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Opposing functions of AEBP2 isoforms fine-tune PRC2 catalytic activity

GSE310209 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 72 samples Submitted 2026/07/15 Platform GPL34290
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 72 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
72 samples: 32 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
Opposing function of AEBP2 isoforms fine-tune PRC2 catalytic activityNucleic acids research · 2026
Summary (written by the submitters)
Polycomb Repressive Complex 2 (PRC2) represses genes through catalyzing H3K27me3, a histone modification essential for maintenance of cellular identity. The complex’s catalytic activity, chromatin localization, and propagation along chromatin are modulated by accessory proteins such as AEBP2, MTF2, JARID2 and PALI, which is specifically required for mouse embryogenesis.
Read the full summary ↓
AEBP2 exists in distinct isoforms: a short isoform that enhances PRC2 catalytic activity and promotes H3K27me3 spreading, facilitating robust gene repression, and a long isoform whose function has remained unclear. Here, we report that the N-terminal region of the long isoform contains a conserved DE-motif that inhibits PRC2 activity, both EZH2 automethylation and H3K27 methylation. Notably, re-expression of the long isoform in Mtf2/Jarid2/Aebp2 triple-knockout mouse embryonic stem cells failed to restore H3K27me3 and caused defective differentiation, unlike the short isoform. These findings uncover an isoform-specific regulatory mechanism by which AEBP2 controls PRC2 activity and contribute to a broader understanding of PRC2’s dynamic regulation during development
Published in
Opposing function of AEBP2 isoforms fine-tune PRC2 catalytic activity
Li Y, Kwon C, Kim H et al. · Nucleic acids research 2026 · PMID 42423305 · doi:10.1093/nar/gkag694
This dataset
Open GSE310209 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 GSE310209_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 PRJNA1365306 and SRA study SRP645533. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42423305) ↗
Study design
32 conditions, mostly in duplicate
E14 WT CUTnTag H3K27me3 ×2 E14 TKO CUTnTag H3K27me3 ×2 E14 TKO AEBP2 long rescue CUTnTag H3K27me3 ×2 E14 TKO AEBP2 short rescue CUTnTag H3K27me3 ×2 E14 WT ChIP AEBP2 ×2 E14 TKO ChIP AEBP2 ×2 E14 TKO AEBP2 long rescue ChIP AEBP2 ×2 E14 TKO AEBP2 short rescue ChIP AEBP2 ×2 +32 more

Supports a between-group comparison across 64 samples.

How we read this: 32 replicated groups read from 72 sample titles; they account for 64 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

+ 32 more — browse all 72 samples with per-sample file links →

Datasets on a similar topic

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