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Single-cell and coupled GRN models of cell patterning in the Arabidopsis thaliana root stem cell niche
BACKGROUND: Recent experimental work has uncovered some of the genetic components required to maintain the Arabidopsis thaliana root stem cell niche (SCN) and its structure. Two main pathways are involved. One pathway depends on the genes SHORTROOT and SCARECROW and the other depends on the PLETHORA...
Autores principales: | , , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2010
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2972269/ https://www.ncbi.nlm.nih.gov/pubmed/20920363 http://dx.doi.org/10.1186/1752-0509-4-134 |
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author | Azpeitia, Eugenio Benítez, Mariana Vega, Iliusi Villarreal, Carlos Alvarez-Buylla, Elena R |
author_facet | Azpeitia, Eugenio Benítez, Mariana Vega, Iliusi Villarreal, Carlos Alvarez-Buylla, Elena R |
author_sort | Azpeitia, Eugenio |
collection | PubMed |
description | BACKGROUND: Recent experimental work has uncovered some of the genetic components required to maintain the Arabidopsis thaliana root stem cell niche (SCN) and its structure. Two main pathways are involved. One pathway depends on the genes SHORTROOT and SCARECROW and the other depends on the PLETHORA genes, which have been proposed to constitute the auxin readouts. Recent evidence suggests that a regulatory circuit, composed of WOX5 and CLE40, also contributes to the SCN maintenance. Yet, we still do not understand how the niche is dynamically maintained and patterned or if the uncovered molecular components are sufficient to recover the observed gene expression configurations that characterize the cell types within the root SCN. Mathematical and computational tools have proven useful in understanding the dynamics of cell differentiation. Hence, to further explore root SCN patterning, we integrated available experimental data into dynamic Gene Regulatory Network (GRN) models and addressed if these are sufficient to attain observed gene expression configurations in the root SCN in a robust and autonomous manner. RESULTS: We found that an SCN GRN model based only on experimental data did not reproduce the configurations observed within the root SCN. We developed several alternative GRN models that recover these expected stable gene configurations. Such models incorporate a few additional components and interactions in addition to those that have been uncovered. The recovered configurations are stable to perturbations, and the models are able to recover the observed gene expression profiles of almost all the mutants described so far. However, the robustness of the postulated GRNs is not as high as that of other previously studied networks. CONCLUSIONS: These models are the first published approximations for a dynamic mechanism of the A. thaliana root SCN cellular pattering. Our model is useful to formally show that the data now available are not sufficient to fully reproduce root SCN organization and genetic profiles. We then highlight some experimental holes that remain to be studied and postulate some novel gene interactions. Finally, we suggest the existence of a generic dynamical motif that can be involved in both plant and animal SCN maintenance. |
format | Text |
id | pubmed-2972269 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-29722692010-11-05 Single-cell and coupled GRN models of cell patterning in the Arabidopsis thaliana root stem cell niche Azpeitia, Eugenio Benítez, Mariana Vega, Iliusi Villarreal, Carlos Alvarez-Buylla, Elena R BMC Syst Biol Research Article BACKGROUND: Recent experimental work has uncovered some of the genetic components required to maintain the Arabidopsis thaliana root stem cell niche (SCN) and its structure. Two main pathways are involved. One pathway depends on the genes SHORTROOT and SCARECROW and the other depends on the PLETHORA genes, which have been proposed to constitute the auxin readouts. Recent evidence suggests that a regulatory circuit, composed of WOX5 and CLE40, also contributes to the SCN maintenance. Yet, we still do not understand how the niche is dynamically maintained and patterned or if the uncovered molecular components are sufficient to recover the observed gene expression configurations that characterize the cell types within the root SCN. Mathematical and computational tools have proven useful in understanding the dynamics of cell differentiation. Hence, to further explore root SCN patterning, we integrated available experimental data into dynamic Gene Regulatory Network (GRN) models and addressed if these are sufficient to attain observed gene expression configurations in the root SCN in a robust and autonomous manner. RESULTS: We found that an SCN GRN model based only on experimental data did not reproduce the configurations observed within the root SCN. We developed several alternative GRN models that recover these expected stable gene configurations. Such models incorporate a few additional components and interactions in addition to those that have been uncovered. The recovered configurations are stable to perturbations, and the models are able to recover the observed gene expression profiles of almost all the mutants described so far. However, the robustness of the postulated GRNs is not as high as that of other previously studied networks. CONCLUSIONS: These models are the first published approximations for a dynamic mechanism of the A. thaliana root SCN cellular pattering. Our model is useful to formally show that the data now available are not sufficient to fully reproduce root SCN organization and genetic profiles. We then highlight some experimental holes that remain to be studied and postulate some novel gene interactions. Finally, we suggest the existence of a generic dynamical motif that can be involved in both plant and animal SCN maintenance. BioMed Central 2010-10-05 /pmc/articles/PMC2972269/ /pubmed/20920363 http://dx.doi.org/10.1186/1752-0509-4-134 Text en Copyright ©2010 Azpeitia et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Azpeitia, Eugenio Benítez, Mariana Vega, Iliusi Villarreal, Carlos Alvarez-Buylla, Elena R Single-cell and coupled GRN models of cell patterning in the Arabidopsis thaliana root stem cell niche |
title | Single-cell and coupled GRN models of cell patterning in the Arabidopsis thaliana root stem cell niche |
title_full | Single-cell and coupled GRN models of cell patterning in the Arabidopsis thaliana root stem cell niche |
title_fullStr | Single-cell and coupled GRN models of cell patterning in the Arabidopsis thaliana root stem cell niche |
title_full_unstemmed | Single-cell and coupled GRN models of cell patterning in the Arabidopsis thaliana root stem cell niche |
title_short | Single-cell and coupled GRN models of cell patterning in the Arabidopsis thaliana root stem cell niche |
title_sort | single-cell and coupled grn models of cell patterning in the arabidopsis thaliana root stem cell niche |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2972269/ https://www.ncbi.nlm.nih.gov/pubmed/20920363 http://dx.doi.org/10.1186/1752-0509-4-134 |
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