A Primate Herpesvirus Uses the Integrator Complex to Generate Viral MicroRNAs

Herpesvirus saimiri (HVS) is a γ-herpesvirus that expresses Sm class U RNAs (HSURs) in latently infected marmoset T cells. By deep sequencing, we identified six HVS microRNAs (miRNAs) that are derived from three hairpin structures located immediately downstream of the 3′ end processing signals of three of the HSURs. The viral miRNAs associate with Ago proteins and are biologically active. We confirmed that the expression of the two classes of viral noncoding RNAs is linked by identifying chimeric HSUR-pre-miRNA transcripts. We show that HVS miRNA biogenesis relies on cis-acting elements specifically required for synthesis and processing of Sm class RNAs. Knockdown of protein components in vivo and processing assays in vitro demonstrated that HVS does not utilize the Microprocessor complex that generates most host miRNAs. Instead, the Integrator complex cleaves to generate the 3′ end of the HSUR and the pre-miRNA hairpin. Exportin-5 and Dicer are then required to generate mature viral miRNAs. ▸ Primary transcripts for HVS miRNAs have snRNAs upstream of pre-miRNA hairpins ▸ HVS miRNA expression relies on snRNA-specific promoter and processing signals ▸ The Integrator complex is required for generation of HVS pre-miRNAs ▸ HVS miRNAs are produced by a Microprocessor-independent, Dicer-dependent pathway