Author response: A simple biophysical model emulates budding yeast chromosome condensation

Cheng, Tammy M.K.; Heeger, Sebastian; Chaleil, Raphaël A. G.; Matthews, Nik; Stewart, Aengus; Wright, Jon D.; Lim, Carmay; Bates, Paul A.; Uhlmann, Frank

doi:10.7554/elife.05565.017

Cited by 2 publications

(1 citation statement)

References 41 publications

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“…By analogy, coalescin molecules on distant loci may form a dimer or dimer of dimer complexes to bring the loci into proximity. However, it is also possible that coalescin serves as a DNA crosslinker independently of the zinc hook, as has been proposed for SMC complexes without a zinc hook (Cheng et al, 2015;Vickridge et al, 2017). Indeed, it is notable that the Gruber lab successfully replaced the globular hinge domain of a bacterial condensin with a zinc hook domain derived from an archaeal Rad50 with no discernible impact on the growth of Bacillus subtilis (Burmann et al, 2017).…”

Section: Molecular Players Sculpting the Higher-order Organization Ofmentioning

confidence: 99%

Emerging views of genome organization in Archaea

Takemata

Bell

2020

Journal of Cell Science

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Over the past decade, advances in methodologies for the determination of chromosome conformation have provided remarkable insight into the local and higher-order organization of bacterial and eukaryotic chromosomes. Locally folded domains are found in both bacterial and eukaryotic genomes, although they vary in size. Importantly, genomes of metazoans also possess higherorder organization into A-and B-type compartments, regions of transcriptionally active and inactive chromatin, respectively. Until recently, nothing was known about the organization of genomes of organisms in the third domain of lifethe archaea. However, despite archaea possessing simple circular genomes that are morphologically reminiscent of those seen in many bacteria, a recent study of archaea of the genus Sulfolobus has revealed that it organizes its genome into large-scale domains. These domains further interact to form defined A-and B-type compartments. The interplay of transcription and localization of a novel structural maintenance of chromosomes (SMC) superfamily protein, termed coalescin, defines compartment identity. In this Review, we discuss the mechanistic and evolutionary implications of these findings.

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Section: Molecular Players Sculpting the Higher-order Organization Ofmentioning

confidence: 99%

Emerging views of genome organization in Archaea

Takemata

Bell

2020

Journal of Cell Science

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In vivo, chromatin is a fluctuating polymer chain at equilibrium constrained by internal friction

Socol

Wang

Jost

et al. 2017

Preprint

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Chromosome mechanical properties determine DNA folding and dynamics, and underlie all major nuclear functions. Here we combine modeling and real-time motion tracking experiments to infer the physical parameters describing chromatin fibers. In vitro, motion of nucleosome arrays can be accurately modeled by assuming a Kuhn length of 35-55 nm. In vivo, the amplitude of chromosome fluctuations is drastically reduced, and depends on transcription. Transcription activation increases chromatin dynamics only if it involves gene relocalization, while global transcriptional inhibition augments the fluctuations, yet without relocalization. Chromatin fiber motion is accounted for by a model of equilibrium fluctuations of a polymer chain, in which random contacts along the chromosome contour induce an excess of internal friction. Simulations that reproduce chromosome conformation capture and imaging data corroborate this hypothesis. This model unravels the transient nature of chromosome contacts, characterized by a life time of ~2 seconds and a free energy of formation of ~1 k B T.. CC-BY 4.0 International license not peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was . http://dx.doi.org/10.1101/192765 doi: bioRxiv preprint first posted online Sep. 24, 2017; Physics of chromosome folding drives and responds to all genomic transactions. In cycling budding yeast cells, large-scale organization of chromosomes in a Rabl-like conformation has been established by imaging and molecular biology approaches (1-4). Yet, the structure of the chromatin fiber at smaller length scales remains more controversial (5). For instance, the recurrent detection of irregular 10-nm fibers by cryo-TEM of thin nuclear sections is questioning the relevance of solenoid or helicoid models of nucleosome arrays (6)(7)(8). This problem has not been clarified by probing the motion of chromosomes in vivo, although dynamic measurements offer a unique opportunity to infer structural properties of genome organization (9). Indeed, we and others have shown that chromosome dynamics in yeast is characterized by sub-diffusive behavior detected by a non-linear temporal variation of the mean square displacement (MSD) of chromosome loci (10-16):( ) = Γwith , , and t the anomaly exponent, amplitude, and time interval, respectively. A subdiffusive response was detected over a broad temporal time scale covering four time decades with an anomaly exponent in the range 0.4-0.6. This response appeared to be consistent with the Rouse model, a generic polymer model that describes chromosomes as a series of beads connected by elastic springs. The length of the springs is related to the mechanical properties of chromatin fiber, namely equal to twice its persistence length (hereafter denoted as the Kuhn length b). The link between the flexibility and the amplitude of the MSD (17) suggested that chromosomes are highly flexible in yeast with b of 1-5 nm (10). Inconsistent with structural and mechanical mode...

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Author response: A simple biophysical model emulates budding yeast chromosome condensation

Cited by 2 publications

References 41 publications

Emerging views of genome organization in Archaea

Emerging views of genome organization in Archaea

In vivo, chromatin is a fluctuating polymer chain at equilibrium constrained by internal friction

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