A Dynamic Gene Regulatory Network Model That Recovers the Cyclic Behavior of Arabidopsis thaliana Cell Cycle

PLoS Computational Biology
Elizabeth Ortiz-GutiérrezElena R Alvarez-Buylla

Abstract

Cell cycle control is fundamental in eukaryotic development. Several modeling efforts have been used to integrate the complex network of interacting molecular components involved in cell cycle dynamics. In this paper, we aimed at recovering the regulatory logic upstream of previously known components of cell cycle control, with the aim of understanding the mechanisms underlying the emergence of the cyclic behavior of such components. We focus on Arabidopsis thaliana, but given that many components of cell cycle regulation are conserved among eukaryotes, when experimental data for this system was not available, we considered experimental results from yeast and animal systems. We are proposing a Boolean gene regulatory network (GRN) that converges into only one robust limit cycle attractor that closely resembles the cyclic behavior of the key cell-cycle molecular components and other regulators considered here. We validate the model by comparing our in silico configurations with data from loss- and gain-of-function mutants, where the endocyclic behavior also was recovered. Additionally, we approximate a continuous model and recovered the temporal periodic expression profiles of the cell-cycle molecular components involved, thus s...Continue Reading

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Citations

Nov 28, 2015·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Claude Gérard, Albert Goldbeter
Feb 23, 2017·Annual Review of Plant Biology·Iris MeierDavid E Evans
Mar 19, 2019·The New Phytologist·Elena R Alvarez-BuyllaAdriana Garay-Arroyo
Feb 15, 2018·Development, Growth & Differentiation·Juan A Arias Del AngelMariana Benítez
Feb 2, 2018·Proceedings of the National Academy of Sciences of the United States of America·Reed S SorensonLeslie E Sieburth
Jan 8, 2019·Journal of Experimental Botany·Andrew J MillarTomasz Zielinski
Sep 5, 2019·Frontiers in Immunology·Jennifer EncisoCarlos Villarreal
Feb 3, 2021·Proceedings of the National Academy of Sciences of the United States of America·Camila GoldyRamiro E Rodriguez
Jul 14, 2019·Trends in Plant Science·Amy Marshall-Colón, Daniel J Kliebenstein
Mar 23, 2021·Frontiers in Plant Science·Mónica L García-GómezElena R Álvarez-Buylla

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Methods Mentioned

BETA
ubiquitination

Software Mentioned

Atalia
R
BoolNet

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