Fig. 4
From: Temperature-dependent regulation of upstream open reading frame translation in S. cerevisiae
Changes in temperature result in changes in translation of some uORFs. a, b Scatterplots of normalized read densities. The mRNA densitymORF was calculated as the number of RNA-seq reads mapped to the corresponding mORF coding region normalized to the total number of RNA-seq reads. The RPF densityuORF was calculated as the number of ribosomal footprint reads (ribosome protected fragments) mapped to the uORF coding region normalized to the total number of RPF reads. TEuORF was calculated as RPF densityuORF divided by mRNA densitymORF at either 20, 30, or 37 °C. a Scatterplots of mRNA densities (i), RPF densities (ii), and translational efficiencies (TEs; (iii)) for cells grown at 30 °C (x-axis) and 20 °C (y-axis). The scatterplot of TEs also shows uORFs exhibiting ≥ 2-fold changes in both TEuORF and relative TE (TEuORF/TEmORF) at a false discovery rate (FDR) < 0.1. Red circles represent uORFs meeting these criteria whose translation is activated at 20 °C as compared to 30 °C (N = 16), while blue circles represent uORFs whose translation is repressed at 20 °C as compared to 30 °C (N = 20). The open circles are AUG uORFs while the filled circles are NCC uORFs. b Same as in a, except the circles represent read densities for cells grown at 30 °C (x-axis) and 37 °C (y-axis). As before, the scatterplot of TEuORF (iii) shows uORFs with ≥ 2-fold changes in both TE and relative TE at FDR < 0.1. Red circles represent uORFs whose translation is activated at 37 °C as compared to 30 °C (N = 24), while blue circles represent uORFs whose translation is repressed at 37 °C as compared to 30 °C (N = 52). Open circles, AUG uORFs; filled circles, NCC uORFs