Fig. 4: Transcriptome-wide identification of ALKBH8-regulated mRNAs.

a Mass spectrometry analysis of cm5U, mcm5U and mcm5s2U levels in tRNAs from CTL, A8-KO and A8-OE HCT116 cells, 3 biological replicates. b OP-Puro labeling of global translation levels in CTL and A8-KO HCT116 cells, 3 biological replicates. c Schematic of RNA-seq (up) and Ribo-seq (bottom) experiments. d Fold change of ribosome density in A site for each codon after ALKBH8 depletion. 2 independent sequencing experiments, P values were calculated using Wald test with Benjamini–Hochberg correction. e–g Cumulative distributions of ribosome density change (e), mRNA change (f), and relative ribosome density change (TE) (g) for codon-rich, codon-poor, and total transcripts. All the genes were divided into codon-rich genes (top 20%) and codon-poor genes (bottom 20%) based on the content of 5A-ending codons (including AAA, CAA, GAA, AGA, and GGA). 2 independent sequencing experiments, Two-sided Mann–Whitney test. h–j Cumulative distributions of ribosome density change (h), mRNA change (i), and relative ribosome density change (j) for codon-rich, codon-poor, and total transcripts. All the genes were divided into codon-rich genes (top 20%) and codon-poor genes (bottom 20%) based on the content of 5G-ending codons (including AAG, CAG, GAG, AGG, and GGG). 2 independent sequencing experiments, Two-sided Mann–Whitney test. Source data are provided as a Source Data file.