Biology subjects

Harju, J.

Publications and source records attributed to Harju, J..

5 recordsLinked to original sources

bioRxiv2024

Loop-extruder mediated rigidity can globally order bacterial chromosomes

Many bacterial chromosomes show large-scale linear order, so that a locuss genomic position correlates with its position along the cell. In the model organism E. coli, for instance, the left and right arms of the circular chromosome lie in different cell halves. However, no mechanisms that anchor loci to the cell poles have been identified, and it remains unknown how this so-called "left-ori-right" organization arises. Here, we construct a biophysical model that explains how global chromosome order could be established via an active loop extrusion mechanism. Our model assumes that the motor protein complex MukBEF extrudes loops on most of the E. coli chromosome, but is excluded from the terminal region by the protein MatP, giving rise to a partially looped ring polymer structure. Using 3D simulations of loop extrusion on a chromosome, we find that our model can display stable left-ori-right chromosomal order in a parameter regime consistent with prior experiments. We explain this behavior by considering the effect of loop extrusion on the bending rigidity of the chromosome, and derive necessary conditions for left-ori-right order to emerge. Finally, we develop a phase diagram for the system, where order emerges when the loop size is large enough and the looped region is compacted enough. Our work provides a mechanistic explanation for how loop-extruders can establish linear chromosome order in E. coli, and how this order leads to accurate gene positioning within the cell, without locus anchoring.

biophysics↗

bioRxiv2024

Resolving interface structure and local internal mechanics of mitotic chromosomes

The interface of chromosomes enables them to interact with the cell environment and is crucial for their mechanical stability during mitosis. Here, we use Atomic Force Microscopy (AFM) to probe the interface and local micromechanics of the highly condensed and complex chromatin network of native human mitotic chromosomes. Our AFM images provide detailed snapshots of chromatin loops and Sister-Chromatids Intertwines. A scaling analysis of these images reveals that the chromatin surface has fractal nature. AFM-based Force Spectroscopy and microrheology further show that chromosomes can resist severe deformations, elastically recovering their initial shape following two characteristic timescales. Localized indentations over the chromatids reveal that the spatially varying micromechanics of the chromatin network is largely governed by chromatin density. Together, our AFM investigation provides new insights into the structure and local mechanics of mitotic chromosomes, offering a toolbox for further characterization of complex biological structures, such as chromosomes, down to the nanoscale.

biophysics↗

bioRxiv2023

Loop-extruders alter bacterial chromosome topology to direct entropic forces for segregation

Entropic forces have been argued to drive bacterial chromosome segregation during replication. In many bacterial species, how-ever, specifically evolved mechanisms, such as loop-extruding SMC complexes and the ParABS origin segregation system, contribute to or are even required for chromosome segregation, suggesting that entropic forces alone may be insufficient. The interplay between and the relative contributions of these segregation mechanisms remain unclear. Here, we develop a biophysical model showing that purely entropic forces actually inhibit bacterial chromosome segregation until late replication stages. By contrast, our model reveals that loop-extruders loaded at the origins of replication, as observed in many bacterial species, alter the effective topology of the chromosome, thereby redirecting and enhancing entropic forces to enable accurate chromosome segregation during replication. We confirm our model predictions with polymer simulations: purely entropic forces do not allow for concurrent replication and segregation, whereas entropic forces steered by specifically loaded loop-extruders lead to robust, global chromosome segregation during replication. Finally, we show how loop-extruders can complement locally acting origin separation mechanisms, such as the ParABS system. Together, our results illustrate how changes in the geometry and topology of the polymer, induced by DNA-replication and loop-extrusion, impact the organization and segregation of bacterial chromosomes.

biophysics↗

bioRxiv2023

Ion-mediated condensation controls the mechanics of mitotic chromosomes

During mitosis in eukaryotic cells, mechanical forces generated by the mitotic spindle pull the sister chromatids into the nascent daughter cells. How do mitotic chromosomes achieve the necessary mechanical stiffness and stability to maintain their integrity under these forces? Here, we use optical tweezers to show that ions involved in physiological chromosome condensation are crucial for chromosomal stability, stiffness and viscous dissipation. We combine these experiments with high-salt histone-depletion and theory to show that chromosomal elasticity originates from the chromatin fiber behaving as a flexible polymer, whereas energy dissipation can be explained by interactions between chromatin loops. Taken together, we show how collective properties of mitotic chromosomes, a biomaterial of incredible complexity, emerge from molecular properties, and how they are controlled by the physico-chemical environment.

biophysics↗

bioRxiv2022

Multi-contact statistics distinguish models of chromosome organization

Chromosome organization in both eukaryotes and prokaryotes is highly regulated. Organizing mechanisms, such as loop-extrusion, have been extensively studied using Hi-C methods, which measure pairwise contacts between chromosomal regions. New multi-contact methods additionally measure which chromosomal contacts occur simultaneously. Here, we develop three predictors of baseline multi-contact frequencies given pairwise contact data, corresponding to distinct physical limits, and argue that a comparison between data and prediction can lead to biological insight. We test these predictors for two simulated polymer models with cross-linking or loop-extrusion, and find that simulated three-point contacts are only predicted by the physically appropriate approximation. Finally, we apply our approach to previously published experimental multi-contact data from human chromosomes. Strikingly, we discover that observed three-point contact frequencies are well predicted by a formula based on loop-extrusion, suggesting that multi-contact data can give insight into chromosome organization mechanisms.

biophysics↗