Identification and quantitative analysis of the major determinants of translation elongation rate variation

Ribosome profiling provides a detailed view into the complex dynamics of translation. Although the precise relation between the observed ribosome footprint densities and the actual translation elongation rates remains elusive, the data clearly suggest that elongation speed is quite heterogeneous along the transcript. Previous studies have shown that elongation is locally regulated by multiple factors, but the observed heterogeneity remains only partially explained. To dissect quantitatively the different determinants of elongation speed, we here use probabilistic modeling to estimate transcript-specific initiation and local elongation rates from ribosome profiling data. Using this model-based approach, we estimate the fraction of ribosomes (∼ 9%) undetected by the current ribosome profiling protocol. These missing ribosomes come from regions harboring two or more closely-stacked ribosomes, and not accounting for them leads to a substantial underestimation of translation efficiency for highly occupied transcripts. We further quantify the extent of transcriptand position-specific interference between ribosomes on the same transcript, and infer that the movement of ∼ 2.5% of ribosomes is obstructed on average, with substantial variation across different genes. The extent of interference also varies noticeably along the transcript sequence, with a moderately elevated level near the start site and a significantly pronounced amount near the termination site. However, we show that neither ribosomal interference nor the distribution of slow codons is sufficient to explain the observed level of variation in the elongation rate. Instead, we find that electrostatic interaction between the ribosomal exit tunnel and specific parts of the nascent polypeptide governs the elongation rate variation as the polypeptide makes its initial pass through the tunnel. Once the N-terminus has escaped the tunnel, the hydropathy of the nascent polypeptide within the ribosome plays a major role in modulating the elongation speed. We provide evidence that our results are consistent with evolutionary signals and the known biophysical properties of the exit tunnel. 1 . CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/090837 doi: bioRxiv preprint first posted online Dec. 1, 2016;