Disome and trisome profiling reveal targets of ribosome quality control

The ribosome-associated protein quality control (RQC) system that resolves stalled translation events is activated when ribosomes collide and form disome, trisome or higher order complexes. However, it is unclear whether this system distinguishes collision complexes formed on defective mRNAs from those with functional roles on endogenous transcripts. Here, we performed disome and trisome footprint profiling in yeast and found collisions were enriched on diverse sequence motifs known to slow translation. When 60S recycling was inhibited, disomes accumulated at stop codons and could move into the 3’UTR to reinitiate translation. The ubiquitin ligase and RQC factor Hel2/ZNF598 generally recognized collisions but did not trigger degradation of endogenous transcripts. However, loss of Hel2 triggered the integrated stress response, via phosphorylation of eIF2alpha, thus linking these pathways. Our results suggest that Hel2 has a role in sensing ribosome collisions on endogenous mRNAs and such events may be important for cellular homeostasis. 31 samples are included in the study (4 mRNA-Seq, 4 monosome footprints, 21 disome footprints, and 2 trisome footprints). Read sizes were examined according to lengths relevant for each type of analysis and aligned by 5' or 3' ends, as noted. Samples also differ according to media conditions (3-AT, anisomycin, etc.) and genotype. Some samples serve as biological replicates, as noted.