title: Regulatory logic and pattern formation in the early sea urchin embryo.
abstract: We model the endomesoderm tissue specification process in the vegetal half of the early sea urchin embryo using Boolean models with continuous-time updating to represent the regulatory network that controls gene expression. Our models assume that the network interaction rules remain constant over time and the dynamics plays out on a predetermined program of cell divisions. An exhaustive search of two-node models, in which each node may represent a module of several genes in the real regulatory network, yields a unique network architecture that can accomplish the pattern formation task at hand--the formation of three latitudinal tissue bands from an initial state with only two distinct cell types. Analysis of an eight-gene model constructed from available experimental data reveals that it has a modular structure equivalent to the successful two-node case. Our results support the hypothesis that the gene regulatory network provides sufficient instructions for producing the correct pattern of tissue specification at this stage of development (between the fourth and tenth cleavages in the urchin embryo).
authors.affiliation: Duke University, Physics Department, Box 90305, Durham, NC 27708, USA. Electronic address: sunmyboy@gmail.com.
authors.forename: Mengyang
authors.initials: M
authors.lastname: Sun
authors.affiliation: Department of Chemical and Systems Biology, Stanford University School of Medicine, 269 Campus Drive, CCSR Building, Stanford, CA 94305, USA. Electronic address: xianrui.cheng@gmail.com.
authors.forename: Xianrui
authors.initials: X
authors.lastname: Cheng
authors.affiliation: Duke University, Physics Department, Box 90305, Durham, NC 27708, USA; Duke University, Duke Center for Systems Biology, Durham, NC 27708, USA. Electronic address: socolar@phy.duke.edu.
authors.forename: Joshua E S
authors.initials: JE
authors.lastname: Socolar
mesh_terms: D000818:Animals; D019521:Body Patterning / Q000502:physiology*; D002454:Cell Differentiation / Q000502:physiology*; D053263:Gene Regulatory Networks / Q000235:genetics / Q000502:physiology*; D005855:Germ Layers / Q000196:embryology*; D008954:Models, Biological; D012617:Sea Urchins / Q000196:embryology*
keywords: Boolean models; Cell fates; Gene regulation; Network dynamics