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.
This project is still ongoing. Due to technical difficulties encountered in data production and in recruiting a post-doctoral fellow, it was decided in October 2020 to reconfigure the final part of the project into a PhD project in line with the first part, thus securing the availability of experimental data. The PhD project has started on December 1st, 2021, to investigate the use of Deep Learning-based approaches (Artificial Intelligence) to decipher cellular mechanism in plant morphogenesis.
Publications:
Arpòn J, Gaudin V, Andrey P (2018). A method for testing random spatial models on nuclear object distributions. Plant Chromatin Dynamics : Methods and Protocols, M. Bemer & C. Baroux (Eds.), Methods in Molecular Biology, vol. 1675, pp. 493–507. Humana Press, New York, NY.
Arpón J, Sakai K, Gaudin V, Andrey P (2021). Spatial modeling of biological patterns shows multiscale organization of Arabidopsis thaliana heterochromatin. Scientific Reports, 11, 323.
Capilla-Pérez, L., Durand, S., Hurel, A., Lian, Q., Chambon, A., Taochy, C., Solier, V., Grelon, M., and Mercier, R. (2021). The synaptonemal complex imposes crossover interference and heterochiasmy in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 118: 1–11.
Christophorou, N., She, W., Long, J., Hurel, A., Beaubiat, S., Idir, Y., Tagliaro-Jahns, M., Chambon, A., Solier, V., Vezon, D., Grelon, M., Feng, X., Bouche, N., and Mezard, C. (2020). AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization. PLoS Genet. 16: 1–23.
Coen, O., Lu, J., Xu, W., De Vos, D., Péchoux, C., Domergue, F., Grain, D., Lepiniec, L., and Magnani, E. (2019). Deposition of a cutin apoplastic barrier separating seed maternal and zygotic tissues. BMC Plant Biol. 19: 1–20.
Coen, O., Lu, J., Xu, W., Pateyron, S., Grain, D., Péchoux, C., Lepiniec, L., and Magnani, E. (2020). A TRANSPARENT TESTA Transcriptional Module Regulates Endothelium Polarity. Front. Plant Sci. 10: 1–14.
Cromer, L., Jolivet, S., Singh, D.K., Berthier, F., De Winne, N., De Jaeger, G., Komaki, S., Prusicki, M.A., Schnittger, A., Guérois, R., and Mercier, R. (2019). Patronus is the elusive plant securin, preventing chromosome separation by antagonizing separase. Proc. Natl. Acad. Sci. U. S. A. 116: 16018–16027.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.
Laruelle E, Belcram K, Trubuil A, Palauqui JC, Andrey P (2022). Large-scale analysis and computer modeling reveal hidden regularities behind variability of cell division patterns in Arabidopsis thaliana embryogenesis. eLife, 11, e79224.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.
Romeiro Motta, M., Zhao, X., Pastuglia, M., Belcram, K., Roodbarkelari, F., Komaki, M., Harashima, H., Komaki, S., Kumar, M., Bulankova, P., Heese, M., Riha, K., Bouchez, D., and Schnittger, A. (2022). B1‐type cyclins control microtubule organization during cell division in Arabidopsis. EMBO Rep. 23: 1–18.
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.
Vrielynck, N., Schneider, K., Rodriguez, M., Sims, J., Chambon, A., Hurel, A., De Muyt, A., Ronceret, A., Krsicka, O., Mézard, C., Schlögelhofer, P., and Grelon, M. (2021). Conservation and divergence of meiotic DNA double strand break forming mechanisms in Arabidopsis thaliana. Nucleic Acids Res. 49: 9821–9835.
Communications in conferences:
Andrey P (2023). TBA. Plant Computational Biology Workshop, 4-8 September 2023, Sainsbury Lab, Cambridge, UK. (Invited speaker).
Andrey P (2022). Computational approaches to decipher cell division patterns in plant embryo. Plant Computational Biology Workshop, 29 August–2 September 2022, ENS Lyon (invited speaker).
Lefranc S, Kodera C, Biot E, Ouddah A, Durrmeyer A, Uyttewaal M, Bouchez D and Andrey P (2022). Computational analysis of cell division patterns in the shoot apical meristem. In Proceedings of the First European conference: From genes to plant architecture : the shoot apical meristem in all its states, Toumaï Conference Center Poitiers (France), 28–30 November 2022.
Andrey P (2020). Statistical modeling of spatial interactions in biological patterns, with application to plant nuclear organization. Quantitative BioImaging Conference, Jan 6-9, Oxford, UK.
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, Andrey P, Arpon J, Sakai K, Del Prete S (2017). Spatial 3D modelling of nuclear architecture in plants. Presented at 3D CHROME Symposium “Modelling of 3D Genome Organization: Integrating Genomics and Microscopy Data”, 2-3 Octobre, Gif-Sur Yvette, France.
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, Sweeden.
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.
P Andrey, « Modélisation 3D des patrons de divisions cellulaires au cours de l'embryogenèse précoce chez Arabidopsis thaliana », réunion du pôle Morphogenèse, Signalisation, Modélisation de l’IJPB, 29 avril 2014, Versailles.
P Andrey, “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, 26–28 Juin 2013 (conférence invitée).
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, 26–28 Juin 2013 (conférence invitée).
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.
Datasets:
Belcram K; Palauqui JC (2022), A collection of 3D images of Arabidopsis thaliana embryos, https://doi.org/10.15454/HIIBKW, Recherche Data Gouv, V1.
Gaudin V, Andrey P (2019). A collection of 3D images of Arabidopsis thaliana cell nuclei, https://doi.org/10.15454/1HSOIE, Recherche Data Gouv, V1.
