Global reorganization of budding yeast chromosome conformation in different physiological conditions

Dultz, Elisa; Tjong, Harianto; Weider, Elodie; Herzog, Mareike; Young, Barry P.; Brune, Christiane; Müllner, Daniel; Loewen, Christopher; Alber, Frank; Weis, Karsten

doi:10.1083/jcb.201507069

Cited by 36 publications

(45 citation statements)

References 60 publications

(96 reference statements)

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“…The authors propose that this association likely results from multiple independent anchoring sites. Moreover, using a genome-wide screen, they identified a novel role for histone deacetylases in chromatin association with the nuclear periphery and provided further evidence for the previously described role of the transcriptional coactivator SAGA complex in peripheral gene repositioning in response to galactose activation [30]. …”

Section: Gene Expression Regulation By Npcs In Yeastmentioning

confidence: 91%

“…Recent, work from the Weis lab has shown that during activation, the association of the GAL locus with the NPC involves large genome rearrangements that position several chromosomal domains in close proximity to the nuclear envelope [30]. The authors propose that this association likely results from multiple independent anchoring sites.…”

Section: Gene Expression Regulation By Npcs In Yeastmentioning

confidence: 99%

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Nuclear pore complexes and regulation of gene expression

Raı́ces

D’Angelo

2017

Current Opinion in Cell Biology

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Nuclear pore complexes (NPCs), are large multiprotein channels that penetrate the nuclear envelope connecting the nucleus to the cytoplasm. Accumulating evidence shows that besides their main role in regulating the exchange of molecules between these two compartments, NPCs and their components also play important transport-independent roles, including gene expression regulation, chromatin organization, DNA repair, RNA processing and quality control, and cell cycle control. Here we will describe the recent findings about the role of these structures in the regulation of gene expression.

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Section: Gene Expression Regulation By Npcs In Yeastmentioning

confidence: 91%

Section: Gene Expression Regulation By Npcs In Yeastmentioning

confidence: 99%

Nuclear pore complexes and regulation of gene expression

Raı́ces

D’Angelo

2017

Current Opinion in Cell Biology

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“…All these observations highlight the highly dynamic nuclear envelope and the variability of nuclear size and shape (Stone et al, 2000; Webster et al, 2009). Accurate determination of the nuclear envelope position using fluorescence microscopy is technically challenging and is mostly performed in two dimensions (2D) (Dultz et al, 2016). Recent techniques have been proposed to explore the nuclear geometry in 3D (Zhao et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

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

Wang

Kamgoué

Normand

et al. 2016

Journal of Cell Science

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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.

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“…Fluorescently-labeled operator-binding proteins attach to each operator array forming two fluorescent spots (Figure 4 A), where the inter-spot distance is affected by the growth conditions (Figure 4 B). (Dultz et al, 2016;Shechtman et al, 2017), the mean inter-loci distance was observed to be dependent on the growth condition (mean ± standard deviation: 339 ± 174 in dextrose and 434 ± 193 in galactose). Crucially, while previous 3D datasets were recorded over hours at ~1 image per second (Shechtman et al, 2017), the current method acquires hundreds of images per second, producing a large library of suitable cell images in only a few minutes (N = 8,996 for dextrose and 11,074 for galactose, recorded in <5 and <10 minutes, respectively).…”

Section: Measuring Chromosomal Compaction States In Saccharomyces Cermentioning

confidence: 96%

High-throughput multicolor 3D localization in live cells by depth-encoding imaging flow cytometry

Weiss

Ezra

Goldberg

et al. 2019

Preprint

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Imaging flow cytometry replaces the canonical point-source detector of flow cytometry with a camera, unveiling subsample details in 2D images while maintaining high-throughput. Here we show that the technique is inherently compatible with 3D localization microscopy by point-spread-function engineering, namely the encoding of emitter depth in the emission pattern captured by a camera. By exploiting the laminar-flow profile in microfluidics, 3D positions can be extracted from cells or other objects of interest by calibrating the depth-dependent response of the imaging system using fluorescent microspheres mixed with the sample buffer. We demonstrate this approach for measuring fluorescently-labeled DNA in vitro and the chromosomal compaction state in large populations of live cells, collecting thousands of samples each minute. Furthermore, our approach is fully compatible with existing commercial apparatus, and can extend the imaging volume of the device, enabling faster flowrates thereby increasing throughput. RESULTS Device and functionalityAn illustration of the device is shown in Figure 1 A. Samples are loaded into the instrument and then directed through a multilaser-illuminated imaging volume. Emission light from the sample is captured by a 60X objective, relayed through a series of lenses, divided into separate spectral channels, and directed onto a camera, whose readout rate is synchronized with the flow speed. As a first demonstration, we show how an astigmatism can be incorporated into the system. By inserting a cylindrical lens between two of the aforementioned relay lenses (see Methods), the axial and lateral focal planes of the instrument are bifurcated, thus an object closer to the objective will appear focused laterally, but defocused axially and vice versa (Figures 1 B, C). The extent of the astigmatism contains information about the depth of the emitter, but is not a direct measurement of the z position. The typical 3D calibration used in microscopy (Huang et al., 2008) is therefore inapplicable and the incorporation of PSF engineering into flow imaging necessitates a novel 3D calibration procedure, which we describe below.

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Global reorganization of budding yeast chromosome conformation in different physiological conditions

Abstract: Movement of the GAL locus to the nuclear periphery is part of a large-scale rearrangement of chromosome architecture induced by glucose withdrawal and is regulated by the activities of histone acetyltransferases and histone deacetylases.

Cited by 36 publications

References 60 publications

Nuclear pore complexes and regulation of gene expression

Nuclear pore complexes and regulation of gene expression

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

High-throughput multicolor 3D localization in live cells by depth-encoding imaging flow cytometry

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