host restricts KSHV lytic activation through NMD

Here, we demonstrate that NMD contributes to restriction of the DNA virus, Kaposi sarcoma-associated herpesvirus (KSHV). Lytic reactivation of KSHV, which is the etiological agent of Kaposi's sarcoma as well as primary effusion lymphoma (PEL), is significantly enhanced upon knockdown of NMD factors. Coupling RNA-sequencing and transcriptome-wide identification of phospho-UPF1 (p-UPF1) bound RNAs we define NMD substrates in the PEL cell line TREx-BCBL1-RTA. Moreover, we demonstrate that NMD targets both cellular and viral transcripts, including the mRNA encoding the viral transcription factor, replication and transcription activator (RTA), to restrict KSHV reactivation. Unexpectedly, we identified an NMD-regulated feedforward loop that couples activation of the unfolded protein response (UPR) with transcriptional activation of RTA. Collectively, our study describes an intricate relationship between cellular targets of an RNA QC pathway and KSHV lytic gene expression, and demonstrates that NMD can function as a cell intrinsic restriction mechanism acting upon DNA viruses.