Genomewide Mapping and Screening of Kaposi's Sarcoma-Associated Herpesvirus (KSHV) 3′ Untranslated Regions Identify Bicistronic and Polycistronic Viral Transcripts as Frequent Targets of KSHV MicroRNAs

Kaposi's sarcoma-associated herpesvirus (KSHV) encodes over 90 genes and 25 microRNAs (miRNAs). The KSHV life cycle is tightly regulated to ensure persistent infection in the host. In particular, miRNAs, which primarily exert their effects by binding to the 3′ untranslated regions (3′UTRs) of target transcripts, have recently emerged as key regulators of KSHV life cycle. Although studies with RNA cross-linking immunoprecipitation approach have identified numerous targets of KSHV miRNAs, few of these targets are of viral origin because most KSHV 3′UTRs have not been characterized. Thus, the extents of viral genes targeted by KSHV miRNAs remain elusive. Here, we report the mapping of the 3′UTRs of 74 KSHV genes and the effects of KSHV miRNAs on the control of these 3′UTR-mediated gene expressions. This analysis reveals new bicistronic and polycistronic transcripts of KSHV genes. Due to the 5′-distal open reading frames (ORFs), KSHV bicistronic or polycistronic transcripts have significantly longer 3′UTRs than do KSHV monocistronic transcripts. Furthermore, screening of the 3′UTR reporters has identified 28 potential new targets of KSHV miRNAs, of which 11 (39%) are bicistronic or polycistronic transcripts. Reporter mutagenesis demonstrates that miR-K3 specifically targets ORF31-33 transcripts at the lytic locus via two binding sites in the ORF33 coding region, whereas miR-K10a-3p and miR-K10b-3p and their variants target ORF71-73 transcripts at the latent locus through distinct binding sites in both 5′-distal ORFs and intergenic regions. Our results indicate that KSHV miRNAs frequently target the 5′-distal coding regions of bicistronic or polycistronic transcripts and highlight the unique features of KSHV miRNAs in regulating gene expression and life cycle.