GEO series
Noncanonical PRC2 chromatin association reveals a key role of EZHIP in intergenerational epigenetic memory transition [RNA-Seq]
GSE289641
Mus musculus (mouse)
RNA-seq (gene expression)
68 samples
Submitted 2025/11/18
Platform GPL28330
At a glance
RNA-seq (gene expression) · mouse · 68 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
- 68 samples: 23 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
- EZHIP restricts noncanonical PRC2 binding and regulates H3K27me3 intergenerational inheritance and reprogrammingCell stem cell · 2025
Summary (written by the submitters)
Epigenetic memory undergoes drastic reprogramming in intergenerational gamete-to-embryo transition. H3K27me3, a histone mark catalyzed by PRC2 (Polycomb Repressive Complex 2), is an evolutionally conserved histone mark that plays essential roles in stably repressing developmental genes to maintain cell-type-specific programs. In mice, H3K27me3-mediated epigenetic memory, however, undergoes both resetting at classic Polycomb targets and inheritance of broad H3K27me3 domains that mediate noncanonical imprinting (noncanonical H3K27me3 domains) during early embryogenesis.
Read the full summary ↓
How such erasure and inheritance are achieved simultaneously remains elusive. Here, through temporal profiling of chromatin occupancy, we show that PRC2 associates with H3K27me3 at both Polycomb targets and noncanonical domains in growing oocytes. PRC2 then pre-disassembles and dissociates from chromatin in mature oocytes, before H3K27me3 erasure at Polycomb targets after fertilization. PRC2 reappears at Polycomb targets in blastocysts when H3K27me3 initiates restoration. By contrast, noncanonical H3K27me3 domains persist to blastocysts, where PRC2 rapidly rebinds by the end of 1-cell embryos until blastocysts. Mechanistically, we found that such noncanonical PRC2 action is regulated by EZHIP, a PRC2 inhibitory factor. By doing so, EZHIP plays a key role in both H3K27me3 erasure and intergenerational inheritance, as well as H3K27me3 re-establishment. Ezhip is highly translated around fertilization, which strongly restricts PRC2 activity, leading to gradual decrease of H3K27me3. Upon knockout of maternal Ezhip, PRC2 becomes hyperactive, binds promiscuously in the genome and deposits widespread H3K27me3. Consequently, H3K27me3 allelic bias and noncanonical imprinting, including imprinted X chromosome inactivation, are impaired. Unexpectedly, the widespread ectopic H3K27me3 paradoxically causes de-repression of H3K27me3 targets, possibly due to dilution of H3K27me3 effectors. Loss of Ezhip further attenuates H3K27me3 restoration at Polycomb targets during peri-implantation, and leads to gene dysregulation and sub-lethality after implantation. Taken together, we uncover PRC2 noncanonical chromatin association during the parental-to-embryonic transition and identify Ezhip as a crucial regulator for both erasure and inheritance of intergenerational epigenetic memories.
Published in
Zeng Y, Kong F, Xu Z et al.
· Cell stem cell 2025
· PMID 41118764
· doi:10.1016/j.stem.2025.09.009
This dataset
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.
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 GSE289641_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1223869 and SRA study SRP563993. Searching any of these in the dataset finder brings you back here.
Study design
23 conditions, mostly in duplicate
EZHIP_WT_Bl_RNAseq ×7
EZHIP_mHet_Bl_RNAseq ×7
EZHIP_mKO_Bl_RNAseq ×7
EZHIP_WT_E425_RNAseq ×4
EZHIP_mKO_E425_RNAseq ×4
EZHIP_KO_FGO_RNAseq ×3
EZHIP_mKO_8C_RNAseq ×3
EZHIP_WT_FGO_RNAseq ×2
+16 more
Supports a between-group comparison across 67 samples.
