Herpesvirus-encoded lncRNA targets host splicing by interacting with splicing factors

Kaposi’s sarcoma-associated herpesvirus (KSHV) encodes multiple short and long noncoding RNAs which contribute to viral latency, persistence, host gene regulation, and immune evasion. The Antisense-to-Latency Transcript (ALT) is a ~ 10 kb long noncoding RNA (lncRNA) located on the opposite strand of the major latency-associated region encoding the latency associated nuclear antigen, vCyclin, vFLIP, the Kaposin’s and 12 microRNA genes. ALT is a nuclear lncRNA that is lowly expressed during latency, but strongly upregulated during lytic replication. Using RNA antisense purification and quantitative mass spectrometry (RAP-MS) in lytically induced primary effusion lymphoma cells, we identified 51 human and 3 viral proteins that directly interact with ALT. Of these enriched proteins, 48 are splicing factors, including core and alternative splicing proteins, such as U2AF2, PTBP1/2, SRSF1/3 and MBNL1. Interaction and co-localization of ALT was confirmed with various splicing factors in ribonucleoprotein complexes. We further identified that induction of lytic replication in lymphoid and epithelial cells leads to thousands of host gene splicing changes, which are partially restored upon perturbation of ALT expression. Finally, transient knockdown of ALT strongly inhibits viral reactivation and virion production. Hence, by splicing factors interactions, ALT interferes with host gene expression. Our results uncover a novel mechanism that shifts gene expression from the host to the virus late during the viral replication cycle to efficiently produce progeny virus and potentially antagonize host immune defenses.