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Super resolution imaging of 3D chromatin folding in Arabidopsis

English title Super resolution imaging of 3D chromatin folding in Arabidopsis
Applicant Baroux Célia
Number 198171
Funding scheme COST (European Cooperation in Science and Technology)
Research institution Institut für Pflanzen- und Mikrobiologie Universität Zürich
Institution of higher education University of Zurich - ZH
Main discipline Cellular Biology, Cytology
Start/End 01.05.2021 - 30.04.2025
Approved amount 318'388.00
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All Disciplines (3)

Discipline
Cellular Biology, Cytology
Genetics
Molecular Biology

Keywords (6)

Imaging; Histones; Arabidopsis; Reprogramming; Super-resolution; Chromatin

Lay Summary (French)

Lead
How the genome folds, packs and distributes in the cell's nucleus matters for gene expression, repair and replication. The genome's organizing principles largely remain a mystery and only starts being investigated, mostly in animal models. Yet, plant genomes have much to reveal, especially in relation to the extraordinary plasticity of plant cells.
Lay summary
Chez les Eukaryotes (plantes, animaux, champignons..), le genome est encapsulé dans le noyau, un compartiment cellulaire qui offre une plateforme de regulation de l'expression des gènes mais aussi de la reparation et réplication du génome. Au cours des dernières années, les chercheurs ont montré un nouveau niveau de régulation qui s'opère en trois dimensions dans le noyau. La distribution spatiale, la segmentation  en domaines et les degrés de compaction du génome ne sont pas aléatoires et varient en fonction du type cellulaire ou de son état physiologique. Un nouvel élan a été donné qui a créé le champ de recherche '3D Genomics' . Celui ci s'appuie sur les synergies de plusieurs disciplines, la biologie moléculaire, l'imagerie de pointe à haute résolution, le traitement d'image et la modélisation mathématique. Quels sont les principes d'organisation spatiale instruisant les fonctions du génome? Comment ces principes se retrouvent-ils ou diffèrent entre animaux, plantes ou champignons? Quel est leur impact pour le fonctionnement de la cellule, de l'organisme? Notre projet contribue à réponde à cette question, par la description de domaines choisis dans le génome de la plante modèle Arabidopsis, concernant leur distribution spatiale et degré de compaction, leur composition épigénétique, et leur dynamique (ou stabilité) dans un contexte de reprogrammation cellulaire.
Direct link to Lay Summary Last update: 16.03.2021

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Abstract

Three-dimensional (3D) genomics aims at gaining a holistic view of 3D genome organization, linking functional chromatin domains across different scales with genome function, such as transcription. International consortia exist that implement concerted efforts to resolve 3D genome organization principles mostly in animal or yeast models, with projected benefits to contribute to disease and health control in human and animals. Plants as eukaryote models are notoriously missing from these efforts although several groups worldwide contributed to the adaptation of 3D genomics approaches for plant nuclei and genomes. Intensifying efforts on plant models bears the promise of new knowledge on the mechanisms underlying cellular reprogramming in plants; being at the basis of their remarkable physiological and developmental adaptation abilities. Our group has expertise in 3D chromatin studies in the model plant Arabidopsis in relation to cell fate and cell response to light. We recently moved towards super resolution imaging using Stimulated Excitation Depletion microscopy which allows down to 30nm lateral and 50-70nm axial resolution in our experimental setup. Recent findings on chromatin structure in differentiated plant cells or cells lacking linker histones and resembling pluripotent cells suggest plant-specific principles of chromatin architecture and nanodomains organization that need to be resolved, however, at even higher resolution using single molecule microscopy imaging. In this context we propose two pilot studies aiming for establishing super-resolution, single molecule based microscopy imaging of chromatin in Arabidopsis focusing on two biological questions, related to our work: (i) the architecture of the chromatin fiber and spatial distribution of nucleosome clutches and nanodomains of differing packing density in differentiated vs pluripotent cells, (ii) the 3D architecture of a plant-specific topological domain mediating silencing of foreign DNA elements in partnership with Dr. S Grob, who discovered it. For both projects we will also test an innovative super resolution microscopy imaging platform developed by the Pelkmans’ lab at the University of Zürich (BEAM) and offering a significantly higher versatility and ease of use compared to techniques based on stochastic optical reconstruction (STORM) imaging. Collectively the work will (i) benchmark the use of super resolution imaging for elucidating chromatin architecture at nanoscale in plants, an approach largely missing in the community, and (ii) provide a first insight into chromatin packing and folding at the nanoscale in a model plant (Arabidopsis). In addition, these pilot studies will shed light onto plant chromatin organizing principles at an unprecedented scale and will greatly contribute the objectives of the International Nucleome Consortium COST action, to which the project is related.
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