Extensive 5'-Surveillance Guards Against Non-Canonical NAD-Caps of Nuclear mRNAs in Yeast

The ubiquitous redox coenzyme nicotinamide adenine dinucleotide (NAD) acts as a noncanonical cap structure on prokaryotic and eukaryotic ribonucleic acids. Here we find that in budding yeast, NAD-RNAs are abundant (>1400 species), short (<170 nt), and mostly correspond to mRNA 5'-ends. The modification percentage of transcripts is low (<5%). NAD incorporation occurs mainly during transcription initiation by RNA polymerase II, which uses distinct promoters with a YAAG core motif for this purpose. Most NAD-RNAs are 3'-truncated. At least three decapping enzymes, Rai1, Dxo1, and Npy1, guard against NAD-RNA at different cellular locations, targeting overlapping transcript populations. NAD-mRNAs are not translatable in vitro. Our work indicates that in budding yeast, most of the NAD incorporation into RNA seems to be disadvantageous to the cell, which has evolved a diverse surveillance machinery to prematurely terminate, decap and reject NAD-RNAs. Overall design: NAD-RNA and All-cap-RNA profiling in wild type (WT) and mutant deletion of Npy1(n)/Dxo1(d)/Rai1(r) yeast strains. Please note that [1] each *_merge_genome.wig file was generated from three replicates and is linked to the corresponding rep1 sample records [2] the rawHits*.txt and Stat*.txt data was generated from multiple samples as indicated in the corresponding sample description field and are linked as Series supplementary files.