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Polycomb Chromatin Topology Enables Long-Range Enhancer Recruitment during Craniofacial Development [RNA-seq]

GSE295406 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2026/04/08 Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 24 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
24 samples: 8 conditions, mostly in triplicateGroups 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
Polycomb chromatin topology enables long-range enhancer recruitment during craniofacial developmentNature communications · 2026
Summary (written by the submitters)
Little is known about how three-dimensional chromatin topology shapes mammalian craniofacial development. In mouse cranial neural crest cells, a Polycomb Repressive Complex 2 (PRC2)-dependent chromatin architecture is established before migration. This configuration maintains craniofacial gene promoters poised and connects them with distal Polycomb tethering elements, positioning promoters in spatial proximity to future long-range enhancers.
Read the full summary ↓
Deletion of Ezh2 disrupts this early topology, causing inappropriate gene derepression in post-migratory craniofacial subpopulations where these genes are normally silenced, and failure of long-range enhancer recruitment where activation is required, thereby impairing proper gene expression. We further identify a distal Polycomb tethering element essential for Hoxa2 enhancer recruitment across topologically associating domains. Thus, Polycomb acts not only as a transcriptional repressor, but also as a chromatin-folding organizer that prepares developmental genes for later activation, by facilitating subsequent recruitment of distal active enhancers previously not in contact. Polycomb-mediated topology therefore orchestrates the transition from progenitor plasticity to precise spatiotemporal control of morphogenetic gene programs during neural crest development and face formation.
Published in
Polycomb chromatin topology enables long-range enhancer recruitment during craniofacial development
Ben Zouari Y, Joshi O, Salvi A et al. · Nature communications 2026 · PMID 42135326 · doi:10.1038/s41467-026-73065-5
This dataset
Open GSE295406 in finder → Find more mouse RNA-seq 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 GSE295406_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1254616 and SRA study SRP580783. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42135326) ↗
Study design
8 conditions, mostly in triplicate
RNASeq_FNP_E11.5_WT ×3 RNASeq_Mx_E11.5_WT ×3 RNASeq_Md_E11.5_WT ×3 RNASeq_PA2_E11.5_WT ×3 RNASeq_FNP_E11.5_Ezh2cKO ×3 RNASeq_Mx_E11.5_Ezh2cKO ×3 RNASeq_Md_E11.5_Ezh2cKO ×3 RNASeq_PA2_E11.5_Ezh2cKO ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 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
Datasets on a similar topic

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