Related papers: Gene activity fully predicts transcriptional burst…
We propose a stochastic model for gene transcription coupled to DNA supercoiling, where we incorporate the experimental observation that polymerases create supercoiling as they unwind the DNA helix, and that these enzymes bind more…
Timely up- or down-regulation of gene expression is crucial for cellular differentiation and function. While gene upregulation via transcriptional activators has been extensively investigated, gene silencing remains understudied, especially…
Experimental evidences show that in gene transcription, RNA polymerase has the possibility to be stalled at certain position of the transcription template. This may be due to the template damage, or protein barriers. Once stalled,…
We study the response of an autoregulated gene to a range of concentrations of signal molecules. We show that transcriptional leakage and noise due to translational bursting have the opposite effects. In a positively autoregulated gene,…
Control of transcription presides over a vast array of biological processes, including those mediated by gene regulatory circuits that exhibit multistability. Within these circuits, two- and three-gene network motifs are particularly…
A general class of stochastic gene expression models with self regulation is considered. One or more genes randomly switch between regulatory states, each having a different mRNA transcription rate. The gene or genes are self regulating…
In recent times whole-genome gene expression analysis has turned out to be a highly important tool to study the coordinated function of a very large number of genes within their corresponding cellular environment, especially in relation to…
The intrinsic stochasticity of gene expression can lead to large variations in protein levels across a population of cells. To explain this variability, different sources of mRNA fluctuations ('Poisson' and 'Telegraph' processes) have been…
Cells are known to utilize biochemical noise to probabilistically switch between distinct gene expression states. We demonstrate that such noise-driven switching is dominated by tails of probability distributions and is therefore…
Over the last several decades it has been increasingly recognized that stochastic processes play a central role in transcription. Though many stochastic effects have been explained, the source of transcriptional bursting (one of the most…
Appropriate regulation of gene expression is essential to ensure that protein synthesis occurs in a selective manner. The control of transcription is the most dominant type of regulation mediated by a complex of molecules such as…
Gene expression is controlled primarily by interactions between transcription factor proteins (TFs) and the regulatory DNA sequence, a process that can be captured well by thermodynamic models of regulation. These models, however, neglect…
Cells integrate signals and make decisions about their future state in short amounts of time. A lot of theoretical effort has gone into asking how to best design gene regulatory circuits that fulfill a given function, yet little is known…
Mutation is a critical mechanism by which evolution explores the functional landscape of proteins. Despite our ability to experimentally inflict mutations at will, it remains difficult to link sequence-level perturbations to systems-level…
This paper considers adiabatic reduction in a model of stochastic gene expression with bursting transcription considered as a jump Markov process. In this model, the process of gene expression with auto-regulation is described by fast/slow…
This paper considers adiabatic reduction in both discrete and continuous models of stochastic gene expression. In gene expression models, the concept of bursting is a production of several molecules simultaneously and is generally…
mRNA-protein assemblies play a fundamental role in forming membraneless compartments within cells, whose functions may include activating, inhibiting, and localizing reactions. Recruitment of proteins into droplets can diminish cell to cell…
We examine immunostaining experimental data for the formation of the strip 2 of $even-skipped$ ($eve$) transcripts on $D.$ $melanogaster$ embryos. An estimate of the factor converting immunofluorescence intensity units into molecular…
Transcription factor binding sites vary in their specificity, both within and between species. Binding specificity has a strong impact on the evolution of gene expression, because it determines how easily regulatory interactions are gained…
In this manuscript we propose a mathematical framework to couple transcription and translation in which mRNA production is described by a set of master equations while the dynamics of protein density is governed by a random differential…