Gene Regulatory Network Dynamical Logical Models for Plant Development.
Methods Mol Biol
; 2395: 59-77, 2022.
Article
em En
| MEDLINE
| ID: mdl-34822149
ABSTRACT
Mathematical and computational approaches that integrate and model the concerted action of multiple genetic and nongenetic components holding highly nonlinear interactions are fundamental for the study of developmental processes. Among these, gene regulatory network (GRN) dynamical models are very useful to understand how diverse types of regulatory constraints restrict the multigene expression patterns that characterize different cell fates. In this chapter we present a hands-on approach to model GRN dynamics, taking as a working example a well-curated and experimentally grounded GRN developmental module proposed by our group the flower organ specification gene regulatory network (FOS-GRN). We demonstrate how to build and analyze a GRN model according to the following steps:
(1) integration of molecular genetic data and formulation of logical rules specifying the dynamic behavior of each gene; (2) determination of steady states (attractors) corresponding to each cell type; (3) validation of the GRN model; and (4) extension of the deterministic model with the inclusion of stochasticity in order to model cell-state transitions dependent on noise due to fluctuations of the involved gen products. The methodologies explained here in detail can be applied to any other developmental module.Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Flores
/
Redes Reguladoras de Genes
Idioma:
En
Revista:
Methods Mol Biol
Assunto da revista:
BIOLOGIA MOLECULAR
Ano de publicação:
2022
Tipo de documento:
Article
País de afiliação:
Estados Unidos