How we read this: 23 replicated groups read from 68 sample titles; they account for 67 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
- GSM8795706 EZHIP_WT_FGO_RNAseq_rep1 EZHIP_WT_FGO_RNAseq
- GSM8795707 EZHIP_Het_FGO_RNAseq_rep1 EZHIP_Het_FGO_RNAseq
- GSM8795708 EZHIP_KO_FGO_RNAseq_rep1 EZHIP_KO_FGO_RNAseq
- GSM8795709 EZHIP_KO_FGO_RNAseq_rep2 EZHIP_KO_FGO_RNAseq
- GSM8795710 EZHIP_WT_FGO_RNAseq_rep2 EZHIP_WT_FGO_RNAseq
- GSM8795711 EZHIP_Het_FGO_RNAseq_rep2 EZHIP_Het_FGO_RNAseq
- GSM8795712 EZHIP_KO_FGO_RNAseq_rep3 EZHIP_KO_FGO_RNAseq
- GSM8795713 EZHIP_WT_PN5_RNAseq_rep1 EZHIP_WT_PN5_RNAseq
- GSM8795714 EZHIP_mHet_PN5_RNAseq_rep1 EZHIP_mHet_PN5_RNAseq
- GSM8795715 EZHIP_mKO_PN5_RNAseq_rep1 EZHIP_mKO_PN5_RNAseq
- GSM8795716 EZHIP_WT_PN5_RNAseq_rep2 EZHIP_WT_PN5_RNAseq
- GSM8795717 EZHIP_mHet_PN5_RNAseq_rep2 EZHIP_mHet_PN5_RNAseq
- GSM8795718 EZHIP_mKO_PN5_RNAseq_rep2 EZHIP_mKO_PN5_RNAseq
- GSM8795719 EZHIP_WT_L2C_RNAseq_rep1 EZHIP_WT_L2C_RNAseq
- GSM8795720 EZHIP_WT_L2C_RNAseq_rep2 EZHIP_WT_L2C_RNAseq
- GSM8795721 EZHIP_mHet_L2C_RNAseq_rep1 EZHIP_mHet_L2C_RNAseq
- GSM8795722 EZHIP_mHet_L2C_RNAseq_rep2 EZHIP_mHet_L2C_RNAseq
- GSM8795723 EZHIP_mKO_L2C_RNAseq_rep1 EZHIP_mKO_L2C_RNAseq
- GSM8795724 EZHIP_mKO_L2C_RNAseq_rep2 EZHIP_mKO_L2C_RNAseq
- GSM8795725 EZHIP_WT_8C_RNAseq_rep1 EZHIP_WT_8C_RNAseq
- GSM8795726 EZHIP_mHet_8C_RNAseq_rep1
- GSM8795727 EZHIP_mKO_8C_RNAseq_rep1 EZHIP_mKO_8C_RNAseq
- GSM8795728 EZHIP_mKO_8C_RNAseq_rep2 EZHIP_mKO_8C_RNAseq
- GSM8795729 EZHIP_WT_8C_RNAseq_rep2 EZHIP_WT_8C_RNAseq
- GSM8795730 EZHIP_mKO_8C_RNAseq_rep3 EZHIP_mKO_8C_RNAseq
- GSM8795731 EZHIP_WT_Bl_RNAseq_rep1 EZHIP_WT_Bl_RNAseq
- GSM8795732 EZHIP_WT_Bl_RNAseq_rep2 EZHIP_WT_Bl_RNAseq
- GSM8795733 EZHIP_mHet_Bl_RNAseq_rep1 EZHIP_mHet_Bl_RNAseq
- GSM8795734 EZHIP_mHet_Bl_RNAseq_rep2 EZHIP_mHet_Bl_RNAseq
- GSM8795735 EZHIP_mKO_Bl_RNAseq_rep1 EZHIP_mKO_Bl_RNAseq
- GSM8795736 EZHIP_mKO_Bl_RNAseq_rep2 EZHIP_mKO_Bl_RNAseq
- GSM8795737 EZHIP_WT_Bl_RNAseq_rep3 EZHIP_WT_Bl_RNAseq
- GSM8795738 EZHIP_WT_Bl_RNAseq_rep4 EZHIP_WT_Bl_RNAseq
- GSM8795739 EZHIP_WT_Bl_RNAseq_rep5 EZHIP_WT_Bl_RNAseq
- GSM8795740 EZHIP_WT_Bl_RNAseq_rep6 EZHIP_WT_Bl_RNAseq
- GSM8795741 EZHIP_WT_Bl_RNAseq_rep7 EZHIP_WT_Bl_RNAseq
- GSM8795742 EZHIP_mHet_Bl_RNAseq_rep3 EZHIP_mHet_Bl_RNAseq
- GSM8795743 EZHIP_mHet_Bl_RNAseq_rep4 EZHIP_mHet_Bl_RNAseq
- GSM8795744 EZHIP_mHet_Bl_RNAseq_rep5 EZHIP_mHet_Bl_RNAseq
- GSM8795745 EZHIP_mHet_Bl_RNAseq_rep6 EZHIP_mHet_Bl_RNAseq
+ 28 more — browse all 68 samples with per-sample file links →
Datasets on a similar topic
- GSE289642 Noncanonical PRC2 chromatin association reveals a key role of EZHIP in intergenerational epigenetic memory transition [ChIP-Seq, Cut & Run] 107 samples shares ezhip, prc2, intergenerational, noncanonical, epigenetic, transition, 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, rna-seq
- GSE264673 EPOP Restricts PRC2.1 Targeting to Chromatin by Directly Modulating Enzyme Complex Dimerization (RNA-Seq) 12 samples shares prc2, chromatin, rna-seq
- GSE318278 Self-clustering of three CBX2 molecules drives PRC2 to promote facultative heterochromatinization of Polycomb target genes [RNA-Seq] 4 samples shares prc2, chromatin, rna-seq
- GSE278534 EZHIP-mediated PRC2 inhibition is required to maintain H3K27me3-dependent imprinting post fertilization 76 samples shares ezhip, prc2
- GSE278811 EZHIP-mediated PRC2 inhibition is required to maintain H3K27me3-dependent imprinting post fertilization [ChIP-Seq] 77 samples shares ezhip, prc2
- GSE293160 SKP1A-mediated degradation of PRC2 triggers activation of Polycomb-silenced gene [RNA-seq] 24 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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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.