Ribosomal protein targets of Rap1 are repressed in edelfosine. (A) Volcano plot of genes downregulated in response to edelfosine as identified by RNA-seq transcriptome analysis. Targets of Rap1 are colored red. Genes confirmed by qPCR are labeled. (B) Venn diagram showing the overlap between genes strongly downregulated in edelfosine (<−2 ln(FC)) and genes known to be bound by Rap1 (Lieb et al., 2001), including ribosomal protein genes. (C) qPCR of genes identified in A compared to their RNA-seq values. Bars represent mean ± SD for three independent experiments while circles represent individual experiments. (D) The isogenic wild type (KM014) or the indicated Rap1 mutants were serial diluted onto defined solid medium containing 20 μM edelfosine (EDLF) or vehicle (Ctrl) and incubated at 30°C for 2 d. The first dilution of rap1-17 cells was A₆₀₀ ∼1, while the other two strains were A₆₀₀ ∼0.1, which was experimentally determined to normalize strain growth on control plates.