GEO series

SKP1A-mediated degradation of PRC2 triggers activation of Polycomb-silenced gene [RNA-seq]

GSE293160 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2025/08/25 Platform GPL19057

At a glance

RNA-seq (gene expression) · mouse · 24 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: 24 samples: 11 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: SKP1A bound to Polycomb-silenced genes mediates degradation of PRC2 and preconditions their activationMolecular cell · 2025

Summary (written by the submitters)

Polycomb group (PcG) proteins are evolutionarily conserved repressors of developmental genes. Paradoxically, the same PcG proteins also play roles in gene activation via mechanisms that are not yet fully understood. Here, we found that S-phase kinase-associated protein 1A (SKP1A), an essential factor of SCF (SKP1A/CULLIN1/F-box) ubiquitin ligases and a subunit of the PCGF1 (Polycomb group RING finger protein 1) component of Polycomb repressive complex 1 (PCGF1-PRC1), mediates the link between PcG-dependent gene regulation and ubiquitin-dependent proteasomal degradation.

Read the full summary ↓

By using differentiating mouse embryonic stem cells, we found that SKP1A removes EED, a core component of Polycomb repressive complex 2 (PRC2) that is bound to PcG target gene promoters, via proteasomal degradation, and it thereby sensitises these genes for subsequent activation. Furthermore, we show that SKP1A removes EED from the Meis2 promoter in the midbrain of developing mouse embryos, leading to Meis2 gene expression. In summary, we reveal here a previously unknown role of SKP1A in activating PcG-target genes via the proteasomal degradation of PRC2. This implies that SKP1A-containing PCGF1-PRC1 may confer reversibility on PcG-mediated gene silencing for robust spatiotemporal regulation of target genes.

Published in

SKP1A bound to Polycomb-silenced genes mediates degradation of PRC2 and preconditions their activation

Kondo T, Ito S, Takano J et al. · Molecular cell 2025 · PMID 40858113 · doi:10.1016/j.molcel.2025.08.004

This dataset

Open GSE293160 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 GSE293160_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 PRJNA1242981 and SRA study SRP573740. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40858113) ↗

Study design

11 conditions, mostly in duplicate

EED f/f+3i_RNA-seq ×2 EED f/f EB day1_RNA-seq ×2 EED f/f EB day2_RNA-seq ×2 EED KO+3i_RNA-seq ×2 EED KO EB day1_RNA-seq ×2 EED KO EB day2_RNA-seq ×2 EED KO+WT EED+3i_RNA-seq ×2 EED KO+WT EED EB day1_RNA-seq ×2 +5 more

Supports a between-group comparison across 22 samples.

How we read this: 11 replicated groups read from 24 sample titles; they account for 22 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

GSM8877628 EED f/f+3i_RNA-seq_rep1 EED f/f+3i_RNA-seq
GSM8877629 EED f/f+3i_RNA-seq_rep2 EED f/f+3i_RNA-seq
GSM8877630 EED f/f EB day1_RNA-seq_rep1 EED f/f EB day1_RNA-seq
GSM8877631 EED f/f EB day1_RNA-seq_rep2 EED f/f EB day1_RNA-seq
GSM8877632 EED f/f EB day2_RNA-seq_rep1 EED f/f EB day2_RNA-seq
GSM8877633 EED f/f EB day2_RNA-seq_rep2 EED f/f EB day2_RNA-seq
GSM8877634 EED KO+3i_RNA-seq_rep1 EED KO+3i_RNA-seq
GSM8877635 EED KO+3i_RNA-seq_rep2 EED KO+3i_RNA-seq
GSM8877636 EED KO EB day1_RNA-seq_rep1 EED KO EB day1_RNA-seq
GSM8877637 EED KO EB day1_RNA-seq_rep2 EED KO EB day1_RNA-seq
GSM8877638 EED KO EB day2_RNA-seq_rep1 EED KO EB day2_RNA-seq
GSM8877639 EED KO EB day2_RNA-seq_rep2 EED KO EB day2_RNA-seq
GSM8877640 EED KO+WT EED+3i_RNA-seq_rep1 EED KO+WT EED+3i_RNA-seq
GSM8877641 EED KO+WT EED+3i_RNA-seq_rep2 EED KO+WT EED+3i_RNA-seq
GSM8877642 EED KO+WT EED EB day1_RNA-seq_rep1 EED KO+WT EED EB day1_R…
GSM8877643 EED KO+WT EED EB day1_RNA-seq_rep2 EED KO+WT EED EB day1_R…
GSM8877644 EED KO+WT EED EB day2_RNA-seq_rep1 EED KO+WT EED EB day2_R…
GSM8877645 EED KO+WT EED EB day2_RNA-seq_rep2 EED KO+WT EED EB day2_R…
GSM8877646 EED KO+N-KR EED+3i_RNA-seq_rep1 EED KO+N-KR EED+3i_RNA-…
GSM8877647 EED KO+N-KR EED+3i_RNA-seq_rep2 EED KO+N-KR EED+3i_RNA-…
GSM8877648 EED KO+N-KREED EB day1_RNA-seq_rep1
GSM8877649 EED KO+N-KR EED EB day1_RNA-seq_rep2
GSM8877650 EED KO+N-KR EED EB day2_RNA-seq_rep1 EED KO+N-KR EED EB day2…
GSM8877651 EED KO+N-KR EED EB day2_RNA-seq_rep2 EED KO+N-KR EED EB day2…

Datasets on a similar topic

GSE263260 SKP1A-mediated degradation of PRC2 triggers activation of Polycomb-silenced genes : Gene expression 1 12 samples shares prc2, polycomb-silenced, skp1a-mediated, degradation, activation, triggers
GSE297309 SKP1A-mediated degradation of PRC2 triggers activation of Polycomb-silenced gene [CUT&Tag] 108 samples shares prc2, polycomb-silenced, skp1a-mediated, degradation, activation, triggers
GSE297094 SKP1A-mediated degradation of PRC2 triggers activation of Polycomb-silenced gene [ChIP-seq 2] 73 samples shares prc2, polycomb-silenced, skp1a-mediated, degradation, activation, triggers
GSE263263 SKP1A-mediated degradation of PRC2 triggers activation of Polycomb-silenced genes : CUT&Tag 1 20 samples shares prc2, polycomb-silenced, skp1a-mediated, degradation, activation, triggers
GSE293161 SKP1A-mediated degradation of PRC2 triggers activation of Polycomb-silenced gene [ChIP-seq] 16 samples shares prc2, polycomb-silenced, skp1a-mediated, degradation, activation, triggers
GSE263265 SKP1A-mediated degradation of PRC2 triggers activation of Polycomb-silenced genes : CUT&Tag 2 12 samples shares prc2, polycomb-silenced, skp1a-mediated, degradation, activation, triggers
GSE289641 Noncanonical PRC2 chromatin association reveals a key role of EZHIP in intergenerational epigenetic memory transition [RNA-Seq] 68 samples shares prc2, rna-seq
GSE272602 DNA glycosylases Ogg1 and Mutyh mediate gene expression of PRC2 targets important for memory formation (RNA-Seq) 24 samples shares prc2, rna-seq

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