Fig. 3: Proteomics links Pol I activity, ribosomal content and metabolism.

a–f Proteomes of nematodes treated with control (Ctrl) RNAi, tif-1A RNAi or ncl-1 RNAi were analyzed at AD2, AD6 and AD12. Each condition has five biological replicates of n = 700 worms. a, b Box plots showing log2 fold changes of selected immune response (CLEC), heat stress response (HSP), oxidative stress response (GST), and ribosomal (Ribosome) proteins as well as vitellogenins (VIT), comparing tif-1A KD (a) and ncl-1 KD (b) nematodes to age-matched controls. Each dot represents one protein, the median fold change within each group is shown as a bold line, the lower and upper limits of the boxplot indicate the first and third quartile, respectively, and the whiskers show the most up- and down-regulated proteins. The expression levels and Q values of individual proteins are reported in Supplementary Data 1–3. c, d Proteins differentially expressed (log2 fold change > 0.58, Q value < 0.05) in tif-1A KD (c) and ncl-1 KD (d) versus Ctrl RNAi animals on AD12 were classified using WormCat, and the two top enriched categories (Ribosome and Metabolism) with their subgroups are presented (analysis details are shown in Supplementary Data 8 and 9). e Box plots showing log2 fold changes of selected mitochondrial proteins between AD2 and AD12 Ctrl RNAi animals are presented. Either all measured mitochondrial proteins (‘mitochondrion’) or distinct categories (‘mito-protein complex’, ‘mito-respirasome’ and (‘mito-translation’) are shown. f Box plots showing log2 fold changes of selected mito-ribosome components in tif-1A RNAi and ncl-1 RNAi worms compared to age-matched controls. The expression levels and Q values of individual proteins are reported in Supplementary Data 10 (for e) and 11 (for f). In a, b, e and f the Wilcoxon rank-sum test was used for statistical analysis; Bonferroni correction was performed to adjust for multiple comparisons. ns = not significant, ****P < 0.0001, ***P < 0.001, **P < 0.01, *P < 0.05. All statistical tests used were two-sided, the exact P values and statistical analyses are reported in the Source Data file.