Figure 3.

Sequence motifs in the vicinity of the initiation site and ribosome occupancy. The figure displays sequence motif logos of the sequence spanning between positions −15 and +18 relative to the initiating AUG for two yeast genes sets—high ribosome-occupancy genes and low ribosome-occupancy genes (Arava et al, 2003). The sequence logos show an interesting signature of enrichment in Adenine nucleotides upstream to the initiating AUG codon in genes with high ribosome occupancy (A), accompanied with particular nucleotide preference at positions +5 and +6 (B). The 5′ UTR sequence of low ribosome-occupancy genes is also enriched with Adenine nucleotides (C), yet to a much lower extent. Genes with low ribosome occupancy show no nucleotide preference downstream to the initiating AUG codons (D). For this display, high ribosome-occupancy and low ribosome-occupancy genes (204 and 206 genes, respectively) were defined as genes at the top and at the bottom of the ribosome-occupancy distribution (occupancy>0.85, or occupancy<0.6 correspondingly). The 5′ UTR sequences of the investigated genes were derived from the study by Nagalakshmi et al (2008); the coding regions were downloaded from SGD web site. Sequence logos were created using WebLogo (Crooks et al, 2004).