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

Abstract NAD is a key component of cellular metabolism and also serves as an alternative 5’cap on short noncoding RNAs. The function of NAD in RNA, however, remains poorly understood. We investigated NAD capping of RNAs in HIV-1 infected cells, as HIV-1 is responsible for the depletion of the NAD/NADH cellular pool and causes intracellular pellagra. We used NAD captureSeq on HIV-1 infected/noninfected cells and revealed that four snRNAs (U1, U4ATAC, U5E, and U7) and four snoRNAs (SNORD3G, SNORD102, SNORA50A, and SNORD3B) lost their NAD cap when infected with HIV-1. Here, we provide evidence that the loss of the NAD cap increases the stability of the U1-HIV-1 pre-mRNA duplex. We also show that decreasing the amount of NAD-capped U1 snRNA by overexpressing the NAD RNA decapping enzyme DXO leads to a marked increase in HIV-1 infectivity. Moreover, an experimental increase of NAD capped RNAs improves the efficiency of splicing of HIV-1 and cellular RNAs and lowers HIV-1 infectivity. Our experiments show a potential dual role of U1 snRNA in HIV-1 infection and present the first possible function of NAD-capped RNAs in eukaryotic antiviral responses.