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DNA methylation constrains nucleosome retention in sperm and H3K4 methylation deposition in early mouse embryos [RNA-seq 2]

GSE229238 Mus musculus (mouse) DNA methylation 42 samples Submitted 2024/10/21 Platform GPL17021
At a glance

DNA methylation · mouse · 42 samples

What it is
DNA methylationChemical marks on DNA that help switch genes on or off.
Organism
Mus musculus (mouse)
Samples
42 samples: 22 × Early 4 cell stage embryo Dnmt3a f/+ ; Dnmt3b f/+ sperm derived vs 20 × Early 4 cell stage embryo Dnmt3a f/- ; Dnmt3b f/- ; Stra8-iCre tg sperm derivedGroups 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
DNA methylation modulates nucleosome retention in sperm and H3K4 methylation deposition in early mouse embryosNature communications · 2025
Summary (written by the submitters)
DNA methylation serves a stable gene regulatory function in mature somatic cells. In the germ line and during early embryogenesis, however, DNA methylation undergoes global erasure and re-establishment to support germ cell and embryonic development. While de novo DNA methylation during male germ cell development is essential for setting genomic imprints, possible other intergenerational roles for paternal DNA methylation following fertilization are unknown.
Read the full summary ↓
To address this question, we reduced the level of DNA methylation in developing male germ cells through conditional gene deletion of the de novo DNA methyltransferases DNMT3A and DNMT3B in undifferentiated spermatogonia. Mutant male germ cells nevertheless completed their differentiation to sperm. We observed that DNMT3A serves a largely maintenance-like methylation function at many intragenic sites in undifferentiated spermatogonia while DNMT3B catalyzes de novo methylation during spermatogonial differentiation. In spermatogonia, the acquisition of DNA methylation and deposition of H3K4me3 occur mutually exclusive. Failing de novo DNA methylation in spermatogonia leads to increased nucleosome occupancy in mature sperm at sites with high CpG content, reinforcing the model that DNA methylation constrains nucleosome retention in sperm. To assess the impact of altered sperm chromatin in the formation of embryonic chromatin, we measured H3K4me3 occupancy at paternal and maternal alleles in 2-cell embryos using a highly sensitive transposon-based tagging assay for modified chromatin. Our data show that reduced DNA methylation in sperm renders paternal alleles permissive for H3K4me3 establishment in early embryos, independently from paternal inheritance of sperm born H3K4me3. Together, this study provides first evidence that paternally inherited DNA methylation directs chromatin formation during early embryonic development.
Published in
DNA methylation modulates nucleosome retention in sperm and H3K4 methylation deposition in early mouse embryos
Fanourgakis G, Gaspa-Toneu L, Komarov PA et al. · Nature communications 2025 · PMID 39774947 · doi:10.1038/s41467-024-55441-1
This dataset
Open GSE229238 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 GSE229238_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 PRJNA953620 and SRA study SRP431595. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39774947) ↗
Study design
22 × Early 4 cell stage embryo Dnmt3a f/+ ; Dnmt3b f/+ sperm derived vs 20 × Early 4 cell stage embryo Dnmt3a f/- ; Dnmt3b f/- ; Stra8-iCre tg sperm derived

Supports a between-group comparison across 42 samples.

How we read this: 2 replicated groups read from 42 sample titles; they account for 42 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

+ 2 more — browse all 42 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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