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USP17L promotes the 2-cell program through deubiquitination of H2AK119ub1 and ZSCAN4 [ChIP-Seq]

GSE282421 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 18 samples Submitted 2025/06/13 Platform GPL28330
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 18 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
18 samples: 9 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
USP17L promotes the 2-cell-like program through deubiquitination of H2AK119ub1 and ZSCAN4Nature communications · 2025
Summary (written by the submitters)
Zygotic genome activation (ZGA) is the first transcription event after fertilization. A minor wave of ZGA (minor ZGA) precedes and is essential for the major wave of ZGA (major ZGA) in two-cell (2C) mouse embryos. A subset of minor ZGA genes (known as “2C” genes) are also activated in a rare population of embryonic stem cells (ESCs) (2C-like cells), which possess expanded developmental plasticity to both embryonic and extra-embryonic tissues, like 2-cell embryos.
Read the full summary ↓
However, the functions of these 2C genes remain to be fully understood. Here, through knockdown, overexpression, and biochemical analyses, we find that one family of such 2C genes, Usp17l, plays essential roles in both transcriptional and post-translational regulation of the 2C program. Specifically, USP17LE, a member of the USP17L family, deubiquitinates H2AK119ub1 and promotes the expression of Dux and the downstream 2C genes, including Zscan4, Tcstv1, and retrotransposons such as MERVL, in ESCs. Moreover, USP17LE deubiquitinates and stabilizes ZSCAN4. In mouse pre-implantation embryos, Dux is marked by strong H2AK119ub1 at most stages except for the 1-cell and early 2-cell stages, and overexpression of Usp17le reduces H2AK119ub and further promotes the activation of Dux and 2C genes. Thus, our findings identify USP17L as a key regulator of the 2C program.
Published in
USP17L promotes the 2-cell-like program through deubiquitination of H2AK119ub1 and ZSCAN4
Shi P, Lu X, Jin K et al. · Nature communications 2025 · PMID 40750602 · doi:10.1038/s41467-025-62303-x
This dataset
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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 GSE282421_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 PRJNA1188559 and SRA study SRP546469. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40750602) ↗
Study design
9 conditions, mostly in duplicate
Ctrl_L2C_H2AK119ub1 ×2 Usp17le_OE_L2C_H2AK119ub1 ×2 Usp17l_KD_L2C_H2AK119ub1 ×2 Ctrl_L2C_H3K27me3 ×2 Usp17le_OE_L2C_H3K27me3 ×2 Usp17l_KD_L2C_H3K27me3 ×2 WT_H3K9me3 ×2 Usp17l_KD4_H3K9me3 ×2 +1 more

Supports a between-group comparison across 18 samples.

How we read this: 9 replicated groups read from 18 sample titles; they account for 18 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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