GEO series

Systematic investigation reveals extensive Epstein-Barr virus transcriptional regulation of the human genome

GSE303478 Homo sapiens Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing 217 samples Submitted 2026/06/08 Platform GPL24676Platform GPL34284

Summary

We systematically investigate interactions between Epstein-Barr virus (EBV) transcriptional regulators (vTRs) and the human genome. Starting with 16 known and candidate vTRs, we identify nine whose introduction into human cells results in substantial alterations to host gene expression. Genome-scale determination of vTR genomic binding events and alterations to chromatin accessibility reveals a detailed map of EBV's functional interactions with the human genome, including >100,000 vTR binding events impacting almost a quarter of all human genes. BMRF1 emerges as a potent regulator, impacting >7,000 genes and altering >37,000 chromatin regions. Our results provide new evidence that EBV RTA interacts with and stabilizes the binding of human RBPJ. Network analysis reveals that many human genes are targeted by multiple EBV vTRs, highlighting the vast coordinated impact of EBV on human gene expression. This study provides a valuable, extensive resource for examining EBV-induced alterations to human gene regulation, with data available on multiple platforms.

Published in

Dexheimer PJ, Hass MR, Edsall LE et al. · Cell genomics 2026 · PMID 42456663 · doi:10.1016/j.xgen.2026.101303

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Direct links to NCBI, no account and no request form: the whole study as GSE303478_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 217 samples. Raw sequencing reads are also available from ENA.

Whole study · RAW.tar ↓ Series matrix ↓ All supplementary files ↗ Raw reads on ENA ↗

Also filed as BioProject PRJNA1295495 and SRA study SRP602723. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42456663) ↗

Study design

13 conditions, mostly in triplicate

cGFP tagged BMRF1 stable transfection ×3 nGFP tagged EBNA1 stable transfection ×3 nGFP tagged EBNA2 stable transfection ×3 nGFP tagged EBNA3A stable transfection ×3 nGFP tagged EBNA3B stable transfection ×3 nGFP tagged EBNA3C stable transfection ×3 nGFP tagged EBNALP stable transfection (TREx) ×3 cGFP tagged RTA stable transfection ×3 +6 more

Supports a between-group comparison across 39 samples.

13 replicated groups read from the first 40 of 217 sample titles; they account for 39 of them. Check it against the sample list below before relying on it.

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