GEO series

Altered Cofactor Recruitment and Nucleosome Dynamics Underlie Bisphenol A's Impact on Estrogen Receptor-Mediated Transcriptional Bursting [CUT&Tag]

GSE251649 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 45 samples Submitted 2025/06/02 Platform GPL18573

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 45 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: 45 samples: 45 samples, each with a distinct title — no replicated groupsGroups 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: Altered cofactor recruitment and nucleosome dynamics underlie bisphenol A's impact on ERα-mediated transcriptional burstingiScience · 2025

Summary (written by the submitters)

Gene regulation is complex, involving the coordination of hundreds of proteins to initiate transcription. At individual loci, transcriptional initiation is stochastic, resulting in short periods of nascent RNA synthesis known as transcriptional bursts. To understand how altered Estrogen Receptor α (ERα) function and cofactor recruitment regulates transcriptional bursting, we utilized single molecule imaging of estrogen responsive genes in Bisphenol A (BPA) treated cells.

Read the full summary ↓

We observe that cells treated with BPA exhibited TFF1 burst initiation rates and sizes which were indistinguishable from cells induced with Estradiol (E2). However, we observed a 50% reduction in the number of active alleles in BPA treated cells. This effect is gene specific, as GREB1 was unperturbed. Although we observed no difference in chromatin accessibility, the TFF1 promoter exhibited an altered structure which coincided with reduced ERα and cofactor binding. Lastly, deletion of the enhancer locus removed the BPA effect, indicating that enhancer function was perturbed. Our results demonstrate gene specific effects of altered ERα recruitment and function which lead to a reduction of transcriptionally permissive states. Our work supports the model that the initial estrogen response occurs from alleles in primed transcriptionally permissive states with additional inactive alleles contributing to the cellular response over time.

Published in

Altered cofactor recruitment and nucleosome dynamics underlie bisphenol A's impact on ERα-mediated transcriptional bursting

Day CR, Yaşar P, Adedoyin G et al. · iScience 2025 · PMID 40678530 · doi:10.1016/j.isci.2025.112864

This dataset

Open GSE251649 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 GSE251649_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 PRJNA1055019 and SRA study SRP479140. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40678530) ↗

Study design

45 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 45 sample titles: 45 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

GSM7984579 EtOH-1-ERa-Cut&TAG
GSM7984580 EtOH-2-ERa-Cut&TAG
GSM7984581 EtOH-3-ERa-Cut&TAG
GSM7984582 E2-1-ERa-Cut&TAG
GSM7984583 E2-2-ERa-Cut&TAG
GSM7984584 E2-3-ERa-Cut&TAG
GSM7984585 BPA-1-ERa-Cut&TAG
GSM7984586 BPA-2-ERa-Cut&TAG
GSM7984587 BPA-3-ERa-Cut&TAG
GSM7984588 EtOH-1-FoxA1-Cut&TAG
GSM7984589 EtOH-2-FoxA1-Cut&TAG
GSM7984590 EtOH-3-FoxA1-Cut&TAG
GSM7984591 E2-1-FoxA1-Cut&TAG
GSM7984592 E2-2-FoxA1-Cut&TAG
GSM7984593 E2-3-FoxA1-Cut&TAG
GSM7984594 BPA-1-FoxA1-Cut&TAG
GSM7984595 BPA-2-FoxA1-Cut&TAG
GSM7984596 BPA-3-FoxA1-Cut&TAG
GSM7984597 EtOH-1-27ac-Cut&TAG
GSM7984598 EtOH-2-27ac-Cut&TAG
GSM7984599 EtOH-3-27ac-Cut&TAG
GSM7984600 E2-1-27ac-Cut&TAG
GSM7984601 E2-2-27ac-Cut&TAG
GSM7984602 E2-3-27ac-Cut&TAG
GSM7984603 BPA-1-27ac-Cut&TAG
GSM7984604 BPA-2-27ac-Cut&TAG
GSM7984605 BPA-3-27ac-Cut&TAG
GSM7984606 EtOH-1-MED1-Cut&TAG
GSM7984607 EtOH-2-MED1-Cut&TAG
GSM7984608 EtOH-3-MED1-Cut&TAG
GSM7984609 E2-1-MED1-Cut&TAG
GSM7984610 E2-2-MED1-Cut&TAG
GSM7984611 E2-3-MED1-Cut&TAG
GSM7984612 BPA-1-MED1-Cut&TAG
GSM7984613 BPA-2-MED1-Cut&TAG
GSM7984614 BPA-3-MED1-Cut&TAG
GSM8607163 EtOH-1-BRG1-Cut&TAG
GSM8607164 EtOH-2-BRG1-Cut&TAG
GSM8607165 EtOH-3-BRG1-Cut&TAG
GSM8607166 E2-1-BRG1-Cut&TAG

+ 5 more — browse all 45 samples with per-sample file links →

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

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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.