Modeling the Epigenetic Landscape in Plant Development.

Methods Mol Biol
Authors
Keywords
Abstract

Computational mechanistic models enable a systems-level understanding of plant development by integrating available molecular experimental data and simulating their collective dynamical behavior. Boolean gene regulatory network dynamical models have been extensively used as a qualitative modeling framework for such purpose. More recently, network modeling protocols have been extended to model the epigenetic landscape associated with gene regulatory networks. In addition to understanding the concerted action of interconnected genes, epigenetic landscape models aim to uncover the patterns of cell state transition events that emerge under diverse genetic and environmental background conditions. In this chapter we present simple protocols that naturally extend gene regulatory network modeling and demonstrate their use in modeling plant developmental processes under the epigenetic landscape framework. We focus on conceptual clarity and practical implementation, providing directions to the corresponding technical literature. The protocols presented here can be applied to any well-characterized gene regulatory network in plants, animals, or human disease.

Year of Publication
2018
Journal
Methods Mol Biol
Volume
1819
Pages
357-383
Date Published
2018
ISSN
1940-6029
DOI
10.1007/978-1-4939-8618-7_17
PubMed ID
30421413
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