Fig. 6: SICFA analysis reveals early biochemical pathways of 5-FU on RNA post-transcriptional modifications.

a Heatmap showing the stability and abundance change patterns (transformed log₂FC) of 15 proteins in early response to 5-FU treatment. b Network depicting bioinformatics enrichment analysis for proteins with significant stability changes at 4 h. Gene nodes are colored by log₂FC, and biological process node sizes represent the number of contained genes. c Bar charts showing the log₂FC values for stability (SICFA) and abundance of pseudouridine synthases (PUS1, PUS3, PUS10, TRUB1, TRUB2) at different time points following 5-FU treatment. Chemical structures illustrate the conversion of uridine to pseudouridine catalyzed by the PUS family. d Bar chart depicting the log₂FC values for stability and abundance of DUS3L (tRNA-dihydrouridine synthase) at different time points. The chemical structure shows the conversion of uridine to 5,6-dihydrouridine. e Bar charts showing the log₂FC values for stability and abundance of TRMT2A and EMG1, which are involved in methylation modifications of uridine and pseudouridine, respectively, at different time points after 5-FU treatment. The chemical structures illustrate these methylation modifications. f Volcano plots showing the fold change (log₂FC) and statistical significance (−log₁₀(p value)) of tRNA modifications after 5-FU treatment for 4 h (left) and 24 h (right), compared to the control group. The p values from two-sided empirical Bayes t tests without adjustment, with n = 3 cell replicates. Significantly downregulated tRNA modifications are marked in orange, upregulated ones in blue, and unchanged modifications in gray. Source data are provided as a Source Data file.