Fig. 3

Significant TE changes identified by ribosome footprinting or polysomal RNA sequencing. a Circular heatmap representing the protein-coding genes with significant changes in TE (Babel, FDR < 0.1, Z-test with Benjamini–Hochberg correction, n = 3 biologically independent RPL10 WT and R98S Ba/F3 clones), identified by polysomal RNA sequencing (outer circle) or ribosome footprinting (middle circle). Corresponding protein changes, when available, are shown in the inner circle. The color scale represents the signed p-value associated to the change (which indicates both significance and direction of the change). Statistically significant changes are indicated by a star (*) and correspond to FDR < 0.1 for TE changes (Babel, Z-test with Benjamini–Hochberg correction, n = 3 biologically independent RPL10 WT and R98S Ba/F3 clones) and p-value < 0.01 for protein change (T-test on normalized spectra from quantitative mass spectrometry, n = 3 biologically independent RPL10 WT and R98S Ba/F3 clones). Only genes with at least 10 aligned ribosome footprints or polysomal RNA reads and at least 10 reads in the corresponding mRNA sequencing dataset for each sample are considered. Genes not passing this threshold or genes with no corresponding protein mass spectrometry measurement are indicated as not available. b Representation of the normalized RPFs for RPL10 WT and R98S Ba/F3 clones aligned to PSPH 5’ untranslated region (5’UTR), coding sequence (CDS, in yellow), and 3’UTR (ENSMUST00000031399). Four arrows indicate the upstream ORFs (positions: 10–369; 373–447; 463–561; 613–681) as predicted by altORFev (10.1093/bioinformatics/btw736). These plots contain pooled data from three RPL10 WT versus three R98S Ba/F3 clones. c Percentages of significant protein changes (quantitative mass spectrometry, T-test, p-value < 0.01) associated with significant mRNA changes (differential expression analysis by DESeq2, two-sided Wald test with Benjamini–Hochberg correction, FDR < 0.1, n = 3 biologically independent RPL10 WT and R98S Ba/F3 clones) and/or with significant TE changes (Babel, Z-test with Benjamini–Hochberg correction, FDR < 0.1, n = 3 biologically independent RPL10 WT and R98S Ba/F3 clones) or neither. Both ribosome footprinting and polysomal RNA sequencing matching mRNA-sequencing datasets were considered for changes in mRNA levels. Changes in TE identified by ribosome footprinting and/or polysomal RNA sequencing were both considered. d Scatterplot representing the correlation between the log2-transformed fold change (RPL10 R98S versus RPL10 WT) in RPF counts and the log2-transformed fold change in polysomal RNA-sequencing counts. e Scatterplots representing the correlation between the log2-transformed fold changes (RPL10 R98S versus RPL10 WT) in RPF counts (on the left) or polysomal RNA-sequencing counts (on the right) and the log2-transformed fold change in normalized protein spectral counts. Cor Pearson correlation coefficient