Elongationless start–stop elements are stress-resilient translation gates that are more repressive than uTranslons

Start-stop elements are translation regulatory elements in 5' untranslated regions (UTR) of eukaryotic transcripts, consisting of a start codon immediately followed by a stop codon. In contrast to canonical upstream Translons (uTranslons), they exclude elongation which creates unique properties. We conducted a comprehensive, carefully controlled comparison of human start-stop elements and uTranslons both at a genome-wide level and with targeted reporter assays. We found that start-stops and uTranslons were similar with respect to their presence in the 5' UTRs of hundreds of genes, in particular transcription factors and signaling molecules, the low transcript levels of the corresponding genes, short RNA half-lives, and the negative effect on downstream translation. However, start-stop containing genes were translationally even more repressed than genes with uTranslons. Analysing the start-stop architecture and diverse ribosome footprinting datasets, we found evidence for a start-stop-specific mechanism that involves repeat cycling between initiation, termination, ribosome splitting, and 60S rejoining-a process possibly modulated by ASCC3 and eIF1. This cycling explained increased ribosome retention at start-stops and was-in contrast to ribosome retention at uTranslons-independent of the global initiation state. Finally, we showed that the start-stop element in human ATF4 augments the core regulatory model by controlling translation of the uTranslons.