Extended Data Fig. 4: Additional data for Figs. 4 and 5.
a) tRNA-seq replicate data for HEK293T cells related to Fig. 4a–d. Pearson’s values for comparing the fraction tRNA reads for the biological replicates under different preQ1 and queuine treatments. b) MEF cells, Northern blots for Q-modifiable tRNAs: tRNATyr, tRNAAsp, tRNAHis, and tRNAAsn. 5S rRNA is the loading control. Lines indicated preQ1 and queuine treatments are replicates. c) Heatmap of expression of individual tRNA anticodon families, cognate tRNATyr/His/Asn/Asp are indicated by arrows. All tRNA normalized to 0Q samples without preQ1 treatment. mt: mitochondrial tRNA. d) mRNA-seq replicate data for HEK293T cells related to Fig. 4g–k. Pearson’s values for replicates of input and polysome samples. e) PreQ1 versus 0Q input mRNA (left) and polysome mRNA (right). Red, preQ1/0Q > 2. Blue, 0Q/preQ1 > 2. The 117 ribosomal protein genes (named RPL/RPS) are highlighted in brown. f) Gene ontology (GO) analysis for biological process and molecular function of genes with significant change in TE. Blue: TE < 0.2 in preQ1/0Q. Red: TE > 5 in preQ1/0Q. g) mRNA expression heatmap of 98 “blue” genes, normalized to 0Q input sample. h) mRNA expression heatmap of 154 “red” genes, normalized to 0Q input sample. i) Comparing codon usage of the 4 amino acids decoded by Q-modifiable tRNAs affected by preQ1 treatment. X-axis represents the codon usage (CU) of the blue transcripts in Fig. 4h, and y-axis represents the codon usage of the red transcripts in Fig. 4h. C-ending codons are in blue, U-ending codons are in green. j) Codon usage of genes in Fig. 4h. Blue: TE < 0.2 in preQ1/0Q. Red: TE > 5 in preQ1/0Q. Grey: all other genes. Unprocessed blots are available in source data.
