Related papers: Transcription factor clusters regulate genes in eu…
Under dilute in vitro conditions transcription factors rapidly locate their target sequence on DNA by using the facilitated diffusion mechanism. However, whether this strategy of alternating between three-dimensional bulk diffusion and…
Understanding transcription factor dynamics is crucial for unraveling the regulatory mechanisms of gene expression that underpin cellular function and development. Measurements of transcription factor subcellular movements are essential for…
The ability of eukaryotic cells to squeeze through constrictions is limited by the stiffness of their large and rigid nucleus. However, migrating cells are often able to overcome this limitation and pass through constrictions much smaller…
Cells sense external concentrations and, via biochemical signaling, respond by regulating the expression of target proteins. Both in signaling networks and gene regulation there are two main mechanisms by which the concentration can be…
Regulatory networks have evolved to allow gene expression to rapidly track changes in the environment as well as to buffer perturbations and maintain cellular homeostasis in the absence of change. Theoretical work and empirical…
In order to survive, reproduce and (in multicellular organisms) differentiate, cells must control the concentrations of the myriad different proteins that are encoded in the genome. The precision of this control is limited by the inevitable…
Proteins and nucleic acids form non-Newtonian liquids with complex rheological properties that contribute to their function in vivo. Here we investigate the rheology of the transcription factor NANOG, a key protein in sustaining embryonic…
The endoplasmic reticulum (ER), a cellular organelle that forms a cell-spanning network of tubes and sheets, is an important location of protein synthesis and folding. When the ER experiences sustained unfolded protein stress, IRE1 proteins…
A model is proposed to study the process of hypoxia-induced angiogenesis in cancer cells. The model accounts for the role played by the vascular endothelial growth factor (VEGF)-A in regulating the oxygen intake. VEGF-A is dynamically…
The simultaneous expression of the hunchback gene in the numerous nuclei of the developing fly embryo gives us a unique opportunity to study how transcription is regulated in living organisms. A recently developed MS2-MCP technique for…
Gene expression is a readily-observed quantification of transcriptional activity and cellular state that enables the recovery of the relationships between regulators and their target genes. Reconstructing transcriptional regulatory networks…
Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from…
Motivation: Modelling methods that find structure in data are necessary with the current large volumes of genomic data, and there have been various efforts to find subsets of genes exhibiting consistent patterns over subsets of treatments.…
Deciphering gene regulatory networks is a central problem in computational biology. Here, we explore the use of multi-modal neural networks to learn predictive models of gene expression that include cis and trans regulatory components. We…
Single-molecule narrowfield microscopy is a versatile tool to investigate a diverse range of protein dynamics in live cells and has been extensively used in bacteria. Here, we describe how these methods can be extended to larger eukaryotic,…
Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…
We investigate the dynamical properties of the transcriptional regulation of gene expression in the yeast Saccharomyces Cerevisiae within the framework of a synchronously and deterministically updated Boolean network model. By means of a…
The Unfolded Protein Response is the cell mechanism for maintaining the balance of properly folded proteins in the endoplasmic reticulum , the specialized cellular compartment. Although it is largely studied from a biological point of view,…
Translation is a key step in the synthesis of proteins. Accordingly, cells have evolved an intricate array of control mechanisms to regulate this process. By constructing a multi-component mathematical framework for translation we uncover…
Motivation: The regulation of gene expression during tissue development is extremely complex. One of the key regulatory mechanisms of gene expression involves the recognition of regulatory motifs by various proteins in the promoter regions…