High resolution microscopy reveals the nuclear shape of budding yeast during cell cycle and in various biological states

Abstract

How spatial organization of the genome depends on nuclear shape is unknown, mostly because accurate nuclear size and shape measurement is technically challenging. In large cell populations of the yeast Saccharomyces cerevisiae, we assessed the geometry (size and shape) of nuclei in three dimensions with a resolution of 30 nm. We improved an automated fluorescence localization method by implementing a post-acquisition correction of the spherical microscopic aberration along the z-axis, to detect the three dimensional (3D) positions of nuclear pore complexes (NPCs) in the nuclear envelope. Here, we used a method called NucQuant to accurately estimate the geometry of nuclei in 3D throughout the cell cycle. To increase the robustness of the statistics, we aggregated thousands of detected NPCs from a cell population in a single representation using the nucleolus or the spindle pole body (SPB) as references to align nuclei along the same axis. We could detect asymmetric changes of the nucleus associated with modification of nucleolar size. Stereotypical modification of the nucleus toward the nucleolus further confirmed the asymmetric properties of the nuclear envelope.

Extent and context dependence of pleiotropy revealed by high-throughput single-cell phenotyping

“…We applied Wishbone separately to cells belonging to each of the three cell types defined by morphometric analysis (unbudded, small-budded, and large-budded cells). The trends describing how morphological features vary across Wishbone-defined cell-division trajectories are consistent with previous observations of how morphology changes as yeast cells divide (75,76) (Fig 4A; line plots). For example, Wishbone sorts fixed-cell images in such a way that cell area increases throughout the course of cell division (Fig4A; upper left panel), and nuclear elongation occurs just before nuclear division (Fig4A; lower left panel).…”

Mapping the native organization of the yeast nuclear pore complex using nuclear radial intensity measurements

“…3A and Dataset S1, sheet 2). Diploid cells are larger than haploid cells, so the experiment also served to test accuracy against variations in the nuclear diameter (35). Assuming that the NPC structure is identical in haploid and diploid cells (SI Appendix, To provide an independent estimate of accuracy in a more complex setting, we used strains simultaneously expressing 2 different yEGFP-tagged Nups (Fig.…”

Geometrical characterization of fluorescently labelled surfaces from noisy 3D microscopy data

“…The increasing use of 3D imaging in fluorescence microscopy applications, with confocal microscopy being now mainstream, has allowed for the acquisition of large amounts of 3D data in both biological and physical systems. Examples include biological studies of the morphological changes that occur during cell migration (Soll, Soll et al, 2000), the microbial cell shape (Ursell et al, 2014), the cellular packings during tissue morphogenesis (Hayashi & Carthew, 2004;Lecuit & Lenne, 2007) and early embryonic development (Pierre et al, 2016) and even the geometry of the cell nucleus at the subcellular scale (Kim et al, 2015;Wang et al, 2016). Studies of the mechanics of emulsions in soft-matter physics also rely on the ability to characterize the geometry of individual droplets (Brujić et al, 2002;Zhou et al, 2006).…”