HIV-1 infection affects NAD capping of host cell snRNA and snoRNA

NAD besides its key role in cellular metabolism can serve as an alternative 5’ cap at several short non-coding RNAs. However, the function of the NAD cap remains elusive. Here, we investigate NAD capping of RNAs upon HIV-1 infection, which is associated with intracellular pellagra – depletion of NAD/NADH cellular pool. We applied NAD captureSeq on HIV-1 infected/noninfected cells and we revealed that four snRNAs (U1, U4ATAC, U5E and U7) and four snoRNAs (snord3G, snord102, snorA50A and snord3B) lost NAD cap upon HIV-1 infection. Interestingly, U1 snRNA was previously shown to be essential for HIV-1 replication. We provide evidence that the NAD cap reduces the stability of the U1 - HIV-1 pre-mRNA duplex. The importance of NAD RNA cap in HIV-1 infection was further supported by NAD decapping enzyme DXO overexpression, which led to increase in HIV-1 infectivity. This is the first example of NAD cap function in mammalian cells and suggests a general role of non-canonical RNA caps in antiviral innate immunity response. To identify RNAs with reduced NAD capping, we prepared four NAD captureSeq libraries from the sRNA fraction of MT4 noninfected and HIV-1 infected cells. NAD captureSeq relies on selective reaction of ADP-ribosyl cyclase (ADPRC) with 4-pentyn-1-ol and with NAD-RNA. After CuAAC reaction, the NAD capped RNA is tagged with biotin and captured on streptavidin beads. Captured RNA is then reversely transcribed and cDNA is used for preparation of NAD captureSeq library. To sort out non-specifically interacting RNA, ADPRC is omitted in negative control samples. To assess expression levels of sRNAs +/- HIV-1 infection, we generated sRNA-seq datasets from noninfected and HIV-1-infected MT-4 cells in triplicates.