GEO series

Cohesin recruitment to promoters and enhancers by general transcription factors and chromatin regulators

GSE283958 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 47 samples Submitted 2025/06/09 Platform GPL24247

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 47 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: 47 samples
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: Cohesin stabilization at promoters and enhancers by common transcription factors and chromatin regulatorsEpigenetics & chromatin · 2025

Summary (written by the submitters)

Background Cohesin is a major regulator of three-dimensional genome organization and gene expression. Cohesin binds to DNA and dynamically extrudes a DNA loop, often bringing two cis-regulatory elements physically close together. Extruding cohesin molecules can be stalled or stabilized when they encounter a CTCF insulator protein on DNA, thereby anchoring a DNA loop.

Read the full summary ↓

However, many enhancer-promoter loops that are bound by cohesin lack CTCF and it is not clear how cohesin is recruited to these sites in the genome. Results Here, we investigate the localization patterns of cohesin, as well as general chromatin state and localization of transcription factors WDR5, SP1, and NFYA in mouse embryonic stem cells. The SP1 and NFYA transcription factors are ubiquitously expressed proteins known to regulate expression of genes associated with a variety of cellular processes, while WDR5 is a core component of multiple complexes that regulate chromatin. Cohesin co-binds promoters and enhancers with WDR5, with SP1, or with NFYA in mESCs and other cell types. Cohesin co-immunoprecipitates with WDR5, SP1, and NFYA and cohesin simultaneously binds to the same chromatin molecules with these proteins. At co-bound sites, depletion of cohesin does not alter binding of WDR5, SP1, or NFYA;, however depletion of WDR5, SP1, or NFYA decreases cohesin binding. Conclusions These results indicate that general transcription factors and chromatin regulators recruit cohesin to specific sites in chromatin and thereby serve as structural regulators of enhancer-promoter loops via the recruitment of cohesin.

Published in

Cohesin stabilization at promoters and enhancers by common transcription factors and chromatin regulators

Bryan AF, Justice M, Stutzman AV et al. · Epigenetics & chromatin 2025 · PMID 40490791 · doi:10.1186/s13072-025-00598-2

This dataset

Open GSE283958 in finder → Find more mouse 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 GSE283958_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 PRJNA1196388 and SRA study SRP550552. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40490791) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 47 more — browse all 47 samples with per-sample file links →

Datasets on a similar topic

GSE296438 Transcription factor NFYA directs male meiotic entry by facilitating accessible chromatin at the promoters of genes expressed during meiosis [scRNA-seq & scATAC-seq] 10 samples shares transcription, promoters, chromatin
GSE295340 Polycomb Chromatin Topology Enables Long-Range Enhancer Recruitment during Craniofacial Development [ChIP-seq] 42 samples shares recruitment, chromatin
GSE339012 Mega-Enhancers Compartmentalize Transcriptionally Active Long Genes in the Brain [ChIP-Seq] 22 samples shares transcription, enhancers
GSE314045 Rotational settings quantize nucleosome movement by chromatin regulators 15 samples shares regulators, chromatin
GSE283906 RXR-Mediated Remodeling of Transcriptional and Chromatin Landscapes in APP Mouse Brain: Insights from Integrated Single-Cell RNA and ATAC Profiling 10 samples shares transcription, chromatin
GSE237534 INO80 / SWR remodelers regulate Pol II transcription through BRD2 and chromatin landscape 217 samples shares transcription, chromatin
GSE217970 Mapping putative enhancers in mouse oocyte and early embryo reveals TCF3/12 as key folliculogenesis regulators 164 samples shares regulators, enhancers
GSE200323 Establishment of chromatin architecture interplays with embryo hypertranscription 158 samples shares transcription, chromatin

Search all mouse ChIP / ATAC / CUT&Tag datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.