In the nucleus of eukaryotic cells, a significant portion of the genome consists of lamina-associated domains, which are preferentially located at the nuclear periphery. However, how the remaining parts of the genome are exactly radially organized in the nucleus remains largely unknown. During my lecture I will describe a method named Genomic loci Positioning by Sequencing (GPSeq), which allows for genome-wide measurements of the distance to the nuclear lamina. Using GPSeq, we generated reproducible maps of the radial organization of the genome in human cells, at various resolutions, that revealed radial gradients of genomic and epigenomic features, gene expression, as well as A/B compartments and chromatin loops. We assessed the contribution of various features in predicting radiality, and found GC-content to have the strongest predictive power at all resolutions. Finally, we show that, by combining GPSeq radial information with Hi-C intra- and trans-chromosomal contacts, we are able to build whole-genome structure predictions much more accurately than possible thus far. Our data demonstrate that GPSeq is a powerful method to study genome architecture and reveal that the cell nucleus has a much finer level of radial organization than previously appreciated.

Lumenogenesis is a common mechanism in plant and animals that consists in creating, gaps, and lumens between cells to allow the formation of ducts. The creation of tubes occurs following several scenarios that are worth comparing. In this presentation I will present our understanding of how small canaliculi are formed by hepatocytes in livers. These canaliculi collect the secreted bile and their morphogenesis is very poorly understood.  Deficient formation leads defects in bile flows and consequently diseases (cholestasis). We adopted a deconstrutivist approach to understand how an osmotically driven growth of canaliculi can anisotropically lead to the development of a tube. I will show how single hepatocytes (the main cellular constituents of the liver) can be induced to form spherical hemi-lumen by contact with an inert material, demonstrating that lumenogenesis initiation does not require the concomitant development of lumen in the neighboring cells. I will then show how the spatial geometry of extra cellular matrix provides a guidance tool to favor the development of tubulogenesis in the direction of lowest intra-cellular tension. Lastly, I will show the existence of special protrusions crossing the lumen cavity, bridging, suturing, the developing lumen to putatively minimize its extension in the lateral direction, and consequently favoring its extension along the tubular axis.

References:

[1]  Zhang, Y. et al. Biomimetic niches reveal the minimal cues to trigger apical lumen formation in single hepatocytes. Nat Mater, doi:10.1038/s41563-020-0662-3 (2020).

[2]  Li, Q. et al. Extracellular matrix scaffolding guides lumen elongation by inducing anisotropic intercellular mechanical tension. Nat Cell Biol 18, 311-318, doi:10.1038/ncb3310 (2016).

[3]  Stoecklin, C. et al. A New Approach to Design Artificial 3D Microniches with Combined Chemical, Topographical, and Rheological Cues. Advanced Biosystems 0, 1700237, doi:doi:10.1002/adbi.201700237 (2018).

[4]  Dasgupta, S., Gupta, K., Zhang, Y., Viasnoff, V. & Prost, J. Physics of lumen growth. Proc Natl Acad Sci U S A 115, E4751-E4757, doi:10.1073/pnas.1722154115 (2018).

Actively regulated symmetry breaking, which is ubiquitous in biological cells, underlies phenomena such as directed cellular movement and morphological polarization. Here, we investigate how an organ-level polarity pattern emerges through symmetry breaking at the cellular level during the formation of a mechanosensory organ. Combining theory, genetic perturbations and in vivo imaging, we study the development and regeneration of the fluid-motion sensors in the zebrafish’s lateral line. We find that two interacting symmetry-breaking events—one mediated by biochemical signalling and the other by cellular mechanics—give rise to precise rotations of cell pairs, which produce a mirror-symmetric polarity pattern in the receptor organ.