Reference : mRNA translation rate modeling with an extended TASEP incorporating tRNAs modifications
Scientific congresses and symposiums : Poster
Life sciences : Biochemistry, biophysics & molecular biology
http://hdl.handle.net/2268/240145
mRNA translation rate modeling with an extended TASEP incorporating tRNAs modifications
English
Joiret, Marc mailto [Université de Liège - ULiège > > In silico medecine-Biomechanics Research Unit >]
Rapino, Francesca mailto [Université de Liège - ULiège > > Stem Cells-Cancer Signaling >]
Close, Pierre mailto [Université de Liège - ULiège > > Stem Cells-Cancer Signaling >]
Geris, Liesbet mailto [Université de Liège - ULiège > Département d'aérospatiale et mécanique > Génie biomécanique >]
5-Sep-2019
A0
Yes
Yes
International
EMBO Workshop - Protein Synthesis and Translational Control
from 04-09-2019 to 07-09-2019
European Molecular Biology Organization
Heidelberg
Germany
[en] mRNA ; ribosome ; elongation rate ; TASEP ; electrostatic interaction ; ribosome exit tunnel ; codon usage ; tRNA modifications ; Ribo-Seq ; bioinformatics ; computational biology
[en] Translational regulation through synonymous codon usage has been recently shown to play an important role in health and disease. Modified tRNAs are important actors involved in regulating protein expression levels by optimizing the decoding of differentially used codons, nevertheless their contribution in protein synthesis dynamics remain unclear. Totally Asymmetric Simple Exclusion Process (TASEP) models have been used to quantify the transcripts translation rate by ribosomes. Our work aims at extending TASEP modeling to accommodate for tRNA modifications effects. We generated a computational stochastic model quantifying protein synthesis rates. The algorithm uses ribosome residence time per codon from transcripts codons sequences, relative transcripts abundance and tables of (modified or not) tRNA relative abundance. Important features in the model include the elongation rate variation caused by charged amino-acids in the ribosomal exit tunnel, proline ring opening delay at the peptide transfer center and optionally transcript secondary structure slow down effects. The model allows to compare relative protein expression levels as well as RiboSeq profiles in different scenarios with a controllable pool of ribosomes.
We intend to use our model to help understand how codon usage and tRNA modifications dynamically interact and impact on protein synthesis.
Biomech research Unit - GIGA Institute GIGA In silico medicine
F.R.S.-FNRS - Fonds de la Recherche Scientifique ; FWO - Fonds Wetenschappelijk Onderzoek Vlaanderen ; ERC - European Research Council
Joint-t-against-Osteoarthritis; EOS grant n° 30480119; ERC grant agreement n°772418 (INSITE)
Researchers ; Professionals ; Students
http://hdl.handle.net/2268/240145
EMBO European Molecular Biology Organization. The abstract should not be cited in bibliographies. Material contained herein should be treated as personal communication and should be cited as such only with the consent of the author.
H2020 ; 772418 - INSITE - Development and use of an integrated in silico-in vitro mesofluidics system for tissue engineering

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