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EPOP and MTF2 Activate PRC2 Activity through DNA-sequence specificity

GSE306783 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 34 samples Submitted 2026/01/09 Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 34 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
34 samples: 28 distinct titles, 6 of them repeatedGroups 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 and MTF2 Activate PRC2 Activity through DNA-sequence specificitybioRxiv : the preprint server for biology · 2025
Summary (written by the submitters)
The Polycomb repressive complex 2 (PRC2) establishes transcriptionally silent chromatin by catalyzing histone H3 lysine 27 trimethylation (H3K27me3). Although cofactors such as MTF2 and JARID2 are known to direct PRC2 to nucleation sites and stimulate its catalytic activity, the role of the PRC2-associated factor EPOP has remained unclear and even controversial.
Read the full summary ↓
Here, we combine biochemical reconstitution and a cellular EED-rescue system to define EPOP’s contribution to initial PRC2 recruitment and de novo H3K27me3 deposition. We show that EPOP, like MTF2, directly stimulates PRC2 histone methyltransferase activity in vitro. In vivo, EPOP is dispensable for initial PRC2 recruitment but promotes de novo H3K27me3 deposition in cooperation with MTF2 and JARID2. Mechanistically, electrophoretic mobility shift assays and reconstituted chromatin substrates reveal that EPOP and MTF2 enhance PRC2–nucleosome binding in a sequence- and chromatin-dependent manner: EPOP preferentially potentiates activity on GA-rich dinucleosomes, whereas MTF2 favors GCN-rich substrates. Together, these findings position EPOP as a positive regulator of PRC2 function during the establishment of H3K27me3 domains, and reveal a paradigm in which distinct cofactors confer DNA-sequence-specific control of de novo H3K27me3 deposition.
Published in
EPOP and MTF2 Activate PRC2 Activity through DNA-sequence specificity
Granat J, Liu S, Popoca L et al. · bioRxiv : the preprint server for biology 2025 · PMID 41040190 · doi:10.1101/2025.09.25.678634
This dataset
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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 GSE306783_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 PRJNA1312105 and SRA study SRP614054. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41040190) ↗
Study design
28 distinct titles, 6 of them repeated
mESC, EED rescue 24h, WT background, HA-EED C… ×2 mESC, EED rescue 0h, EPOPKO background, HA-EE… ×2 mESC, EED rescue 24h, EPOPKO background, HA-E… ×2 mESC, EED rescue 24h, WT background, H3K27me3… ×2 mESC, EED rescue 0h, EPOPKO background, H3K27… ×2 mESC, EED rescue 24h, EPOPKO background, H3K2… ×2

How we read this: Read from 34 sample titles: 28 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
Datasets on a similar topic

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