Ranjith Padinhateeri

During meiosis, the exchange of genetic material (“recombination”) is essential to bring about genetic variation in offspring. To carry out the recombination, homologous pairs of DNA have to come into proximity and align, which is inherently a polymer dynamics problem. In fission yeast, this is accomplished by the extensive nuclear oscillation that applies a pulling force on the chromosome polymers. In this work, we investigate the competition between the pulling force that tries to facilitate the alignment and the intra-chromatin interactions that assist the chromatin folding. The crucial role played by the intra-chromatin interaction for a range of pulling forces and loci locations is highlighted here. Upon comparing our results with the experimental findings, we not only reaffirm the enhancement of contact probability with loci-dependent pulling but also get a meaningful interpretation of the chromosome unfolding and pairing at different stages of movement.

Chromatin is an actively remodeled polymeric system whose organization emerges from the interplay of equilibrium interactions and ATP-dependent processes. Recent in vitro experiments show that nucleosome spacing and ATP-dependent remodeler activity significantly influence chromatin condensate properties. Here, guided by these observations, we develop a hierarchy of coarse-grained models that systematically dissect the roles of nucleosome spacing, remodeler-mediated binding-unbinding kinetics, and active force generation in governing condensate dynamics. We demonstrate that nucleosome spacing heterogeneity is a key determinant of condensate material properties. Condensates formed from regularly spaced fibers exhibit enhanced internal mixing, whereas those assembled from disordered spacing develop pronounced structural correlations, increased entanglement, and suppressed internal dynamics. Incorporating remodeler-like binding-unbinding nonequilibrium kinetics drives local structural reorganization, leading to condensate swelling and a substantial acceleration of internal relaxation. In condensates of heterogeneous fibers, contrasts in spacing and activity robustly drive spatial segregation, giving rise to stable core-shell architectures. Strikingly, when dipolar forces are coupled to hydrodynamic interactions, serving as a minimal representation of active nucleosome translocation, condensates exhibit enhanced center-of-mass motion. Together, our results establish a predictive coarse-grained framework that quantitatively links structural heterogeneity and active processes to emergent chromatin-like condensate organization, mechanics, and transport.

The nature of the chromatin polymer and its properties are tightly coupled to its function. By analyzing recent microscopy data, we show that chromatin segments at ∼ 10–100 kb scales exhibit anomalously broad bond-length fluctuations and acute local angles beyond the scope of existing polymer models. Using polymer simulations at nucleosome resolution and systematic coarse-graining, we show that chromatin at these scales requires a non-equilibrium description. We develop a data-constrained non-equilibrium model that explains these anomalous fluctuations, in which coarse-grained beads experience extensile, angular, and stochastic active forces. Our work provides an experimentally guided framework for incorporating active processes and suggests that the nature of activity is scale-dependent. The model quantitatively reproduces three-dimensional distance distributions across scales and enables inference of effective elastic and active parameters, providing a unified framework for active chromatin simulations and the study of its 3D organization.

Chromosomal translocations, arising from unresolved double-stranded DNA breaks (DSBs), play a central role in genome instability and evolution. A prevailing hypothesis suggests that the probability of translocation between two chromatin segments depends on both their spatial proximity and the likelihood of DSB formation and rejoining. To test this, we perform Monte Carlo simulations of chromatin model polymers with varying levels of compaction and three-dimensional organization. Our results reveal that translocation probability cannot be fully explained by simple two-segment contact probabilities. Instead, it is strongly modulated by the global polymer compaction, which increases the incidence of multisegment contacts and introduces higher-order contributions. We further demonstrate that translocation probability exhibits a nontrivial functional dependence on both contact probability and DSB probability. We propose an empirical formula to compute translocation probability and provide analytical arguments for simple cases. Together, our findings highlight the critical role of chromatin organization in shaping the landscape of genome rearrangements and provide a framework to quantitatively predict translocation events from underlying polymer features and breakage statistics.

Protein molecules must efficiently locate specific DNA sequences within the densely packed chromatin of the cell nucleus. We investigate how the spatial organisation of chromatin, specifically its organisation into Topologically Associating Domains (TADs), fundamentally affects this search process. Using exact analytical theory and simulations of different models of chromatin, we show that target search within compact, highly connected chromatin domains can leverage intersegmental jumps to significantly decrease search times. Further, we establish that there exists an optimal degree of polymer compaction that minimizes the search time for proteins to find their targets. For highly folded domains, our results suggest that rather than bulk diffusion, intersegmental transfers – jumping between chromatin segments that are close together in space – drive the optimal search process. Remarkably, when we analyse 8,355 TAD structures across the human genome, we find that their natural connectivity matches with the theoretical optimum predicted by our model. The structural organisation within TADs significantly reduces protein search times far beyond what is achievable through classical facilitated diffusion. In essence, our work suggests that packaging of chromatin inside the nucleus has implications beyond spatial organisation, and is also intricately linked to the dynamics of proteins inside the nuclear environment.

Fungal centromeres are clustered near microtubule organizing centers to help adopt the Rabl chromosomal organization. The role of centromere clustering in driving large-scale changes in structural and functional chromatin assembly remains unclear. Here, using Hi-C and superresolution microscopy, we show that cell cycle-dependent centromere declustering and clustering states in Cryptococcus neoformans drive global changes in the 3D genome architecture. Centromeres and telomeres are scattered around the nuclear periphery at interphase ^G1 , and this arrangement constrains the interarm interactions within a chromosome, providing a unique interphase ^G1 chromosome organization. Moreover, centromeres and telomeres are organized as separate compartments, segregating them from active euchromatic regions. Polymer modeling reveals that the transition from the unclustered to clustered centromere state during the cell cycle involves changes from a globular to an elongated chromosome architecture. Strikingly, while clustered centromeric regions replicate early in most yeasts, C. neoformans centromeres replicate late in S-phase, hinting at a possible link between centromere clustering dynamics and CEN DNA replication timing. Overall, our study uncovers several unique organizational principles governing the dynamic genome architecture in an evolutionarily diverged basidiomycete yeast.

How the 3D organization of chromatin affects gene translocation is an open question. By Monte Carlo simulation of translocation events in folded chromatin, we examine how the probability of translocation ( T _ij ) is influenced by chromatin compaction and the occurrence of double-stranded DNA breaks (DSBs). Our results show that, beyond the two-segment contact probability, T _ij depends on the overall compaction of the polymer and has a non-trivial contribution from multi-bead contacts and the probability of DSBs. We propose an empirical formula and provide analytical arguments for simple cases.

Fungal centromeres are clustered near microtubule organizing centers to help adopt the Rabl chromosomal organization. The role of centromere clustering in driving large-scale changes in structural and functional chromatin assembly remains unclear. Here, using Hi-C and super-resolution microscopy, we show that cell cycle-dependent centromere declustering and clustering states in Cryptococcus neoformans drive global changes in the 3D genome architecture. Centromeres and telomeres are scattered around the nuclear periphery at interphase ^G1 , and this arrangement constrains the inter-arm interactions within a chromosome, providing a unique interphase ^G1 chromosome organization. Moreover, centromeres and telomeres are organized as compartments, segregating them from active euchromatic regions. Polymer modeling reveals that the transition from the unclustered to clustered centromere state during the cell cycle involves changes from a globular to an elongated chromosome architecture. Strikingly, while clustered centromeres replicate early in most yeasts, C. neoformans centromeres replicate late in S-phase, hinting a possible link between centromere clustering dynamics and CEN DNA replication timing. Overall, our study uncovers several unique organizational principles governing the dynamic genome architecture in an evolutionarily diverged basidiomycete yeast.