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Monitoring rapid degradation of NANOG reveals UTP15 maintains pluripotency by regulating nascent transcripts

GSE276879 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 30 samples Submitted 2025/10/23 Platform GPL24247
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: 15 conditions, mostly in duplicateGroups 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
Monitoring rapid degradation of NANOG reveals UTP15 maintains pluripotency by regulating nascent transcriptsNature communications · 2025
Summary (written by the submitters)
Master transcription factors (MTFs) are key regulators in cell fate determination. However, an approach to profile MTF’s direct transcriptional targets together with their associated RNA-binding proteins (RBPs), is still lacking. Here, we applied 5-ethynyluridine RNA metabolic labelling and click chemistry to map the dynamics of the transcriptional targets and the RBPs interacting with the newly transcribed RNAs upon acute NANOG degradation in mouse embryonic stem cells (mESCs).
Read the full summary ↓
We identified UTP15, a classic rRNA-biogenesis regulator, acts as a key activator of pluripotency-associated gene transcription independently of rRNA biogenesis. Importantly, NANOG-regulated transcription enhances UTP15 binding to transcription start sites (TSSs), associated with increased Pol II binding and more active transcription. Moreover, UTP15 promotes the assembly of Pol II biomolecular condensates, thereby potentially driving pluripotency gene transcription. Collectively, our study uncovers a NANOG-nascent transcript-UTP15 regulatory axis to activate pluripotency gene transcription, providing a distinct approach for studying MTF’s function during cell fate determination.
Published in
Monitoring rapid degradation of NANOG reveals UTP15 maintains pluripotency by regulating nascent transcripts
Deng M, He D, Wang X et al. · Nature communications 2025 · PMID 41361183 · doi:10.1038/s41467-025-67018-7
This dataset
Open GSE276879 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 GSE276879_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 PRJNA1159330 and SRA study SRP531911. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41361183) ↗
Study design
15 conditions, mostly in duplicate
UTP15_CLIP-seq ×2 UTP15_ChIP-seq_Input ×2 UTP15_ChIP-seq_IP ×2 UTP15_ChIP-seq_ActD ×2 UTP15_ChIP-seq_Ctrl ×2 UTP15_ChIP-seq_NANOG_NoIAA ×2 UTP15_ChIP-seq_NANOG_AddIAA ×2 polII_ChIP-seq_0h_Input ×2 +7 more

Supports a between-group comparison across 30 samples.

How we read this: 15 replicated groups read from 30 sample titles; they account for 30 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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