GEO series

WDR5 Remodels NANOG Condensates to Drive Transcriptional Programs and Sustain Stem Cell Identity [ChIP-seq]

GSE299636 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 28 samples Submitted 2025/11/19 Platform GPL24247

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 28 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: 28 samples: 13 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: WDR5 remodels NANOG condensates to drive transcriptional programs and sustain stem cell identityNature communications · 2026

Summary (written by the submitters)

Stem cell pluripotency relies on a finely tuned interplay between transcription factors and epigenetic regulators. Here, we identify a direct interaction between NANOG, a master pluripotency transcription factor, and WDR5, a core component of the SET1/MLL complex that is essential for maintaining stem cell identity. Mechanistically, WDR5 reshapes the prion-like structures of NANOG into dynamic, liquid-liquid phase-separated (LLPS) condensates, facilitating its recruitment to pluripotency-associated promoters and activating target gene expression.

Read the full summary ↓

X-ray crystallography and NMR spectroscopy reveal that the NANOG homeodomain engages WDR5 through an extensive structural interface distinct from previously characterized short linear motifs. The NANOGR153A mutation disrupts its interaction with WDR5, leading to impaired LLPS formation, reduced chromatin co-occupancy, and diminished levels of active histone marks (H3K4me3 and H4K16ac), ultimately compromising the pluripotency of embryonic stem cells. Furthermore, pharmacological inhibition of the WDR5-NANOG interaction using a WIN motif inhibitor robustly suppresses leukemia stem cell expansion in vivo, highlighting its therapeutic potential. Collectively, this study uncovers an LLPS-mediated regulatory mechanism whereby WDR5 modulates NANOG condensate dynamics to sustain stem cell identity in both physiological and pathological contexts.

Published in

WDR5 remodels NANOG condensates to drive transcriptional programs and sustain stem cell identity

Wang D, Shi X, Xie J et al. · Nature communications 2026 · PMID 41565645 · doi:10.1038/s41467-026-68623-w

This dataset

Open GSE299636 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 GSE299636_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 PRJNA1275807 and SRA study SRP592068. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41565645) ↗

Study design

13 conditions, mostly in duplicate

mESC, WT, H3K4me3 ChIP-seq, ×2 mESC, R153A, H3K4me3 ChIP-seq, ×2 mESC, WT, H4K16ac ChIP-seq, ×2 mESC, R153A, H4K16ac ChIP-seq, ×2 mESC, Ctrl, Nanog ChIP-seq, ×2 mESC, HD, Nanog ChIP-seq, ×2 mESC, WT, Nanog ChIP-seq, ×2 mESC, R153A, Nanog ChIP-seq, ×2 +7 more

Supports a between-group comparison across 26 samples.

How we read this: 13 replicated groups read from 28 sample titles; they account for 26 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

GSM9042395 mESC, WT, H3K4me3 ChIP-seq, rep1 mESC, WT, H3K4me3 ChIP-…
GSM9042396 mESC, WT, H3K4me3 ChIP-seq, rep2 mESC, WT, H3K4me3 ChIP-…
GSM9042397 mESC, R153A, H3K4me3 ChIP-seq, rep1 mESC, R153A, H3K4me3 Ch…
GSM9042398 mESC, R153A, H3K4me3 ChIP-seq, rep2 mESC, R153A, H3K4me3 Ch…
GSM9042399 mESC, WT, H4K16ac ChIP-seq, rep1 mESC, WT, H4K16ac ChIP-…
GSM9042400 mESC, WT, H4K16ac ChIP-seq, rep2 mESC, WT, H4K16ac ChIP-…
GSM9042401 mESC, R153A, H4K16ac ChIP-seq, rep1 mESC, R153A, H4K16ac Ch…
GSM9042402 mESC, R153A, H4K16ac ChIP-seq, rep2 mESC, R153A, H4K16ac Ch…
GSM9042403 mESC, Ctrl, Nanog ChIP-seq, rep1 mESC, Ctrl, Nanog ChIP-…
GSM9042404 mESC, Ctrl, Nanog ChIP-seq, rep2 mESC, Ctrl, Nanog ChIP-…
GSM9042405 mESC, HD, Nanog ChIP-seq, rep1 mESC, HD, Nanog ChIP-se…
GSM9042406 mESC, HD, Nanog ChIP-seq, rep2 mESC, HD, Nanog ChIP-se…
GSM9042407 mESC, WT, Nanog ChIP-seq, rep1 mESC, WT, Nanog ChIP-se…
GSM9042408 mESC, WT, Nanog ChIP-seq, rep2 mESC, WT, Nanog ChIP-se…
GSM9042409 mESC, R153A, Nanog ChIP-seq, rep1 mESC, R153A, Nanog ChIP…
GSM9042410 mESC, R153A, Nanog ChIP-seq, rep2 mESC, R153A, Nanog ChIP…
GSM9042411 mESC, input, rep1 mESC, input,
GSM9042412 mESC, input, rep2 mESC, input,
GSM9042413 mESC, Ctrl, Wdr5 ChIP-seq, rep1 mESC, Ctrl, Wdr5 ChIP-s…
GSM9042414 mESC, Ctrl, Wdr5 ChIP-seq, rep2 mESC, Ctrl, Wdr5 ChIP-s…
GSM9042415 mESC, HD, Wdr5 ChIP-seq, rep1 mESC, HD, Wdr5 ChIP-seq,
GSM9042416 mESC, HD, Wdr5 ChIP-seq, rep2 mESC, HD, Wdr5 ChIP-seq,
GSM9042417 mESC, WT, Wdr5 ChIP-seq, rep1 mESC, WT, Wdr5 ChIP-seq,
GSM9042418 mESC, WT, Wdr5 ChIP-seq, rep2 mESC, WT, Wdr5 ChIP-seq,
GSM9042419 mESC, R153A, Wdr5 ChIP-seq, rep1 mESC, R153A, Wdr5 ChIP-…
GSM9042420 mESC, R153A, Wdr5 ChIP-seq, rep2 mESC, R153A, Wdr5 ChIP-…
GSM9042421 mESC, ChIP Input, rep1
GSM9042422 mESC, ChiP Input, rep2

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GSE276879 Monitoring rapid degradation of NANOG reveals UTP15 maintains pluripotency by regulating nascent transcripts 30 samples shares nanog
GSE141505 ZFP982 confers mouse embryonic stem cell characteristics by regulating expression of Nanog, Zfp42, and Dppa3 8 samples shares nanog

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