GEO series

Decoding 3D chromatin architecture reveals distinct enhancer classes underlying hierarchical gene regulation in prostate cancer

GSE314777 Homo sapiens (human) Other 10 samples Submitted 2026/06/15 Platform GPL34284

At a glance

human · 10 samples

Organism: Homo sapiens (human)
Samples: 10 samples: 5 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.
Paper: Decoding 3D chromatin architecture reveals distinct enhancer classes underlying hierarchical gene regulation in prostate cancerGenome biology · 2026

Summary (written by the submitters)

Background: The transcription process is controlled by non-coding regulatory elements, more than 70% of which are putative enhancers. These enhancers comprise over 600,000 regions and are marked by histone modifications. However, the mechanisms by which altered enhancers in cancer cooperate within the three-dimensional chromatin architecture to drive oncogenic programs remain poorly understood.

Read the full summary ↓

Results: By integrating 201 H3K27ac ChIP seq datasets from prostate, we identify 3,216 high confidence prostate cancer-specific putative enhancers. Ultra high resolution chromatin interaction profiling by Region Capture Micro-C at a representative chr6q24.1 locus reveals that these enhancers form cancer specific, highly nested interactions with promoters that coalesce into a multi connected hub absent in normal prostate cells. CRISPR/Cas9 perturbations of these enhancers, examined one by one, distinguish enhancer classes within the hub. Deletion of a central enhancer collapses hub-wide enhancer activities and architecture, leading to the downregulation of target genes, impaired proliferation, and reduced clonogenic growth. In contrast, deletion of a redundant enhancer results in minimal transcriptional changes, as neighboring enhancers rescue cancer signaling through compensatory architectural rewiring that strengthens alternative enhancer-promoter interactions. We also observe that FOXA1, a pioneer transcription factor activated in prostate cancer, directly binds to these enhancers and regulates distinct enhancer classes, leading to varying degrees of chromatin accessibility and gene expression changes. Conclusions: These findings suggest that enhancers function in a coordinated manner, forming multi-connected cancer-specific chromatin interaction hubs, with distinct enhancer classes contributing differently to gene regulation. This study advances our ability to modulate gene expression in a cell type-specific manner, opening new avenues for precision therapies.

Published in

Decoding 3D chromatin architecture reveals distinct enhancer classes underlying hierarchical gene regulation in prostate cancer

Cao H, Wu Z, Ji B et al. · Genome biology 2026 · PMID 42487124 · doi:10.1186/s13059-026-04178-9

This dataset

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Download · which file do I need?

Direct links to NCBI, 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.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE314777_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

Also filed as BioProject PRJNA1392580. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42487124) ↗

Study design

5 conditions, mostly in duplicate

22Rv1_RCMC_WT ×2 22Rv1_RCMC_NTC ×2 22Rv1_RCMC_cPCE_del ×2 22Rv1_RCMC_rPCE_del ×2 RWPE1_RCMC_WT ×2

Supports a between-group comparison across 10 samples.

How we read this: 5 replicated groups read from 10 sample titles; they account for 10 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

GSM9410352 22Rv1_RCMC_WT_R1 22Rv1_RCMC_WT
GSM9410353 22Rv1_RCMC_WT_R2 22Rv1_RCMC_WT
GSM9410354 22Rv1_RCMC_NTC_R1 22Rv1_RCMC_NTC
GSM9410355 22Rv1_RCMC_NTC_R2 22Rv1_RCMC_NTC
GSM9410356 22Rv1_RCMC_cPCE_del_R1 22Rv1_RCMC_cPCE_del
GSM9410357 22Rv1_RCMC_cPCE_del_R2 22Rv1_RCMC_cPCE_del
GSM9410358 22Rv1_RCMC_rPCE_del_R1 22Rv1_RCMC_rPCE_del
GSM9410359 22Rv1_RCMC_rPCE_del_R2 22Rv1_RCMC_rPCE_del
GSM9410360 RWPE1_RCMC_WT_R1 RWPE1_RCMC_WT
GSM9410361 RWPE1_RCMC_WT_R2 RWPE1_RCMC_WT

Datasets on a similar topic

GSE314776 Decoding 3D chromatin architecture reveals distinct enhancer classes underlying hierarchical gene regulation in prostate cancer [ChIP-Seq] 24 samples shares architecture, hierarchical, underlying, chromatin, decoding, distinct, enhancer, prostate
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GSE286581 Ablation of Linker Histone H1.4 Reveals Focal Regulation of AP-1 Directed Enhancers and Chromatin Accessibility [4sU] 6 samples shares chromatin, enhancer
GSE272080 3D chromatin-based variant-to-gene maps across 57 human cell types reveal the cellular and genetic architecture of autoimmune disease susceptibility [captureC] 6 samples shares architecture, chromatin
GSE268035 STAG2 Mutations Reshape the Cohesin-Structured Spatial Chromatin Architecture to Drive Gene Regulation in Acute myeloid Leukemia 541 samples shares architecture, chromatin
GSE215328 Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [hESC_H9_d049_ChIP_Seq] 135 samples shares architecture, chromatin
GSE316337 Multi-omics profiling reveals microbiota, metabolite, lipid, and immunological heterogeneity underlying distinct pathophysiological mechanisms of age-related endotypes in type 1 diabetes 54 samples shares underlying, distinct
GSE289467 Intraindividual epigenetic heterogeneity underlying phenotypic subtypes of advanced prostate cancer [CUT&Tag] 50 samples shares underlying, prostate

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