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

Yamamoto, T.; Kinoshita, Kazuhisa; Hirano, Takeshi

doi:10.1016/j.bpj.2023.08.006

Cited by 3 publications

(3 citation statements)

References 60 publications

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“…It is mainly because of the fact that diffusion length l d decreases or the brush height increases with increasing the polymerization rate k p0 and the condensation of polymers due to the slow polymer dynamics plays only a minor role, see eqs. ( 31) and (32).…”

Section: Discussionmentioning

confidence: 99%

“…In our recent theory, we have predicted that the DFCs at the interface between FCs and GC are polymer brushes of nascent pre-rRNAs that are swollen to accommodate RBPs in the brush [6]. There are analogous systems with DNA − DNA brushes with DNA-binding proteins, such as histones [26,27], transcription factors [28], and Structural Maintenance of Chromosome proteins [29][30][31][32]. Second, nascent pre-rRNAs are end-grafted to the surface via Pol Is that add nucleoside triphosphates (which are monomers of RNAs) to the nascent pre-rRNAs.…”

Section: Introductionmentioning

confidence: 99%

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Polymer brush inspired by ribosomal RNA transcription

Yamamoto

2023

Eur. Phys. J. E

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Pre-ribosomal RNAs are synthesized during the transcription by RNA polymerase I molecules localized at the surfaces of a nucleolus subcompartment. Inspired by the ribosomal RNA transcription, we here develop a scaling theory of a brush of polymers, where monomers are added to their grafted ends in the steady state. Our theory predicts that monomers newly added to the polymers stay at the vicinity of the surface due to the slow dynamics of the polymers and thus the polymer volume fraction increases with increasing the polymerization rate. The excluded volume interaction between polymers and reactant monomers suppresses the diffusion of reactant monomers and thus decreases the polymerization rate. The extent of the suppression of monomer diffusion increases with increasing the polymerization rate because the diffusion length decreases, rather than the condensation of polymers due to their slow dynamics.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Polymer brush inspired by ribosomal RNA transcription

Yamamoto

2023

Eur. Phys. J. E

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“…Collectively, these chromatin modifications influence its physical attributes, such as compaction and stiffness. Additionally, chromosomal loci can be physically constrained via tethering to external non-chromatin structures such as spindle microtubules, the nuclear lamina in interphase, matrix attachment regions (MARs), and scaffold attachment regions (SARs), or via internal tethering at the base of chromatin loops or by regions of entanglement [1][2][3][4][5]. Involved in a diversity of biological functions, tethering can be permanent and firm, as with the attachments at telomeres and centromeres in yeast [6][7][8][9][10][11].…”

Section: Introductionmentioning

confidence: 99%

Polymer Modeling Reveals Interplay between Physical Properties of Chromosomal DNA and the Size and Distribution of Condensin-Based Chromatin Loops

Kolbin,

Walker,

Hult

et al. 2023

Genes

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Transient DNA loops occur throughout the genome due to thermal fluctuations of DNA and the function of SMC complex proteins such as condensin and cohesin. Transient crosslinking within and between chromosomes and loop extrusion by SMCs have profound effects on high-order chromatin organization and exhibit specificity in cell type, cell cycle stage, and cellular environment. SMC complexes anchor one end to DNA with the other extending some distance and retracting to form a loop. How cells regulate loop sizes and how loops distribute along chromatin are emerging questions. To understand loop size regulation, we employed bead–spring polymer chain models of chromatin and the activity of an SMC complex on chromatin. Our study shows that (1) the stiffness of the chromatin polymer chain, (2) the tensile stiffness of chromatin crosslinking complexes such as condensin, and (3) the strength of the internal or external tethering of chromatin chains cooperatively dictate the loop size distribution and compaction volume of induced chromatin domains. When strong DNA tethers are invoked, loop size distributions are tuned by condensin stiffness. When DNA tethers are released, loop size distributions are tuned by chromatin stiffness. In this three-way interaction, the presence and strength of tethering unexpectedly dictates chromatin conformation within a topological domain.

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Regulation of condensin II by self-suppression and release mechanisms

Yoshida,

Kinoshita,

Shintomi

et al. 2024

MBoC

Self Cite

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In vertebrates, two distinct condensin complexes, condensin I and condensin II, cooperate to drive mitotic chromosome assembly. It remains largely unknown how the two complexes differentially contribute to this process at a mechanistic level. We have previously dissected the role of individual subunits of condensin II by introducing recombinant complexes into Xenopus egg extracts. Here we extend these efforts by introducing a modified functional assay using extracts depleted of topoisomerase IIα (topo IIα), which allows us to further elucidate the functional similarities and differences between condensin I and condensin II. The intrinsically disordered C-terminal region of the CAP-D3 subunit (the D3 C-tail) is a major target of Cdk1 phosphorylation, and phosphorylation-deficient mutations in this region impair condensin II functions. We also identify a unique helical structure in CAP-D3 (the D3 HEAT docker) that is predicted to directly interact with CAP-G2. Deletion of the D3 HEAT docker, along with the D3 C-tail, enhances the ability of condensin II to assemble mitotic chromosomes. Taken together, we propose a self-suppression mechanism unique to condensin II that is released by mitotic phosphorylation. Evolutionary implications of our findings are also discussed.

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

Cited by 3 publications

References 60 publications

Polymer brush inspired by ribosomal RNA transcription

Polymer brush inspired by ribosomal RNA transcription

Polymer Modeling Reveals Interplay between Physical Properties of Chromosomal DNA and the Size and Distribution of Condensin-Based Chromatin Loops

Regulation of condensin II by self-suppression and release mechanisms

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