Deconstructing the individual steps of vertebrate translation initiation

In eukaryotes, the number of ribosomes synthesizing a given protein depends on how many are recruited to its mRNA, their success in navigating its 5' untranslated region (UTR) and whether they recognize its start codon. Initiation of translation is a rate limiting step in protein synthesis and key to gene expression control 1, but despite this centrality it remains poorly understood 2,3. Here we introduce ribosome complex profiling (RCP-seq) to capture the transcriptome-wide occupancy of scanning, initiating, elongating and terminating ribosome complexes in a higher eukaryote. We track scanning and elongating ribosomes across all 5' UTRs in zebrafish, which enable us to assess the individual regulatory contributions from the three stages of initiation: ribosome recruitment, scanning of the 5' UTR and recognition of the start codon. Our data sheds light on small subunit recruitment to mRNAs presenting evidence for the threading model and demonstrates that sequence features regulate this recruitment. We estimate the processivity of scanning ribosomes as they traverse the 5' UTR and show that the repressive effects of upstream open reading frames depend on the efficiency of both translation initiation and termination. Finally, we determine the optimal initiation contexts by directly estimating the conversion of scanning to elongating ribosomes and demonstrate specific regulation of translation initiation at the endoplasmic reticulum. Our results open for the possibility of deconvoluting translation initiation into separate stages and provides the first view of global occupancy of ribosomal small subunits in a vertebrate.