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CTCF depletion uncouples the role of enhancer-promoter interactions and higher-order chromatin hubs in gene regulation during cellular differentiation [ChIPmentation]

GSE263637 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 42 samples Submitted 2025/03/03 Platform GPL21697Platform GPL30173
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 42 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
42 samples: 15 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
CTCF depletion decouples enhancer-mediated gene activation from chromatin hub formationNature structural & molecular biology · 2025
Summary (written by the submitters)
Enhancers and promoters interact in 3D chromatin structures to regulate gene expression. The mechanisms that drive the formation of these structures and their function during cellular differentiation are incompletely understood. Here, we study the structure-function relationship of the genome in a lymphoid-to-myeloid differentiation system at very high resolution.
Read the full summary ↓
We demonstrate a close correlation between binding of regulatory proteins, formation of chromatin interactions, and gene expression. By integrating analysis of single-allele topologies and computational modeling, we show that tissue-specific gene loci are organized into chromatin hubs, characterized by cooperative interactions between multiple enhancers, promoters, and CTCF-binding sites. Depletion of CTCF leads to a near-complete loss of these structures, which indicates that CTCF-mediated interactions provide a scaffold for chromatin hub formation. In contrast, the effects of CTCF depletion on gene expression are relatively mild and can be explained by rewired enhancer-promoter interactions. Together, our results demonstrate an instructive role for enhancer-promoter interactions in gene regulation during cellular differentiation, which does not depend on cooperative interactions in chromatin hubs.
Published in
CTCF depletion decouples enhancer-mediated gene activation from chromatin hub formation
Karpinska MA, Zhu Y, Fakhraei Ghazvini Z et al. · Nature structural & molecular biology 2025 · PMID 40360814 · doi:10.1038/s41594-025-01555-z
This dataset
Open GSE263637 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 GSE263637_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 PRJNA1098618 and SRA study SRP500715. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40360814) ↗
Study design
15 conditions, mostly in triplicate
BLaER, SMC1A_ChIP_0h ×3 BLaER, SMC1A_ChIP_12h ×3 BLaER, SMC1A_ChIP_24h ×3 BLaER, SMC1A_ChIP_72h ×3 BLaER, SMC1A_ChIP_96h ×3 BLaER, MED26_ChIP_0h ×3 BLaER, MED26_ChIP_12h ×3 BLaER, MED26_ChIP_24h ×3 +9 more

Supports a between-group comparison across 40 samples.

How we read this: 15 replicated groups read from 42 sample titles; they account for 40 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

+ 2 more — browse all 42 samples with per-sample file links →

Datasets on a similar topic

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