Fig. 2: Increased translation of uORFs/uoORFs in mitotically arrested cancer cells.

a Schematic overview of ORF types detected by PRICE. dORF downstream open reading frame, iORF internal open reading frame, ncRNA noncoding RNA, uORF upstream open reading frame, uoORF upstream overlapping open reading frame. b Proportion of ORFs of each type identified in U-2 OS cells treated with vehicle (Control), BI2536 (0.1 µM), Nocodazole (0.5 µM), Taxol (1 µM), or STLC (5 µM) for 16 h. “Variant” refers to ORFs that contain a stop codon but cannot be categorized as CDS or truncated CDS. “Orphan” refers to ORFs that do not fit into any of the described categories. c Venn diagram showing the number of uORFs/uoORFs identified by PRICE in U-2 OS cells arrested in mitosis with BI2536 (0.1 µM), Nocodazole (0.5 µM), Taxol (1 µM), or STLC (5 µM) for 16 h. d Bar plot showing the combined scores for the GO database “Biological Process” obtained by Enrichr analysis of the common genes described in (c). P values were calculated using a one-sided Fisher’s exact test. Raw P values were adjusted using the Benjamini–Hochberg procedure. e Percentage of translation initiation site codons from uORFs/uoORFs in U-2 OS cells treated with vehicle (Control), BI2536 (0.1 µM), Nocodazole (0.5 µM), Taxol (1 µM), or STLC (5 µM) for 16 h. f Volcano plot illustrating the translation efficiency (TE) of all predicted uORFs/uoORFs in U-2 OS cells treated with 0.5 µM Nocodazole for 16 h. compared to asynchronous cells. The x-axis represents the log2 fold change in TE for uORFs/uoORFs. The y-axis indicates the significance of changes in TE. uORFs/uoORFs with increased TE are highlighted in red, while those with decreased TE are highlighted in blue. Data from two technical replicates. g Read distribution of representative uORFs/uoORFs with increased TE in mitotically arrested U-2 OS cells. RiboSeq (upper panels) and RNA-Seq (lower panels) reads are shown for the 5’UTR and the start of the CDS. Prolif proliferating, Noco Nocodazole.