Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
Biophys J
2023 Oct 03;12219:3869-3881. doi: 10.1016/j.bpj.2023.08.006.
Show Gene links
Show Anatomy links
Elasticity control of entangled chromosomes: Crosstalk between condensin complexes and nucleosomes.
Yamamoto T
,
Kinoshita K
,
Hirano T
.
???displayArticle.abstract???
Condensin-mediated loop extrusion is now considered as 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 chromosome-like structures in Xenopus egg extracts, although these structures are somewhat different from those assembled by wild-type condensin complexes. In the absence of topoisomerase II (topo II), the mutant condensin complexes produce an unusual round-shaped structure termed a bean, which consists 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. We consider that this peculiar structure serves as a model system to study how DNA entanglements, nucleosomes, and condensin functionally crosstalk with each other. To gain insight into how the bean structure is formed, here we construct a theoretical model. Our theory predicts that the core is formed by attractive interactions between mutant condensin complexes, whereas the halo is stabilized by the energy reduction through 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 suppress the assembly of nucleosomes.
Alipour,
Self-organization of domain structures by DNA-loop-extruding enzymes.
2012, Pubmed
Alipour,
Self-organization of domain structures by DNA-loop-extruding enzymes.
2012,
Pubmed
Blossey,
The dynamics of the nucleosome: thermal effects, external forces and ATP.
2011,
Pubmed
Bracha,
Entropy-driven collective interactions in DNA brushes on a biochip.
2013,
Pubmed
Brackley,
Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization.
2013,
Pubmed
Brackley,
Ephemeral Protein Binding to DNA Shapes Stable Nuclear Bodies and Chromatin Domains.
2017,
Pubmed
Bruinsma,
Chromatin hydrodynamics.
2014,
Pubmed
Choppakatla,
Linker histone H1.8 inhibits chromatin binding of condensins and DNA topoisomerase II to tune chromosome length and individualization.
2021,
Pubmed
,
Xenbase
Clemson,
An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles.
2009,
Pubmed
Ganji,
Real-time imaging of DNA loop extrusion by condensin.
2018,
Pubmed
Goloborodko,
Chromosome Compaction by Active Loop Extrusion.
2016,
Pubmed
Goloborodko,
Compaction and segregation of sister chromatids via active loop extrusion.
2016,
Pubmed
Hassler,
Structural Basis of an Asymmetric Condensin ATPase Cycle.
2019,
Pubmed
Hirano,
Condensin-Based Chromosome Organization from Bacteria to Vertebrates.
2016,
Pubmed
Joseph,
Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos.
2017,
Pubmed
Kimura,
ATP-dependent positive supercoiling of DNA by 13S condensin: a biochemical implication for chromosome condensation.
1997,
Pubmed
,
Xenbase
Kinoshita,
Balancing acts of two HEAT subunits of condensin I support dynamic assembly of chromosome axes.
2015,
Pubmed
,
Xenbase
Kinoshita,
A loop extrusion-independent mechanism contributes to condensin I-mediated chromosome shaping.
2022,
Pubmed
,
Xenbase
Kong,
Human Condensin I and II Drive Extensive ATP-Dependent Compaction of Nucleosome-Bound DNA.
2020,
Pubmed
Lee,
Cryo-EM structures of holo condensin reveal a subunit flip-flop mechanism.
2020,
Pubmed
Leidescher,
Spatial organization of transcribed eukaryotic genes.
2022,
Pubmed
Naumova,
Organization of the mitotic chromosome.
2013,
Pubmed
Pommier,
Roles of eukaryotic topoisomerases in transcription, replication and genomic stability.
2016,
Pubmed
Rosa,
Structure and dynamics of interphase chromosomes.
2008,
Pubmed
Ryu,
Bridging-induced phase separation induced by cohesin SMC protein complexes.
2021,
Pubmed
Sakai,
Modeling the functions of condensin in chromosome shaping and segregation.
2018,
Pubmed
Sasaki,
MENepsilon/beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles.
2009,
Pubmed
Sekimoto,
Temperature hysteresis and morphology of volume phase transition of gels.
1993,
Pubmed
Shintomi,
Reconstitution of mitotic chromatids with a minimum set of purified factors.
2015,
Pubmed
,
Xenbase
Shintomi,
Mitotic chromosome assembly despite nucleosome depletion in Xenopus egg extracts.
2017,
Pubmed
,
Xenbase
Shintomi,
Guiding functions of the C-terminal domain of topoisomerase IIα advance mitotic chromosome assembly.
2021,
Pubmed
,
Xenbase
Socol,
Rouse model with transient intramolecular contacts on a timescale of seconds recapitulates folding and fluctuation of yeast chromosomes.
2019,
Pubmed
Sunwoo,
MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles.
2009,
Pubmed
Terakawa,
The condensin complex is a mechanochemical motor that translocates along DNA.
2017,
Pubmed
Uneyama,
Multi-chain slip-spring model for entangled polymer dynamics.
2012,
Pubmed
Wang,
Achieving Molecular Fluorescent Conversion from Aggregation-Caused Quenching to Aggregation-Induced Emission by Positional Isomerization.
2021,
Pubmed
Yamamoto,
Loop extrusion driven volume phase transition of entangled chromosomes.
2022,
Pubmed
Yamamoto,
Triblock copolymer micelle model of spherical paraspeckles.
2022,
Pubmed
Yamamoto,
Transcription Driven Phase Separation in Chromatin Brush.
2016,
Pubmed
Yamamoto,
Transcription dynamics stabilizes nucleus-like layer structure in chromatin brush.
2017,
Pubmed
Yamazaki,
Functional Domains of NEAT1 Architectural lncRNA Induce Paraspeckle Assembly through Phase Separation.
2018,
Pubmed
Yamazaki,
Paraspeckles are constructed as block copolymer micelles.
2021,
Pubmed