Fig. 1

Translation Inhibitors Block Ribosome Footprints on Protein Coding Sequences. a Distribution of whole transcriptome reads (black) and ribosome footprints in the absence of translation inhibitors (blue) and after translation inhibition by DMDA-PatA (red), harringtonine (green) or puromycin (yellow) on the eEF2 transcript. The grey box shows a zoom onto the junction between 5’ UTR and coding sequence. Note: ribosome pileup on the AUG start codon in the control ribosome profiling sample and the appearance of peaks on non-initiation codons in the presence of harringtonine. b – d Scatter plots of the translation efficiency (TE-) score (ratio of number of RNAse resistant footprints to the number of whole transcriptome reads) on annotated protein coding sequences (CDS) versus the fraction of ribosome footprints that resist to treatment by the translation inhibitors DMDA-PatA (B), harringtonine (C, Harr) and puromycin (D, Puro). The following subfamilies of mRNAs are highlighted: Histones (yellow circles), huge CDS of more than 15 kb (red squares), transcripts with ribosomes stalled on the AUG translation initiation codon (>30 % of CDS ribosome footprints on AUG +/− 1 nucleotide, blue circles). e Cumulative frequency distribution of the fraction of drug resistant ribosome footprints for annotated protein coding transcripts (solid lines) and ORFs of snoRNAs (squares). b–e Data shown are from annotated protein coding sequences that have at least 100 whole transcriptome reads and at least 100 ribosome footprints. The same cutoffs were used for snoRNAs in (E). See also Additional file 1: Figure S2