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SPS - Saclay Plant Sciences

Project 4: Modelling developmental mechanisms

Coordination: Philippe Andrey / Patrick Laufs

Abstract:

This project aims at developing modelling and systems biology approaches for a better understanding of two key developmental processes in plants: embryo morphogenesis and seed maturation.

Embryogenesis is a complex process by which a single zygotic cell gives rise to a mature embryo consisting of different organized cell types. For this, cellular growth and division, patterning and cell differentiation have to be properly regulated. We developed a new computational framework for modelling cell divisions in real cell shapes observed in 3D images and showed that the early, stereotyped cell division patterns in Arabidopsis can be explained using a unique rule linking mother cell geometry and division plane positioning. These results suggest that self-organized processes could play a more important role than previously thought in plant early morphogenesis.
During the following maturation phase, the embryo accumulates specific storage products and becomes progressively tolerant to desiccation, thus preparing the seed to dispersal. This requires the activation of specific spatio-temporal programs that are determined by a group of interacting, partially redundant transcription factors whose expression is tightly regulated, in part via mechanisms affecting chromatin modifications. Chromatin is a dynamic structure, the organization of which is linked with overall nuclear architecture and with the regulation of gene expression. We developed a new, highly sensitive protocol to quantify gene expression in microdissected tissues from wildtype and mutant seeds.  We also generated a collection of 3D images from identified cell types in wildtype and mutant plant nuclei. Analyzing these data with newly developed spatial modelling tools highlighted a multiscale organization of constitutive heterochromatin in A. thaliana and complementary roles of proteins from the CRWN family in the regulation of this organization.

Objectives:

The project was divided in two parts, with the objective of modelling :

1. the spatio-temporal patterns of cell divisions during early embryogenesis;

2. nuclear organization and gene network transcriptional regulation during seed maturation

Main results:

Part 1 of the project :

- establishment of a collection of segmented and annotated images of embryos up to 16C stage;

- development of a computational model of cell division in 3D;

- a new cell division rule linking mother cell geometry and division plane positioning, predictive of cell division patterns in the early embryo.

Part 2 of the project :

- a new RNAseq protocol with high sensitivity for transcriptomic analysis in seed microdissected tissues;

- an image collection of wildtype and mutant plant nuclei from identified cell types;

- identification of principles and determinants of spatial organization of constitutive heterochromatin.

Prospects:

Part 1:

- based on the developed computational model, study the interplay between cell division and growth and their role in the emergence of embryo asymmetry at the heart stage;

- study the contributions of specific regulators to the control of cell division orientation by characterizing cell division patterns in early embryos of mutants.

Part 2:

- apply the developed spatial models to analyze and compare nuclear organizations in different seed cell types;

- based on the collected transcriptomics data, model the gene regulation networks that subtend seed maturation, taking into account spatial constraints.

Publications (as of September, 2019):

Moukhtar J, Trubuil A, Belcram K, Legland D, Khadir Z, Urbain A, Palauqui JC, Andrey P (2019). Cell geometry determines symmetric and asymmetric division plane selection in Arabidopsis early embryos. PLoS Computational Biology, 15, e1006771.

Sakai K, Taconnat L, Borrega N, Yansouni J, Brunaud V, Paysant-Le Roux C, Delannoy E, Martin Magniette ML, Lepiniec L, Faure JD, Balzergue S, Dubreucq B (2018). Combining laser-assisted microdissection (LAM) and RNA-seq allows to perform a comprehensive transcriptomic analysis of epidermal cells of Arabidopsis embryo. Plant Methods, 14, 10.

Del Prete S., Arpón J., Sakai K., Andrey P., Gaudin V. (2014). Nuclear Architecture and Chromatin Dynamics in Interphase Nuclei of Arabidopsis thaliana. Cytogenetic and Genome Research 143, 28-50.

Communications in conferences:

Laruelle L, Moukhtar J, Trubuil A, Belcram K, Legland D, Khadir Z, Palauqui JC, Andrey P (2019). Deciphering cell division patterns in plant early embryogenesis by combining 3D image analysis and computer modelling. Plant Growth and Form : International Symposium on Quantitative Plant Morphodynamics, 9–11 September 2019, Heidelberg, Germany (invited).

