Alphaherpesviruses remodel the cellular transcriptome to deplete m6A-containing transcripts

Virus infections are accompanied by major transcriptional changes in the host cell. We systematically investigated whether infection with viruses from different virus families specifically affects transcripts containing m6A, the most common internal modification of mRNA. Alphaherpesviruses were found to extensively alter m6A processing of infected cells. Overall design: To investigate the effect of alphaherpesviruses on m6A methylated transcripts, we infected Swine Testicle cells (ST) with Pseudorabies virus (PRV) for 16 hours or HEK-T cells with Herpes simplex virus type I (HSV-1) for 16 hours. In addition, ST cells that were depleted of different m6A readers (YTHDF1, YTHDF2 and YTHDF3, YTHDC1 or YTHDC2) were infected with PRV for 16 hours. We then performed RNA-seq to determine gene expression differences to determine the impact alphaherpesvirus infection has on m6A methylated transcripts.