Based on a non-equilibrium mechanism for spatial pattern formation we study how position information can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of cells in a developing multicellular organism. As an example we study the developmental problems of domain formation and proportion regulation in the presence of noise, as well as in the presence of cell flow. We find that networks that solve this task exhibit a hierarchical structure of information processing and are of similar complexity as developmental circuits of living cells. Proportion regulation is scalable with system size and leads to sharp, precisely localized boundaries of gene expression domains, even for large numbers of cells. A detailed analysis of noise-induced dynamics, using a mean-field approximation, shows that noise in gene expression states stabilizes (rather than disrupts) the spatial pattern in the presence of cell movements, both for stationary as well as growing systems. Finally, we discuss how this mechanism could be realized in the highly dynamic environment of growing tissues in multi-cellular organisms.
Networks of gene regulation govern morphogenesis, determine cell identity and regulate cell function. But we have little understanding, at the local level, of which logics are biologically preferred or even permitted. To solve this puzzle, we studied the consequences of a fundamental aspect of gene regulatory networks: genes and transcription factors talk to each other but not themselves. Remarkably, this bipartite structure severely restricts the number of logical dependencies that a gene can have on other genes. We developed a theory for the number of permitted logics for different regulator…
During organismal development, biochemical reaction networks sense and respond to mechanical forces to coordinate embryonic patterning with embryo morphogenesis. Factors such as cortical tension, cell density, and matrix mechanical properties influence differentiation and cell fate decisions by modulating gene regulatory signaling networks. A major goal in synthetic development is to construct gene regulatory circuits that program the patterning and morphogenesis of synthetic multicellular structures. However, in the synthetic context, little is known regarding how the physical properties of t…
The first cell fate decisions in the developing fly embryo are made very rapidly : hunchback genes decide in a few minutes whether a given nucleus follows the anterior or the posterior developmental blueprint by reading out the positional information encoded in the Bicoid morphogen. This developmental system constitutes a prototypical instance of the broad spectrum of regulatory decision processes that combine speed and accuracy. Traditional arguments based on fixed-time sampling of Bicoid concentration indicate that an accurate readout is not possible within the short times observed experimen…
A spontaneously patterning reaction diffusion network, containing an integrated activator inhibitor and substrate depletion mechanism, specifies trichoblast cell fate in Arabidopsis roots
Institute of Systems, Molecular and Integrative Biology. University of Liverpool（利物浦大学生物系统、分子与整合生物学研究所）；School of Biosciences. University of Nottingham（诺丁汉大学生物科学学院）