Moukhtar J., Laruelle, E., Trubuil, A., Belcram, K., Legland, D., Khadir, Z., Palauqui, J.-C., Andrey, P. (2019). Combining 3D image analysis and computer modeling to understand cell division patterns in plant early embryogenesis. Quantitative BioImaging Conference, 8-11 January 2019, Rennes, France.

Andrey P (2018). Image analysis and computer modelling of cell divisions in plant early embryogenesis. Phycomorph COST Action Workshop : “Imaging seaweed cells and tissues”, 12–13 November 2018, Roscoff, France (invited).

Andrey P (2017). Modeling 3D cell division patterns in plant early embryogenesis. CLIPS 2017 : Multiscale Live Imaging in Human, Animal and Plant Health, 12–13 septembre 2017, Gif-sur-Yvette, France (invited).

Gaudin V (2016). Spatial 3D modelling of plant nuclear architecture, International Symposium on Nuclear Dynamics in Plants, 16 November, Tokyo, Japan.

Andrey P (2015). Modeling spatial distributions and patterns in biological imaging. GDR 2588, Third Mini-symposium on BioImage Informatics, 23–24 novembre 2015, Institut Pasteur, Paris (invited).

Arpón J, Del Prete S, Sakai K, Andrey P, Gaudin G (2015) Spatial 3D modelling of plant nuclear architecture, INUPRAG Meeting, 6-8 October, Nancy, France.

Moukhtar J, Belcram K, Trubuil A, Legland D, Palauqui JC, Andrey P (2015). Computational modelling of cell division patterns during plant early embryogenesis. International Workshop on Image Analysis Methods for the Plant Sciences, 21–22 septembre 2015, Louvain-la-Neuve, Belgium (orateur).

Arpon J, Sakai K, Del Prete S, Gaudin V, Andrey P (2015). A spatial statistical approach to analyze and model nuclear architecture. International Workshop on Image Analysis Methods for the Plant Sciences, 21–22 septembre 2015, Louvain-la-Neuve, Belgium.

Arpón J, Sakai K, Del Prete S, Gaudin V, Andrey P (2015). Recent developments on the statistical spatial modeling of nuclear architecture in A. thaliana. International Plant Nuclear Consortium Meeting, 3-5 July, Olomouc, Czech Republic.

Arpón J, Del Prete S, Sakai K, Andrey P, Gaudin V (2015) Spatial 3D modelling of plant nuclear architecture, European Workshop on Plant Chromatin, 25-26 June, Upssala, Sweden.

Balzergue S., Borrega N., Yansouni J., Brunaud V., Delanoye E., Faure J.D., Dubreucq B. « Low RNAseq microdissected plant tissue », International Symposium on Microgenomics, Paris, France, May 15-16 2014.

Andrey P, “Modelling cell division patterns in Arabidopsis thaliana early embryos”. First TEFOR Symposium, December 16, 2013, Paris (invited talk).

Arpón J, Sakai K, Del Prete S, Gaudin V, Andrey P. Image analysis and spatial modelling of nuclear organisation in Arabidopsis thaliana. First Meeting of the International Plant Nuclear Group, Oxford Brookes University, June 26–28, 2013 (invited talk).

Sakai K, Del Prete S, Arpón J, Andrey P, Gaudin V, “Nuclear architecture and genome functions in Arabidopsis thaliana”, First Meeting of the International Plant Nuclear Group, Oxford Brookes University, June 26–28, 2013 (invited talk).

Présentation du projet-phare ”Modélisation des mécanismes développementaux” du LabEx ”Sciences des Plantes de Saclay” P Andrey, K Belcram, B Dubreucq, V Gaudin, P Laufs, J Moukhtar, JC Palauqui, A Trubuil, A Urbain & L Lepiniec, Septièmes Journées de Biologie cellulaire du Grand Campus, 14-15 Mai 2012, Institut Curie, Orsay.