GEO series

Z-DNA formation induces the totipotent-like state and primes Zscan4-dependent chromatin compartmentalization [scRNA-seq]

GSE291990 Mus musculus (mouse) Single-cell RNA-seq 2 samples Submitted 2025/12/11 Platform GPL18573Platform GPL19057

At a glance

Single-cell RNA-seq · mouse · 2 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Mus musculus (mouse)
Samples: 2 samples
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: Z-DNA formation regulates the totipotent-like state and primes Zscan4-dependent chromatin compartmentalizationNature structural & molecular biology · 2026

Summary (written by the submitters)

A remarkable transition during murine development is the progression from the 1-cell embryo to the 2-cell stage, accompanied by the activation of a specific set of embryonic genes, epigenome reprogramming, and nuclear architecture reorganization. Some of these characteristics are recapitulated in vitro with the spontaneous emergence of 2-cell-like cells from mouse embryonic stem cells, which exhibit a transcriptomic signature resembling the 2-cell stage, including the expression of genes such as Dux, Zscan4, and the repetitive element MERVL, and a more relaxed chromatin state.

Read the full summary ↓

Here, we show that inter-and intra-chromosomal interactions, driven by Zscan4 chromatin factors, form during this transition and segregate into a distinct genomic compartment (Z compartment). Mechanistically, the formation of Z-DNA, an alternative DNA conformation regulated by polyamine levels, promotes the emergence of totipotent-like cells and the establishment of the Z compartment. This compartment is characterized by a decrease in active histone marks and a reduced expression of genes associated with differentiation and late developmental processes. Overall, these findings suggest that Z-DNA formation may play a dual role, first in activating ZGA genes and later in guiding genome compartmentalization to safeguard the totipotent-like state by restricting the expression of non-ZGA genes within a permissive chromatin environment.

Published in

Z-DNA formation regulates the totipotent-like state and primes Zscan4-dependent chromatin compartmentalization

Shajahan S, Loe-Mie Y, Asselin L et al. · Nature structural & molecular biology 2026 · PMID 41703099 · doi:10.1038/s41594-026-01751-5

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 GSE291990_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1236296 and SRA study SRP570472. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41703099) ↗

Samples in this study

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Datasets on a similar topic

GSE291992 Z-DNA formation induces the totipotent-like state and primes Zscan4-dependent chromatin compartmentalization 47 samples shares z-dna, compartmentalization, zscan4-dependent, totipotent-like, formation, chromatin, induces
GSE289305 Alterations in chromatin architecture promote totipotent-like features in a DUX-dependent manner [RNA-Seq] 27 samples shares totipotent-like, chromatin

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