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LncRNA adapters determine SWI/SNF complex occupancy at gene regulatory elements [ATAC-seq]

GSE262057 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 12 samples Submitted 2024/11/27 Platform GPL18573
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 12 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
12 samples: 3 × HUVEC, ATAC-seq, Control, 30 minutes, vs 3 × HUVEC, ATAC-seq, BRG1 PROTAC, 30 minutes, vs 3 × HUVEC, ATAC-seq, BRG1 PROTAC, 60 minutes, vs 3 × HUVEC, ATAC-seq, BRG1 PROTAC, 240 minutes,Groups 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
Long non-coding RNAs direct the SWI/SNF complex to cell type-specific enhancersNature communications · 2025
Summary (written by the submitters)
The coordination of chromatin remodeling is essential for DNA accessibility and gene expression control. The highly conserved and ubiquitously expressed SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex plays a key role in regulating gene expression in a context-dependent manner. SWI/SNF actively maintains open chromatin states across the genome and responds dynamically to cellular signals.
Read the full summary ↓
However, the precise mechanisms determining how SWI/SNF is targeted to specific genomic sites remain elusive. In this study we demonstrate that long non-coding RNAs (lncRNAs) are pivotal in the binding of the SWI/SNF complex to specific genomic targets. The interaction between SWI/SNF and lncRNAs is essential for the recruitment of the complex to gene regulatory elements, where it plays a critical role. We show that trans-acting lncRNAs direct the SWI/SNF complex to cell-specific enhancers, with lncRNA knockdowns leading to a genome-wide redistribution of SWI/SNF away from these enhancers. This redistribution impacts the expression of genes connected to these enhancers, underscoring the critical role of lncRNAs in the specific targeting of SWI/SNF to DNA. This insight into the targeting mechanisms of SWI/SNF by lncRNAs has broad implications, from understanding the processes of gene expression control to identifying therapeutic targets in diseases associated with SWI/SNF dysfunction, such as cancer.
Published in
Long non-coding RNAs direct the SWI/SNF complex to cell type-specific enhancers
Oo JA, Warwick T, Pálfi K et al. · Nature communications 2025 · PMID 39747144 · doi:10.1038/s41467-024-55539-6
This dataset
Open GSE262057 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 GSE262057_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 PRJNA1090117 and SRA study SRP496770. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39747144) ↗
Study design
3 × HUVEC, ATAC-seq, Control, 30 minutes, vs 3 × HUVEC, ATAC-seq, BRG1 PROTAC, 30 minutes, vs 3 × HUVEC, ATAC-seq, BRG1 PROTAC, 60 minutes, vs 3 × HUVEC, ATAC-seq, BRG1 PROTAC, 240 minutes,

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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
Datasets on a similar topic

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