GEO series

EPOP Restricts PRC2.1 Targeting to Chromatin by Directly Modulating Enzyme Complex Dimerization (RNA-Seq)

GSE264673 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2025/12/12 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 12 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Mus musculus (mouse)
Samples: 12 samples: 12 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: EPOP restricts PRC2.1 targeting to chromatin by directly modulating enzyme complex dimerizationNature communications · 2026

Summary (written by the submitters)

Polycomb repressive complex 2 (PRC2) mediates developmental gene repression as two classes of holocomplexes, PRC2.1 and PRC2.2. EPOP is an accessory subunit specific to PRC2.1, which also contains PCL proteins. Unlike other accessory subunits that collectively facilitate PRC2 targeting, EPOP was implicated in an enigmatic inhibitory role, together with its interactor Elongin BC.

Read the full summary ↓

We report an unusual molecular mechanism whereby EPOP regulates PRC2.1 by directly modulating its oligomerization state. EPOP disrupts the PRC2.1 dimer and weakens its chromatin association, likely by disabling the avidity effect conferred by the dimeric complex. Congruently, an EPOP mutant specifically defective in PRC2 binding enhances genome-wide enrichments of MTF2 and H3K27me3 in mouse epiblast-like cells (EpiLCs). Elongin BC is largely dispensable for the EPOP-mediated inhibition of PRC2.1. EPOP defines a distinct subclass of PRC2.1, which uniquely maintains an epigenetic program by preventing the over-repression of key gene regulators in the continuum of pluripotency and differentiation.

Published in

EPOP restricts PRC2.1 targeting to chromatin by directly modulating enzyme complex dimerization

Gong L, Liu X, Yang X et al. · Nature communications 2026 · PMID 41519789 · doi:10.1038/s41467-025-68280-5

This dataset

Open GSE264673 in finder → Find more mouse RNA-seq 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 GSE264673_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1103785 and SRA study SRP503692. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41519789) ↗

Study design

12 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 12 sample titles: 12 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

GSM8225382 EPOP-Mutant mESCs grown in 2i media, Replicate 1, RNA
GSM8225383 EPOP-Mutant mESCs grown in 2i media, Replicate 2, RNA
GSM8225384 EPOP-Mutant mESCs grown in 2i media, Replicate 3, RNA
GSM8225385 EPOP-Mutant EpiLCs, Replicate 1, RNA
GSM8225386 EPOP-Mutant EpiLCs, Replicate 2, RNA
GSM8225387 EPOP-Mutant EpiLCs, Replicate 3, RNA
GSM8225388 EPOP-WT mESCs grown in 2i media, Replicate 1, RNA
GSM8225389 EPOP-WT mESCs grown in 2i media, Replicate 2, RNA
GSM8225390 EPOP-WT mESCs grown in 2i media, Replicate 3, RNA
GSM8225391 EPOP-WT EpiLCs, Replicate 1, RNA
GSM8225392 EPOP-WT EpiLCs, Replicate 2, RNA
GSM8225393 EPOP-WT EpiLCs, Replicate 3, RNA

Datasets on a similar topic

GSE306783 EPOP and MTF2 Activate PRC2 Activity through DNA-sequence specificity 34 samples shares epop, prc2
GSE289641 Noncanonical PRC2 chromatin association reveals a key role of EZHIP in intergenerational epigenetic memory transition [RNA-Seq] 68 samples shares prc2, chromatin
GSE263885 Chromatin repression by PRC2 results in reduced gene expression driving key features of CD8 T cell exhaustion [RNA-seq] 20 samples shares prc2, chromatin
GSE289642 Noncanonical PRC2 chromatin association reveals a key role of EZHIP in intergenerational epigenetic memory transition [ChIP-Seq, Cut & Run] 107 samples shares prc2, chromatin
GSE263938 Chromatin repression by PRC2 results in reduced gene expression driving key features of CD8 T cell exhaustion 34 samples shares prc2, chromatin
GSE318279 Self-clustering of three CBX2 molecules drives PRC2 to promote facultative heterochromatinization of Polycomb target genes 33 samples shares prc2, chromatin
GSE270581 Chromatin distribution alterations of histone modifacations and PRC2 complex caused by Rack7 deletion in primary astrocyte [ChIP-Seq] 24 samples shares prc2, chromatin
GSE244650 Targeting lysozyme 2 in endocardium promotes rapid recovery by modulating remote injury signals 13 samples shares modulating, targeting

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