Loop extrusion driven volume phase transition of entangled chromosomes

Yamamoto, T.; Schiessel, Helmut

doi:10.1016/j.bpj.2022.06.014

Cited by 5 publications

(3 citation statements)

References 47 publications

(46 reference statements)

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“…To extend our theory to the mechanism of mitotic chromosome assembly, it is necessary to consider the loop extrusion activity of condensin complexes and the strand-passing activity of topo II. If condensin complexes localized to the core start to extrude loops, they will generate tension of the DNAs entangled in the core so that the DNAs in the halo are reeled into the core (Yamamoto and Schiessel, 2022). The magnitude of the interaction between wild-type condensin complexes may be smaller than the magnitude of the interaction between mutant condensin complexes because CAP-G subunits counteract with CAP-D2 subunits (Kinoshita et al, 2015).…”

Section: Discussionmentioning

confidence: 99%

“…The formation of nucleosomal loops in the halo stiffens the entangled DNA network because they reel DNAs out of the core and decrease the number of DNA units in the elastically effective part of entangled DNA in the core. Recently, a similar concept was used to theoretically predict the contribution of the loop extrusion process to the selfassembly of entangled bare DNAs (Yamamoto and Schiessel, 2022). The electrostatic aspect of the nucleosome assembly, such as the charge inversion (Park et al, 1999, Nguyen andShklovskii, 2001), is a classical subject of soft matter physics.…”

Section: Introductionmentioning

confidence: 99%

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Elasticity control of entangled chromosomes: Crosstalk between condensin complexes and nucleosomes

Yamamoto

Kinoshita

Hirano

2023

Biophysical Journal

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Elasticity control of entangled chromosomes: Crosstalk between condensin complexes and nucleosomes

Yamamoto

Kinoshita

Hirano

2023

Biophysical Journal

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“…The formation of nucleosomal loops in the halo stiffens the entangled DNA network because they reel DNAs out of the core and decrease the number of DNA units in the elastically effective part of entangled DNA in the core. Recently, a similar concept was used to theoretically predict the contribution of the loop extrusion process to the self-assembly of entangled bare DNAs (Yamamoto and Schiessel, 2022). The electrostatic aspect of the nucleosome assembly, such as the charge inversion (Park et al, 1999, Nguyen and Shklovskii, 2001), is a classical subject of soft matter physics.…”

Section: Introductionmentioning

confidence: 99%

Elasticity control of entangled chromosomes: crosstalk between condensin complexes and nucleosomes

Yamamoto

Kinoshita

Hirano

2022

Preprint

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Condensin-mediated loop extrusion is now considered the main driving force of mitotic chromosome assembly. Recent experiments have shown, however, that a class of mutant condensin complexes deficient in loop extrusion can assemble abnormal chromosome-like structures in Xenopus egg extracts. In the absence of topoisomerase II (topo II), the mutant condensin complexes produce an unusual round-shaped structure termed a `bean', which is composed of a DNA-dense central core surrounded by a DNA-sparse halo. The mutant condensin complexes accumulate in the core whereas histones are more concentrated in the halo than in the core. To get insights into how the bean structure is formed, here we construct a theoretical model. Our theory predicts that the core is produced by the attractive interactions between mutant condensin complexes whereas the halo is stabilized by the energy reduction by the selective accumulation of nucleosomes. The formation of the halo increases the elastic free energy due to the DNA entanglement in the core, but the latter free energy is compensated by condensin complexes that protect DNAs from nucleosome assembly. Understanding this peculiar structure is likely to enrich our understanding of how DNA entanglements, nucleosomes, and condensin functionally cross-talk with each other.

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Molecular dynamics simulations of nucleosomes are coming of age

Fedulova,

Armeev,

Romanova

et al. 2024

WIREs Comput Mol Sci

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Understanding the function of eukaryotic genomes, including the human genome, is undoubtedly one of the major scientific challenges of the 21st century. The cornerstone of eukaryotic genome organization is nucleosomes—elementary building blocks of chromatin about 10 nm in size that wrap DNA around an octamer of histone proteins. Nucleosomes are integral players in all genomic processes, including transcription, DNA replication and repair. They mediate genome regulation at the epigenetic level, bridging the discrete nature of the genetic information encoded in DNA with the analog physical nature of the intermolecular interactions required to access that information. Due to their relatively large size and dynamic nature, nucleosomes are difficult objects for experimental characterization. Molecular dynamics (MD) simulations have emerged over the years as a useful tool to complement experimental studies. Particularly in recent years, advances in computing power, refinement of MD force fields and codes have opened up new frontiers in terms of simulation timescales and quality for nucleosomes and related systems. It has become possible to elucidate in atomistic detail their functional dynamics modes such as DNA unwrapping and sliding, to characterize the effects of epigenetic modifications, DNA and protein sequence variation on nucleosome structure and stability, to describe the mechanisms governing nucleosome interactions with chromatin‐associated proteins and the formation of supranucleosome structures. In this review, we systematically analyzed all‐atom MD simulation studies of nucleosomes and related structures published since 2018 and discussed their relevance in the context of older studies, experimental data, and related coarse‐grained and multiscale studies.This article is categorized under: Software > Molecular Modeling Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods Structure and Mechanism > Computational Biochemistry and Biophysics

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Loop extrusion driven volume phase transition of entangled chromosomes

Cited by 5 publications

References 47 publications

Elasticity control of entangled chromosomes: Crosstalk between condensin complexes and nucleosomes

Elasticity control of entangled chromosomes: Crosstalk between condensin complexes and nucleosomes

Elasticity control of entangled chromosomes: crosstalk between condensin complexes and nucleosomes

Molecular dynamics simulations of nucleosomes are coming of age

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