GEO series

Human Papillomavirus Genomes Associate with Active Host Chromatin during Viral Genome Maintenance [4C-seq]

GSE294036 Homo sapiens (human) Other 7 samples Submitted 2025/07/07 Platform GPL24676

At a glance

human · 7 samples

Organism: Homo sapiens (human)
Samples: 7 samples: 4 × 9E cells, extrachromosomal HPV31, biol vs 3 × 6E cells, integrated HPV31, biolGroups 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: Human papillomavirus genomes associate with active host chromatin during persistent viral infectionPLoS pathogens · 2025

Summary (written by the submitters)

Human papillomaviruses (HPVs) maintain their genomes as minichromosomes in the nuclei of infected keratinocytes. This study investigates the association of HPV31 genomes with host chromatin using both HiC and 4C-seq chromosome conformation capture techniques. We show that HPV31 genomes preferentially associate with transcriptionally active A compartments of host chromatin, regions of open chromatin defined by ATAC-seq, and super-enhancers defined by Brd4 and H3K27ac ChIP-seq.

Read the full summary ↓

The viral genome association sites were also highly correlated with genomic loci previously identified as common HPV integration sites in cervical cancers. Recent studies have shown that transcriptionally active sites are prone to dsDNA breaks, and we find a strong correlation among dsBREAK datasets with transcriptionally active and open regions of host chromatin and the HPV31 genome association sites defined in our study. These findings suggest that HPV genomes associate with cellular transcriptional epicenters to maintain active viral gene expression during persistent infection, but also indicate that the susceptibility of these regions to dsDNA breaks could explain their propensity for viral DNA integration in HPV-associated cancers.

Published in

Human papillomavirus genomes associate with active host chromatin during persistent viral infection

Warburton A, Markowitz TE, Miranda JL et al. · PLoS pathogens 2025 · PMID 40892869 · doi:10.1371/journal.ppat.1013454

This dataset

Open GSE294036 in finder → Find more human datasets →

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 (GSE294036_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 PRJNA1247935. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40892869) ↗

Study design

4 × 9E cells, extrachromosomal HPV31, biol vs 3 × 6E cells, integrated HPV31, biol

Supports a between-group comparison across 7 samples.

How we read this: 2 replicated groups read from 7 sample titles; they account for 7 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

GSM8896992 6E cells, integrated HPV31, biol rep 1 6E cells, integrated HP…
GSM8896993 6E cells, integrated HPV31, biol rep 2 6E cells, integrated HP…
GSM8896994 6E cells, integrated HPV31, biol rep 3 6E cells, integrated HP…
GSM8896995 9E cells, extrachromosomal HPV31, biol rep 1 9E cells, extrachromoso…
GSM8896996 9E cells, extrachromosomal HPV31, biol rep 2 9E cells, extrachromoso…
GSM8896997 9E cells, extrachromosomal HPV31, biol rep 3 9E cells, extrachromoso…
GSM8896998 9E cells, extrachromosomal HPV31, biol rep 4 9E cells, extrachromoso…

Datasets on a similar topic

GSE304818 Highly active chromosome regions preferentially associate with two perispeckle networks that partition the interchromatin space. 50 samples shares associate, chromatin, active
GSE230342 Chromatin conformation dynamics during CD4+ Tcell activation implicates autoimmune disease associated genes and regulatory elements (HiC) 6 samples shares associate, chromatin
GSE273054 Differential chromatin accessibility analysis elucidates mechanisms of coronary artery disease-associated genetic variation 119 samples shares associate, chromatin
GSE278549 PBAF associates with repressed chromatin to enable REST occupancy 61 samples shares associate, chromatin
GSE303855 Mechanistic and Epigenetic Partitioning of Lamina-Associated Chromatin Revealed by a Genome-Wide Imaging Screen 45 samples shares associate, chromatin
GSE244275 Altered enhancer-promoter interaction leads to MNX1 expression in pediatric acute myeloid leukemia with t(7;12)(q36;p13) [4C-Seq] 10 samples shares 4c-seq
GSE284199 New insights into the cis-regulation of the CFTR gene in pancreatic cells [4C-seq] 9 samples shares 4c-seq
GSE282510 Multi-omics analysis in primary T cells elucidates mechanisms behind disease associated genetic loci [Hi-C] 108 samples shares associate

Search all human datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.