An overview of known targets of cellular or viral targets is given in tables 2 and 3.Table 2 Cellular Targets of viral miRNAs.Table 3 Viral Targets of viral miRNAs.
From the targets identified to date (Table 1, Figure 1) it is apparent that viral miRNAs play an important role in immune evasion by inhibiting immune surveillance and extending the life of the infected host cell. Table 1 Immunomodulatory viral miRNAs.
One substrate of IKBKE is the interferon regulatory factor 3 (IRF3), downstream of the TLR signaling pathway. Therefore, repression of IKBKE by miR-K12-11 attenuates IFN signaling and decreases the antiviral response of the host [33]. Interestingly, the NF-kappa-B inhibitor NFKBIA/IkappaBaphla is also down-regulated by KSHV-miR-K12-1, leading to NFKB activation and maintenance of latency (see below) [33].
We used the 3'UTR reporter assay to screen the 14 miRs in the cluster, and identified miR-K1 as the miR that targeted IkaaB-alpha (Supplementary We used the 3'UTR reporter assay to screen the 14 miRs in the cluster, and identified miR-K1 as the miR that targeted IkaaB-alpha (Supplementary Information, Fig.S7a).
An analysis of IKK members revealed that miR-K12-1 directly inhibits NFKBIA/IKBalpha, thus increasing NF-kappaB activity and inhibiting lytic replication.
Our dataset also confirmed 12 out of 29 validated KSHV miRNA targets with expression in our dataset(>40%). Confirmed interactions include those with BACH1, FOS, CDKN1A(p21), TNFRSF12A(TWEAKR), RAD21 and RBL2 mRNAs, whose regulation had previously been validated at the level of protein expression. A list summarizing the recovery of previously published targets of the KSHV and EBV miRNAs is presented in Table S9. NIHMS333942-supplement-01 Table S9 Recovery of previously published targets for KSHV or EBV miRNAs.
As KSHV putative direct targets we extracted transcripts that were significantly down-regulated significantly in the replicate experiments, and which contained at least one seed-match to one of the KSHV miRNAs. We identified 704 putative direct targets in DG-75 cells (Figure 3B), and 980 putative direct targets in EA.hy926 cells (Figure 3C). A complete list of putative direct targets can be found in Dataset S2 for DG-75 cells and in Dataset S3 for EA.hy926 cells. The overlap between the two datasets contained 153 putative direct targets (Dataset S4).
