ArticlePloS one2013
Complex degradation processes lead to non-exponential decay patterns and age-dependent decay rates of messenger RNA.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
25 citing papers in PubMed.
- How memory and adaptation cost shape cell phenotypic dynamics in response to fluctuating environments.bioRxiv : the preprint server for biology · 2025Article
- Analysis of a detailed multi-stage model of stochastic gene expression using queueing theory and model reduction.Mathematical biosciences · 2024Article
- The minimal intrinsic stochasticity of constitutively expressed eukaryotic genes is sub-Poissonian.Science advances · 2023Article
- The minimal intrinsic stochasticity of constitutively expressed eukaryotic genes is sub-Poissonian.bioRxiv : the preprint server for biology · 2023Article
- Incorporating age and delay into models for biophysical systems.Physical biology · 2021Article
- Queuing Models of Gene Expression: Analytical Distributions and Beyond.Biophysical journal · 2020Article
- Critical role of deadenylation in regulating poly(A) rhythms and circadian gene expression.PLoS computational biology · 2020Article
- The Dynamics of Cytoplasmic mRNA Metabolism.Molecular cell · 2020Article
- Kinetic CRAC uncovers a role for Nab3 in determining gene expression profiles during stress.Nature communications · 2017Article
- Article
- Universal Poisson Statistics of mRNAs with Complex Decay Pathways.Biophysical journal · 2016Article
- Degradation Parameters from Pulse-Chase Experiments.PloS one · 2016Article
- Regulation of the Na+/K+-ATPase Ena1 Expression by Calcineurin/Crz1 under High pH Stress: A Quantitative Study.PloS one · 2016Article
- Single-molecule modeling of mRNA degradation by miRNA: Lessons from data.BMC systems biology · 2015Article
- A master equation and moment approach for biochemical systems with creation-time-dependent bimolecular rate functions.The Journal of chemical physics · 2014Article
- Transcriptome-wide analysis of trypanosome mRNA decay reveals complex degradation kinetics and suggests a role for co-transcriptional degradation in determining mRNA levels.Molecular microbiology · 2014Article
- Stochastic kinetics on networks: when slow is fast.The journal of physical chemistry. B · 2014Article
- Contributions of cell growth and biochemical reactions to nongenetic variability of cells.Biophysical journal · 2014Article
- Unveiling the hidden structure of complex stochastic biochemical networks.The Journal of chemical physics · 2014Article
- Periodic mRNA synthesis and degradation co-operate during cell cycle gene expression.Molecular systems biology · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Experimental studies on mRNA stability have established several, qualitatively distinct decay patterns for the amount of mRNA within the living cell. Furthermore, a variety of different and complex biochemical pathways for mRNA degradation have been identified. The central aim of this paper is to bring together both the experimental evidence about the decay patterns and the biochemical knowledge about the multi-step nature of mRNA degradation in a coherent mathematical theory. We first introduce a mathematical relationship between the mRNA decay pattern and the lifetime distribution of individual mRNA molecules. This relationship reveals that the mRNA decay patterns at steady state expression level must obey a general convexity condition, which applies to any degradation mechanism. Next, we develop a theory, formulated as a Markov chain model, that recapitulates some aspects of the multi-step nature of mRNA degradation. We apply our theory to experimental data for yeast and explicitly derive the lifetime distribution of the corresponding mRNAs. Thereby, we show how to extract single-molecule properties of an mRNA, such as the age-dependent decay rate and the residual lifetime. Finally, we analyze the decay patterns of the whole translatome of yeast cells and show that yeast mRNAs can be grouped into three broad classes that exhibit three distinct decay patterns. This paper provides both a method to accurately analyze non-exponential mRNA decay patterns and a tool to validate different models of degradation using decay data.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.