U of T study identifies how Epstein–Barr virus reprograms human genes during infection

Findings show a viral protein activates a large cluster of microRNAs usually seen only in early development

A study from the University of Toronto’s Department of Molecular Genetics has identified how the Epstein–Barr virus (EBV) alters human gene regulation during infection. The findings show that a viral protein, BZLF1, activates a cluster of human microRNAs (miRNAs) typically expressed only in embryonic cells.

The research, published in PLOS Pathogens, was led by postdoctoral fellow Ashley Campbell and Professor Lori Frappier. Using RNA sequencing, the team compared cells containing dormant and active EBV infections.

“Our research identified microRNAs that change in expression when cells are latently or lytically infected with EBV,” said Campbell. “We found more than 100 miRNAs changed between latent and lytic infection, including a human miRNA, miR-409-3p, not previously associated with EBV, which promotes lytic infection.

MicroRNAs are short RNA molecules that regulate gene expression, helping control how genes are turned on and off in the cell. The Frappier Lab found that during EBV’s active phase, known as “lytic,” a viral protein called BZLF1 turns on the DLK1–DIO3 locus. This area of the human genome has many microRNAs and long noncoding RNAs.

This locus, also known as C14MC, is normally active only during embryonic development, when cells are rapidly dividing and differentiating into tissues. In adult cells, this region is silenced. The study shows that EBV reactivates this embryonic developmental program, creating cellular conditions that favour viral replication and persistence.

“This work is helping us understand how EBV is altering the cellular environment, including genetic pathways regulated by miRNAs during lytic infection,” said Campbell. “We are also identifying a new role for a viral protein, BZLF1, in activating the expression of transcripts where select miRNAs originate from within the human genome.”

The study also found that BZLF1 binds directly to regulatory regions of the DLK1–DIO3 locus. This binding triggers the expression of long noncoding RNAs like MEG8, MEG9, and MIR381HG, which produces miRNAs that help support viral replication.

 “We found that a viral protein, BZLF1, goes to the largest miRNA cluster in the human genome, C14MC,” Campbell explained. “However, we do not yet know what cellular factors are bringing it there.”

By identifying this mechanism, the study helps explain how EBV maintains infection in human cells and provides broader insight into its role in virus-associated diseases and cancers.

“In the long term, this work can help identify cellular pathways that are regulated and could be targeted to treat EBV-related diseases,” said Campbell. “We are also excited to look at other miRNAs found in the study, see what genes they are regulating, and their significance during EBV infection.”

This research was supported by the Canadian Institutes of Health Research (CIHR) and the Natural Sciences and Engineering Research Council of Canada (NSERC).