The Role of Criticality of Gene Regulatory Networks in Morphogenesis

Hyobin Kim, Hiroki Sayama

Research output: Contribution to journalArticle

Abstract

Gene regulatory network (GRN)-based morphogenetic models have recently gained an increasing attention. However, the relationship between microscopic properties of intracellular GRNs and macroscopic properties of morphogenetic systems has not been fully understood yet. Here we propose a theoretical morphogenetic model representing an aggregation of cells, and reveal the relationship between criticality of GRNs and morphogenetic pattern formation. In our model, the positions of the cells are determined by spring-mass-damper kinetics. Each cell has an identical Kauffman’s NK random Boolean network (RBN) as its GRN. We varied the properties of GRNs from ordered, through critical, to chaotic by adjusting node in-degree K. We randomly assigned four cell fates to the attractors of RBNs for cellular behaviors. By comparing diverse morphologies generated in our morphogenetic systems, we investigated what the role of the criticality of GRNs is in forming morphologies. We found that nontrivial spatial patterns were generated most frequently when GRNs were at criticality. Our finding indicates that the criticality of GRNs facilitates the formation of nontrivial morphologies in GRN-based morphogenetic systems.

Original languageEnglish
JournalIEEE Transactions on Cognitive and Developmental Systems
DOIs
Publication statusAccepted/In press - 2018 Jan 1
Externally publishedYes

Fingerprint

Genes
Agglomeration
Kinetics

Keywords

  • cell fate.
  • Cell signaling
  • criticality
  • gene regulaoty network (GRN)
  • Kinetic theory
  • Microscopy
  • morphogenetic pattern
  • Morphogenetic system
  • Morphology
  • Perturbation methods
  • random Boolean network (RBN)
  • Springs
  • Switches

ASJC Scopus subject areas

  • Software
  • Artificial Intelligence

Cite this

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abstract = "Gene regulatory network (GRN)-based morphogenetic models have recently gained an increasing attention. However, the relationship between microscopic properties of intracellular GRNs and macroscopic properties of morphogenetic systems has not been fully understood yet. Here we propose a theoretical morphogenetic model representing an aggregation of cells, and reveal the relationship between criticality of GRNs and morphogenetic pattern formation. In our model, the positions of the cells are determined by spring-mass-damper kinetics. Each cell has an identical Kauffman’s NK random Boolean network (RBN) as its GRN. We varied the properties of GRNs from ordered, through critical, to chaotic by adjusting node in-degree K. We randomly assigned four cell fates to the attractors of RBNs for cellular behaviors. By comparing diverse morphologies generated in our morphogenetic systems, we investigated what the role of the criticality of GRNs is in forming morphologies. We found that nontrivial spatial patterns were generated most frequently when GRNs were at criticality. Our finding indicates that the criticality of GRNs facilitates the formation of nontrivial morphologies in GRN-based morphogenetic systems.",
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