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De novo formation of cis-regulatory contacts in the absence of NIPBL-driven chromatin loop extrusion

GSE256073 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 30 samples Submitted 2026/02/18 Platform GPL28330
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 30 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
30 samples: 25 distinct titles, 5 of them repeatedGroups 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
De novo formation of cis-regulatory contacts in the absence of NIPBL-driven chromatin loop extrusionNature genetics · 2026
Summary (written by the submitters)
NIPBL promotes chromatin loop extrusion by the cohesin complex until it stalls at convergently oriented CTCF sites, forming structural loops. In contrast, a large fraction of loops connecting cis-regulatory elements (CREs) can be maintained in the absence of cohesin. However, whether de novo establishment of CRE loops requires loop extrusion remains unclear.
Read the full summary ↓
To address this question, we characterized the formation of structural and CRE loops during the mitosis-to-G1-phase transition in the absence of NIPBL. Structural loop formation was impaired proportionally to loop length. Computational modeling supports these observations, suggesting that NIPBL enhances cohesin extrusion beyond NIPBL’s known loading function. Importantly the majority of CRE loops, regardless of length, was established independently of loop extrusion. While globally gene activation showed little impairment, NIPBL loss delayed the formation of CRE loops involving weak enhancers. Collectively, our findings reveal that post-mitotic establishment of regulatory contacts and gene transcription can occur independently of chromatin loop extrusion.
Published in
De novo formation of cis-regulatory contacts in the absence of NIPBL-driven chromatin loop extrusion
Aboreden NG, Zhao H, Yang JH et al. · Nature genetics 2026 · PMID 41974991 · doi:10.1038/s41588-026-02565-3
This dataset
Open GSE256073 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 GSE256073_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 PRJNA1077991 and SRA study SRP490357. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41974991) ↗
Study design
25 distinct titles, 5 of them repeated
nipbl_noc_0h_clone ×2 nipbl_noc_1h_with_auxin_clone ×2 nipbl_noc_45min_with_auxin_clone ×2 nipbl_noc_4h_no_auxin_clone ×2 nipbl_noc_4h_with_auxin_clone ×2

How we read this: Read from 30 sample titles: 25 distinct titles with little repetition. 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
Datasets on a similar topic

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