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Extensive mutual influences of SMC complexes shape 3D genome folding

GSE269952 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 176 samples Submitted 2024/12/21 Platform GPL28330
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 176 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
Mus musculus (mouse)
Samples
176 samples: 43 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
Extensive mutual influences of SMC complexes shape 3D genome foldingNature · 2025
Summary (written by the submitters)
Mammalian genomes are folded by the distinct actions of SMC complexes which include the chromatin loop-extruding cohesin, the sister-chromatid cohesive cohesin, and the mitotic chromosome-associated condensins 1-3. While these complexes function at different stages of the cell cycle, they co-exist on chromatin during the G2/M-phase transition, when genome structure undergoes a dramatic reorganization 1,2.
Read the full summary ↓
Yet, how distinct SMC complexes affect each other and how their mutual interplay orchestrates the dynamic folding of 3D genome remains elusive. Here, we engineered all possible cohesin/condensin configurations on mitotic chromosomes to delineate the concerted, mutually influential action of SMC complexes. We find that: (i) Condensin disrupts extrusive-cohesin binding at CTCF sites, thereby promoting the disassembly of interphase TADs and loops during mitotic progression. Conversely, extrusive-cohesin impedes condensin mediated mitotic chromosome spiralization. (ii) Condensin diminishes cohesive-cohesin peaks and, conversely, cohesive-cohesin antagonizes condensin-mediated mitotic chromosome longitudinal shortening. Co-presence of extrusive- and cohesive-cohesin synergizes these effects and dramatically inhibits mitotic chromosome condensation. (iii) Extrusive-cohesin positions cohesive-cohesin at CTCF binding sites. However, cohesive-cohesin by itself cannot be arrested by CTCF molecules, is insufficient to establish TADs or loops and lacks loop extrusion capacity, implying non-overlapping function with extrusive-cohesin. (iv) Cohesive-cohesin restricts extrusive-cohesin mediated chromatin loop expansion. Collectively, our data describe a comprehensive three-way interplay among major SMC complexes that dynamically sculpts chromatin architecture during cell cycle progression.
Published in
Extensive mutual influences of SMC complexes shape 3D genome folding
Zhao H, Shu L, Qin S et al. · Nature 2025 · PMID 40011778 · doi:10.1038/s41586-025-08638-3
This dataset
Open GSE269952 in finder → Find more mouse 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 GSE269952_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 PRJNA1124163 and SRA study SRP514090. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40011778) ↗
Study design
43 conditions, mostly in duplicate
flag_configuration4_clone16_9aa_S ×4 flag_configuration4_clone17_9aa_S ×4 configuration5_short_release_clone ×3 configuration5_clone ×3 configuration7_short_release_clone ×3 configuration6_clone ×3 configuration6_light_load_clone ×3 configuration9_clone ×2 +116 more

Supports a between-group comparison across 95 samples.

How we read this: 43 replicated groups read from 176 sample titles; they account for 95 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

+ 136 more — browse all 176 samples with per-sample file links →

Datasets on a similar topic

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