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. 2023 Mar 11;35(6):1848–1867. doi: 10.1093/plcell/koad075

Figure 5.

Figure 5.

Upstream open reading frames (uORFs) alter the translation efficiency (TE) of mRNAs in wheat. A) Cumulative distributions of the TEs of mRNAs with uORFs. A 2-sided Wilcoxon test was performed. B) TE of uORFs with and without an AUG start codon and their downstream mORFs. The left panel shows TEs of AUG uORFs and non-AUG uORFs. The right panel shows TEs of mORFs with and without an AUG uORF. The “w/o uORF” group represents 1,000 randomly selected mORFs without uORFs. Two-sided Wilcoxon tests were performed. C) Kozak sequences of uORFs and main ORFs (mORFs). A chi-square test was performed. D) Several genes with uORFs alter the mORF TE. The TEs of the uORFs and mORFs across developmental stages are anticorrelated. E and F) Coverage of Ribo-seq reads in TabZIP53-5AE) and TaCCR2-5DF). Read coverage was normalized by the million reads mapped to nuclear coding sequences. In the region upstream of the mORF, the sequencing reads support the expression of uORFs. Green boxes, uORFs. The base sequences and the length of the uORFs (uORFTabZIP53-5A, uORFTaCBL1-1B) can be found in Supplemental Data Set 10. G) Schematic of the dual-luciferase system used to investigate the effect of uORFs on the translation of mORFs. 35S, cauliflower mosaic virus 35S promoter. REN, Renilla reniformis luciferase; LUC, firefly luciferase. Del indicates the deletion of a uORF. H–K) The effect of the different cassettes on the LUC/REN activity H and J) and LUC/REN mRNA level I and K) associated with the mORF in the dual-luciferase reporter system. P-values were calculated using 2-sided Student's t-test. uORFTabZIP53-5A and uORFTaCCR2-5 were derived from TabZIP53-5A and TaCCR2-5D, respectively. H and I) TabZIP53-5A. J and K) TaCCR2-5D. Mean and standard error are shown. L) A frequency distribution histogram of the correlation between the TEs of uORFs and those of their mORFs. TEs of uORFs and their mORFs were calculated, respectively. All replicates from 3 developmental stages were used. The Spearman correlation coefficients were used to measure the correlation.