Biology subjects

Harju, J.

Publications and source records attributed to Harju, J..

8 recordsLinked to original sources

bioRxiv2026

Counting to two: how phages decide between lysis and lysogeny

Upon infecting a bacterium, temperate phages must decide between killing the cell to reproduce (lysis) and entering a symbiotic lifestyle (lysogeny). This choice is often informed by the cells state and by the number of infecting phage particles, or multiplicity of infection (MOI). Because the copy numbers of all phage genes scale identically with MOI, an MOI-dependent decision requires a rapidly established asymmetry between the lytic and lysogenic pathways. We introduce a minimal model showing how a simple coupling to host machinery (e.g. a protease) can generate such an asymmetry. Our analytical model yields scaling laws that predict how the lysislysogeny decision responds to perturbations of the host. It also quantitatively predicts stochastic features of infection outcomes, such as lysogeny probabilities, consistent with experimental data. By reducing complex regulatory networks to their essential components, our framework reveals the organizing principles of lysislysogeny decisions across phage species.

biophysics↗

bioRxiv2026

Spatially correlated fluctuations govern relative chromatin motion

Essential nuclear processes require pairs of chromosomal loci to find each other in three-dimensional space. Polymer models of chromosome dynamics typically assume that the stochastic forces driving such locus motion are spatially uncorrelated, implying that relative diffusion follows directly from single-locus dynamics. Here we show that this assumption fails in living cells. Using live-cell imaging in fly embryos and mouse embryonic stem cells, we find that pairwise locus distances diffuse markedly slower than predicted for independent fluctuations. Combining stochastic trajectory analysis with polymer simulations, we demonstrate that this slowdown arises from non-equilibrium spatially correlated fluctuations (SCFs) in the nucleoplasm, which cause nearby loci to move coherently. We establish three experimentally testable signatures of SCFs: fluctuation amplitudes plateau at large distances, are independent of genomic separation, and show an anomalous temporal scaling. All three predictions are confirmed experimentally, including for loci on separate chromosomes. ATP depletion and disruption of cohesin-mediated loop extrusion reveal that both active processes and crosslinking contribute to correlation magnitudes. Because SCFs slow relative motion preferentially at short distances, they reduce encounter frequencies while prolonging encounter durations, generating a trade-off with direct implications for gene regulation. Our results identify spatially correlated fluctuations as a fundamental determinant of relative motion in confined active polymers.

biophysics↗

bioRxiv2025

Learning the dynamic organization of a replicating bacterial chromosome from time-course Hi-C data

Bacterial chromosomes are in continual motion as they undergo concurrent transcription, replication, and segregation. Time-course Hi-C experiments hold promise for studying chromosome organization across the cell cycle, but interpreting Hi-C data from dynamic systems remains challenging. Here, we develop a fully data-driven 4D Maximum Entropy approach to extract a model for the dynamic organization of a replicating bacterial chromosome directly from time-course Hi-C and microscopy data. After validating our 4D data-driven model for Caulobacter crescentus against independent microscopy data, we infer quantitative information about changes in chromosome organization across the bacterial replication cycle. Our model reveals a sustained global linear organization of the C. crescentus chromosome during replication, as well as dynamic patterns of local chromosome extension induced by the replication forks. We use these data-driven inferences to constrain a mechanistic model for a replicating bacterial chromosome. Our model demonstrates that origin-pulling by a ParABS -like system, together with loop extrusion by condensin, can explain our inferred large-scale chromosome segregation patterns. The inferred replication-induced local changes in chromosome compaction, however, require additional mechanisms, which we attribute to replication-induced NAP unbinding and positive supercoiling. Overall, our work introduces a rigorous data-driven framework for quantitatively interpreting time-course Hi-C data, and offers new mechanistic insights into bacterial chromosome organization across the cell cycle.

biophysics↗

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↗