uORF analysis.

A single transcript isoform per gene was selected as described above except for the minimal UTR length, which was set to 12 nt. We then used the zebrafish uORF dataset from Johnstone et al.⁶⁶, which contains location and translation efficiency information, to identify weakly and highly translated uORFs at 2 hpf as described above for mRNAs. We calculated per-uORF DMS-seq accessibility profiles by applying the 2–8% rules described above, for uORFs longer than 150 nt For shorter uORFs, the DMS accessibility was computed with 150-nt regions starting at the uORF AUG initiation codon. Global uORF accessibility values were derived as described above. uORFs containing fewer than ten A and C bases were removed from this analysis.