Systematic characterization of the conformation and dynamics of budding yeast chromosome XII

Albert, Benjamin; Mathon, Julien; Shukla, Avanish; Saad, Hicham; Normand, Christophe; Léger-Silvestre, Isabelle; Villa, David; Kamgoué, Alain; Mozziconacci, Julien; Wong, Hua; Zimmer, Christophe; Bhargava, Poonam; Bancaud, Aurélien; Gadal, Olivier

doi:10.1083/jcb.201208186

Cited by 50 publications

(85 citation statements)

References 48 publications

(70 reference statements)

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“…the fact that loci at larger genomic distance from the centromere moved over longer distances during the same time interval. Figure 5b–e shows measured MSD for four loci on four different chromosomes (including the rDNA-carrying chromosome 12, whose spatial configuration is quite different from the other chromosomes [64]) over time intervals in the range of 16 ms to 100 s. As previously pointed out, the MSD obeyed a subdiffusive power law with an exponent ~0.5, roughly consistent with the Rouse polymer model [18, 37, 41, 44, 64]. The model reproduced this behavior relatively well over almost four orders of magnitude of time.…”

Section: Resultsmentioning

confidence: 99%

Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations

et al. 2017

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BackgroundThe structure and mechanical properties of chromatin impact DNA functions and nuclear architecture but remain poorly understood. In budding yeast, a simple polymer model with minimal sequence-specific constraints and a small number of structural parameters can explain diverse experimental data on nuclear architecture. However, how assumed chromatin properties affect model predictions was not previously systematically investigated.ResultsWe used hundreds of dynamic chromosome simulations and Bayesian inference to determine chromatin properties consistent with an extensive dataset that includes hundreds of measurements from imaging in fixed and live cells and two Hi-C studies. We place new constraints on average chromatin fiber properties, narrowing down the chromatin compaction to ~53–65 bp/nm and persistence length to ~52–85 nm. These constraints argue against a 20–30 nm fiber as the exclusive chromatin structure in the genome. Our best model provides a much better match to experimental measurements of nuclear architecture and also recapitulates chromatin dynamics measured on multiple loci over long timescales.ConclusionThis work substantially improves our understanding of yeast chromatin mechanics and chromosome architecture and provides a new analytic framework to infer chromosome properties in other organisms.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-017-1199-x) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations

et al. 2017

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“…The motion of chromosome loci was recorded using a brightfield microscope and analyzed using a customized high-throughput tracking software based on the Multiple-Target Tracing algorithm (Supplemental Fig. S1; Sergé et al 2008;Albert et al 2013). Because physical tethering of chromosomes may occur at the nuclear periphery (Heun et al 2001;Hediger et al 2002), the nucleus was divided into two regions of equal surfaces, and every tracked locus was automatically assigned to a central or peripheral localization based on the segmentation of the first image of the acquisitions (see image in Fig.…”

Section: Resultsmentioning

confidence: 99%

“…The movements of chromosome loci were systematically analyzed using a custom software that was developed in Matlab (Mathworks) (Sergé et al 2008;Albert et al 2013 [source code at http://jcb.rupress.org/ content/202/2/201/suppl/DC1, and the executable file at ftp:// intermtt:MTTinterface@ftp.laas.fr/]). This software enabled us to extract (x, y) coordinates by Gaussian fitting, to reconstruct the trajectories, and to compute the MSD and the step distribution function (see Supplemental Video 1).…”

Section: Discussionmentioning

confidence: 99%

High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome

et al. 2013

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Chromosome dynamics are recognized to be intimately linked to genomic transactions, yet the physical principles governing spatial fluctuations of chromatin are still a matter of debate. Using high-throughput single-particle tracking, we recorded the movements of nine fluorescently labeled chromosome loci located on chromosomes III, IV, XII, and XIV of Saccharomyces cerevisiae over an extended temporal range spanning more than four orders of magnitude (10 -2 -10 3 sec). Spatial fluctuations appear to be characterized by an anomalous diffusive behavior, which is homogeneous in the time domain, for all sites analyzed. We show that this response is consistent with the Rouse polymer model, and we confirm the relevance of the model with Brownian dynamics simulations and the analysis of the statistical properties of the trajectories. Moreover, the analysis of the amplitude of fluctuations by the Rouse model shows that yeast chromatin is highly flexible, its persistence length being qualitatively estimated to <30 nm. Finally, we show that the Rouse model is also relevant to analyze chromosome motion in mutant cells depleted of proteins that bind to or assemble chromatin, and suggest that it provides a consistent framework to study chromatin dynamics. We discuss the implications of our findings for yeast genome architecture and for target search mechanisms in the nucleus.

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“…A home-made PDMS chamber connected to a microfluidic pump (Fluigent S.A.) allowed trapping of cells under a constant flow of growth medium for more than 2 h. Confocal microscopy was performed as previously described (Albert et al, 2013). Electron microscopy was performed as previously described (Albert et al, 2011).…”

Section: Methodsmentioning

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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Systematic characterization of the conformation and dynamics of budding yeast chromosome XII

Abstract: Comprehensive analysis of the intranuclear territories and motion of budding yeast chromosome XII loci suggests that long-range chromosome architecture is mainly determined by the physical principles of polymers.

Cited by 50 publications

References 48 publications

Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations

Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations

High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome

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

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