Global RNA stability profiling in human NBDY knockout using TimeLapse-seq

We previously identified a conserved human microprotein NoBody/NBDY that can interact with the mRNA decapping complex through EDC4 and affects the expression of an NMD (nonsense-mediated decay) substrate. However, it remains unclear the exact mechanism of NBDY-regulated RNA stability change and whether this is the direct cause/consequence of its modulation of P-body structure/numbers. Here we present a global profile of RNA stability in human NBDY knockout cells via TimeLapse-seq. By comparing this dataset to our previous work done in DCP2 KO cells, we demonstrate that NBDY is a specificity factor of the 5'-3' RNA decay. In addition, these data indicate a role of NBDY in cell cycle and other signaling transduction processes as well. RNA isolated from cells +/- s4U feed was subjected to oxidative-nucleophilic-aromatic-substitution chemistry and sequenced. All sequencing for experimental samples was performed in duplicate per condition assessed, while negative controls were performed as single replicates without s4U treatment.