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The placentalia specific histone H3.4 promotes germ cell development and reproductive fitness [ChIP-seq]

GSE291272 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 41 samples Submitted 2026/04/06 Platform GPL17021Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 41 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
41 samples: 12 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
The eutherian-specific histone H3.4 promotes germ cell development and reproductive fitnessNature communications · 2026
Summary (written by the submitters)
Genes involved in chromatin remodeling during sperm development are under strong evolutionary pressure to optimize reproductive fitness In mice, the histone H3.4 variant, encoded by the single copy H3f4 gene, is essential for spermatogenesis. H3.4 is highly expressed in spermatogonia and replaces progressively canonical H3 histones during spermatogonial expansion and differentiation.
Read the full summary ↓
Phylogenetic analysis shows that H3f4 is specific to the placental lineage and originates from an ancestral H3.2 gene existing prior to the divergence of placental and marsupial mammals over 100 million years ago. Situated in a majorly truncated histone cluster, placental H3f4 orthologs show increased synonymous and non-synonymous substitution rates compared to analogous marsupial H3.2 genes. H3f4 carries four non-synonymous substitutions relative to H3.2 genes. To understand the impact of evolutionary sequence divergence on reproductive fitness, we reverted three of four non-synonymously substituted residues in H3f4 to those present in H3.1 (H3f4V24A, H3f4H42R, H3f4S98A) while leaving H3f4C96 intact which is identical to H3.1C96. When expressed from both alleles, neither single nor triple reversion of diverged residues affected spermatogenesis much. In contrast, hemizygous expression of the triply reverted H3f4H3.1 allele on a H3f4-deficiency background caused an >40% reduction in testis weight associated with death of pachytene spermatocytes, impaired differentiation of spermatids and aberrant expression of thousands of genes during spermatid elongation. Hemizygous expression of individual residue substitution alleles revealed that residues V24 and H42 of H3.4 promote spermatogenesis, while residue S98 is neutral. Together, our study shows that H3f4 has been subject to positive evolutionary selection, promoting male reproductive fitness.
Published in
The eutherian-specific histone H3.4 promotes germ cell development and reproductive fitness
Komarov PA, Bammer PC, Liang CY et al. · Nature communications 2026 · PMID 42248887 · doi:10.1038/s41467-026-73954-9
This dataset
Open GSE291272 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 GSE291272_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 PRJNA1232701 and SRA study SRP568412. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42248887) ↗
Study design
12 conditions, mostly in duplicate
SgU_wt_H3.3 ×2 SgU_tg_H3.3 ×2 SgU_tg_Myc ×2 SgD_wt_H3.3 ×2 SgD_tg_H3.3 ×2 SgD_tg_Myc ×2 ScLZ_wt_H3.3 ×2 ScLZ_tg_H3.3 ×2 +21 more

Supports a between-group comparison across 24 samples.

How we read this: 12 replicated groups read from 41 sample titles; they account for 24 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

+ 1 more — browse all 41 samples with per-sample file links →

Datasets on a similar topic

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