Figure 3.

Cells with U₃₄ Modification Defects Exhibit Gene Expression Hallmarks of Proteotoxic Stress

(A–C) Log2 fold changes (mutant/WT) in mRNA abundance and gene-level ribosome occupancy in U₃₄ modification-deficient strains grown in YPD (n = 3). Color annotation is as in Figure 2B.

(D) Hierarchically clustered heat map of ribosome occupancy data from (A)–(C).

(E) Venn diagram of the overlap between significantly downregulated (Benjamini-corrected p < 0.01) genes in U₃₄ modification-deficient strains.

(F) GO term enrichment in genes significantly downregulated in ncs2Δ, elp6Δ, and ncs2Δelp6Δ strains was summarized and visualized in semantic similarity-based scatter plots using REViGO. x axis: likeliness of meaning between GO terms; y axis: Benjamini-corrected p values of statistical significance for GO category enrichment; symbol size: frequency of GO term in database.

(G) Venn diagram of the overlap between significantly upregulated genes.

(H) GO term enrichment in genes upregulated in ncs2Δelp6Δ calculated as in (F).

(I) Growth defects of strains lacking Rpn4, which controls expression of the UPS via the proteasome-associated control element (PACE).

See also Figure S4 and Table S2.