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Landscape of the Epstein-Barr virus-host chromatin interactome and gene regulation

GSE281522 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 41 samples Submitted 2025/04/06 Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 41 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Homo sapiens (human)
Samples
41 samples: 17 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; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
Landscape of the Epstein-Barr virus-host chromatin interactome and gene regulationThe EMBO journal · 2025
Summary (written by the submitters)
The three-dimensional (3D) chromatin structure of Epstein–Barr virus (EBV) within host cells and the underlying mechanisms of chromatin interaction and gene regulation, particularly those involving EBV’s noncoding RNAs (ncRNAs), have remained incompletely characterized.
Read the full summary ↓
In this study, we employed state-of-the-art techniques of 3D genome mapping, including protein-associated chromatin interaction analysis with paired-end tag sequencing (ChIA-PET), RNA-associated chromatin interaction technique (RDD), and super-resolution microscopy, to delineate the spatial architecture of EBV in human lymphoblastoid cells. We systematically analyzed EBV-to-EBV (E–E), EBV-to-host (E–H), and host-to-host (H–H) interactions linked to host proteins and EBV RNAs. Our findings reveal that EBV utilizes host CCCTC-binding factor (CTCF) and RNA polymerase II (RNAPII) to form distinct chromatin contact domains (CCDs) and RNAPII-associated interaction domains (RAIDs). The anchors of these chromatin domains serve as platforms for extensive interactions with host chromatin, thus modulating host gene expression. Notably, EBV ncRNAs, especially Epstein–Barr-encoded RNAs (EBERs), target and interact with less accessible regions of host chromatin to repress a subset of genes via the inhibition of RNAPII-associated chromatin loops. This process involves the cofactor nucleolin (NCL) and its RNA recognition motifs, and depletion of either NCL or EBERs alters expression of genes crucial for host infection control, immune response, and cell cycle regulation. These findings unveil a sophisticated interplay between EBV and host chromatin.
Published in
Landscape of the Epstein-Barr virus-host chromatin interactome and gene regulation
Tian SZ, Yang Y, Ning D et al. · The EMBO journal 2025 · PMID 40425856 · doi:10.1038/s44318-025-00466-5
This dataset
Open GSE281522 in finder → Find more human 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 GSE281522_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1184196 and SRA study SRP544271. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40425856) ↗
Study design
17 conditions, mostly in duplicate
EBERs_RDD_combined ×3 MALAT1_RDD_combined ×3 ATAC-seq_EBERsNC ×3 miR-BART_RDD_combined ×2 v-snoRNA1_RDD_combined ×2 RNAPII_ChIA-PET_EBERsNC ×2 RNAPII_ChIA-PET_EBERsKD ×2 RNAPII_ChIA-PET_HEK293T_NCLNC ×2 +13 more

Supports a between-group comparison across 37 samples.

How we read this: 17 replicated groups read from 41 sample titles; they account for 37 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

+ 1 more — browse all 41 samples with per-sample file links →

Datasets on a similar topic

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