Extended Data Fig. 2: Translational downregulation of 5’TOP mRNAs during infection.

a. In uninfected cells, specific genes highly enriched in association with the 80 s ribosome were identified. A heatmap of differential gene expression between total and 80 s or total and polysome samples is annotated above with 5’TOP genes in red. Beneath: 20 nucleotide sequence motifs of 82 known or potential 5’TOP genes were generated using weblogo.berkely.edu. b. Log₂FC changes in 5’TOP mRNAs contained in 80S or polysome fractions from mock infected or infected samples from Fig. 1. Red and blue bars indicate increases and decreases in Log₂FC enrichment over total RNA, respectively. c. Log₂FC comparison of total mock versus infected or 80S mock versus infected samples. While also downregulated at the transcript level, more robust loss from 80S samples was detected in infected samples. DESeq2 uses Wald tests to evaluate the significance of differential expression and applies Benjamini-Hochberg (BH) correction to control the false discovery rate (FDR). Adjusted p-values (padj) identify significantly differentially expressed genes after multiple testing correction. The adjusted p-value cutoff was set above 0.01 and the Log₂FC threshold was set to 1.1. For a–c, data is derived from 3 biologically independent experiments.