GEO series
Polycomb Chromatin Topology Enables Long-Range Enhancer Recruitment during Craniofacial Development [ChIP-seq]
GSE295340
Mus musculus
Genome binding/occupancy profiling by high throughput sequencing
42 samples
Submitted 2026/04/08
Platform GPL17021Platform GPL24247
Summary
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. 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
Ben Zouari Y, Joshi O, Salvi A et al.
· Nature communications 2026
· PMID 42135326
· doi:10.1038/s41467-026-73065-5
This dataset
Download
Direct links to NCBI, no account and no request form: the whole study as GSE295340_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 42 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1254229 and SRA study SRP580689. Searching any of these in the dataset finder brings you back here.
Study design
39 conditions, each sampled once — no replicated groups
ChipSeq_PA2_E11.5_WT_H3K27ac ×2
Read from the first 40 of 42 sample titles: 39 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM8945962 ChipSeq_Progenitors_E8.5_WT_H3K27ac
- GSM8945963 ChipSeq_FNP_E11.5_WT_H3K27ac
- GSM8945964 ChipSeq_Mx_E11.5_WT_H3K27ac
- GSM8945965 ChipSeq_Md_E11.5_WT_H3K27ac
- GSM8945966 ChipSeq_PA2_E11.5_WT_H3K27ac
- GSM8945967 ChipSeq_FNP_E11.5_Ezh2cKO_H3K27ac
- GSM8945968 ChipSeq_Mx_E11.5_Ezh2cKO_H3K27ac
- GSM8945969 ChipSeq_Md_E11.5_Ezh2cKO_H3K27ac
- GSM8945970 ChipSeq_PA2_E11.5_Ezh2cKO_H3K27ac
- GSM8945971 ChipSeq_FNP_E11.5_WT_H3K4me2
- GSM8945972 ChipSeq_Mx_E11.5_WT_H3K4me2
- GSM8945973 ChipSeq_Md_E11.5_WT_H3K4me2
- GSM8945974 ChipSeq_PA2_E11.5_WT_H3K4me2
- GSM8945975 ChipSeq_FNP_E11.5_Ezh2cKO_H3K4me2
- GSM8945976 ChipSeq_Mx_E11.5_Ezh2cKO_H3K4me2
- GSM8945977 ChipSeq_Md_E11.5_Ezh2cKO_H3K4me2
- GSM8945978 ChipSeq_PA2_E11.5_Ezh2cKO_H3K4me2
- GSM8945979 ChipSeq_FNP_E11.5_WT_H3K27me3
- GSM8945980 ChipSeq_Mx_E11.5_WT_H3K27me3
- GSM8945981 ChipSeq_Md_E11.5_WT_H3K27me3
- GSM8945982 ChipSeq_PA2_E11.5_WT_H3K27me3
- GSM8945983 ChIPseq_Input_NebNextUltra
- GSM8945984 ChipSeq_PA2_E11.5_HIRE1-del_H3K27me3
- GSM8945985 ChipSeq_PA2_E11.5_HIRE1-del_H3K27ac
- GSM8945986 ChipSeq_PA2_E11.5_Control_H3K27me3
- GSM8945987 ChipSeq_PA2_E11.5_Control_H3K27ac
- GSM8945988 ChipSeq_Md_E11.5_HIRE1-del_H3K27me3
- GSM8945989 ChipSeq_Md_E11.5_HIRE1-del_H3K27ac
- GSM8945990 ChipSeq_Md_E11.5_Control_H3K27me3
- GSM8945991 ChipSeq_Md_E11.5_Control_H3K27ac
- GSM9562050 ChipSeq_PA2_E11.5_WT_H3K27ac_1
- GSM9562051 ChipSeq_PA2_E11.5_WT_H3K27me3_1
- GSM9562052 Input_PA2_E11.5_WT
- GSM9562053 ChipSeq_PA2_E11.5_Hoxa2PTE-36kb-del_H3K27ac_1
- GSM9562054 ChipSeq_PA2_E11.5_Hoxa2PTE-36kb-del_H3K27me3_1
- GSM9562055 Input_PA2_E11.5_Hoxa2PTE-36kb-del
- GSM9562056 ChipSeq_FNPMxMdPA2_E11.5_WT_CTCF_1
- GSM9562057 ChipSeq_FNPMxMdPA2_E11.5_Ezh2cKO_CTCF_1
- GSM9562058 Input_FNPMxMdPA2_E11.5_WT
- GSM9562059 Input_FNPMxMdPA2_E11.5_Ezh2cKO
+ 2 more — browse all 42 samples with per-sample file links →
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