ArticleRNA (New York, N.Y.)2001
Computational modeling of eukaryotic mRNA turnover.
Article in RNA (New York, N.Y.), 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed, 138 citations in OpenAlex.
- Cytoplasmic mRNA decay and quality control machineries in eukaryotes.Nature reviews. Genetics · 2025Review
- RNA degradation triggered by decapping is largely independent of initial deadenylation.The EMBO journal · 2024Article
- The role of polymers in enabling RNAi-based technology for sustainable pest management.Nature communications · 2024Review
- Analysis of a detailed multi-stage model of stochastic gene expression using queueing theory and model reduction.Mathematical biosciences · 2024Article
- Solving stochastic gene-expression models using queueing theory: A tutorial review.Biophysical journal · 2024Review
- Distilling dynamical knowledge from stochastic reaction networks.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- The minimal intrinsic stochasticity of constitutively expressed eukaryotic genes is sub-Poissonian.Science advances · 2023Article
- Article
- The minimal intrinsic stochasticity of constitutively expressed eukaryotic genes is sub-Poissonian.bioRxiv : the preprint server for biology · 2023Article
- Rapid nuclear deadenylation of mammalian messenger RNA.iScience · 2023Article
- Article
- Poly(A) tail dynamics: Measuring polyadenylation, deadenylation and poly(A) tail length.Methods in enzymology · 2021Article
- Tob2 phosphorylation regulates global mRNA turnover to reshape transcriptome and impact cell proliferation.RNA (New York, N.Y.) · 2020Article
- The Dynamics of Cytoplasmic mRNA Metabolism.Molecular cell · 2020Article
- Inverted translational control of eukaryotic gene expression by ribosome collisions.PLoS biology · 2019Article
- Article
- C3P3-G1: first generation of a eukaryotic artificial cytoplasmic expression system.Nucleic acids research · 2019Article
- An mRNA decapping mutant deficient in P body assembly limits mRNA stabilization in response to osmotic stress.Scientific reports · 2017Article
- Article
- Stochastic modeling of biochemical systems with multistep reactions using state-dependent time delay.Scientific reports · 2016Article
6 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The process of eukaryotic gene expression involves a diverse number of steps including transcription, RNA processing, transport, translation, and mRNA turnover. A critical step in understanding this process will be the development of mathematical models that quantitatively describe and predict the behavior of this complex system. We have simulated eukaryotic mRNA turnover in a linear multicomponent model based on the known mRNA decay pathways in yeast. Using rate constants based on experimental data for the yeast unstable MFA2 and stable PGK1 transcripts, the computational modeling reproduces experimental observations after minor adjustments. Subsequent analysis and a series of in silico experiments led to several conclusions. First, we demonstrate that mRNA half-life as commonly measured underestimates the average life span of an mRNA. Second, due to the properties of the pathways, the measurement of a half-life can predominantly measure different steps in the decay network. A corollary of this fact is that different mRNAs will be affected differentially by changes in specific rate constants. Third, the way to obtain the largest change of levels of mRNA for the smallest changes in rate is by changing the rate of deadenylation, where a large amount of regulation of mRNA decay occurs. Fourth, the 3'-to-5' degradation of mRNA shows mRNA-specific rates of degradation that are dependent on the 5' structure of the mRNA. These programs can be run over the Web, are adaptable to other eukaryotes, and provide outputs as graphs and virtual northern gels, which can be directly compared to experimental data. Therefore, this model constitutes a useful tool for the quantitative analysis of the process and control of mRNA degradation in eukaryotic cells.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.