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Fig. 4 | BMC Genomics

Fig. 4

From: Comparative ribosome profiling uncovers a dominant role for translational control in Toxoplasma gondii

Fig. 4

Open reading frames in 5′ leader sequences (uORFs) are abundant in Toxoplasma. a Based on the presence of a start and a downstream in-frame stop codon, some Toxoplasma transcripts contain more than 14 non-overlapping uORFs. b-c Individual Toxoplasma transcripts with an upstream translated uORFs (red arrow) exhibit reduced ribosome occupancy at the cognate canonical protein coding sequences. Ribo-seq (red peaks) and RNA-seq (blue peaks) read pile-up on ToxoDB (blue) and PASA-updated (black) transcript structures. d Weighted position-specific scoring matrices (PSSMs) around (±10 nucleotides) annotated ATG of transcripts lacking uORFs. Vertical axis represents weighted relative entropy (WRENT). e Cumulative WRENT scores around ATG start codons along the coding transcripts. Dotted lines indicate median WRENT scores of uORF and CDS, and the proportion of uORFs (~90%) with WRENT scores less than the median CDS WRENT score. f Predicted secondary structure ensemble free energies (EFEs) in a sliding 35-nt window on 5′ UTRs, CDSes, and 3′ UTRs. A more negative EFE indicates more stable secondary structures. g The secondary structure EFE correlates with translation efficiency in CDSes. See also Additional file 3: Figure S2 and Additional file 4: Table S1

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