Transcriptome maps of general eukaryotic RNA degradation factors

RNA degradation pathways underlie RNA processing, the regulation of RNA levels, and the surveillance of aberrant or poorly functional RNAs in cells. Here we provide transcriptome-wide RNA-binding profiles of 30 general RNA degradation factors in the yeast S. cerevisiae. The profiles define the distribution of factors between RNA classes. They are also consistent with the canonical degradation pathway for closed-loop forming mRNAs after deadenylation. Modeling based on mRNA half-lives suggests that most degradation factors bind already to intact mRNAs, whereas decapping factors are recruited only for mRNA degradation, consistent with decapping being a rate-limiting step. Global analysis suggests that the nuclear surveillance machinery, including the complexes Nrd1/Nab3, TRAMP4, and the exosome, targets aberrant nuclear RNAs, pre-processes snoRNAs, and regulates attenuated genes. Finally, mRNA transcript optimality is the most predictive feature for binding of decapping factors and the Xrn1 exonuclease to mRNA, consistent with rapid 5´-degradation of inefficiently translated mRNAs. We used photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) to systematically generate transcriptome-wide protein binding profiles for 30 general RNA degradation factors in the yeast Saccharomyces cerevisiae. Biological replicates are collected for all 30 degradation factors.