Origins of binary gene expression in post-transcriptional regulation by microRNAs
@article{Bose2012OriginsOB, title={Origins of binary gene expression in post-transcriptional regulation by microRNAs}, author={I Bose and Sumana Ghosh}, journal={The European Physical Journal E}, year={2012}, volume={35}, pages={1-8} }
AbstractMicroRNA-mediated regulation of gene expression is characterised by some distinctive features that set it apart from unregulated and transcription-factor-regulated gene expression. Recently, a mathematical model has been proposed to describe the dynamics of post-transcriptional regulation by microRNAs. The model explains the observations made in single-cell experiments quite well. In this paper, we introduce some additional features into the model and consider two specific cases. In the…
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References
SHOWING 1-10 OF 86 REFERENCES
Positive feedback, stochasticity and genetic competence.
- BiologyPhysical biology
- 2007
The appearance of bimodal protein distributions in B. subtilis cell population is explained in the framework of three possible scenarios: the system is monostable in a deterministic description and stochasticity in gene expression is solely responsible for the appearance of the two expression states.
Graded and binary responses in stochastic gene expression.
- BiologyPhysical biology
- 2004
The theoretical results on binary response provide a good description of the 'all-or-none' phenomenon observed in an eukaryotic system.
MicroRNAs can generate thresholds in target gene expression
- BiologyNature Genetics
- 2011
It is shown that regulation by miRNAs establishes a threshold level of target mRNA below which protein production is highly repressed, and near this threshold, protein expression responds sensitively to target mRNA input, consistent with a mathematical model of molecular titration.
Stochastic mRNA Synthesis in Mammalian Cells
- BiologyPLoS biology
- 2006
The results demonstrate that gene expression in mammalian cells is subject to large, intrinsically random fluctuations and raise questions about how cells are able to function in the face of such noise.
Slowly Produced MicroRNAs Control Protein Levels*
- BiologyThe Journal of Biological Chemistry
- 2010
A mechanistic model consisting of four state variables and nine kinetic parameters that account for transcript sequestration and degradation via miRNA-mRNA complex formation is constructed and predicts that, even when present in low copy number, miRNAs can exert potent effects on protein concentration.
Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations.
- MathematicsBiophysical journal
- 2001
Quantitative Characteristics of Gene Regulation by Small RNA
- BiologyPLoS Biology
- 2007
The results demonstrate that sRNA provides a novel mode of gene regulation, with characteristics distinct from those of protein-mediated gene regulation; these include a threshold-linear response with a tunable threshold, a robust noise resistance characteristic, and a built-in capability for hierarchical cross-talk.
Small Regulatory RNAs May Sharpen Spatial Expression Patterns
- BiologyPLoS Comput. Biol.
- 2007
This work explores the possibility that small RNAs participate in sharpening a gene expression profile that was crudely established by a morphogen, and points out the functional significance of some mechanistic properties, such as mobility of smallRNAs and the irreversibility of their interactions.