Fig. 4: NPM1 depletion triggers ribosome pausing.

Data comparing Apc^loxP/loxPKras^G12D/+Npm1^loxP/loxP and Apc^loxP/loxPKras^G12D/+ intestinal epithelial cells, sampled 3 days after induction (n = 4 per group) a, Translation efficiency scatter with differentially expressed transcripts at the total cytoplasmic RNA level (x axis) compared to changes at the RPF level (y axis). Transcripts are color-coded depending on their change being significant at the total and RPF level (both up and both down), or exclusively at the RPF level (RPF up and RPF down) (P_adj < 0.1). No transcript was detected to be changed exclusively at the total cytoplasmic RNA level. b, GSEA for Hallmark gene sets on transcripts ranked according to changes at the RPF level. c, GSEA for Hallmark gene sets on genes ranked according to changes at the proteome level. d, Enrichment profiles from the GSEA for the Hallmark sets E2F targets, G2M checkpoint and MYC targets V1. Left, Enrichment profiles of RPFs. Right, Enrichment profiles of proteomics data. Enrichment scores were calculated using the weighted Kolmogorov–Smirnov test implemented in the fGSEA package. Significance and normalization were assessed using empirical permutation testing; P values were adjusted using the Benjamini–Hochberg method. Normalized enrichment scores (NES) and P_adj values are shown in the plots. e, Quantification of genes shared by the leading edges of both RPFs and proteomics (within the same pathway) are displayed as violins (Npm1^+/+ (WT) condition in gray, Npm1^loxP/loxP (KO) condition in red). Each plot represents scaled abundances of RPF-normalized reads and protein intensities; the number of genes in the shared leading edge is displayed above each panel. The box plots within the violins extend from the 25th to 75th percentile, with the lines plotted at the median. The whiskers extend to the minimum and maximum values, no further than 1.5 times the interquartile range from the hinges. Outliers beyond the end of the whiskers are not plotted. f, Ribosome pause site distribution across transcript CDS, with induced sites in red, resolved sites in blue and maintained sites in gray. g, Ribosome pause site distribution across genes belonging to the leading edges of the pathways indicated. For each pathway, the pause distribution is shown for those genes belonging to the leading edge of both RPFs and proteins, or to the leading edge exclusively for proteins (only protein) or RPFs (only RPFs). The number of genes in each of these categories is indicated above the plots. Color coding of the pause sites as in f. Note that the number of genes in the shared category is different than in e as we are displaying only transcripts for which ribosomes pause sites were confidently identified. h, Metagene plot of all transcripts detected in the Riboseq experiment with more than 50 average reads aligned to their CDS. The plot represents the variation in ribosome occupancy across the 5′ untranslated region (UTR) (first panel), their CDS (second panel) or their 3′ UTR (third panel). The gray shaded area represents the standard deviation of the delta ribosome occupancy across the four biological replicates assayed per group.

Source data