The m(6)A reader YTHDC2 is essential for escape from KSHV SOX-induced RNA decay

The role of N6-methyladenosine (m(6)A) modifications has increasingly been associated with a diverse set of roles in modulating viruses and influencing the outcomes of viral infection. Here, we report that the landscape of m(6)A deposition is drastically shifted during Kaposi’s sarcoma–associated herpesvirus (KSHV) lytic infection for both viral and host transcripts. In line with previous reports, we also saw an overall decrease in host methylation in favor of viral messenger RNA (mRNA), along with 5′ hypomethylation and 3′ hypermethylation. During KSHV lytic infection, a major shift in overall mRNA abundance is driven by the viral endoribonuclease SOX, which induces the decay of greater than 70% of transcripts. Here, we reveal that interlukin-6 (IL-6) mRNA, a well-characterized, SOX-resistant transcript, is m(6)A modified during lytic infection. Furthermore, we show that this modification falls within the IL-6 SOX resistance element, an RNA element in the IL-6 3′ untranslated region (UTR) that was previously shown to be sufficient for protection from SOX cleavage. We show that the presence of this m(6)A modification is essential to confer SOX resistance to the IL-6 mRNA. We next show that this modification recruits the m(6)A reader YTHDC2 and found that YTHDC2 is necessary for the escape of the IL-6 transcript. These results shed light on how the host cell has evolved to use RNA modifications to circumvent viral manipulation of RNA fate during KSHV infection.