Position-dependent codon occurrence is associated with patterns of translational efficiency and ribosomal occupancy...

All life depends on the reliable translation of RNA to protein according to complex interactions between translation machinery and RNA sequence features. While ribosomal occupancy and codon frequencies vary across coding regions, well-established metrics for computing coding potential of RNA do not capture such positional dependence. Here, we investigate positional bias in codon usage, which contextually accounts for the position of protein-coding signals embedded within coding regions. We demonstrate the existence of position-dependent patterns of codon frequency in the human transcriptome and describe these patterns using our POsition-Specific Codon Occurrence (POSCO) score that is more consistently associated with translation-initiating codons than other common sequence features. We further show that the patterns described by POSCO are not accounted for by other common scores, including position-dependent GC content, consensus sequences, and the presence of signal peptides in the translation product. More importantly, POSCO defines a spectrum of translational efficiency and local tRNA adaptation index (tAI). High POSCO scores correspond to the highest initial tAI values, which increase over the downstream length of the transcript, forming a translational highway. Meanwhile, low POSCO scores exhibit the lowest initial tAI values followed by a previously undescribed translational valley. An inverse correlation was found between POSCO score and ribosomal occupancy near the start codon. We also find that POSCO defines a spectrum of local folding energies, with high-POSCO transcripts showing the most stable folding immediately after the start codon. Finally, we examine the relationship between POSCO intensity and functional enrichment. We find that transcripts with start codons showing the highest POSCO are enriched for functions relating to development of musculoskeletal, cardiovascular, neurological, gastrointestinal, sensory, and other body systems. Furthermore, transcripts with high POSCO are depleted for functions related to immune response and detection of chemical stimulus. These findings lay important groundwork to improve our understanding of the regulation of translation, the calculation of coding potential, and the classification of RNA transcripts.