Distal nucleotides affect the rate of stop codon read-through

A key step in gene expression is the recognition of the stop codon to terminate translation at the correct position. However, it has been observed that ribosomes can misintrepret the stop codon and continue the translation in the 3' UTR region, which is called stop codon read-through (SCR). It has been suggested that these events would occur on a programmed basis, but the underlying mechanisms are still not well understood. Here, we present a strategy for the comprehensive identification of SCR events in the D. melanogaster transcriptome by evaluating the ribosomal density profiles. For each identified event, the associated ribosomal leak rate was estimated. With the sequences associated to SCR events, we performed a statistical characterization of the frequency of nucleotide use in the proximal region to the stop codon. We observed that the nucleotide usage pattern in transcripts with the TGA codon is different from the pattern in those transcripts ending in the TAA codon, suggesting the existence of at least two mechanisms that could alter the translational termination process. We have even observed that distal nucleotides can also affect the SCR rate. Furthermore, we developed linear regression models for each of the three stop codons, and we show that the models using the nucleotides at informative positions outperforms those models that consider the entire sequence context to the stop codon.