mRNA-sequencing of 293T-no dice transfected with miR-16, miR-214, or KSHV-miR-K6-5p

The viral miRNA miR-K6-5p encoded by the DNA tumor virus Kaposi's sarcoma-associated herpesvirus exhibits offset, sequence similarity with the tumor suppressive cellular miR-15/16 family, as well as sharing a short seed match to the cellular miR-214 (nts 2-7). We investigated how gene regulation by the viral miR-K6-5p is related to regulation by these cellular miRNAs by performing transcriptome analysis. mRNA-Seq was done in HEK 293T NoDice cells (Bogerd et al., RNA 2014) lacking Dicer which severely impaired the maturation of miRNAs thereby eliminating confounding effects of endogenously expressed miR-15/16 family. We transfected mature miRNA mimics of miR-16, miR-K6-5p wild-type, a variant of miR-K6-5p with a U at nt 1 instead of a C to control of RISC loading (miR-K6 5'U), miR-214, or a control mimic into NoDice cells, and harvested total RNA 2 days post-transfection. Overall design: Gene expression changes due to expression of miR-16, miR-214, KSHV-miR-K6-5p were measured by mRNA-sequencing