Optimizing information flow in small genetic networks. IV. Spatial coupling

T.R. Sokolowski, G. Tkacik, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).


Journal Article | Published | English
Department
Abstract
We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying signals subject to gene regulatory noise? Here we extend our information-theoretic framework for gene regulation to spatially extended systems. As an example, we consider a lattice of nuclei responding to a concentration field of a transcriptional regulator (the "input") by expressing a single diffusible target gene. When input concentrations are low, diffusive coupling markedly improves information transmission; optimal gene activation functions also systematically change. A qualitatively new regulatory strategy emerges where individual cells respond to the input in a nearly step-like fashion that is subsequently averaged out by strong diffusion. While motivated by early patterning events in the Drosophila embryo, our framework is generically applicable to spatially coupled stochastic gene expression models.
Publishing Year
Date Published
2015-06-15
Journal Title
Physical Review E Statistical Nonlinear and Soft Matter Physics
Volume
91
Issue
6
Article Number
062710
IST-REx-ID

Cite this

Sokolowski TR, Tkacik G. Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2015;91(6). doi:10.1103/PhysRevE.91.062710
Sokolowski, T. R., & Tkacik, G. (2015). Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter Physics, 91(6). https://doi.org/10.1103/PhysRevE.91.062710
Sokolowski, Thomas R, and Gasper Tkacik. “Optimizing Information Flow in Small Genetic Networks. IV. Spatial Coupling.” Physical Review E Statistical Nonlinear and Soft Matter Physics 91, no. 6 (2015). https://doi.org/10.1103/PhysRevE.91.062710.
T. R. Sokolowski and G. Tkacik, “Optimizing information flow in small genetic networks. IV. Spatial coupling,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 6, 2015.
Sokolowski TR, Tkacik G. 2015. Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter Physics. 91(6).
Sokolowski, Thomas R., and Gasper Tkacik. “Optimizing Information Flow in Small Genetic Networks. IV. Spatial Coupling.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 6, 062710, American Institute of Physics, 2015, doi:10.1103/PhysRevE.91.062710.

Link(s) to Main File(s)
Access Level
OA Open Access

Export

Marked Publications

Open Data IST Research Explorer

Search this title in

Google Scholar