Improved Determination of Subnuclear Position Enabled by Three-Dimensional Membrane Reconstruction

Zhao, Y., Schreiner, S. M., Koo, P. K., Colombi, P., King, M. C., Mochrie, S. G. (July 2016) Improved Determination of Subnuclear Position Enabled by Three-Dimensional Membrane Reconstruction. Biophys J, 111 (1). pp. 19-24. ISSN 0006-3495

DOI: 10.1016/j.bpj.2016.05.036


Many aspects of chromatin biology are influenced by the nuclear compartment in which a locus resides, from transcriptional regulation to DNA repair. Further, the dynamic and variable localization of a particular locus across cell populations and over time makes analysis of a large number of cells critical. As a consequence, robust and automatable methods to measure the position of individual loci within the nuclear volume in populations of cells are necessary to support quantitative analysis of nuclear position. Here, we describe a three-dimensional membrane reconstruction approach that uses fluorescently tagged nuclear envelope or endoplasmic reticulum membrane marker proteins to precisely map the nuclear volume. This approach is robust to a variety of nuclear shapes, providing greater biological accuracy than alternative methods that enforce nuclear circularity, while also describing nuclear position in all three dimensions. By combining this method with established approaches to reconstruct the position of diffraction-limited chromatin markers-in this case, lac Operator arrays bound by lacI-GFP-the distribution of loci positions within the nuclear volume with respect to the nuclear periphery can be quantitatively obtained. This stand-alone image analysis pipeline should be of broad practical utility for individuals interested in various aspects of chromatin biology, while also providing, to our knowledge, a new conceptual framework for investigators who study organelle shape.

Item Type: Paper
Subjects: organs, tissues, organelles, cell types and functions > organelles, types and functions > endoplasmic reticulum
Investigative techniques and equipment > imaging
organism description > yeast > Saccharomyces > Schizosaccharomyces pombe
CSHL Authors:
Communities: CSHL labs > Koo Lab
Depositing User: Matthew Dunn
Date: 12 July 2016
Date Deposited: 16 Sep 2019 18:47
Last Modified: 16 Sep 2019 18:59
PMCID: PMC4945324
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