Sense codon-misassociated eRF1 elicits widespread ribosome stalling and induction of quality control

The rescue pathway of stalled ribosomes and ribosome-associated quality control (RQC) serves as a surveillance system for aberrant translation that senses ribosome collisions. Although the molecular mechanism has been extensively studied, the endogenous contexts of ribosome collision rescued by the system are poorly understood. Here, beginning with a study of the codon specificity of the eukaryotic translation termination factor eRF1, we show that transient binding of eRF1 to the UUA sense codon leads to ribosome collision and provides a constitutive source of rescue substrates in humans. eRF1-selective Monosome-Seq and Disome-Seq revealed that eRF1 was recruited not only to stop codons but also to near-cognate sense codons, including the UUA codon. The eRF1 on UUA codons delays translation elongation but does not trigger the termination reaction. Remarkably, Disome-Seq with the depletion of ASCC3 and 4EHP, key factors for the ribosome rescue and translation initiation repression, showed that ribosomes stalled at UUA codons consist of a subpopulation suppressed by those factors. Failure of ribosome collision repression by ASCC3-4EHP triggers stress response, such as expression of the stress-induced transcription factor ATF3. This study highlights the impact of sense codon misrecognition by the termination factor on translation homeostasis in human cells.