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Characterization of induced cohesin loop extrusion trajectories in living cells [ChIP-seq]

GSE277608 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 147 samples Submitted 2025/06/26 Platform GPL30173Platform GPL24676Platform GPL18573
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 147 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
147 samples: 39 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
Characterization of induced cohesin loop extrusion trajectories in living cellsNature genetics · 2025
Summary (written by the submitters)
The cohesin complex shapes chromosomes by DNA loop extrusion, but individual extrusion trajectories were so far unappreciable in vivo. Here, we developed and validated TArgeted Cohesin Loader (TACL), a system enabling the strong activation of anchored loop extrusion from dozens of defined genomic sites in living cells. Studying their individual loop extrusion trajectories revealed that extruding cohesin-STAG2 stops not only at domain boundaries but at all flanking CTCF sites, engaging them in a complex transient looping network that supports intradomain contacts.
Read the full summary ↓
Cohesin-STAG1 cannot associate with weak CTCF binding sites and fails to similarly support intradomain interactions. NIPBL-MAU2 remains associated with cohesin when stalled at looping CTCF sites, suggesting these factors may also be required for loop stabilization. TACL induces cohesin traffic jams and illegal loops with divergent CTCF sites, demonstrating that stalled cohesin can block extruding cohesin in vivo. Genes exposed to TACL-induced loop extrusion were collectively hindered in transcription and the underlying chromatin altered its accessibility and reduced its H3K27ac marks. Thus, by enabling the study of individual loop extrusion trajectories in vivo, we could assign new functions to players, identify new looping networks and uncover an interplay between loop extrusion, gene transcription and chromatin composition.
Published in
Characterization of induced cohesin loop extrusion trajectories in living cells
Han R, Huang Y, Robers MJ et al. · Nature genetics 2025 · PMID 41102415 · doi:10.1038/s41588-025-02358-0
This dataset
Open GSE277608 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 GSE277608_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 PRJNA1162893 and SRA study SRP533652. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41102415) ↗
Study design
39 conditions, mostly in duplicate
C17,TACL-ON,Input, ×7 C17,mCherry,Input, ×6 C17,TACL-OFF,Input, ×3 C17_RAD21AID_SC1,TACL-ON,Input, ×3 C17_RAD21AID_SC6,mCherry,Input, ×3 C17,TACL-ON,FLAG, ×2 C17,TACL-ON,H3K27ac, ×2 C17,TACL-ON,H3K4me3, ×2 +88 more

Supports a between-group comparison across 90 samples.

How we read this: 39 replicated groups read from 147 sample titles; they account for 90 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

+ 107 more — browse all 147 samples with per-sample file links →

Datasets on a similar topic

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