Biology subjects

Padinhateeri, R.

Publications and source records attributed to Padinhateeri, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Active Nucleosome Sliding, Eviction, and Reassembly Dynamics Can Regulate Chromatin Condensate Organization

At the nucleosome scale, chromatin is an actively remodeled polymeric system whose organization is continuously reshaped by ATP-dependent remodelers that slide, evict, and reassemble nucleosomes along DNA. However, how the local structural rearrangements generated by such remodeling events influence condensate-scale organization and dynamics remains poorly understood. Here, we introduce a coarse-grained model of chromatin condensates composed of short polymers that explicitly incorporates enzyme-assisted nucleosome sliding together with nucleosome eviction and reassembly, coupled to Langevin relaxation dynamics. By explicitly accounting for the DNA length sequestered within individual nucleosomes, the model captures the steric constraints and local conformational relaxation that accompany nucleosome sliding, eviction, and reassembly. We find that nucleosome activity drives condensate swelling, enhances condensate-size fluctuations, and promotes internal mixing. In condensates containing both active and passive polymers, differences in nucleosome activity further induce radial segregation, with active polymers enriched near the periphery and passive polymers concentrated in the interior. These results identify active nucleosome remodeling as a physical mechanism for regulating chromatin condensate structure, fluidity, and spatial organization.

biophysics↗

bioRxiv2026

Interplay of Structural Heterogeneity and Active Remodeling Controls Chromatin Condensate Organization and Dynamics

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, 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 non-equilibrium kinetics drives local structural reorganization, leading to condensate swelling and a substantial acceleration of internal relaxation. In a condensate 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. SIGNIFICANCE STATEMENTChromatin forms dynamic condensates in living cells that play important roles in genome organization and regulation. Recent in vitro experiments have shown that condensate properties are strongly influenced by the arrangement of nucleosomes, the protein complexes around which DNA is wrapped, along chromatin fibers and by ATP-dependent remodeling activity. However, the mechanisms linking these molecular processes to condensate behavior remain poorly understood. Using a hierarchy of coarse-grained models, we identify the distinct roles of structural heterogeneity, remodeler-mediated kinetics, and active force generation in chromatin condensates. By providing a mechanistic explanation for experimental observations, our work establishes a physical framework connecting chromatin architecture and energy-consuming processes to condensate organization, dynamics, and function.

biophysics↗

bioRxiv2026

Data-driven polymer modeling reveals how scale-dependent active fluctuations shape chromatin organization

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.

biophysics↗

bioRxiv2025

Predicting statistics of gene translocation events: role of chromatin compaction and double-strand DNA break

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 (Tij) is influenced by chromatin compaction and the occurrence of double-stranded DNA breaks (DSBs). Our results show that, beyond the two-segment contact probability, Tij 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.

biophysics↗

bioRxiv2025

Spatio-temporal chromosomal arrangements by late-replicating heterochromatin

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 interphaseG1, and this arrangement constrains the inter-arm interactions within a chromosome, providing a unique interphaseG1 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. SignificanceChromosomes occupy the nuclear space in many ways. Primary chromosomal arrangements are such that centromere regions of different chromosomes either form a cluster, as in yeasts, or are scattered around the nuclear periphery, more common in metazoans. Exceptionally, centromeres show cell cycle stage-specific clustering in the basidiomycete fungus Cryptococcus neoformans. We show that the spatial positioning and the refractory nature of centromeres and telomeres shape the arrangement and large-scale organization of chromosomes in C. neoformans. Metazoan-like late-replicating centromeres in C. neoformans possibly favor the unclustered/scattered centromere state in S-phase, not commonly found in fungi. Our results not only highlight the remarkable genome plasticity of C. neoformans but also raise the possibility that centromere replication timing determines genome organization principles.

genomics↗

bioRxiv2025

Polymer dynamics reveal stage-wise unfolding and homologous pairing of chromosomes in S. pombe

During meiosis, the exchange of genetic material ("recombination") is essential to bring up the genetic variation in offspring. To carry out the recombination, homologous pairs of DNA have to come in proximity and align. In fission yeast, this is accomplished by the extensive nuclear oscillation that applies pulling force on the chromosomes. 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 location 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 in different stages of movement.

biophysics↗

bioRxiv2024

Interplay between cohesin kinetics and polymer relaxation modulates chromatin-domain structure and dynamics

Even though the three-dimensional static organization of chromatin is highly studied, chromatin is a dynamic structure, and time-dependent changes are crucial for biological function. While it is known that both intra-chromatin interaction and loop extrusion are crucial to understanding chromatin organization, what is their respective role in deciding the nature of spatial and temporal organization is not clear. Simulating a model with active loop extrusion and intra-chromatin interactions, we show that under certain conditions, the measurable dynamic quantities are dominated by the loop extrusion, even though the population-averaged contact map (structure) can be dominated by intra-chromatin interactions, with loop extrusion playing no major role. Our results show that the dynamic scaling exponents with loop extrusion are consistent with the experimental observations and can be very different from those predicted by existing fractal-globule models for chromatin. We argue that one needs to measure both the structure and dynamics simultaneously to unambiguously interpret the organization of chromatin.

