Single-cell and coupled GRN models of cell patterning in the Arabidopsis thaliana root stem cell niche

Azpeitia, Eugenio; Benítez, Mariana; Vega, Iliusi; Villarreal, Cuauhtémoc Calderón; Álvarez-Buylla, Elena

doi:10.1186/1752-0509-4-134

Cited by 65 publications

(88 citation statements)

References 93 publications

(179 reference statements)

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“…Importantly, this hypothesis was experimentally verified (Scacchi et al, 2010). The crosstalk between auxin and CKs observed at the transition zone and the means by which auxin regulates the pattern and maintenance of the root SCN in conjunction with other transcription factors have also been studied with theoretical tools (Muraro et al, 2011;Azpeitia et al, 2010). This body of research has provided important clues about hormone function and highlights how the combined use of experimental and theoretical approaches can improve our understanding of the crosstalk among hormones.…”

Section: Theoretical Approaches To the Study Of Hormones In The Rootmentioning

confidence: 90%

Hormone symphony during root growth and development

Garay‐Arroyo¹,

Sánchez²,

García‐Ponce³

et al. 2012

Developmental Dynamics

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Hormones regulate plant growth and development in response to external environmental stimuli via complex signal transduction pathways, which in turn form complex networks of interaction. Several classes of hormones have been reported, and their activity depends on their biosynthesis, transport, conjugation, accumulation in the vacuole, and degradation. However, the activity of a given hormone is also dependent on its interaction with other hormones. Indeed, there is a complex crosstalk between hormones that regulates their biosynthesis, transport, and/or signaling functionality, although some hormones have overlapping or opposite functions. The plant root is a particularly useful system in which to study the complex role of plant hormones in the plastic control of plant development. Physiological, cellular, and molecular genetic approaches have been used to study the role of plant hormones in root meristem homeostasis. In this review, we discuss recent findings on the synthesis, signaling, transport of hormones and role during root development and examine the role of hormone crosstalk in maintaining homeostasis in the apical root meristem.

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Section: Theoretical Approaches To the Study Of Hormones In The Rootmentioning

confidence: 90%

Hormone symphony during root growth and development

Garay‐Arroyo¹,

Sánchez²,

García‐Ponce³

et al. 2012

Developmental Dynamics

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“…In an attempt to explain the robust patterning of the root SCN of Arabidopsis thaliana in terms of the dynamics of known molecular regulators, Azpeitia and collaborators recently postulated several GRN dynamical models [ 32 ]. The models are grounded on experimental evidence of the interactions among the main molecular regulators of root SCN patterning.…”

Section: Arabidopsis Thaliana Root Stem Cell Niche (Scn) Grnmentioning

confidence: 99%

Descriptive vs. Mechanistic Network Models in Plant Development in the Post-Genomic Era

Dávila-Velderrain

Martínez-García

Álvarez-Buylla

2015

Methods in Molecular Biology

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Network modeling is now a widespread practice in systems biology, as well as in integrative genomics, and it constitutes a rich and diverse scientific research field. A conceptually clear understanding of the reasoning behind the main existing modeling approaches, and their associated technical terminologies, is required to avoid confusions and accelerate the transition towards an undeniable necessary more quantitative, multidisciplinary approach to biology. Herein, we focus on two main network-based modeling approaches that are commonly used depending on the information available and the intended goals: inference-based methods and system dynamics approaches. As far as data-based network inference methods are concerned, they enable the discovery of potential functional influences among molecular components. On the other hand, experimentally grounded network dynamical models have been shown to be perfectly suited for the mechanistic study of developmental processes. How do these two perspectives relate to each other? In this chapter, we describe and compare both approaches and then apply them to a given specific developmental module. Along with the step-by-step practical implementation of each approach, we also focus on discussing their respective goals, utility, assumptions, and associated limitations. We use the gene regulatory network (GRN) involved in Arabidopsis thaliana Root Stem Cell Niche patterning as our illustrative example. We show that descriptive models based on functional genomics data can provide important background information consistent with experimentally supported functional relationships integrated in mechanistic GRN models. The rationale of analysis and modeling can be applied to any other well-characterized functional developmental module in multicellular organisms, like plants and animals.

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“…Other works have evidenced that genes such as SCARECROW (SCR) or SHORTROOT (SHR) play a very significant role during the development of central cells in root meristems [7,19].…”

Section: It Has Been Found That In the Case Of The Root Meristem Of Amentioning

confidence: 99%

“…• The quiescent center is formed by a group of four cells which generally speaking do not divide after embryogenesis and whose main function is to regulate the cell spatial structure of the plant, that is, to inhibit differentiation of the initial cells with which they are in direct contact and to serve as a cell reservoir in order to replace damaged cells [7].…”

Section: The Root Stem Cell Nichementioning

confidence: 99%

Space-time dynamics of Stem Cell Niches: a unified approach for Plants

Pérez

López²,

Padilla

2013

Journal of Integrative Bioinformatics

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SummaryMany complex systems cannot be analyzed using traditional mathematical tools, due to their irreducible nature. This makes it necessary to develop models that can be implemented computationally to simulate their evolution. Examples of these models are cellular automata, evolutionary algorithms, complex networks, agent-based models, symbolic dynamics and dynamical systems techniques.We review some representative approaches to model the stem cell niche in Arabidopsis thaliana and the basic biological mechanisms that underlie its formation and maintenance. We propose a mathematical model based on cellular automata for describing the space-time dynamics of the stem cell niche in the root. By making minimal assumptions on the cell communication process documented in experiments, we classify the basic developmental features of the stem-cell niche, including the basic structural architecture, and suggest that they could be understood as the result of generic mechanisms given by short and long range signals. This could be a first step in understanding why different stem cell niches share similar topologies, not only in plants. Also the fact that this organization is a robust consequence of the way information is being processed by the cells and to some extent independent of the detailed features of the signaling mechanism. IntroductionStudies on stem cell from diverse systems have shown that their behavior is controlled by extracellular cues from the niche (long and short range signals) and by intrinsic genetic programs within the stem cell itself [1].Although important progress has been made in understanding these signaling processes, it is still open to a large extent what mechanisms are essential for the formation and maintenance of stem cell niches. In particular, whether some of these mechanisms are common and if it is possible to consider a basic or "universal" architecture for the stem cell niche which is conserved throughout a wide range of organisms. The purpose of this paper is twofold. On the one hand, we review some of the most representative approaches to model stem cell niches and their dynamics. On the other hand, we present a unified approach in an attempt to capture the basic cell communication features (both short and long range) that are necessary to explain the appearance, formation and robustness of the niche. We intend to provide a generic minimal framework, i.e., that can in principle account for the features of the niches that are

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Single-cell and coupled GRN models of cell patterning in the Arabidopsis thaliana root stem cell niche

Cited by 65 publications

References 93 publications

Hormone symphony during root growth and development

Hormone symphony during root growth and development

Descriptive vs. Mechanistic Network Models in Plant Development in the Post-Genomic Era

Space-time dynamics of Stem Cell Niches: a unified approach for Plants

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