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Broad H3K4me3 controls transcription output and timing during spermatid development

GSE242515 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 111 samples Submitted 2024/09/03 Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 111 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
111 samples: 51 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
SETD1B-mediated broad H3K4me3 controls proper temporal patterns of gene expression critical for spermatid developmentCell research · 2025
Summary (written by the submitters)
Male germ cells express a complex transcriptome under tight temporal regulation during their development. However, our knowledge of the epigenetic regulation of crucial stages in this process, such as meiotic onset, remains limited. Here, by dissecting a comprehensive map of the dynamic epigenomic landscape in developing mouse male germ cells, we uncover mutually exclusive shifts in the repressive histone marks H3K9me2, H3K9me3 and H3K27me3 during the mitosis-to-meiosis transition and completion of meiotic recombination.
Read the full summary ↓
These dynamic shifts coincide with temporal changes in global transcriptional output, retrotransposon activity, and the silencing of mitotic/meiotic genes during spermatogenesis. In addition, we identify Setd1b-mediated broad H3K4me3 domains in both mouse and human spermatids. These broad H3K4me3 domains promote Pol II occupancy and transcription, resulting in high gene expression in spermatids. Setd1b ablation leads to a complete loss of broad H3K4me3, and the redistribution of Pol II from broad H3K4me3 promoters to regular H3K4me3 promoters, thereby compromising temporal gene expression and ultimately hampering spermiogenesis. These findings reveal that dynamic epigenetic changes orchestrate stage-specific gene expression in spermatogenesis, with Setd1b-mediated broad H3K4me3 serving as a crucial regulator that controls the timing of stage-specific gene expression in spermatids.
Published in
SETD1B-mediated broad H3K4me3 controls proper temporal patterns of gene expression critical for spermatid development
Lin Z, Rong B, Lyu R et al. · Cell research 2025 · PMID 40033033 · doi:10.1038/s41422-025-01080-0
This dataset
Open GSE242515 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 GSE242515_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 PRJNA1013787 and SRA study SRP459034. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40033033) ↗
Study design
51 conditions, mostly in duplicate
Input.RS ×3 H3K27ac.RS2 ×2 H3K27ac.RS4 ×2 H3K27ac.RS8 ×2 H3K27me3.RS2 ×2 H3K27me3.RS4 ×2 H3K27me3.RS8 ×2 H3K36me3.RS2 ×2 +51 more

Supports a between-group comparison across 103 samples.

How we read this: 51 replicated groups read from 111 sample titles; they account for 103 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

+ 71 more — browse all 111 samples with per-sample file links →

Datasets on a similar topic

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