Abstract
We describe the first genome wide analysis of translation based on a model aimed at capturing the physical and dynamical aspects of this process. The Ribosomal Flow Model (RFM) is a computationally efficient approximation of the Totally Asymmetric Exclusion Process (TASEP) model (e.g. see [1]). The RFM is sensitive to the order of codons in the coding sequence, the tRNA pool of the organism, interactions between ribosomes and their size (see Figure [1]). The RFM predicts fundamental outcomes of the translation process, including translation rates, protein abundance and ribosomal densities [2] and the relation between all these variables, better than alternative (’non-physical’) approaches (e.g. see [3,4]). In addition, we show that the RFM model can be used for accurate inference of initiation rates, the effect of codon order on protein abundance and the cost of translation. All these variables could not be inferred by previous predictors.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Shaw, L.B., et al.: Totally asymmetric exclusion process with extended objects: a model for protein synthesis. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 68, 021910 (2003)
Ingolia, N.T., et al.: Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324, 218–223 (2009)
dos Reis, M., et al.: Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res. 32, 5036–5044 (2004)
Tuller, T., et al.: Determinants of protein abundance and translation efficiency in s. cerevisiae. PLoS Comput. Biol. 3, e248 (2007)
Kudla, G., et al.: Coding-sequence determinants of gene expression in escherichia coli. Science 324, 255–258 (2009)
Welch, M., et al.: Design parameters to control synthetic gene expression in escherichia coli. PLoS One 4, e7002 (2009)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Reuveni, S., Meilijson, I., Kupiec, M., Ruppin, E., Tuller, T. (2011). A Ribosome Flow Model for Analyzing Translation Elongation. In: Bafna, V., Sahinalp, S.C. (eds) Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science(), vol 6577. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-20036-6_34
Download citation
DOI: https://doi.org/10.1007/978-3-642-20036-6_34
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-20035-9
Online ISBN: 978-3-642-20036-6
eBook Packages: Computer ScienceComputer Science (R0)