Figure 6

Ribosome profiling reveals global down-regulation of translation. (A) Kernel density estimation plot showing decreased ribosome occupancy on mRNAs in Maf1^−/−livers. The x-axis shows translation efficiency scores (calculated as the average translation efficiency scores for all transcripts (splice site variants, alternative TSSs, etc.) derived from one gene, see Materials and Methods), the y-axis the score density. KS Kolmogorov–Smirnov test. (B) MvA plot showing the average of translation efficiency scores in the WT and Maf1^−/− liver samples (x-axis) and the log2 fold change in Maf1^−/− versus WT samples (y-axis). Each dot represents the average score for all transcripts derived from one gene. The red and orange dots indicate score changes with adjusted p values ≤ 0.05 and ≤ 0.1, respectively, as determined by limma. (C) GSEA analysis⁵⁹ with the indicated gene set (genes encoding proteins involved in translation, TOP genes, and genes encoding ribosomal proteins). The x-axis shows genes ranked by decreasing fold change from left to right, the y-axis shows the running enrichment score for the gene set as the analysis progresses through the ranked list. (D) Immunoblots of liver lysates from WT or Maf1^−/− mice performed with antibodies directed against the indicated proteins. The lower panel shows the quantification of the signals normalized to γ-tubulin. Image acquisition was performed with the Odyssey Imaging System (LI-COR Biosciences) software (www.licor.com/bio/image-studio/), (version 2.1.10). The three panels are from the same gel, but image acquistion of RPS18 and RPL37A was performed on different channels.