Figure 5. Kinetics of Translation and mRNA Decay Impacts Alternate EJC Occupancy.

(A) A scatterplot of fold-change in CASC3-EJC occupancy with and without cycloheximide (CHX; x axis) and fold-change in RNPS1-EJC with and without CHX (y axis). Each dot represents a canonical transcript for each GRChg38 known gene and is colored as indicated in the legend (bottom right). Green outlined dots: ribosomal protein genes. Dotted red line: linear regression. Top left corner: coefficient of determination (R²).

(B) Top 5 GO term keywords and their enrichment p values in CASC3-EJC enriched transcripts (from A) in the absence (left) or presence of CHX (right).

(C) Boxplots showing distribution of ribosome occupancy (y axis) of transcript groups on y axis. Median values are shown to the right of each boxplot. Top: p values (Wilcoxon rank sum test). Bottom: number of transcripts in each group. Ribosome occupancy estimates were based on Kiss et al. (2017).

(D) Scatterplot as in (A) comparing fold-change in CASC3-EJC versus RNPS1-EJC footprint read counts in –CHX (x axis) and +CHX (y axis) conditions.

(E) Boxplots as in (C) showing distribution of ribosome occupancy estimates of transcript groups from (D) as indicated on the bottom.

(F) Comparison of fold-change in CASC3-EJC or RNPS1-EJC footprint reads at canonical EJC sites from ribosomal protein (RP)-coding mRNAs or non-ribosomal (non-RP)-protein coding mRNAs. Top: p values (Wilcoxon rank sum test).

(G) Boxplots as in (C) and (E) above comparing mRNA half-life of transcript groups from (D) as indicated on the bottom. mRNA half-life data are from Tani et al. (2012).

See also Figure S5.