ArticlePLoS computational biology2018
Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources.
Article in PLoS computational biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 9 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
9 citing papers in PubMed, 13 citations in OpenAlex.
- eIF3 mRNA selectivity profiling reveals eIF3k as a cancer-relevant regulator of ribosome content.The EMBO journal · 2023Article
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- Variability in mRNA translation: a random matrix theory approach.Scientific reports · 2021Article
- Codon-based indices for modeling gene expression and transcript evolution.Computational and structural biotechnology journal · 2021Review
- Correction: Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources.PLoS computational biology · 2019Article
- Modelling and measuring intracellular competition for finite resources during gene expression.Journal of the Royal Society, Interface · 2019Article
- Networks of ribosome flow models for modeling and analyzing intracellular traffic.Scientific reports · 2019Article
- Novel insights into gene expression regulation during meiosis revealed by translation elongation dynamics.NPJ systems biology and applications · 2019Article
Corrections and comments
- Erratum issued
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent studies have demonstrated how the competition for the finite pool of available gene expression factors has important effect on fundamental gene expression aspects. In this study, based on a whole-cell model simulation of translation in S. cerevisiae, we evaluate for the first time the expected effect of mRNA levels fluctuations on translation due to the finite pool of ribosomes. We show that fluctuations of a single gene or a group of genes mRNA levels induce periodic behavior in all S. cerevisiae translation factors and aspects: the ribosomal densities and the translation rates of all S. cerevisiae mRNAs oscillate. We numerically measure the oscillation amplitudes demonstrating that fluctuations of endogenous and heterologous genes can cause a significant fluctuation of up to 50% in the steady-state translation rates of the rest of the genes. Furthermore, we demonstrate by synonymous mutations that oscillating the levels of mRNAs that experience high ribosomal occupancy (e.g. ribosomal "traffic jam") induces the largest impact on the translation of the S. cerevisiae genome. The results reported here should provide novel insights and principles related to the design of synthetic gene expression circuits and related to the evolutionary constraints shaping gene expression of endogenous genes.
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