Eukaryotic AUG initiation contexts consist of a broad range of nucleotide patterns associated with distinct...

In eukaryotes, translation initiation is extensively modulated by cis-regulatory sequences located on the mRNA along with trans-acting factors which influence the lifetime of the codon-anticodon interaction in the P site of the scanning 43S complex and eventually control ribosome assembly. Here, we analyzed sequences around AUG start codons to account for mutually dependent or mutually exclusive nucleotide combinations that influence start codon recognition. By comparing the initiation contexts of annotated coding sequences in six model eukaryotes, we show that their nucleotide features are highly species-specific. Searching for accurate consensus nucleotide patterns around AUG start codons identifies multiple nucleotide patterns rather than a single consensus sequence in each eukaryote. Importantly, these patterns highlight distinct nucleotide features around the conserved purine at position -3 across eukaryotes, known to strongly influence initiation efficiency. Finally, computing a species-specific score for any AUG context shows that these diverse nucleotide features associate with specific biological functions.