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ZBTB16/PLZF regulates self-renewal and differentiation of juvenile spermatogonial stem cells through an extensive transcription factor-chromatin poising network

GSE276673 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 20 samples Submitted 2025/01/03 Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 20 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
20 samples: 10 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
ZBTB16/PLZF regulates juvenile spermatogonial stem cell development through an extensive transcription factor poising networkNature structural & molecular biology · 2025
Summary (written by the submitters)
Spermatogonial stem cells (SSCs) balance self-renewal versus differentiation/spermatogenesis to ensure continuous sperm production. Here, we uncover multiple roles for the transcription factor ZBTB16/PLZF in juvenile mouse undifferentiated spermatogonia (uSPG). ZBTB16 activates genes in uSPG promoting self-renewal and cell cycle progression to maintain uSPG and transit-amplifying states.
Read the full summary ↓
Remarkably, in uSPG, ZBTB16, SALL4, SOX3 all co-localize at over 12,000 promoters regulating uSPG and meiosis. These regions feature broad H3K4me3 and H3K27ac, DNA hypomethylation, RNAPol2 and often CTCF. Hi-C analyses reveal robust 3D physical interactions among these co-bound promoters, revealing a transcription factor and higher-order active chromatin interaction network within uSPG that poises meiotic promoters for subsequent activation. Conversely, these factors do not occupy germline-specific promoters driving spermiogenesis, which instead lack promoter-promoter physical interactions and bear DNA hypermethylation, even when active. Overall, ZBTB16 promotes uSPG cell cycle progression and colocalizes with SALL4, SOX3, CTCF and RNAPol2 to establish a novel and extensive chromatin poising network.
Published in
ZBTB16/PLZF regulates juvenile spermatogonial stem cell development through an extensive transcription factor poising network
Yi C, Kitamura Y, Maezawa S et al. · Nature structural & molecular biology 2025 · PMID 40033150 · doi:10.1038/s41594-025-01509-5
This dataset
Open GSE276673 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 GSE276673_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 PRJNA1158670 and SRA study SRP531457. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40033150) ↗
Study design
10 conditions, mostly in duplicate
ChIPSeq_P7_Testis_WT_SALL4 ×2 ChIPSeq_P7_Testis_WT_SOX3 ×2 ChIPSeq_P7_Testis_WT_TBP ×2 ChIPSeq_P7_Testis_WT_Pan-RNAPol2 ×2 ChIPSeq_P7_Testis_WT_RNAPol2Ser5P ×2 ChIPSeq_P7_Testis_WT_RNAPol2Ser2P ×2 ChIPSeq_P7_Testis_Null_SALL4 ×2 ChIPSeq_P7_Testis_Null_SOX3 ×2 +2 more

Supports a between-group comparison across 20 samples.

How we read this: 10 replicated groups read from 20 sample titles; they account for 20 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
Datasets on a similar topic

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