5 conditions, mostly in duplicate

wild type nuclei, No Dam, No spermidine, ×2 wild type nuclei, 0.78 nM Dam, No spermidine, ×2 wild type nuclei, 1.56 nM Dam, No spermidine, ×2 wild type nuclei, 3.12 nM Dam, No spermidine, ×2 wild type nuclei, 6.25 nM Dam, No spermidine, ×2

Supports a between-group comparison across 10 samples.

How we read this: 5 replicated groups read from 10 sample titles; they account for 10 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

GSM8862800 wild type nuclei, No Dam, No spermidine, rep 1 wild type nuclei, No Da…
GSM8862801 wild type nuclei, 0.78 nM Dam, No spermidine, rep 1 wild type nuclei, 0.78 …
GSM8862802 wild type nuclei, 1.56 nM Dam, No spermidine, rep 1 wild type nuclei, 1.56 …
GSM8862803 wild type nuclei, 3.12 nM Dam, No spermidine, rep 1 wild type nuclei, 3.12 …
GSM8862804 wild type nuclei, 6.25 nM Dam, No spermidine, rep 1 wild type nuclei, 6.25 …
GSM8862805 wild type nuclei, No Dam, No spermidine, rep 2 wild type nuclei, No Da…
GSM8862806 wild type nuclei, 0.78 nM Dam, No spermidine, rep 2 wild type nuclei, 0.78 …
GSM8862807 wild type nuclei, 1.56 nM Dam, No spermidine, rep 2 wild type nuclei, 1.56 …
GSM8862808 wild type nuclei, 3.12 nM Dam, No spermidine, rep 2 wild type nuclei, 3.12 …
GSM8862809 wild type nuclei, 6.25 nM Dam, No spermidine, rep 2 wild type nuclei, 6.25 …

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

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