Fig. 1

Identification of mRNAs whose levels and translation are altered by Fhit. a The workflow for identifying mRNAs under translational control by Fhit is shown. E1 cells are H1299 cells with a stably transfected empty vector and D1 cells are H1299 cells with a stably transfected, ponasterone A-inducible FHIT transgene. Duplicate cultures of each cell line were treated with Ponasterone A, and cytoplasmic extracts were used for RNA-Seq and ribosome profiling (RIBO-Seq). b Fhit induction in D1 but not E1 cells was confirmed by Western blotting. c The log₂ change in steady state levels of the mRNA transcriptome is shown as a function of RNA-Seq read counts. All mRNAs that underwent a statistically-significant change in association with Fhit expression (p < 0.05) are indicated with red circles, and we arbitrarily selected a 1.5-fold change as a cutoff for further study. These transcripts and their fold changes are listed in Additional file 4. d The log₂ fold change in coding region RIBO-Seq for each mRNA is shown as a function of RNA-Seq read counts. Statistically significant changes are indicated by red circles as in c. These transcripts and their fold changes are listed in Additional file 7. e RiboDiff was used to normalize the coding region RIBO-Seq data in d to the RNA-Seq data in c. Fhit-mediated changes in the resulting Average Ribosome Density (ARD) are plotted as a function of RNA-Seq read counts. Again a cutoff of 1.5-fold was selected. mRNAs that underwent a statistically-significant change with Fhit (p < 0.05) are labeled and indicated with red dots