5′-end NAD+ cap in human cells promotes RNA decay through DXO-mediated deNADding

Eukaryotic mRNAs generally possess a 5′-end m 7 G cap that promotes their translation and stability. However, mammalian mRNAs can also carry a 5′-end nicotinamide adenine dinucleotide (NAD + ) cap that, in contrast to the m 7 G cap, does not support translation but instead promotes mRNA decay. The mammalian and fungal noncanonical DXO/Rai1 decapping enzymes efficiently remove NAD + caps and cocrystal structures of DXO/Rai1 with 3′-NADP + illuminates the molecular mechanism for how the “deNADding” reaction produces NAD + and 5′-phosphate RNA. Removal of DXO from cells increases NAD + -capped mRNA levels and enables detection of NAD + -capped intronic snoRNAs, suggesting NAD + caps can be added to 5′-processed termini. Our findings establish NAD + as an alternative mammalian RNA cap and DXO as a deNADding enzyme modulating cellular levels of NAD + -capped RNAs. Collectively, these data reveal mammalian RNAs can harbor a 5′-end modification distinct from the classical m 7 G cap that promotes, rather than inhibits, RNA decay.