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Reprogramming of H3K36me2 guides lineage- and locus-specific post-implantation DNA methylation [ChIP-Seq]

GSE273314 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 159 samples Submitted 2025/09/27 Platform GPL28330Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 159 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
159 samples: 69 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
Reprogramming of H3K36me2 guides lineage-specific post-implantation de novo DNA methylationNature cell biology · 2025
Summary (written by the submitters)
In mammals, DNA methylation is rapidly re-established after implantation following global erasure in pre-implantation embryos, the regulation of which, however, is not completely understood. Here, by mapping H3K36me2 in pre- and post-implantation mouse embryos, we unravel the dynamic reprogramming of H3K36me2 in mouse early development and its role in post-implantation de novo DNA methylation.
Read the full summary ↓
Parental H3K36me2 was progressively lost by the 8-cell stage, while de novo H3K36me2 was established at putative enhancers after ZGA mediated by histone acetylation, followed by genome-wide deposition after implantation. H3K36me2 was however excluded from the inactive X chromosome. Catalytic mutation of NSD1, the major H3K36me2 methyltransferase, compromised post-implantation development and DNA methylation re-establishment, with extra-embryonic lineages more severely affected than embryonic lineages. De novo DNA methylation establishment in embryonic lineages partially bypassed H3K36me2/3 through elevated DNMT3B expression. Mechanistically, the PWWP domain of DNMT3A, but not that of DNMT3B, confers strict requirement of H3K36me2/3 for DNA methylation, while DNMT3B is a “leaky” reader of H3K36 methylation. Nevertheless, germline-specific genes, including those contain CpG islands at promoters, still require H3K36me2 to be efficiently methylated and silenced. Amid global remethylation, DNA methylation valleys (DMVs) escape de novo DNA methylation, where PRC1 and H2AK119ub1 antagonize H3K36me2 invasion. Thus, reprogramming of H3K36me2 is required for early embryogenesis and regulates lineage- and locus-specific post-implantation DNA methylation establishment.
Published in
Reprogramming of H3K36me2 guides lineage-specific post-implantation de novo DNA methylation
Lu X, Wang L, Liu B et al. · Nature cell biology 2025 · PMID 41219433 · doi:10.1038/s41556-025-01805-8
This dataset
Open GSE273314 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 GSE273314_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 PRJNA1141408 and SRA study SRP522836. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41219433) ↗
Study design
69 conditions, mostly in duplicate
SKO_mESC_10k_S2_20k_K36me3 ×3 FGO_H3K36me2 ×2 MII_H3K36me2 ×2 1C_H3K36me2 ×2 2C_H3K36me2 ×2 4C_H3K36me2 ×2 8C_H3K36me2 ×2 ICM_H3K36me2 ×2 +81 more

Supports a between-group comparison across 139 samples.

How we read this: 69 replicated groups read from 159 sample titles; they account for 139 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

+ 119 more — browse all 159 samples with per-sample file links →

Datasets on a similar topic

Search all mouse ChIP / ATAC / CUT&Tag datasets in GEO →

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