Figure 4. Ribosomes translate detectable reading frames on lncRNAs.

(A) Schematic of AUG start site detection using two harringtonine samples (from 120 s and 150 s treatment). The start site is an AUG codon with a peak in footprint density – higher occupancy than flanking codons – selected as the highest occupancy among peaks at AUGs. (B) AUG start sites typically show the highest footprint density among all codons, not just all AUGs with peaks. (C) AUG start sites typically fall in the first few hundred nt of transcripts, and (inset) near the beginning of the transcript. (D) AUG start sites are typically among the first AUG codons on transcripts, with relative positions shown in the histogram and absolute index shown in the pie chart (i.e., nearly half of AUG start sites are the first AUG on the transcript overall). (E) Overall ribosome occupancy is higher in the ORFs downstream of AUG start sites, relative to the overall density on the transcript. (F) Footprints on As downstream of detected AUG start sites and upstream of the stop codon are biased towards the frame of the ORF. Annotated protein-coding genes show similar reading frame bias within the ORF but not in the 5′ UTR (upstream) or 3′ UTR (downstream).