biophysics↗

bioRxiv2024

Shear flow as a tool to distinguish microscopic activities of molecular machines in a chromatin loop

Several types of molecular machines move along biopolymers like chromatin. However, the details about the microscopic activity of these machines and how to distinguish their modes of action are not well understood. We propose that the activity of such machines can be classified by studying looped chromatin under shear flow. Our simulations show that a chromatin-like polymer with two types of activities (constant or local curvature-dependent tangential forces) exhibits very different behavior under shear flow. We show that one can distinguish both activities by measuring the nature of a globule-to-extended coil transition, tank treading, and tumbling dynamics.

biophysics↗

bioRxiv2023

Role of diffusion and reaction of the constituents in spreading of histone modification marks

Cells switch genes ON or OFF by altering the state of chromatin via histone modifications at specific regulatory locations along the chromatin polymer. These gene regulation processes are carried out by a network of reactions in which the histone marks spread to neighboring regions with the help of enzymes. In the literature, this spreading has been studied as a purely kinetic, non-diffusive process considering the interactions between neighboring nucleosomes. In this work, we go beyond this framework and study the spreading of modifications using a reaction-diffusion (RD) model accounting for the diffusion of the constituents. We quantitatively segregate the modification profiles generated from kinetic and RD models. The diffusion and degradation of enzymes set a natural length scale for limiting the domain size of modification spreading, and the resulting enzyme limitation is inherent in our model. We also demonstrate the emergence of confined modification domains without the explicit requirement of a nucleation site. We explore polymer compaction effects on spreading and show that single-cell domains may differ from averaged profiles. We find that the modification profiles from our model are comparable with existing H3K9me3 data of S. pombe.

biophysics↗

bioRxiv2023

Protein search processes mediated by chromatin topology

We investigate the role of compaction of chromatin domains in modulating search kinetics of proteins. Collapsed conformations of chromatin, characterised by long loops which bring distant regions of the genome into contact, and manifested structurally as Topologically Associated Domains (TADs) affect search kinetics of DNA associated transcription factors and other proteins. In this study, we investigate the role of the compactness of chromatin on the dynamics of proteins using a minimal model. Using analytical theory and simulations, we show that an optimal compaction exists for which the residence time of proteins on a chromatin-like polymer backbone is minimum. We show that while bulk diffusion is an advantageous search strategy for extended polymers, for highly folded polymer domains, intersegmental transfers allow optimal search. We extend these results to more detailed polymer models - using the Freely Rotating Chain model, a Lennard-Jones bead-spring polymer model, which approximates chromatin behavior. We show that our results continue to hold for these polymer models, with a minimum residence time at an optimum polymer compaction. Finally, we also analyse the dynamics of proteins on networks generated using experimental chromatin conformation data from 8355 TADs extracted from human chromosomes. Our analysis suggests that TADs exist near this zone of optimality, indicating that chromatin conformations can play a crucial role in modulating protein search strategies.

biophysics↗

bioRxiv2023

Nonequilibrium switching of segmental states can influence compaction of chromatin

Knowledge about the dynamic nature of chromatin organization is essential to understand the regulation of processes like DNA transcription and repair. While most models assume protein organization and chemical states along chromatin as static, experiments have shown that these are dynamic and lead to the switching of chromatin segments between different physical states. To understand the implications of this inherent nonequilibrium switching, we present a diblock copolymer model of chromatin, with switching of its segmental states between two states, mimicking active/repressed or protein unbound/bound states. We show that competition between switching timescale Tt, polymer relaxation timescale{tau} p, and segmental relaxation timescale{tau} s can lead to non-trivial changes in chromatin organization, leading to changes in local compaction and contact probabilities. As a function of the switching timescale, the radius of gyration of chromatin shows a non-monotonic behavior with a prominent minimum when Tt {approx}{tau} p and a maximum when Tt {approx}{tau} s. We find that polymers with a small segment length exhibit a more compact structure than those with larger segment lengths. We also find that the switching can lead to higher contact probability and better mixing of far-away segments. Our study also shows that the nature of the distribution of chromatin clusters varies widely as we change the switching rate. Significance statementDifferent cells in multicellular organisms have the same DNA but different functions. The function of any given cell type can be time-dependent. The current understanding is that differences in gene expression arising from local compaction and the probability for far-away regulatory segments to come in contact play an important role in establishing these differences. The necessary structural variations are achieved through a combination of changes in the chemical and physical states of chromatin regions. In this paper, we present a model for chromatin accounting for the dynamic switching of chromatin regions between different chemical and physical states. We demonstrate the implications of such switching in determining the local 3D structure of chromatin.

