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Spatial modeling of biological patterns shows multiscale organization of Arabidopsis thaliana heterochromatin

The spatial organization in the cell nucleus is tightly linked to genome functions such as gene regulation. Similarly, specific spatial arrangements of biological components such as macromolecular complexes, organelles and cells are involved in many biological functions. Spatial interactions among e...

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Autores principales: Arpòn, Javier, Sakai, Kaori, Gaudin, Valérie, Andrey, Philippe
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7801681/
https://www.ncbi.nlm.nih.gov/pubmed/33431919
http://dx.doi.org/10.1038/s41598-020-79158-5
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author Arpòn, Javier
Sakai, Kaori
Gaudin, Valérie
Andrey, Philippe
author_facet Arpòn, Javier
Sakai, Kaori
Gaudin, Valérie
Andrey, Philippe
author_sort Arpòn, Javier
collection PubMed
description The spatial organization in the cell nucleus is tightly linked to genome functions such as gene regulation. Similarly, specific spatial arrangements of biological components such as macromolecular complexes, organelles and cells are involved in many biological functions. Spatial interactions among elementary components of biological systems define their relative positioning and are key determinants of spatial patterns. However, biological variability and the lack of appropriate spatial statistical methods and models limit our current ability to analyze these interactions. Here, we developed a framework to dissect spatial interactions and organization principles by combining unbiased statistical tests, multiple spatial descriptors and new spatial models. We used plant constitutive heterochromatin as a model system to demonstrate the potential of our framework. Our results challenge the common view of a peripheral organization of chromocenters, showing that chromocenters are arranged along both radial and lateral directions in the nuclear space and obey a multiscale organization with scale-dependent antagonistic effects. The proposed generic framework will be useful to identify determinants of spatial organizations and to question their interplay with biological functions.
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spelling pubmed-78016812021-01-13 Spatial modeling of biological patterns shows multiscale organization of Arabidopsis thaliana heterochromatin Arpòn, Javier Sakai, Kaori Gaudin, Valérie Andrey, Philippe Sci Rep Article The spatial organization in the cell nucleus is tightly linked to genome functions such as gene regulation. Similarly, specific spatial arrangements of biological components such as macromolecular complexes, organelles and cells are involved in many biological functions. Spatial interactions among elementary components of biological systems define their relative positioning and are key determinants of spatial patterns. However, biological variability and the lack of appropriate spatial statistical methods and models limit our current ability to analyze these interactions. Here, we developed a framework to dissect spatial interactions and organization principles by combining unbiased statistical tests, multiple spatial descriptors and new spatial models. We used plant constitutive heterochromatin as a model system to demonstrate the potential of our framework. Our results challenge the common view of a peripheral organization of chromocenters, showing that chromocenters are arranged along both radial and lateral directions in the nuclear space and obey a multiscale organization with scale-dependent antagonistic effects. The proposed generic framework will be useful to identify determinants of spatial organizations and to question their interplay with biological functions. Nature Publishing Group UK 2021-01-11 /pmc/articles/PMC7801681/ /pubmed/33431919 http://dx.doi.org/10.1038/s41598-020-79158-5 Text en © The Author(s) 2021, corrected publication 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Arpòn, Javier
Sakai, Kaori
Gaudin, Valérie
Andrey, Philippe
Spatial modeling of biological patterns shows multiscale organization of Arabidopsis thaliana heterochromatin
title Spatial modeling of biological patterns shows multiscale organization of Arabidopsis thaliana heterochromatin
title_full Spatial modeling of biological patterns shows multiscale organization of Arabidopsis thaliana heterochromatin
title_fullStr Spatial modeling of biological patterns shows multiscale organization of Arabidopsis thaliana heterochromatin
title_full_unstemmed Spatial modeling of biological patterns shows multiscale organization of Arabidopsis thaliana heterochromatin
title_short Spatial modeling of biological patterns shows multiscale organization of Arabidopsis thaliana heterochromatin
title_sort spatial modeling of biological patterns shows multiscale organization of arabidopsis thaliana heterochromatin
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7801681/
https://www.ncbi.nlm.nih.gov/pubmed/33431919
http://dx.doi.org/10.1038/s41598-020-79158-5
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