Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast

Conference paper

DOI: 10.1007/978-3-319-31957-5_3

Part of the Lecture Notes in Computer Science book series (LNCS, volume 9649)
Cite this paper as:
Wang H., McManus J., Kingsford C. (2016) Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast. In: Singh M. (eds) Research in Computational Molecular Biology. RECOMB 2016. Lecture Notes in Computer Science, vol 9649. Springer, Cham


Ribosome profiling quantitatively captures ribosome locations during translation. The resulting profiles of ribosome locations are widely used to study translational speed. However, an accurate estimation of the ribosome location depends on identifying the A-site from ribosome profiling reads, a problem that was previously unsolved. Here, we propose a novel method to estimate the ribosome A-site positions from high-coverage ribosome profiling reads. Our model allows more reads to be used, accurately explains the 3-nt periodicity of ribosome profiling reads from various lengths, and recovers consistent ribosome positions across different lengths. Our recovered ribosome positions are correctly highly skewed towards a single frame within a codon. They retain sub-codon resolution and enable detection of off-frame translational events, such as frameshifts. Our method improves the correlation with other estimates of codon decoding time. Further, the refined profiles show that yeast wobble-pairing codons are translated slower than their synonymous Watson-Crick-pairing codons. These results provide evidence that protein synthetic rate can be tuned by codon usage bias.


Ribosome profiling A-site recovery Translation rate 

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  1. 1.Computational Biology Department, School of Computer ScienceCarnegie Mellon UniversityPittsburghUSA
  2. 2.Department of Biological SciencesCarnegie Mellon UniversityPittsburghUSA

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