biophysics↗

bioRxiv2022

Predicting scale-dependent chromatin polymer properties from systematic coarse-graining

Simulating chromatin is crucial for predicting genome organization and dynamics. Even though coarse-grained bead-spring polymer models are commonly used to describe chromatin, the relevant bead dimensions, elastic properties, and the nature of inter-bead potentials are unknown. Using publicly available nucleosome-resolution contact probability (Micro-C) data, we systematically coarse-grain chromatin and predict quantities essential for polymer representation of chromatin. We compute size distributions of chromatin beads for different coarse-graining scales, quantify fluctuations and distributions of bond lengths between neighboring regions, and derive effective spring constant values. Unlike the prevalent notion, our findings argue that coarse-grained chromatin beads must be considered as soft particles that can overlap, and we derive an effective inter-bead soft potential and quantify an overlap parameter. We also compute angle distributions between neighboring bonds giving insights into intrinsic folding and local bendability of chromatin. While the nucleosome-linker DNA bond angle naturally emerges from our work, we show that there are two populations of local structural states. The bead sizes, bond lengths, and bond angles show different mean behavior at Topologically Associating Domain (TAD) boundaries and TAD interiors. We integrate our findings into a coarse-grained polymer model and provide quantitative estimates of all model parameters, which can serve as a foundational basis for all future coarse-grained chromatin simulations.

biophysics↗

bioRxiv2021

Size-dependent secondary nucleation and amplification of α-synuclein amyloid fibrils

The size of the amyloid seeds is known to modulate their autocatalytic amplification and cellular toxicity. However, the seed size-dependent secondary nucleation mechanism, toxicity, and disease-associated biological processes mediated by -synuclein (-Syn) fibrils are largely unknown. Using the cellular model and in vitro reconstitution, we showed that the size of -Syn fibril seeds not only dictates its cellular internalization and associated cell death; but also the distinct mechanisms of fibril amplification pathways involved in the pathological conformational change of -Syn. Specifically, small-sized fibril seeds showed elongation possibly through monomer addition at the fibril termini; whereas longer fibrils template the fibril amplification by surface-mediated nucleation as demonstrated by super-resolution microscopy. The distinct mechanism of fibril amplification, and cellular uptake along with toxicity suggest that breakage of fibrils into different sizes of seeds determine the underlying pathological outcome of synucleinopathies.

neuroscience↗

bioRxiv2021

Spatiotemporal solidification of α-synuclein inside the liquid droplets

Liquid-liquid phase separation (LLPS) and subsequent liquid-to-solid transition is implicated in membraneless organelles formation as well as disease associated protein aggregation. However, how liquid-to-solid transition is initiated inside a liquid droplet remains unclear. Here, using studies at single droplet resolution, we show that liquid-to-solid transition of -synuclein (-Syn) liquid droplets is associated with significant changes in the local microenvironment as well as secondary structure of the protein, which is prominently observed at the center of the liquid droplets. With the ageing of liquid droplets, the "structured" core at the center gradually expands and propagates over entire droplets. Further, during droplet fusion, smaller, homogeneous droplets progressively dissolve and supply proteins to the larger, heterogeneous droplets containing solid-like core at their center. The present study will significantly help to understand the physical mechanism of LLPS and liquid-to-solid transition in biological compartmentalization as well as in protein aggregation associated with human neurodegenerative disorders. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/465113v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@2a3406org.highwire.dtl.DTLVardef@bd8148org.highwire.dtl.DTLVardef@172b4eaorg.highwire.dtl.DTLVardef@1c3965f_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2021

Role of non-specific interactions in the phase-separation and maturation of macromolecules

