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

Abstract

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.

Polymer brush inspired by ribosomal RNA transcription

“…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).…”

“…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.…”

Regulation of condensin II by self-suppression and release mechanisms

“…In another study, a modified assay was established to address the function of recombinant condensin I in egg extracts depleted of endogenous topoisomerase IIα (topo IIα; Kinoshita et al. , 2022 ; Yamamoto et al. , 2023 ).…”