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Pervasive and programmed nucleosome distortion patterns on single mammalian chromatin fibers

GSE288933 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 162 samples Submitted 2026/01/29 Platform GPL29177Platform GPL28352
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 162 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
162 samples: 41 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
Pervasive and programmed nucleosome distortion on single chromatin fibresNature · 2026
Summary (written by the submitters)
We present a genome-scale method to map the single-molecule co-occupancy of structurally distinct nucleosomes, subnucleosomes, and other protein-DNA interactions via long-read high-resolution adenine methyltransferase footprinting.
Read the full summary ↓
Iteratively Defined Lengths of Inaccessibility (IDLI) classifies nucleosomes on the basis of shared patterns of intranucleosomal accessibility, into: i.) minimally-accessible chromatosomes; ii.) octasomes with stereotyped DNA accessibility from superhelical locations (SHLs) +/-1 through +/-7; iii.) highly-accessible unwrapped nucleosomes; and iv.) subnucleosomal species, such as hexasomes, tetrasomes, and other short DNA protections. Applying IDLI to mouse embryonic stem cell (mESC) chromatin, we discover widespread nucleosomal distortion on individual mammalian chromatin fibers, with >85% of nucleosomes surveyed displaying degrees of intranucleosomally accessible DNA. We observe epigenomic-domain-specific patterns of distorted nucleosome co-occupancy and positioning, including at enhancers, promoters, and mouse satellite repeat sequences. Nucleosome distortion is programmed by the presence of bound transcription factors (TFs) at cognate motifs; occupied TF binding sites are differentially decorated by distorted nucleosomes compared to unbound sites, and degradation experiments establish direct roles for TFs in structuring binding-site proximal nucleosomes. Finally, we apply IDLI in the context of primary mouse hepatocytes, observing evidence for pervasive nucleosomal distortion in vivo. Further genetic experiments reveal a role for the hepatocyte master regulator FOXA2 in directly impacting nucleosome distortion at hepatocyte-specific regulatory elements in vivo. Our work suggests extreme—but regulated—plasticity in nucleosomal DNA accessibility at the single-molecule level. Further, our study offers an essential new framework to model transcription factor binding, nucleosome remodeling, and cell-type specific gene regulation across biological contexts.
Published in
Pervasive and programmed nucleosome distortion on single chromatin fibres
Yang MG, Richter HJ, Wang S et al. · Nature 2026 · PMID 42056506 · doi:10.1038/s41586-026-10418-6
This dataset
Open GSE288933 in finder → Find more 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 GSE288933_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 PRJNA1221005 and SRA study SRP562286. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42056506) ↗
Study design
41 conditions, mostly in duplicate
E14_mESC_Rep30_Seq ×4 E14_mESC_Rep31_Seq ×4 E14_mESC_Rep32_Seq ×4 E14_mESC_Rep33_Seq ×4 E14_mESC_Rep34_Seq ×4 E14_mESC_Rep35_Seq ×4 E14_mESC_Rep36_Seq ×4 E14_mESC_Rep37_Seq ×4 +89 more

Supports a between-group comparison across 106 samples.

How we read this: 41 replicated groups read from 162 sample titles; they account for 106 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

+ 122 more — browse all 162 samples with per-sample file links →

Datasets on a similar topic

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