Phase separation of biomolecules could be mediated by both specific and non-specific interactions. How the interplay between non-specific and specific interactions along with polymer entropy influences phase separation is an open question. We address this question by simulating self-associating molecules as polymer chains with a short core stretch that forms the specifically interacting functional interface, and longer non-core regions that participate in non-specific/promiscuous interactions. Our results show that the interplay of specific (strength,{epsilon} sp) and non-specific interactions (strength,{epsilon} ns) could result in phase separation of polymers and its transition to solid-like aggregates (mature state). In the absence of{epsilon} ns, the polymer chains do not dwell long enough in the vicinity of each other to undergo phase separation and transition into a mature state. On the other hand, in the limit of strong{epsilon} ns, the assemblies cannot transition into the mature state and form a non-specific assembly, suggesting an optimal range of interactions favoring mature multimers. In the scenario where only a fraction (Nfrac) of the non-core regions participate in attractive interactions, we find that a slight modifications to either{epsilon} ns or Nfrac can result in a dramatically altered self-assembled states. Using a combination of heterogeneous and homogeneous mix of polymers, we establish how this interplay between interaction energies dictates the propensity of biomolecules to find the correct binding partner at dilute concentrations in crowded environments. Author SummaryBiological function relies on the ability of biomolecules to bind to specific interaction partners. In the crowded cellular milieu, the process of biomolecules binding to specific interaction partners to carry out a function is non-trivial. A mere diffusion-limited meeting of interaction partners in space does not ensure biomolecular function. Rather, even when in contact these molecules have to find the correct orientations to carry out function. Further, for dynamic biomolecules such as polymers, the functional configuration is often one of several possible configurations. In this scenario, assuming the functional configuration after binding involves overcoming of a significant entropic barrier. Therefore, the interacting biomolecules have to dwell in contact long enough before they reorganize to find the functional orientation! While functional contacts offer an enthalpic gain, they are often only a small fraction of all protein-protein interactions. Therefore, in this paper, we study the role played by non-functional, promiscuous interactions in shaping the thermodynamics and kinetics of formation of specific interactions. Our results suggest that there exists an optimal range of non-specific interaction strengths which promotes the process of biomolecular complexes finding the functional configurations.

biophysics↗

bioRxiv2021

High fidelity epigenetic inheritance: Information theoretic model predicts k-threshold filling of histone modifications post replication

Beyond the genetic code, there is another layer of information encoded as chemical modifications on histone proteins positioned along the DNA. Maintaining these modifications is crucial for survival and identity of cells. How the information encoded in the histone marks gets inherited, given that only half the parental nucleosomes are transferred to each daughter chromatin, is a puzzle. Mapping DNA replication and reconstruction of modifications to equivalent problems in communication of information, we ask how well enzymes can recover the parental modifications, if they were ideal computing machines. Studying a parameter regime where realistic enzymes can function, our analysis predicts that, pragmatically, enzymes may implement a threshold - k filling algorithm which fills unmodified regions of length at most k. This algorithm, motivated from communication theory, is derived from the maximum a posteriori probability (MAP) decoding which identifies the most probable modification sequence based on available observations. Simulations using our method produce modification patterns similar to what has been observed in recent experiments. We also show that our results can be naturally extended to explain inheritance of spatially distinct antagonistic modifications.

biophysics↗

bioRxiv2021

Spatiotemporal organization of chromatin domains: role of interaction energy and polymer entropy

Chromatin is known to be organized into multiple domains of varying sizes and compaction. While these domains are often imagined as static structures, they are highly dynamic and show cell-to-cell variability. Since processes such as gene regulation and DNA replication occur in the context of these domains, it is important to understand their organization, fluctuation and dynamics. To simulate chromatin domains, one requires knowledge of interaction strengths among chromatin segments. Here, we derive interaction strength parameters from experimentally known contact maps and use them to predict chromatin organization and dynamics. Taking two domains on the human chromosome as examples, we investigate its 3D organization, size/shape fluctuations, and dynamics of different segments within a domain, accounting for hydrodynamic effects. Considering different cell types, we quantify changes in interaction strengths and chromatin shape fluctuations in different epigenetic states. Perturbing the interaction strengths systematically, we further investigate how epigenetic-like changes can alter the spatio-temporal nature of the domains. Our results show that heterogeneous weak interactions are crucial in determining the organization of the domains. Computing effective stiffness and relaxation times, we investigate how perturbations in interactions affect the solid-like and liquid-like nature of chromatin domains. Quantifying dynamics of chromatin segments within a domain, we show how the competition between polymer entropy and interaction energy influence the timescales of loop formation and maintenance of stable loops.

biophysics↗

bioRxiv2020

Continuous variable response, kinetic gating and connectivity that govern IS topology are perturbed in hyperinsulinemia

Understanding kinetic control of biological processes is as important as identifying components that constitute pathways. Insulin-signaling (IS) is central for almost all metazoans and its perturbations are associated with various diseases and aging. While temporal phosphorylation changes and kinetic constants have provided some insights, constant or variable parameters that establish and maintain signal topology are poorly understood. Our iterative experimental and mathematical simulation-based approaches reveal novel kinetic parameters that encode concentration and nutrient dependent information. Further, we find that pulsatile fasting insulin rewires IS akin to memory and in anticipation of a fed response. Importantly, selective kinetic gating of signals and maximum connectivity, between metabolic and growth-factor arms under normo-insulinemic states, maintains network topology. In addition to unraveling kinetic constraints that determine cascade architecture, our findings will help in identifying novel therapeutic strategies that conserve coupling between metabolic and growth-factor arms, which is lost in diseases and conditions of hyperinsulinemia.

bioinformatics↗