Related papers: Systems Biophysics of Gene Expression
Complex systems with tightly coadapted parts frequently appear in living systems and are difficult to account for through Darwinian evolution, that is random variation and natural selection, if the constituent parts are independently coded…
The expression of genes usually follows a two-step procedure. First, a gene (encoded in the genome) is transcribed resulting in a strand of (messenger) RNA. Afterwards, the RNA is translated into protein. Classically, this gene expression…
Transcription factors (TFs) are key regulators of gene expression. Based on the classical scenario in which the TF search process switches between one-dimensional motion along the DNA molecule and free Brownian motion in the nucleus, we…
In biochemical signaling, information is often encoded in oscillatory signals. However, the advantages of such a coding strategy over an amplitude encoding scheme of constant signals remain unclear. Here we study the dynamics of a simple…
Systems biology approaches combining theoretical modeling with experiments have been singularly successful in uncovering novel features of cellular phenomena. One such feature is that of binary gene expression in which the expression level…
Fluctuations in the measured mRNA levels of unperturbed cells under fixed conditions have often been viewed as an impediment to the extraction of information from expression profiles. Here, we argue that such expression fluctuations should…
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 order to express specific genes at the right time, the transcription of genes is regulated by the presence and absence of transcription factor molecules. With transcription factor concentrations undergoing constant changes, gene…
With the increasing amount of experimental data on gene expression and regulation, there is a growing need for quantitative models to describe the data and relate them to the different contexts. The thermodynamic models reviewed in the…
Gene expression has a stochastic component owing to the single molecule nature of the gene and the small number of copies of individual DNA binding proteins in the cell. We show how the statistics of such systems can be mapped on to quantum…
The development of new techniques to quantitatively measure gene expression in cells has shed light on a number of systems that display oscillations in protein concentration. Here we review the different mechanisms which can produce…
In the simplest view of transcriptional regulation, the expression of a gene is turned on or off by changes in the concentration of a transcription factor (TF). We use recent data on noise levels in gene expression to show that it should be…
There is increasing evidence that protein binding to specific sites along DNA can activate the reading out of genetic information without coming into direct physical contact with the gene. There also is evidence that these distant but…
Gene expression in individual cells is highly variable and sporadic, often resulting in the synthesis of mRNAs and proteins in bursts. Bursting in gene expression is known to impact cell-fate in diverse systems ranging from latency in HIV-1…
A proof is presented that gene regulatory networks (GRNs) based solely on transcription factors cannot control the development of complex multicellular life. GRNs alone cannot explain the evolution of multicellular life in the Cambrian…
Gene regulation is a complex process involving the role of several genomic elements which work in concert to drive spatio-temporal expression. The experimental characterization of gene regulatory elements is a very complex and…
This paper presents a real-time simulation involving ''protozoan-like'' cells that evolve by natural selection in a physical 2D ecosystem. Selection pressure is exerted via the requirements to collect mass and energy from the surroundings…
It often is emphasized that gene expression is noisy. A seemingly contradictory view is that control mechanisms have been optimized to squeeze as much information as possible out of a limited number of molecules. Here we revisit these…
Numerous transcription factors self-assemble into different order oligomeric species in a way that is actively regulated by the cell. Until now, no general functional role has been identified for this widespread process. Here we capture the…
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…