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CRISPR screen decodes SWI/SNF chromatin remodeling complex assembly

GSE268206 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 56 samples Submitted 2025/04/28 Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 56 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
56 samples: 20 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
CRISPR screen decodes SWI/SNF chromatin remodeling complex assemblyNature communications · 2025
Summary (written by the submitters)
The SWI/SNF (or BAF) complex is an essential chromatin remodeler that regulates DNA accessibility at developmental genes and enhancers. SWI/SNF subunits are among the most frequently mutated genes in cancer and neurodevelopmental disorders. These mutations are often heterozygous loss-of-function alleles, indicating a dosage-sensitive role for SWI/SNF subunits in chromatin regulation.
Read the full summary ↓
However, the molecular mechanisms that regulate SWI/SNF subunit dosage to ensure proper complex assembly remain largely unexplored. We performed a genome-wide CRISPR KO screen, using epigenome editing in mouse embryonic stem cells, and identified Mlf2 and Rbm15 as regulators of SWI/SNF complex activity. First, we show that MLF2, a poorly characterized chaperone protein, regulates a subset of SWI/SNF target genes by promoting chromatin remodeling activity. Next, we find that RBM15, part of the m6A RNA methylation writer complex, controls m6A modifications on specific SWI/SNF mRNAs to regulate protein levels of these subunits. Misregulation of m6A methylation causes overexpression of core SWI/SNF subunits leading to the assembly of incomplete complexes lacking the catalytic ATPase/ARP subunits. These data indicate that targeting modulators of SWI/SNF complex assembly may offer a potent therapeutic strategy for diseases associated with impaired chromatin remodeling.
Published in
CRISPR screen decodes SWI/SNF chromatin remodeling complex assembly
Schwaemmle H, Soldati H, Lykoskoufis NMR et al. · Nature communications 2025 · PMID 40447637 · doi:10.1038/s41467-025-60424-x
This dataset
Open GSE268206 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 GSE268206_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 PRJNA1115128 and SRA study SRP509438. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40447637) ↗
Study design
20 conditions, mostly in triplicate
DMSO_MLF2-dTAG ×3 8hdTAG13_MLF2-dTAG ×3 DMSO_SMARCA4-dTAG ×3 8hdTAG13_SMARCA4-dTAG ×3 DMSO_MLF2-dTAG_RNA ×3 3hdTAG13_MLF2-dTAG_RNA ×3 8hdTAG13_MLF2-dTAG_RNA ×3 24hdTAG13_MLF2-dTAG_RNA ×3 +14 more

Supports a between-group comparison across 54 samples.

How we read this: 20 replicated groups read from 56 sample titles; they account for 54 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

+ 16 more — browse all 56 samples with per-sample file links →

Datasets on a similar topic

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