Genome-wide Survey of Ribosome Collision

Ribosome movement is not always smooth and is rather often impeded. For ribosome pauses, fundamental issues remain to be addressed, including where ribosomes pause on mRNAs, what kind of RNA/amino acid sequence causes this pause, and the physiological significance of this attenuation of protein synthesis. Here, we survey the positions of ribosome collisions caused by ribosome pauses in humans and zebrafish using modified ribosome profiling. Collided ribosomes, i.e., disomes, emerge at various sites: Pro-Pro/Gly/Asp motifs; Arg-X-Lys motifs; stop codons; and 3′ untranslated regions. The electrostatic interaction between the charged nascent chain and the ribosome exit tunnel determines the eIF5A-mediated disome rescue at the Pro-Pro sites. In particular, XBP1u, a precursor of endoplasmic reticulum (ER)-stress-responsive transcription factor, shows striking queues of collided ribosomes and thus acts as a degradation substrate by ribosome-associated quality control. Our results provide insight into the causes and consequences of ribosome pause by dissecting collided ribosomes. [Display omitted] •Disome profiling reveals widespread ribosome collisions in vertebrates•Ribosomes are in queues at Pro-Pro/Gly/Asp, Arg-X-Lys, stop codons, and 3′ UTRs•The positively charged nascent chain weakens the eIF5A-mediated rescue of disomes•The stalled disomes on XBP1u mRNA are an endogenous substrate of RQC Han et al. survey ribosome collision sites across the transcriptome by sequencing disome footprints in humans and zebrafish and find that inefficient contexts for elongation, termination, and recycling of ribosomes contributes to the collision of ribosomes. They also uncover XBP1u as an endogenous target of ribosome-associated quality control.