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.
Footnotes
Competing interests
The authors declare no competing or financial interests.
Author contributions
R.W. performed microscopy, analyzed data, wrote image analysis scripts and wrote the manuscript; A.K. conceived and wrote image analysis scripts and analyzed data; C.N. constructed strains, analyzed data and wrote the manuscript; I.L.-S. performed electron microscopy and wrote the manuscript; T.M. computed spherical aberration and wrote the manuscript; O.G. designed experiments, analyzed data, and wrote the manuscript. All authors reviewed the results and approved the final version of the manuscript.
Funding
This work was supported by the Agence Nationale de la Recherche (ANDY) and Initiative d'excellence of Université de Toulouse (Clemgene and Nudgene). Deposited in PMC for immediate release.
Data availability
The NucQuant software implementing the methods described in this paper is available to download at GitHub (https://github.com/ogadal/nucquant).
Supplementary information
Supplementary information available online at http://jcs.biologists.org/lookup/doi/10.1242/jcs.188250.supplemental
- Received February 17, 2016.
- Accepted November 1, 2016.
- © 2016. Published by The Company of Biologists Ltd
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed.
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