GEO series

Preventing CpG hypermethylation in oocytes safeguards mouse development [RNA-seq]

GSE234965 Mus musculus (mouse) DNA methylation 533 samples Submitted 2025/03/27 Platform GPL17021Platform GPL24247

At a glance

DNA methylation · mouse · 533 samples

What it is: DNA methylationChemical marks on DNA that help switch genes on or off.
Organism: Mus musculus (mouse)
Samples: 533 samples
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: Preventing CpG hypermethylation in oocytes safeguards mouse developmentDevelopmental cell · 2025

Summary (written by the submitters)

DNA methylation (DNAme) controls gene expression, genome stability and cell identity in many mammalian organisms. Genomes of most somatic cells and spermatozoa are largely methylated, apart from CpG-dense sequences including gene promoters1. In mouse oocytes, DNAme is mostly limited to transcribed regions2,3. The mechanisms restricting global DNAme acquisition in developing oocytes and the relevance thereof for regulating gene expression and embryo development after fertilization are unknown.

Read the full summary ↓

Here we show that the histone H3 lysine 36 dimethyl (H3K36me2) demethylases KDM2A and KDM2B redundantly execute multiple chromatin functions during oocyte development, which are vital to pre- and post-implantation development. Firstly, by serving as recruitment factors of variant Polycomb Repressive Complex 1 (vPRC1), they control genome-wide H2A mono-ubiquitination deposition (H2AK119u1) and PRC1-dependent gene repression4. Secondly, as demethylases, KDM2A/KDM2B prevent global H3K36me2 accumulation, thereby impeding DNMT3A-catalyzed de novo DNAme within PRC1-controlled promoter, genic, and intergenic regions, and even at non-PRC1-controlled CpG-dense gene promoters5. Decisively, we demonstrate that aberrant Dnmt3a-dependent DNAme established in Kdm2a/Kdm2b double mutant oocytes represses transcription from maternal loci in two-cell embryos and impairs pre-implantation development. Hence, KDM2A/KDM2B are essential for defining the appropriate oocyte DNA methylome which in turn conveys competence for early embryonic development. Our research implies that the reprogramming capacity eminent to early embryos is insufficient to erase aberrant DNAme from maternal chromatin. Lastly, our work shows that early development is vulnerable to gene dosage haplo-insufficiency effects, possibly in a parental-specific manner.

Published in

Preventing CpG hypermethylation in oocytes safeguards mouse development

Kawamura YK, Ozonov EA, Papasaikas P et al. · Developmental cell 2025 · PMID 40902605 · doi:10.1016/j.devcel.2025.08.005

This dataset

Open GSE234965 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 GSE234965_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 beta-value tables or raw IDAT files among the supplementary files.

Also filed as BioProject PRJNA983814 and SRA study SRP443902. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40902605) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 533 more — browse all 533 samples with per-sample file links →

Datasets on a similar topic

GSE234968 Preventing CpG hypermethylation in oocytes safeguards mouse development 612 samples shares hypermethylation, preventing, safeguards, oocytes
GSE234967 Preventing CpG hypermethylation in oocytes safeguards mouse development [Cut&Run] 17 samples shares hypermethylation, preventing, safeguards, oocytes
GSE271862 The Sotos syndrome gene Nsd1 safeguards bivalent developmental enhancers in poised states through restraining excessive H3K27me3 deposition [RNA-Seq] 18 samples shares safeguards, rna-seq
GSE247849 RNA Surveillance by the RNA Helicase MTR4 Determines Volume of Mouse Oocytes [polyA_RNA-seq-Nu_Cy] 13 samples shares oocytes, rna-seq
GSE262431 RNA Surveillance by the RNA Helicase MTR4 Determines Volume of Mouse Oocytes [day 14 total_RNA-seq-Nu_Cy] 12 samples shares oocytes, rna-seq
GSE266388 Histone methyltransferase SETDB1 safeguards mouse fetal hematopoiesis by suppressing activation of cryptic enhancers [RNA-seq] 12 samples shares safeguards, rna-seq
GSE247848 RNA Surveillance by the RNA Helicase MTR4 Determines Volume of Mouse Oocytes [polyA_RNA-seq] 12 samples shares oocytes, rna-seq
GSE276261 EOMES safeguards TSC chromatin accessibility by directing BRG1 to TSC-associated loci [RNA-seq] 45 samples shares safeguards, rna-seq

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.