Indexed on: 04 Jun '13Published on: 04 Jun '13Published in: Genomics
Accurate and efficient gene expression requires that protein translation initiates from mRNA transcripts with high fidelity. At the same time, indiscriminate initiation of translation from multiple ATG start-sites per transcript has been demonstrated, raising fundamental questions regarding the rate and rationale governing alternative translation initiation. We devised a sensitive fluorescent reporter assay for monitoring alternative translation initiation. To demonstrate it, we map the translation initiation landscape of a Saccharomyces cerevisiae gene (RMD1) with a typical ATG sequence context profile. We found that up to 3%-5% of translation initiation events occur from alternative out-of-frame start codons downstream of the main ATG. Initiation from these codons follows the ribosome scanning model: initiation rates from different start sites are determined by ATG order, rather than their context strength. Genomic analysis of S. cerevisiae further supports the scanning model: ATG codons downstream rather than upstream of the main ATG tend to have higher context scores.