RT Journal Article
SR Electronic
T1 Identification and quantitative analysis of the major determinants of translation elongation rate variation
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 090837
DO 10.1101/090837
A1 Khanh Dao Duc
A1 Yun S. Song
YR 2017
UL http://biorxiv.org/content/early/2017/03/21/090837.abstract
AB 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 transcript- and 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.